Chapter 1A

May 11, 2006

12:28 PM

Chapter 1A: Biochemistry
Enzymes
The Kinetic Role of the Enzyme
1. The Two Laws of Thermodynamics:
#1: Energy cannot be created or destroyed (but it can be mutated)
#2: The disorder (entropy) of the unierse tends to increase
2. !ibbs" free energy: #! $ #% & T#'
% $ entha(py) which is heat energy (#% $ #E & *#+)
T $ temperature
' $ entropy
,. 'tandard free energy change (#!o") is #! with a(( reactants and products
present at 1 - concentration) and p% $ .
#!
o
" $ &/T(n0"e1 (0" is the ratio of reactants to products at e1ui(ibrium)
#! $ #!o" 2 /T(n0 (so we can re(ate #! to #!o")
0 is the ratio of reactants to products at the time (not at
e1ui(ibrium)
3. 4 cata(yst (owers the actiation energy (Ea) of a reaction without changing the
#!
5t (owers the Ea by stabi(izing the transition state
5t does not get consumed in the reaction
6. 'ee diagram:







Enzyme Structure and Function
7. 8acts about enzymes:
-ost of them are g(obu(ar ,&9 fo(ded proteins (this a((ows for the
speci:city of the actie site)
The actie site is shaped such that the transition state of the
reaction is stabi(ized
5t is so speci:c shape&wise that it can een recognize di;erent
stereoisomers of a mo(ecu(e
*roteases are enzymes which c(eae proteins
Their actie site usua((y has a serine because its <% group can
act as a nuc(eophi(e to attac= the carbony( carbon of an amino
acid to brea= the peptide bond
4 recognition poc=et is a site on the c(eaing enzyme c(ose to
the actie site which binds to speci:c amino acid residues in the
substrate and a((ows the serine in the actie site to cut at the
right p(ace
.. >ays to regu(ate enzyme actiity:
?oa(ent modi:cation (i.e. phosphory(ation@dephosphory(ation)
The phosphate is usua((y added to@remoed from serine)
threonine) or tyrosine
*roteo(ytic c(eaage
The enzyme is ca((ed a zymogen before being actiated to form
an actie enzyme (thin= !5 tract)
4ssociation with other po(ypeptides
'ometimes there can be regu(atory subunits which bind to the
enzyme and regu(ate it
4((osteric regu(ation
>hen di;erent mo(ecu(es bind to a((osteric sites on the enzyme
(thin= feedbac= regu(ation)

Basic Enzyme Kinetics
A. 'aturation =inetics:





+maB $ the reaction rate when the enzyme is saturated
0m $ the amount of substrate necessary to reach a reaction e(ocity of
C.6 +maB
1. ?ooperatiity is when we hae a mu(ti&unit enzyme) and the binding of
substrate to one subunit increases the aDnity of other subunits for their
substrates
This resu(ts in a sigmoida( reaction e(ocity graph because as more
substrates are bound to enzyme) the e(ocity sudden(y shoots up
because aDnity is increased
1. There are mu(tip(e ways to inhibit enzymes:
?ompetitie inhibition: compete with the substrate to bind at the
actie site
+maB wi(( stay the same
0m wi(( increase
Eon&competitie inhibition: the inhibitor binds to a site <T%E/ than the
actie site and renders the enzyme use(ess
+maB decreases
0m stays the same

Other
1. Know your amino acids (make chart elsewhere)

Enzymes and ?e((u(ar /espiration
Energy Metabolism and the Defnitions of Oidation and Reduction
1. %igh&(ee( energetics of (ife: energy is stored in reduced mo(ecu(es (i=e
carbohydrates and fats) then they are oBidized to produce 4T* and ?<2
(creating 4T* is a non&spontaneous process so this is a(( one big coup(ed
reaction)
1. <Bidation means:
4ttach oBygen (or increase # of bonds to oBygen)
/emoe hydrogen
/emoe e(ectrons
1. /eduction
/emoe oBygen (or decrease # of bonds)
4dd hydrogen
4dd e(ectrons

!ntroduction to "ellular Res#iration
1. The 3 steps of ce((u(ar respiration are: g(yco(ysis (cytop(asm)) pyruate
dehydrogenase comp(eB (*9?) (mitochondria( matriB)) 0rebs cyc(e
(mitochondria( matriB)) e(ectron transport@oBidatie phosphory(ation (inner
mitochondria( membrane)

$lycolysis
,A1.. 'ee :gure:









1. <era((:
Ta=e a g(ucose mo(ecu(e (7 ?"s) and ma=e it into 2 pyruate mo(ecu(es
(, ?"s each)
2 4T*"s used) 3 4T*"s generated (per g(ucose) not per pyruate)
2 E49%"s generated from E492"s
1. Eote that:
*hosphofructo=inase is a FcommittedF step because it uses 4T* and is
thus irreersib(e as we(( as because 8&1)7&G* can on(y be used in
g(yco(ysis (no other pathways)
1. 8ermentation:
This is not a FstepF in ce((u(ar respiration un(ess it is an anaerobic
enironment) in which case something has to be done in order to
regenerate the E49% which was formed from E492 during g(yco(ysis
5n yeast) the pyruate is conerted to ethano(
5n anima(s) the pyruate is conerted to (actate

The %yru&ate Dehyrogenase "om#le
1. 'ee :gure:










1. <era((: ta=e the pyruate from g(yco(ysis (, ?"s) and ma=e it into an acety(&
?o4 unit (2 ?"s)) (osing a ?<2 in the process
Each pyruate gies us 1 E49%) which means 2 E49% tota( per
g(ucose
1. Eote that:
The *9? is regu(ated by 4-* (ee(s: when they are high) it means that
4T* is (ow and so the *9? is stimu(ated to action
The T** is a non&protein mo(ecu(e & a Fprosthetic groupF & which is part
of the enzyme (attached to its actie site)
4s opposed to E492) which is a co&factor (necessary to the
enzyme"s function) but doesn"t actua((y interact with it)

The Krebs "ycle
1. 'ee :gure:










1. <era((: ta=e the acety( unit (2 ?"s)) combine it with oBa(oacetate (3 ?"s)) then
go through a cyc(e which wi(( re(ease 2 ?<2"s and create E49%) 849%2) !T*)
etc.
*er g(ucose: 7 E49%) 2 849%2) 2 !T*

"om#artmentalization of $lucose "atabolism in Eu'aryotes
1. The intermembrane space of the mitochondria is continuous with the
cytop(asm of the ce(( because the outer mitochondria( membrane has (arge
porins that (et eerything through
1. The inner membrane of the mitochondria is fo(ded into FcristaeF) which a((ows
for more membrane surface area
1. *ro=aryotes do eerything in the cytop(asm (no membrane&bound organe((es)
so they do not hae to import the E49% produced in g(yco(ysis into the
mitochondria (this saes energy)

Electron Trans#ort and Oidati&e %hos#horylation
1. 'ee :gure:










1. <era((: eery time the e(ectrons get passed to a member of the ET? (i.e. that
member is reduced)) energy is re(eased
1. 'peci:cs:
, of the members are (arge proteins comp(eBes with heme prosthetic
groups or iron&su(fur e(ectron&transfer systems
The 2 other members are sma((er e(ectron carriers that can actua((y
moe
The :na( member of the chain reduces oBygen to water (adds e(ectrons
and protons to oBygen)
1. <ther names of the ET? members (ma=e sure you understand why):
F4F a(so =nown as E49% dehydrogenase) coenzyme H reductase
FGF a(so =nown as cytochrome ? reductase
F?F a(so =nown as cytochrome ? oBidase
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tota( amount of 4T* produced per g(ucose mo(ecu(e
using the fo((owing facts:
Each E49% mo(ecu(e pumps 1C protons across the inner membrane as
it goes through the ET?
Each 849%2 mo(ecu(e pumps 7 protons (it enters at G)
The 4T* synthase produces 1 4T* for eery 3 protons
8or eu=aryotes) each E49% produced in g(yco(ysis on(y produces 1.6
4T* (whi(e bacteria produce 2.6)
This is because eu=aryotes hae to eBpend energy getting the
E49% into the mitochondria( matriB


Chapter 1B
Saturday, June 03, 2006
6:21 PM

Chapter 1B: Gene Expression

9E4 and the !enetic ?ode
D() Structure
The bui(ding b(oc=s of 9E4 are deoByribonuc(eoside 6" triphosphates
(genera((y named dET*"s):
o /ibose sugar without an oBygen
o 4 string of , phosphates attached to the 6" carbon of the ribose
o 4romatic base (adenine) guanine) thymine) or cytosin) attached to the
1" carbon of the ribose
4 a ! are purines (deried from purine) and hae 2 carbon rings
? a T are pyrimidines (deried from pyrimidine) and hae 1
carbon ring
o <% group on the ," carbon
Euc(eoside is bust the ribose sugar and the aromatic base) whi(e a nuc(eotide
is a nuc(eoside 2 the phosphates

*o(ynuc(eotide se1uences are connected when the phosphate on the 6" carbon
of one dET* forms a phosphodiester bond to the ," <% of another dET* (this is
where we get the 6"&c," direction from)
o The phosphates are hydro(yzed in this process (energy re(easingd
spontaneous) so that there is on(y one phosphate bonded to the <%
group) not a chain of ,
o This means that pyrophosphate is a F(eaing groupF) and when this
subse1uent(y gets hydro(yzed again) a (ot of energy is re(eased &&
which is what dries the entire po(ymerization reaction forward

9E4 structure is a right&handed doub(e he(iB he(d together by hydrogen bonds
between comp(ementary strands of 9E4 (understand eery part of this
statemente)
o The 2 9E4 strands are anti&para((e( (6" s. ,")
o The %&bonds are a(ways either between 4 and T or ? and ! (i.e. purine
2 pyrimidineethis is because the shapes of the mo(ecu(es are
conducie for %&bonding in that way)
o Gecause the he(iB is coi(ed) we end up with the bases stac=ed on top of
each other and this a((ows them to bond hydrophobica((y and hae an
der >aa(s reactions) which increases the mo(ecu(e stabi(ity
Ginding 2 9E4 strands together is ca((ed hybridization@annea(ing) and
separating them is me(ting@denaturation
o The temperature at which ha(f of a so(ution of 9E4 is me(ted is ca((ed
the Tm

9i;erence between pro=aryotes and eu=aryotes:
o *ro=aryotes further stabi(ize their (circu(arf) genome by twisting the
circ(e around on itse(f to form supercoi(s (it a(ready has Fregu(arF coi(s
because of 9E4"s he(iB nature)
o Eu=aryotes stabi(ize their 9E4 bye
>rapping it around g(obu(ar proteins ca((ed histones (beads on
a string)
FGeadF is a nuc(eosome & 9E4 wrapped around an
octamer of histones
F'tringF between the beads is F(in=erF 9E4
Then we pac= the nuc(eosomes together to ma=e chromatin

The Role of D()
?entra( 9ogma of -o(ecu(ar Gio(ogy:
o 9E4 information is copied onto a comp(ementary strand ca((ed m/E4
o m/E4 trae(s to the cytop(asm where the ribosome (with the he(p of
r/E4 and t/E4) ta=e its information to ma=e proteins

There are many causes of genetic mutations (g+ (ight) interca(ation) mista=es
in rep(ication) etc.) but here are the , =inds of mutations:
o *oint mutations: sing(e base pair substitution
-issense point mutations: cause one amino acid to rep(ace
another
Eonsense point mutations: cause a stop codon to rep(ace a
regu(ar codon
?onseratie missense point mutation: when the new amino
acid is simi(ar enough to the o(d one that the protein for a((
intents and purposes does not change much
'i(ent mutations: when the error does not change the amino
acid being encoded or when it occurs in a part of the gene that
does not encode for protein (i.e. introns)
o 5nsertion mutations: adding nuc(eotides into the 9E4 se1uences
This usua((y causes frameshift mutations) which is when the
Freading frameF is thrown o; and the ribosome does not FreadF
the m/E4 in the correct sets of ,
o 9e(etion mutations: remoa( of nuc(eotides from the se1uence
This can a(so cause frameshift mutations

D() Re#lication
9E4 rep(ication is semi&conseratie) which means that when you ta=e a
doub(e&stranded 9E4 he(iB apart and copy it) you ma=e 2 new doub(e&
strandseand one strand in each of the doub(e&strand is from the FparentF 9E4
he(iB
*o(ymerization (cata(yzed by 9E4 po(ymerase) is the process of adding new
dET*"s (nuc(eotides) to a nascent 9E4 chain
o 5t is 4L>4`' in the 6"&c," direction
9E4 po(ymerase re1uires a temp(ate (thus it is more appropriate(y ca((ed 9E4&
dependent 9E4 po(ymerase)
o Thus the temp(ate is /E49 in the ,"&c6" direction) since the resu(ting
combination of new and o(d strands must be anti&para((e(
9E4 po(ymerase re1uires a primer (it cannot start a new 9E4 chain on its
own)
o 4n /E4 po(ymerase enzyme ca((ed primase does the priming) :((ing it
in with /E4 nuc(eotides which are (ater rep(aced by 9E4

5n order to start 9E4 rep(ication) we hae to unwind the doub(e he(iB and then
separate the Fannea(edF strands
o %e(icase does G<T% of these bobs
5t starts at a speci:c (ocation ca((ed the origin of rep(ication
o Gecause unwinding the strand at one (ocation wi(( cause it to wind
more tight(y at another (ocation) we re(iee the pressure by using
topoisomerase enzymes to cut and re&wind the 9E4
o The unwound sing(e 9E4 strands are not ery stab(e on their own) so
we stabi(ize them with sing(e&strand binding proteins

<ne prob(em is that as rep(ication proceeds to either side of the origin of
rep(ication) thin= about the rep(ication for=s that are createdeon(y one ha(f of
the for= can be trae(ed on in a ,"&c6" direction) which is how we need to be
reading the temp(ate
o Thus we hae (eading and (agging strands) where the (agging strand is
actua((y made up of many sma((er F<=aza=i fragmentsF which are
created in a 6"&c," direction
The fragments are (ater boined up by 9E4 (igase) another
enzyme

Eu=aryotic s. *ro=aryotic /ep(ication:
o Eu=aryotic rep(ication: we hae many di;erent rep(ication bubb(es)
which means that on a particu(ar chromosone) there are many di;erent
origins of rep(ication
o *ro=aryotic rep(ication: it is ca((ed FthetaF rep(ication
/emember it is a circu(ar genomeewe start at on(y <EE origin
of rep(ication) and as it proceeds to both sides the genome
starts to (oo= (i=e the h symbo(

5n more detai(: pro=aryotic 9E4 po(ymerase
o There are actua((y , di;erent =inds of 9E4 po(ymerase: 5) 55) and 555
9E4 po(ymerase 5 remoes the primer and rep(aces it with 9E4
5t has 6"&c," eBonuc(ease actiity) which means that it
traerses the primer in the 6"&c," direction) remoing
nuc(eotides as it goes
9E4 po(ymerase 55 is un=nown
9E4 po(ymerase 555 does the main bob of e(ongating the (eading
strand
5t can go bac=wards for short times to :B mista=es: this
is ca((ed ,"&c6" eBonuc(ease actiity

!ene EBpression
R() and Transcri#tion
/E4 is di;erent from 9E4 in the fo((owing ways:
o 5t is (norma((y) sing(e&stranded
o 5t has a(( the same bases as 9E4 eBcept it uses uraci( (g) instead of
thymine (T)
o The ribose sugar is not deoBy) meaning that on the 2" carbon there is
an <% group
This group ma=es /E4 (ess stab(e (can mutate more) because
the <% group is c(ose enough to the phosphate to attac= it and
in so doing brea= up an /E4 po(ymer

*ro=aryote s. eu=aryote
o *ro=aryotes are Fpo(ycistronicF) which means that a sing(e m/E4
strand codes for more than one po(ypeptide (not because of di;erent
reading frames but because they are one after another)
4(though the proteins are usua((y re(ated in function

Transcri#tion
<nce again we are doing po(ymerization@chain e(ongation) eBcept this time it
is using /E4 po(ymerase (no primer needed) instead of 9E4 po(ymerase
o /E4 po(ymerase does not hae ,"&c6" eBonuc(ease actiity) so
transcription is not as re(iab(e as rep(ication
-ore di;erences from rep(ication:
o 5nstead of the origin of rep(ication we hae the Fstart siteF (and it on(y
goes in one direction)
The se1uence of nuc(eotides immediate(y before the start site is
ca((ed the FpromoterF) and this is where /E4 po(ymerase goes
:rst to get actiated
o <n(y one of the 9E4 strands is going to get transcribed to /E4) and it
is ca((ed the temp(ate@non&coding@transcribed@anti&sense strand
The other strand is ca((ed the coding@sense strand) because the
nuc(eotides it ho(ds are the ones which wi(( actua((y be used
(remember because the m/E4 which gets transcribed is
comp(ementary to the anti&sense strand) bust as the sense
strand is)

?omparing pro=aryotic and eu=aryotic transcription:
o Location of transcription
*ro=aryotes do it free in the cytop(asm
Eu=aryotes ma=e m/E4 in the nuc(eus then transport it outside
into the cytop(asm
o *rimary transcript and m/E4
*ro=aryotes" primary transcript (i.e. the m/E4 that comes
straight o; the transcription process) is ready to be trans(ated
right away (actua((y) since eerything happens in the
cytop(asm) trans(ation starts on a chain of m/E4 een before its
transcription is comp(etef)
Eu=aryotes" primary transcript is E<T ready to go & it is modi:ed
eBtensie(y before trans(ation:
'p(icing (remoe the stu;) ca((ed introns) that don"t code
for proteins (i=e regu(atory se1uenceseand bust hae the
FeBonsF) or the part that actua((y codes for protein)
The /E4 transcript GE8</E sp(icing occurs is
ca((ed heterogeneous nuc(ear /E4 (hn/E4)
4dd 6" cap to he(p with trans(ation
4ttach ," po(y&4 tai( to protect against eBonuc(eases
o /E4 po(ymerase(s)
There are , di;erent =inds of /E4 po(ymerases for eu=aryotes
(note that this is iipped from before) when */<04/`<TE' were
the ones with , 9E4 po(ymerases):
/E4 po(ymerase 5 (transcribe r/E4)
/E4 po(ymerase 55 (transcribe m/E4)
/E4 po(ymerase 555 (transcribe t/E4)
o /egu(ation of transcription
5t"s bust genera((y more comp(eB in eu=aryotes than in
pro=aryoteseeu=aryotes hae se1uence&speci:c transcription
factors) T4T boBes) etc.

Translation
The important structure here is transfer /E4 (t/E4)) which has a site ca((ed an
FanticodonF to bind to the m/E4 and an Famino acid acceptorF site
o 4ttaching the amino acid to the t/E4 re1uires hydro(yzing one 4T*eso
:rst we get aminoacy( 4-*
o 4nd then we attach that to the t/E4 (Ft/E4 (oadingF@Famino acid
actiationF)) which is unfaorab(e but drien forward by ta=ing o; the
4-*
o 4nd at the end) we hae aminoacy( t/E4
The amino acid&t/E4 bond is 4L'< high energy) and so when
we brea= it to attach the amino acid to the po(ypeptide chain)
we can use that energy to drie the reaction forward
o The who(e Fmatch amino acid with t/E4F process is hand(ed by
aminoacy(&t/E4 synthetases

/ibosome stu;e
o 5t"s basica((y this big huge mass of po(ypeptides and m/E4
o There are two subunits: (arge and sma((
o >hen the subunits are attached together) the ribosome is good to go
and there are , binding sites:
* site (peptidy(&t/E4)) i.e. where the growing po(ypeptide chain
whi(e sti(( attached to t/E4 is (ocated in trans(ation
4 site (aminoacy(&t/E4)) i.e. acceptor site & where each new
t/E4 de(iers its amino acid

*ro=aryotic trans(ation
o 8irst(y remember that trans(ation starts een when transcription is sti((
going
4(so =now that -gLT5*LE ribosomes wor= on the same m/E4 at
once & this is ca((ed a po(yribosome
o 5nitiation:
Trans(ation does not begin at the 6" end of the m/E4eit"s bust a
bit further down the chaine
8irst there is a FpromoterF ca((ed the Fribosome binding
siteF a=a F'hine 9a(garno se1uenceF) and then the
actua( start codon
To actua((y start initiation we hae to put together the ribosome)
so we do: sma(( subunit 2 initiation factors 2 m/E4 2 (arge
subunit (in that order) (cost one G!)
Then we attach the :rst aminoacy(&t/E4 comp(eB to the start
codon) which sits in the * site
The amino acid is a(ways formy(&methionine (a modi:ed
methionine)
o E(ongation:
The neBt aminoacy(&t/E4 enters the 4 site (cost one G!)
Then Fpeptidy( transferaseF actiity causes the * site amino
acid to peptide bond with this new amino acid
Then trans(ocation: the new t/E4 2 new amino acid moes into
the * site (cost one G!)
'o you wi(( notice that trans(ation of the po(ypeptide goes from
E&terminus to ?&terminus
o Termination:
>hen a stop codon appears in the 4 site) we get a Fre(ease
factorF instead of t/E4 in the 4 site) which causes peptidy(
transferase to hydro(yze the bond between the (ast t/E4 and
the comp(eted po(ypeptide
The ribosome separates into subunits and we"re good to go

9i;erences in eu=aryotic trans(ation (there are bust a few):
o The ribosome is AC' instead of .C'
o m/E4 is processed after transcription) before trans(ation starts
o The E&termina( amino acid is p(ain methionine) instead of f-et (formy(
methionine)


?hapter 2
'unday) june C3) 2CC7
11:22 4-

Chapter ": #icro$iolo%y

+iruses
*iral Structure and Function
'tu; about iruses:
o +iruses are infectious agents that attac= a(( (ife forms (p(ants) anima(s)
protists) and bacteria)
o They are Fob(igate intrace((u(ar parasitesF) which meanse
<b(igate: they %4+E to be intrace((u(ar (if they are outside the
ce(() they can do no harm)
5ntra: as intimated aboe) they hae to be inside
*arasite: they Ffeed o;F the ce(("s mechanisms & they cannot
surie on their own
o They re(y on Fhost machineryF as much as possib(e) which means that
they use the ce(("s abi(ity to trans(ate 9E4@/E4) ma=e proteins) etc.
o They are '*E?585? & they on(y attac= certain ce((s & the ones which hae
receptors on their surface which match the irus" shape
'tructure of iruses:
o 4(( iruses hae a nuc(eic acid genome pac=aged in a protein she((
The genome can be either:
9E4 or /E4
'ing(e or doub(e&stranded
Linear or circu(ar
The nuc(eic acid of a irus is <EL` its genome and nothing e(se
(as opposed to regu(ar ce((s which hae non&genomic nuc(eic
acid materia() such as m/E4) t/E4) etc.)
The protein coat is ca((ed the FcapsidF) and we c(assify iruses
based on the shape of the capsid (i.e. its morpho(ogy):
%e(ica( capsids are rod&shaped
*o(yhedra( capsids are mu(tip(e&sided geometric surfaces
'urrounding the capsid there is an Fene(opeF & the irus gets
this from the membrane of the %<'T ?ELLe
5t contains:
*hospho(ipids) proteins) and carbohydrates from
the host membrane
*roteins encoded by the ira( genome itse(f
4 irus ac1uires its ene(ope by budding through the
host membrane
o They are '-4LL (much sma((er than the host ce((s they infect)
The protein pac=aging for the genome is rigid) so it cannot
accommodate FeBpansionF
The irus dea(s with this by being eDcient (again by using host
machinery wheneer possib(e) and a(so by using mu(tip(e
reading frames so that a sing(e strand of 9E4@/E4 can encode
more than one protein se1uence)

Bacterio#hage +ife "ycles
The :rst part:
8irst the iruses binds to the eBterior of a bacteria( ce(( (so we are
focusing on bacteria here) as shown by the tit(e FbacteriophageF (ife
cyc(es) & and this is ca((ed FattachmentF or FadsorptionF
Then the ira( genome (but not the ene(ope or the capsidf) is inbected
into the host ce((
Then we go into the (ytic cyc(e </ the (ysogenic cyc(e
Lytic cyc(e (this one goes bang bang bang):
<nce the genome is in) it gets transcribed@trans(ated right away by the
host ce(("s po(ymerases and ribosomes
<ne of the :rst gene products is hydro(ase) which destroys the
</5!5E4L genome (i.e. the genome of the hostewe don"t need
that anymoref)
Then we hae 9E4@/E4 rep(ication to ma=e mu(tip(e copies of the
irus" genome) using the nuc(eotide bases which are the resu(t of the
hydro(ysis of the host genome
?apsid proteins are a(so made for a(( these new ira( genomes) so they
can become rea( iruses
8ina((y we get an enzyme ca((ed (ysozyme) which destroys the bacteria(
ce(( wa((
Eow the ce(( -E-G/4EE sti(( remains) but because the ce(( wa((
is destroyed) osmotic pressure causes the ce(( to (yse) and a((
those new iruses come out
Lysogenic cyc(e (coming in a(( 1uiet&(i=e):
The idea here is that the irus doesn"t destroy the host ce(( right away)
(i=e it does in the (ytic cyc(eewhen it enters the ce(() it bust
incorporates itse(f into the host genome and 9<E' E<T !ET
Ek*/E''E9 (transcription is b(oc=ed by a repressor protein)
4t this point the ira( genome is ca((ed a prophage
Gut the thing is) now eery time that host ce(( reproduces itse(f) the
irus wi(( reproduce as we((
4nd then at a certain pointeEk?5'5<E happens) which is when the ira(
genome eBcises itse(f from the host genome and is now (oose and free
in the bacteria( ce(( & and then the (ytic cyc(e starts
'ometimes when it eBcises itse(f) it ta=es some of the host ce(("s
genome a(ong with it and this gies it a new feature (i.e. the
irus sudden(y codes for a protein which metabo(izes ga(actose)
& this is ca((ed transduction
9i;erences for anima( iruses (as opposed to bacteriophages a=a bacteria&
inading iruses):
The receptors on the ce(( surface which the irus binds to are not jg'T
for the irus & they are ino(ed in the ce(("s regu(ar function as we((
>hen iruses enter anima( ce((s) it"s not by FinbectionF & it is usua((y by
endocytosis (which is not possib(e with bacteriophages because of the
ce(( wa(()
This means that the irus has to be uncoated after it enters the
ce(() because un(i=e bacteriophages they do E<T (eae their
capsid outside during the penetration process
9i;erences in cyc(es:
Lytic cyc(e the same
There is a new one ca((ed the productie cyc(e: it is the same as
the (ytic cyc(e) but it does not destroy the host ce(( because the
iruses eBit the ce(( by FbuddingF through the membrane (this is
how they coat themse(es with the membrane as we(()
Lysogenic cyc(e the same) eBcept it is ca((ed a FproirusF
instead of a prophage

*iral $enomes
Let"s thin= about what =ind of proteins a irus must encode or carry based on
its genome type:
(2) /E4 iruses (i.e. a piece of sing(e&stranded ira( /E4 which seres
as m/E4):
<0 obious(y we can do trans(ation right away because it wi((
sere as m/E4) so a(( we need to worry about is how to
rep(icate the /E4 so that more iruses can be madeeso we
need /E4&dependent /E4 po(ymerase (but we don"t hae to
%4+E it with usewe can bust encode it) then (et the ribosomes
ma=e it)
(&) /E4 iruses (i.e. a piece of sing(e&stranded /E4 that is
comp(ementary to the actua( ira( /E4):
%ere we can"t do trans(ation right away & we hae to ma=e the
rea( strand :rst from the comp(ementary strand) so it must
?4//` /E4&dependent /E4 po(ymerase
/etroiruses (i.e. (2) /E4 iruses which undergo (ysogeny) which
means they incorporate into the host genome):
The prob(em with (ysogeny is that the irus needs to become
doub(e&stranded 9E4 in order to :t into the host genome)
meaning that they need to undergo the process ca((ed Freerse
transcriptionF & an enzyme ca((ed /E4&dependent 9E4
po(ymerase can do this
Gut they on(y hae to EE?<9E the enzyme) because when the
/E4 gets into the ce(( it can get trans(ated by the ribosome
right away
9oub(e&stranded 9E4 iruses:
These boys encode enzymes re1uired for dET* synthesis and
9E4 rep(icationeeen though yes) the host ce(( wi(( hae these
enzymes too. The issue is that the host ce(( wi(( on(y create
those dET*"s and rep(icate the 9E4 when it is time for the ce((
5T'EL8 to rep(icateethus the irus needs to bring its own crap if
it wants to go by its own time tab(e

*ro=aryotes
!ntroduction
The main di;erence between pro=aryotes and eu=aryotes is that pro=aryotes
do not hae a nuc(eus or any other membrane&bound organe((e) for that
matter (howeer they can sti(( carry out a(( the same (ife processes as a
eu=aryote can)
Liing organisms in genera( are c(assi:ed using many (ee(sethe highest is
=ingdom) and there are 6: pro=aryotes) sing(e&ce((ed eu=aryotes) fungi) p(ants)
and anima(s

Bacterial Structure and "lassifcation
'o we are ta(=ing about the bacteria( ce((ei.e. a pro=aryotee
?ontents of the cytop(asm:
/eca(( there are no membrane&bound organe((es
The genome is a doub(e&stranded ?5/?gL4/ 9E4 chromosome (no
nuc(eus@histones)
Transcription and trans(ation happen in the same p(ace) at the
same time
Gacteria( ribosomes are structura((y di;erent than eu=aryotic
ones) a(though they do the same thing (this a((ows us to ma=e
drugs that target on(y bacteria( ribosomes)
There is a(so a p(asmid) which is genetic materia( but E<T part of the
genomeeit is bust o; by itse(fean FeBtrachromosoma( genetic
e(ementF
The p(asmid encodes gene products that gie an adantage to
the ce(() and a(so orchestrate eBchange of genetic information
between bacteria (conbugation)
?e(( membrane@ce(( wa((:
There is a ce(( wa(( (preents osmotic pressure&re(ated prob(ems) and a
ce(( membrane
The ce(( wa(( is composed of peptidog(ycan & a combination of
amino acids and sugars that is uni1ue to pro=aryotes
This ce(( wa(( is usua((y what anti&biotics target) because if they
can brea= it) then the ce(( wi(( burst due to osmosis
!ram staining of the ce(( wa((:
Gacteria can a(so be c(assi:ed based on the resu(t of a !ram
staining of the ce(( wa((: !ram&negatie bacteria stain wea=(y
and !ram&positie bacteria stain strong(y
!ram&negatie bacteria hae a (re(atie(y) thin (ayer of
peptidog(ycan in their ce(( wa(( (it is this stu; that gets
stained)) but then a(so an 4995T5<E4L (ayer outside that
made of (ipopo(ysaccharides that proides additiona(
protection
Getween the 2 (ayers is the Fperip(asmic spaceF)
where we hae enzymes that =i(( anti&biotics (so
gram&negatie bacteria is rea((y good against
anti&biotics not on(y because it has more (ayers of
protection but a(so because it has a doub(e (ayer)
!ram&positie bacteria bust hae the ce(( wa(() which has
a rea((y thic= (ayer of peptidog(ycan in it
EndotoBins s. eBotoBins:
EndotoBins are a norma( part of the outside (ayer of !ram&
negatie bacteriaebut they can be bad if a (ot of bacteria die
and their outer membranes disintegrate and re(ease these
endotoBins
The body"s immune system responds by re(easing tons
of chemica(s) which causes the body to go into septic
shoc= (b(ood enters the tissues) b(ood pressure drops)
etc.)
EBotoBins are a(ways bad & they are toBic substances re(eased
by both !ram&negatie and !ram&positie bacteria that =i((
other bacteria so that the re(easing bacteria can hae a chance
to (ie
?apsu(e@g(ycoca(yB:
5t"s bust a stic=y (ayer of po(ysaccharide that surrounds the bacteria(
ce(( (sometimes around a who(e bacteria( co(ony)
5t ma=es the bacteria hard for the immune system to get to) and a(so
a((ows the bacteria to stic= to smooth surfaces
8(age((a:
This is bust a (ong) whip&(i=e :(ament which bacteria can use to get
around (at the cost of 4T*)
5t brea=s down to:
8i(ament
%oo=
Gasa( structure (anchor the iage((um to the outside of the
bacteria( ce(( and rotates the rod and the rest of the iage((um
as necessary)
'ee :gure:





The iage((a moes the bacteria according to a process ca((ed
chemotaBis) where the bacteria :gures out which direction to go in for
food by using chemoreceptors to detect changing concentrations of
some substance
*i(i:
This is a (ong probection on the bacteria( surface which is ino(ed in
attaching to di;erent surfaces
>e a(so hae the :mbriae) which are sma((er and do the same thing

Bacterial $ro,th Re-uirements and "lassifcation
9i;erent terms:
-edium: is the enironment where the bacteria grow (but this is E<T
their food)
-ost common medium is agar) based on seaweed
*(ating: putting bacteria onto a dish with some sort of medium to see if
they wi(( grow
?o(ony: a crop of bacteria which hae grown in some p(ace
-inima( medium: agar p(us on(y g(ucose (to feed the bacteria)
>i(d&type bacteria: a type of bacteria which has 4LL the characteristics
that are natura( for that particu(ar species
*(a1ue: Fc(earF spot amongst a co(ony (or a F(awnF) when growth is
dense) where bacteria hae died
?(assifying bacteria by how they eat:
>e sub&c(assify based on carbon source and energy source:
4utotrophs use ?<2 as their carbon source
%eterotrophs re(y on organic nutrients created by other
organisms (i.e. g(ucose)
?hemotrophs get their energy from chemica(s
*hototrophs get their energy from (ight
'o we can combine these terms to hae FchemoautotrophF)
FphotoautotrophF) etc.
The (ast important type is FauBotrophF) where the bacteria needs
something beyond carbon@energy to (ie) i.e. Farginine auBotrophF
where the bacteria needs to get arginine from somewhere since it can"t
ma=e it on its own
?(assify based on temperature:
Each bacteria grows optima((y or maybe een can on(y surie at
certain temperaturese
-esophi(es: moderate temperatures (around ,C o?)
Thermophi(es: ery hot (up to 1CC o?)
*sychrophi(es: co(d (around C o?)
?(assify based on oBygen uti(ization and to(erance:
Gacteria which re1uire oBygen to do metabo(ism (i.e. cannot do
anything in its absence): ob(igate aerobes
Gacteria who don"t re1uire oBygen (but might sti(( used it): anaerobes
8acu(tatie anaerobes: use oBygen when aai(ab(e) but don"t
EEE9 it to surie
To(erant anaerobes: neer use oBygen but can grow in its
presence
<b(igate anaerobes: don"t use oBygen and are in fact poisonous
'ome bacteria do anaerobic respiration) which is when bacteria do ce((
respiration but with the eBterna( e(ectron receptor being something
<T%E/ than oBygen (i.e. nitrate) carbon dioBide) su(fur oBide)
?(assify based on shape:
'ee tab(e:






Bacterial +ife "ycle
Gacteria produce aseBua((y: each ce(( bust produces doub(e the ce((u(ar
components) then rep(icates the genome) then sp(its (no meiosis)
recombination) etc.)
o This means that genetic diersity is neer introduced into bacteria ia
reproduction
Gacteria( growth :gure:

Gacteria( growth (in idea( conditions) is eBponentia( (so the (og of the
popu(ation count grows (inear(y with time)
%oweer) before getting into FeBponentia( growth modeF a=a the F(og
phaseF) there is a F(ag phaseF where ce(( diision does not occur (this is
because the bacteria hae to ma=e a(( the ce((u(ar components needed
for diision)
Then at the end) there is a Fstationary phaseF where they don"t grow
anymore because there aren"t any more nutrients
'ometimes bacteria form FendosporesF) which is (i=e hibernation when
conditions for growth are bad
This means they get tough) thic= eBterna( she((s made of peptidog(ycan
They can surie ery hot temperatures) so if we want to c(ean
something comp(ete(y we hae to ma=e it ery high temperature
The metabo(ic reactiation of endospores is ca((ed FgerminationF

$enetic Echange Bet,een Bacteria

8ungi
Fungal Structure
Fungal +ife "ycles

4danced Topic: /ecombinant 9E4

&Chapter " Addendum'

$enetic Echange Bet,een Bacteria
<0 :rst (et"s rea(ize that there are , ways that bacteria do FmutateF or at (east
ac1uire new genetic materia( (remember that reproduction is not going to be
one of these) since they reproduce aseBua((y):
o Transduction (remember how the (ysogenic cyc(e wor=s)
o Transformation (it"s a bit weird) but pretty much you dump bacteria
into a cu(ture then add pure 9E4) then the bacteria wi(( ta=e up the
9E4)
o ?onbugation (<0) this is the most common onee(et"s ta(= about this)

The high&(ee( concept of conbugation is that bacteria( ce((s touch each other
physica((y and then transfer genetic information
o The genetic information norma((y transferred is =nown as the F8F
factor) which is FeBtrachromosa( 9E4F in that it is not part of the
norma( bacteria( circu(ar chromosome
o The way this wor=s is that there ma(e and fema(e bacteria( ce((s
-a(e ce((s are F82F) meaning that they hae the 8 factor
8ema(e ce((s are F8&F) meaning that they receie the 8 factor
from the ma(e (a(though the 8 factor is copied) so the origina(
ma(e ce(( remains ma(e)
o 'o you can see that the F8F factor & thus the genes which are on it & is
de:nite(y going to be a part of the FnewF genetic materia( receied by
a bacteria( ce((
There is a(so) howeer) another situation in which een more
information is transferred
This is a situation in which the 8 factor is actua((y integrated
into the -45E !EE<-E of the bacteria( ce((
'o what does this meanl 5t means that when the ce(( is copying
the 8 factor in preparation for transfer to the fema(e ce(() some
of the origina( genome gets copied a(ong with it and so the
fema(e ce(( gets een more than it bargained for
These ce((s are ca((ed %fr or Fhigh fre1uency of recombinationF
ce((s

8ungi
Fungal Structure
<0 so now we"re ta(=ing about fungi. /emember that they are the ,rd
=ingdom that we rea((y get into during this courseethe others being
pro=aryotes (of which bacteria is one) and anima(s
'o the fungi is its own =ingdomebut at a higher (ee() it is bust a mu(ti&ce((ed
eu=aryote

<0) some 1uic= shots:
o 8ungi hae a ce(( wa(( made from chitin (di;erent materia( than p(ant
and bacteria( ce(( wa((s)
o 4(( fungi are chemoheterotrophs
/eca(( FchemoF means that they get energy from chemica(s
rather than the sun (photo)
/eca(( FheteroF means that they use organic materia(s from
other organisms as their carbon source) un(i=e autotrophs which
use ?<2
o -ost fungi are ob(igate aerobes (means that they must be in an
oBygen&rich enironment)

The hierarchy for fungi structure is as fo((ows
o ?e(( (of course)
o %ypha ((ong :(ament of ce((s boined end to end)) of which there are 2
=inds
'eptate hyphae hae the ce((s separated by wa((s
4septate hyphae hae E< separation) meaning that the
cytop(asmic contents and nuc(ei are shared amongst a(( the
ce((s
o -yce(ium (a meshwor= of hyphae)
o Tha((us (many myce(ium) which resu(t in a structure isib(e to the
na=ed eye)

Fungal +ife "ycles
<0) (et"s :rst rea(ize that fungi reproduce both seBua((y and aseBua((y

Let"s ta(= about aseBua( reproduction
o This occurs by budding) fragmentation) or spore production
Gudding: a new sma((er ce(( grows outward from an eBisting one
8ragmentation: the myce(ium is bro=en into sma(( pieces which
then grow into their own myce(iums
'pore production: many spores form from one ce((
/eca(( from the concept of the bacteria( spore that the
funga( spore has a tough wa(( resistant to enironmenta(
eBtremes
o T%E -45E *<5ET: since it is 4'Ekg4L) the resu(ting Fo;springF wi((
a(ways be identica( genetic c(ones of the origina( ce((

Let"s ta(= about seBua( reproduction
o The one point to understand for seBua( reproduction is that a(( fungi are
%4*L<59) which is opposite to the dip(oid ce((s that humans hae
%ap(oid means that they on(y hae one copy of each =ind of
chromosome
o 'o when the fungi reproduce seBua((y) what happens is that two
hap(oids combine together to ma=e a dip(oid) but then they separate to
more hap(oids
>hen they are in the dip(oid stage) chromosome may
(ostensib(y) get switched around so that when they sp(it to
ma=e hap(oids again) there is new genetic materia(
4nd so these hap(oids bust undergo mitosis to ma=e more of
themse(es


?hapter ,
Tuesday) june 1,) 2CC7
m:3. 4-

Chapter (: Generali)ed Eukaryotic Cells

*art 1: The <rgane((es
Huic= oeriew of organe((es in the ce(( and the number of membranes they
hae surrounding them:
o Euc(eus (2): contain and protect 9E4) transcription) partia( assemb(y of
ribosomes
o -itochondria (2): produce 4T*
o /ibosomes (C): synthesize proteins
o /E/ (1): synthesis and modi:cation of secretory) membrane&bound)
and organe((e proteins
o 'E/ (1): detoBi:cation and g(ycogen brea=down in (ierd steroid
synthesis in gonads
o !o(gi (1): modi:cation and sorting of protein) some synthesis
o Lysosomes (1): contain acid hydro(ases that digest arious substances
o *eroBisomes (1): metabo(ize (ipids and toBins using %2<2

The (ucleus
The genomic materia( (9E4) is organized into chromosomes
o Each chromosome has a FcentromereF in the midd(e to he(p with
mitosis and meiosis
They a(so hae te(omeres at the ends ((arge numbers of
repeated 9E4 se1uences) which he(p to protect the
chromosome from degradation
o 'ome parts of the chromosome are organized into regions ca((ed
FheterochromatinF) which are tight(y pac=ed and the genes are
inaccessib(e
Gut other regions ca((ed euchromatin are more (oose(y pac=ed
and here the genes are actie
The nuc(eus is supported by a cytos=e(eton&ana(og ca((ed Fnuc(ear matriBF or
Fnuc(ear sca;o(dF

The nuc(eo(us is a region within the nuc(eus that ma=es ribosomes) so it has
9E4) /E4 po(ymerases) r/E4) and the protein components of the ribosome
o The ribosome is *4/T54LL` assemb(ed here by the nuc(eo(us & the r/E4
is transcribed and the ribosoma( subunits are attached) and then it is
sent out into the cytop(asm so that trans(ation (remember a((
trans(ation happens in the cytop(asm) can happen and we add the
necessary proteins
This a(so he(ps to preent the trans(ation of hn/E4) which cou(d
happen if we had fu((y functioning ribosomes in the nuc(eus

The nuc(ear ene(ope is the FmembraneF that surrounds the nuc(eus & in fact it
is 2 (ipid bi(ayer membranes
o 4t some points) the inter&membrane space is continuous with the
(umen of the endop(asmic reticu(um
o The ene(ope a(so has Fnuc(ear poresF that a((ow sma(( items to di;use
into the nuc(eus from the cytop(asm
Gigger items are on(y a((owed in if they hae a Fnuc(ear
(oca(ization se1uenceF

Mitochondria
-itochondria hae their own mini&genome & it is a circu(ar 9E4 mo(ecu(e
o They hae their own way of doing eerything & 9E4 rep(ication)
trans(ation) ribosomes) etc.
o 5t is on(y passed from the mother to the chi(dren (Fmaterna(
inheritanceF)
The endosymbiotic theory of mitochondria( eo(ution suggests that the
mitochondria was once an independent unice((u(ar organism (iing within
(arger ce((s
o This is because it can do a(( this stu; & ma=e its own 9E4) etc.

Endo#lasmic Reticulum
The E/ is basica((y bust a (arge system of fo(ded membrane
There are 2 types:
o The rough E/ has ribosomes bound to its surface) thus it is the site of
protein synthesis for proteins targeted to enter the secretory pathway
o The smooth E/ doesn"t ma=e proteinsebut it contains enzymes for
steroid hormone synthesis or in the degradation of enironmenta(
toBins

-ore on the secretory pathway:
o <0 so there are two sites for trans(ation in the ce((: on the rough E/
and on ribosomes which are bust free in the cytop(asm
o Gasica((y) any protein synthesized on the rough E/ wi(( end up either:
secreted into the eBtrace((u(ar enironment) as an integra( p(asma
membrane protein) and in the membrane </ interior of the E/) !o(gi)
or (ysosomes
The way the proteins get to and from a(( these compartments is
by trae(ing in esic(es (so in a sense we ?<gL9 say that they
are a(( contiguous)

Eery protein has an amino acid se1uence that determines >%E/E it wi(( get
trans(ated
o 'o the idea is that it binds to any random ribosome :rst and starts
trans(atingebut once the se1uence has been attached) the Fsigna(
recognition partic(e ('/*)F binds to the who(e ribosome and now we
hae a ribosome&'/* comp(eB that binds to the rough E/
4nd then from there) as the protein is trans(ated it goes into the
rough E/ (where a signa( peptidase cuts o; the unnecessary
part)

5ntegra( membrane proteins are di;erent & these a(so hae Fsigna( se1uencesF
that cause their trans(ation to be (oca(ized to the E/ membrane) but there are
a few di;erences:
o 4s trans(ation is happening) the hydrophobic transmembrane domains
are threaded through the E/ (umen
o 4fter trans(ation is comp(ete) the Fsigna( se1uencesF are E<T c(eaed
o;

The rough E/ a(so does g(ycosy(ation and disu(:de bond formation for proteins

The $olgi "om#le
5t is a group of membranous sacs stac=ed together (i=e co((apsed bas=etba((s
5t has the fo((owing functions:
o -odi:cation of proteins made in the rough E/
o 'orting and sending proteins to their correct destinations
o 'ynthesizing macromo(ecu(es (i.e. po(ysaccharides) to be secreted

The !o(gi is diided into cis) media() and trans
o The protein&containing esic(es coming o; the E/ go to the cis stac=
and eentua((y eBit at the trans stac= in a speci:c direction (as
determined by the !o(gi in concert with specia( signa(s on the protein
itse(f)
o To be more speci:c) once a protein (eaes the !o(gi) there are 2
secretory pathways it can go on:
?onstitutie secretory pathway: it goes direct(y to the ce((
surface and eBits no matter what
/egu(ated secretory pathway: they stay in their secretory
esic(es but don"t actua((y eBit unti( they get signa(ed to

+ysosomes
They do both autophagy (se(f&eating) when intrace((u(ar components are
messed up) and they participate in phagocytosis (when the ce(( engu(fs
something from the outside wor(d and it is now inside the ce(( to be bro=en
down) and (ast(y crinophagy (digesting unneeded eBcess secretory products)
The enzymes which digest stu; are ca((ed acid hydro(ases) because they on(y
wor= in acidic enironments

%eroisomes
They are ca((ed peroBisomes because hydrogen peroBide is a by&product of the
metabo(ic reactions they perform) which inc(ude:
o Lippid brea=down
o 9etoBi:cation of drugs in the (ier
Een though hydrogen peroBide is damaging) this is not an issue because
peroBisomes a(so hae an enzyme ca((ed cata(ase that conerts %2<2 &c %2<
2 <2

*art 2: 'tructura( E(ements of the 4nima( ?e((

Membranes of the Eu'aryotic "ell
The membrane inc(udes: phospho(ipids) g(yco(ipids) and cho(estero(
o *hospho(ipids are g(ycero( attached to two fatty acids and a phosphory(
group (maybe phosphory( cho(ine)
o !(yco(ipids hae fatty acids but then carbohydrate side chains
8atty acids form mice((es) but phospho(ipids form bi(ayer membranes (due to
steric hindrance)

*roteins are part of the membraned they perform many di;erent functions
o 'ome are ce((&surface receptors) which sit on the outside of the bi(ayer
and bind signa( mo(ecu(es that come a(ong) such as hormones) then
re(ay this message into the ce((
o <thers are channe( proteins) which se(ectie(y a((ow ions or mo(ecu(es
to cross the membrane
4nother way to c(assify proteins is integra( (goes through the entire
membrane and thus has portions in the membrane and portions out of the
membrane) or periphera( (pure(y on one side of the membrane or the other &
attached to integra( membrane proteins)
o /emember that proteins get embedded in the membrane as they are
made in the rough E/ & and then the esic(e comes and FfusesF with
the membrane

The membrane can be described with a Fiuid mosaic mode(F) where things
can moe (atera((y but not up and down (due to hydrophi(ic@hydrophobic
repu(sion)

The iuidity of a membrane is a;ected by what =ind of (ipids are in there
o 'aturated fatty acids on the phospho(ipids mean they are straighter
and thus easier to pac= together & this means we are LE'' 8Lg59
because the phospho(ipids are c(oser together
o ?ho(estero( :ts itse(f in between the (ipids and brea=s up the continuity
(thus ma=ing it -</E 8Lg59)

%assi&e Transmembrane Trans#ort
8aci(itated di;usion happens with: channe( proteins and carrier proteins
o ?hanne( proteins are bust a protein with an opening that the ion can
trae( through
'ometimes they are Fo(tage gatedF or F(igand gatedF) which
means that they can open and c(ose in response to o(tage
changes or (igand binding
o ?arrier proteins (4L'< transmembrane) don"t hae a tunne() but they
hae it so that the ion binds to the protein on one side of the
membrane) then the protein undergoes a conformationa( change so
that the mo(ecu(e moes to the other side of the membrane
There are di;erent =inds of carrier proteins:
gniports (transport one mo(ecu(e at a time)
'ymports (carry two mo(ecu(es in the same direction)
4ntiports (carry two mo(ecu(es in opposite directions)

There are a(so other things ca((ed pores where they are big enough that they
are E<T se(ectie in what they a((ow to pass
o These things are made by po(ypeptides ca((ed porins

)cti&e Trans#ort
5n actie transport) mo(ecu(es are moed against a gradient (not a(ways
concentration & it cou(d be e(ectrochemica( as we(()
o *rimary actie transport is coup(ed with 4T* hydro(ysis
o 'econdary actie transport is coup(ed to the iow of some other ion
9<>E its e(ectrochemica(@concentration gradient (this is di;erent from
the antiport in faci(itated di;usion because there we hae both ions
moing 9<>E their concentration gradients)

The (a.K )T%ase and the Resting Membrane %otential
, Ea2 out) 2 02 in
o Gut the thing is) 0 ions (ea= bac= <gT through potassium (ea=
channe(s) which means we end up with an oera(( positie charge
outside the membrane

The ro(es of the Ea@0 4T*ase are:
o -aintain osmotic ba(ance
o Estab(ish the resting membrane potentia(
o *roide the sodium concentration gradient for driing secondary actie
transport

Endocytosis and Eocytosis
Endocytosis is when the ce(( membrane inaginates to form a esic(e ca((ed an
FendosomeF
There are , =inds of endocytosis:
o *hagocytosis: non&speci:c upta=e of (arge particu(ate matter into a
phagocytic esic(e
o *inocytosis: non&speci:c upta=e of sma(( mo(ecu(es and eBtrace((u(ar
iuid
o /eceptor&mediated endocytosis: this is speci:c & the site of endocytosis
is a pit coated with c(athrin and has receptors that bind to speci:c
substrates
?(athrin is a :brous protein inside the ce(( that FanchorsF the
receptor proteins
Then the pit inaginates as usua( and stu; gets bro=en down
(a(though the receptor is returned to the coated pit once more)

"ell/Surface Rece#tors
The , main =inds of ce((&surface receptors are (igand&gated ion channe(s)
cata(ytic receptors) and !&protein coup(ed receptors
o ?ata(ytic receptors cause enzyme actiity to start or stop when
something binds to it (often this enzyme is a =inase or phosphatase)
5t is often the side chain hydroBy( of serine) threonine) or
tyrosine that gets phosphory(ated
o !&protein coup(ed receptors
These wor= by actiating a second messenger) which is a
mo(ecu(e that wi(( spread out to een more receptors to start
enzyme actiity going
'o the idea is that the receptor wou(d actiate !&proteins which
wou(d actiate adeny(y( cyc(ase enzymes (for eBamp(e) which
wou(d create cyc(ic 4-* mo(ecu(es which wou(d actiate protein
=inases@phosphatases) and thus the e;ect of a sing(e receptor is
mu(tip(ied manifo(d

4(so note that there are inhibitory !&protein (in=ed receptors
4nd a(so that sometimes phosphop(ipase ? is actiated instead of adeny(y(
cyc(ase

The "ytos'eleton
The cytos=e(eton not on(y proides support for the ce(() but 4L'< he(ps with
moement and substance transport
?ytos=e(eton is made up of microtubu(es ((argest)) intermediate :(aments) and
micro:(aments (sma((est)ethey are a(( proteins

The microtubu(e is made up of a(pha and beta g(obu(ar proteins which are
paired up (dimerized) and then made into a sheet which then ro((s into a tube
o >e can e(ongate the tube at the end by adding more a(pha@beta
sheets) but on(y at one end because the other end is anchored to the
microtubu(e organizing center (-T<?)) near the nuc(eus
o >ithin the -T<? is a pair of centrio(es & these are the things which are
going to moe out to the opposite ends of the ce(( during ce(( diision

9uring mitosis) we hae a Fmitotic spind(eF where we hae one pair of
centrio(es at either end of the ce((
o 'ome microtubu(es branch out in a star shape from the centrio(es) and
we ca(( these the FasterF
o <ther microtubu(es connect to the chromosomes) and we ca(( these
Fpo(ar :bersF
The po(ar :bers connect to the =inetochore :bers) which
connect to the =inetochore) which connects to the centrosome
of the chromosome

The -T<? is essentia( for mitosis) but the centrio(es are note(this has been
proed eBperimenta((y and a(so by (oo=ing at p(ants) who do not hae
centrio(es)

?i(ia are sma(( hairs on the ce(( surface which moe iuids past the ce(( surface
(thin= mucoci(iary esca(ator)
8(age((um is a (arge tai( which moes the ce(( by wigg(ing
Goth ci(ia and iage((a are made up of a m22 arrangement of microtubu(es)
where each microtubu(e is bound to its neighbor by a contracti(e protein ca((ed
dynein which causes moement of the :(aments past each other
o 4nd then the ci(ia@iage((a is anchored to the p(asma membrane by a
Fbasa( bodyF) which has the same structure as a centrio(e (a ring of m
trip(ets of microtubu(es)
o Eote that the structure and motie mechanism is di;erent for
pro=aryotic ci(ia@iage((ae

-icro:(aments are rods formed in the cytop(asm from the po(ymerization of
the g(obu(ar protein actin
o These guys are responsib(e for gross moements of the entire ce(() (i=e
pinching it in ha(f during mitosis and Famoeboid moementF) when
changing the cytop(asmic structure cause the cytop(asm and the rest
of the ce(( to moe in one direction

5ntermediate :(aments are not composed of a sing(e po(ypeptide (such as
actin) or a(pha@beta tubu(in)
o They are a(so di;erent from microtubu(es@micro:(aments in that they
are permanent) not continua((y re&assemb(ed and disassemb(ed
o They are good at proiding strong ce(( structure

"ell )dhesion and "ell 0unctions
'o basica((y there are di;erent ways to (in= ce((s together) and a big
determinant of this is whether or not we want to a((ow substances to go
between the ce((s

Tight bunctions are bands that wrap a(( the way around the ce((s
o This not on(y preents the passage of substances between ce((s) but it
a(so stops proteins in the p(asma membrane from going whereer they
want & thin= about intestina( ce((s) and how the baso(atera( surface is
theoretica((y continuous with the apica( surface) eBcept that since they
hae these things wrapped a(( the way around) stu; can"t moe from
the apica( to the baso(atera(
9esmosomes don"t sea( ce((s together but they do attach them by (in=ing in
certain spots) not a(( the way around the ce((
o Gasica((y we hae :bers that go a(( the way between ce((s) and are
anchored in the p(asma membranes by a p(a1ue made by the protein
=eratin and then are further attached to intermediate :(aments (thus
they don"t moe within the Fiuid mosaicF because they are anchored)
!ap bunctions are opening between ce((s that a((ow ions) amino acids) and
carbohydrates to miBebut not po(ypeptides or organe((es because they are
bigger
o They a(so a((ow for action potentia(s to pass

*art ,: The ?e(( ?yc(e and -itosis
'ee :gure: (be sure to (abe( what happens at each phase)










'ome ce((s are permanent(y stuc= in interphase (thin= neurons) and thus the
on(y way to rep(enish them is to dee(op stem ce((s from e(sewhere
?ancer occurs when this ce(( cyc(e screws up and reproduction happens too
fast
o 'ometimes this happens due to a gene which mutates (this is ca((ed an
oncogene)


?hapter 3
>ednesday) june 13) 2CC7
12:32 *-

Chapter *: Genetics and E+olution

*art 1: !enetics
The +anguage of $enetics
'ometimes when the 2 a((e(es of a gene are di;erent) the dominant a((e(e is
not eBpressed but rather there can be:
o 5ncomp(ete dominance & when there is a b(ended miB of both a((e(es
(i.e. red 2 white $ pin=)
o ?odominance & when the a((e(es are both eBpressed) but they are not
b(ended (i.e. thin= b(ood ce((s)
-ore comp(icated stu; can happen during inheritance:
o *(eiotropism: when a(tering one gene can seem to a;ect mu(tip(e
unre(ated things (i.e. eyes) foot)
o *o(ygenism: when mu(tip(e genes a;ect a sing(e trait (i.e. more than
one gene wi(( a;ect height)
o *enetrance: the (i=e(ihood that a person with a gien genotype wi((
eBpress a certain phenotype (because genes don"t a(ways direct(y (ead
to certain traits & perhaps they bust increase the probabi(ity of a trait)
(i=e cancer)
o Epistasis: when the eBpression of one gene depends on another gene
(i.e. a((e(e for cur(y hair doesn"t matter if one is ba(d)

Meiosis
'ee diagram:















/andom notes:
o The mabor sources of ariabi(ity are random segregation and
recombination
o /ecombination ta=es a (ong time) so meiotic prophase ta=es most of
the time in meiosis
o 'ometimes meiosis 55 does E<T begin immediate(y after te(ophase 5

Eon&disbunction is when chromosomes fai( to separate during anaphase (either
homo(ogous chromosomes in anaphase 5 or sister chromatids in anaphase 55)
>hen the non&disbunctie gametes fuse with norma( gametes) this can resu(t
in:
o Trisomy (zygote has , copies of a chromosome)
o -onosomy (one copy of a chromosome)
The e;ect of trisomy@monosomy (when not fata() cou(d be:
o 9own"s 'yndrome (trisomy of #21)
o Turner"s 'yndrome (1 k but no ` chromosome)
gsua((y when seB chromosome are ino(ed) eBterna(
appearance wi(( be ma(e if there is at (east one ` chromosome
%oweer a(most eeryone wi(( be steri(e and menta((y retarded

Mendelian $enetics
-ende("s Laws:
o *rincip(e of 'egregation: 2 a((e(es of an indiidua( are separated and
passed on to the neBt generation sing(y
o Law of 5ndependent 4ssortment: the a((e(es of one gene wi(( separate
into gametes independent(y of a((e(es for another gene
'ome more terms:
o Test cross: when we cross a p(ant for un=nown genotype with a (pure&
breeding) one of =nown genotype
o 81 generation: the progeny of a test cross

+in'age
Lin=age is the fai(ure of genes to disp(ay independent assortment (i.e. when
they are on the same chromosome)

5n any gien cross between genes on the same chromosome) some
phenotypes of the progeny wi(( demonstrate (in=age and some wi(( not
o Gy ana(yzing the ratio between these two) we can predict how far apart
on the chromosome the genes are because we =now that crossing oer
is proportiona( to distance apart
o The Ffre1uency of recombinationF is gien as the number of
recombinant phenotypes resu(ting from a cross diided by the tota(
number of progeny

Se +in'age and %edigrees
Traits determined by genes on the k or ` chromosome are ca((ed FseB&(in=ed
traitsF
o k&(in=ed traits are fre1uent) but `&(in=ed traits are much more rare
o -en are FhemizygousF for k&(in=ed traits because they on(y hae one k
chromosome and thus they eBpress whateer a((e(e they hae) een if
it is recessie

*edigrees are charts of a fami(y that can be used to determine the nature of a
gene
?onentions:
o -a(es are s1uares and fema(es are circ(es
o 4 cross (mating) is represented by a horizonta( (ine connecting the
ma(e and fema(e
o <;spring from a cross are connected to their parents by a ertica( (ine
and to their sib(ings by a horizonta( (ine
o 5ndiidua(s anicted by a trait being studied are shaded in
<rder of ana(ysis:
o 5s the a((e(e that causes the trait dominant or recessiel
o 5s the gene ino(ed carried on a seB chromosomel
o 5f the disease is seB&(in=ed) is it on the k or ` chromosomel
o ?a(cu(ate the probabi(ities of inheritance where necessary.
o 5f more than one trait is ino(ed) go through 'teps 1&3 for each) then
determine the re(ationship between the two traits

%o#ulation $enetics
*opu(ation genetics describes the inheritance of traits in popu(ations oer time
o *opu(ation is de:ned as Fmembers of a species that mate and
reproduce with each otherF
o 5nstead of thin=ing about genomes of particu(ar species) we thin=
about gene poo(s
o 4nd a =ey ariab(e is Ffre1uency of an a((e(eF in a popu(ation) which is
the number of a((e(es that eBist diided by the number of tota( a((e(es

The F%ardy&>einberg LawF states that the fre1uencies of a((e(es in the gene
poo( of a pop(uation wi(( not change oer time) proided that the fo((owing
assumptions are true:
o There is no mutation
o There is no natura( se(ection
o There is random mating
o There is no migration
o The popu(ation is suDcient(y (arge to preent random drift in a((e(e
fre1uencies
/andom drift is when random things happen to change a((e(es &
something which can hae a signi:cant e;ect in sma((er
popu(ations since by de:nition they are unab(e to hae enough
ariabi(ity and size to FeBpungeF the randomness

>e can a(so use the concept of a((e(e fre1uency to do this:
o >e =now * 2 p $ 1
o Thus *2 2 2*p 2 p2 $ 1
Then *2 wou(d be the percentage of F**F) 2*p wou(d be the
percentage of *p) and p2 wou(d be the percentage of pp
4(so) since we =now that a((e(e fre1uencies tend to remain the
same oer time) we can conc(ude that genotype fre1uencies wi((
a(so remain constant oer time
>e hae the idea of F%ardy&>einbergF e1ui(ibrium) which is when the a((e(e
fre1uencies no (onger change within a popu(ation
o 5t ta=es one generation to reach this & that is) if we start out with
mating pure&breeding species) the genotypes of their chi(dren wi(( be
di;erent from their genotypes) but that"s <0 because the pure&
breeding species were not in %&> e1ui(ibrium
o The true e1ui(ibrium ta=es one generation to achiee

*art 2: Eo(ution
E&olution by (atural Selection
4 =ey term in eo(ution is :tness: it is how successfu( an anima( is in passing
on its a((e(es to future generations (E<T how we(( they are adapted to an
enironment) or how we(( it can feed) etc.)
o Thus :tness can be conferred simp(y by haing tons of progeny

8irst(y (et"s note that natura( se(ection wi(( E<T introduce genetic diersityd i.e.
it cannot create new a((e(esea(( natura( se(ection does is a(ter a((e(e
fre1uencies by acting on the genetic diersity present at the time
%oweer there are some things which 9< introduce genetic ariabi(ity:
o Eew a((e(es: as a resu(t of mutations in the genome (but remember
that to hae a (asting e;ect) this mutation must introduce itse(f in the
!E/- L5EEf)
o Eew combinations of a((e(es: this is when we hae independent
assortment) recombination) and random segregation during meiosis
This wi(( E<T create new a((e(es) but it can produce di;erent
phenotypes that are then Fnatura((y se(ected onF and thus a
certain =ind of phenotype wi(( increase in fre1uency and thus
those a((e(es wi(( as we((

There are di;erent FmodesF of natura( se(ection that can hae di;erent e;ects
on a popu(ation:
o 9irectiona( se(ection: po(ygenic traits often fo((ow a be((&cured
eBpression) which means that if we remoe the eBtremes at one end)
the entire cure wi(( shift so as to remain Fnorma(F
o 9iergent se(ection: possib(y natura( se(ection cou(d remoe the
popu(ation in the -599LE of a be(( cure) meaning that we on(y (eae
the two eBtremes & this wou(d sp(it the popu(ation in two and possib(y
een mean the creation of new species
o 'tabi(izing se(ection: se(ect against G<T% eBtremes of a popu(ation)
which dries up the number of anima(s at the aerage een more
o 4rti:cia( se(ection: humans interene by contro((ing who mates with
who
o 'eBua( se(ection: there is no random se(ection of mating but rather
anima(s wou(d mate with other anima(s based on mutua( attraction due
to some mating disp(ay
o 0in se(ection: how sometimes you might sacri:ce yourse(f for your =in
and thus the process of natura( se(ection might not wor=...

The S#ecies "once#t and S#eciation
4 species is a group of organisms which are capab(e of reproducing with each
other seBua((y
o Eot on(y that) but their o;spring a(so hae to be capab(e of
reproducing with each otherf (thus horses and don=eys are not from
the same species because a(though they can reproduce and create a
mu(e) the mu(e is steri(e)
There are 2 main c(asses of reasons why species do not more often try to
mate with each other:
o *re&zygotic barriers: this is where the hybrid zygote cannot een be
formedefor mu(tip(e reasons:
Eco(ogica( (i.e. physica( boundaries)
Tempora( (mating times are not oer(apping)
-echanica( (i.e. practica( size issues)
Gehaiora( (you hae to perform a certain ritua( :rst)
!ametic (the sperm&egg recognition system doesn"t :t)
o *ost&zygotic barriers (preent the dee(opment) suria() or
reproduction of hybrid indiidua(s)

F'peciationF is the creation of a new speciesehoweer a(( new species must
come from eBisting species
There are di;erent ways this happens) howeer:
o 4nagenesis is when one bio(ogica( species simp(y morphs into another
a(together
o ?(adogenesis is when we hae FbranchingF) where one species
diersi:es and becomes 2 or more new species
'ometimes this is due to geographica( iso(ation: Fa((opatric
iso(ationF
'ometimes it happens in the same area (perhaps due to
diergent se(ection): Fsympatriac iso(ationF

>e can c(assify organisms based on these assumptions because we can
anticipate species wi(( eo(eefor eBamp(e:
o >e =now that re(ated species wi(( share physica( characteristics) thus
Fhomo(ogous structuresF are physica( features shared by 2 di;erent
species as a resu(t of a common ancestor
/e(ated) Fana(ogous structuresF sere the same function in 2
di;erent species but are E<T due to common ancestry
4 resu(ting phenomenon is Fconergent eo(utionF) when 2
di;erent species come to share 4 L<T of ana(ogous structures
due to simi(ar se(ectie pressures) but it is E<T because they
eo(ed from the same species
The opposite of this is Fdiergent eo(utionF) when
diergent se(ection causes c(adogenesis
4nd :na((y) Fpara((e( eo(utionF is when 2 species go
through simi(ar eo(utionary changes due to simi(ar
se(ectie pressures

Taonomy
>e c(assify organisms in . di;erent categories: =ingdom) phy(um) c(ass) order)
fami(y) genus) and species
0now Tab(e 3.2

'ome important terms:
o ?epha(ization means that there is the dee(opment of a head region
with a brain and sensory organs
o Gi(atera( symmetry: this is when we sp(it something down the midd(e
and see if the two sides are mirror images of each other

The Origin of +ife
oep


?hapter 6
-onday) june 27) 2CC7
7:,A *-

Chapter ,: -er+ous and Endocrine .ystems

*art 1: Eeurona( 'tructure and 8unction
!ntroduction
%igh (ee(: rea(ize that the nerous and endocrine system are
interconnectedefor eBamp(e) the pituitary and the adrena(s (both endocrine
g(ands) are contro((ed by the nerous system

Structure of the (euron
'ee 8igure 1) pg. 1Amenote the:
o ?e(( body (a=a soma)
o 9endrites
o 4Bon
o 4Bon termina(s
'igna( direction goes from dendrites to aBon
?e(( body inc(udes the nuc(eus) as we(( as most norma( ce(( bio(ogy
processese
o 'o it has a ce(( membrane and a cytop(asm as usua(e
Gipo(ar neurons hae one dendrites) whi(e mu(ti&po(ar neurons hae mu(tip(e
dendrites
o %oweer) note that a(( neurons on(y hae <EE aBon

The )ction %otential
'ee 8igure in notes (thin=ing about the ce(( membranee)
o Ea) ?a) ?( concentrated outside
0 concentrated inside
o Ea@0 4T*&ase ebects , Ea and brings in 2 0) but 0 are a((owed to (ea=
bac= out through 0 (ea= channe(
This resu(ts in a negatie charge inside the ce(( of &.C m+
(norma((y)
o There are 2 main o(tage&gated channe(s & one for Ea and the other for
0
>hen the membrane potentia( reaches the thresho(d (&6C m+))
the o(tage&gated channe(s open and we get depo(arization
9epo(arization brings us to 2,C m+

'o after each time a neuron :res) there is are 2 refractory periodse
o 4G'<LgTE: the o(tage&gated Ea channe(s are resetting and there is no
chance for more Ea to get through
o /EL4T5+E: the membrane is hyper&po(arized and so on(y an eBtra&(arge
stimu(us wi(( set o; another action potentia(
This is because the 0 channe(s hae not c(osed yet and so (ots
of negatie charge is sti(( coming in (in the form of positie
charge (eainge)
'ee 8igure ,) pg. 1m,e(et"s ta(= through ite
o >e"re norma((y at &.C m+ but upon the arria( of an eBtra&ce((u(ar
signa() we get a bit of sodium coming into the ce((e
o >hen enough comes in that we get to &6C m+) the o(tage&gated Ea
channe(s open and positie charge enters the ce(( unti( we get to 2,C
m+
o 4t this point) the Ea channe(s c(ose and 0 channe(s open so that there
is a rush of negatie charge into the ce((
o 'o much negatie charge comes into the ce(( that we actua((y go -</E
EE!4T5+E than norma( & down to around &mC m+
o >e recoer from this state through action ia the 0 (ea= channe(s (E<T
the o(tage&gated ones) and the Ea@0 4T*&ase

Let"s ta(= about sa(tatory conductione'ee 8igure 6) pg. 1m6
o Eote that mye(in coats the neuron (Fmye(in sheathsF) and there are
on(y openings at speci:c points a(ong the neuron
-ye(in is made by 'chwann ce((s
-ye(in ma=es the ce(( membrane impermeab(e to ions
o The openings are ca((ed Eodes of /anier and there are Ea o(tage&
gated channe(s c(ustered at the nodes which a((ow for tons of Ea entry
at those separated points
o 'o this resu(ts in rapid conduction and bursts of Ea at the nodes & the
rapid FbumpingF e;ect which resu(ts is =nown as Fsa(tatory conductionF

Syna#tic Transmission
There are , di;erent things which a neuron can synapse onto:
o -usc(e ce((s
o !(ands
o <ther neurons
There are di;erent =inds of synapses:
o E(ectrica( (i.e. gap bunctions found in the functiona( syncytium of the
heart)
o ?hemica( (where action potentia( are conerted to chemica( signa(s) i.e.
neurotransmitters)
'ee 8igure 7enoticee
o The (igand&gated Ea channe(s (these open and cause an action
potentia( on the second neuron)
o The neurotransmitter&containing esic(es in the :rst neuron
o The ca(cium iniuB
This happens on the :rst neuron as a resu(t of the action
potentia(
The ca(cium causes the esic(es to fuse with the ce(( membrane
and re(ease their neurotransmitters
4fter the neurotransmitters are re(eased) they are ta=en up by the pre&
synaptic neuronethen they are either recyc(ed) bro=en down) etc.
o i.e. acety(cho(inesterase brea=s down acety(cho(ine and thus causes
the signa( to shut down

Eote that neurotransmitters can be either eBcitatory or inhibitory & they can
either depo(arize or hyperpo(arize the post&synaptic neuron
o i.e. !4G4 causes the membrane potentia( become more negatie
o EBamp(es of other ET"s: gamma&aminobutyric acid (!4G4)) serotonin)
and norepinephrine
Eote that a gien pre&synaptic neuron can on(y re(ease one =ind of ET) but a
post&synaptic neuron can receie mu(tip(e types of ET"s (in fact this is
probab(y how spatia( summation wou(d wor=)

Summation
The :rst thing to note is that once an action potentia( begins) the speed and
magnitude do E<T change (i.e. the a((&or&none princip(e)
o The on(y thing that can a;ect the speed is the size of the aBon
'o the =ey thing is the regu(ation of whether or not the action potentia( :res at
a((
The re(ease of neurotransmitters by one 4* on one pre&synaptic neuron is
usua((y not enough to bring the post&synaptic membrane to thresho(d

'o the decision is madeebased on how many E*'* (eBcitatory post&synaptic
potentia() and 5*'* (inhibitory post&synaptic potentia() we gete
There are a(so 2 =inds of summation:
o Tempora( (when a sing(e aBon termina( :res so 1uic=(y that the e;ects
of mu(tip(e :res combine)
o 'patia( (we combine the e;ects of mu(tip(e aBon termina(s to see if
they (ead to a depo(arization eBceeding &6C m+)

*art 2: <rganization of the %uman Eerous 'ystem
Functional Organization
There are , functions of the nerous system:
o 'ensory & receie information coming from the outside to the inside
o 5ntegratie & processing the information and deciding what to do with it
o -otor & sending information from the ?E' to the e;ectors (thus it is not
on(y musc(e they innerate) but g(ands as we(()

'o there are di;erent =inds of neurons to go a(ong with this:
o 4;erent: carry information from the sensory organs to the ?E'
o E;erent: carry information from the ?E' to the e;ectors
i.e. motor neurons

/eieB arcs: these things are nerous system pathways that start with
something being sensed and end with an e;ector performing some action
o -ono&synaptic reieB arc: this is when there are bust 2 neurons and 1
synapse ino(ed) for eBamp(e if a sensory neuron senses a musc(e
stretching) then sends the sing(e a(ong its aBon to the spina( cord
where it synapses with a motor neuron) which sends bac= a signa( to
some musc(e to contract in response
o 9i&synaptic reieB arc: when the sensory neuron synapses with more
than one post&synaptic neuron
'o not on(y the motor neurone
Gut a(so synapse with an Finhibitory interneuronF which wou(d
then go and synapse with a neuron contro((ing another musc(e
to cause it to re(aB
'o we end up with one musc(e contracting and the other
re(aBing (this is an eBamp(e of reciproca( inneration)

'ee pg. 2C1e(et"s ta(= about the organization of the nerous system
o 'omatic s. autonomic:
'omatic is s=e(eta( musc(e (most(y o(untary reieBes) and
conscious sensation
4utonomic is smooth musc(e and interna( organs (most(y
ino(untary)
Eote that both somatic and autonomic hae a;erent and
e;erent functions
o >e can further brea= down the E88E/EET part of the autonomic
diision into sympathetic and para&sympathetic:
'ympathetic is associated with the :ght or iight response)
adrena(ine) epinephrine) etc. (basica((y dea(ing with stress)
*arasympathetic is associated with resting and FruminatingF
(means the digestion of food)

'ee notes for chartema=e sure you understand >%` for each one (so donqt
hae to memorize)
a$le ,.1 is the same thin%...

)natomical Organization
'ee 8igure in notesenote:
o !ang(ions are a c(uster of soma (ce(( bodies) which are (ocated outside
the ?E' (<gT'59Ef)
o 'ympathetic gang(ion are interconnected so that the :ght@iight
response can be coordinated
o Getween epinephrine and norepinephrine: one is a hormone and the
other is a neurotransmitter (l & chec= into thise)

?E' anatomica( organization
o 8i(( this in...

'ee Tab(e in notese

*E' anatomica( organization
o 4(( neurons entering and eBiting the ?E' are carried by 12 pairs of
Fcrania( neresF (go to the brainstem) and ,1 pairs of Fspina( neresF
(go to the spina( cord)
o <ther than that) we hae to understand that there are di;erent nere
organizations for the somatic nerous system) the autonomic
sympathetic nerous system) and the autonomic parasympathetic
nerous system

'omatic nerous system
o 4;erent
'o now we are ta(=ing about sensory neuronse
The neuron set&up is that we hae a (ong dendrite going from
the sensory receptor ((et"s say the s=in on the bac= of the hand)
to the ce(( body) which is (ocated in a Fdorsa( root gang(ionF
The dorsa( root gang(ion is a bunch of somatic sensory
ce(( bodies c(umped together) and it is Fdorsa(F meaning
that it is Fto the bac= ofF the spina( cord
5t is protected by the ertebra( co(umn but not by the
meninges
Then from that ce(( body) the aBon eBtends into the spina( cord
where it synapses somewhere either in the spina( cord or the
brain stem
o E;erent
8irst rea(ize that it is the somatic E') meaning that on(y s=e(eta(
musc(e ce((s are innerated) meaning that the on(y e;erent
neurons are -<T</ EEg/<E'
The motor neurons hae ce(( bodies (and therefore dendrites) in
the brain stem or entra( (front) portion of the spina( cord) and
then hae a (ong aBon to the s=e(eta( musc(e
They use acety(cho(ine as their neurotransmitter
4utonomic nerous system
o 4;erent
This is not on the -?4T because we don"t =now too much about
it yet...
o E;erent
<ne characteristic common to both sympathetic and
parasympathetic is that instead of a sing(e neuron going from
?E' to e;ector) there are two: ca((ed the Fpre&gang(ionicF and
Fpost&gang(ionicF neurons
This is because we hae one neuron coming out of the spina(
cord) but instead of going to the e;ector it goes to a gang(ion
(c(uster of ce(( bodies)eand then from there another neuron
comes out to go to our e;ector
The sympathetic and para&sympathetic di;er in terms of the
(ocation of the gang(ion) the types of neurotransmitters used)
etce'ee tab(e:











The adrena( g(and is an important part of the nerous system & there are 2 of
them) one aboe each =idney
There are 2 parts to the adrena( g(and: corteB (outer portion) and medu((a
(inner portion)
o The corteB is an endocrine g(and & it secretes g(ucocorticoid (a=a
cortiso() and minera(ocorticoid (a=a a(dosterone)
o The medu((a is part of the sympathetic nerous system & it is basica((y
an eo(ed bunch of post&gang(ionic neurons that are stimu(ated by
pre&gang(ionic neurons
>hen they are stimu(ated) they re(ease epinephrine (a=a
adrena(ine)) which is a fast&acting hormone that p(ays a big ro(e
in the :ght&or&iight response
'o remember: norepinephrine is an ET) whi(e epinephrine is a hormone (a=a
49/EE4L5EE)

*art ,: 'ensation
Ty#es of Sensory Rece#tors
$ustation and Olfaction
1earing and the *estibular System
*ision2 Structure and Function

*art 3: The Endocrine 'ystem
1ormone Ty#es2 Trans#ort and Mechanisms of )ction
Let"s reiew the di;erence between endocrine and eBocrine g(andse
o Endocrine g(ands are 9g?TLE'' g(ands that secrete products into the
b(oodstream ia capi((aries such that the products eentua((y go to
other ce((s with appropriate receptors
o EBocrine g(ands are those whose products empty into the eBterna(
wor(d ia 9g?T'
Eote that the !5 tract counts as the eBterna( wor(d (thus the
pancreas is an eBocrine g(and)

The two types of steroid hormones are peptide hormones and steroid
hormonesethere are signi:cant di;erences between the two) see tab(e:


























<ther facts about hormones:
o *eptide hormones are diided into two types: po(ypeptides and amino
acid deriaties
!(ucose is an eBamp(e of a po(ypeptide
Epinephrine is an eBamp(e of an amino acid deriatie & it is
based on tyrosine and secreted by the adrena( medu((a
o 4s for steroids) the only body parts which secrete them are:
8or seBua(ity) reproduction) dee(opment etc: the testes)
oaries) and p(acenta
8or water ba(ance and other processes: adrena( corteB

Organization and Regulation of the 1uman Endocrine System
Endocrine system is a(( about maintaining homeostasis: which is to =eep the
body conditions within certain (imits
o i.e. ?a(citonin & decreases ca(cium concentrations in the b(ood

`ou hae to rea(ize that there are mu(tip(e (ee(s of hormona( contro(
o The (owest (ee( is how hormones direct(y contro( bodi(y functions) for
eBamp(e a(dosterone wou(d a;ect water retention in the =idneys
o Gut then there are Ftropic hormonesF) most(y re(eased by the anterior
pituitary) which contro( those hormones by inhibiting or stimu(ating
their re(ease
o 4nd then een on top of the tropic hormones) there is a neuro(ogica(
(ayer of contro( in that the hypotha(amus (brain tissuef) re(eases
Fre(easingF and FinhibitingF factors (a=a hormones) to the pituitary so
as to contro( the tropic hormones

The hypotha(amic&pituitary contro( aBise
o This contro( aBis is basica((y the re(ationship between the
hypotha(amus and the pituitary g(and
o The two are connected ia the Fhypotha(amic&pituitary porta( systemF
a=a the Fhypotha(amic&hypophysia( porta( systemF (since the pituitary
g(and is a(so =nown as the hypophysis)
The hypotha(amus is diided intoe
o 4nterior (adenohypophysis): this is a norma( endocrine g(and in that it
is a;ected by the re(easing@inhibiting factors and it re(eases hormones
o *osterior (neurohypophysis): this is a neuroendocrine g(and in that it is
composed of brain tissue (hence FneuroF) but it re(eases hormones
4ctua((y the hormones are made in the hypotha(amus and
re(eased from the posterior pituitaryethe posterior pituitary is
basica((y bust a bunch of aBons

Ma3or $lands and their 1ormones
#emori)e a$le ,./0 p%. ""(

&Chapter , Addendum'

"(S )natomical Organization
&1ll this in23'

*art ,: 'ensation
Ty#es of Sensory Rece#tors
Two ery broad categories of sensory receptors are eBteroreceptors (detect
stimu(i from the outside wor(d) and interoreceptors (detect interna( stimu(i)

There are 6 types of sensory receptors: mechanoreceptors) chemoreceptors)
nociceptors) thermoreceptors) and e(ectromagnetic receptors
o -echanoreceptors: most basica((y) these receptors respond to
mechanica( disturbances such as pressure) ibration) etc.
8or eBamp(e we hae the *acinian corpusc(e) which sends an
action potentia( wheneer its membrane is depressed
4(so there is the auditory hair ce(() which (as we wi(( (ater
discuss) is in the inner ear and detects ibrations from sound
waes
4(so) those things that detect stretch in the intestina( wa(( and
signa( that gastrin re(ease are mechanoreceptors
o ?hemoreceptors: these guys (predictab(y) respond to particu(ar
chemica(s
8or eBamp(e) o(factory receptors detect airborne chemica(s
!ustatory chemoreceptors detect chemica(s in the food we eat
which gie it its taste
?hemoreceptors in the medu((a as we(( as carotid and aortic
arteries detect changes in b(ood p%) ?<2) <2) etc.
o Eociceptors: these are pain receptors which wor= by detecting
chemica(s that are re(eased when tissue is damaged (yes) this means
that they are simp(e chemoreceptors in a way)
<ne thing that we notice with these guys is that they can be
imprecise && that"s why we get things (i=e referred pain) which is
when we fee( pain in our arm during a heart attac= for eBamp(e
o Thermoreceptors: changes in temperature
o E(ectromagnetic receptors: stimu(ated by e(ectromagnetic waes && i.e.
the rods@cones of the eyef

There are a(so proprioceptors:
o These are basica((y receptors which a((ow us to be aware of ourse(es &&
i.e. what position is our body in) etc.

$ustation and Olfaction
<0 :rst) this is bust an app(ication of chemoreceptors

!ustation is taste) and basica((y there are 3 main =inds of taste receptors on
the tongue that respond to di;erent chemica(s and te(( us what we are
FtastingF
o 'weet receptors detect g(ucose
o 'a(ty receptors detect sodium (Ea2)
o Gitter receptors detect basicity
o 'our receptors detect acidity
The unit of taste is the Ftaste budF) and it consists of epithe(ia( ce((s
surrounding a Ftaste poreF where the hairs are (ocated which detect those
di;erent things

<(faction is taste) and here the receptors are high in the nasa( caity
?hemica(s in the air come through the mucus

1earing and the *estibular System
5ntroduction
o 9iscuss the anatomy of the ear.
.ee 4i%ure 15.160 p%. (*5
5t is diided into the outer) midd(e) and inner ear:
<uter:
The *5EE4 directs sound waes into the ear
The sound waes trae( through the E4/ ?4E4L
which is sea(ed at the end by the T`-*4E5?
-E-G/4EE (a=a eardrum)
-idd(e:
<era(( it is bust an 45/&85LLE9 ?4+5T` that (in=s
up with the E4'<*%4/`Ek through the
Eg'T4?%54E TgGE
gsua((y the Eustachian tube is b(oc=ed but
sometimes it is open so that the pressure
from inside the ear can e1ui(ibrate with
atmospheric pressure during things (i=e
yawning
5nside this air&:((ed caity we hae T%/EE '-4LL
G<EE': the ma((eus (hammer)) incus (ani()) and
stapes (stirrup)
These bones are a(( attached by F%5E!E'F
& and the ma((eus is connected to the
tympanic membrane and the stapes is
attached to the membrane which
separates the midd(e ear from the inner
ear (this is how sound from the outside
gets conducted through this inner
portionf)
5nner:
<0 here there are T>< mabor sensory structures)
each with a di;erent purpose:
+E'T5GgL4/ 4**4/4Tg': it is for our
sense of e1ui(ibrium (more on this (ater)
?<?%LE4: it is (i=e a coi(ed tube (i=e a
snai( that (ies within a bony caity ca((ed
the L4G`/5ET%
5t is separated from the midd(e ear
by the <+4L >5E9<> and /<gE9
>5E9<>
%earing is our perception of sound
o >hat do we remember from physics that is important herel
%igh s. (ow sounds (i.e. pitch) correspond to high&fre1uency
and (ow&fre1uency waes
'oft s. (oud sounds correspond to the 4-*L5Tg9E of the wae
'ound transduction is a mu(ti&step process
o >hat"s the oera(( pathway for how hearing wor=sl
4ir waes &c mechanica( ibrations &c iuid waes &c chemica(
signa(s &c action potentia(s
o !o into a (itt(e more detai( for each step.
.ee 4i%ure 15.170 p%. (*"
The sound waes trae( through the ear cana( and hit the
tympanic membrane) which causes the three bones in the
midd(e ear to ibrate in se1uence
The (ast bone in the se1uence ('T4*E') is attached to the <+4L
>5E9<> which is connected to the coch(ea of the inner ear
The coch(ear has iuid in it and waes are created in this iuid
which actiate the 'EE'</` %45/ ?ELL' inside the coch(ear as
they moe through
The waes moe through the entire coch(ea and the ibration
energy FeBitsF at the /<gE9 >5E9<>) which goes bac= into
the midd(e ear area
The hair ce((s get stimu(ated and action potentia(s are :red in
the primary sensory neurons which bring the signa( to the brain)
and o; we gof
The coch(ea of the inner ear is :((ed with iuid
o 9iscuss the anatomy of the coch(ea in more detai(.
There are , para((e( Fchanne(sF which are :((ed with iuid:
estibu(ar duct) coch(ear duct (in the midd(e)) and tympanic
duct
The estibu(ar and tympanic ducts are continuous (they
meet at the tip of the coch(ear at the opening =nown as
the %EL5?<T/E-4) and they contain iuid =nown as
*E/5L`-*%
The coch(ear duct is :((ed with EE9<L`-*%
The coch(ear duct contains the </!4E <8 ?</T5) which is
where a(( the action happens:
.ee 4i%ure 15."50 p%. (**
<0 so the organ sits on the G4'5L4/ -E-G/4EE and is
coered by the TE?T</54L -E-G/4EE
>hen iuid waes moe through the coch(ea) they
disp(ace these membranes and they cause the hair ce((s
of the organ of ?orti to moe side to side
.ee 4i%ure 15."10 p%. (*,
The idea is that there are 'TE/E<?5L54 stic=ing
out of the hair ce((s and they hae Fprotein
bridgesF between them. >hen the ci(ia
bend@moe around as waes pass by) these
bridges are a;ected and they respond by opening
ion channe(s to a((ow ca(cium re(ease) action
potentia(s) etc.
g(timate(y the signa(s get passed down the
?<?%LE4/ EE/+E
'ounds are processed :rst in the coch(ea
o EBp(ain how we account for di;erent *5T?%E' of sound.
<0 this is a(( about the G4'5L4/ -E-G/4EE (remember what
that isl). The parts of the membrane that are near the round
and oa( windows is 'T588 4E9 E4//<>) but it is wider and
more ieBib(e in the midd(e of the coch(ea (the part furthest
from the round@oa( windows)
4nd the higher&fre1uency waes create maBima( disp(acement
of the basi(ar membrane EE4/ the windows) whereas the (ower&
fre1uency waes disp(ace maBima((y at that dista( end
Thus by :guring out where the hair ce((s are sending the most
action potentia(s) we can :gure out the fre1uency of the waes
and thus the pitchf *retty sic=f
o %ow about (oudnessl
<0 this is a (itt(e more basic & it"s bust the amp(itude of the
wae) which wi(( a;ect the 8/EHgEE?` of the action potentia(s
sent
%earing (oss may resu(t form mechanica( or neura( damage
o 9iscuss the , forms of hearing (oss.
?onductie hearing (oss: sound can"t get through the eBterna(
or midd(e ear. This cou(d be as simp(e as ear waB p(ugging the
ear cana( to diseases which impede the ibration of one of the
bones
'ensorineura( hearing (oss: this is when the structures of the
inner ear get damaged. 8or eBamp(e) hair ce((s can degenerate
oer time and cause presbycusis
?entra( hearing (oss: the neura( pathway from the ear to the
centra( corteB is damaged (this is the most rare)

4s for the E4/ 4E9 EHg5L5G/5g-...
o The semi&circu(ar cana(s of the ear detect motion and therefore he(p
the body to maintain e1ui(ibrium
o just (i=e with sound) they wor= on the basis of hairs detecting
moement and then sending neura( impu(ses
o <ther ba(ance&monitoring organs in the ear:
gtric(e &c for static e1ui(ibrium
'accu(e &c for (inear acce(eration

*ision2 Structure and Function
5ntroduction
o %ow does ision wor=l %ow is this re(ated to the way a camera wor=sl
Gecause (ight enters the eye through the *g*5L and is focused
by a LEE' on a (ight&sensitie surface && the /ET5E4
just as with a camera) the pupi( can adbust to contro( how
much (ight gets in
Then the photoreceptors of the retina transduce (ight energy
into an e(ectrica( signa(
Then the signa( goes through arious neura( pathways
The Eye is *rotected by the '=u((
o 9iscuss the EkTE/E4L anatomy of the eye.
.ee 4i%ure 15."60 p%. (,5.
5t"s pretty basicewe hae a bony caity in the face ca((ed an
</G5T that is formed by the facia( bones of the s=u((
There are 7 EkT/5E'5? E`E -g'?LE' which attach to the outer
surface of the eye and contro( its moement
The eye(ids c(ose oer the top part of the eye
The L4?/5-4L 4**4/4Tg' is a system of g(ands and ducts that
=eeps a iow of tears washing oer the cornea so that it is moist
and c(ean
The E4'<L4?/5-4L 9g?T drains these tears into the
nasa( caity
o 9iscuss the 5ETE/E4L 4E4T<-` of the eye.
.ee 4i%ure 15."80 p%. (,1
There are 2 compartments of the eye) and they are separated
by a LEE'
8/<ET ?<-*4/T-EET:
This is most(y :((ed with 4HgE<g' %g-</) a (ow&
protein p(asma&(i=e iuid
G4?0 ?<-*4/T-EET: this is most(y :((ed with the
+5T/E<g' G<9`) which is a matriB that he(ps maintain
the shape of the eyeba((
o Ta(= about the path of (ight through the eye.
5t comes through the ?</EE4) which is a transparent dis=
continuous with the '?LE/4
Light goes through the a1ueous humor) through the opening of
the pupi() and hits the LEE'
The (ight rays are bent so that they focus on the /ET5E4
There is a spot on the retina ca((ed the <*T5? 95'0) from
which neurons of the isua( pathway eBit the eye as the
<*T5? EE/+E
/ight neBt to this optic dis= is the 8<+E4 surrounded by
the -4?gL4) which together are the regions of the retina
with the -<'T 4?gTE ision
*hotoreceptors Transduce Light into E(ectrica( 'igna(s
o Huic=(y compare@contrast rods and cones.
/ods and cones are the 2 =inds of *%<T</E?E*T</' in the eye
/ods are <+E/4LL more numerous (2C:1 ratio)) but cones are
more concentrated in the 8<+E4
/ods are more for mono&chromatic night&time ision and (ow&
(ight enironments) whi(e cones are good for %5!%&4?g5T` and
?<L</ ision during the daytime
o 9iscuss the structure of rods and cones.
.ee 4i%ure 15.(80 p%. (,8
<0 there are T%/EE main segments:
<uter segment that touches that *5!-EET E*5T%EL5g-
of the retina
5nner segment that ho(ds the mabor organe((es (i=e
nuc(eus) 4T*@protein synthesis) etc.
Gase segment that synapses with the bipo(ar ce((s
o Ta(= about isua( pigments. %ow do they wor=l
These are bound to the ce(( membranes in the <gTE/
'E!-EET' of the photoreceptors
Their bob is to do the 4?Tg4L T/4E'9g?T5<E from (ight energy
to a change in membrane potentia(
/ods hae <EL` <EE =ind of isua( pigment: /%<9<*'5E
?ones hae , di;erent =inds but they are a(( c(ose(y
re(ated to rhodopsin
Each of the , cone pigments absorbs a particu(ar
wae(ength of (ight the most & /E9) !/EEE) or GLgE
(these are the basic co(ors of (ight) as you =now)
o 'o what actua((y happens when the (ight hits those rods or conesl
&1ll this in23'
9efects in isua( acuity
o 4(right) so the dea( is that (ight goes through the cornea and the (ens
before hitting the pupi(
Goth the cornea and the (ens change the path of the (ight to a
certain degree such that the rays arrie eBact(y on the retina
%oweer) if the cornea@(ens are improper(y bent) the (ight may
be focused too far in front of the retina) or too far behind it
o There are , ways this can go wrong:
-`<*54: (ight is focused in front of the retina && this causes
nearsightedness
>e correct this by putting a concae (dierging) (ens in
front of the eye
%`*E/<*54: (ight is focused behind the retina && this causes
farsightedness
>e correct by putting a coneB (conerging) (ens in front
of the eye
*/E'G`<*54: in genera() the inabi(ity to accommodate (focus) &&
this occurs when the (ens (oses ieBibi(ity due to aging


?hapter 7
Tuesday) june 2.) 2CC7
A:2A *-

Chapter /: Circulatory0 9ymphatic0 and :mmune .ystems

*art 1: The ?ircu(atory 'ystem
"om#onents of the "irculatory System
The circu(atory system hand(es many duties:
o 9istribution of nutrients from the digestie tract) (ier) and adipose
(fat) tissue
o Transport oBygen from the (ungs to the entire body) and carbon dioBide
from the tissues bac= to the (ungs
o Transport metabo(ic waste products from tissues to the eBcretory
system (i.e. the =idneys)
o Transport hormones from the endocrine g(ands to the targets and
proide feedbac=
o -aintain homeostasis of body temperature
o %emostasis (b(ood c(otting)
'ome terms:
o *erfusion: the iow of b(ood through a tissue
o 5schemia: inade1uate b(ood iow through a tissue (resu(ts in
predictab(yebui(d&up of waste) inade1uate oBygen distribution) etc.)
o 4noBia: b(ood iow is <0) but oBygen distribution is reduced

<f a(( the di;erent things that b(ood trae(s through (heart) eins) arteries)
etc.) & the capi((aries are the structures which a((ow materia(s from the b(ood
to di;use into the surrounding tissue (this because their wa((s are thin
enough)

The heart can be diided (on a macro (ee() into two sides & (eft and right
o The right side of the heart pumps b(ood to the (ungs (this is ca((ed the
pu(monary circu(ation)) and the (eft side pumps the oBygenated b(ood
to the rest of the body (this is ca((ed the systemic circu(ation)
Eow thin= capi((aries again & capi((aries are the on(y p(ace where b(ood"s
contents can be eBchanged with the surroundings) and so in each circu(ation
system they wi(( on(y pass through one set (either in the (ungs or in the
tissues) before going bac= to the heart
o %oweer) there are things ca((ed Fporta( systemsF where b(ood passes
through 2 sets of capi((ary systems before returning to the heart
o There are , porta( systems:
%epatic (b(ood goes through intestina( capi((aries) then into the
hepatic ein) then through (ier capi((aries) then :na((y bac= to
the heart)
%ypotha(amic&hypophysea( porta( system (b(ood passes through
capi((aries in the hypotha(amus and then a(so in the pituitary
g(and)
0idney
o The idea is that porta( systems are for direct transport of substances
from one p(ace to another) without haing to go through the heart

The 1eart
Each side of the heart (right@pu(monary and (eft@systemic) has two chambers:
atrium and entric(e
o The b(ood arriing from eins co((ects in the atrium and then is pumped
into the entric(e and then into the arteries to either go to the brain or
the rest of the body
0now 8igure 2) pg. 22m

The heart has its own nutrient needs) so there is are Fcoronary arteriesF which
branch from the aorta and then surround the wa(( of the heart ((i=e a crown)
hence FcoronaryF)) eentua((y end up in the coronary eins which empty into
the coronary sinus which empties into the right atrium

+a(es in the circu(atory system are used to ensure that b(ood on(y iows one
way & bi&directiona( iow can be a prob(em due to pressure di;erentia(s (for
eBamp(e) the right entric(e is of higher pressure than the right atrium) so
un(ess there was a a(e between the two) we wou(d see b(ood going from the
entric(e into the atrium which is not productie
o /ight atrioentricu(ar a(e: bicuspid a=a mitra( a(e
o Left atrioentricu(ar a(e: tricuspid a(e
o 'emi(unar a(es: between the (arge arteries and the entric(es
o +a(es in the enous system & this is necessary because after the b(ood
passes through the capi((aries) a (ot of its FpressureF is gone and so it is
harder for it to continue moing forward
?ontraction of s=e(eta( musc(e a(so he(ps this because it
s1ueezes the eins and thus increases the pressure within them

4 cardiac cyc(e is made up of diasto(e and systo(e
o 9iasto(e: when the 4+ a(es are open and the atria are s1ueezing
b(ood into the entric(es
o 'ysto(e: when the 4+ a(es are c(osed but the semi(unar a(es are
open as the contraction of entric(es sends b(ood into the arteries
4t the beginning of systo(e) the 4+ a(es c(ose (F(ubF)
4t the end) the semi(unar a(es c(ose (FdubF)

?ardiac output (L@min) $ stro=e o(ume (L@beat) r heart rate (beats@min)
o 4th(etes (who hae stronger hearts) hae (ower heart rates because
their stro=e o(umes are higher

<ne way to increase stro=e o(ume is to stretch the heart more) since it wi((
contract more forcefu((y to return to its origina( state
o The way to do this is ca((ed the F8ran=&'tar(ing mechanismF) which is
when we increase enous return) which means putting more b(ood into
the heart from the eins
o There are 2 main ways to increase enous return:
5ncrease the tota( o(ume of b(ood in the circu(atory system (by
retaining water)
?ontract the (arge eins

4ction potentia(s causing contraction of the cardiac musc(e are spread through
the musc(es of the heart because the ce((s act as a Ffunctiona( syncytiumF)
which means that for a(( intents and purposes) the ce((s are connected
because there are gap bunctions between the ce((s that a((ow e(ectrica( signa(s
to moe from ce(( to ce((
o The atria"s functiona( syncytium (and therefore the signa(s that pass
through it) is iso(ated from the entricu(ar syncytium by the Fcardiac
conduction systemF
/eca(( from another chapter that not on(y do o(tage&gated (FfastF) sodium
channe(s propagate the action potentia() but Fs(ow ca(cium channe(sF do as
we(( because they stay open (onger and thus the possibi(ity of tetanus@signa(
bui(d&up is e(iminated
o There are ino(utions of the membrane in cardiac ce((s ca((ed t&tubu(es)
which a((ow the o(tage depo(arization to reach the heart of a ce(( & this
causes the '/ to re(ease ca(cium and a(so a((ows the entry of ca(cium
from the eBtrace((u(ar enironment (of course as you reca(() ca(cium is
necessary for musc(e contraction)

gn(i=e s=e(eta( musc(e) the action potentia(s in the heart are not started by
nerous or endocrine signa(s & instead they are started automatica((y from
within the heart & a region of the right atrium ca((ed the sinoatria( ('4) node
5n these ce((s) the o(tage di;erence neer returns to &mC m+ (as the rest of
the body does) but rather bust to &66 m+) which means that the spontaneous
(ea=age of sodium into the ce(( can set o; the o(tage&gated sodium channe(s
o The on(y thing is) these are Fs(owF channe(s) and so the
depo(arization@repo(arization of the '4 node ce((s is 1uite a bit s(owere

'o once an action potentia( starts in the '4 node) it goes into the atria but
a(so through the Finternoda( tractF to the atrioentricu(ar node) where it
pauses for a second (to a((ow the action potentia( and associated contraction
to spread throughout the atria) and then into the 4+ bund(e (a=a bund(e of
%is) then into the *ur=inbe :bers) which spread out to coer the entric(es
o Eote that the :bers spread out from the bottom of the entric(es
upwards) so that the b(ood is pumped upwards from the entric(es to
the aorta@arteries

The autonomic nerous system (as mentioned) doesn"t cause the heart to
beat) but it can regu(ate how 84'T it beats by inhibiting the depo(arization of
the '4 node
o 5t is the parasympathetic system that does this) and the main nere is
ca((ed the Fagus nereF) which has pregang(ionic aBons synapsing in
gang(ia near the node) then post&gang(ionic aBons going from the
gang(ia to the '4 node and re(easing 4ch to inhibit the '4 node (this is
ca((ed the Faga( toneF)
o The sympathetic nerous system a(so a;ects the heart & this happens
when the heart needs to be beat 1uic=er@output more per beat
'ympathetic post&gang(ionic neurons innerate the heart by
re(easing norepinephrine
The adrena( medu((a secretes epinephrine which binds to
receptors on the heart

1emodynamics
G(ood iow is basica((y the resu(t of opposing forces: the di;erence in pressure
between arteries and eins s. the friction from the wa((s of the esse( (ca((ed
FresistanceF)
o The e1uation describing this is <hm"s (aw: (de(ta)* $ H B / (* $
pressure) H $ b(ood iow) / $ resistance)
>e change pressure by increasing the force or rate of cardiac
contraction
>e change resistance by constricting arterio(ar smooth musc(e
(ca((ed precapi((ary sphincters) so that the arteries are s(ower)
which increases resistance

*eriphera( resistance is the resistance of the entire systemic circuit
o The periphera( resistance is contro((ed by the sympathetic nerous
system & it is a(ways proiding at (east a base (ee( of resistance by
innerating the precapi((ary sphincters & this constant nerous system
input is ca((ed Fadrenergic toneF
o The sympathetic nerous system is a(so ab(e to diert b(ood iow to
tissues which need it more at certain timese

8or a b(ood pressure of 12C@AC:
o 'ysto(ic b(ood pressure: 12C mm%g
o 9iasto(ic b(ood pressure: AC mm%g
o *u(se pressure: 3C mm%g

G(ood pressure is ta=en with a sphygmomanometer) which is a b(ood pressure
cu;
o The cu; cuts o; b(ood iow to the arm be(ow it and then the pressure is
re(eased unti( an audib(e sound is heard & this is the Fsystemic arteria(
pressureF) because it means that the pressure in the artery is bust high
enough to oercome the pressure of the cu;
>hen we can hear sounds the :rst time) we say that it is the
Fsysto(ic pressureF because that is the highest pressure which
there wi(( eer be && it is the arteria( b(ood pressure right after
systo(e
Then the cu; continues to be (oosened unti( the sound cannot
be heard anymore & this is because the cu; is (oose enough that
the b(ood iows smooth(y through the upper arm arteries and
does not FpoundF into the sides of the wa((s when it is going
through the former(y restricted area where the cu; was & this is
the diasto(ic pressure
o Eote that diasto(ic pressure remains high een between heartbeats
because the wa((s of the aorta@arteries are e(astic and muscu(ar) so
they shrin= a (ot when not :((ed with b(ood to maintain the same
pressure
This is important because that high pressure needs to be
maintained in order to drie b(ood iow throughout the body at
a(( times

Last(y) there is the concept of F(oca( autoregu(ationF) which is when the tissues
contro( the resistance (i.e. di(ation) of the capi((aries in their (oca( area
according to how much nutrient inta=e@waste management they need
o This is good because then the nerous system doesn"t hae to do a((
this wor= contro((ing eerything

"om#onents of Blood
There are 2 parts to b(ood & the part that is (i1uid (Fp(asmaF) and the part that
is composed of ce((s (ca((ed Fformed e(ementsF)
o *(asma consists of 66s of the b(ood o(ume) and it contains a bunch of
stu; that is bust disso(ed) such as e(ectro(ytes) bu;ers) sugars) b(ood
proteins) (ipoproteins) carbon dioBide) oBygen) metabo(ic waste
products) etc.

The b(ood proteins inc(ude:
o 4(bumin: he(ps to maintain oncotic pressure) which is the portion of
osmotic pressure in the capi((aries due on(y to the p(asma proteins
o 5mmunog(obu(ins: essentia((y they are antibodies) thus they are
important for the immune system
o 8ibrinogen: this is essentia( for b(ood c(otting
o Lipoproteins: you =now what these aree

<ther disso(ed substances:
o 'ugars: are most(y g(ucose
o >aste products: most(y urea (nitrogen brea=down product of amino
acids)) bi(irubin (brea=down product of heme)

The other component of b(ood (besides p(asma and a(( the disso(ed things
inside it) is the formed e(ements & red b(ood ce((s (erythrocytes)) white b(ood
ce((s ((eu=ocytes)) p(ate(ets) etc.
o /G?"s are 3C&36s of a(( b(ood (so they are the mabority of the formed
e(ements)
This portion is =nown as the FhematocritF
o >G?"s@p(ate(ets are around 1s of the tota(e
4(( b(ood ce((s are made from stem ce((s in the bone marrow

>hen who(e b(ood c(ots) there is a iuid portion and a so(id c(ot & the iuid
portion is serum) which is made up of p(asma minus the proteins in it used for
c(otting (thin= :brinogen)

/G? stu;
o The hormone erythropoeitin (made in the =idney) stimu(ates /G?
production in the bone marrow
o 4ged /G?"s are eaten by phagocytes in the sp(een and (ier
o /G?"s (ast 12C days
o 5t has no nuc(eus or other organe((es & it must re(y on g(yco(ysis for 4T*
(that"s why it is an ob(igatory g(ucose user)
o 5t has a biconcae shape because it needs to maBimize its surface area
because it carries a (ot of oBygen from (ungs to tissues and carbon
dioBide from tissues to (ungs
o 5t contains mi((ions of hemog(obin mo(ecu(es) which is what a((ows it to
carry oBygen
>G? stu;
o The (eu=ocyte (>G?)"s ro(e is to :ght infection and dispose of ce((s
o >G?"s are norma( ce((s (i.e. they hae a(( the organe((es)
o 'ome >G?"s (macrophages and neutrophi(s) moe by amoeboid
moti(ity (craw(ing)) which means that they can craw( out of capi((ary
interce((u(ar bunctions and roam free in T5''gE' so as to hunt enemies
o There are 7 types of >G?"s: macrophage) G ?e(() T ?e(() neutrophi()
eusinophi() basophi(
'ee Tab(e 7.1) pg. 23, isf there is timee

*(ate(et stu;
o They are (i=e /G?"s in that they hae no nuc(ei and a (imited (ifespan
o Their function is to aggregate at the site of damage to a b(ood esse(
wa(( and form a Fp(ate(et p(ugF) which wi(( he(p to stop b(eeding
4nother b(ood protein ca((ed :brin forms a mesh to ho(d the
p(ate(et p(ug together
8ibrin comes from the p(asma protein :brinogen & this is
cata(yzed by another protein ca((ed thrombin
r'o a p(asma protein is bust a protein disso(ed in the
p(asmafr
>hen eerything tries) it becomes a scab
4 b(ood c(ot or FthrombusF is bust a scab ioating in the
b(oodstream && not goodf
o Lots of other substances are ino(ed in hemostasis & inc(uding +itamin
0) which a (ot of the proteins depend on

Trans#ort of $ases

<Bygen transport
o <Bygen is carried on hemog(obin) which is a comp(eB protein in /G?"s

%emog(obin has 3 po(ypeptide subunits) each subunit

containing one mo(ecu(e of heme

%eme is a (arge mu(ti&ring structure that has a sing(e iron atom

bound at its center

The iron atom binds to oBygen

o /emember that hemog(obin demonstrate FcooperatieF binding) which
is when we hae a tense@re(aBed conformation for the hemog(obin
mo(ecu(es

>hen it is tense) the aDnity for oBygen is (owereand ice ersa

for re(aBed
The idea is that the more subunits bound) the higher the
aDnity of the other subunits for oBygen...

This is important so that it can hae (ower aDnity in the tissues

(so that myog(obin can ta=e it) but higher in the (ungs (so that it
can ta=e the oBygen from the a(eo(i)
o ?ertain factors stabi(ize the tense con:guation) meaning that in the
presence of these factors) hemog(obin is more (i=e(y to be tense

These factors abound in tissues which are in need of oBygen:

%igh ?<2 partia( pressure (wou(d be the case with a (ot
of g(yco(ysis@?4? stu;)
9ecreased p% (from (actic acid bui(d up)
5ncreased temperature (again as a resu(t of a(( this
metabo(ic actiity)

The (essened aDnity of hemog(obin in response to these factors

is ca((ed the FGohr e;ectF

?arbon dioBide transport

o ?<2 is transported through the b(ood in , main ways:

4s carbonic acid@protons) due to the e1ui(ibrium of ?<2 2 %2<

t&&c %2?<, t&&c %?<,
&
2 %
2

Gound to hemog(obin (but not the oBygen binding sites)

9isso(ed in the b(ood (it is a bit more po(ar than <2 and so it
can disso(e)

Echange of Substances )cross the "a#illary 4all
, =inds of things need to be ab(e to pass between the endothe(ia( ce((s that
ma=e up the capi((ary wa((: nutrients) waste products) and >G?"s
The entry and eBit of water from the capi((aries is important to note:
o 8irst(y) rea(ize that water has a great tendency to iow <gT of the
capi((aries because of a) the iuid pressure created by the heart"s
pumping action and b) the high osmo(arity of the tissues
o >e dea( with this by ma=ing the p(asma of the b(ood 4L'< of ery high
osmo(arity & this is where a(bumin comes in) because it is too (arge to
(eae the capi((aries and so it wi(( stay in the b(oodstream and gie it
high osmo(arity
4s we discussed ear(ier) the part of osmotic pressure caused
jg'T by these proteins is the Foncotic pressureF
Thin= about itesomething (i=e Ea?( in the b(oodstream
wou(d E<T he(p the osmotic gradient because it can
(eae the capi((aries and go into the tissues as we((f
4s we go through a capi((ary) we wi(( see that water s1ueezes out of the
tissues at the beginning) but as we get c(oser to the end) the iuid pressure
decreases and the oncotic pressure becomes more powerfu() resu(ting in
water coming G4?0 into the capi((ary from the tissues

There are some medica( conditions re(ated to water in the tissues:
o 9uring iniammation) the endothe(ia( ce((s of the capi((aries retract so
that the intrace((u(ar c(efts are bigger so that more white b(ood ce((s
can get to the tissues
Gut this means that water can get into the tissues as we(()
causing them to swe(( and producing a condition =nown as
FedemaF

The +ym#hatic System
This is another system for iuid distribution in the body
5t is not FconnectedF to the heart) so iow through this system is managed by
a(es) smooth musc(es in the wa((s) etc.
The iuid iowing through this (ca((ed F(ymphF) is :(tered by (ymph nodes)
which are part of the immune system & they contain tons of >G?"s that can
initiate an immune response to anything foreign in the (ymphe
The biggest (ymph esse( is the thoracic duct) which sma((er (ymph esse(s
empty intoethe thoracic duct empties into the (eft subc(aian ein (near the
nec=)

*art 2: The 5mmune 'ystem
There are , =inds of immunity: innate) humora() and ce((&mediated

!nnate !mmunity
This is genera() non&speci:c protection which the body proides against
arious inaders
%ere are the main components of innate immunity:
o '=in (stops the entry of micro&organisms)
o Tears) sa(ia) and b(ood (contain (ysozyme) which =i((s bacteria)
o !astric (stomach) acidity) which destroys many pathogens which are
ingested with food or swa((owed after being passed out of the
respiratory tract
o -acrophages and neutrophi(s indiscriminate(y phagocytize micro&
organisms
o The Fcomp(ement systemF) which is a group of 2C b(ood proteins that
non&speci:ca((y bind to the surface of foreign ce((s and destroy them

1umoral !mmunity5 )ntibodies5 and B/"ells
Eow we are ta(=ing about antibodies (4b) or a(so =nown as immunog(obu(ins
(5g)) which recognize ce((s speci:ca((y) bind to them) then destroy them
o Each anti&body mo(ecu(e is composed of 2 copies of 2 di;erent
po(ypeptides & the F(ight chainF and the Fheay chainF
o 4(so) the anti&body mo(ecu(e can be diided into the Fconstant regionF
and the Fariab(e regionF
The Fconstant regionF is the same for a(( the antibodies in the
same ?L4'' & the c(asses being 5g!) 5g4) 5g-) 5g9) and 5gE
The ariab(e regions are ariab(e because they are the parts
that recognize di;erent antigens and bind to them
The antigens are the things on the bad ce((s that identify
them to the antibodiesethey can be a protein on the ce((
surface) sometimes the entire ce(( (when it is sma(()
4s you wou(d eBpect) many times the F:ttingF is
based on ,&9 conformation

>hen an anti&body binds to an antigen) di;erent things can happen:
o Ginding of antibody can inactiate the antigen (i.e. preent a irus from
binding to ce((s)
o Ginding of antibody can induce phagocytosis of a partic(e by
macrophages and neutrophi(s
o The presence of antibodies on the surface of a ce(( can actiate the
comp(ement system to form ho(es in the ce(( membrane and (yse the
ce((

4ntibodies (remember they are bust proteins in the b(oodf) are produced by G
ce((s & there are mi((ions of di;erent types of G ce((s) and they each code for
one speci:c antibody protein
o The way this wor=s is that the G ce((s each hae a di;erent genome)
meaning that they wi(( each code for a di;erent =ind of protein
o The reason they hae a di;erent genome is because as they are made
from stem ce((s in the bone marrow) 9E4 recombination happens and
so each G ce(( has a s(ight(y di;erent genome and thus ma=es a
di;erent antibody
o >hen an antigen matching the G ce((s comes a(ong) it binds to an
antibody mo(ecu(e on the G ce(( surface and this te((s the G ce(( to
pro(iferate and di;erentiate
o 5t di;erentiates into 2 di;erent =inds of ce((s: p(asma ce((s and memory
ce((s
*(asma ce((s get to wor= right away) ma=ing antibodies for this
antigen that origina((y bound to the G ce(( and re(easing them
into the b(ood
-emory ce((s don"t re(ease anything but they hang around)
dormant) waiting to see that antigen again
o This way of se(ecting G ce((s to mature (because not a(( of them are
going to bind to an antigen) meaning that not a(( of them wi((
pro(iferatef) is ca((ed Fc(ona( se(ectionF

The :rst time this who(e process wor=s) it is ca((ed the Fprimary immune
responseF & it is not fast enough to preent symptoms of the infection from
occurring because it ta=es time for the G ce((s to pro(iferate and then produce
antibodies
Gut the neBt time the immune system sees this bacteria) the Fsecondary
immune responseF happens which is because there are a(ready tons of
memory ce((s ready to go

"ell/mediated !mmunity and the T "ell
'o there are 2 =inds of T ce((s: T he(pers (a=a F?93 ce((sF) and T =i((ers
(cytotoBic T ce((s) a=a F?9A ce((sF)
o T he(per ce((s actiate G ce((s) T =i((er ce((s) and other ce((s of the
immune system & so they don"t rea((y do anything themse(es but are
of course crucia( to the immune response
5t communicates with other ce((s by re(easing specia( hormones
ca((ed (ympho=ines and inter(eu=ins
Eote that it is the host of the %5+ irus && i.e. this is where %5+
attac=s
o T =i((er ce((s destroy abnorma( host ce((s (i.e. irus&infected host ce((s)
cancer ce((s) foreign ce((s i.e. s=in graft) etc.)

T ce((s are made in the thymus g(and (hence FTF)) and the idea is that during
chi(dhood) T/5LL5<E' of di;erent T ce((s are produced (di;erent as in speci:c
for di;erent antigens)
o 4s we progress through chi(dhood) the thymus g(and remoes the T
ce((s which recognize antigens from our <>E ce((s (fai(ure to do so wi((
cause an auto&immune reaction) which we don"t want)
o 4nd then for each of the other T ce((s) when they sense an antigen
they wi(( pro(iferate (as the G ce((s do) and then it"s good times

The recognition mechanism for T ce((s wor=s genera((y through recognizing
certain proteins on the ce(( surface of some suspect ce((
<ne important group of ce((&surface proteins is the mabor histocompatibi(ity
comp(eB (-%?)) of which there are 2 types: c(ass 5 and c(ass 55
o -%? ?(ass 5 proteins ta=e random samp(es of peptide from inside the
ce(( and disp(ay it on the surface
This a((ows T ce((s to monitor the interna( contents of a ce(( by
bust (oo=ing at the membrane surface & ery usefu( when the
ce(( is irus&infected and so the irus is disp(ayed on the ce((
surface
Thus -%? ?(ass 5 proteins are found on E+E/` ?ELL of the body
o -%? ?(ass 55 proteins are used to disp(ay fragments of ce((s which hae
a(ready been recognized as bad and chopped up by macrophages or G
ce((s
<n(y macrophages and G ce((s do this && thus they are =nown as
Fantigen&presenting ce((sF
'o the di;erence between ?(ass 5 and 55 is that the peptide
presented in ?(ass 5 may not be bad) whereas in ?(ass 55 it is
a(ways bad and in fact has a(ready been recognized as such
4nyways) the reaction chain for -%? ?(ass 55 is that the T he(per
ce(( wi(( recognize it) then actiate G ce((s and stimu(ate
pro(iferation of T =i((er ce((s) then once a(( that stu; is bui(t up
then the infection wi(( 95E

Other Tissues !n&ol&ed in the !mmune Res#onse
The tonsi(s are masses of (ymphatic tissue in the bac= of the throat that
FcatchF pathogens which enter the body through respiration or ingestion
o The appendiB does the same thing but is (ocated around the (arge
intestine
Eeither of these two guys is essentia( for


?hapter .
'unday) june 11) 2CC7
.:,6 *-

Chapter 6: ;i%esti+e and Excretory .ystems

*art 1: The 9igestie 'ystem

O&er&ie, of the $! Tract
The basic idea of digestion is that we brea= down food into its most basic
parts by enzymes (hence the term Fenzymatic hydro(ysisF)
%ere are the di;erent foods types and their associated hydro(ytic enzymes:
o 1 trig(yceride &&&&pancreatic (ipase&&&&c 2 fatty acids 2 1 monog(yceride
o *o(ysaccharide &&&&ptya(in (a=a sa(iary amy(ase) and pancreatic
(ipase&&&&c disaccharides
o 9isaccharides &&&&brush border disaccharidases&&&c monosaccharides
o *o(ypeptide &&&&gastric acidity@pepsin) pancreatic proteases (trypsin and
chymotrypsin)&&&&c dipeptides and tripeptides
o 9ipeptides and tripeptides &&&&brush border peptidases&&&&c amino acids

>e ca(( the ce((s (ining the !5 (umen Fepithe(ia( ce((sF (as opposed to
endothe(ia() or anything e(se) because epithe(ia( ce((s are those which (ine the
outside of the body (i.e. s=in ce((s)eand the !5 tract is considered to be open
to the outside wor(d
The di;erent sides of an epithe(ia( ce(( are apica( (faces inside the (umen) and
baso(atera( (the sides and FbottomF of the ce(()
o There are tight bunctions between apica( ce((s so that nothing can get
between those ce((s un(ess it is supposed to

The !5 tract has its own nerous system (means that it can do signa(
integration for some things instead of haing to go a(( the way bac= to the
?E')) and so !5 tract moti(ity is contro((ed by neres but a(so by hormones
o The parasympathetic nerous system stimu(ates moti(ity and re(aBes
sphincters
o The sympathetic nerous system does the opposite

There are two =inds of secretion: endocrine and eBocrine
o Endocrine eBcretions re(ease their products into the b(oodstream (so
thin= hormones)
8or eBamp(e: pancreas
o EBocrine eBcretions g'g4LL` re(ease their products into ducts which
eentua((y bring them somewhere (in this case) into the !5 (umen)
8or eBamp(e: (ier) ga((b(adder) and pancreas (yes you can be
both eBocrine and endocrine)
4(so) some ce((s in the wa((s of the gut itse(f secrete
things (i.e. gob(et ce((s secrete mucus)
EBocrine g(ands are composed of specia(ized epithe(ia( ce((s
which are further organized into sacs ca((ed FaciniF

The $astrointestinal Tract
'ee 8igure 6 (pg. 27C)
o -outh &c esophagus &c (ower esophagea( sphincter (a=a cardiac
sphincter) &c stomach &c py(oric sphincter &c duodenum &c bebunum &c
i(eum &c i(eoceca( a(e &c co(on &c eBterna( ana( sphincter

The mouth does fragmentation) (ubrication) and some enzymatic digestion
o 'a(ia contains sa(iary amy(ase and (ysozyme (=i((s bacteria) thus
he(ps with immunity)
The pharynB) or throat) contains openings to both the esophagus (eating) and
the trachea (breathing)
o The esophagus has two sphincters (upper esophagea( and (ower
esophagea() which regu(ate the moement of food
The stomach does the fo((owing: partia( digestion of food) regu(ated re(ease of
food into the sma(( intestine) and destruction micro&organismsethe fo((owing
things he(p it to do so:
o 4cidity (=i((s microorganisms) hydro(yzes proteins) conerts pepsinogen
to pepsin)
o *epsin (a gastric enzyme for proteo(ysis) thus it brea=s down food
proteins but a(so actiates chymotrypsin and trypsin)
o -oti(ity (brea=s up food partic(es and a(so moes them through)
o 'phincters (the py(oric sphincter stops too much food from going into
the duodenum & this depends on acidity and stretching in the
duodenum)
?ho(ecysto=inin is the main enzyme that does this
o !astrin (this is another hormone secreted by F! ce((sF in the stomach
wa(( & it stimu(ates acid and pepsin secretion and gastric moti(ity)
!astrin secretion is stimu(ated by food in the stomach or by
parasympathetic stimu(ation
%istamine acts as a co&factor for the stimu(ation of acid
secretion by gastrin (so sometimes we b(oc= histamine to =eep
acidity (ee(s down)
The sma(( intestine comp(etes digestion as we(( as most of absorptionehere
are the =ey features:
o 'urface area (the sma(( intestine has a (arge surface area because of
its (ength) fo(ds) i((i) and microi((i)
+i((i are macroscopic probections into the intestine) microi((i are
sma((er ones
o 5ntestina( i((useit has , important structures:
?api((aries (absorb the brea=down products of carbs and
proteinsethey become eins and eentua((y the hepatic porta(
ein) which ta=es them to the (ier)
Lactea(s (absorb the brea=down products of dietary fatse
become (ymphatic esse(s which become the thoracic duct and
empties into the genera( b(oodstream && thus bypassing the
(ier)
*eyer"s patches ((ymphocytes on the i((i which he(p to protect
against gut pathogens and toBins)
o Gi(e and pancreatic secretions in the duodenum (pancreatic secretions
are digestie enzymes and bicarbonated bi(e secretions are made from
cho(estero( and he(ps to digest fats)
Gi(e is stored in the ga((b(adder unti( needed
The bi(e duct and the pancreatic duct merge at the sphincter of
<ddi and so they u(timate(y both arrie into the !5 (umen from
the same opening
o 9uodena( enzymes (besides the ones from the pancreas):
?e((s in the wa(( of the duodenum secrete stu; to actiate
pancreatic enzymes (i.e. entero=inase actiates trypsinogen)
'ome enzymes of the duodenum wa(( do their wor= 4T the wa(( &
they don"t go into the (umen (i.e. the brush border
disaccharidases)
o 9uodena( hormones:
?ho(escysto=inin (??0): secreted in response to fats in the
duodenumd causes the pancreas to secrete digestie enzymesd
stimu(ates ga((b(adder contractiond decreases gastric moti(ity
'ecretin: re(eased in response to acid in the duodenumd causes
pancreas to re(ease bicarbonate as a bu;er which wi(( neutra(ize
%?( (this is because duodena( p% needs to be =ept neutra( or
een s(ight(y basic for the pancreatic enzymes to function)
Enterogastrone: decreases stomach emptying
o jebunum and i(eum: these are the (ater parts of the sma(( intestinee
they absorb the stu; that the duodenum did not absorb
The ro(e of the co(on (a=a (arge intestine) is to absorb water and minera(s) and
to form and store feces unti( defecation
o <era(() it goes from the cecum to the rectum
The appendiB is a(so here & it has a (ymphatic function
o The ana( sphincter is made up of interna( smooth musc(e (autonomic
contro() and eBterna( s=e(eta( musc(e (o(ntary contro()
o The co(on contains (ots of bacteria which metabo(ize undigested
materia( (gas is a fre1uent by&product of this)
?o(onic bacteria are important because they =eep dangerous
bacteria from pro(iferating (because they wi(( compete with
them for space and nutrients) and because they supp(y +itamin
0) for b(ood c(otting

The $! )ccessory Organs
The !5 accessory organs are the pancreas) (ier) and ga((b(adder

EBocrine pancreas re(eases: pancreatic amy(ase) pancreatic (ipase) nuc(eases
(for 9E4@/E4)) pancreatic protease
o 5t a(so re(eases zymogens: trypsin) chymotrypsin)
procarboBypeptidase) proco((agenase
o The pancreatic secretions are contro((ed by the hormones ??0 and
secretin

Endocrine pancreas is a(so within the pancreas & it is sma(( regions ca((ed the
is(ets of Langerhans
o There are , =inds of ce((s in these Fis(etsF) and they each secrete a
uni1ue hormone:
4(pha ce((s re(ease g(ucagon
Geta ce((s re(ease insu(in
9e(ta ce((s re(ease somatostatin (this inhibits digestie
processes)

'o the pancreas has a huge ro(e in maintaining b(ood g(ucose
o Lowering b(ood g(ucose: insu(in causes the remoa( of sugar from the
b(oodstream to be stored in ce((sethis is important not on(y so that the
ce((s can get their energy) but a(so because eBcess g(ucose cause
neurona( and rena( damage
o /aising b(ood g(ucose: g(ucagon) epinephrine (adrena( corteB)) and
cortiso( (adrena( corteB) a(( raise b(ood g(ucose
Low b(ood g(ucose is fata( because ce((s wi(( die) so the ro(e of
these , guys is ery important (whereas insu(in not so much
because e(eated b(ood g(ucose isn"t that bade)

The (ier secretes bi(e) and the ga((b(adder stores bi(e
o Gi(e is made up of bi(e acids) which are a(so ca((ed bi(e sa(ts when they
are deprotonated
4 ga((stone is a (arge crysta( formed from bi(e but with
ingredients in the wrong proportions
o The (ier"s ro(e is more in processing the food) not with digesting
theme
5t stores sugar as g(ycogen) ma=es proteins from amino acids)
dea(s with toBins) etc.
5t produces most of the b(ood proteins that circu(ate in the
p(asma

) Day in the +ife of Food
?arbohydrates
o G(ah b(ah b(ahe<0 now we hae monosaccharidesewe ta=e them into
the intestina( epithe(ia( ce(( by actie transport (more speci:ca((y a
symport) which ta=es in sugar whi(e a((owing sodium to iow in down its
concentration gradient as we(()
This gradient is created by Ea@0 4T*&ases which ta=e Ea out of
the ce(( and into the interstitium (not the !5 (umen)
o <nce the concentration in the epithe(ia( ce(( is high enough) a gradient
eBists which wi(( a((ow their faci(itated di;usion (uniport) into the
capi((aries
o The increased b(ood sugar (ee(s cause the Geta ce((s of the pancreatic
is(ets of Langerhans to secrete insu(in) which means that not on(y the
(ier but a(so other ce((s of the body wi(( ta=e up) uti(ize) and store
g(ucose
*roteins
o G(ah b(ah b(ahe<0 now we hae dipeptides and tripeptides
o The brush border peptidases brea= them down into peptides
o They get absorbed into the epithe(ia( ce((s the same as
monosaccharides (symport with sodium)) and then faci(itated di;usion
uniport into the capi((aries
8ats
o G(ah b(ah b(ahe<0 now we hae monog(ycerides and fatty acidsethey
di;use into the epithe(ia( ce((s by themse(es (since they are sma(( and
hydrophobicf)
o <nce they get into the epithe(ia( ce((s) we conert them bac= to
trig(ycerides and pac=age them in chy(omicrons
o The chy(omicrons enter the (actea(s and eentua((y go into the main
b(oodstream
o 4s they bypass ce((s) the ce((s ta=e up the fat
5n particu(ar) adipocytes and (ier ce((s hae (ipoprotein (ipase)
which hydro(yzes the trig(ycerides bac= into monog(ycerides
and fatty acids) which di;use into the ce((s and do stu;

*itamins
(Eothing)

*art 2: The EBcretory 'ystem
O&er&ie,
The =idneys main(y do eBcretionebut the (ier) (arge intestine) and s=in are a((
ino(ed as we((f

Lier
o The (ier hand(es many wastes by modifying them and re(easing them
into bi(e) which eentua((y gets eBcreted (a(though) yes) most bi(e is
recyc(ed) && especia((y it does this for (arge </ hydrophobic waste
products
o The (ier a(so ma=es urea and re(eases it into the b(oodstream to be
:(tered out at the =idney (the urea comes from nitrogen which comes
from protein brea=down)
?o(on
o The co(on doesnqt rea((y eBcrete anything) but it -<9585E' the
eBcrement by reabsorbing water and ions etc. from the stu; that is
passing through the !5 tract
'=in
o '=in produces sweat) which is simi(ar to urine in that it contains water)
urea) and ions && thus s=in is in a way) eBcretory
%oweer) it is not */5-4/5L` eBcretory because the main
function of sweating is temperature contro() not eBcretion
issuese

0idneys
o The =idney has , main parts to its operation:
8i(tration (iuids and sma(( mo(ecu(es (eae the b(ood and enter
the tubu(es of the =idney)
'e(ectie reabsorption (some of the :(trate goes bac= into the
b(ood)
?oncentration and di(ution (decide whether to ta=e out een
more (i1uid to ma=e the urine concentrated) or to (eae it in
there)
o 'ee tab(e:






)natomy of the Ecretory System
G(ood goes into the =idney from a rena( artery) and (eaes the =idney ia the
rena( ein
The ureter ta=es urine from the =idney to the urinary b(adder
o The b(adder wor=s (i=e the ana( sphincter does & interna( (ayer of
smooth musc(e) eBterna( (ayer of s=e(eta( musc(e
The =idney has an outer region (corteB) and inner region (medu((a)
o The medu((a is organized into Fmedu((ary pyramidsF) which empty at
the tip (Fpapi((aF) into a space ca((ed the ca(yB
o The ca(yces conerge to form the rena( pe(is) which empties into the
ureter
The functiona( unit of the =idney is the nephron) which is essentia((y a rena(
tubu(e which receies :(trate at one end and empties into a co((ecting duct at
the other end (which wou(d be the papi((a) if we go macroscopic)
o 5n more detai() here is the path of b(ood@:(trate:
4;erent arterio(e &c g(omeru(us (ba(( of capi((aries) &c e;erent
arterio(e
*ressure di;erences between the g(omeru(us and the c(ose(y
associated FGowman"s ?apsu(eF) which is a part of the rena(
tubu(e) cause iuid to (ea= out from the b(ood into the capsu(e
(a(though of course) substances which are too big to di;use
such as proteins wi(( stay in the b(ood)
o 5n more detai() here is se(ectie reabsorption:
'ome of the :(trate in the tubu(e is stu; that we 9<E"T want to
(ose) so it di;uses G4?0 from the rena( tubu(e to peritubu(ar
capi((aries) which become enu(es and then eins and then the
rena( ein
This most(y happens in the FproBima( cono(uted tubu(eF
(*?T)) which is c(ose to the Gowman"s capsu(e
4(( so(ute moement is accompanied by water moement)
which means that the *?T is where most reabsorption of water
ta=es p(aceethe concentration of urine is determined (ater) by
re(atie(y :ner&tuned changes
'e(ectie reabsorption is se(ectie in that it on(y reabsorbs
certain substances) but it is E<T se(ectie when it comes to how
-g?% is reabsorbed & it absorbs a(( the so(ute it can (again)
so(ute concentration issues are dea(t with L4TE/ on in the
tubu(e)
o ?oncentration and di(ution
The (ast part of the tubu(e (dista( tubu(e) ta=es care of this & the
determination of how concentrated the urine is going to be
(basica((y how much water and sa(t do we =eep in the urine)
Eerything is contro((ed by two hormones: 49% and a(dosterone
49% is anti&diuretic hormone) which means that it
preents diuresis (water (oss in urine)ethus when 49% is
actie) we are going to hae a (ot of reabsorption of
water in the dista( tubu(e meaning that the urine is going
to be high(y concentrated
49% is a dehydration thing) meaning that
dehydration is one of the primary things which
sets it o;
4(dosterone causes Ea2 to be reabsorbed more by the
nephron) causing the p(asma to hae higher osmo(arity)
which wi(( ma=e the person thirsty and a(so increase
water retentionethis wi(( increase b(ood o(ume which
increases b(ood pressure
4(dosterone is a b(ood pressure thing) meaning
that (ow b(ood pressure is one of the main things
that sets it o;

0now 8igure 13) pg. 2A1
o Gowman"s capsu(e &c proBima( cono(uted tubu(e &c descending (imb
of the (oop of %en(e &c ascending (imb of the (oop of %en(e &c dista(
cono(uted tubu(e &c co((ecting duct

The (oop of %en(e is a Fcountercurrent mu(tip(ierF) which basica((y means that
the (imbs of the (oop of %en(e hae di;erent permeabi(ities and go in opposite
directions
o The descending (imb is permeab(e to water) so (ots of water (eaes and
the :(trate becomes ery sa(ty
The osmotic gradient a((owing this is maintained by the fact
that the asa recta (eBtensions of the e;erent arterio(es) run
around the (oop of %en(e and ta=e up this water that has been
eBcreted
o Then in the ascending (imb) a(( that so(ute (eaes because it is
permeab(e to so(ute but not to watereso the urine is ery
concentrated at this point
o Eow a(( the so(ute is in the medu((ary interstitium) and it can sere as a
gradient to ta=e water out of the :(trate in the co((ecting duct proided
that the correct transporters are in p(ace due to the 49%@a(dosterone

'ee 8igure for b(ood pressure contro(:














/ena( regu(ation of p%
o The =idney contro(s p% by eBcreting %?<,& when it is too basic) and %2
when it is too acidic
o The enzyme Fcarbonic anhydraseF hand(es this by conerting ?<2 &c
%2?<, &c % 2 %?<,) at which point the =idney can eBcrete either the
%2 or the %?<,&
?arbonic anhydrase is found in a(( the nephron"s epithe(ia( ce((s)
eBcept for the ones in the thin part of the (oop of %en(e (which
are metabo(ica((y inactie)

Endocrine Role of the Kidney
0now the chart on pg. 2A3


?hapter A
-onday) june C6) 2CC7
A:,, 4-

Chapter 8 < #uscle and .keletal .ystems

-usc(e
Types of musc(e:
o 'triated
?ardiac (ino(untary contro()
'=e(eta( (o(untary contro()
o 'mooth (in the wa((s of ho((ow organs i.e. !5 tract) urinary system) etc.)
(ino(untary contro()

S'eletal Muscle
-usc(es wor= by manipu(ating the s=e(eton of the body & thus to be e;ectie)
they must be attached to bones
o They are attached at either end of the musc(e to bones) ia tendons
made of co((agen
o They contract (musc(es can ne+er eBpand) to proide di;erent =inds of
moement:
8(eB (reduce ang(e of the boint)
EBtend (increase ang(e of the boint)
4bduct (moe away from the body)
4dduct (moe toward the body)
<ne of the two bones boined by a s=e(eta( musc(e is c(oser to the body) and
stays in p(ace when the musc(e contractseso it is the other bone that is
moing c(oser or farther away
o The point on the non&moing bone where the musc(e attaches is ca((ed
the ForiginF
o The point on the moing bone is ca((ed the FinsertionF
<ftentimes) musc(es are paired or grouped in order to either coordinate the
same moement (synergistic) or the opposite moements (antagonistic) i.e.
bicep s. tricep)

'tructure@physio(ogy of s=e(eta( musc(e (see 8igure 2) pg. 2AA)
o -usc(e tissue is bro=en down into connectie tissue and contracti(e
tissue
The contracti(e tissue is he(d together in bund(es ca((ed fascic(es
o >ithin each fascic(e there are :ne musc(e :bers) ca((ed myo:berse
which are each actua((y bust one huge ce((
These musc(e ce((s@musc(e :bers are syncytia) meaning that
they are the product of many ce((s fused together (which means
that they are often mu(ti&nuc(eate)
o Each musc(e ce((@:ber has a specia(ized ce(( membrane ca((ed the
sarco(emma) which is the norma( p(asma membrane 2 po(ysaccharide
and co((agen (this a((ows it to fuse with tendon :bers)
o >ithin each musc(e ce((@:ber there are sma((er units ca((ed myo:bri(s)
and it is these which proide the force of contraction for the musc(e
o >ithin each myo:bri( there are sarcomeres (aid down end to end
Each sarcomere consists of an oer(apping arrangement of
po(ymerized actin :(aments (ca((ed thin :(aments) and myosin
:(aments (ca((ed thic= :(aments)
'ee :gure:





'(iding 8i(ament -ode( of -usc(e ?ontraction
o The basic idea is that within each sarcomere of each myo:bri( of each
myo:ber of each fascic(e of each musc(eethe thin and thic= :(aments
s(ide across each other so that they oer(ap een moree
This causes each sarcomere of each myo:bri( of each myo:ber
of each fascic(e of each musc(eeto '%</TEEf %ence musc(e
contractionf
o This F:(ament s(idingF is powered by the enzyme FmyosinF) which uses
4T* hydro(ysis (note that of course this is a di;erent myosin than the
:(ament which ma=es up the thic= :(amentsf)
o The entire s(iding process is ca((ed a contracti(e cyc(e:
The myosin FheadF binds to a Fmyosin binding siteF on the actin
:(ament (the tai( is a(ready bound to the myosin :(ament)ethis
is a(so ca((ed Fcross bridge formationF
4t this point it is a(so bound to 49* and *i) from a
preious contraction (you wi(( see why)
The Fpower stro=eF occurs) where the myosin head pu((s the
actin chain past itse(f (i.e. the ang(e between the head and the
tai( decreases)
%ere the 49* gets re(eased so that we can...
Gind a EE> 4T* mo(ecu(e to the myosin) which causes it to (et
go of the actin
4T* gets hydro(yzed and the myosin head gets coc=ed bac= and
bound to a new binding site again

EBcitation&?ontraction ?oup(ing (basica((y) a way to contro( the automatic
reaction which wou(d otherwise occur wheneer we had actin) myosin) and
4T* a(( in the same enironment)
o The idea is that the Ftroponin&tropomyosinF comp(eB preents
contraction when ?a22 is not present
o Gasica((y) tropomyosin is a (ong :brous protein which winds around the
thin (actin) :(ament) b(oc=ing a(( the binding sitesethis means that
myosin cannot bindf
o Gut troponin is a g(obu(ar protein associated with tropomyosin that)
when bound to ?a22) undergoes a conformationa( change which wi((
moe tropomyosin out of the way) so that the actin :(aments can bind
o 'o basica((yeeerything is contro((ed by cytop(asmic ?a22 (ee(sf

The Eeuromuscu(ar junction and 5mpu(se Transmission
o <0 the idea is that the neuromuscu(ar bunction is the synapse between
the aBon termina( and the myo:ber (musc(e ce(() & this is where a
neurona( signa( wou(d cause the ce(( to do stu;
The interesting thing howeer is that un(i=e norma( synaptic
c(efts where it is on(y a certain point) the neuromuscu(ar
bunction is (i=e a (ong trough@inagination of the musc(e ce(( &
this is so that a signa( neurona( signa( can depo(arize a (arge
region of the musc(e ce(( at oncef
The neurotransmitter is acety(cho(ine
The F(ong troughF is ca((ed the motor end p(ate
o The rest is easye4ch causes Ea iniuB) which depo(arizes the post&
synaptic membrane (Fend p(ate potentia(F)) which opens up more
o(tage&gated sodium channe(s (if it is big enough) and causes an
action potentia(
<ne coo( thing: since action potentia(s are basica((y a ce((&
surface sort of dea() the interior of the myo:ber (musc(e ce(()
won"t rea((y fee( iteso we use transerse tubu(es (t&tubu(es) to
a((ow the action potentia( to reach the interior of the ce((
Then once the action potentia( arries in the interior courtesy of
the t&tubu(es) the sarcop(asmic reticu(um does its thing
The '/ is a huge smooth endop(asmic reticu(um which
comp(ete(y surrounds each myo:bri(eit stores ?a22) so
when it gets that 4*) it (ets out the ca(cium which then
a((ows the musc(e to contract

-echanics of ?ontraction (i.e. di;erent ways to ary contraction strength)
o 'tart with the sma((est possib(e musc(e contraction: it is the FtwitchF)
which is when on(y one motor neuron goes o;) and so on(y the
myo:bers which are connected to it contract
o 8orce of contraction can be increased by:
/ecruiting motor units: setting o; more motor neurons) so that
a(( of their associated myo:bers go o; as we((
8re1uency summation: so that the ?a22 neer gets fu((y
se1uestered by the '/

Energy 'torage in the -yo:berea few 1uic= shots:
o The compound creatine phosphate is an Fintermediate&termF energy
storage mo(ecu(e that reforms 4T* from 49* 2 *i
o -yog(obin de(iers the oBygen to the musc(e (necessary for ce((u(ar
respiration to produce more 4T*) by ta=ing <2 from hemog(obin as
hemog(obin trae(s through the b(oodstream with oBygen attached

0eener fact:
o The (ength of a musc(e (i.e. when uncontracted) how much oer(ap
there is between the thin and thic= :(aments) a;ects contraction
strength & too much oer(ap and the :(aments wi(( interfere with each
other) too (itt(e oer(ap and not enough crossbridges can be formed for
a powerfu( contraction
This is ca((ed the F(ength&tensionF re(ationship

"ardiac Muscle "om#ared to S'eletal Muscle
'imi(arities:
o 'arcomeres (thus cardiac musc(e is striated because of the FstripesF)
bust (i=e s=e(eta( musc(e)
o T&tubu(es
o Troponin&tropomyosin
o Length&tension re(ationship (een more signi:cant here because un(i=e
s=e(eta( musc(e) where the bones pretty much ensure that the (ength
stays the same) the heart can eBpand and contract and the musc(es
>5LL be a;ected)
9i;erences:
o The musc(e ce((s (myo:bers) are not syncytia() meaning that they a((
on(y hae one nuc(eus
o 4(( the musc(e ce((s are interconnected by gap bunctions ca((ed
Finterca(ated dis=sF) which a((ow action potentia(s to go through the
who(e heart (so functiona((y it is (i=e a syncytium because a(( the ce((s
are on some (ee( FconnectedF)
o -otor neurons do E<T determine the contraction of the heart
musc(eseit"s contro((ed instead by the pacema=er ce((s
o The action potentia( in cardiac musc(e is dependent not on(y on FfastF
sodium channe(s) but a(so sodium&ca(cium channe(s) which are
'L<>E/ to respondethat is why the action potentia( graph (oo=s (i=e
this:





o /easons for the Fp(ateau phaseF:
Longer contraction duration: which a((ows for comp(ete
entricu(ar emptying
Longer refractory period: preents summation and tetanus
(wou(d be dead(y in the heart)

Smooth Muscle "om#ared to S'eletal Muscle
'imi(arities:
o ?ontracti(e cyc(e
o /o(e of ?a22
9i;erences:
o 5t has Ffunctiona( syncytiaF instead of Frea(F syncytia) bust (i=e cardiac
ce((s
o 4ction potentia(s are a miB between s=e(eta( and cardiac:
'ometimes it is a Fspi=eF (i=e s=e(eta( (a(though -g?%) -g?%
s(ower)
'ometimes it has a Fp(ateauF (i=e cardiac musc(e for pro(onged
contractions
o There are no sarcomeres & the thin and thic= :(aments are instead bust
hanging around in the cytop(asm (hence the smooth rather than
striated appearance)
o Earrower and shorter than s=e(eta( musc(e ce((s
Eo t&tubu(es (as mentioned aboe) they are so sma(( that this is
not necessary)
4gain because of the sma((er size) the '/ is not necessary
because ca(cium can bust come through the membrane
o Eo troponin&tropomyosineinstead we use ca(modu(in and myosin (ight&
chain =inase
o The neurons which induce contraction are not somatic (as they are
with musc(e) but instead are autonomic

The '=e(eta( 'ystem
The ertebrate s=e(eta( system p(ays 6 ro(es:
o 'upport the body
o *roide a framewor= for moement
o *rotect ita( organs
o 'tore ca(cium
o 'ynthesize e(ements of b(ood i.e. red@white b(ood ce((s and p(ate(ets
(this is ca((ed hematopoiesis)
The ertebrate endos=e(eton is diided into:
o 4Bia( components (s=u(() ertebra( co(umn) ribcage)
o 4ppendicu(ar components (eerything e(se)

"onnecti&e Tissue
4(( types of connectie tissue are deried from the :brob(ast
o 8ibrob(ast can turn into adipocytes) chondrocytes (carti(age)) and
osteocytes (bone)
o 5t can secrete 85G/<g' materia( such as co((agen (strength@stabi(ity)
and e(astin (e(asticity)
There are two genera( categories of connectie tissue:
o Loose connectie tissue inc(udes adipose tissue and the eBtrace((u(ar
matriB
The eBtrace((u(ar matriB inc(udes g(ycosaminog(ycans) which are
so(ated by waterethis gies tissues their thic=ness and
:rmness
o 9ense connectie tissue refers to bones) tendons) and (igaments

Macrosco#ic Bone Structure
Two primary bone shapes: iat (ribs) s=u(() etc.) and (ong ((imbs)
o 8(at bones do hematopoiesis and protect organs
o Long bones are for support and moement
-ore on (ong bone structure:
o -ain shaft is diaphysis
o 8(ared end is epiphysis

Two types of bone structure: compact or spongy
o ?ompact bone is hard and dense
o 'pongy bone is porous
-ost bones are spongy surrounded by a (ayer of compact bone
The diaphysis of (ong bones is a tube composed of compact bone

Gone marrow: it is non&bony materia( found in the shafts of (ong bones and in
the pores of spongy bones
o /ed marrow: found in spongy bone within iat boneseit is the site of
erythropoiesis
4ctiity is increased by erythropoietin
o `e((ow marrow: found in shafts of (ong boneseit is inactie

Microsco#ic Bone Structure
"artilage
Bone $ro,th and Remodeling6 the "ells of Bone
+igaments5 Tendons5 and 0oints

&Chapter 8 Addendum'

Microsco#ic Bone Structure
Gone is composed of 2 principa( ingredients: co((agen and hydroByapatite
o The dea( is that co((agen is (aid down in an ordered structure
o 4nd then hydroByapatite (ca(cium phosphate crysta(s) forms around
this framewor= and ma=e the bone strong and inieBib(e

Eow thin= about it on a more macro (ee( & the di;erences between spongy
and compact bone
o 'pongy bone is (i=e a sponge in terms of structure & there are bust
many spi=es of bone surrounding marrow&(i=e caities (ca((ed spicu(es
or trabecu(ae)
o ?ompact bone has a speci:c structure) and the most basic unit of this
structure is the osteon

<0) (et"s brea= down the osteon
'tarting from the center) there is a %aersian cana( where there are
b(ood esse(s) (ymph esse(s) and neres
Then there are (ayers of bone ca((ed (ame((ae surrounding this center
(i=e concentric rings
There are tiny channe(s ca((ed cana(icu(i coming out from the ho(e)
going through the (ame((ae) and ending up in spaces ca((ed (acunae
There is an osteocyte & mature bone ce(( & in each (acunae and so it is
through the cana(icu(i (channe(s) that the osteocytes can contact each
other) get nutrients from the b(ood) etc.

"artilage
?arti(age is something that is found between bones (i.e. at boints)
5t is strong but ieBib(e) so we see it in p(aces of the body where we need that
ieBib(e yet strong support) such as: (arynB) trachea) outer ear) etc.
?arti(age is secreted by chondrocytes

There are , =inds of carti(age:
o %ya(ine: strong and '<-E>%4T ieBib(e
8ound in (arynB) trachea) boints
o E(astic: more ieBib(e than hya(ine carti(age
'o we see this in the outer ear) epig(ottis) etc.
o 8ibrous: ery rigid and a good support
The interertebra( dis=s of the spina( co(umn & we don"t need
much ieBibi(ity but we want 'g**</T here

?arti(age is E<T innerated and it 9<E' E<T hae b(ood esse(s
o 'o it gets its nutrition from the surrounding iuid
o Gut it sti(( doesn"t hae a direct supp(y) which means that carti(age
inburies ta=e a (ong time to hea(

Bone $ro,th and Remodeling6 the "ells of Bone
<0) :rst remember that (ong bones ((i=e in our arms and (egs) are made up of
a diaphysis (the tube) and the epiphysis (the iared ends)

>hen we are chi(dren) there is an epiphysea( p(ate between the diaphysis and
the epiphysis
o >e produce carti(age here and thus the diaphysis and epiphysis are
forced apart) and the bone becomes (onger
o Then the carti(age is rep(aced by bone) so eerything hardens and the
(ength increase is permanent
o 4fter puberty) androgens@estrogens cause the epiphysea( dis= to ossify
so that no more growing can occur

>hat about when we are adu(tsl >e(( there is no more growth at the
epiphysea( p(ate) but what we do hae is the bone continua((y being degraded
and then remade & this process is ca((ed remode(ing
o L4`5E! 9<>E G<EE:
<0 so we hae osteob(asts in the bone and they bust (ay down
co((agen and hydroByapatite (we =now this)
Gut then at a certain point) it is comp(ete(y surrounded by a((
this bone it has (aid down
4t this point it stops (aying down the bone and bust stays in that
space of its own
The space is ca((ed a (acuna (sound fami(iarl)
4nd the osteob(ast is now ca((ed an osteocyte (sound
fami(iarl)
o 9E'T/<`5E! G<EE:
The ce((s which do this are ca((ed osteoc(asts & they disso(e the
hydroByapatite ca(cium phosphate crysta(s) and the bone bust
co((apses

<f course there are a(so conse1uences regarding hormone actiity here
o The more osteob(asts wor=) the more hydroByapatite crysta(s they
disso(e) and thus the more ca(cium and phosphate is in the
b(oodstream
o Thus in order to maintain constant ca(cium (ee(s and phosphate
(ee(s) hormones contro( osteob(ast s. osteoc(ast actiity as we(( as
contro( the rate of ?a absorption from the intestine
o Tab(e:








+igaments5 Tendons5 and 0oints
/eca(( that (igaments and tendons are considered to be dense connectie
tissue) which means that they are strong and they contain a (ot of co((agen
o Gones are the other type of dense connectie tissue

Tendons connect bones to musc(e
Ligaments connect bones to other bones
o The point of connection is ca((ed a j<5ET
5mmoab(e boints are ca((ed synarthroses) and basica((y this
means that the 2 bones are fused together (i.e. s=u(()
'(ight(y moab(e boints are ca((ed amphiarthroses (i.e. ertebra(
bones)
8ree(y moab(e boints are diarthroses (i.e. e(bow) =nee) etc.)

Thin=ing more about boints:
o They are a(( (ubricated by synoia( iuid
o The surfaces of the 2 bones which contact each other are perfect(y
smooth because they are (ined by hya(ine carti(age
/eca(( that carti(age has no direct nutrition@materia(s supp(y &&
this is why it is easy for them to get iniamed) sti;) etc. (thin=
arthritic =nees)


?hapter m
Tuesday) june C7) 2CC7
A:3. 4-

Chapter 7: =espiratory and .kin .ystems

The /espiratory 'ystem
Functions
The basic idea is that organisms need oBygen to do oBidatie phosphory(ation
o 'ing(e&ce((ed eu=aryotes can bust get it by di;usion
o 'imp(e mu(ti&ce((ed eu=aryotes can do the same
o Gut comp(eB mu(ti&ce((u(ar eu=aryotes (i=e us need to hae a who(e
respiratory system to do this
<ther things the respiratory system does:
o p% regu(ation: remember there is a ba(ance between ?<2 t&&&carbonic
anhydrase&&&c carbonic acid
Thus the more ?<2 we breathe out) the (ess acid we hae) and
so the p% of the b(ood goes up
%yperenti(ation: too much breathingd causes the b(ood
to be too basic
%ypoenti(ation: too (itt(e breathingd causes the b(ood to
be too acidic
o Thermoregu(ation: we (ose heat when breathing out
o *rotection from disease and particu(ate matter: air has to go through
barriers before reaching the (ungs) where they can do harm

)natomy of the Res#iratory System
The respiratory tract is the passageway used by gases to enter and eBit the
(ungs:
o Eose: warm@humidify the aird a(so :(ter is with nasa( hairs and stic=y
mucus
o EasopharynB: open space behind the nose
o *harynB: basica((y the throat
o LarynB: at the bottom of the throateit has , functions:
0eeps the airway open (made entire(y of carti(age)
%as the epig(ottis) which can sea( the trachea whi(e swa((owing
so that food is not FbreathedF in
?ontains the oca( cords) which ibrate when air is passed by
them to create sound
o Trachea: a passageway that must remain open (again carti(age preent
its co((apse)
o Gronchi: branches of the trachea (on(y 2) (again carti(age preents
their co((apse)
o Gronchio(es: branches of the bronchi (E< carti(age)
Their wa((s are made of smooth musc(e) so these are the guys
which get eBpanded and contracted to contro( air iow into the
system
o 4(eo(ar 9ucts: l
o 4(eo(i: tiny sacs (one ce(( (arge) at the end of bronchio(es
They hae thin wa((s which a((ow them to eBchange oBygen with
the b(ood

/o(e of the respiratory epithe(ium in protecting against disease and foreign
obbects
o Gasica((y unti( we get to the a(eo(i) the ce((s which (ine the wa((s of the
respiratory tract are epithe(ia( ce((s) which are too thic= to do gas
eBchange (because they are thic= and ?<Lg-E4/) & so air bust gets
passed (or ?<E9g?TE9) through these areas
o 'ome of the epithe(ia( ce((s (ca((ed gob(et ce((s) secrete a (ayer of stic=y
mucus
o <ther epithe(ia( ce((s hae ci(ia which sweep this (ayer of mucus up
towards the pharynB
o 4t the pharynB) the mucus traps the pathogens and inha(ed partic(es
and can either cough it out or swa((ow them

Gut the actua( air eBchange ta=es p(ace in the a(eo(i) a(eo(ar ducts) and the
ery sma((est bronchi (ca((ed respiratory bronchio(es)
o This is ca((ed the Frespiratory zoneF and the epithe(ium bust consists of
a sing(e (ayer of s1uamous (FiatF) epithe(ia( ce((s ca((ed the simp(e
s1uamous epith(ium
o *rotection here is di;erent because we can"t hae mucus here or e(se it
wou(d stop the di;usion) so instead we use Fa(eo(i macrophagesF

This is stu; secreted by FType 2 a(eo(ar (ining ce((sF (FType 1F is the
s1uamous epithe(ia( (ayer) and it reduces surface tension on the a(eo(i so
that they don"t co((apse (the water mo(ecu(es on the surface of the a(eo(i
wou(d c(ump together and Fshrin=F the who(e thing)

%ulmonary *entilation
>e get air in and out of the (ungs by doing:
o 5nspiration (contract the diaphragm to en(arge the (ungs and the chest
caity) which wi(( draw air in)
The diaphragm is under the (ungs and is norma((y shaped (i=e a
dome) but it iattens when contracted so that the chest caity 2
(ungs are drawn downward
The intercosta( musc(es (between the ribs) a(so contract during
inspiration) which pu((s the ribs upward and further eBpands the
chest caity
o EBpiration (the (ungs spontaneous(y wi(( recoi( and push stu; out & no
muscu(ar wor= needed)
Gut sometimes the abdomina( musc(es can get in on the act if
they contract) because this wi(( press upward on the diaphragm
which wi(( shrin= the size of the (ungs een more and push the
air out

The (ungs are e(astic bags that if not for the he(p of other parts of the body)
wou(d co((apse in on themse(es
o The reason why they don"t is because of the Fp(eura( spaceF & which is
between the iscera( p(eura( membrane ((ines the (ungs) and the
parieta( p(eura( membrane ((ines the inside of the chest caity)
o The two p(eura( membranes are drawn together because:
'urface tension on the water mo(ecu(es (ining the membrane
-</E 5-*</T4ETL`: there is a negatie pressure in there) so
the membranes are Fsuc=edF together
o This Fsuc=ing attachmentF between the two (ayers is the same reason
why when the chest caity eBpands) the (ungs eBpand with it (when
the chest eBpands) the p(eura( pressure decreases een more and so
the (ungs eBpand too)

$as Echange
The idea for the pu(monary circu(ation is that the b(ood needs to hae some
way of coming from the heart (deoBygenated)) passing through the (ungs)
then going bac= to the heart (now oBygenated) so that it can be pumped to
the rest of the body where oBygen is needed
This who(e arrangement is ca((ed the Fpu(monary circu(ationF
o *u(monary artery comes from the heart
o 4rtery branches into pu(monary capi((aries a=a a(eo(ar capi((aries
o 4 few capi((aries go to E4?% a(eo(us and get the oBygen ia di;usion
(whi(e giing Fbac=F ?<2 of course)
These gases di;use through the Frespiratory membraneF) which
is the combination of the a(eo(ar epithe(ium 2 interstitia( (i1uid
2 capi((ary endothe(ium
o Then the capi((aries become enu(es
o The enu(es eentua((y become the pu(monary ein) which ta=es
eerything bac= to the heart

/andom fact: pu(monary edema is when there is iuid in the (ungs resu(ting
from increased b(ood pressure
o The idea is that increased b(ood pressure wi(( eBpand the a(eo(ar
capi((aries beyond that which they can natura((y di(ate) so iuid wi((
come out into the (ungs and the a(eo(i
o Eorma((y) we :B this by haing the (ymphatic system carry interstitia(
iuid out of the (ungs

The eBchange of gases is a(( a resu(t of Fpartia( pressuresFethe idea is that
anytime you hae a co((ection of gases) they wi(( co((ectie(y create a tota( gas
pressure
o Each gas" indiidua( contribution to that pressure is proportiona( to its
abundance within the miBture (i.e. tota( gas pressure 1CC torr) <2
ma=es up 2Cs of the gasepartia( pressure of <2 wi(( be 2C torr)
o 4nd of courseegas wants to go from a p(ace of higher pressure to
(ower pressure
o 'o when we breathe air in and it goes into our a(eo(i) the <2 is going
to di;use into the a(eo(ar capi((aries" b(ood unti( the partia( pressure
between the two p(aces is the same (and ?<2 going the other way) of
coursee)

Regulation of Res#iration
The big boss here is the Frespiratory contro( centerF) which is in the medu((a of
the brain stemeit responds to stimu(i by adbusting the rate and depth of
breathing
'ee tab(e:









<ther interesting points: the wa((s of bronchi and the (arger bronchio(es
contain smooth musc(e) which can contract to c(ose o; the bronchi
o This is good when they are contracting so as to b(oc= irritants from
going further
o Gut it can a(so be bad when a((ergy attac=s cause the mast ce((s here
to re(ease histamine) which causes bronchoconstriction and stops
breathing
>e dea( with this by administering epinephrine@anti&histamines)
which wi(( cause bronchodi(ation

The '=in
Structure
5t is the (argest organ in the body (by size and weight)
5t protects us from pathogens and eBcessie water eaporation) and it
regu(ates body temperature
5t has , (ayers (see 8igure 6) pg. ,17):
o Epidermis (outermost)
o 9ermis (in the midd(e)
o %ypodermis@subcutaneous tissue (inner mostd it is essentia((y an
insu(ating (ayer of fat)

The epidermis is basica((y (ayers upon (ayers of epithe(ia( ce((s (ca((ed
strati:ed s1uamous epithe(ia( ce((s) & these guys are a(ways reproducing & the
top (ayers get s(oughed o; and they are rep(aced by (ayers at the bottom
(ca((ed the stratum basa(e)
o The ce((s are a(so F=eratinizedF) which means that they are surrounded
by the protein =eratin) which wi(( ma=e them waterproof since it is
hydrophobic
o The ce((s a(so hae Fme(aninF) which absorbs the g+ (ight from the sun
so that the under(ying tissues don"t get damaged

The dermis hase
o G(ood esse(s (both for the dermis and a(so the epidermis)
o 'ensory receptors
o 'weat@oi( g(ands) hair fo((ic(es

Tem#erature Regulation by the S'in
There are basica((y 3 ways to cope with co(d weather:
o ?ontraction of s=e(eta( musc(es: either ino(untary (shiering) or
o(untary (bumping up and down)
o 5nsu(ating fat in the s=in which conseres the heat we generate
through metabo(ism
o F?utaneous asoconstrictionF) which is when we constrict the b(ood
esse(s in the dermis so that we don"t (ose heat ia conduction from
the b(ood running through there
The sympathetic nerous system a(so causes this & that"s why
the s=in can become co(d and pa(e when someone is frightened
o ?(othing (duh)

4nd for /ELE4'5E! heat when it is too warme
o 'weating: (oss of heat by eaporation
o ?onduction: heat (oss by conduction (esp. due to di(ating the
cutaneous b(ood esse(s)


?hapter 1C
-onday) ju(y 1.) 2CC7
,:C2 *-

Chapter 15: =eproducti+e .ystems and ;e+elopment

The /eproductie 'ystems
The Male Re#roducti&e System
>hen we are ta(=ing about <gT'59E T%E G<9`) the 2 principa( ma(e
reproductie structures are the scrotum and the penis
o The scrotum is basica((y bust a bag of s=in containing the ma(e gonads
(a=a testic(es@testes)
The testes hae 2 ro(es:
'ynthesize sperm (i.e. spermatogenesis)
'ecrete ma(e seB hormones a=a androgens into the
b(oodstream
5nteresting point: the testes hae to be =ept at a speci:c
temperature (ee( which is in fact (ower than the rest of the
body && this is why it is =ept outside the FmainF part of the body

.ee 4i%ure 10 p%. ("1

<0 (et"s thin= about testes anatomye
o >ithin the testes we hae seminiferous tubu(es (this is where sperm is
created)
Getween these tubu(es we hae the testicu(ar interstitium)
which is where we hae Leydig ce((s which synthesize
androgens (such as testosterone)
o 4nyways) the seminiferous tubu(es empty into the epididymis) which is
a (ong tube coi(ed on the bac= of each testic(e
o 8rom there we go to the as deferens
'perm goes from the as deferens into the inguina( cana()
where it meets the other as deferens (from the other testes) to
form a common ebacu(atory duct (so this is where the sperm
waits before ebacu(ation)
4(so contributing to the ebacu(atory duct are the Faccessory
g(andsF) which create semen (a nourishing enironment for the
sperm) which combines with the sperm
The g(ands are:
'emina( esic(es: contributes fructose and other
stu;
*rostate g(and: a(=a(ine secretions for neutra(izing
acidity within the urethra and the agina
Gu(bourethra( g(and: iscous and a(=a(ine
secretion (for (ubrication and neutra(iziation)
o 8rom there we go to the urethra) which is in the penis (so we are now
in the penis)

Let"s ta(= about erections & the reason why we get erections is because there
is erecti(e tissue in the penis with specia( eins and capi((aries that can ta=e a
(ot of b(ood at high pressure) thus becoming sti;
o This erecti(e tissue is found in the corpus caernosum and the corpus
spongiosum of the penis

The , stages of the ma(e seBua( act are: arousa() orgasm) and reso(ution
o 4rousa(:
*4/4'`-*4T%ET5? input
There are 2 stages here:
Erection (di(ate and :(( the arteries supp(ying the enous
tissue to cause swe((ing)
Lubrication (bu(bourethra( g(ands secrete a iscous
mucus which seres as (ubricant)
o <rgasm:
'`-*4T%ET5? stimu(ation@input
There are 2 stages:
Emission (so this is when the sperm from the as
deferens and the semen from the accessory g(ands
combine in the urethra to prepare to (eae)
Ebacu(ation (semen is prope((ed out of the urethra by
rhythmic contractions of musc(es surrounding the base
of the penis)
Eote that this is a /E8LEk reaction performed
wheneer there is semen in the urethra
o /eso(ution:
'`-*4T%ET5? input
This is bust the return to a norma() unstimu(ated state && so the
arteries sering the penis constrict) there is (ess b(ood
accumu(ated in the penis) etc.
4bout 2&, minutes

Let"s ta(= about semen:
o <n(y 2s sperm
o 7Cs semina( esic(es output
o ,6s prostate g(and output
o ,s bu(bourethra( g(and output

S#ermatogenesis
Huic=(y) the basics:
o 'o spermatogenesis is basica((y a ma(e doing meiosis to produce a
hap(oid gamete ca((ed spermatozoa (a=a sperm)
>hen fema(es do this) the resu(tant gamete is ca((ed FoaF) a=a
egg
o 8erti(ization occurs when a sperm) after haing been deposited into the
fema(e genita( tract) swims to meet the egg and enters it) thus
producing a zygote
Eotab(y then) the on(y thing the ma(e contributes to the
eentua( human is the genes & eerything e(se is from the egg
(this is why the 9E4 of the mitochondria is materna((y
inheritedf)

'perm synthesis is done in the seminiferous tubu(es of the testes
o 'erto(i ce((s are found in the wa((s of the tubu(e and so a sperm starts
from the outer wa(( and moes inward towards the (umen
o Gy the time it reaches the (umen) meiosis has been comp(eted and it is
ready to go) so we deposit it into the (umen and are o; to the races

'ee the fo((owing :gure ($e sure to add comments >rom a$le 15.10 p%.
("*):
















-ore on the conersion of spermatids into spermatozoa:
o 'o we get the 9E4 chromosomes condensing) the cytop(asm shrin=ing)
and the ce(( shape changing so that we hae a head (contains nuc(eus)
and a tai( (the iage((um)
The base of the tai( is (i=e a Fnec=F) and there are many
mitochondria here which produce energy using fructose so that
the iage((um can moe
-ore on the headeit contains:
4crosome (contains hydro(ytic enzymes for penetration
of the oum"s protectie (ayers)
Gindin (protein on the sperm"s surface that attaches to
receptors on the membrane surrounding the oum)

Let"s ta(= about the hormones which contro( spermatogenesis:
o Testosterone & stimu(ates the diision of spermatogonia
o Lutenizing hormone (L%) & stimu(ates the Leydig ce((s to secrete
testosterone
o 8o((ic(e&stimu(ating hormone (8'%) & stimu(ates the 'erto(i ce((s
o 5nhibin & inhibits 8'% re(ease (for negatie feedbac= reasons)
4re you surprised that the 'erto(i ce((s produce this thingl

De&elo#ment of the Male Re#roducti&e System
'o (et"s remember & when we are bust an embryo) we 9< hae a seB) but it"s
bust that we hae not seen the seB yet in terms of a repro. system that is
either distinctie(y ma(e or fema(e
5nstead) we hae F>o(Dan ductsF and F-u((erian ductsF at the same time
o >o(Dan ducts can *<TEET54LL` turn into ma(e interna( genita(ia:
epididymis) semina( esic(es) and as deferens
o -u((erian ducts can *<TEET54LL` turn into fema(e interna( genita(ia:
fa((opian tubes) uterus) and agina
Then the dea( is that the F`F chromosome wi(( determine which of these 2
structures 9<E' end up dee(oping
o 5f there is no F`F) then the -u((erian ducts wi(( dee(op (a(ong with the
eBterna( fema(e genita(ia) and the >o(Dan ducts wi(( ta=e a hi=e
o 5f there 5' a F`F) then the -u((erian 5nhibiting 8actor is secreted to shut
down the -u((erian ducts) and instead we get testosterone which
encourages the >o(Dan dee(opment

'ee the fo((owing :gure (insert comments >rom para%raph on p%. ("6):














The )ndrogens
'traight&up de:nition: a(( hormones ino(ed in the dee(opment and
maintenance of ma(e characteristics are ca((ed FandrogensF
o The primary androgen is of course testosterone
o Gut howeer) it has to be conerted to dihydrotestosterone in the ce((s
of target tissues before it has any e;ect

Testosterone is produced during dee(opment as needed in order to dee(op
the ma(e interna( and eBterna( genita(ia
o Gut then after that) it fa((s to (ower (ee(seunti( pubertye
o 4t puberty) it increases again so that sperm is producedea(so so we
get the dee(opment and maintenance of ma(e secondary seBua(
characteristics
Eotab(y we get oice deepening) epiphysis fusion (bones)) etc.

Female Re#roducti&e System2 )natomy and De&elo#ment
.ee 4i%ure ,0 p%. ((5

<0 so there is a (ot of homo(ogous dee(opment here (i.e. simi(ar to ma(es) &&
because there are those non&di;erentiated structures in embryos
o 5nstead of testes we hae oaries) which secrete E'T/<!EE' (the
fema(e seB hormones)
o The L4G5<'?/<T4L '>ELL5E!' grow into the scrotum for the ma(e)
but into the F(abia maboraF of the agina
o 5nstead of the penis we get the c(itoris
gnder the c(itoris we hae the urethra( opening) where urine
(eaes
'urrounding this opening we hae the (abia minora
o >e a(so hae the opening of the agina between the (abia minora

4fter this we are getting to the agina and interna( fema(e genita(ia where
there is E< %<-<L<!` because it dee(ops from the -u((erian ducts) which
are 95'T5E?TL` fema(e
o >e hae the agina) which is basica((y a tube
o The uterus opens into the agina) and this opening is ca((ed the ceriB
o The uterus has mu(tip(e (ayers of (ining in it:
Endometrium & nourishes a dee(oping embryo (or is shed each
month to cause menstruation)
-yometrium & (ayer of smooth musc(e which ma=es up the wa((
of the uterus
o ?oming out of the uterus there are 2 fa((opian tubes which end in
:mbriae
o The :mbriae contact the oarye(so the egg goes from the oary into
the 8a((opian tubese)

The fema(e seBua( act has the same stages as the ma(e one:
o 4rousa(:
4gain *4/4'`-*4T%ET5?
4gain diided into 2:
Erection & c(itoris and (abia minora contain erecti(e tissue
and become engorged with b(ood
Lubrication & proided by mucus secreted by Gartho(in"s
g(ands and the agina( epithe(ium
o <rgasm
4gain '`-*4T%ET5?
5t a(so ino(es musc(e contractions (which inc(ude the widening
of the ceriB so that sperm can moe into the uterus)
%oweer) no ebacu(ation
o /eso(ution
4gain '`-*4T%ET5?
Gut it ta=es 2C&,C minutes instead of 2&,

Oogenesis and O&ulation
The :rst di;erence is that the Fgonia"sF are produced when the fema(es are
E-G`/<' && as opposed to on(y when they become teenagers
o 'o basica((y we hae (arge numbers of oogonia being produced when
the fema(e is an embryo
o 'ome of these become primary oocytes but !< E< 8g/T%E/ unti(
puberty for the fema(e
o Then eery month) a few oocytes mature into oa

-eiosis in fema(es
o This is di;erent too in that when we get ce(( diision (for both -eiosis 5
and 55) the resu(ting species are not the same
4fter -eiosis 5 we get the main egg (has most of the cytop(asm)
and the :rst po(ar body (ha(f the 9E4 as re1uired but ery (itt(e
cytop(asm)
4fter -eiosis 55 && which bust happens to the main egg && we get
the main egg and the second po(ar body
o 'o the resu(t is that meiosis resu(ts in on(y <EE !4-ETE) not four
o 4(so because of the way that on(y a few oocytes go at a time for
fema(es) most oocytes are stuc= in *rophase 5 for a L<E! timee
Gut when it comes their turn to become eggs (remember this
happens to bust 1 or 2 per month)) they re&enter the meiotic
cyc(e and continue on to form the egg which wi(( hopefu((y be
ferti(ized
%oweer many oocytes neer get this and so they die

>hat actua((y happens is that the egg does -eiosis 5 and becomes a
secondary oocyte) then it goes into the fa((opian tube (i.e it is ou(ated) && but
note that -eiosis 55 has not happened yet so there is sti(( more to go
o 5n fact the way it wor=s is that the secondary oocyte on(y goes on to do
-eiosis 55 if a sperm enters (ferti(izes) it
>hen a sperm does enter) the 9E4 does not fuse unti( the egg
:rst :nishes doing -eiosis 55) and then they fuse
o 'o if the woman does not hae seB that month) then when
menstruation occurs) it is not a mature egg ce(( that is (ost but rather a
secondary oocyte

Let"s ta(= about fo((ic(e dee(opmente
o The fo((ic(e is something that surrounds the primary oocyte
'o eery primary oocyte is surrounded by a fo((ic(e & basica((y
the fo((ic(e is made up of granu(osa ce((s && they support and
nurture and he(p with dee(opment (the ma(e e1uia(ent is the
serto(i ce((s)
o The :rst FphaseF of the fo((ic(e is the Fprimordia(F fo((ic(e
Then it becomes a Fprimary fo((ic(eF when the granu(osa ce((s
pro(iferate to form seera( (ayers around the oocyte
4t this stage the oocyte a(so adds some
mucopo(ysaccharides ca((ed the Fzona pe((ucidaF (inside
the granu(osa (ayer)
4nd there is a(so the Ftheca( ce((sF added (<gT'59E the
granu(osa (ayer)
The theca( ce((s) since they are the
FinterstititumF) are (i=e the Leydig ce((s in the
ma(e && so unsurprising(y they are G<T%
stimu(ated by L%
g(timate(y on(y one fo((ic(e per month becomes a mature or
F!raa:anF fo((ic(e
The !raa:an fo((ic(e bursts and the secondary oocyte
goes into the fa((opian tube
The oocyte =eeps its granu(osa ce((s though and
they are now ca((ed the corona radiata

The Menstrual "ycle
Huic= introduction for estrogen@progesteronee
o Goth estrogen and progesterone p(ay a ro(e in the menstrua( and
pregnancy
o The fo((ic(e synthesizes estrogen
o 4fter ou(ation) the remaining fo((icu(ar ce((s form the corpus (uteum
and secrete estrogen and progesterone

Eow to the cyc(eethere are T>< ways to describe it) and they di;er based on
which part of the reproductie system we are considering the changes to
o EE9<-ET/54L ?`?LE:
, stages: pro(iferatie phase) secretory) and menstrua(
*ro(iferatie: estrogen produced by the fo((ic(e induces
endometria( pro(iferation (i.e. it gets thic=er and
prepares for imp(antation)
'ecretory: this happens after ou(ation and so the corpus
(uteum is formed and it secretes estrogen and
progesterone to further dee(op the endometrium
%ere we see secretion of g(ycogen) (ipids) and
other materia(e
-enstrua(: so we assume that ferti(ization does not
occur) which means that the corpus (uteum decreases)
thus estrogen and progesterone do as we(() thus the
endometria( (ining fa((s o;
o <+4/54E ?`?LE:
, stages: fo((icu(ar) ou(atory) (utea( phases
8o((icu(ar: so here a primary fo((ic(e matures and secretes
estrogen
The estrogen acts (oca((y to cause that fo((ic(e to
:nish o; meiosis 5
<u(atory: now the oocyte is a secondary oocyte) and
ou(ation occurs and it (eaes the oary
5t trae(s down the 8a((opian tube towards the
uterus
Lutea(: now the oary doesn"t hae the egg anymore)
but it has the (eftoer granu(osa ce((s from the fo((ic(e
which once housed the eggethese ce((s turn into the
corpus (uteum and secretes the estrogen and
progesterone which starts the secretory phase in the
endometrium

<0 (et"s a(so ta(= about pituitary hormones and how they a;ect this who(e
process
o The chief ones are 8'% and L% (note that they are stimu(ated by
gonadotropin re(easing hormone) re(eased by the hypotha(amus)
o 'ee :gure ($e sure to la$el usin% in>ormation >rom p%. ((,):



















1ormonal "hanges During %regnancy
<0) so now we"re ta(=ing about pregnancy && what happens to hormonesl
(note that they hae to di;er in '<-E way from non&pregnant situations
because if they didn"t) the uterine (ining wou(d get s(oughed o; as usua( and
the imp(anted embryo is screwed)
o 5t"s a(( about feedbac= cyc(ese
*regnancy means constant high (ee(s of estrogen and
progesterone
Therefore there is negatie feedbac= on the pituitary and we
don"t hae L% re(ease
>hich means that there is no ou(ation (see preious
:gure)
Gut then how do we preent corpus (uteum degeneration from
occurring (this is what happens when L% decreases)l >e
preent it through the secretion of human chorionic
gonadotropin (h?!)) which is secreted by the p(acenta

The p(acenta is basica((y what ends up after the zygote imp(ants itse(f into the
endometrium

9ee(opment
Fertilization and "lea&age
<0 (et"s ta(= about how ferti(ization happens
o 8irst the egg & reca(( that after it is ou(ated) it sti(( has two (ayers
around it: the zona pe((ucida (bust outside the membrane) and the
corona radiata (outside the zona pe((ucida)
o Then the sperm & if intercourse occurs and it is deposited near the
ceriB) then it gets capacitated (FactiatedF) and attempts to swim
through the uterus towards the secondary oocyte (egg) in the 8a((opian
tube
o 5f we are (uc=y (or un(uc=yf)) a sperm penetrates the corona radiata
and the zona pe((ucida and then gets into the egg
5t accomp(ishes this penetration of the protectie (ayers using
the Facrosome reactionF) which is when the acrosome in the
sperm head re(eases hydro(ytic enzymes
4(so in this process we see the Facrosoma( processF
which stic=s out of the sperm) going to the ite((ine (ayer
(the zona pe((ucida) and binds to it using FbindinF
o <nce the sperm is inside) the secondary oocyte does meiosis 55 and we
get an ootid 2 second po(ar body
o The ootid becomes an oum (more mature ersion)
o The sperm and egg nuc(ei fuse and we get our zygoteeand we are
good to gof

Eow how about when stu; goes wrongl 8or eBamp(e *<L`'*E/-` & when
mu(tip(e sperm enter the egg
o >e hae 2 ways to preent thise
84'T GL<?0: the egg p(asma membrane depo(arizes) which
preents additiona( sperm from fusing with the membrane
'L<> GL<?0: due to the depo(arization) ca(cium enters the ce((
and causes the Fcortica( reactionF
The Fcortica( reactionF means that:
The space between the ite((ine (ayer and the
p(asma membrane swe((s
The ite((ine (ayer hardens
The p% in the egg changes) which causes
increased metabo(ism and protein synthesis

?LE4+4!E: so this is a(( about how the zygote dee(ops after ferti(ization
o 5t a(( happens through the process of embryogenesis
4nd the :rst step of embryogenesis is c(eaage & the zygote
undergoes many ce(( diisions and we end up with a ba(( of ce((s
ca((ed the -</gL4
4fter the moru(a we get the b(astocyst
The b(astocyst has an inner and outer ce(( mass
(basica((y a ba(( inside a ba(()
The Finside ba((F stic=s to the Foutside ba((F at one end of
the caity
>e end up with the inner ce(( mass becoming the
embryo
>e end up with the outer ce(( mass becoming the
trophob(ast) which becomes the chorion (part of
the p(acenta)

!m#lantation and the %lacenta
<0 so the b(astocyst gets to the uterus (remember it started in the 8a((opian
tubes) and imp(ants
o This ta=es about <EE >EE0 (after ferti(ization)
5mp(antation is faci(itated through the secretion of endometrium&(ysing
proteases re(eased by the trophob(ast (outer (ayer of the b(astocyst as you
reca(()
4nd so right now we hae the trophob(ast between the embryo and the
mother"s wa(( && and so nutrients etc. are eBchanged through the trophob(ast
Eentua((y the p(acenta forms) which is specia(ized for this transfer of
nutrients
o This ta=es about , months
>hat is the signi:cance of thatl 5t is that unti( we get the
p(acenta up and running) we sti(( need the corpus (uteum for its
estrogen and progesterone producing abi(ity
Therefore human chorionic gonadotropin is important && this is
re(eased by the chorion (reca(( that the trophob(ast basica((y
bust turns into the chorion)

5t shou(d a(so be noted that part of p(acenta( dee(opment is the formation of
p(acenta( i((i && these are probections from the p(acenta into the endometrium
which a((ow the eBchange of substances from the materna( b(oodstream to the
infant"s
o Eote that the b(ood itse(f neer gets transferredf

Eow :na((y (et"s thin= about the inner ce(( massewhat becomes of itl
o >e(( it"s not on(y the embryo && a(so we get the amnion) yo(= sac) and
a((antois
The amnion is a membrane that surrounds a iuid&:((ed caity in
which the embryo resides (so Fwater brea=ingF is when the
amnion brea=s and a(( this water comes out)
`o(= sac stores yo(= for repti(es and birds) but for humans it is
the p(ace for /G? synthesis
4((antois & it forms the b(ood esse(s for the umbi(ica( cord)
which transports b(ood between the embryo and the p(acenta

%ost/!m#lantation De&elo#ment
<0 a few things happen hereegastru(ation and then neuru(ation

8irst (et"s ta(= about gastru(ation:
o 5t is basica((y the dee(opment of the embryo into a structure with ,
distinct (ayers: endoderm) mesoderm) and ectoderm
o 8o((owing is a tab(e describing which body parts come from which
(ayer:










Then after gastru(ation is neura(ation && the formation of the nerous system
o >hat we do is we pinch o; a (ayer of ectoderm (remember this is
where the nerous system dee(ops from) to form the dorsa( neura(
grooe) which becomes the neura( tube
<ther ectoderma( ce((s go to other parts of the body to from the
*E'

Last(y) (et"s thin= about dee(opment from a macro iew
o >e can diide it into embryonic and feta( stage
Gefore A wee=s we hae the embryonic stage
%ere organogenesis occurs: the dee(opment of organ
systems
4fter A wee=s we are considered a FfetusF so it is the feta( stage
<rganogenesis has comp(eted so now the systems are
bust growing and maturing

Di7erentiation
<0 so di;erentiation is basica((y the process of ce(( specia(ization & they get
better at certain abi(ities and decrease in others
*rimitie ce((s in an ear(y embryo hae the potentia( to become any ce(( type)
and they are thus ca((ed T<T5*<TEET ?ELL'
o 4t some point in their (ife) the fate of totipotent ce((s is determined &&
so they aren"t specia(ized yet) but we 0E<> what they are going to be
&& so this is FdeterminationF
9etermination can be induced by a ce(("s enironment </ it can
be pre&programmed
o Later on they actua((y di;erentiatee

just to screw things oer) there is a(so Fde&di;erentiationF) which is
di;erentiation bac=wards
o This can cause cancerf

Birth and +actation
/emember that birth is a(so =nown as FparturitionF
o Girth in genera( is dependent on the contractions of musc(es in the
uterine wa(( which wi(( push the baby out
%ow can this happen) based on the fact that progesterone
usua((y preents the uterine from contracting during
pregnancyl 5t"s because oBytocin is re(eased by the posterior
pituitary and a(so the estrogen:progesterone ratio changes
o >hen the actua( contractions begin) we get a positie feedbac= cyc(e
where the stretch of the ceriB causes the uterine contractions to
increase in intensity) which ma=es the ceriB stretch more) etc.

>e can diide (abor into , stages:
o 9i(ation of the ceriB (way more so than norma()
o 4ctua( birth: baby goes through the ceriB and birth cana(
o EBpu(sion of the p(acenta

<0 now (et"s thin= about mi(= secretion
o 8irst(y) the breasts get bigger during pregnancy due to the estrogen
and progesterone which the p(acenta re(eases
%oweer they preent mi(= from being re(eased
o 4fter birth) estrogen and progesterone decrease (thus mi(= is not
preented from being re(eased) and insetad we get pro(actin re(eased
from the anterior pituitary && the pro(actin cuases mi(= to be produced
o >hen it comes time for the mi(= to actua((y be re(eased) the baby
suc=(es the breast which causes oBytocin to be re(eased from the
posterior pituitary) which further a((ows Fmi(= (et&downF (i.e. the re(ease
of mi(=)