c

c
c
c
c
c
c
c
c
c
c
c
Introduction: Themes in the Study of Life9/7/2010 8:38:00 AM
×




: properties due to the arrangement and interactions
of parts as complexity increases









 



  studying a small component


 Biologist have to understand how these components
work together by studying how components interact as a whole,cconstructs
models for the dynamic behavior of whole biological systems, used instead
of reductionism.







c
The Biosphere: All environments on Earth inhabited by life.
Ecosystems: All the living and non-living things in a particular area.
Communities: Entire array of organism in an ecosystem.
Populations: Individuals of a species living in a specified area.
Organisms: Individual living things.
Organs and Organ systems: Carry out a particular function in the body.
Tissues: A group of similar cells.
Cells: Life¶s fundamental unit of structure and function.
Organelles: Functional components that make up a cell.
Molecules: Chemical structure consisting of two or more atoms.




 












!


 "




Cell: the lowest level of organization that can perform all activities required
for life.
Prokaryotic cells: (Bacteria and Archae)
1) has membrane 2) the DNA is not enclosed 3) don¶t have organelles
Eukaryotic cells: (Plants and Animals)
1) has membrane 2) has organelles 3)DNA in nucleus





!


×
#
$
%





Taxonomy: the branch of biology that names and classifies species
Three Domains of Life:
Domain Bacteria: Prokaryotic
Domain Archaea: Prokaryotic
Domain Eukarya: Eukaryotic (Protista, Fungi, Plantae and Animalia)

Charles Darwin and Evolution

On the Origin of Species by Means of Natural Selection: 1) Contemporary
species arose for succession of ancestors and 2)Species are naturally
selected, natural environment ³selects´ for the propagation of certain traits.

&
  '(

1) Discovery Science: Describing nature through observation and analysis in
order to acquire empirical data
Inductive Reasoning: generalizations form a large number of specific
observations

2) Hypothesis-based Science: Explaining nature through hypotheses

Hypothesis: tentative answer to a well-framed question
Deductive Reasoning: from general observation to specific conclusions:
-If all organisms are made of cells and humans are organisms, then humans
are composed of cells.
Theory: broader than a hypothesis, they are general, can lead to new
hypothesis and there is a lot of evidence to support it
 ater: The Molecule that Supports Life 9/7/2010 8:38:00 AM

The polarity of water molecules result in hydrogen bonding.




)

1.c !




 water molecules attract each other due to polarity,
surface tension
2.c Ability to 




, since they are bonded, its harder for
them to move
3.c ×* 
 upon freezing
4.c å


 as a solvent
+

 water molecules¶ property to cling to other materials

,




-


×
 energy of motion
,
 total amount of kinetic energy due to molecular motion



,
 the amount of heat that must be absorbed or lost for 1g of
that substance to change heat



 intensity of that heat due to average kinetic energy
!

 heat require to raise the temperature of 1g of water by 1 degree

)
",
 


,

Heat is absorbed when H-bonds break, heat is released when h-bonds are
made
 ater can absorb or release a large amount of heat with only a slight
change in its own temperature

× 

!

× 
 transformation from liquid to gas
,
å 
: heat liquid must absorb for 1g to be converted to gas
× 

!
 as liquids evaporate, its remaining surface cools, it
helps stabilize temperatures in organisms and bodies of water






 homogenous mixture of substances

 dissolving agent

 dissolved substance
+(

 water is solvent
,

: water loving
, 
 fear water, could not dissolve but disperse

!
!


Concentration is expressed in moles/ liter
Molecular mass: the sum of all the masses of all atoms in a molecule
1 mole= 6.02 X 10^23
Example:
1 molar solution glucose. Glucose= C6(H2O)6
((C=6 X12))+((H=12X6X1))+((O=6X16))=180

Acids and Bases

Acidic and basic conditions affect living organisms
A hydrogen atom in a hydrogen bond between two water molecules can shift
from one to another
In pure water: [H+] and [OH-] are equal (10^-7)

Acids: donor of protons [H+] or more hydronium ions [H3O+]

Bases: receiver of protons or donor of [OH-] hydroxide ions
Strong bases and acids completely dissociate

pH Scale
Buffer: substance able to release or take up [H+] in order to maintain a
stable concentration, minimize changes in concentrations of [H+] and [OH-],
most buffers consist of an acid-base pair that reversibly combine with [H+]

From pH to molar concentration

pH= -log[H+]
[H+]=10^(-pH)

Dissociation of  ater
H2O + H2Oâ H3O+ + OH-
Carbon and the Molecular Diversity of Life9/7/2010 8:38:00 AM


!

 the study of carbon compounds
Organic compounds range from simple molecules to colossal ones
å

  the idea that organic compounds arise only in organisms; was
disproved when chemists synthesized these compounds

×
! 



c Electron configuration is the key to an atom¶s characteristics, it
determines the kinds and number of bonds an atom will form with other
atoms
c  ith four valence electrons, carbon can form four covalent bonds with a
variety of atoms (hydrogen, oxygen, and nitrogen)
c This tetravalence makes large, complex molecules possible
c In molecules with multiple carbons, each carbon bonded to four other
atoms has a tetrahedral shape
c However, when two carbon atoms are joined by a double bond, the
molecule has a flat shape

,: organic molecules consisting of carbons and hydrogens

'

‡'
 are compounds with the same
molecular formula but different structures and
properties:
±

 have different covalent
arrangements of their atoms
±.




 have the same covalent
arrangements but differ in spatial
arrangements
±×

 are isomers that are mirror
images of each other
A small number of chemical groups are key to the functioning of biological
molecules:
A number of characteristic groups are often attached to skeleton of organic
molecules
Functional groups: are the components of organic molecules that are most
commonly involved in chemical reactions.
The arrangement of functional groups give each molecule its unique
properties.



&'  

. 
1.c Hydroxyl Group: -OH Since the oxygen has a strong electronegativity, it
takes away hydrogen¶s electron, this allows for hydrogen bonding, being
hydrogen partially positive.
2.c Carbonyl Group: -C=O Major constituents of sugars.  hen it is grouped
within a carbon skeleton it is a ketone.  hen it is at the end of the carbon
skeleton it is an aldehyde.
3.c Carboxyl Group: -COOH Carries a proton that it can give up when it gets
in water. (Acids)
4.c Amino Group: -NH 2 Tend to be basic, they are proton acceptors. Name
c
of compound is amine.
5.c Sulfhydryl Group: SH The name of the coumpound is a thiol. It is
sensitive to oxidation. which resembles a hydroxyl group. These groups
interact to help stabilize the structure of many proteins.
6.c Phosphate Group: OPO32- Used in sugar metabolism to get energy out of
sugar, it is highly negative and it sensitive to hydrolysis. It may be use as
an on and off switch.
7.c Methyl Group: -CH3 A carbon bonded to three hydrogen atoms. Addition
to DNa affects genes. Arangement in methyl groups affects there shape
and function.

Assymetric Carbon:????
A carbon with four different substituent. Enantiomers
NO ATP
Chapter 5: The Structure and Function of Large
Biological Molecules 9/7/2010 8:38:00 AM

!



&


c Carbohydrates
c Lipids
c Proteins
c Nucleic Acids

Macromolecules are polymers, built from monomers

Polymer: a long molecule consisting of many similar building blocks
Monomers: small building-block molecule
Three Classes of polymers: carbohydrates, proteins, and nucleic acids





/

c Condensation Reaction: (Dehydration Reaction) Occurs when two
monomers bond together through the loss of a water molecule
c Enzymes: macromolecules that speed up the dehydration process
c Hydrolysis: a reaction that is the reverse of dehydration, it breaks
polymers

! 

Carbohydrates include sugars and the polymers of sugars, source of energy
and they are building materials
Monosaccharide: simplest carbohydrate, single sugar
Polysaccharides: polymers composed of many sugar building-blocks,

Sugars
Monosaccharides have molecular formulas that are usually multiples of CH2O
Glucose (C6H12O6) is the most common monosaccharide
Monosaccharides are classified by:
-Location of carbonyl group
If their carbonyls are within the molecule, they are Ketoses.
If their carbonyls are at the end of the molecule, they are Aldoses.
-The number of carbons in the carbon skeleton
Though often drawn as linear skeleton, in aqueous solutions many sugars
form rings. Monosaccharide serve as a major fuel for cells and raw material
for building molecules.

Glycosidic bond: formed through dehydration, ending in a bond between an

oxygen atom and two carbohydrates

Polysaccharides have storage and structural roles determined by its sugar

monomers and the positions of glycosidic linkages.




Lipids are large biological molecules that do not form polymers
They are hydrophobic, they have little or no affinity to water
They are fats, phospholipids and steroids


 consist of carboxyl group attached to a long carbon skeleton,
they are made through dehydration reaction 
-Fats are constructed from two types of smaller molecules: fatty acids and
Glycerol, a three-carbon alcohol with a hydroxyl group attached to each
carbon
-In a fat, three fatty acids are joined to glycerol by an ester linkage, creating
a triacylglycerol, or triglyceride

Ester bond: bond made by dehydration, between a carbon and oxygen

-Saturated fatty acids have the maximum number of hydrogen atoms

possible and no double bonds, solid at room temperature
-Unsaturated fatty acids have one or more double bonds, liquid

  

: two fatty acids and a phosphate group attached to glycerol,
they are important because they can assemble into a bi-layer with
hydrophobic tails pointing to the interior making a permeable membrane



: lipids characterized by a carbon skeleton consisting of four fused
rings
Cholesterol, an important steroid is a component in animal cell membranes



Proteins have many structures and many functions.
-Enzymes are a type of protein that acts as a catalyst to speed up chemical
reactions
-Amino acids are organic molecules with carboxyl and
amino groups and an alpha carbon (center carbon) and an
R
-Amino acids differ in their properties due to differing side chains, called R
groups
-A protein consists of one or more polypeptides which are made of many
amino acids linked by peptide bonds






1.c Primary: Its unique sequence of amino acids
2.c Secondary: Coils and folds in a polypeptide chain, alpha helices and beta
pleated sheets, which result from hydrogen bonds
3.c Tertiary: Arrangement of all atoms of a protein
a.c Tertiary structure is determined by interactions between R groups,
rather than interactions between backbone constituents
b.c These interactions between R groups include hydrogen bonds, ionic
bonds, hydrophobic interactions, and van der  aals interactions
c.c Strong covalent bonds called disulfide bridges may reinforce the
protein¶s structure
4.c Quaternary: results when two or more polypeptide chains form one
macromolecule
-Hemoglobin is a globular protein consisting of four polypeptides: two
alpha and two beta chains

!


+
+

‡c Acidic R groups contain a carboxylic acid functional group, -COOH.
‡c Basic R groups contain an amino (not amide) functional group, -NH2,
which attracts a proton to form -NH3.
‡c Neutral polar R groups are neither acidic nor basic, but they contain a
highly electronegative atom such as oxygen, nitrogen, or sulfur.
 ‡c Neutral nonpolar R groups contain mostly carbon and hydrogen (alkyl
groups). They may also contain nitrogen or sulfur, but the effect of
those atoms is diminished due to the size of the alkyl portion.


/
#!
%


+! 




A slight change in a primary structure can affect a protein¶s structure and
ability to function
Sickle-cell disease, an inherited blood disorder, results from a single amino
acid substitution in the protein hemoglobin

Protein structures are sensitive to their solvent and can be unfolded by
alterations in pH, salt concentration, temperature, etc.

0

+

The amino acid of a sequence of a polypeptide is programmed by a unit of
inheritance called gene.
Genes are made of DNA, a nuecleic acid.
Two types of nucleic acid:
1.c Deoxyribonucleic acid (DNA): DNA
directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls
protein synthesis, which occurs in
ribosomes
2.c Ribonucleic acid (RNA)


0

+

-Nucleic acids are polymers called
polynucleotides, made of monomers called nucleotides
-Each nucleotide consists of a nitrogenous base, a pentose sugar, and a
phosphate group
-The portion of a nucleotide without the phosphate group is called a
nucleoside=c nitrogenous base + sugar)

 


0



1.c Pyrimidines (cytosine, thymine, and uracil) have a single six-membered
ring
2.c Purines (adenine and guanine) have a six-membered ring fused to a five-
membered ring

-Adjacent nucleotides are joined by covalent bonds that form between the ±
OH group on the 3p carbon of one nucleotide and the phosphate on the 5p
carbon on the next
-These links create a backbone of sugar-phosphate units with nitrogenous
bases as appendages
-The sequence of bases along a DNA or mRNA polymer is unique for each
gene

‡In DNA, the sugar is deoxyribose; in
RNA, the sugar is ribose



%0+%
,

*
The DNA has two polynucleotide spiraling around an imaginary axis, forming
a 


*
In the DNA double helix, the two backbones run in opposite 5p M 3p
directions from each other, an arrangement called 



The nitrogenous bases in DNA pair up through hydrogen bonds.
Nitrogenous bases bonding:
Adenine (A)-Thymine (T) or (U) Uracil in RNA
Guanine (G)-Cytosine (C)


KNO :
Proteins, depending on their R group, hydrophobic or hydrophilic, charges
The Chemical Context of Life 9/7/2010 8:38:00 AM

×

! 

&
 anything that takes up space and has mass
×

 a substance that cannot be broken down to other substances by
chemical reactions
!  a substance consisting of two or more elements

×

 those required by an organism in only minute quantities

+ 



+  the smallest unit of matter that still retains the properties of an
element, made up of protons, neutrons, and electrons
Atoms of various elements differ in number of subatomic particles
+

 where protons and neutron are tightly packed
+
0 
 number of protons in nucleus, unique to an element
&0 
 sum of protons plus neutrons
+
&: Atoms¶ total mass, similar to its mass number
'
 Atoms of the same element that have different numbers of
neutrons



'
 decay spontaneously,
giving off particles and energy


×


×

×
: the capacity to cause change


×
 energy that matter has
because of its location or structure
The electrons of an atom differ in amounts of potential energy
×


1


2 An electron¶s state of potential energy
 hen the energy is lost , it releases energy in form of heat or light
(photons)

å



 electrons in the outermost shell

Elements with full valence electrons are chemically inert
(noble gasses)
An orbital is the three-dimensional space when an electron
is found 90% of the time
Each electron shell consists of a specific number of orbitalsc


In a # 
, atoms share electrons equally: H2
In a 
, one atom is more
electronegative, the atoms don¶t share electrons equally and
this causes partial positive and partial negative charges

'
 when atoms strip electrons from their bonding
partners. After the transfer of electrons, both atoms have
charges. Ions are weaker than covalent bonds.
Ion: a charged atom
,
 1/20 strength of a covalent bond
Interactions between partial negative and partial positive caused by
hydrogen molecules. They give us specificity in biology.

å
)'

 only attracted when really close together,
you need a lot of these interactions to make strong connection

Molecular Shape and Function

!




!



: the making and breaking of chemical bonds

 are starting materials,  are ending materials
×(


 : rate of the forward reaction is equal to the rate of the reverse.
Chemical reactions make and break covalent bonds
2H2 + O2â 2H2O
Chapter 6: A Tour of a Cell 9/7/2010 8:38:00 AM

&
 
132Light Microscope (LM): visible light passes through a specimen and
magnifies the image. But we can¶t get the detail because the wavelength is
too big. Can be used to see a living cell, but once the cell is stained, the cell
dies.
The Quality of Images Depend on:
Magnification: the ratio of an object¶s image size to its real size
Resolution: the measure of clarity of the image

Techniques:
c Brightfield (unstained)
c Brightfield (stained)
c Phase-contrast
c Differential-interference-contrast
c Fluorescence
c Confocal

142Electron Microscope (EM): has a shorter wavelength and lets us see

details of macromolecules.

Techniques:
Scanning electron microscopes: focus beam of electrons onto the surface,
3D images
Transmission electron microscopes (TEMS): beams go through a specimen,
used to study internal structures.

!
 


Cell fractionation takes cells apart and separates the major organelles from
one another, it enables scientists to determine the function of organelles.
Uses spinning to separate cells and organelles apart.

!



Basic features of all cells:

1.c Plasma Membrane
2.c Cytosol: Semi-fluid substance
3.c Chromosomes (genes)
4.c Ribosomes


!

35/

Uc Nucleoid: DNA in an unbound region, no nucleus
Uc No membrane-bound organelles
Uc Cytoplasm bound by plasma membrane

45×/

Uc DNA in a nucleus that is bounded by a membranous nuclear envelope
Uc Membrane-bound organelles
Uc Cytoplasm in the region between the plasma membrane and nucleus
Uc Much larger than prokaryotic cells

The  

is a selective barrier (polar bi-layer) that allows

sufficient passage of oxygen, nutrients, and waste to service the volume of
every cell

The logistics of carrying out cellular metabolism sets limits on the size of
cells. Cells can only get so big. Surface area increases while total volume
remains constant

+
!

Nucleus: Protected by a nuclear membrane (two membrane) which has
pores that lets things in and out. Inside, it has chromatin and nucleolus.
The mRNA comes out of the pores and links to a ribosome in the rough
endoplasmic reticulum.
0

Uc Contains most of the cell¶s genes and is usually the most conspicuous
organelle
Uc The 



encloses the nucleus, separating it from the
cytoplasm
Uc The nuclear membrane is a double membrane; each membrane consists
of a lipid bilayer
Uc Pores regulate the entry and exit of molecules from the nucleus
Uc The shape of the nucleus is maintained by the 

,which is
composed of protein
Uc In the nucleus, DNA and proteins form genetic material called   

Uc Chromatin condenses to form discrete   

Uc The 
is located within the
nucleus and is the site of ribosomal
RNA (rRNA) synthesis




Uc Particles made of ribosomal RNA
and protein
Uc Ribosomes carry out protein
synthesis in two locations:
-In the cytosol (free ribosomes)
-On the outside of the endoplasmic reticulum or the nuclear envelope (bound
ribosomes)

Endomembrane System: regulates protein traffic and performs metabolic

functions in the cell

! 

×




35c 0




45c × 


 
-The endoplasmic reticulum (ER) accounts for more than half of the total
membrane in many eukaryotic cells
-The ER membrane is continuous with the nuclear envelope
-There are two distinct regions of ER:
-Smooth ER, which lacks ribosomes
-Rough ER, with ribosomes studding its surface
3.c .
+  shipping and receiving center, sorts and packages
materials to transport vesicles
4.c 
 A lysosome is a membranous sac of hydrophilic enzymes
that can digest macromolecules
Phagocytosis:
Autophagy: Process used to recycle organelles
]5c å

Food Vacuoles: formed by phagocytosis
Contractile Vacuoles: pumps excess water out of cells
Central vacuoles: holds organic compounds and water, a storage area,
allows plant cells to become larger than animal and bacterial cells
*5c  &


-These components are either continuous or connected via transfer by
vesicles





1.c &
 
 are the sites of cellular respiration which generates ATP,
contains ribosomes. They have a smooth outer and inner membrane
folded into cristae (which provides large surface area). The inner
membrane creates two compartments: intermembrane space and
mitochondrial matrix.
2.c !  family of the plastids,in plants and algae where
photosynthesis takes place, contains ribosomes. Structure: thylakoid,
membrane sacs stacked to form granum, which contains chlorophyll. The
inner fluid is called stroma.
3.c 
*

 oxidative organelle, they use oxidation to degrade
different types of molecules
Î5c !/


#The cytoskeleton is a network of fibers extending throughout the
cytoplasm. It organizes the cell¶s structures and activities, anchoring
many organelles. The cytoskeleton helps to support the cell and maintain
its shape.
-It interacts with motor proteins to produce motility. Inside the cell,
vesicles can travel along ³monorails´ provided by the cytoskeleton.
-Composed of three types of molecular structures:
Uc Microtubules: (tubiline)Hollow tubes, maintain cell shape, cell mobility,
chromosome movement in cell division, and organelle movement.
Uc Microfilaments: (actin) two intertwined strands of actin, maintain cell
shape, muscle contraction, citoplasmic streaming, cell division
Uc Intermediate filamenents: (keratin) Fibrous protein cable, anchorage of
nucleus, formation of nuclear lamina
Membrane Structure and Function 9/7/2010 8:38:00 AM

&


The plasma membrane separates the living cell from its surroundings, it
exhibits selective permeability, allowing substances to cross it more easily
than others.
Membranes are made of proteins and lipids (phospholipids are most
abundant).
The fluid mosaic model states that a membrane is a fluid structure with a
mosaic of various proteins embedded in it.


&
&


Uc Integral Proteins: Big ones that traverse

the bi-layer.
Uc Peripheral proteins: the ones outside of
the bi-layer.

&

 


Uc Phospholipids and proteins of plasma membrane can move within the bi-
layer, they cannot flip-flop.
Uc Membranes must be fluid to work properly; they are usually about as fluid
as salad oil. Unsaturated fatty acids are not tightly packed, saturated are.
Uc The steroid cholesterol has different effects on membrane fluidity at
different temperatures:
-At warm temperatures (such as 37°C), cholesterol restrains movement of
phospholipids.
-At cool temperatures, it maintains fluidity by preventing tight packing.


*&6 
&




1.c Transport: Active and Passive
2.c Enzymatic activity
3.c Signal transduction
4.c Cell-cell recognition
5.c Intercellular joining
6.c Attachment to the cytoskeleton and extracellular matrix

-Cells recognize each other by binding to surface molecules, often

carbohydrates, on the plasma membrane
-Membrane carbohydrates may be covalently bonded to lipids (forming


) or more commonly to proteins (forming  

)
-Carbohydrates on the external side of the plasma membrane vary among
species, individuals, and even cell types in an individual






&


Uc Membranes have distinct inside and outside faces
Uc The asymmetrical distribution of proteins, lipids, and associated
carbohydrates in the plasma membrane is determined when the
membrane is built by the ER and Golgi apparatus
Uc Glycosolated Proteins will not be found in the cytoplasm, only in the
membrane
m

 An animal cell membrane will be more fluid at room temperature
if it contains: more cis-unsaturated and polyunsaturated fatty acid«not
cholesterol, not longer fatty acids because the longer the stiffer and not
trans because they are not natural.
m

 Regions of the plasma membrane called lipid rafts ³have high
concentrations´ of cholesterol. Consequently, the proteins in lipids rafts.:
Tend to stay clustered together.
m

  hich of the following amino acids would most likely be present
in the transmembrane domain of an integral membrane protein?: a
hydrophobic acid like valine, because it is on a hydrophobic area of the
membrane

 &

 

35

  Movement due to concentration gradients
(differences), through diffusion
%

 is the tendency for molecules to spread out evenly into the
available space
%
×(


  As many molecules cross one way as cross in the
other direction
 
the diffusion of water across a selectively permeable membrane,
from the region of lower solute concentration to the region of higher solute
concentration (tendency of water to move to areas of higher solute
concentrations).




%

 Passive Diffusion Through Proteins
Uc 


%

: transport proteins speed the passive movement
of molecules across the plasma membrane
Uc Channel proteins provide corridors that allow a specific molecule or ion to
cross the membrane
Uc ! 
 




Yc Aquaporins, for facilitated diffusion of water
Yc Ion channels that open or close in response to a stimulus (gated
channels)
SCREEEEEEEEEEEEEEEEEN SHOOOOOOOOOOOOOT
45+

  Allow passage of hydrophilic substances, moves
substances against their concentration gradient, requires ATP, allows cells to
maintain concentration gradients that differ from their surroundings
! 


 hydrophilic channel that select molecules or ions can use
as a tunnel.
!



 bind to molecules and shuttle them across the
membrane, requires energy


 #
  1+

 2
[Na+] outside, [K+] inside, both are moving against their concentration
gradients. For every molecule of ATP, the protein can transport 3 [Na+] out
and 2[K+]. Every time we go to one cycle of ATPase, we generate an
electron potential on the cell
since we are shipping three
cations out and only two in.

' &


&




(ATPase & the Bacteria
Proton Pump)
-Membrane potential: voltage
difference across a
membrane, distribution of
positive and negative ions
-Electrochemical Gradient: ion¶s concentration gradient, membrane
potential.

! 
Contransport: when active transport of a solute indirectly drives transport of
another solute

5c / +
 &



Exocytosis: transport vesicles migrate to the membrane, fuse with it, and
release their contents
Endocytosis: the cell takes in macromolecules by forming vesicles form the
plasma membrane
There are three types of Endocytosis:
Phagocytosis: cellular eating
Pinocytosis: cellular drinking
Receptor-mediated Endocytosis


)



!



 the ability of a solution to cause a cell to gain or lose water
35, 

 Solute concentration is less than that inside the cell,
cell gains water.
45'

Solute concentration is the same as that inside the
cell, no net water movement across the plasma membrane.
5,


 Solute concentration is greater than that inside the
cell, cell loses water.

 

, the control of water balance, is a necessary adaptation
for life in such environments

)

!

 )
-Cell walls maintain water balance
c Plant cell in hypotonic solution swells until wall opposes uptake, the cell is
now 

‡If a plant cell and its surroundings are isotonic, there is no net movement
of water into the cell; the cell becomes 
(limp), and the plant may
wilt
‡In a hypertonic environment, plant cells lose water; eventually, the
membrane pulls away from the wall, a usually lethal effect called
 


m

: Fructose because there¶s no concentration inside the cell and
sucrose cant move.
m

Î Glucose because it has a higher concentration inside the cell.
m

] The cell has more solutes
Question 6:
Introduction to Metabolism 9/7/2010 8:38:00 AM

 ork requires energy in form of ATP which is produced through the

oxidation of glucose to CO2.

Metabolism: the totality of an organism¶s chemical reactions

-Catabolic: release energy by breaking down complex molecules into
simple compounds (favorable reactions)
-Anabolic: consume energy to build complex molecules from simpler ones

×

×
 the capacity to cause change, it can be converted from one form to
another
-


×
 motion

 ×
7,
 movement of atoms or molecules


×
 matter possesses because of its location or structure
!

×
 potential energy available for release in a chemical
reaction


 
 study of energy transformations
‡!

 (liquid in a thermos) is isolated from its surroundings
‡

energy and matter can be transferred between the system
and its surroundings
Spontaneous Process: process hat doesn¶t require, without the input of
energy, usually an exorgonic process





 

c
1!

×
2 the energy of the universe is
constant. Energy can be transferred and transformed, but it cannot be
created or destroyed.
- During every energy transfer or transformation, some energy is unusable,
and is often lost as heat
c 
 Every energy transfer or transformation increases the
entropy (disorder) of the universe
-Energy flows into an ecosystem in the form of light and exits in the form of
heat
º




 
ºree Energy: energy that can do work when temperature and pressure are
uniform
‡The change in free energy (¨G)during a process is related to the change in
enthalpy, or change in total energy (¨‰), change in entropy (¨ ), and
temperature in Kelvin
):
¨G = ¨‰ ± ¨
‡Only processes with a negative ¨G are spontaneous
-H must decrease and/or S must increase.
‡Spontaneous processes can be 

 to perform work, in other words
they usually are exorgonic reactions that can drive endergonic ones



×
8

8×(


 
Free energy: measure of a system¶s instability, its tendency to change to a
more stable state.
During spontaneous change, free energy decreases and stability of a system
increases
Equilibrium: state of maximum stability
A process is spontaneous and can perform work only when its moving
toward equilibrium

×(


 &

 
c Reactions in a closed system eventually reach equilibrium and then do no
work
c Cells are not in equilibrium; they are open systems experiencing a
constant flow of materials
c A defining feature of life is that metabolism is never at equilibrium
c A catabolic pathway in a cell releases free energy in a series of reactions

An exergonic reaction proceeds with a net release of free energy and is

spontaneous
An endergonic reaction absorbs free energy from its surroundings and is
nonspontaneous

Question 1: C
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c Mechanical
c Transport
c Chemical
To do work, cells manage energy resources by energy coupling, the use of
an exorgonic process to drive an endergonic one.



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c The bonds between the phosphate groups of ATP¶s tail can be broken by
hydrolysis
c Energy is released from ATP when the terminal phosphate bond is broken
c This release of energy comes from the chemical change to a state of
lower free energy, not from the phosphate bonds themselves
c ATP has a high free energy because of its four negatively charged
oxygens and wants to go to more stable state by releasing a phosphate
and giving off energy.
c In the cell, the energy from the exergonic reaction of ATP hydrolysis can
be used to drive an endergonic reaction. Overall, the coupled reactions
are exorgonic.

Question 2: E






+
c ATP is a renewable resource hat can be regenerated by adding a
phosphate group to ADP
c The energy to phospholyrate ADP come from caablolic reactions in the
cells.
SLIDE 21 is supposed to say exorgonic
Question 3: C

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Enzymes speed up metabolic reactions by lowering energy barriers
Catalyst: facilitates a reaction but is not consumed by it.
Enzyme: catalytic protein


+

×



c Activation Energy: the initial energy needed to start a chemical reaction,
it is often supplied in form of heat from the surroundings.
c Enzyme catalyze reactions by lowering the activation energy barrier
c Enzymes do not affect the change in free-energy (¨G); instead, they
hasten reactions that would occur eventually

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c ×

 the reactant that an enzyme acts on
c ×
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* formed when an enzyme binds to its
substrate
c +



 region where the substrate binds to the enzyme
c The active site can lower an EA barrier by:
-Orienting substrates correctly
-Straining substrate bonds
-Providing a favorable microenvironment
-Covalently bonding to the substrate
×
,

:
c Cofactors: non-protein enzyme helpers
c Coenzymes: organic cofactors

Question 5: A

 
×

×

An enzyme¶s activity can be affected by:
-General environmental factors such a as energy and pH
-Chemicals that specifically influence the enzyme
Each enzyme has an optimal temperature in which it can function
Each enzyme has an optimal pH in which it can function.

×
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Competitive Inhibitors: bind to the active site of an enzyme, competing with
the substrate
Non-competitive (Allosteric) Inhibitors: bind to another part of an enzyme,
causing the enzyme to change shape and making the active site less
effective.



×

Metabolic pathways are tightly regulated


! Switch on or off the genes that encode specific
enzymes
+



 Protein¶s function at one site is affected by binding
of a regulatory molecule at another site
Compartmentalization:

Eliminate Slide 30 and 31

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Feedback Inhibition: the end product of a metabolic pathway shuts down the
pathway, it prevents a cell from wasting chemical resources by synthesizing
more product than is needed.

Question 6: C
Question 7: D
Question 8: B
Question 9: A
Question 10: C
Question 11: B
Cellular Respiration 9/7/2010 8:38:00 AM

!




Catabolic Pathways yield energy by oxidizing organic fuels
Cellular respiration consumes oxygen and organic molecules and yields ATP
‡Although carbohydrates, fats, and proteins are all consumed as fuel, it is
helpful to trace cellular respiration with the sugar glucose:
C6H12O6 + 6O2  6CO2 + 6H2O + Energy (ATP + heat)






*
Oxidation Reactions/ Redox Reactions: chemical reactions that transfer
electrons between reactants
In Oxidation, a substance loses an electron or is oxidized
In reduction, a substance gains electrons or is reduced(to a negative charge)
Some redox reactions change the electron sharing in covalent bonds:
methane (CH4) being oxidized and converting into carbon dioxide (CO2)




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Electro form organic compounds are usually first transferred to NAD+, a
coenzyme electron acceptor.
NAD+ is an oxidizing agent during cellular respiration
Each NADH (the reduced form of NAD+) represents stored energy that is
used to synthesize ATP
NADH passes the electrons to the electron transport chain
Unlike an uncontrolled reaction, the electron transport chain passes
electrons in a series of steps instead of one explosive reaction
Oxygen pulls electrons down the chain in an energy-yielding tumble
The energy yielded is used to regenerate ATP
NADH enters the ETC first, generating more energy. FADH2 enters later,
generating less energy.

 



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1. Glycolysis: the breaking down of a glucose molecule into two pyruvates
2. Citric Acid/ Kreb Cycle: completes the breakdown of glucose
3. Oxidative Phosphorylation: accounts for most of the ATP synthesis
Screen shot 2

Substrate Level Phosphorylation- Reducing Equivalence

Glycolysis and the Citric Acid Cycle form a small amount of ATP through
substrate-level Phosphorylation. ADP is phosphorolated in an enzyme.
Oxidative Phosphorylation accounts for 90% of ATP generated

Glycolisis
Breaks down glucose into two pyruvates
Occurs in the cytoplasm and has two major phases:
-Energy Investment Phase: 2 ATP in
-Energy Payoff Phase: 4 ATP
Net Gain: 2 pyruvtes, 2 ATP, 2 H2O, 2 NADH
Screen Shot3

Citric Acid Cycle

‡Before the citric acid cycle can begin, pyruvate must be converted to acetyl
CoA. It does this by losing a carbon as CO2 and binding to the enzyme
acetyl. Generates: 1 NADH
‡The citric acid cycle, also called the Krebs cycle, takes place within the
mitochondrial matrix.
‡Generates: 1 ATP, 3 NADH, and 1 FADH2



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The Kreb Cycle has eight steps.
The acetyl group of acetyl CoA joins the cycle by combining with
oxaloacetate, forming cirtrate.
Seven steps decompse the citrate back to oxaceloacetate, making the
process a cylce.
The NADH and FADH2 produced by the cycle relay electron extracted from
food to the electron transport chain.

Oxidative Phosphorolation
*


  


 
 


 
+


‡Following glycolysis and the citric acid cycle, NADH and FADH2 account for
most of the energy extracted from food
‡These two electron carriers donate electrons to the

 
 
chain, which powers ATP synthesis via oxidative Phosphorylation

The Pathway of Electron Transport

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Electron transfer in the ETC causes proteins to pump H+ from the
mitochondrial matrix to the intermembrane space.
H+ then moves back, passing through channels of ATP synthesis
This is an example of chemiosmosis, the use of energy in a H+ gradient to
drive cellular work
‡The energy stored in a H+ gradient across a membrane couples the redox
reactions of the electron transport chain to ATP synthesis
‡The H+ gradient is referred to as a proton-motive force, emphasizing its
capacity to do work

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‡During cellular respiration, most energy flows in this sequence:
glucose NADH electron transport chain proton-motive force
ATP
‡About 40% of the energy in a glucose molecule is transferred to ATP during
cellular respiration, making about 38 ATP




 
+
 

*

UCellular respiration requires O2 to produce ATP
‡Glycolysis can produce ATP with or without O2 (in aerobic or anaerobic
conditions)
‡In the absence of O2, glycolysis couples with fermentation to produce ATP
‡Fermentation consists of glycolysis plus reactions that regenerate NAD+,
which can be reused by glycolysis
‡Two common types are alcohol fermentation and lactic acid fermentation

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‡In lactic acid fermentation, pyruvate is reduced by NADH, forming lactate
as an end product, with no release of CO2, generating two ATP
‡Lactic acid fermentation by some fungi and bacteria is used to make cheese
and yogurt
‡Human muscle cells use lactic acid fermentation to generate ATP when O2 is
scarce




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‡Both processes use glycolysis to oxidize glucose and other organic fuels to
pyruvate
‡The processes have different final electron acceptors: an organic molecule
(such as pyruvate) in fermentation and O2 in cellular respiration
‡Cellular respiration produces much more ATP




 


+















Gycolysis and the citric acid cycle are major intersections to various catabolic
and anabolic pathways
Biosynthesis (Anabolic pathways) precursor molecules may come directly
from food, from glycolysis, or from the citric acid cycle



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‡Feedback inhibition
‡If ATP $ respiration speeds up; ATP respiration slows down
‡Control of catabolism is based mainly on regulating the activity of enzymes
at strategic points in the catabolic pathway


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9/7/2010 8:38:00 AM