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Biology Lesson 1 Chemistry Review and Enzymes

Thermodynamics
H S
-TS
- + - Spontaneous at all temperatures
+ - + Non-spontaneous at all temperatures
- - + Spontaneous at low temperatures
+ + - Spontaneous at high temperatures
G = H - TS
G = G + RTlnQ
G = -RTlnK
eq








Kinetics
Catalyst speeds up a reaction by lowering the activation energy by providing an alternate mechanism
(pathway) for the reaction to occur
A catalyst lowers the E
a
in both directions, is not consumed in a rxn, and does not shift the equilibrium.

Reaction Coordinate Diagrams


Enzyme Kinetics
Michaelis-Menton Kinetics
Higher Km, lower affinity for substrate
Substrate Specificity

G<0 K
eq
>1
G>0 K
eq
<1
G=0 K
eq
=1
K
eq
Meaning
K >> 1 Products favored at eq.
K << 1 Reactants favored at eq.
K ~ 1 Considerable Prod/React
present at eq.
] [
] [
max
S K
S V
V
m


Competitive Inhibition
-Inhibitor binds to the active site
-Changes K
m
but not V
max



Non-competitive Inhibition
-Inhibitor binds somewhere other than the active site
-Changes V
max
not K
m



Cooperativity
Sigmoidal curve
Hemoglobin vs. myoglobin
Bohr Effect - H
+
and CO
2
decrease the affinity of
hemoglobin for O
2








Enzyme Regulation
1) Allosteric Regulation (ex. feedback inhibition)
2) Phosphorylation (covalent modification)
-Ser, Thr, and Tyr residues can be phosphorylated by kinases (use ATP hydrolysis) or phophorylases
-Phosphatases dephosphorylate enzymes
-Phosphorylation can either activate or inhibit an enzyme depending upon the enzyme
3) Zymogens inactive precursors that become active upon proteolytic cleavage
4) Cofactors involvement of metal ions or organic molecules (coenzymes)
5) Association with other peptides
Biology Lesson 2 Cellular Metabolism
Metabolism
Catabolism vs. Anabolism
Oxidation/Reduction


Catabolism of Glucose (oxidation of glucose):
C
6
H
12
O
6
+ 6O
2
6CO
2
+ 6H
2
O

Anaerobic Catabolism of Glucose
1) Glycolysis (cytosol) substrate-level phosphorylation
2) Fermentation (production of ethanol) or production of lactate

Aerobic Catabolism of Glucose
1) Glycolysis (cytosol) substrate-level phosphorylation
2) PDC (Mitochondrial Matrix)
3) Krebs Cycle (Mitochondrial Matrix)
4) Electron Transport Chain (Mitochondrial Inner Membrane) oxidative phosphorylation


Mitochondrial Structure
Outer membrane, intermembrane space, inner membrane, matrix


Regulation of Glycolysis
ENZYME ACTIVATED BY INHIBITED BY
Hexokinase Glucose-6-P (minor)
PFK-1
AMP
Fructose-6-P
Fructose-2,6-BP (liver)
Insulin
ATP
Fructose-1,6-BP
Citrate
Glucagon
Pyruvate Kinase AMP
Fructose-1,6-BP
ATP
Acetyl CoA
Phosphorylation
Alanine


Gluconeogenesis Production of glucose; the reverse of glycolysis (uses a few different enzymes)
-occurs mainly in the liver (but also the kidneys)


Glycogen Metabolism glucose polymer for glucose storage in the liver and muscles
-insulin activates glycogen synthesis
-glucagon and epinephrine promote degradation


Cori cycle lactate transported to the liver for conversion back to glucose
Glucose Catabolism
Glycolysis
(cytosol)
Glucose
(6C)
2ATP 2ADP
4ADP 4ATP 2NADH 2NAD
+
2 Pyruvate
(3C)
2NADH 2NAD
+
2CO
2
2 Acetyl-CoA
(2C)
( ach e)
TCA Cycle
(Kreb's Cycle)
3NADH 3NAD
+
FAD FADH
2
GDP GTP
ADP ATP
1 for e pyruvat
2CO
2
(1 for each pyruvate)
(per Acetyl-CoA)
Lactate
(3C)
Ethanol + CO
2
N
A
D +
N
A
D
H
N
A
D
H
N
A
D
+
A
n
a
e
r
o
b
i
c
C
o
n
d
i
t
i
o
n
s
Electron
Transport
Chain
ATP
Synthase
H
+
NAD
+
NADH
FADH
2
FAD
1/2O
2
+2H
+
H
2
O
H
+
e
-
e
-
e
-
ADP ATP
mitochondrial matrix
low [H
+
]
intermembrane space
high [H
+
]
Yield Per
Glucose
2ATP
2GTP
10NADH
2FADH
2
25ATP
3ATP
32ATP Total*


1NADH = 2.5 ATP
1FADH
2
= 1.5 ATP
Glucose
Glucose-6-Phosphate (G-6-P)
Fructose-6-Phosphate (F-6-P)
Fructose-1,6-Bisphosphate (FBP)
Glyceraldehyde-3-P (G-3-P)
1,3-Bisphosphoglycerate (BPG)
3-Phosphoglycerate (3-PG)
2-Phosphoglycerate (2-PG)
Phosphoenolpyruvate (PEP)
Pyruvate
Dihydroxyacetonephosphate (DHAP)
Glyceraldehyde-3-P (G-3-P)
1,3-Bisphosphoglycerate (BPG)
3-Phosphoglycerate (3-PG)
2-Phosphoglycerate (2-PG)
Phosphoenolpyruvate (PEP)
Pyruvate
ATP
ATP
ATP ATP
ATP
ATP
ADP
ADP
ADP ADP
ADP
ADP
NAD
+NADH
NAD
+ NADH
Hexokinase
Glucosephosphate
Isomerase
Aldolase
Triosephosphate
Isomerase
Glyceraldehyde-3-Phosphate
Dehydrogenase
Phosphoglycerate
Kinase
Phosphoglycerate
Mutase
Enolase
Pyruvate
Kinase
Major
Regulatory
Step
H
2
O H
2
O
TCA Cycle (Krebs Cycle or Citric Acid Cycle)



Regulation of the TCA Cycle
ENZYME ACTIVATED BY INHIBITED BY
Citrate Synthase ADP
Acetyl-CoA
Citrate
Succinyl-CoA
ATP and NADH (lesser extent)
Isocitrate Dehydrogenase ADP
Ca
2+

ATP and NADH (minor)
-Ketoglutarate Dehyrogenase ADP
Ca
2+

Succinyl-CoA
NaDH
ATP (minor)
Pyruvate Carboxylase Acetyl-CoA

Overall Regulation of Glucose Metabolism
Low ATP/ADP and NADH/NAD
+
Ratios Catabolism activated and Biosynthesis inhibited
High ATP/ADP and NADH/NAD
+
Ratios Biosynthesis activated and Catabolism inhibited

Electron Transport Chain


1NADH = 2.5 ATP
1FADH
2
= 1.5 ATP



Chemiosmosis The electron transport chain establishes a proton gradient (establishing an electrochemical potential) which powers ATP synthase.
Lipid Metabolism
Dietary Intake to Storage
Triacylglycerides converted to fatty acids and monoacylglycerides for absorption out of the small intestine.
Reassembled into triacylglycerides and transported via chylomicrons to adipose tissue for storage.


From Adipose Tissue to Energy Production
Triacylglycerides converted to fatty acids and glycerol by hormone-sensitive lipases
-Activated by glucagon and epinephrine in response to fasting, exercise, or stress
-Glycerol transported to liver for glycolysis or gluconeogenesis
-Fatty acids transported through the bloodstream to tissues in need (heart and muscles primary)


-oxidation




-Unsaturated fatty acids produce 1 less FADH
2
for each double bond
O
O
SCoA
O
Catabolism of Stearic Acid (18C)
9 Acetyl CoA
8 NAD
+
8 NADH
8 FAD
8 FADH
2
27 NAD
+
27 NADH
9 FAD
9 FADH
2
18 CO
2
CAC Cycle
ATP
AMP + PP
i
2P
i
(Equivalent to 2ATP consumed)
9 GDP
9 GTP
(equal to 9ATP)
8 Rounds of -oxidation

NADH FADH
2
ATP
-oxidation
8 8 -2
CAC Cycle 27 9 9
Total 35 (= 87.5 ATP) 17 (= 25.5 ATP) 7 TOTAL: 120 ATP

Photosynthesis
6CO
2
+ 6H
2
O C
6
H
12
O
6
+ 6O
2



Light reactions take place in the thylakoid membrane.
Dark reactions take place in the stroma.

Chlorophylls absorb red light (600-700nm) and blue light (400-500nm).
Antennae chlorophyll molecules pass light energy to reaction centers.


Photophorphorylation
Photosystems are part of an electron transport chain that creates a proton gradient.
The proton gradient powers ATP synthase.


Chloroplasts





Light Reactions

Dark Reactions (Calvin Cycle)





Ribulose-1,5-bisphosphate
(5C)
3-Phosphoglycerate
(3C)
Glyceraldehyde-3-phosphate
(3C)
Dihydroxyacetone phosphate
(3C)
Glyceraldehyde-3-phosphate
(3C)
3 CO
2
+ H
2
O
6 ATP
6 ADP
6 NADPH
6 NADP
+
3 ATP
3 ADP
Glycolysis
Carbohydrates
stay in the cycle


Biology Lesson 3 Molecular Biology
DNA and RNA
Nucleoside (ribose + base) vs. nucleotide (ribose + base + 3 phosphates)
Purines (guanine and adenine) and pyrimidines (cytosine, thymine, and uracil)


















Nucleoside

NH
O
O N
O
H OH
H H
H H
O P O
O
-
O
P O
O
-
O
P
-
O
O
-
O
sugar
base
triphoshpate
Nucleotide

N
N
H
NH
2
O
C
NH
N
H
O
O
T
NH
N
H
O
O
U
Pyrimidines
(CUT the PY)




DNA double helix (right-handed helix)
Antiparallel strands

Complementary

Held together by H-bonding

Base stacking

Watson-Crick base pairing
G-C: 3 Hydrogen bonds
A-T: 2 Hydrogen bonds





Chromosome Organization
Prokaryotes - One circular chromosome (supercoiled by DNA gyrase)

Eukaryotes Many linear chromatin (called chromosomes when condensed during mitosis)
Wrapped around nucleosomes (histone octamers)
Have centromeres and telomeres




Replication (Making DNA from a DNA template)
1) Helicase unwinds DNA helix and separates strands forming the replication fork at the origin.
Topoisomerase unravels DNA ahead of the replication bubble to relieve tension.

2) Single-strand binding proteins bind and stabilize the single stranded DNA.

3) Primase lays RNA primers on the leading (only once) and lagging strand (many times).

4) DNA polymerase (III*) elongates new strands complementary to the leading strand (continuously) and the
lagging strand (discontinuously) in the 5 3 direction (for both).
The fragments on the lagging strand are called Okazaki fragments.

5) DNA ligase joins the Okazaki fragments together (seals the backbone).

6) DNA Polymerase (Pol I*) replaces the RNA primers with DNA


Semiconservative new DNA has one parent strand and one daughter strand

Replication of the telomeres (by telomerase) in eukaryotes

Energy provided by breaking high energy phosphate bonds during formation of phosphodiester linkages.

Reverse Transcriptase polymerase in retroviruses that synthesizes DNA from an RNA template



Prokaryotic DNA polymerases
DNA Pol Function Exonuclease Activity
DNA Pol I Replace Primers and DNA repair 3 to 5 and 5 to 3 exonuclease
DNA Pol II ??? SOS ??? ???
DNA Pol III Primary pol for elongation 3 to 5 exonuclease




Differences between Prokaryotes and Eukaryotes
Prokaryotes Eukaryotes
1 Circular chromosome Many linear chromatin
Supercoiled (by DNA gyrase) Wrapped around nucleosomes (histone octamers)
1 origin of replication Many origins of replication
Bi-directional Bi-directional
DNA Repair
Proofreading 35 exonuclease can remove the last nucleotide if an error occurs during replication.



Nick Translation 53 exonuclease activity of DNA Pol I following replication



Mismatch Repair DNA is methylated prior to replication (prokaryotes); this allows for the parent strand
(methylated) and daughter strand (not methylated) to be distinguished after replication and
any errors during replication in the daughter strand to be repaired.
Several enzymes and proteins are involved.
1) The area around the mismatch is removed on the daughter strand.
2) DNA Pol III fills in the gap.
3) DNA ligase seals the backbone.



Base-excision Repair 1) A damaged base is removed leaving an AP site.
2) An AP endonuclease removes the rest of that nucleotide.
3) An exonuclease removes several more nucleotides.
4) DNA Pol I fills in the gap.
5) DNA ligase seals the backbone.



Nucleotide-excision Repair most common form of repair for damage caused by UV light.
1) The area around the damage is removed.
2) DNA Pol I fills in the gap.
3) DNA ligase seals the backbone.
Protein Synthesis
Prokaryotes

Eukaryotes


Transcription (Making RNA from a DNA template)
1) RNA Pol binds promoter region and begins unzipping DNA.
Promoter region contains a -35 sequence and Pribnow box in prokaryotes.
Promoter region often contains a TATA box in eukaryotes.

2) RNA Pol begins transcribing (forming complementary RNA) at the start site (5 3 direction).
It is the template (or non-coding) strand only that is being transcribed.

3) Transcription is terminated at a special sequence.

Template Strand (Non-coding, anti-sense) vs. Coding Strand (Sense)
Transcription is the principle site of gene regulation.

Gene a DNA sequence encoding for a protein.
Monocistronic (eukaryotes) vs. polycistronic (prokaryotes)

Prokaryotes Eukaryotes
1 RNA polymerase 3 RNA polymerases
(RNA pol I for rRNA nucleolus)
(RNA pol II for mRNA)
(RNA pol III for tRNA)
Promoter is -35 sequence and
Pribnow box (-10)
Promoter is often TATA box (-25)
Occurs in the cytoplasm Occurs in the Nucleus
Coupled transcription/translation Not coupled (Occur in separate compartments)
No mRNA processing 5CAP, poly A tail, splicing out introns

Lac Operon (Transcription Regulation)
The Lac genes allow for the catabolism of lactose.
The repressor binds to operator preventing transcription.
Lactose binds the repressor removing it from the operator.
Translation (Making a peptide from mRNA)
1) Initiation Small ribosomal subunit binds to mRNA near the 5 end (along with many initiation factors).
Shine-Dalgarno sequence at -10 in prokaryotes; other sequences in eukaryotes

2) Met-tRNA (fMet in prokaryotes) binds to the start codon (AUG) via its anticodon will be the P site.
Aminoacyl site (A site), peptidyl site (P site) and exit site (E site)

3) Large ribosomal subunit binds.

4) Elongation - 2
nd
charged tRNA binds at the A site (requires GTP hydrolysis).

5) Ribosome catalyzes peptide bond formation.

6) Translocation (APE) requires GTP hydrolysis.

7) Termination release factor binds when stop codon appears in the A site.

rRNA, tRNA, and mRNA

Charging tRNA requires ATP hydrolysis.

Ribosomes 70S (50S&30S) in prokaryotes and 80S (60S&40S) in eukaryotes)
Eukaryotic RNA polymerases
RNA pol I rRNA
RNA pol II mRNA
RNA pol III tRNA

Post-translational modifications may be made at the ER or Golgi body.

Genetic Code: Degenerate

Replication Transcription Translation
Begins at Origin of Replication Start Site
(upstream promoter region)
Start Codon(AUG)
(upstream Shine-
Dalgarno seq (prok)
acts as ribosome
binding site)
Elongation Enzyme DNA Polymerase RNA Polymerase Ribosome
Where occurs (prokaryotes) Cytoplasm Cytoplasm Cytoplasm
Where occurs (eukaryotes) Nucleus Nucleus Cytoplasm




Genetic Code

Start Codon
AUG

Stop Codons
UGA U Go Away
UAA U Are Away
UAG U Are Gone
Molecular Biology Techniques
PCR (Polymerase Chain Reaction) DNA amplification
1) Denaturation DNA strands are separated with heating (>90C)

2) Annealing The sample is cooled (~55C) to allow primers specific to the target sequence to anneal to
the template strands of the target sequence.

3) Elongation Taq polymerase replicates the templates (~70C)


4) Thermal cycling is repeated many times.




Restriction Enzymes endonucleases that cut dsDNA at a specific sequence leaving either sticky ends or blunt
ends.
Eco RI cuts at the palindromic sequence 5' GAATTC 3'







Gene Cloning Transferring a gene from one cell to another to impart the genes function.
Plasmids small circular dsDNA that has an origin of replication, many restriction sites, and
often antibiotic resistance and a promoter.

A gene is inserted into a plasmid using restriction enzymes and DNA ligase.

The plasmid is used to transform bacteria (bacteria take up the plasmid).

Can also be used in eukaryotes as well (needs eukaryotic promoter and poly A signal).



Hybridization DNA microarrays can be used to detect the presence and amount of specific DNA or RNA
sequences
1) PCR (DNA with Taq polymerase; RNA with Reverse Transriptase)

2) DNA is denatured and single strands are allowed to anneal (when complementary) to single
stranded probe DNA on an array

3) A marker (often a fluorophore) allows for the detection and quantification of hybridized sequences.


Biology Lesson 4 Genetics and Evolution
Genetics
Gene genetic material coding for a single gene product (peptide, rRNA or tRNA)
Locus the chromosomal location of a gene
Allele one variant of a gene
Homologous chromosomes chromosomes that code for the same set of genes (but may have different alleles),
one received from each parent

Genotype vs. phenotype

Law of segregation separation of alleles in the haploid gametes

Law of independent assortment genes assort independently to the progeny

Homozygous vs. heterozygous
Pure breeding or True-breeding strain

Dominant vs. recessive

Complete Dominance when a heterozygote has the phenotype of only 1 of the alleles (the dominant one)

Incomplete dominance phenotypes of the progeny are blends of the parental phenotypes
(ex. snap dragons homozygous red crossed with homozygous white gives pink progeny)

Codominance both inherited alleles are completely expressed (ex. blood types ABO)

1) Homozygous yellow peas (dominant) are crossed with homozygous green peas (recessive). The F1
generation is then self-crossed. What will be the phenotypic ratios in the F2 generation?





2) For peas, yellow is dominant to green and round is dominant to wrinkled. Two heterozygous yellow, round
pea plants are crossed (YyRr). What are the phenotypic ratios in the F1 generation?





3) How would you figure out if a yellow pea plant had the homozygous or heterozygous genotype?




Pleiotropism when a gene has multiple phenotypes associated with its expression

Polygenism when multiple genes affect a trait

Penetrance probability an organism with a specific genotype will express a particular phenotype

Expressivity term describing the variation of phenotype for a specific genotype

Epistasis occurs when the expression of a gene is dependent upon another gene

Autosomes vs. sex chromosomes (X and Y)

Sex-linked Genes
Y-linked traits rare as there are very few genes on the Y-chromosome
All Y-linked disorders are passed on to all male offspring (but to no female offspring)
X-linked traits males only receive a single copy of the X-chromosome from their mother

Mitochondrial inheritance from the mother any genetic disorders coded by the mitochondrial DNA will be
passed on to all offspring

Turner Syndrome (X) offspring (female) have only a single X chromosome resulting from nondisjunction
Kleinfelter Syndrome (XXY) offspring (male) have an extra X chromosome resulting from nondisjunction

3) Color-blindness is the result of an X-linked recessive allele. What is the probability that a colorblind father
and a normal mother (homozygous) have a colorblind child (son or daughter)?






4) What is the probability that a heterozygous mother (a carrier) and a normal father have a colorblind
daughter? A color blind son?





Mutations
Most mutations are deleterious to the cell.

Point mutation (substitution, insertion, deletion) change of a single nucleotide
Missense mutation point mutation leading to a codon coding for a different amino acid
Nonsense mutation point mutation leading to a stop codon

Frame-shift mutations insertion or deletion leading to a change in the reading frame of a gene

Mutations in replication low level of natural mutations that occur during replication

Mutagens and carcinogens agents causing mutation (carcinogens when they cause cancer)



Interphase
G1
S

Protein and nucleic acid synthesis to prepare for replication; production of organelles
DNA Replication
Prophase I Longest phase
Chromosomes condense and tetrad formation (homologous pairs)
Recombination
Disappearance of the nuclear envelope and polarization of the centrioles (MTOCs)
Metaphase I Chromosomes line up on metaphase plate
Spindle fibers attach at centromeres via kinetochores
Anaphase I Spindle fibers pull homologous chromosomes apart towards the centrioles
Cleavage furrow begins forming
Telophase I Nuclear membranes reform
Completion of cytokinesis
Prophase II Chromosomes condense
Disappearance of the nuclear envelope and polarization of the centrioles (MTOCs)
Metaphase II Chromosomes line up on metaphase plate
Spindle fibers attach at centromeres via kinetochores
Anaphase II Spindle fibers pull sister chromatids apart towards the centrioles
Cleavage furrow begins forming
Telophase II Nuclear membranes reform
Completion of cytokinesis
Nondisjunction failure of tetrads to separate during meiosis I or sister chromatids in meiosis II
(ex. Down syndrometrisomy 21)
(ex. Turner Syndrome (X) only a single X chromosome)
(ex. Kleinfelter Syndrome (XXY) an extra X chromosome)

Translocation movement of a segment of one chromosome to another non-homologous chromosome
(ex. Down syndrome chromosome 21 14)

Recombination (single and double crossovers)


Linked genes genes on the same chromosome that probably will not undergo independent assortment
-the closer together on the chromosome the greater the linkage between genes
-the likelihood of recombination increases with distance between genes



5) Lets say that the color and size gene for an organism lie on the same chromosome:
B = blue, b = green, L = large, l = small
Two organisms that are heterozygous for bothcolor and size with the dominant alleles paired on one
chromosome and the recessive alleles paired on the other are crossed and the offspring are as follows:
Phenotype Number
Blue and Large 70
Blue and Small 3
Green and Large 4
Green and Small 23
Which are the recombinant phenotypes?


Population Genetics
Hardy-Weinberg Equilibrium allele frequencies remain constant in a gene pool for a population in equilbrium
p + q = 1
Assumptions for equilibrium
1. Random mating
2. No mutations
3. No selection (natural or otherwise)
4 No migration
5. Large population size
(No genetic drift)
p = frequency of dominant allele
q = frequency of recessive allele

p
2
+ 2pq + q
2
= 1
p
2
= frequency of homozygous dominant genotype
2pq = frequency of heterozygous genotype
q
2
= frequency of homozygous recessive genotype

Evolution
Fitness the ability of an organism to pass on its alleles

Natural Selection differential reproduction of an organism based upon fitness in its environment
1) Stabilizing Selection Selection against the extremes (for the averages)
2) Directional Selection Selection against one extreme (but favoring the opposite extreme)
3) Disruptive (Divergent) Selection Selection against the averages (for the extremes)
4) Artificial Selection directional selection done by humans with selecting for traits in animals and crops
5) Sexual Selection Differential mating between males and females

Species organisms that are capable of reproduction of fit offspring

Speciation
Polymorphism when multiple phenotypes exist within a population

Adaptation an inherited trait that confers greater fitness
Specialization an adaptation to a specific function or environment

Inbreeding increased likelihood of mating between organisms with similar genotypes (limits genetic variation)
Outbreeding - increased likelihood of mating between organisms with different genotypes

Genetic Drift random change in allele frequencies in a population
-smaller populations are more susceptible to genetic drift

Bottleneck dramatic decrease in size of a population making it susceptible to genetic drift

Ontogeny and Phylogeny Similarities in stages of development (ontogeny) can be used to determine
evolutionary relationships between organisms.

Convergent Evolution two species possess the same analogous structures unrelated to a common ancestor
Divergent Evolution divergent leading to distinct populations/species
Parallel Evolution similar evolutionary changes in different species due to similar environmental pressures

Symbiosis
1) Parasitism when a species requires another species as a host to live, harming the host in the process
2) Commensalism an organism requires another species as a host to live, but doesnt harm or benefit the host
in the process
3) Mutualism symbiotic relationship between two organisms that confers fitness on both
Origin of Life Prebiotic Soup?I decided not to present the current scientific beliefs regarding this topic as I
simply dont have a lot of faith in them. But it is still required material and Ill let you find another resource
for this section. My apologies.
Biology Lesson 5 - Microbiology
Viruses
Non-living, parasitic, infectious agent that can only replicate within a host cell.
-Viruses infect every type of living organism (plant, animal, bacteria, archaebacteria).
-Structure - nucleic acid encased in a protein capsid (enveloped or nonenveloped)
-Genome can be linear or circular and can be either dsDNA, ssDNA, dsRNA, or ssRNA.
-Relatively small genomes that can often be read in different reading frames.
-Typically uses hosts replication, transcription, and translation machinery.
-Much smaller than prokaryotic or eukaryotic cells




Bacteriophage Life Cycles
Lytic Cycle
1) Adsorption Bind cell surface via tail (host cell specific interactions)
2) Penetration puncture cell wall and membrane and inject genome into the host cell
3) Hydrolase (a viral gene product) is produced and degrades the hosts genome.
4) Replication of the viral genome (many copies) and synthesis of much capsid protein
5) Assembly of new virus particles
6) Production of lysozyme to degrade the cell wall resulting in cell lysis and release of virus particles.

Lysogenic Cycle
1) Adsorption Bind cell surface via tail (host cell specific interactions)
2) Penetration puncture cell wall and membrane and inject genome into the host cell
3) Integration of the phage genome into the host genome
4) Dormancy viral genes not expressed by viral genome is transmitted to all progeny during cell division
5) Activation excision of viral DNA and entrance into the lytic cycle


Animal cell viruses have similar cycles to the lytic and lysogenic.
Viruses of eukaryotes often have a lipid bilayer envelope and enter the host cell via endocytosis and exit by
budding out of the host cell.


Host cells contain restriction enzymes that will degrade viral DNA. Bacteria methylate their own DNA to
distinguish it from foreign DNA.


Transduction transfer of genetic material via a virus in the lysogenic cycle.

Virus Types (by genome)
[+] RNA viruses viral genome is ssRNA which can also serve directly as mRNA
-must code for an RNA-dependent RNA polymerase for viral replication






[-] RNA viruses viral genome is ssRNA which is anti-sense (-) and therefore complementary to the mRNA
coding for the viral genes.
Must code for an RNA-dependent RNA polymerase and include this polymerase in its capsid
to be infectious

[+] RNA
(can serve
as mRNA)
[-] RNA
[-] RNA
(assembled
into capsids
for new viruses)
RNA-dep
RNA Pol
RNA-dep
RNA Pol
viral proteins
t
r
a
n
s
l
a
t
i
o
n





Retroviruses [+] RNA viruses that convert their genomes into dsDNA for incorporation into the hosts
genome; must encode an RNA-dependent DNA polymerase (reverse transcriptase)

Prokaryotes
cilia
flagellum
ribosomes
plasmid
supercoiled
circular
chromosome
plasma membrane
cell wall


-Single circular dsDNA genome and possibly the presence of a plasmid(s).
-No nucleus, membrane bound organelles or mitotic apparatus.
-Coupled transcription and translation.

Eubacteria vs. Archaebacteria

Classifications of Bacteria
cocci
(spherical)
bacilli
(rod-shaped)
spirilla
(spiral-shaped)


Gram Positive Bacteria stain dark purple during gram staining
-have cell membrane and cell wall (peptidoglycan)
Gram Negative Bacteria stain pink during gram staining
-have cell membrane, cell wall and outer lipopolysaccharide layer (contains endotoxins)


Flagellar Propulsion bacterial flagellum used by motile bacteria for locomotion
Chemotaxis- movement is directed toward chemoattractants or away from chemorepellents
(sensed by chemoreceptors)
-powered by ATP hydrolysis
Fission
Reproduction simply through growth, DNA replication, and cell division.
Doubling times vary but can be as short as 20 minutes under ideal conditions.



Endospores dormant form produced by some bacteria under harsh conditions.
-have a thick peptidoglycan coat and can survive through extreme conditions

Aerobes can survive in an oxygen environment
Anaerobes do not require oxygen to survive
Facultative Anaerobes Can carry out out metabolic processes with or without oxygen


Conjugation


-way to share genetic information adding to diversity
-common way of conferring antibiotic resistance genes
Fungi
Eukaryotes including yeast (unicellular) and a variety of multicellular forms.
Have a cell wall made of chitin.


Asexual Reproduction
1) Budding A fungal cell simply grows out of an existing fungal cell until distinct.
2) Spore Formation procuded by mitosis, spores will germinate under favorable condition to become active.



Sexual Reproduction

Biology Lesson 6 Eukaryotic Cells






Mitochondrial Structure

-PDC and Krebs Cycle occur in the matrix
-ETC Complexes are located in the inner membrane
-Protons are pumped (actively) from the matrix to
the intermembrane space
-ATP synthase is located in the inner membrane and
synthesizes ATP on the matrix side


Organelle Function
Nucleus DNA storage and site of transcription
Surrounded by a nuclear envelope (2 lipid bilayers) through which nuclear pores regulate
traffic of large molecules
Contains the nucleolus (dark spot which is the site of rRNA synthesis)
Ribosomes Translation of mRNA into proteins (present in both pro- and eukaryotes)
Rough ER ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to
form glycoproteins destined for secretion or integration into the membrane
Smooth ER Synthesis of lipids (membrane) and hormones often for export from the cell
Breakdown of toxins in liver cells
Golgi Apparatus Modification (glycosylation) and packaging of proteins into vesicles for secretion or
transport to cellular destinations (like lysosomes)
Mitochondria Site of ATP synthesis via ATP Synthase as a result of oxidative phosphorylation (PDC,
Krebs cycle and the Electron Transport Chain)
Site of fatty acid catabolism (-oxidation)
Have their own DNA (circular) and ribosomes for self-replication
Lysosomes Contains acid hydrolases (digestive enzymes) and have pH~5
Degradation of old organelles or phagocytosed materials
Produced from the Golgi Apparatus
Not present in plant cells
Peroxisomes Involved in the breakdown (involving hydrogen peroxide) of many substances including,
fatty acids, amino acids, and various toxins
Carry out the glyoxalate cycle in germinating plant seeds
Centrioles Source of the spindle apparatus used for cell division (acts as a microtubule organizing
center a.k.a. MTOC)
Not present in plant cells
Vacuoles Fluid-filled membrane-bound vesicles used for transport, storage of nutrients and other
substances, pumping excess water out of a cell, and cell rigidity (in plants)
Chloroplasts Site of photosynthesis in plant cells

Animal cells have lysosomes and centrioles (not present in plant cells).

Plant cells have cell walls, chloroplasts and a central vacuole (not present in animal cells).

Cell Walls
Bacteria Made of peptidoglycans
Archaebacteria Polysaccharides (not peptidoglycans though)
Fungi Made of chitin
Plant cells Made of cellulose
Animal cells None


Protein Trafficking
ribosome
mRNA
nascent
peptide
Rough ER
signal
peptide
N-terminus
signal
recognition
particle (SRP)
signal
peptide
cleaved
ER lumen
SRP binds signal peptide,
translation stalls, and
the ribosome is transported to the ER
SRP directs ribosome
with nascent peptide to
the ER membrane
Translation resumes and
signal peptide is cleaved




plasma membrane
(integral membrane or secreted)
organelles
(ex. lysosomes, ER)
Golgi
Apparatus
cis
trans
Plasma Membrane
Fluid Mosaic Model Components free to move in 2D throughout the membrane
Composed of phoshpolipids, glycolipids and cholesterol
Cholesterol adds rigidity to the membrane
Unsaturated fatty acids increase membrane fluidity

Hydrophobic molecules and small polar molecules (uncharged) can cross the membrane
(ex. CO
2
, O
2
, lipids (including certain hormones), some drugs)

peripheral
membrane
protein
transmembrane
protein
integral membrane protein
polysaccharides


Membrane Proteins
Peripheral membrane proteins adhere to membrane surface via electrostatic interactions

Integral membrane proteins anchored to and embedded in the membrane

Transmembrane proteins Spans the membrane and includes channel proteins, carrier proteins, porins

Cell Receptors - recognition glycoproteins on the cell surface that interact with hormones or other molecules
and relay signals into the cell

Adhesion proteins
Gap Junctions allow exchange of nutrients and cell-to-cell communication (ex. cardiac muscle cells)
Tight Junctions completely encircles cells and seals the space between them to prevent leakage
-(ex. intestinal cells)
Desmosomes spot welds between cells that adhere them to one another and give mechanical strength
-anchored to the cytoskeletons of each cell (ex. skin cells)
Plasmodesmata narrow channels allowing the exchange of nutrients in plant cells

Glycocalyx carbohydrate coating on the cell wall of some bacteria and the plasma membrane of some animal
cells; functions in adhesion, barrier to infection, or cell-cell recognition

Membrane Transport
Passive Transport
1)Simple Diffusion (ex. CO
2
, O
2
, lipids, some drugs)
2) Facilitated Diffusion diffusion of ions/polar solutes via a carrier protein (channel protein) (ex. glucose)

Active Transport - works against the concentration gradient and requires energy (ATP hydrolysis)
1) Primary (ex. Na/K pump3Na
+
pumped out and 2K
+
pumped into cell fueled by ATP hydrolysis)
2) Secondary uses one solutes gradient (established by ATP hydrolysis) to accomplish the transport of
another (Na
+
/glucose cotransport)














Cell Signaling and Second Messengers (G-Proteins)
1) Ligand binds G-protein receptor
2) G-protein receptor activates G-protein which binds GTP (exchanges GTP for GDP)
3) G-protein activates Adenylate Cyclase (ATP cAMP)
4) cAMP acts as a 2
nd
messenger activating a series of proteins and transcription factors



Osmosis and plasmolysis vs. cytolysis
Hypertonic, hypotonic, isotonic


Exocytosis vs. endocytosis
Phagocytosis and pinocytosis
Receptor-mediated endocytosis


Cytoskeleton
Microtubules made from tubulin in a 9+2 arrangement
-functions as a railroad for intracellular transport
-found in the spindle apparatus of mitosis (MTOCs/centrioles) and in flagella and cilia

Intermediate filaments support and maintain the shape of the cell

Microfilaments made from actin and involved in cellular motility, muscle contraction, and cytokinesis



Mitosis



















Cell Cycle
G1
G2
S
Inter
M
i
t
o
s
i
s
p
r
o
p
h
a
s
e
m
e
t
a
p
h
a
s
e
a
n
a
p
h
a
s
e
t
e
l
o
p
h
a
s
e
phase
Summary of Mitosis
Interphase
G1
S
G2

Protein and nucleic acid synthesis to prepare for replication; production of organelles
DNA Replication
Continued growth in preparation for mitosis
Prophase Chromosomes condense
Nuclear envelope disappears
Polarization of the centrioles (MTOCs)
Metaphase Chromosomes line up on metaphase plate
Spindle fibers attach at centromeres
Anaphase Spindle fibers pull sister chromatids apart towards the centrioles
Cleavage furrow begins forming
Telophase Nuclear membranes reform
Completion of cytokinesis

*
*
*
*
prophase
metaphase
anaphase
telophase
and
cytokinesis

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