Biology Lesson 1 – Chemistry Review and Enzymes Thermodynamics

H S -TΔS - + - Spontaneous at all temperatures + - + Non-spontaneous at all temperatures - - + Spontaneous at low temperatures + + - Spontaneous at high temperatures

G = H - TS G = G + RTlnQ G = -RTlnKeq 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 Ea 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 Keq>1 G>0 Keq<1 G=0 Keq=1

Keq Meaning K >> 1 Products favored at eq. K << 1 Reactants favored at eq. K ~ 1 Considerable Prod/React

present at eq.

][

][max

SK

SVV

m

Competitive Inhibition -Inhibitor binds to the active site -Changes Km but not Vmax

Non-competitive Inhibition -Inhibitor binds somewhere other than the active site -Changes Vmax not Km

Cooperativity Sigmoidal curve Hemoglobin vs. myoglobin Bohr Effect - H+ and CO2 decrease the affinity of hemoglobin for O2 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): C6H12O6 + 6O2 → 6CO2 + 6H2O 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) Kreb’s 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 2NADH2NAD+

2 Pyruvate(3C) 2NADH2NAD+

2CO2

2 Acetyl-CoA(2C)

( ach e)

TCA Cycle(Kreb's Cycle)

3NADH3NAD+FAD FADH2

GDP GTP

ADP ATP

1 for e pyruvat

2CO2

(1 for each pyruvate)

(per Acetyl-CoA)

Lactate(3C)

Ethanol + CO2

NAD +

NADHNADH

NAD+

An

aero

bic

Con

dit

ion

s

ElectronTransport

Chain

ATPSynthase

H+

NAD+NADH FADH2 FAD1/2O2+2H+ H2O

H+ e-e-

e-

ADP ATPmitochondrial matrix

low [H+]

intermembrane space

high [H+]

Yield PerGlucose2ATP2GTP10NADH2FADH2

25ATP

3ATP

32ATP Total*

1NADH = 2.5 ATP 1FADH2 = 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

ATPATP

ADP

ADP

ADP ADP

ADPADP

NAD+NADH

NAD+NADH

Hexokinase

GlucosephosphateIsomerase

Aldolase

TriosephosphateIsomerase

Glyceraldehyde-3-PhosphateDehydrogenase

PhosphoglycerateKinase

PhosphoglycerateMutase

Enolase

PyruvateKinaseMajor

RegulatoryStep

H2OH2O

TCA Cycle (Kreb’s 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 Ca2+

ATP and NADH (minor)

-Ketoglutarate Dehyrogenase ADP Ca2+

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 1FADH2 = 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 FADH2 for each double bond

O

O

SCoA

O

Catabolism of Stearic Acid (18C)

9 Acetyl CoA

8 NAD+

8 NADH

8 FAD

8 FADH2

27 NAD+

27 NADH

9 FAD

9 FADH2

18 CO2

CAC Cycle

ATP

AMP + PPi 2Pi

(Equivalent to 2ATP consumed)

9 GDP

9 GTP(equal to 9ATP)

8 Rounds of -oxidation

NADH FADH2 ATP

-oxidation 8 8 -2 CAC Cycle 27 9 9

Total 35 (= 87.5 ATP) 17 (= 25.5 ATP) 7 TOTAL: 120 ATP

Photosynthesis

6CO2 + 6H2O → C6H12O6 + 6O2

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 CO2 + H2O

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

ON

O

HOH

HH

HH

OPO

O-

O

PO

O-

O

P-O

O-

O

sugar

basetriphoshpate

Nucleotide

N

NH

NH2

O

CNH

NH

O

O

TNH

NH

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 – 3’5’ exonuclease can remove the last nucleotide if an error occurs during replication. Nick Translation – 5’3’ 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 5’CAP, 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 - 2nd 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 mRNARNA 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 gene’s 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 syndrome—trisomy 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 p2 + 2pq + q2 = 1 p2 = frequency of homozygous dominant genotype 2pq = frequency of heterozygous genotype q2 = 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 doesn’t 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 don’t have a lot of faith in them. But it is still required material and I’ll 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 host’s 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 host’s 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 serveas mRNA)

[-] RNA [-] RNA(assembledinto capsids

for new viruses)

RNA-depRNA Pol

RNA-depRNA Pol

viral proteins

translation

Retroviruses – [+] RNA viruses that convert their genomes into dsDNA for incorporation into the host’s

genome; must encode an RNA-dependent DNA polymerase (reverse transcriptase)

Prokaryotes

cilia

flagellum

ribosomes

plasmid

supercoiledcircular

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 Kreb’s Cycle occur in the matrix -ETC Complexes are located in the inner membrane -Proton’s 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,

Kreb’s 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

nascentpeptide

Rough ERsignalpeptide

N-terminus

signalrecognition

particle (SRP)

signalpeptidecleaved

ER lumen

SRP binds signal peptide,translation stalls, and

the ribosome is transported to the ER

SRP directs ribosomewith nascent peptide to

the ER membrane

Translation resumes andsignal peptide is cleaved

plasma membrane

(integral membrane or secreted)

organelles(ex. lysosomes, ER)

GolgiApparatus

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. CO2, O2, lipids (including certain hormones), some drugs)

peripheralmembrane

protein

transmembraneprotein

integral membrane proteinpolysaccharides

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. CO2, O2, 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 pump—3Na+ 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 ‘2nd 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

Mitosispr

opha

sem

etap

hase

anap

hase

telop

hase

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

anaphasetelophase

andcytokinesis