Uworld Biology Master - DNA/CELL GROWTH/GENETICS/PROK/EUK/VIRUS

*CELL GROWTH*

*CELL GROWTH*

Steps in Eukaryotic DNA replication - function of the ffg - topoisomerase II, helicase, ssDNA-BP, primase, DNA polymerases α + β, range h, DNA poly γ, DNA ligase - are telomeres synthesized? 5) DNA synthesized by _____ 6) RNA primers removed by _____ 7) RNA replaced with DNA by ______

1) supercoils removed by DNA topoisomerase II 2) helicase unwinds DNA strands 3) ssDNA-BP stabilize DNA & prevents reannealing 4) RNA primers synthesized by primase, 5) DNA synthesized by DNA poly α + β 6) RNA primers removed by range h, 7) DNA replaced with DNA by DNA poly γ, 8) okazaki fragments joined by DNA ligase, - telomeres synthesized by telomerase

Steps in prokaryotic DNA replication - function of the ffg - topoisomerase II, helicase, ssDNA-BP, primase, DNA polymerase III, DNA poly I, DNA ligase, leading and lagging strands - are telomeres synthesized? 5) DNA synthesized by _____ 6) RNA primers removed by _____ 7) RNA replaced with DNA by ______

1) supercoils removed by dna topoisomerase II 2) helicase unwinds DNA strands;disrupts Hbond 3) ssDNA-BP stabilize DNA & prevents reannealing 4) RNA primers synthesized by primase, 5) DNA synthesized by DNA poly III in 5' to 3' 6) RNA primers removed by DNA poly I, 7) RNA replaced with DNA by DNA poly I, 8) okazaki fragments joined by DNA ligase - leading - continuous toward rep. fork - lagging - discontinuous away from rep. fork - telomeres not synthesized

Fluid Mosaic Model - *what migrates? - in what direction?*

Cell membrane is said to be fluid because - it's various non-phospholipid stuff are able to migrate *laterally* through the entire phospholipid rich surface of the cell in all direction

Describe process of fermentation & glyconeogenesis - pyruvate oxidizes ____→_____ - in Glyconeogenesis ____ is converted to ____ - For Proks; pyruvate → enzyme → - For Euks; pyruvate → enzyme → - Is O₂ required for either? - are the active during anaerobic conditions?

Fermentation = No O₂ required - metabolizes pyruvate under anaerobic conditions to oxidize NADH → NAD⁺ For Proks; Pyruvate + NADH←(pyruvate decarboxylase) → Acetaldehyde + CO₂ ←(Alcohol dehydrogenase) → Ethanol + NAD⁺ For Euks; Pyruvate + NADH ← (lactate dehydrogenase)→ Lactic acid + NAD⁺ Glyconeogenesis = No O₂ required - Process by which non-carbohydrate carbon sources are converted into glucose Both do not require O₂; ∴ are active during anaerobic conditions in both Prok & Euks

Differences & Similarities btw Genetic Drift & Bottle neck - caused by? - effect on genetic diversity, allele pop size, survival

Genetic Drift = Chance event, - eg- sampling error Bottle neck = Not by chance, -eg- natural disasters, human destruction BOTH - ↓ genetic diversity - ↑probability of a beneficial allele being removed and deleterious allele becoming fixed - can cause extinction in small population

Genetic Linkage During recombination, what happens when; - 2 genes are located close to each other - 2 genes are located far from each other - composition of recombinants to parental in new homoC

Genetic Linkage = ↑parental/non-recombinant - Tendency of allele in close proximity to remain on same chromosome & be inherited together by offspring 2 genes located close to each other - tend to hang on to each other and transfer together rather than combine with others - ∴ New HomoC = ↓recombinants, ↑parental 2 genes located far from each other - tend to be free to combine with others - ∴ New HomoC = ↑recombinants, ↓parental

- Genetic Recombination - Recombinants - Parental

Genetic Recombination = Crossing over events Recombinants - Only the new combinations of alleles - from mom and dad and vice versa Parental - Original combinations that already existed in the parent

Given a homodimer with 225 residue monomer - Calculate # of AA residues - Calculate # of nucleotides in mRNA sequence - Calculate molecular weight of the protein

# of AA residues = 225 x 2 = 450 total AA # of nucleotides in mRNA sequence = # AA in protein × 3 nucleotides per codon = 450 AA × 3 nucleotides = 1,350 nucleotides molecular weight of the protein = # AA in protein × molecular weight of an AA = 450 AA × 110 Da = 49,500 Da 1350 mRNA nucleotides must be translated to form 50,000Da or 50kDa protein

Diff btw (Proto) Oncogenes, Tumor suppressing cells and Pro-apoptotic proteins - what do they code for? - what do they promote? - what do they inhibit?

(Proto)-Oncogenes eg p53, Rb - code for cell growth factors or receptors - mutated or over-expressed gene that induces uncontrolled cell growth - by promoting cell cycle progression or inhibiting apoptosis Tumor suppressing genes - code for DNA repair enzymes. - repress uncontrolled/cancerous cell growth via apoptosis In cancer; ↑Oncogenes; ↓Tumor suppressing genes → Ignores Apoptosis pathways Pro-apoptotic proteins - would not lead to DNA repair, but would prevent tumor development via apoptosis (cell death pathways)

*GENETICS AND EVOLUTION*

*GENETICS AND EVOLUTION*

*VIRUSES*

*VIRUSES*

- *region of DNA responsible for binding mRNA during prokaryotic transcription? - region of RNA responsible for binding ribosomes during prokaryotic translation?*

- *TATA box upstream Promoter region* with help of RNA Poly and TFs on mRNA strand - *Shine-Dalgarno sequence upstream start codon* on mRNA strand

*Similarities*

- Both have double-stranded DNA - Both of their mRNAs can be *bound by multiple ribosomes* in the cytoplasm - Under anaerobic condition, → glycolysis, fermentation and gluconeogenesis are active in both Euks and Proks - Because no O₂ required - Krebs cycle and the ETC are only active in the presence of a final electron acceptor, such as O₂ (aerobic) or inorganic ions (anaerobic) - Both can reproduce sexually.

*Diff between Conjugation, Transduction, Transformation & Transfection*

- Conjugation - Transfer of genetic info from one prok cell to another vis direct contact --> eg- F factor (sex pilus), plasmids (genes) -Transduction -Transfer DNA from one prok to another by bacteriophage - Transformation - Cellular uptake of foreign DNA from environment -eg- dead stuff - Transfection - Transfer of genetic material (plasmid) from Prok to Euks

Where are the following regions found on a chromosome? - *Heavily methylated region* - Centromere - *Histone-rich region* - *G-C rich region* - *A-T rich region* - Telomere - p - q

- Heavily methylated region - Centromere = center - Histone-rich region = G-C (light bands) and A-T (dark bands) - G-C rich region = light band/less condensed /euchromatin region = transcriptionally active - A-T rich region = dark bands/condensed /heterochromatin region = transcriptionally inactive - Telomere = ends - p = short arm - q = long arm

If radioactively labelled cytosines was added to a culture in the middle of prophase, and then growth was halted at the end of telophase. Where would radioactively labelled DNA be found?

- No where - DNA is replicated in S phase. - Prophase is in M phase. Since all of the DNA that would be present at the end of telophase had already been synthesized in S phase, none of the cytosines would be incorporated into the DNA of any cells in the culture.

In a group of insect where 60% have red eyes, 30% have apricot eyes, 5% have white eyes, and 5% have pink eyes. Which of these eye colors would be designated the wild type? - *what is wild type - what are the others called?*

- Red Wild type = the most prevalent, (naturally occurring in the "wild") phenotype for a certain trait. - white, pink, and apricot are due to genetic variations of the gene that codes for eye color.

Steps in Translation (IET) - from binding of subunit to *dissociation*

- Requires Energy 1) Small (40S) subunit binds 5'cap of mRNA Large (60S) subunit binds tRNA 2) Ribosome continues to elongate chain by reading each mRNA in 5' to 3' direction 3) stop codon is read & release factors induces dissociation of ribosome-mRNA complex

Anaphase - Unique for? - what happens in mitosis and meiosis I and II - *what is non-disjunction?*

- Separation/ Non-disjunction Anaphase (mitosis) - No recombination - Sister Chromatids separate *(diploid)* Anaphase I (meiosis) - *After recombination* - Homo Chromosomes separate Anaphase II (meiosis) - No recombination - Sister Chromatids separate *(haploid)* Non-disjunction - occurs then sister chromatids fail to separate properly during anaphase → resulting in one daughter cell having unequal #s of chromosomes compared to others

What is test cross? -* what does it determine? - what is crossed with what? - can it be used for all or any of these (monohybrid, dihybrid, or polyhybrid)*

- determines unknown genotypes of organism --> homo or heterozygote - unknown is crossed with known *homozygous recessive* individual, - can be used for monohybrid, dihybrid, or polyhybrid.

pre-mRNA post-transcriptional modifications - 4 steps to mature mRNA

- occur at the non-coding (antisense) DNA strand in nucleus 1) 7-mGT (5'cap) is added to 5' end, 2) poly AAA tail is added to 3' end, 3) splicing done by spliceosome (snRNP + proteins) - introns removed and exons joined together 4) alternative splicing combines different exons to acquire different gene products from a single mRNA transcript - mature mRNA formed

Replication Stress - where & when does it occur - how is it repaired?

- occurs when DNA synthesis is arrested(stops) at the S phase of Euk cell cycle ------------ X B/4 replication / After replication Replication Stress response factors - repairs stalled fork → to continues replication

Steps in Transcription (I,E,T) - start with topoisomerase, promoter region, RNA poly binding, directions, end with mRNA

1) helicase(unwind) and topoisomerase(-supercoil) the DNA double helix 2) TF and RNA Poly II bind TATA box in promoter region 3) As RNA Poly II travels down and reads DNA strand in 3' to 5' direction, it unravels double helix & relies on the complementary bases to catalyze the synthesis of pre-mRNA strand which grows in the 5' to 3' direction

Goal of 5'cap and Poly A tail

5'cap - recognized by ribosome during translation and prevents degradation Poly A tail - The chain of adenosine nucleotides prevents degradation and facilitates export of mature mRNA from nucleus to cytoplasm

Chargaff rules/pairing

AG - Purines CUT - Pyrimidines A=T - (less energy needed to break) G≡C (largest) G>A>T>U>C (smallest)

Difference between Adaptive radiation & Speciation

Adaptive Radiation = Darwin finches(diff beaks) - diversifying characteristics in a subgroup of individual from a single species - subgroup has a new role diff from others - BUT... can still mate with each other - ↓competition=↑fitness Speciation = New species - Adaptive Radiation gone wrong - New species from previously existing species - When species develop different characteristics (over many years) and get to a point that they become new species and - CANNOT mate with each other anymore

Ribosome-mRNA complex - make up of ribosomes - *where does it translocate to and why?* - # of ribosomes for Proks and Euks

All ribosomes have (r)proteins + (r)RNA - translate mRNA sequence into proteins - translocate to rough ER to synthesize secretory lysosomal or integral membrane protein Euks = 60S+40S = 80S ribosomes Proks = 50S+30S = 70S ribosomes

Difference btw Alternate Splicing & Gene Duplication & *Epigenetic modification* - what generates what? - eg

Alternate Splicing - *Several proteins* are generated from *a single pre-mRNA transcript* - eg- during splicing Gene Duplication = Evolutionarily related genes - *Several proteins* are generated from *multiple similar genes or single gene* - Due to unequal crossing over - overtime they can carry out distinct roles at different times during life cycle Epigenetic modification = No change in sequence - eg - Methylation and demethylation - *one protein sequences* generate *several different gene expressions* - leads to alternative gene expression without changes in the sequence of the nucleic acid itself.

Animal cell plasma membranes contain; (4)

Animal cell plasma membranes contain; - phospholipids, - cholesterol, - glycolipids (lipids + sugar groups), - glycoproteins (proteins + sugar groups - carbohydrates - transmembered protein - integral protein

Classification based on - morphology (shape) - habitat - O₂ dependence

Bacilli (rod) Cocci (spherical) Spirilli (spiral) Thermophiles (↑T°) Acidophiles (↓pH) Halophiles (↑Salt) Aerobic (O₂ needed) - Kreb, ETC (in Euk only) Anaerobic (No O₂ required) - Glycolysis, Fermentation, Glyconeogenesis, ETC (in Prok only)

Diff btw Bacteria, Archaea, Eukarya

Bacteria - Unicellular - Nucleus Absent - Organelles Absent - Cell wall with peptidoglycan Present - Cellular division by Binary fission - Circular Chromosome Archaea - Unicellular - Nucleus Absent - Organelles Absent - *No peptidoglycan cell wall* - Cellular division by Binary fission - Circular Chromosome Eukarya - *Unicellular or multicellular* - Nucleus Present - Organelles Present - No peptidoglycan cell wall - Cellular division by Mitosis - Linear Chromosome

What is cell determination? - what is it due to? What is cell differentiation? - what is it due to? What is inductive signaling? - how does it occur? why? what is the goal of cell transplant

Cell Determination - Specification of cell fate -due to inductive signaling btw cells in embryo Cell Differentiation - Acquisition of unique/specialized/biochemical/structural/ cellular characteristics in the embryo - due to inductive signaling Inductive signaling = communication with surrounding cells - occurs when an inducer/signaling cell releases chemical signals that act on neighboring cells by regulating the expression of specific genes - signaling provides the cell with positional & fate determining info required for proper development. During cell transplant - Goal is to determine whether donor neural cells would continue to develop independently → into the tissue of choice OR →assume a diff tissue type or cell fate (due to communication with surrounding cells aka inductive signaling)

What are the 2 Nervous System cell types? functions? - what are the CNS & PNS glial cells & functions - does Neural crest cells have inductive or inhibitory influence on Neural tube formation? - what happens when a disease (eg spinal bifida) affects the neural tube dev? how dos it affect neural crest

Cell Migration in embryogenesis - movt of cells into their final positions within the embryo - eg- Neural tube → give rise to CNS - Neural crest → give rise to PNS Nervous System cell types 1) Neurons - conduct electrical signals 2) Glial - Support neural functions CNS glial cells that arise from neural tube - Oligodendrocytes - form myelin sheaths around neurons - Astrocytes - provide support, anchor neurons to nutrient supply source PNS glial cells that arise from neural crest - Schwann cells - similar to Oligodendrocytes - Satellite cells - similar to Astrocytes Neural crest cells have no substantial inductive or inhibitory influence on Neural tube formation ∴ when a disease (eg spinal bifida) affects the neural tube dev, Neural crest cells are not involved in the pathology & will continue to act normally as temporary migratory cells that give rise to diverse lineages of cell in PNS

Difference btw Heterochromatin and Euchromatin - What is chromatin? What are the charges of each of the components - How are they wound - how does DNA interact with both Histones? Explain

Chromatin = DNA + Histones (eg Nucleosome) DNA = (-) P group Histones = (+) lysine & Arginine basic AAs - interact via dipole intermolecular bonds Heterochromatin = ↓ transcription - tightly bound together - bound by ionic interaction between (-) Phosphate on DNA and (+) lysine on histone Euchromatin = ↑ transcription - loosely bound together - modified by acetylation of K,R - added acetyl group neutralizes the (+) K, R on histone & reduces interaction between histone and DNA

Diff btw Co-dominance & Incomplete dominance - is it observed in Phenotype of homozygous or heterozygous individuals?

Co-dominance = Co-expression -eg- Red + White = Red & White flower Incomplete dominance = Blended/Intermediate -eg- Red + White = Pink flower - Both are observed in Phenotype of *heterozygous* individuals

Diff btw coding (1) and non-coding (5) RNAs - functions

Coding RNA - mRNA - translated into protein by tRNA Non-coding RNA - rRNA - contains ribosomal proteins; enzymatically active - tRNA - pairs mRNA codon with its anticodon to form protein during translation - siRNA - Interfers with translation by binding mRNA and signal for it's degradation - miRNA - Interfers with translation by cleaving mRNA or prevent it from binding to ribosomes - snRNA - (protein + snRNPs) = sliceosome

Diff btw Convergent, Divergent and Parallel evolution

Convergent - Different common ancestor - Diff env; similar unique characteristics - Analogous structures -eg- wings on insect, birds, bat Divergent - Same common ancestor - Diff env; Diff characteristics over time - Homologous structures -eg- forelimbs of vertebrates Parallel evolution - Same common ancestor - Similar env; similar unique characteristics

Diff btw Crossing Over & Alternate Splicing - what kind of diversity do they affect?

Crossing Over = ↑ genetic diversity Alternate Splicing = ↑ protein diversity

Prophase - Unique for? *How does it form? describe* - Diff btw mitosis and meiosis in prophase - *result of daughter cells?*

Crossing over events = Genetic Recombination →Tetrad (4 chromatids) - HomoC line up side by side to form tetrad - Allow physical contact btw paternal and maternal chromosomes at chiasma RESULT - Daughter cell with chromosome containing combination of allele that *differ* from parents mitosis = HomoC DO NOT pair up into tetrads meiosis = √Crossing over + Tetrad formation

Difference between DNA Polymerase and RNA Polymerase I, II and III - which can proofread and which cannot - which transcribe mRNA, rRNA, tRNA, snRNA, miRNA what or duplicate what? - what do they have to do for transcription or translation to be initiated?

DNA Polymerase = replication of *DNA* - can proofread Euks have 3 diff RNA polymerases (RNAPs) RNA polymerase I = transcription of *rRNA* RNA Polymerase II = transcription of *mRNA, snRNA, miRNA* - CANNOT proofread - Must bind to DNA at a promoter region for transcription to be initiated RNA polymerase III = transcription of *tRNA* - tRNA must bind to large ribosome for AA translation to be initiated

DNA polymerase, RNA Polymerase II & Ribosomes - what do they synthesize? - In what direction do they read/synthesize Which degrades quickly? *WHY* - RNA produced from DNA or DNA produced from RNA

DNA polymerase - synthesizes new DNA strands; - reads DNA template in 3' to 5' direction and replicate new strand in 5' to 3' direction RNA Polymerase II - synthesize pre-mRNA - reads DNA anti-sense strand in a 3′ to 5′ direction to transcribe a 5′ to 3′ pre-mRNA Ribosome - synthesize proteins - reads the mRNA transcript in a 5′ to 3′ direction until a stop codon (UAA, UAG, or UGA) is recognized, causing translation termination and polypeptide release. - RNA produced from DNA degrades quickly. - RNA is very unstable on its own, and will only last a short amount of time in the cell.

Diff btw homodimer and heterodimer - what is dimer? - how are they bound together?

Dimer = 2 Monomers = 2 non-covalently bound polypeptide chains homodimer - the polypeptide chains of the 2 monomers have the same sequence heterodimer - the polypeptide chains of the 2 monomers have the diff sequences

- what connects the 2 sister chromatids during prophase? - when does mitotic spindles fibers begin to form? - what is centromere composed of? - If bacteria is exposed to a spindle fiber toxin what happens? - main cause of disjunction?

During Prophase - 2 sister chromatids are connected by *kinetochore* to form a single homologous chromosome During Anaphase The mitotic spindle begins to form when centromere starts migrating to opposite poles of the cell & microtubule filaments grow from them → resulting in spindle fibers Centromere - composed of microtubule organizing centers with a pair of centrioles If bacteria is exposed to a spindle fiber toxin - It might inhibit microtubule polymerization and result in non-disjunction of somatic cells during nuclear division

dNTPs and matureRNA - what joins them? - what attacks what? - exergonic rxn? - what is released? - endergonic rxn? - what bond is formed

During replication - DNA poly joins uncoupled dNTP to the new DNA strand 1) 3'OH from the last nucleotide of growing strand attacks 5'P of an incoming dNTP 2) 2 PPi is cleaved off the dNTP *(exergonic)* -> results in release of H₂O + PPi + Energy 3) PPi is further cleaved into mono(P) to release more energy 4) Energy released is used to form a covalent phosphodiester bond btw the last nucleotide of the growing strand and the incoming dNTP *(endergonic)*

How is a Neural tube & Neural crest formed? - what is neurulation - what happens after gastulation? steps ... Neural tube is precursor of Neural crest precursor of

Ectoderm → Neural plate →Neural groove →Neural tube + Neural crest Neurulation - Formation of the nervous system in vertebrates Following gastulation - the notochord releases signals nagging the ectoderm to thicken & form the neural plate - Neural plate fold inward→form Neural groove - Neural folds converge → create Neural tube Neural tube (precursor of CNS) pinches off ectoderm Neural crest (precursor of PNS) migrate away to give rise to most of the PNS

Uniqueness of RBCs - function - organelles? - are they affected by mit mutations? - do they consume O₂ they transport? - How do they produce energy?

Erythrocytes (RBC) - DO NOT HAVE MIT. - contain (Hgb) - transport O₂ as they expel their nucleus & other organelles during erythropoiesis in bone marrow ∴ Mit mutations cannot affect RBC function - Never consume O₂ they transport - Produce energy via *anaerobic glycolysis*

Method of Cell proliferation in Euks and Prok somatic & germ cells

Euk Somatic Cell - proliferate by completion of M phase Prok Somatic Cell - proliferate via binary fission Euk Germ Cell - proliferate by completion of meiosis

Diff btw Expressivity, Variable expressivity & Penetrance (complete & incomplete)

Expressivity - to what degree a penetrant gene is expressed Variable expressivity = range - 1 genotype → 2+ phenotypes expressed - single genotype give rise to a range of multiple phenotypes - eg- Hearing loss → mild ↔ severe Penetrance = proportion - 1 genotype → % of phenotypes expressed - Proportion of individuals with a genotypes who express the corresponding phenotype Complete Penetrance = genotype - 100% expressed in phenotype -Those with specific genoype *ALL* have ass. phenotype - eg- if you have the genes for being smart, then you'll definitely be smart Incomplete Penetrance genotype - <100% expressed in phenotype - Those with specific genotype but *SOME* express ass. phenotype - eg- you may have the genes for being smart, but you may not actually be smart.

For Proks - Archeae + Bacteria - size ≈ 1-5µm - One Origin of Replication - genetic information in circular chromosome - NO telomeres - NO histones - NO Introns - lacks membrane-bound organelles - NO Nucleus - Haploid DNA is in cytoplasm - tranS and transL occur simultaneously in the cytoplasm - Ribosome = 50S + 30S = 70S - *ETC is located on the plasma membrane.* - *under anaerobic conditions, ATP synthase is active* - *Fermentation yields alcohol in bacteria* - cells division via binary fission, - *Sexual reproduction is via conjugation*

For Euks - Plants, Fungi, Animals - size ≈ 10-30µm - Multiple Origins of Replications - genetic information in linear chromosomes - Have telomere-prevent DNA from unraveling - Have DNA + histone = Chromatin - Have Introns - Have membrane-bound organelles - Have nucleus - Diploid DNA is in nucleus - TranS & Post TranS Mod in nucleus; TranL in cytoplasm. - Ribosome = 60S + 40S = 80S - ETC is located in the Inner Mit Membrane - under anaerobic conditions, ATP synthase is not active - Fermentation yields lactic acid in the muscles of Euks - Cell division is via meiosis (germ cells) and mitosis (somatic cells) - Sexual reproduction is via fusion of gametes (meiosis)

Cell cyecle - phases & function - which is done outside the cell cycle? - what are Restriction Point/Checkpoints - what are the regulated by - what happens to abnormal cells - what happens if it doesn't work - what happens during each check point? - what phase are majority of cancer cells G₀ or interphase & why - what kind of drug do you use to inhibit cell division?

G₀(outside cell cycle)→G1→S→G2→M G1 = Cell growth/Replication S = DNA synthesis/replication G2 = Cell growth/Check for errors in prep for cell division M = Mitosis (Nuclear division) + Cytokinesis (Cytoplasm division) Restriction Point/Checkpoints - Mechanism by which calls regulate their content within the cell cycle - Regulated by → cyclins & cyclin-dependent kinases - some abnormal cells undergo apoptosis, others that can't be repaired continue to divide G1/S Phase transition - cells commit to undergo a division cycle G2/M Phase transition - acts as quality control by stopping cell cycle & checking for abnormalities Cancer cells - uncontrolled cell division/ ↓apotosis - means majority of cells are in interphase & not arrested in G₀ (dormant phase) To inhibit cell division - use drugs that target actively dividing cells in the G1-M phase

Histone acetylation & deacetylation - effect of each process

Histone acetylation = (+) acetyl to histone tail - loosen Heterochromatin → Euchromatin - makes DNA region accessible - up-regulates transcription/gene expression H/deacetylation = (-) acetyl from histone tail - reverts Euchromatin → Heterochromatin - restrict DNA region accessibility - downregulates transcription/gene expression

Classify the following diseases - *Huntington's disease - color-blindness - hemophilia - cystic fibrosis*

Huntington's disease → autosomal dominant cystic fibrosis → autosomal recessive Color-blindness → X-linked recessive hemophilia → X-linked recessive

General overview of cellular respiration - Pyruvate → - main electron carriers for ETC - ETC location in Euks and Proks - How does ATP synthase generate ATP from ADP+Pi - Is ATP synthase active in Proks and Euks under anaerobic conditions? - why or why not?

In Euks Cellular respiration continues when pyruvate is imported into the mitochondria & converted to --> Acetyl CoA Acetyl CoA enters the kreb cycle to generate the necessary electron carriers (NADH + FADH₂) for ETC ETC pumps H⁺ across Inner Mit Membrane; generating a proton gradient --> with O₂ as final electron acceptor ATP synthase - Uses energy of ETC proton gradient to generate ATP from ADP+Pi - Does not directly need O₂ to generate ATP BUT ... The proton gradient by which it function is O₂ dependent in Euks In Proks - No mitochondria - ETC is located on plasma membrane ∴ Under anaerobic conditions, ATP synthase is not active in Euks, but is active in Proks because there is not proton gradient required

Diff btw Sex-linked & Autosomal traits - what creatures have these? - due to allele expressed in? - who is more affected? males/females

In mammals and some insects, genetic traits are passed to next generation in either; Sex Linked Traits - (XX or XY) - due to allele expressed in sex chromosomes - (X) contains more genes than (Y) - *Males are more affected → have only 1(X)* Autosomal Traits - (the other 23 pairs) - due to alleles expressed in autosomes - same # passed from parent to offspring - *both male and female are affected equally*

Diff btw Inbreeding Depression & Random Mating - effect on zygosity, genetic diversity, fitness, fecundity, MHC on offsprings - Why is random mating better - How do you increase heterozygosity among inbreeders

Inbreeding Depression = Mating (relatives); - *↓Heterozygosity=↓genetic diversity=↓fitness* - homozygous for deleterious recessive traits - ↓fecundity (# of offsprings) - ↓MHC - ↓ability to combat infection Random Mating = Mating (non-relatives); outbreeds - *opposite of above* - *↑Heterozygosity*=↑genetic diversity=↑fitness* - ↓ probability of passing familial abnormalities to offspring Random mating better- due to introduction of new genetic material To increase heterozygosity among inbreeders - selectively outbreed with others

*Diff btw Independent assortment & Recombination - How do each explain resemblance to parent and or child*

Independent assortment helps explain why the offspring may not resemble the parent Recombination helps explain why offsprings may not resemble each other → reason why a couple can have ten unique children.

Phases of Cell Division during cell cycle - Guess the ffg stages- correction of errors, duplication of organelles, duplication of DNA, quiescent, cytoplasmic division, nuclear division, separation

Interphase G₀ - quiescent (inactive/dormant) - cell is neither dividing nor preparing to divide - occurs outside of the cell cycle. G₁ - cell growth & duplication of organelles S - REPLICATION/DUPLICATION of DNA G₂ - cell growth, duplication & correction of errors in preparation for cell division M - Mitosis - Separation & Nuclear Division - Cytokinesis - Cytoplasmic Division

What are the benefits of MCH to Natural selection, gene flow, random mating

MHC - encodes surface receptors on cell to help activate adaptive immune system ↑MHC = ↑ability to combat infection = ↑fitness

What are the 2 ways viruses enter the's host cell which method does Non-enveloped (Naked) Viruses & Enveloped Viruses use? - how do they do this? - which binds to receptor protein on cell surface - which forms vesicles? - what kind of drug will inhibit cell entry? - which fuses to host membrane - what is released into the cell with each method?

Many viruses enter host cells via; - receptor-mediated endocytosis (phagocyte) --> (Non-enveloped) OR - by fusing their membrane with the other cell membrane --> (Enveloped) Non-enveloped (Naked) Viruses - Enter cell via receptor-mediated endocytosis → bind specific receptor protein on cell surface → this induces the plasma membrane to bud inward towards the cytosol → then the formed vesicle is pinched off containing both ligand (with capsid) + receptor - A drug that inhibits this inward budding would likely prevent virus from entering cell Enveloped Viruses - Enter cell by fusing their membrane with the host cell membrane - Their capsid is enclosed in a phospholipid membrane & no vesicle is formed - Capsid is then released into the cytosol - A drug that inhibits fusion of viral & cell membrane needed would likely prevent virus from entering cell

Mitochondria - function - Example of tissues that require ATP from Mit - Unique cell that does not have Mit

Mitochondria - allow cell to utilize O₂ in ETC to generate ATP - ∴ Mit defects affect mit active tissue like neurons, muscles, heart, kidney 1) Hepatocytes (liver) → need ATP for carb, protein & lipid synthesis 2) Neurons (nervous system → need ATP for transmission of signals via synapses 3) Myocytes (muscles) → need ATP for contraction & movement RBCs don't have Mitochondria

Mitosis Meiosis - Start with diploid/haploid - end with diploid/haploid, # and type of daughter cells

Mitosis- Interphase → 1(2n) →2(2n) - diploid/genetically identical daughters Meiosis- Interphase → 1(2n) →2(2n) →4(n) - haploid/genetically distinct daughters

Diff & Simil btw Natural selection, gene flow, random mating - caused by? - effect on genetic diversity, fitness, *allele*, pop size, survival

Natural selection = Survival of the fittest Gene flow = due to Migration Random mating = Mating (non-relatives); outbreeds ALL - ↑ genetic diversity due to variation during meiosis (recombination/crossing over) - increase species fitness - introduces new alleles to gene pool - ↑probability of survival - ↑population

Organisms catabolize (breakdown) glucose via; (2) - what do they have in common? - what kind of condition do they occur? aerobic, anaerobic - where does glycolysis occur in Proks & Euks?

Organisms catabolize (breakdown) glucose via; 1) Cellular respiration = yields CO₂ and H₂O C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O 2) Fermentation = yields inorganic waste Pyruvate →Ethanol(Proks) OR Lactic acid(Euks) - Both begin with glycolysis - Glycolysis does not require O₂ ∴ both occur under aerobic & anaerobic conditions - 1Glucose is broken down → Pyruvate → in cytosol of both Euks and Proks

P value > 0.05 and P value < 0.05

P value > 0.05 - means there is a > 5% probability that the result is by chance if null hypothesis is true - ∴ not statistically significant P value < 0.05 - means there is a < 5% probability that the result is by chance if null hypothesis is true - ∴ statistically significant

PROKARYOTES & EUKARYOTES CELLS

PROKARYOTES & EUKARYOTES CELLS

Passive Transport (Simple + Facilitated Diffusion) & Active Transport - *types of stuff allowed to pass through?* - eg

Passive Transport = *No energy needed* if moving down conc gradient (high to low) 1) Simple - *Small Molecules + lipid soluble* - *travel membrane directly*, don't need gates 2) Facilitated - *Large Molecule + charged* - *pass via protein channels or gates* Active Transport =*Need ATP to run pumps* moving against conc gradient (low to high)

Diff btw Phospholipids, Transmembrane proteins, Cholesterol - *types of movt*

Phospholipids(major) = for *lateral movt* - Fluid that allows other non-phospholipid stuff to migrate through them to/out of cell Transmembrane proteins= for *vertical movt* - crosses from ext. env (outer leaflet) to cytoplasm (inner leaflet) of phospholipid bilayer Cholesterol = In Euks only - *At ↑T°; it ↓es fluidity* - *At ↓T°; it ↑es fluidity* to prevent rigidity

Journey of polypeptide chain with signal - where is the signal removed Journey of polypeptide chain without signal - where does post translational modification occur - where do the protein designed for secretion packaged & transported to - what happens at the plasma membrane? - eg of post translational modifications

Presence of a signal sequence on growing polypeptide chain → directs the ribosome-protein complex to → Rough ER → Rough ER Lumen (where signal is removed) The peptide is then repackaged into vesicles & sent to → the golgi body (where some post-translational modification occurs) The protein designed for secretion are packaged & transported in vesicles to → plasma membrane. --> These vesicles then fuse with the plasma membrane & release their content outside the cell post-translational modification - glycosylation - disulfide bond formation - phosphorylation - protein cleavage

Diff btw Prok & Euk secretory pathway

Prok secretory pathway - Lack membrane bound organelles; ∴ utilize special channels in plasma membrane to secrete proteins Euk secretory pathway - Have membrane bound organelles; ∴ utilize Rough ER and Golgi body to secrete proteins

Diff btw Prok and Euk Replication - # of Ori, shape, location - what is monocistronic mRNA & polycistronic mRNA? which is prok or euk?

Proks - circular DNA with single ori in cytoplasm - polycistronic mRNA - one transcript(ion initiation site) per multiple genes Euks - linear DNA with multiple ori in nucleus - allows gene to be copied rapidly & efficiently - monocistronic mRNA - one transcript(ion initiation site) per gene

The sequence below is a portion of an exon of an mRNA transcript. 5′ - UCAAGUGAU - 3′ Write the corresponding DNA coding strand and DNA non- coding strand sequence for this particular transcript?

Sense(coding) DNA - 5′-TCAAGTGAT-3′ mRNA Strand - 5′-UCAAGUGAU-3′ AntiSense(non-coding) DNA -3'-ATCACTTGA-5'

Difference between Stabilizing, disruptive and Directional Selection

Stabilizing = Average phenotypes; ↓diversity Disruptive= Both Extremes phenotypes Directional= 1 Extreme phenotypes; ↓diversity

The founder effect

The founder effect = small initial pop with lots of abnormal allele that gets passed on to future generations - abnormal abundance of an allele in a population derived from a small initial population. - If, by chance, the initial population had an abnormal abundance of a certain allele, this abnormality will generally persist for future generations.

*Law of Independent assortment* - how do chromosomes align -eg - Explain why Prader-Willi and cystic fibrosis are not always inherited together*

The law of independent assortment - says that chromosomes, align independently of each other when being passed from parent to child. -eg-chromosome 7 and chromosome 15 do not directly influence each other's inheritance patterns during meiosis in parental gametes, and can be sent to sperm or eggs in any combination. Explains why Prader-Willi and cystic fibrosis are not always inherited together - one child might have cystic fibrosis as well as Prader-Willi. and another child might have cystic fibrosis, but not Prader-Willi.

Mitochondria DNA - *Functions (3)* - which mitochondria is transmitted to the fetus? *why?* - inherited from whom to whom - how is it diff from nuclear genes

Their main functions include - ATP generation, - heat production, and - beta-oxidation of fatty acids. Only maternal mitochondria are transmitted to the fetus. - because, during fertilization, paternal mitochondria within sperm don't pass into ovum Mitochondrial genes - inherited from affected mothers to offspring females - does not follow Mendelian inheritance patterns Nuclear genes - inherited via autosomal and sex-link - follows Mendelian inheritance patterns, (of inheriting 2 copies of each gene; one from mom & the other from dad)

X-linked Dominant condition X-linked Recessive condition Autosomal Recessive condition Mitochondrial

X-linked Dominant condition - If only X*Y affected →All daughters affected - If only X*X* affected →50% daughters & 50% son affected - Need 1 copy of dominant allele to inherit X-linked Recessive condition - If only X*Y affected →All daughters carriers - If only XX* carrier →50% daughters is carrier & 50% son affected - Need 2 copies of allele to pass to daughter - Need 1 copy of allele to pass to son Autosomal recessive condition (Aa x Aa) - Need 2 copies of (aa) to inherit disease Mitochondrial - If only X*Y affected → 0% of offsprings - If only X*X* affected → 100% of daughters

Zygote = Undergo series of mitotic divisions/cleavages → ___ →eventually lead to __ - what are the 3 different stem cells? . hint (potent) - what do they differentiate into/found? placenta, fetus, or adult? - potency/specialization - which is found in zygotes only - which one can give rise to an entire organism - where do Pluripotent come from?

Zygote = Undergo series of mitotic divisions/cleavages → eventually lead to Fetus Totipotent stem cells → placental + fetus - found only in the zygote (up to 8 cells stage) - Greatest potency/least specialized (can autonomously give rise to an entire organism) - can differentiate into any cell type from an embryo (plancental + fetus) Pluripotent → fetus only - cells of the inner cell mass - can differentiate into any of the 3 germ layers (ie fetus only) Multipotent → fetus + adult - found in both fetus & adult - Least potency/most specialized - can differentiate into cells with many specialized functions ... BUT are limited to a specific lineage (eg can give rise to cells in the nervous system but not other tissues)

Sequence of events from zygote → gastula - diff btw Blastula & Blastocyst - what do each portion of the blastocyst form - what is gastulation?

Zygote→2cells→4cells→Morula →Blastocyst(Trophoblast + Inner cell mass) →Gastula(Endoderm, Mesoderm, Ectoderm) Blastula (non-mammal) /Blastocyst(mammal) - After fertilization, zygote is cleaved into 2 cells → 4 cells →Morula →Blastula (non-mammal) OR Blastocyst (mammal) Blastocyst (mammal) - is cleaved into 2 1) Trophoblast - forms the placenta 2) Inner cell mass - forms the gastula Glastula - Trophoblast + Inner cell mass transform into 3 germ layers via Gastulation Gastulation - Process by which the 3 germ layers form in the developing embryo Germ layers = Endoderm, Mesoderm, Ectoderm - develop into specific structures in body Endoderm(innermost) = digestive organ (liver, pancreas) + lining of digest & respiratory tract Mesoderm(middle) = circulatory + musculoskeletal + urinary + reproductory Ectoderm(outermost) = nervous + integumentary (hair,skin, nails, mouth, nostrils, anus)

Diff btw germ cell and somatic cells - which undergoes mitosis, meiosis? - which is passed on to offsprings or dev after conception? - which have telomeres? - eg

germ cells = sex cell lineage - undergo meiosis to produce gamates - eg sperm, oocytes - passed to offspring via zygote formation in sexual reproduction - inherited and in cells of entire offspring - Have telomeres - expressed somatic cells = non-sex cell lineage -DO NOT undergo meiosis or produce gamates - cannot be passed to offspring; NO zygotes - develop after conception - eg tumor, cancer, skin, muscle, nerve cells - NOT inherited; not in lineage - Have little to no telomeres - but only expressed in cancer cells and cause aging

Diff btw knockout gene and *constitutionally active gene*

knockout gene - gene of interest is removed /disrupted /inactivated → leads to NO protein activity constitutionally active gene - gene of interest is transcribed at constant rate regardless of current cell conditions → leads to protein activity

*Name the germ layer - notochord, melanocyte, myocytes, osteocyte, mucous cells(stomach), sperm & egg, Islet beta cells, Epidermis, Neurons, RBCs, alveolar cells*

notochord = reproductory = Mesoderm melanocyte = skin pigment = Ectoderm myocytes = muscles = Mesoderm osteocyte = bones = Mesoderm mucous cells(stomach) =dig lining = Endoderm sperm & egg = germ cells Islet beta cells = Pancreas = Endoderm Epidermis = Skin = Ectoderm Neurons = nervous = Ectoderm RBCs = circulatory = Mesoderm alveolar cells = resp lining = endoderm

Hardy-Weinburg - Equation - Assumptions - *what is it constant for?*

p²+2pq+q² = 1 p² = freq of homozygotes for dominant disease in population q² = freq of homozygotes for recessive disease in population 2pq = freq of heterozygotes (carrier freq) p + q = 1 p = major allele (homo dominant allele) q = minor allele (homo recessive allele) √ Large population √ Random mating × No natural selection × No new mutations × No gene flow/migration When in H-W eqB - allele freq is constant - heterozygosity is constant

what effect will silencing genes have with the addition of methyl groups to - DNA sequences - mRNA - tRNA

silencing genes by adding methyl groups to - DNA sequences → inhibits transcription - mRNA → inhibits protein translation - tRNA → inhibits protein translation