genetics exam 4 Flashcards

Question

explain the use of mRNA in C. elegans

Answer 1

one experiment involved an mRNA encoded by gene called mex-3 an abundant mRNA in early embryos of C. elegans --> make sense and antisense mex-3 RNA in vitro using cloned genes for mex-3 --> inject either mex-3 antisense RNA or a mix of mex-3 sense and antisense RNA into gonads of C. elegans --> RNA is taken up by eggs and early embryos then you see what happened to the mRNA --> used in situ hybridization for this

Answer 2

- incubate and then subject early embryos in situ hybridization (a laboratory technique that finds and localizes specific DNA or RNA sequences in biological samples) - in this method, labeled probe is added that is complementary to mex-3 mRNA - probe is labeled with green fluorescent dye - if cells express mex-3, the mRNA in cells will bind to the probe and become labeled with green - after incubation with a labeled probe, the cells are washed to remove unbound probe - observe embryos under a microscope the intensity of green color is proportional to [mRNA] --> control is really green (high levels of mex-3 mRNA), injected with mex-3 antisense RNA is moderately green (mRNA levels decreased), injected with dsRNA (no mRNAs detected) this data indicates that dsRNA is more POTENT at SILENCING mRNA than antisense RNA = RNA interference (RNAi) which dsRNA causes the silencing of mRNA

Answer 3

gene silencing mechanisms mediated by miRNAs, siRNAs, or piRNAs RNAi is found in most eukaryotic species - microRNAs (miRNAs) are transcribed from ENDOGENOUS eukaryotic genes (as many as 60% of human genes may be regulated by microRNA) - small interfering RNAs (siRNAs) include those that originate from EXOGENOUS sources (not normally made by cells and those encoded on genome - PIWI-interacting RNAs (piRNAs) are less widely distributed, mostly in ANIMAL GONADS and target transposable elements

Answer 4

they differ mostly in ORIGIN/BIOGENESIS all 3 silence genes, associated with conserved set of proteins and use base complementarity to id mRNA targets

Answer 5

larger precursors - miRNAs = pri-miRNA is made --> folds up on itself to form a HAIRPIN recognized by RNA processing enzymes, cleaved to 70-nt pre-miRNA and exported, cut by dicer to 20-25 bp - siRNA (long dsRNA produced) --> these are either encoded or sometimes produced in response to viral infections, processed into smaller fragments by dicer enzymes - long dsRNAs are artificially introduced into cell will also be processed to siRNAs

Answer 6

they associate with a group of proteins to form silencing complexes --> RNA-Induced Silencing Complex (RISC) [binds to mRNA and causes degradation] or RITS (RNA-induced initiation of transcriptional silencing) [silences mRNA]

Answer 7

- dsRNA molecule that is 20-25 bp long produced from pre-miRNAs and pre-siRNAs by dicer (one strand will be degraded and the other will be retained) - proteins - piRNAs associate with PIWI proteins to form complexes known as piRNA-induced silencing complexes (piRISCS) - all complexes are directed to their target site by base pairing with small RNA review slide 17 of lecture 32

Answer 8

siRNA derived from dsRNA of viral replication and miRNA from pre-miRNA (this is easily manipulated) will form RISC or RITS --> RITS or RISC complex is GUIDED to mRNA target by complementarity between small RNA and mRNA piRNAs cause transcriptional silencing of transposable elements via piRISCs complexes RITS can lead to DNA/histone methylation while RISC leads to mRNA degradation and translation block

Answer 9

RNAi is important form of GENE REGULATION (silences the expression of specific mRNAs but will NEVER INCREASE gene expression) widely used by plants to prevent viral infections siRNAs can be introduced into a cell or produced in cell by genetic engineering to target specific genes for silencing this is huge therapeutic value

Answer 10

Patisiran is a ds siRNA that specifically binds to a genetically conserved seq in 3'-untranslated region of mut and wt transthyretin (TRR) mRNA used for treatment of neuropathy of hereditary transthyretin-mediated amyloidosisin

Answer 11

replication particles with nucleic genomes they must infect LIVING cells to proliferate they can vary with regard to their structure and ability to INFECT DIFF HOSTS

Answer 12

- host range = cell that is infected by virus is called host cell --> host range is number of species that a particular virus can infect - structure = all viruses have NUCLEIC ACID GENOME (DNA or RNA) surrounded by a PROTEIN CAPSID - some viruses have VIRAL ENVELOPE which is derived from plasma membrane of host cell and contains VIRAL SPIKE GLYCOPROTEINS - genome composition = genome of virus can be DNA or RNA, can be ss or ds, and can carry a few of many genes

Answer 13

series of steps that results in the production of new viruses, cycle occurs after a virus has infected a host cell, details of cycles vary from one type of virus to another but they all follow 5-6 basic steps - attachment = virus attaches to surface of a host cell - entry = virus or viral genome enters host cell - integration = some but not all viruses integrate their genome into the genome host cell - synthesis of viral components = viral proteins and RNA or RNA are made by host cell - viral assembly = viral components assemble into virus particles - release = viruses released from host cell AEISAR

Answer 14

viruses may remain INACTIVE or LATENT, during which new viruses ARE NOT MADE some bacteriophages are latent when they are in LYSOGENIC CYCLE HIV usually remains latent for A LONG TIME after RNA genome is reverse transcribed into DNA and integrated into host chromosome some viruses (like herpesviruses) can remain latent as EPISOMES = genetic element that can replicate independently of host genome

Answer 15

HIV causes AIDS, infects human T cells (important in immunity) HIV has RNA genome, retrovirus during cycle, HIV RNA is reverse transcribed into DNA and integrated into a host chromosome (may remain latent for a long time) --> after activation, new HIV particles are made by transcription of HIV and production of new HIV proteins that assemble at plasma membrane and bud from cell HIV carries 9 genes, but some of them encode polyproteins that are cut into multiple proteins by proteolytic processing

Answer 16

has 2 copies of RNA genome that is surrounded by CAPSID --> capsid is surrounded by ENVELOPE that is derived from host cell plasma membrane and is studded with CIRAL SPIKE GLYCOPROTEINS many of the HIV proteins are contained within the virus including REVERSE TRANSCRIPTASE and INTEGRASE (needed during early steps in viral reproductive cycle)

Answer 17

9 genes of HIV can be divided into 5 categories - gag = proteins used for VIRAL ASSEMBLY and CAPSID FORMATION, gene encodes polyprotein that is cleaved into 4 diff proteins (matrix protein, capsid protein, nucleocapsid protein, and p6'-role in release of virions from membranes of infected cells) - pol = enzymes needed for VIRAL REPLICATION AND VIRAL ASSEMBLY, gene encodes a polyprotein that is cleaved into 3 enzymes (HIV protease, reverse transcriptase, and integrase) - vif, vpu = proteins that promote INFECTIVITY and BUDDING - vpr, rev, tat, nef = proteins with REGULATORY FUNCTIONS - env = proteins that are part of VIRAL ENVELOPE --> gene encodes a polyprotein that is cleaved into 2 proteins (gp41 and gp120)

Answer 18

they can only infect host cells that have the required CD4 marker plus the coreceptor (CCR5 or CXCR4)

Answer 19

spike glycoproteins on the HIV bind to receptors on the host cell membrane, the viral envelope fuses with the membrane, releasing the capsid and its contents after HIV enters host cell, ssRNA is reverse transcribed into dsDNA by REVERSE TRANSCRIPTASE --> process begins when a host cell tRNA binds to the HIV RNA (tRNA acts as a primer) --> in series of steps, portions of viral RNA are reverse transcribed into DNA, viral DNA is used as templated to make complementary DNA strand to give dsDNA --> during this process, viral RNA is degraded by RNase H (component of reverse transcriptase) --> dsDNA is integrated into a random position in genome by HIV encoded integrase protein when host cell receives signal to become active, provirus uses host RNA poly to create copies of HIV genome and shorter strands of mRNA which are translated --> assembly of virus particle takes place on INNER SURFACE of cell membrane (in macrophages and vacuoles) HIV enzyme called protease cuts the long chains of HIV proteins into small proteins, the smaller HIV proteins come together with copies of HIV's RNA genetic material and a new virus particle is assembled gag precursor (Pr55gag) is major virion component, gets cleaved into 4 major proteins (matrix, capsid, nucleocapsid, and p6gag) and associates into virions spontaneously --> newly assembled virus buds out from host cell --> during budding, new virus gets covered by cell's cells outer envelope (studded with glycoproteins to help virus bind to CD4 and coreceptors)

Answer 20

viral life cycle have been targeted for antiviral therapy combo therapy of use of multiple anit-HIV drugs like one protease inhibitor with 2 reverse transcriptase inhibitors

Answer 21

+ve strand viruses have RNA genome that can be translated (mRNA like) -ve RNA viruses CANNOT be translated

Answer 22

proofreading mechanism

Answer 23

types A, B, and C but A causes the most infections

Answer 24

orthomyxovirus

Answer 25

NEGATIVE (means cannot be translated), ssRNA has 8 segmented genomes in A and B 3 proteins = M2, hemagglutinin, and neuraminidase in host cell-derived membrane on surface of virion matrix protein M1 underneath, RNA segments covered in nucleoprotein virus attaches to and multiples in the cells of the RESPIRATORY TRACT

Answer 26

1. virus binds to the a respiratory epi cell by hemagglutinin spikes and fuses with the membrane 2. virus is endocytosed into a vacuole and uncoated to release its 8 nucleocapsid segments into the cytoplasm 3. nucleocapsid are transported into nucleus where the - sense RNA is transcribed into + sense strand that will be translated into viral proteins that make up the capsid and spikes 4. (+) sense RNA is used to synthesize glycoprotein spikes inserted into host membrane 5. release of mature virus occurs when viral parts gather at the cell membrane and are budded off with an envelope containing spike 6. (+) sense RNA stands are used to synthesize new - sense RNA stands --> these are assembled into nucleocapsids and transported out of the nucleus to the cell membrane

Answer 27

- hemagglutinin (H) = 18 diff subtypes, most IMPORTANT VIRULENCE FACTOR, binds to host cells - neuraminidase (N) = 11 subtypes, HYDROLYZES MUCUS and ASSISTS VIRAL BUDDING and RELEASE H and N are used to classify the influenza viruses (H1N1) both glycoproteins frequently undergo genetic changes, producing new variant viruses

Answer 28

viral RNA poly is ERROR-PRONE, resulting in constant MUTATIONS and results in AA subs in the viral proteins

Answer 29

one of the genes or RNA stands is sub with a strand from ANOTHER influenza virus of a different animal host by REASSORTMENT

Answer 30

it needs all 8 RNA segments to be present to be an infectious virus

Answer 31

RNA replication will produce a mix of the 8 RNA segs from the avian virus and from the human virus the packaged virus will contain a mix of human and avian RNA segs this is known as REASSORTMENT and produced new combos of HA and NA (antigenic shift)

Answer 32

aquatic birds pigs humans when reassortment occurs, the new virus will have to be very diff from all existing viruses (worldwide epidemics may be a consequence since the entire pop is susceptible to the virus)

Answer 33

large RNA viruses with spaced spikes on envelopes +ve strand RNA (can be translated into mRNA), non -segmented, large RNA genomes common in domesticated animals 7 coronaviruses have been id as causes of human disease, ex: MERS, SARS, SARS-2CoV virus has spikes, nucleocapsids on its RNA viral genome which is enclosed in an envelope

Answer 34

1. binds to host cell receptor ACE-2 2. once endocytosed, its viral genome is released 3. the RNA genome is replicated 4. the viral RNA is transcribed 5. translation of the viral proteins using host machinery 6. assembly of the viral particle 7. formation of the mature virion 8. exocytosis of the new virion

Answer 35

spike protein is a common target for anntibody and vaccine development another strategy = inject indvs with DNA/RNA encoding viral proteins - live attenuated - whole inactivated - RNA - DNA - recombo subunits - recombo viral vectors

Answer 36

a heritable change in gene material mutations provide allelic variations mutations are more likely harmful than beneficial

Answer 37

change in a single base pair/adjacent base pairs it can involve a base substitution this includes transitions and transversions mutations may also involve addition or deletions of short DNA seqs

Answer 38

a change of a pyrimidine (C, T) to another pyrimidine or a purine (A, G) to another purine transitions are more common than transversions

Answer 39

a change of pyrimidine to a purine or vice versa

Answer 40

base subs that DO NOT ALTER the AA seq of the polypep (due to degeneracy of genetic code)

Answer 41

base subs in which AA change does occur ex: sickle cell anemia from glutamic acid to valine if the sub AA has no detectable effect on protein function, the mutation is NEUTRAL this can occur if new AA has similar chem to the AA it replaced

Answer 42

base subs that change a normal codon to a STOP codon (can result in shorter proteins)

Answer 43

addition or deletion of number of nucleotides that is NOT DIVISIBLE BY 3 shifts reading rame so that translation of mRNA resutls in completely diff AA seq downstream of mutation

Answer 44

caused by a 32 bp deletion in CCR5 gene, results in an inactive (undetectable) protein and near complete resistance to HIV-2 infection (present in 13% of N. Europeans)

Answer 45

they can still affect phenotype mutations in the core promoter can change levels of gene expression - up promoter mutations = increase expression - down promoter mutations = decrease expression - regulatory element/operator site = may disrupt ability of gene to be properly regulated - 5'UTR/3'UTR = may alter ability of mRNA to be translated, may alter mRNA stability - splice recognition seq = may alter ability of pre-mRNA to be properly spliced

Answer 46

changes the wt genotype into some new variation

Answer 47

changes mutant allele back to wt also called reversion

Answer 48

decrease the chances of survival most extreme = lethal mutations

Answer 49

enhance survival or reproductive success of an organism environment can affect whether a given mutation is deleterious or beneficial

Answer 50

they affect phenotype only under a defined set of conditions ex: temp-sensitive mutation

Answer 51

germ-line cells = cells that give rise to gametes somatic cells = all other cells

Answer 52

occur directly in sperm or egg or in one of their precursor cells can be passed to next gen where mutation will be found in whole body

Answer 53

those that occur directly in a body cell or in one of its precursor cells, NOT PASSED ONTO NEXT GEN result in patches of affected area, size of patch will depend on timing of mutation (earlier mutation = larger patch) indv with somatic regions that are genotypically diff is called GENETIC MOSAIC

Answer 54

arise spontaneously and continuously during culture, early arising mutants will give rise to LOTS OF MUTANT COLONIES late arising mutants will give rise to FEW RESISTANT COLONIES number of resistant colonies in cultures should FLUCTUATE

Answer 55

1. mutants arise spontaneously and continuously aka spontaneous mutation (if T1-resistant mutants are are already in culture before T1 exposure, then there will be variation and fluctuation which supports the hypothesis that resistance to T1 arises from pre-existing random mutations) 2. T1-resistance mutants arise ONLY AFTER exposure to T1 (in this case, see no fluctuation, any variation among the cultures and aliquots from same large culture should be the SAME) aka induced mutation mutations were continuous and random, they were pre-existing and selected by environmental agent

Answer 56

predicts that the number of tonr (T one resistance) bacteria is very low unless there is a selection, when the numbers created increase

Answer 57

predicts that the number of tonr bacteria will fluctuate in diff bacterial pops and will occur without selection

Answer 58

1. place indv bacterial cells onto growth media 2. incubate overnight to allow formation of bacterial colonies = master plate 3. press velvet cloth onto master plate and then lift gently to obtain a replica of each bacterial colony --> press replica onto 2 secondary plates that contain T1 phage --> incubate overnight to allow growth of mutant cells resistant cells were in the same location on both plates mutations had randomly occurred in absence of selection by T1 became observable with selection for T1 resistance supports random mutation theory

Answer 59

result from abnormalities in cell/biological processes ex: errors in DNA replication, DNA damage from normal cell processes underlying cause originates with the cell

Answer 60

caused by environmental agents agents that are known to alter DNA structure are termed mutagens (can be chemical or physical agents

Answer 61

- depurination - deamination - tautomeric shift - oxidative stress

Answer 62

removal of a purine (A or G) from DNA forming an APURINIC SITE apurinic site can be repaired, however, if the repair system fails then a mutation may result during subsequent rounds of DNA replication (poly will add a random base) --> 3/4 bases are incorrect nucleotide (75% chance of mutation)

Answer 63

removal of an amino group from the cytosine base (other bases are not readily deaminated) DNA repair enzymes can recognize U as an inappropriate base in DNA and remove it however if the repair system fails, G-C to A-T mutat will result during subsequent rounds of DNA replication G-C --> G-U --> A-U --> A-T (NOT T-A)

Answer 64

5-methylcytosine typically occurs at cytosine in CpG di-nt in eukaryotic DNA 5-methylcytosine can be deaminated into THYMINE, a normal constituent of DNA repair enzymes CANNOT determine which of the 2 bases on the 2 DNA strands is the correct base --> for this reason, methylated cytosine bases tend to create hot spots for mutation

Answer 65

spontaneous isomerization of a nitrogen base to an alternative hydrogen-bonding form temporary change in a base structure common, stable form of THYMINE and GUANINE is KETO FORM (RARELY T and G convert to enol form) common stable form of ADENINE and CYTOSINE is the AMINO FORM (RARELY, A and C can convert to an IMINO FORM) rare tautomers can engage in erroneous base pairing

Answer 66

tautomeric shifts and DNA replication can cause mutation to cause mutation, tautomeric shift must occur IMMEDIATELY PRIOR TO REPLICATION T-A --> T-G--> C-G

Answer 67

oxidative DNA damage guanine can be converted to 7,8-dihydro-8-oxoguanine - pairs with adenine during replication (8-oxyG-A) - causes GC base pair --> G-A--> TA base pair 2 steps: chemical alteration of DNA base --> altered pairing by this altered base at next round of DNA replication

Answer 68

many human genetic diseases are caused by an unusual form of mutation called tri-nt repeat expansion (TNRE) certain regions of the chromosome contain tri-nt seqs repeated in tandem --> these repeats are prone to EXPANSION/CONTRACTION in the genome in norm indvs, these seqs are transmitted from parent to offspring intact w/o extra copies but in people with TNRE disorders, length of tri-nt repeat increased above critical size (when threshold number of repeats has been exceeded, disease symptoms occur

Answer 69

insertion = reannealing (of new stand) occurs UPSTREAM of original position deletion = reannealing occurs DOWNSTREAM of original position

Answer 70

FRAGILE X SYNDROME = most common form of inherited mental impairment one end of X-chromosome looks like it's hanging by a thread --> disease is transcribed but NOT TRANSLATED syndrome caused by INCREASE in number of CGG repeats in FMR-1 gene mutated (expanded CGG) region is in part of gene that is transcribed but not translated (5' UTR) DOMINANT, X-LINKED unaffected parents can have affected offspring

Answer 71

200 repeats

Answer 72

silencing of the FMR-1 gene associated with CpG methylation and shift in epigenetic marks of chromatin from euchromatic state to heterochromatic state --> results in NO TRANSCRIPTION of gene increased CGG repeats turn off transcription

Answer 73

if repeat number is greater than 50, correct seq cannot be replicated by replication machinery --> expanded

Answer 74

many tri-nt diseases lead to increases in repeats of a SINGLE AA (repeats in exons, like CAG, resulting in polyglutamine tract in the protein) --> this causes proteins to aggregate with each other which is correlated with progression of disease (like Huntington's)

Answer 75

agents that alter the structure of DNA thereby cause mutations are called mutagens we are concerned about mutagens because: 1. they are often involved in development of HUMAN CANCERS 2. they can cause GENE MUTATIONS that may have harmful effects in future generations mutagenic agents are usually classified as chem or physical mutagens

Answer 76

1. base modifers = covalently modify base structure, some may disrupt pairing by AKLYLATING bases --> base sub mutation 2. intercalating agents = directly interfere with REPLICATION PROCESS (deletions, insertions, frameshift mutations) 3. base analogs = resemble DNA bases, incorporate into DNA and disrupt structure, some tautomerize at high rate --> base sub mutation physical mutagens include radiation (x-rays, gamma rays, ionizing radiation, UV light)

Answer 77

covalently modify the structure of a nt (altered bases are now mispairs) ex: NITROUS ACID replaces amino groups with keto groups, this can change cytosine to uracil and adenine to hypoxanthine (modified bases DO NOT PAIR with appropriate nt in DAUGHTER strand during DNA replication) some chemical mutagens disrupt the appropriate pairing between nucleotides by alkylating bases within the DNA ex: nitrogen mustards (NITROSGUANINE) and ethyl methanesulfonate (EMS) alkylating agents EMS (adds ethyl) and NG (adds met+) to about all bases but mostly G-->O-6-alkylguanine (which mispairs with thymine) causes G:C --> A:T transitions (know that these chemicals are base modifying agents and cause base subs)

Answer 78

contain flat, planar structures that intercalate themselves into double helix --> distorts helical structure when DNA containing these mutagens is replicated, daughter strands may contain single-nt additions/deletions resulting in frameshifts ex: PROFLAVIN, ACRIDINE ORANGE, ICR-191 (know that these chemicals are intercalating agents and cause FRAMESHIFTS)

Answer 79

resemble normal bases become incorporated into daughter strands during DNA replication ex: 5-bromouracil is a THYMINE analog --> can be incorporated into DNA instead of thymine and results in tautomeric shift that pairs with GUANINE A-T --> A-BrU --> G--BrU --> G-C base pairing of 5-BrU with adenine or guanine know that these chemicals are base analogs and cause BASE SUBS and knows steps involved in generating base changes

Answer 80

A:5BU --> A:T or G:5BU --> G:C or G:5BU

Answer 81

includes x-rays and gamma rays has short wavelength and high energy, can penetrate deeply into bio samples has 2 effects on DNA: 1. (indirect) generates ROS, react with DNA --> mutation 2. (direct) break DNA backbone, to give ss or ds breaks, or break glycosidic bond --> AP sites can cause: - base deletions - oxidized bases - single nicks in DNA strands - cross-linking - chromosomal breaks

Answer 82

includes UV light has less energy cannot penetrate deeply into bio molecules causes formation of CROSS-LINKED THYMINE or pyrimidine dimers (joins adjacent Ts on same strand) damage prevents base pairing, blocks replication thymine dimers may cause mutations when DNA strand is replicated

Answer 83

aflatoxin, potent mutagen and carcinogen modifies guanine and adds bulky adduct causes G-->T TRANSVERSIONS

Answer 84

forward mutation (wt-->mut, or his+ --> his-) detect his- by growing all bacterial on MM + histidine then testing colonies on MM alone --> those that grow on MM+ His but not MM alone are his- (because his- needs his to grow) this method takes too long because there's thousands and millions of colonies reverse mutation (mut --> wt, or his- --> his+) detect these by planting the culture of his- bacteria on MM with no his only his+ revertants will grow on MM can screen 10^9 cells on a single plate and detect very low freq of reversion very easily

Answer 85

test uses strains of S. typhimurim that CANNOT synthesize the AA his each has a point mutation (his-) in a gene involved in his biosynthesis --> strain is unable to grow on MM unless his is supplied or reversion mutation occurs, restoring wt seq and ability to synthesize his Ames test monitors rate at which this reversion mutation occurs

Answer 86

used to screen possible carcinogen and mutagens salmonella his auxotroph (requires his to grow) are mixed with rat liver enzymes and plated on media lacking his rat liver extract provides a mix of enzymes that may activate a mutagen live enzymes are required to detect mutagens that are converted to carcinogenic forms by liver test chemical is then added to medium control plates show only a small # of revertants (bacteria cells growing without his) plates inoculated with mutagens/procarcinogens show a larger # of revertants

Answer 87

different Ames strains (TA strains) have diff mutations that can report on distinct mutagenic events some his- mutations are frameshifts, can only be reverted by mutagens that induce frameshifts TA100 = base subs TA1538 = frameshift (-1)

Answer 88

1. an irregularity in DNA structure is detected 2. abnormal DNA is removed 3. normal DNA is resynthesized

Answer 89

PHOTOLYASE can repair thymine dimers --> splits dimers, restoring DNA to its original condition, uses ENERGY of VISIBLE LIGHT for photoreactivation, will not repair dimers in dark ALKYLTRANSFERASE repairs alkylated bases --> transfers methyl or ethyl group from base to cysteine side chain with alkyltransferase protein --> will permanently inactivate alkyltransferase

Answer 90

remove damage (base or DNA backbone) ss nick/gap provides 3' OH for DNA pol I initiation DNA ligase seals nick REMOVE AND REPLACE mechanisms

Answer 91

- base excision repair = cut out base, then cut next to apurinic/aplyrimidinic site and let DNA pol I repair - nt excision repair = cut out seg of DNA around a damaged base

Answer 92

involves enzymes known as DNA N-glycosylases --> these enzymes can recognize an abnormal base and cleave the bond between it and sugar in the DNA via AP endonuclease --> AP site depending on species, this repair system can eliminate abnormal bases like URACIL, 3-METHYLADENINE, and 7-METHYLGUANINE AP endonuclease cleaves backbone upstream of AP site DNA poly I fills in ss gap, using remaining undamaged DNA strand as template ligase seals the nick in backbone

Answer 93

BER CANNOT repair bases with bulky adducts that distort helix or remove multiple, adjacent damaged bases --> unless repaired, these can block TRANSCRIPTION and DNA REPLICATION this is why NER is important --> this type of system can reapir many types of DNA damage including: - thymine dimers (if not repaired by photolyase) and chemically modified bases, missing bases, and some types of crosslinks NER is found in all eukaryotes and bacteria in E. coli, NER system requires 4 key proteins --> UvrA, UvrB, UvrC, UvrD (involved in Ultraviolet light Repair of pyrimidines) --> they will recognize and remove a short seg of damaged DNA, DNA poly and ligase will finish the job UvrA/UvrB complex tracks along DNA in search of damaged DNA --> after damage is detected, UvrA is released and UvrC binds --> UvrC makes cuts on both sides of thymine dimer --> UvrD (helicase) removes damaged region, UvrB and UvrC are released --> DNA poly fills in gap and DNA ligase seals the region

Answer 94

xeroderma pigmentosum (XP), Cockayne syndrome (CS), and PIBIDS common characteristic of all 3 syndromes = increase sensitivity to sunlight XP can be caused by defects in 7 diff NER genes

Answer 95

recognize and correct a base pair mismatch structure of DNA double helix obeys AT/GC rule but during DNA replication, an incorrect base may be added to growing stand by mistake DNA poly have 3'-5' proofreading ability that can detect base mismatches and fix them if proofreading fails, mismatch repair system comes to rescue mismatch repair systems are found in all species important aspect of these systems is that they are specific to newly made strand

Answer 96

using the proteins MutL, MutH, and MutS --> they also direct mismatch removal from newly made strand (proteins named Mut because their absence leads to higher mutation rate than norm)

Answer 97

if can distinguish between parental and daughter strand prior to replication, both strands are methylated --> immediately after replication, parental strand is methylated while daughter is NOT (hemimethylated) in E. coli, A of GATC seqs is methylated

Answer 98

MutS protein slides along DNA and finds mismatch MutL is recruited MutS/MutL complex binds to MutH, which is already bound to hemimethylated seq MutH cuts unmethylated stand with wrong base region including mismatched base removed, leaving gapped DNA repair synthesis resynthesizes removed ssDNA

Answer 99

by recombo repair pathways use undamaged strand as template in resynthesis reaction DNA ds breaks are VERY DANGEROUS --> cause breakage of chromosomes into pieces --> breaks are caused by IONIZING RADIATION and CHEMICAL MUTAGENS (also ROS) --> breaks can cause chromosomal rearrangements and deficiencies may be repaired by 2 mechanisms: - HOMOLOGOUS RECOMBO REPAIR (HRR) - NONHOMOLOGOUS END JOINING (NHEJ) if DSB in dividing cell with sister chromatid available --> break can be repaired using undamaged chromatid as template --> DSB is processed by short digestion of DNA strands (used for strand exchange)

Answer 100

unbroken stands are used as templates to synthesize DNA strands are then broken and rejoined in way that produces separate chromatids because sister chromatids are genetically identical, homologous recombo can be ERROR-FREE repair mech has ss projections that will pair with template

Answer 101

broken ends are recognized by end binding proteins KU70/KU80 proteins form a cross bridge, other proteins are recruited, ends trimmed to generate 5'P and 3'OH --> this processing may result in deletion of small region ends joined by ligase INHERENTLY ERROR-PRONE/MUTAGENIC

Answer 102

by translesion DNA pols but before this --> replicative DNA pols like DNA pol III are sensitive to distortions in DNA --> unable to replicate through DNA lesions, this type of replication requires specialized DNA pols, these pols are induced as part of DNA damage response (SOS response) and will insert any nt into damaged region TLS pols contain active site with loose, flexible pocket --> can accomodate abberant structures in template strand --> neg. consequence of TLS pols = low fidelity (mutation rate is 10-2 to 10-3, higher than 10-8 of replicative pol) when replicative DNA pol encounters damaged region, it is swapped for TLS poly which can tolerate template bases with bulky adducts --> inserts a few bases then falls off, pol III is reattached --> region is replicated but with ERROR-PRONE REPLICATION

Answer 103

to offset differences in number of active sex chromosomes and ensure equal gene expression in both X-chromosome inactivation

Answer 104

occurs by chromosome condensation Barr body is a highly condensed, inactivated X chromosome (typically only seen in females)

Answer 105

female mouse has inherited 2 X chromosomes (one from mother that carries allele conferring white fur Xb and one from father that carries allele conferring black fur XB) random x-chromosome inactivation occurs EARLY in development in some cells, X w/ b (white) allele is activated so only some XB allele is active --> these cells and their descendants only express black fur --> opp is true for cells that inactivated XB (descendants only express white fur) during x-chromosome inactivation, DNA becomes highly compacted, most genes on inactivated X CANNOT be expressed, inactivated X is maintained in an inactive state through replication and cell division (x-chromosome inactivation pattern is passed along to all future somatic cells) ex: calico cat with black and orange fur (they always FEMALE)

Answer 106

mammalian can count their x chromosomes and allow only one of them to remain active --> additional x chromosomes are converted to Barr bodies XX = 1 barr body XY = 0 barr body X0 = 0 barr bodies XXX = 2 barr bodies XXY = 1 barr body

Answer 107

technique of isolating and making many IDENTICAL copies of a gene

Answer 108

- CHROMOSOMAL DNA (the 'insert') = serve as source of DNA segment of interest --> to prepare chromosomal DNA --> obtain cell tissue from organism of interest, break open cells, extract and purify DNA using variety of biochem techniques - VECTOR DNA = usually bacterial plasmid, serve as CARRIER FOR DNA seg that is cloned, can replicate independently of host chromosomal DNA

Answer 109

cell that harbors vector is called HOST CELL (usually E. coli) when vector is replicated inside host cell, DNA that it carries is also replicated the seq of ORIGIN of REPLICATION determines whether a vector can replicate in a particular host cell

Answer 110

1. plasmids = many naturally occurring plasmids have SELECTABLE MARKERS, typically genes conferring ANTIBIOTIC RESISTANCE TO HOST CELL 2. viruses/phages

Answer 111

vector is cleaved with restriction endonuclease and DNA frag from organism of interested is added to the cleaved portion by ligase --> recombo vector DNA is introduced into host cell --> propagation produces many copies of recombo DNA

Answer 112

insertion of chromosomal DNA into a vector requires cutting and joining of DNA frags --> these enzymes are restriction endonucleases or restriction enzymes protect bacterial cells from invasion by foreign DNA (particularly that of bacteriophage) --> these enzymes bind to specific DNA seqs and then cleave the DNA at 2 defined locations, one on each strand they always have accompanying methylase which methylates the same seq, prevents cutting bacteria have methylase and RE, so its own DNA is immune from cutting by RE so methylated DNA IS NOT CUT but UNMETHYLATED IS CUT

Answer 113

at specific sites called palindromic seqs the seq is identical when read in opposite direction in complementary strand BamHI = 5' GGATCC 3' or Sau3AI = 5' GATC 5' ex: 5' AGCT 3' or 5' AAGCTT 3' 3' TCGA 5' 3' TTCGAA 5'

Answer 114

some will digest DNA into fragments with STICKY ENDS = short, ss regions of DNA that can base-pair with another piece of DNA with complementary ss seq some will generate blunt ends --> enzyme NaeI cuts in middle of recognition seq (5' GCCGGC 3') sugar-phosphate backbone of DNA molecules with stick yor blunt ends can be covalently linked together by ligase

Answer 115

ampR --> confers ANTIBIOTIC RESISTANCE to host cell (id cells that have taken up vector) lacZ --> encodes beta-galactosidase (provides means by which bacteria have picked up cloned gene can be id) - origin of replication = allows plasmid to replicate independently of chromosome of bacterial host cell

Answer 116

amp and tet

Answer 117

human chromosomal DNA would generate thousands of frags, typically one frag inserts into plasmic vector at any one time (cut plasmid DNA and human DNA with same restriction enzyme, mis, add ligase) and becomes RECOMBO PLASMID transform E. coli cells with ligation mix, select on amp (or whatever antibiotic plasmid confers resistance to), cells that are able to take up DNA are called COMPETENT CELLS, transformation refers to uptake of plasmid vectors by a bacterial cell, single competent bacterial cell takes up single plasmid molecules and goes on to form a colony on an amp agar plate all bacterial colonies growing on amp plate must have picked up the vector and its ampR gene

Answer 118

colonies may have recircularized plasmid (no insert DNA) or have recombo plasmid, carrying inserted DNA --> this is where lacZ gene comes into play in hybrid vector, chromosomal DNA inserts into lacZ gene, thereby disrupting it (lacZ+ --> lacZ-) --> recirculized vector has FUNCTIONAL lacZ+ gene

Answer 119

2 relevant compounds - IPTG which induces lacZ gene expression - X-Gal = colorless compound that is cleaved by beta-galactosidase into BLUE DYE (color of bacterial colonies will depend on whether or not beta-galactosidase enzyme is function)

Answer 120

in this experiment, when plated on media w/ amp, IPTG, and X-gal --> colonies with RECIRCULARIZED (lacZ+) vectors form BLUE colonies (bad because not recombo) while those with that are hybrid (lacZ-) vectors form white colonies (good because they are recombo plasmids)

Answer 121

- vector gets replicated by host cell many times (this will generate a lot of copies per cell) - bacterial cell divide about every 20 mins(this will generate pop of many millions of cells overnight)

Answer 122

using reverse transcriptase clone of eukaryotic gene made from chromosomal DNA will contains introns, exons, and control regions --> you want to clone a of eukaryotic gene that contains full ORF with NO INTRONS enzyme reverse transcriptase is used to make DNA from RNA --> uses RNA as templated to make complementary DNA (cDNA) 1. add poly-dT primer that binds to the polyA tail of mRNA 2. add reverse transcriptase + dNTPS to synthesize cDNA 3. add RNase H to cut up RNA and generate RNA primers 4. add DNA pol I and ligase to synthesize 2nd DNA strand

Answer 123

advantage of cDNA is that it lacks introns if you want to express human gene in C. color and recover recombo protein, recombo plasmid will need to: - be a cDNA clone (exons/coding seqs only, no introns) - have an E. coli promoter - have an E. coli ribosome binding site - eukaryotic specific post-translational mods will NOT occurs

Answer 124

treating chromosomal DNA with REs can generate tens of thousands of frags after ligation, there is a collection of recombo vectors, with each vector containing a certain frag if the starting material was chromosomal DNA = genomic library if starting material was cDNA, library is called cDNA library

Answer 125

it can copy a specific sequence of DNA without aid of vectors and host cells (must know enough about the gene of interest to have the sequence of 2 short primers) researched much have prior knowledge about the seq if the template DNA to structure the synthetic primers --> specific DNA seg can be amplified from a complex mix of other seqs - you can amplify one gene out of an entire genome/mixture of diff genomes - PCR can be used to amplify very small samples (like in forensics) or retrieved from ancient bio specimens - DNA degrades over time - mtDNA has multiple copies/cell, so there's a better chance of recovering it from ancient samples

Answer 126

to amplify DNA by PCR: 1. template DNA (contains region that needs to be amplifed) 2. oligo-nt primers (complementtary seqs at ends of DNA frag to be amplified, these are synthetic and about 15-20 nts long) 3. deoxynucleoside triphosphates (dNTPs) --> provide precursors for DNA synthesis 4. Taq poly = DNA poly isolated from Taq, THERMOSTABLE enzyme is necessary because PCR involves heating steps that inactivate most other DNA pols

Answer 127

1. denaturation 2. primer annealing 3. primer extension KNOW THIS ORDER 1. add oligo-nt primers 2. heat to separate strands 3. cool and let primers anneal (55-65 C) 4. heat to allow DNA synthesis (Taq works) repeat steps 2 and 3

Answer 128

carried out in a thermocycler all ingredients placed into one tube --> experimenter sets temp range and number of cycles (sequential process of denaturing-annealing-synthesis is repeated for 25-35 cycles) since very little starting template DNA is needed, PCR is highly sensitive

Answer 129

small sample size, no need to culture organism/virus look for amplification of a specific DNA frag characteristic or unqiue to a specific org (use PCR primers that will anneal to DNA only from specific organisms)

Answer 130

used to detect and quantitate amount of RNA in living cells RNA is isolated from a sample, mixed with RT and a primer that will anneal to the 3' end of the RNA (gene-specific primer) generates a ss cDNA which can be used as template DNA in conventional PCR first PCR cycle will convert ss cDNA to dsDNA

Answer 131

used to quantitate the amount of a specific gene or mRNA in a sample real time PCR is carried out in a thermocycler that can measure changes in fluorescence emitted by detector molecules in PCR reaction mix --> can be used to quantify amount of specific piece of DNA or RNA present in sample fluorescence is detected by thermocycler and will increase in proportion to amount of PCR product produced PCR product in tern is proportional to amounnt of DNA or RNA present in original sample this is being used to detect Covid-19 (viral RNA --> cDNA --> amplied in qPCR reaction) greater amount = greater fluorescence

Answer 132

analysis of mutations can provide important info about normal genetic processes mutations can arise spontaneously, be induced by mutagens, or created with rDNA researchers have developed techniques to - make mutations within cloned DNA - introduce these mutant genes into org, replacing the WT copy of gene gene editing = experimentally altering a gene seq

Answer 133

by replacing WT gene with a drug resistance gene recombo is facilitated by homo regions flanking the drug-resistance cassette replacing a WT gene iwth a deleted one, carrying a drug R marker (what you would like to happen) but what actually happens is that the introduced DNA frag carrying drug R integrates at a non-homologous position

Answer 134

make alterations in mouse embryonic stem cells introduce these stem cells into blastocysts implant chimeric blastocyst in pseudo-preg mouse look for offspring who's germline has be modified process is caused by non-homo, ectopic recombo homo recomb is very inefficient, so you can't use single cell zygotes which is why you have to resort to stem cells

Answer 135

freq of homo recombo increased hugle if you can generate a DSB in/next to site where you want recombo to occur DSBs are LETHAL and must be repaired - repair by recombo with homo DNA, injected into cell at same time DSB occurs - if no homo DNA around, repair by berror-prone non-homo end joining (NHEJ) --> generates insertions/deletions that knockout gene

Answer 136

NHEJ = correction leads to constitutive KO HRR correction based on provided template creates KI (knock in) CRISPR/Cas9

Answer 137

virus invades bacterial cell, new spacer is derived from virus and integrated into CRISPR seq, CRISPR RNA is formed, CRISPR RNA guides molecular machinery to target and destroy viral genome RNA produced is complementary to invading phage/plasmid, crDNA base pairs to invading DNA (this is how specific DNA is targeted 2nd RNA, tracrRNA also NEEDED (functional RNA) --> Cas9 recruited, cleavage at site of DNA-RNA base pairing --> crRNA binds next to an NGG PAm seq --> incoming DNA destroyed by dsDNA cleavage Cas9 makes guide RNA that is complementary to where you want to cut (as long as NGG PAM seq is present)

Answer 138

it can make DSBs at specific seqs in genome these breaks have to be repaired if you want to INACTIVATE gene --> can rely on error-prone NHEJ to repair break, introduces deletion/insertion (indels, usually ABOLISH GENE FUNCTION leading to gene KO) if you want to INTRODUCE a specific CHANGE in a gene --> while gRNA/Cas is injected, you also deliver homo 'repair' donor DNA molecule --> DNA can be used to DSB by homo recombo (if DNA carries mutation then mutation will be recombined into repaired chromosome --> produces recombo chromosome with changes you want (KI mutations) CRISPR/Cas9 will continue to cleave perfectly repaired chromosomes --> indel generated by error-prone NHEJ can NO LONGER be cleaved by CRISPR/Cas9 (this version of CRISPR/Cas9 can ONLY generate gene KOs)

Answer 139

during replication, DNA poly connects adjacent deoxy-nts by covalently link 5'-P of one to 3' OH of another nt w/o 3' OH can also be sunthesized = dideoxyribonucleotides of ddNTPS (cannot form bonds) if ddNTP is added to a growing DNA strand, strand can no longer grow --> leads to chain termination the 3' OH group necessary for formation of phosphodiester bond is missing in ddNTPs --> chain terminates at ddG

Answer 140

if you have a mix of dATP and ddATP, some chains will be terminated at EVERY T in template, others will continue to be elongated length of these dd-A terminated chains correspond to position of Ts in template prior to DNA sequencing, DNA must be obtained in large amounts (PCR or cloning) --> target DNA can be cloned into plasmid at site adjacent to primer annealing site --> target DNA is heat denatured into ss --> heat denaturation step provides ss DNA template for modified replication rxn in Sanger DNA sequencing

Answer 141

the A reaction mix contains template primer, DNA poly, dGTP, dCTP, dTTP, dATP, and ddATP at each T in template, either dATP or ddATP can be incorporated --> if ddA is incorporated, synthesis ends but if dA is incorporated, synthesis continues partial termination at each T on template means that some nt chains are terminated, others continue to be elongated the lengths of the nt chains ending in ddATP tells us where each T was in the template, primer is labeled with radioactive 32P so all chains are radioactive too, these chains are resolved on gel and visualized by autoradiography --> you read the seq of synthesized strand (5' to 3'), BOTTOM TO TOP (smaller to larger) T is RED every time ddTTP incorporated opposite A in template, C is PURPLE even time ddCTP incorporated opposite a G in template

Answer 142

the seq of diff colors corresponds to seq of bases in synthesized DNA

Answer 143

method where small DNA frags are randomly generated from larger pieces and sequenced - most efficient and inexpensive way to seq genomes - this method does not require extensive mapping, but the same region may be sequenced multiple times regions of overlap are used to map the frags, relative to one another

Answer 144

1. purify DNA from strains of bacteria --> involves breaking cells open by adding phenol and chloroform, most protein and lipid components go into pheno-chloroform phase --> DNA remains in aqueous phase, which is removed and used in step 2 2. sonicate (using sound waves) DNA to break it into small frags 3. clone DNA frags into vectors, producing a DNA library 4. subject many clones to the procedure of ddDNA sequencing 5. use tools of bioinformatics to id various types of genes in genome

Answer 145

1. to obtain a genetic linkage map of human genome 2. to obtain a physical map of human genome 3. to obtain the DNA seq of entire human genome 4. to develop technology for management of human genome info

Answer 146

rapidly sequencing large amounts of DNA possible because of: - AUTOMATED SEQUENCING with fluro detector - parallel sequencing = simultaneously perform many sequencing runs in multiple, gel-filled capillary tubes - next gen sequencing technologies (NGS) = ability to process thousands or millions of seq reads in parallel

Answer 147

one kind of NGS DNA is fragmented mix of DNA frags with adaptors called sample library frags are attached to beads PCR amplified sequencing reagents flow over beads in wells of plate: dG, dA, dT, dC sequencing by synthesis (SBS) --> PPi is released when nt is added, ATP sulfurylase uses it to make ATP, ATP is used by luciferase to break down luciferin, rxn gives off light detected by a camera in the sequencing machine 1. isolate genomic DNA and break into frags 2. covalently attach oligonucleotide adaptors to 5' and 3' ends of DNA 3. denature DNA into ss and attach beads via red adaptors (only one strand is attached to a bead) 4. emulsify the beads so there is only one bead per droplet, droplets also ocntain PCR reagents that amplify the DNA

Answer 148

it is a nt seq that does not contain any internal stop codons (just one at the end) - in bacteria, long ORFs are contained in chromosomal gene seqs - in eukaryotes, chromosomal coding seqs may be interrupted by introns - in DNA seq, reading of codons could begin with 1st, 2nd, or 3rd nts (called reading frame 1, 2, 3) since there are 2 strands of DNA, in any sdDNA frag, there can be 6 reading frames

Answer 149

it tells you if a ORF encodes a protein similar to a protein characterized and identified in a diff organism basic local alignment search tool searches in databases for AA or nt seq similarity, for whole gene or motifs 'hits' may tell you what similar proteins in other organisms do, from this you can infer the function of your gene/orf/protein

Answer 150

pseudogenes are INACTIVE, 2nd non-functional copy of a gene DNA --> duplication --> mutation --> classical pseudogene formation (inactivating mutation, deletions that remove promoter or mutations in exons that prevent splicing or introduce stop codons into ORFs) processed RNA --> cDNA (only coding seq) --> genomic DNA gets inserted into cDNA --> processed pseudogene (can't be transcribed)

Answer 151

codon bias may influence DNA seq of ORF genetic code is degenerate, but not all synonymous codons are used with equal freq --> unequal use of these codons is related to tRNA abundance in diff orgs expect real ORFs to have codon bias characteristic of other gene IN SAME ORG (YOU SEE CODON BIAS IN CODING REGIONS ONLY)

Answer 152

entire collection of RNA transcripts in a cell transcriptomics seeks to understand the id and abundance of each RNA in cell techniques used: - N. blotting (can only examine 1 mRNA at a time - microarrays or RNAseq, examine ALL mRNAs in cell at once

Answer 153

entire collection of proteins that an org can make proteomics = to understand functional roles of proteins of a species and interplay among proteins

Answer 154

can id all genes that are transcribed DNA microarray is a slide, spotted with a set of synthetic oligonucleotides, representing all of genes in genome each of these oligonucleotides seqs corresponds to part of a known gene --> relative location of each spot on slide is known hybridization experiments with RNA extracted from cells tells you if gene is expressed or not

Answer 155

1. extract mRNA 2. make cDNA reverse transcript, label cDNAs with fluorescent dyes (control = green, experiment = red) 3. hybridize to microarray 4. laser excitation at dye specific Hz 5. detect laser emission 6. computer calculates relative levels of hybridized probe can examine all mRNAs expressed at once indv oligonuccleoides are needed to detect splice variants DARK SHADES = higher expression LIGHT SHADES = lower expression

Answer 156

RNA seq can also be used to assess mRNA expression levels get mRNAs, convert to cDNA seq cDNAs using NGS compare multiple samples number of reads for a particular mRNA is proportional to its level of expression green spots represent DOWNREGULATED genes

Answer 157

AA seq of protein is revealed 2 spectrometers are used - first measures the MASS of a given peptide (that was generated from protein digestion) - second analyzes the peptide after it has been digested into even smaller frags

Answer 158

true this larger size is rooted in a number of cell processes 1. alternative splicing 2. RNA editing 3. post-translational covalent mod

Answer 159

used to separate a mix of diff proteins, separation technique that can distinguish hundreds or even thousands of diff proteins in cell extract --> involves 2 diff gel electrophoresis exps (1st = separates by pH/cahrge interactions and 2nd = separates by size) any given cell of a multicell organism will produce only a subset of proteins in its proteome --> subset that it makes depends on: - cell type - stage of development - environmental conditions

Answer 160

specific spots may be of special interest - proteins which are very abundant in cell type - may be important for that cell's structure or function - spots present in only given circumstance - cells exposed to a hormone versus that are not - spots present only in abnormal cells - very common in cancer cells

Answer 161

to id proteins and measure the MASS-TO-CHARFE RATIO OF IONS next step of 2D gel is to correlate a given spot with a particular protein - spot is cut out from gel - protein is then purified from it - intact peptide, or products from digestion with trypsin may be analyzed by mass spectrometry can id post-translational mod because of size increase from original

Answer 162

protein covalent mods ex: mass of a phosphorylated protein increases by the mass of a phosphate

Answer 163

first 1. sample 2. digestion 3. machine 4. date collected 5. data analysis second 1. sample extraction 2. protein mix 3. machine 4. denatured protein data 5. data analysis

Answer 164

p^2+2pq+q^2

Answer 165

p = dominant allele q = recessive allele allele frequencies are given by p and q genotype frequencies will be given by p^2, 2pq, and q^2

Answer 166

if in Hardy-Weinberg equilibrium = pop IS NOT EVOLVING if not in H-W equ = pop is EVOLVING and one or more the 5 assumptions is being violated

Answer 167

allele freq are preserved and they are in H-W equilibrium

Answer 168

1. calc allele freq from genotype/phenotype freq 2. calc expected numbers of each genotype (use the H-W formula to figure out how many homozygotes and heterozygotes you would expect 3. compare your expected and observed data

Answer 169

1. mutation 2. gene flow 3. non-random mating 4. genetic drift 5. selection

Answer 170

transfer of alleles among pops EMIgration = transfers alleles OUT of a pop IMMIgration = transfers alleles IN

Answer 171

3 biases in mating - ASSORTIVE mating --> positive = similar types of mate, negative = opps attract - ISOLATION by distance --> indvs more apt to mate with neighbor than distantly, located indv, leads to SUBPOPS, proportions of homozygotes larger than predicated by H-W - INBREEDING --> increases homozygosity, recessive traits are expressed and can result in REDUCTION in vigor and reproductive success (inbreeding depression)

Answer 172

results in EXCESS of HOMOZYGOTES compared with random mating and DEFICIENCY of HETEROZYGOTES

Answer 173

closer relations = higher F sibling matings = riskiest (250x increase at 0.001)

Answer 174

H-W assumes INFINITE pop size but real pops are FINITE allele freqs can change from gen to gen as a result of chance of SAMPLING ERROR when gametes are drawn to form next gen GENETIC DRIFT = alelle freq change due to CHANCE, affects SMALLER pops more than larger pops by chance, alleles may be lost from pop --> fixation of particular genotypes in pop GENETIC DRIFT REDUCES GENETIC VARIABILITY genetic drifts are WEAKEST in LARGE pops and STRONGEST in small pops

Answer 175

genetic drift often results from pops passing through a pop bottle neck greater than or equal to consecutive gens when pop size contracts, caused by decrease food supply and increased predation decrease pop size during bottleneck and increase genetic drift, also increases inbreeding

Answer 176

random sampling of original pop to create a new pop founder effect is an example of a pop bottleneck colonists from the mainland colonize an island --> island gene pool is not as variable as the mainland's ex: Amish

Answer 177

H-W assumes no mutation, but mutations do occur mutations produce genetic variation needed for evolution mutation alone is NOT A POWERFUL evolunationary force

Answer 178

MUTATION AND SELECTION TOGETHER make a VERY POWERFUL evolutionary force genotypes (from mutation and recombo) that exhibit differential survival and reproduction = selection - sexual selection selects for traits that improve mating success - natural selection selects for traits advantageous for survival natural selection = survival of the fittest

Answer 179

allele freq CHANGE OVER TIME when diff genotypes have different fitness (pop will evolve) dynamics differ, depending on whether favored allele is dom or recessive - if dom allele is favored = rises SHARPLY, hits plateau, slowly approaches fixation (AA=Aa) --> the unfavored recessive will mostly be in heterozygotes where it is HIDDEN FROM SELECTION, difficult to purge unfavored recessive allele completely - if recessive allele favored = rises SLOWLY at first, aa initially rare (Aa now unfavored, A allele purged from pop)

Answer 180

1. deleterious recessive allele can hide in heretozygote genotype 2. there may be heterozygote advantage 3. freq-dependent selection balanced polymorphism/hterezygote superiority = fitness of heretozygote is greater than that of either homozygotes (when there is heterozygote superiority, neither allele can be eliminated by selection) ex: sickle cell disease with HbS allele

Answer 181

freq-dependent selection occurs when rare alleles have a selective advantage because they are RARE

Answer 182

CCR5 allele = coreceptor for HIV some indvs who are resistant to HIV have CCR5 mutaiton ex: CCR5 delta 32 (frameshift mutation) that introduces a premature stop codon into CCR5 receptor gene, resulting in nonfunctional receptor homozygotes = immune you can get WT-WT, WT-delta 32 dimers that are nonfunctional, and heterozygotes that are once infected = more treatable may increase morbidity

Answer 183

HIGH HIV infection rate and HIGH initial allele freq of 20% in human pop with HIGH HIV INFECTION RATE and high. freq of delta 32 allele = delta 32 can spread rapidly (graph will increase freq)

Answer 184

in areas with LOW HIV infection rates, but HIGH levels of delta-32 --> selection is TOO WEAK to raise delta 32 freq much (graph remains at same freq)

Answer 185

in sub-Saharan African, HIV infection rate is about 25% but delta 32 allele is almost ABSENT under these conditions, delta 32 freq will hardly change

Answer 186

natural selection process that removes harmful genetic variations from a pop

genetics exam 4 Flashcards

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