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Genetics Exam 3 > exam 3 question pool > Flashcards

exam 3 question pool Flashcards

(85 cards)

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1
Q

what are viruses composed of?
most plant and animal viruses have __ genes and viruses that infect bacteria have ___ genes

A

solely DNA or RNA in protein coat

> 10 genes
10-100

HIV–> 9

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2
Q

difference between lytic and lysogenic lifestyle?
cells carrying a prophage are resistant to ?

A

lytic– replication then kill host

lysogenic— integrated into host genome (prophage), replicated, sits dormant can become active

infection by same phage genotype

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3
Q

what is generalized transduction?

A

virus shatters host cells genomes during lytic life cycle

accidentally packed into host DNA instead of viral DNA

movement of 2 genes by same virus

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4
Q

what is specialized transduction?

A

DNA from same region of genome is always taken from the host & put into the next host cell

-lambda phage is example

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5
Q

what is transformation vs transduction?

A

take up of DNA from environment

via phage

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6
Q

how would we culture bacteria in a lab?
what shows on plate & in liquid?

A

mix bacteria + phage, grow, wait for phage to lyse bacteria

plate: bacteria forms lawn, lysed cells form plaques

liquid: bacteria is cloudy, lysis is clear

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7
Q

what is high and low MOI?

A

low MOI <1 phage per cell–> good to assess geno + phenotype

high MOI > 2 phage per cell–> used for complementation, recombination

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8
Q

what is cotransduction?

A

depends on distance between 2 genes

higher frequency for those that are closer together

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9
Q

what happens in complementation if mutant is in same vs different genes?

A

same— F1’s of 2 mutants will be mutant

different genes– 2 mutants will give a normal F1 (complement)

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10
Q

what is the difference between complementation & recombination test?

A

comp: infect at high MO1

recombination:
infect at high MOI for recombination
infect at low MO1–> get geno & phenotype

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11
Q

on a bell shaped curve, when it becomes more normal…..
what is phenotypic variance?

A

less observances deviate from the mean

extend of how individuals deviate from the mean

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12
Q

what are components of Vp?

A

Vp= Vg + Ve

phenotypic varience= variance in genes + variance in environment

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13
Q

what happens when you have 2 true breeding parents?
what about when F1’s cross?

A

Vg=0, only environmental factors work on it–> will have slim peak

3:1 ratio, both Vg and Ve affect–> wide peak, less normal

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14
Q

how to get Vg when dealing with F1 and F2?
how to get heritability?

A

Vg= VpF2 - VpF1

VpF2–> Vg +Ve
VpF1–> Ve

Vg/Vp

if H2 is 0–> parent height has no influence on Childs height

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15
Q

what happens to the mean with a highly vs low heritable trait?

A

high–> mean changes ALOT per generation

low–> mean does not change

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16
Q

how do you identify QTL?
then how do you map it?

A

shows the least of amount of recombination– so less heterozygotes & less frequency of recombination

AND has greatest amount of variation between means of different extremes

recombinant/ total X 100

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17
Q

what are HWE assumptions?

A

infinity large population

no over lapping generations–> complete turnover of genotype at each generations

random mating! (sexual selection is violation)

NO mutation, NO migration, NO selection

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18
Q

for alleles in low frequency, what form are they often found in?

A

heterozygotes

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19
Q

how does HWE work for X linked traits??

A

males :
P + q

females:
P2
2pq
q2

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20
Q

how does migration affect HWE?
how to restore?

A

this will alter allele frequencies OF BOTH populations

— A source of gene flow

after random mating, will restore HWE back

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21
Q

what does inbreeding and assortive mating do to HWE?

A

violates random mating

assortive mating is when mate choice is not random
- impact depends on details of selective mating
- ALTERS allele/ genotype frequencies

inbreeding causes likelihood of more homozygotes
- decrease Aa
-increase AA or aa
- no overall change in allele frequency

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22
Q

what does mutation cause?
mutations can be?

A

halotypes–> collection of mutations on single chromosome

advantageous, deleterious, no effect

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23
Q

what is directional selection?

A

pushes population toward HOMOzygousity

-decreases variation within population, increases differences AMONGST populations

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24
Q

what is balancing selection?
what is over and under dominance?

A

for genes that show complete dominance

– over: heter zygote more fit
- under: homozygot morę fit

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25
what is stabilizing selection?
when natural selection acts to remove deleterious mutantion
26
what do changing allele frequencies occur due to?
random genetic drift
27
what does selection vs random genetic drift do? what is random genetic drift essential for?
selection--increase fitness drift-- alter allele frequencies so it moves away from adaptive peak can lead to phenotypes that selection alone can't
28
source of phenotypic and genetic variation?
genetic + environmental factors --recombination + mutation
29
what is evolution?
change in allele frequencies over time--> populations evolve not individuals
30
what is fitness and selection coefficient?
favored fitness =1 non >1 selection coefficient: 1- fitness
31
what makes evolution inevitable?
mutation, genetic inheritance, differential survival
32
what is the founder effect? allele frequencies will ___ from original population, changes are due to ____?
type of genetic drift-- where small population is established from larger population differ, chance
33
what is a bottleneck?
large populations is reduced by catastrophic event --founder effect is a bottle neck! -- allele frequencies in new population will differ from original population
34
what is molecular evolution?
DNA comparisons with & between specific to help with evolution -phylogenitic trees depict this
35
different proteins have different __?
evolutionary constraints
36
what are synonyms (silent) and non synonymous (replacement) substitutions
silent: change in 3rd base does not change the code sequence -- hidden to selection, higher mutation rate replacement: change in base 1 or 2, which changes the aa -- selection occurs
37
how to test for evidence of selection ? when is it pos or negative selection????
dn (non syn)/synonymous ds null: ratio between species=ratio changes w/in species pos: between species> w/in species neg: between species
38
what composes the backbone of DNA?
deoxyribose phosphate group on 5 carbon
39
what part of DNA has the genetic sequence? what kinds of N bases are there? where does the base attach on the DNA backbone?
the nitrogenous base purines: A and G--> 2 rings prymidines: T and C--> 1 ring 1 prime carbon
40
how many H bonds between A/T and G/C?
A/T--> 2 H bonds G/C has 3 H bonds
41
what coil is DNA, how long is one turn, and how far are the bases separated by, how many base pairs per turn??
R coil 34å 3.4å 10
42
where do DNA binding proteins bind?? and non sequence specific?? how long is human DNA?
major groove bind backbond-- minor groove 1.9m
43
what are indirect & direction impacts of DNA??
indirect: genetic code, gene expression, developement direct: molecular nature, replication, mutation
44
what is the purpose of supercoiling? difference between backward and forward coiling????
for DNA replication, could hinder it Organization of dna Compaction Can regulate gene expression Helps with replication & transcription back: helix opening facilitated forward: helix opening hindered ** when there is a protein**
45
what are essential features of DNA??
sufficient information capacity, ability to replicate, ability to mutate
46
how does DNA replication initiate? and what kind of replication does it follow????
---separation at AT rich region by DNA helicase --semi conservative!!! leading strand always goes towards the replication fork
47
what catalyzes DNA synthesis???? what does it need?
DNA pol 3--> a 5-- 3 polymerase dNTP but must be tri phosphate -DNA template -primase to produce a 3 OH primer to extend off of
48
how do we complete the lagging strand??
DNA pol 1 must remove the primer via 5-3 exonuclease activity 5-3 polymerase fills the gap ligase seals the gap
49
what is the difference between DNA pol 1,2, 3?
1: primer removal mostly 5-3 DNA dep DNA pol 3--5 exonuclease activity 5--3 exonuclease activity--- primer removal 2: usually DNA repair 5-3 DNA dep DNA pol 3--5 exonuclease activity -- proofread 3: DNA synthesis usually 5--3 DNA dep DNA pol 3--5 exonuclease activity
50
what are needed at the replicsome??
DNA pol 1 DNA pol 3 helicase topiosomease ligase primase, RNA primer
51
what happens at the end of replication to the lagging strand?????
removal or RNA primer, DNA gets shorter at the ends
52
what is a telomere & telomerase?
ends of eukaryotic chromosome telomerase: elongates the ends of lagging strand chromosomes - RNA dependent DNA polymerase (RT) uses RNA as a template
53
what are the three steps of telomere elongation?
1:telomerase--- lagging strand template elongation (RT) on the 5--3 end, needs free OH 2:DNA pol 3 for Okazaki fragment synthesis 3: primer removal by DNA pol 1, ligase fills the gaps
54
in what cell types does telomerase have a high & low rate of proliferation??
high: germ, stem, cancer cells low: somatic cells
55
what is the migration equation?
qi=(1-m)qi+mqm qi= allele freq of inhabitants m=percent of individuals contribute to next generation qm=allele frequency of migrants
56
what happens at the end of 3' ends?? what sequence are at the ends???
primers are removed, and cannot be filled, so telomerase comes in and uses RNA template to make 3' end longer, so that the lagging strand can use it as a template to make the ends longer G rich
57
what is gel electrophoresis? what does it separate it based on?? what kind of gel?
departing protein or nucleic acids molecules from another using electrical field --charge, shape, size - agarose
58
what charge does DNA hold?? what chemical tag is put on it??
negative small molecules will travel far, large molecules will not EtBr, binds to sugar phosphate backbone
59
what are the steps of PCR??
denature at 95 anneal the primers on primer extension-- 72, using tax polymerase
59
what is needed for PCR?? each cycle ___ the number of copies in the DNA?
dsDNA with the target sequence nucleotides heat stable DNA pol 2 difference ss DNA primers-- that fit the sequence of the known target - doubles
60
how are PCR products separated??
gel electrophesis separates by their sizes
61
what does ddNTP reaction mixture contain??
DNA stand ss DNA primer DNA pol large Amt of dNTP small amount of ONE ddNTP
62
what are restriction enzymes?? how do restriction enzyme systems work in bacteria?
cut DNA at specific sequences, they restrict the growth of bacteriophages -add methyl group & prevent digestion from restriction enzymes --EcoRI
63
how does molecular cloning work??
have DNA of interesting, digest it with restriction enzymes Eco Ri and Bam HI add the plasmid combine via ligation to put our DNA into our plasmid
64
what does a DNA library contain ?
genomic DNA of organism and those derived from mRNA (complementary DNA libraries)
65
how are recombinant proteins expressed in bacterial cells, what are the components??
promoter protein coding sequence epitope tag helper sequence
66
how does northern blot work?? what is it used for?? what does probing do & what is it??
--RNA length and quantity -separate rRNA on gel - transfer to membrane -hybridize it with a probe --complementary to RNA of interesting binds to RNA via base pairing radioactive, so indicates presence & quantity of RNA
67
what are the 2 controls in northern blot??
EtBr shows staining in the loading control actin is the loading control, will show up if it is viable
68
what is western blot?? how does the antibody work?
shows protein size and quantity -separate protein on gel - transfer to membrane - probe with antibody -antibody binds the protein of interest, which is detect by the secondary antibody -label will indicate presence or quantity
69
what is extending in PCR???? what is pCr? issues?
amplifies DNA of interest, 25-35 cycles, to get full DNA w no over hang primes are extended need template, small length, need to know sequence of flank regions
70
how do you create primers in PCR? sanger sequencing?
top primer is IDENTCAL to coding strand bottom strand is complementary to bottom strand & same as non coding strand --need 2 primers--- -primer is identical to top strand, start on 5' end, near the area where we want to find out
71
how does RT- PCR work??
has mRNA, then we RT to get CDNA==mRNA/cDNA hybrid -Rnase degrades mRNA strand of cDNA is used to make other strand of DNA --then amplify via PCR --quantify via real time PCR
72
what is real time PCR?? how are results interpreted?
- real-time PCR monitors the amplification process in real time using fluorescent dyes or probes if it peaks fast, then there is high RNA concentration peaks late, low RNA concentration
73
what is Sanger sequincing?
The DNA of interest is amplified (e.g., using PCR) if needed. Denaturation: The double-stranded DNA is denatured into single strands, only NEEDS one primer Primer Annealing: A short DNA primer binds to the template strand DNA Synthesis with Chain Termination: DNA polymerase extends the strand using normal deoxynucleotides (dNTPs). Special dideoxynucleotides (ddNTPs) are randomly incorporated, terminating the chain because they lack a 3’-OH group required for further extension. It is a widely used for precise nucleotide sequence of DNA-- DETERMINE DNA -only need 1 primer
74
what are benefits & downfalls the RNA seq?
adv: know RNA accumulation for ALL genes analyzing transcription & RNA processing dis: need genome less abundant RNA hard to study over interpreted as measure of gene expression
75
how does HTS work?
get the RNA or DNA of interest generate a libraries of molecules which then will bind to the target sequence then those sequences will match will the reference in the genome
76
what is ChIP sequencing ? advantages vs dis?
studies protin/DNA interactions adv: find all biding sites of a protein can find postranslation protein modifications dis: need antibody towards protein of interest good negative control limited resolution
77
what is metagenomics?
take sample from environment purify DNA generate library sequence identity species in the sample
78
how does RNA sequence work?
RNA from tissue sequence map to genome then RNA will accumulate in certain genes
79
HTS adv vs diasadv?
adv: find mutation cause phenotype find mutation associate with disease determine best target treatment sequence new genome dis: hard w/o reference genome hard on repeat sequences difficult bioinformatics require
80
what molecules are least likely to contain genomic info?
lipids
82
Polymerase alpha and beta used for??
Alpha for imitation Beta for excision & repair
83
Southern blot??
Same things as northern blot but for DNA
84
The Hershey-Chase experiment used bacteriophages grown on media with radioactive sulphur or radioactive phosphorus. It allowed correlating the transfer of genetic material with the transfer of particular chemical molecules. What was the conclusion of this experiment?
A. It determined that DNA but not proteins is the genetic material
85
Which classes of RNA are transcribed by each eukaryotic RNA polymerase?
RNA Pol I – rRNA; RNA Pol II – mRNA; RNA Pol III – tRNA

Genetics Exam 3 (11 decks)

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