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BIO 375 - Genetics > Exam "4": Translation, Control of Gene Expression, Population Genetics (Bio 375 - Genetics) > Flashcards

Exam "4": Translation, Control of Gene Expression, Population Genetics (Bio 375 - Genetics) Flashcards

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1
Q

amino acid components

A

carboxyl group, amino group, and R group

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2
Q

identity of amino acid is determined by

A

the R group attached to the alpha carbon

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3
Q

in H2O (physiological conditions), the true form of amino acid is

A

charged, with the amino group bearing a positive charge (+NH3) and the carboxyl group bearing a negative charge (COO-)

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4
Q

primary protein structure

A

sequence of amino acids

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5
Q

secondary protein structure

A

folded/twisted polypeptide chain (beta pleated sheet and alpha helix)

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6
Q

tertiary protein structure

A

secondary structure folded further

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7
Q

quaternary protein structure

A

2+ polypeptide chains associated

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8
Q

polypeptides

A

amino acids are joined to each other via peptide bonds formed via dehydration synthesis

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9
Q

dehydration synthesis

A

combining two compounds through removal of water molecules– forms peptide bonds between amino acids, phosphodiester bonds between nucleic acids

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10
Q

hydrolysis

A

breaking of bonds through addition of water

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11
Q

tRNA

A

serves as translating molecule between nucleic acids and amino acids… has characteristic structure with an anticodon and amino acid attachment site

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12
Q

codon

A

found in the mRNA, combinations of three nucleotides – there are 61 “sense” trinucleotide sequences that code for amino acids and 3 “nonsense” trinucleotide sequences that are stop codons

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13
Q

ribosomes read nucleotides of mRNA

A

in groups of three (codons) from 5’ -> 3’

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14
Q

AUG- Met

A

“start” codon when at the beginning of mRNA, but when later in mRNA sequence codes for the amino acid Methionine

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15
Q

sense codons

A

61 codons that code for amino acids

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16
Q

nonsense codons

A

3 stop codons (UAA, UAG, UGA)

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17
Q

degenerate code

A

amino acids may be specified by more than one codon

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18
Q

synonymous codons

A

codons that specify the same amino acid

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19
Q

isoaccepting tRNAs

A

tRNAs that accept the same amino acid but have different anticodons

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20
Q

wobble position

A

third position of codon base pairs weakly with anticodon, where nonconventional base pairing is permitted…. allows the last position of the anticodon to pair weakly with the codon

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21
Q

tRNAs can recognize

A

1-3 different codons

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22
Q

I (inosine)

A

a nitrogenous base only found in tRNA; can base pair with A, U, or C (due to wobble position)

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23
Q

reading frame

A

way in which the codon sequence of a mRNA is read… codons are nonoverlapping so each nucleotide is part of a single codon… is set by position of initiation codon

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24
Q

initiation codon

A

first codon of mRNA to specify an amino acid… usually the first AUG in mRNA – which is N-formylmethionine (modified methionine inserted on “start” AUG) and is removed post translationally

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25
Q

prokaryotic translation

A

takes place in ribosome… ribosome attaches to 5’ end of mRNA and proceeds 3’ down the chain… polypeptide is synthesized starting at amino end (N -> C), with elongation continuing by adding amino acids to carboxyl end

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26
Q

translation stages

A
  1. tRNA loading/charging… 2. initiation… 3. elongation… 4. termination… [with steps 2-4 involving the ribosome]
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27
Q

translation step 1. tRNA loading

A

tRNA molecules must be loaded with correct amino acid (each tRNA is specific for a certain amino acid)– amino acids are loaded onto 3’ end of the tRNA molecule as specified by enzyme aminoacyl-tRNA synthetases

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28
Q

aminoacyl-tRNA synthetase

A

enzymes that facilitate specificity between amino acid and tRNA… there is one of these enzymes for each of the 20 amino acids… each enzyme recognizes one amino acid and their respective tRNA

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29
Q

amino acids are recognized by

A

their different shapes

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30
Q

tRNAs are recognized by

A

their differing sequences (base pairing sequences)

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31
Q

translation step 2. initiation

A

a) IF-3 … b) mRNA binds to 30S … c) IF-2 … d) IF-1

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32
Q

IF-3

A

1st step of initiation – prevents subunit from joining to one another

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33
Q

mRNA binds to 30S

A

2nd step of initiation – using Shine-Dalgarno (consensus sequence found directly upstream of true start codon) and 16S rRNA

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34
Q

IF-2

A

3rd step of initiation – allows initiator tRNA with N-fMet to bind to start codon

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35
Q

IF-1

A

4th step of initiation – allows large subunit to bind to small subunit, securing initiator tRNA in P site

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36
Q

translation step 3. elongation

A

a) EF-Tu-GTP … b) EF-Ts … c) Peptidyl transferase … d) EF-G-GTP

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37
Q

EF-Tu-GTP

A

1st step of elongation – escorts the next tRNA into A site… only permits correct tRNA to be placed into A site… (proofreading enzyme, then after fulfilling proofreading, GTP -> GDP)

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38
Q

EF-Ts

A

2nd step of elongation – recycles EF-Tu-GDP to EF-Tu-GTP (GDP -> GTP)

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39
Q

peptidyl transferase

A

3rd step of elongation – polypeptide on P site tRNA is transferred to amino acid on A site tRNA, catalyzed by large subunit rRNA

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40
Q

EF-G-GTP

A

4th step of elongation – “translocation”… pushes ribosome one codon down mRNA 5’ -> 3’… the tRNA that occupied A site is now in P site (empty tRNA had been moved to E site -> discarded), so A site is available to receive new tRNA (aminoacyl tRNA)

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41
Q

IF

A

initiation factor

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42
Q

EF

A

elongation factor

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43
Q

polypeptide is formed

A

N -> C direction

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44
Q

translation step 4. elongation

A

a) stop codon moves into A site … b) release factors (RF1/RF2, RF3) bind to stop codon and ribosome … c) release factors promote cleavage of polypeptide from tRNA in P site … d) GTP is hydrolyzed to GDP by RF3 and promotes: release of empty tRNA, release of mRNA, and dissociation of ribosomal subunits

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45
Q

prokaryotic ribosome

A

two subunits: 50S and 30S (large and small)… contains three sites that can be occupied by tRNAs (exit stage (E), peptidyl site (P), aminoacyl site (A))

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46
Q

exit site (E)

A

where empty tRNA leaves

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47
Q

peptidyl site (P)

A

where peptide chain grows from tRNA connection

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48
Q

aminoacyl site (A)

A

where tRNAs (charged tRNAs – aminoacyl tRNAs) come into ribosome

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49
Q

eukaryotic translation differences

A

ribosomal subunit sizes (40S and 60S in eukaryotes)… initiation: no Shine-Dalgarno sequence, 5’ cap recognized by small subunit and cap-binding proteins, poly-A tail binds to initiation complex via tail-binding proteins, and more initiation factors involved

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50
Q

control of gene expression

A

regulation of chromatin structure, transcription, mRNA processing, mRNA stability, translation, and posttranslational modification

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51
Q

prokaryotic gene regulation

A

genes with related function are clustered together under the control of a single promoter…. all genes are transcribed into one polycistronic mRNA

52
Q

polycistronic mRNA

A

single mRNA molecule with multiple genes

53
Q

operon

A

group of bacterial structural genes transcribed together… contains a promoter and operator

54
Q

operon components

A

structural genes, regulator gene, operator

55
Q

structural genes

A

multiple genes transcribed into one mRNA; under control of one promoter… encode proteins that are used in metabolism or biosynthesis or that play a structural role in cell

56
Q

regulator gene

A

technically not considered part of operon as it is under control of separate promoter… transcribed and translated into regulator protein and influences transcription of structural genes… genes whose products (either RNA or proteins) interact with other DNA sequences and affect transcription/translation of those sequences

57
Q

regulator protein

A

have domains (each with characteristic structure called a “motif”) that are responsible to binding to DNA… binds to operator

58
Q

operator

A

bound by regulator protein… often overlaps 3’ end of promoter and 5’ end of structural genes

59
Q

binding of operator by regulator protein

A

inhibits binding of RNA polymerase to promoter, and thus preventing transcription

60
Q

regulatory elements

A

affect expression of sequences to which they are physically linked

61
Q

positive control

A

process that stimulate gene expression… regulator protein is an activator that stimulates transcription

62
Q

negative control

A

processes that inhibit gene expression… regulator protein is a repressor that inhibits transcription

63
Q

lac operon

A

first operon to be investigated in great detail, researched by Jacob and Monod in 1961

64
Q

lactose

A

major carbohydrate found in milk… can be metabolized by E.coli in mammalian gut

65
Q

lactose metabolic steps

A
  1. transported across cell membrane by permease… 2. converted into allolactose, galactose, and glucose by beta-galactosidase
66
Q

lac operon components

A

structural genes: lacZ (beta-galactosidase), lacY (permease), lacA (transacetylase)… regulator gene: lacI… promoter: lacP… operator: lacO

67
Q

coordinate induction

A

simultaneous synthesis of several proteins, stimulated by the inducer molecule

68
Q

negative inducible operon

A

regulator protein is a repressor .. transcription is by default off (inhibited) and must be turned on (induced)

69
Q

lac operon (negative inducible)

A

regulator protein is a repressor (negative operon)–> repressor binds to operator and physically blocks binding of RNA polymerase –> transcription is by default off (inhibited) and must be turned on (induced) (inducible operon) –> an inducer (allolactose) binds to repressor and changes its shape to make it inactive… repressor is prevented from binding the operator so RNA polymerase is able to bind promoter and transcription can proceed

70
Q

allosteric protein

A

proteins that change shape upon binding to another molecule… such as an active regulator protein that changes shape after binding with an inducer

71
Q

repressible operon

A

transcription is normally on and must be turned off

72
Q

negative operon

A

regulator protein is a repressor

73
Q

inducible operon

A

transcription is normally off and must be turned on

74
Q

lac operon when lactose is absent

A
  1. active repressor binds to operator… 2. RNA polymerase cannot bind to promoter… 3. transcription prevented
75
Q

lac operon when lactose is present

A
  1. some lactose is converted into allolactose… 2. allolactose inactivates repressor… 3. repressor cannot bind operator… 4. RNA polymerase is able to bind to promoter… 5. structural genes are expressed… 6. lactose is metabolized
76
Q

lac paradox solution

A

basal level of transcription allows minimal production of permease and beta-galactosidase to allow lactose conversion into allolactose

77
Q

lac mutation

A

partial diploid: merozygote (normal haploid genome with plasmid containing an extra lac operon copy) / E.coli strain with an extra copy of lac operon while the remainder of genome is haploid

78
Q

constitutive

A

structural genes that encode essential cellular functions and are expressed continually… such as functional lac enzymes being produced whether lactose is present or not

79
Q

wild type lac operon

A

lacI+ lacP+ lacO+ lacZ+ lacY+ / lacI+ lacP+ lacO+ lacZ+ lacY+

[no beta-galactosidase and permease without allolactose… yes beta-galactosidase and permease with allolactose]

80
Q

lacI- mutation

A

repressor mutation, the repressor is inactive

81
Q

lacIs mutation

A

superrepressor mutation… prevents transcription even in presence of lactose because it has an altered inducer binding site, which means that the inducer can never bind to repressor to release the operator… dominant over I+

82
Q

lacOc mutation

A

operator mutation… repressor cannot bind to the operator so transcription will always occur with/without lactose (constitutive)… dominant over lacO+… only affects genes on same chromosome (cis acting)

83
Q

lacP- mutation

A

promoter mutation… RNA polymerase cannot bind promoter so transcription can never occur… is cis acting

84
Q

types of operons

A

negative inducible… negative repressible… positive inducible… positive repressible

85
Q

negative repressible operon

A

transcription is turned on by default and must be turned off… regulator protein is produced in an inactive form so it cannot bind operator and allows structural genes to be expressed… a corepressor binds to repressor to allosterically alter its shape to an active form… repressor can now bind to operator and halt transcription

86
Q

operon is turned off when needed

A

product U is present at high concentration… enzymatic pathway should be halted… enzymes G, H, and I are not produced

87
Q

positive inducible operon

A

regulator proteins are activators… transcription is off by default with the regulator protein initially produced in inactive form… with precursor present: precursor binds to regulator protein -> activates regulator protein -> regulator protein binds DNA but does not bind to operator -> transcription is activated -> structural genes are expressed

88
Q

positive repressible operon

A

transcription is on by default with regulator protein being produced in active form… if end product is present at high levels: end product binds to activator -> regulator protein is inactivated -> regulator protein does not bind DNA -> transcription is halted and structural genes are not expressed

89
Q

catabolite repression

A

when glucose is present then genes controlling the metabolism of other sugars are repressed…. results from positive (activator) control in response to absence of glucose (catabolite activator protein binds upstream of lac structural promoter in presence of cyclic AMP)… cAMP levels are high when glucose levels are low… works in concert with negative inducible control (cell is more responsible to changes in environment

90
Q

when glucose levels are low

A

cAMP levels are high -> cAMP binds CAP -> cAMP-CAP recruits RNA polymerase to promoter -> lac structural genes are expressed

91
Q

when glucose levels high

A

cAMP levels are low-> cAMP does not bind CAP -> unactivated CAP does not recruit RNA polymerase -> lac structural genes are expressed at a very low level

92
Q

population

A

group of interbreeding members of a single species

93
Q

gene pool

A

set of genetic information carried by the members of a sexually reproducing population

94
Q

allelic frequency

A

frequency of an allele in a gene pool… p= f(A) = 2nAA + nAa / 2N and q = f(a) = 2naa + nAa / 2N… divide by number of alleles in gene pool

95
Q

genotypic frequency

A

frequency of a genotype in a population… f(AA) = # AA individuals / N and f(Aa) = # Aa individuals / N and f(aa) = # aa individuals / N… divide by number of individuals

96
Q

hardy-weinberg law

A

if population is large (genetic drift); no natural selection; random mating (selection); no mutation; and no migration………… then 1. allelic frequencies in gene pool of a population will not change from one generation to the next AND 2. genotypic frequencies will stabilize after one generation of the previous condition to p^2, 2pq, and q^2

97
Q

Hardy-Weinberg equilibrium

A

p^2 + 2pq + q^2… p^2 = frequency of AA genotype, 2pq = frequency of Aa genotype, and q^2 = frequency of aa genotype… p = frequency of A allele and q = frequency of a allele

98
Q

Hardy-Weinberg Details

A

“large” population is any population that is not small… random mating implies that each genotype mates in proportion to its frequency… each H-W applies to one locus (assumptions must hold true for only the locus being studied… a population may be in equilibrium for some loci but not others)

99
Q

implications of Hardy-Weinberg

A
  1. population cannot “evolve” if it meets H-W assumptions– evolution requires changes in allelic frequency; random mating alone does not bring about changes in frequencies, so other factors must be present in order for a population to “evolve”… 2. when in H-W equilibrium, genotypic frequencies are determined by allelic frequencies– heterozygote frequency is greatest when allelic frequency is 0.5 (but never exceeds that frequency); when an allele is at low frequency, most alleles will be found in heterozygotes
100
Q

eugenics

A

the science of improving a human population by controlled breeding to increase the occurrence of desirable heritable characteristics… the breeding of humans to favor certain traits

101
Q

Using Hardy-Weinberg

A

used to estimate the frequency of alleles and genotypes in a population in genetic equilibrium

102
Q

extension of H-W: multiple alleles

A

allelic frequencies: f(A’) = p , f(A’’) = q , f(A’’’) = r … genotypic frequencies: p^2 = f(A’A’) , 2pq = f(A’A’’), , q^2 = f(A’‘A’’) , 2pr = f(A’A’’’) , 2qr = (A’‘A’’’) , r^2 = f(A’'’A’’’)

103
Q

extension of H-W: X-linked alleles

A

allelic frequencies: f(X’) = p , f(X’’) = q … genotypic frequencies: f(X’X’) = p^2 , f(X’X’’) = 2pq , f(X’‘X’’) = q^2 , f(X’Y) = p , f(X’‘Y) = q

104
Q

chi-square test with Hardy-Weinberg Equilibrium

A
  1. Ho and Ha (____ gene with ___ alleles is/is not in Hardy-Weinberg equilibrium for this population)… 2. calculate p and q (and r if applicable)… 3. calculate expected values (using appropriate frequency products, ie p^2, 2pq, q^2, etc)… 4. calculate chi-square… 5. compare to p-table values… 6. conclusion (there is between a ____ and ____ % that any differences between observed and expected values are due to random chance and ____ and ____ % that any differences between observed and expected values are due to some actual physical factor. the p-value is smaller/larger than the significant threshold of p = 0.05, so we reject/fail to reject the Ho and reject/fail to reject the Ha)
105
Q

selection

A

differential reproduction of genotypes based on fitness (relative reproductive success of an individual)… does not produce new alleles (but allows some alleles to be passed to descendants at a greater frequency)… does not act on individual genes (selects combinations of genes)…. types: Natural and Artificial

106
Q

natural selection

A

not human directed, environmentally controlled

107
Q

artificial selection

A

human directed/controlled

108
Q

selection and nonrandom mating

A

affects the probability that certain alleles combine to form genotypes– alters genotypic frequencies

109
Q

positive assortative mating

A

tendency for similar individuals to mate

110
Q

negative assortative mating

A

tendency for dissimilar individuals to mate

111
Q

inbreeding

A

preferential mating between related individuals (positive assortative mating for relatedness)… affects all genes… leads to departure from H-W equilibrium, increased proportion of homozygotes, decreased proportion of heterozygotes, and increased incidence of genetic diseases

112
Q

outbreeding

A

negative assortative mating for unrelatedness

113
Q

outcrossing

A

avoidance of mating between related individuals

114
Q

genetic rescue

A

introduction of new genetic variation into an inbred population

115
Q

identical by descent

A

two alleles of a homozygote are descended from same ancestral allele (inbreeding)

116
Q

identical by state

A

two alleles of a homozygote are identical in structure and function but are from two different copies in ancestors (outbreeding)

117
Q

inbreeding coefficient (F)

A

measure of probability that two alleles are identical by descent… varies from 0 to 1 (with 0 indicating random mating and 1 indicating that all alleles are identical by descent)… if F=1 then self-fertilization or cloning has occurred

118
Q

effect of inbreeding on H-W

A

increase in homozygotic frequencies– f(AA) = p^2 + Fpq ; f(aa) = q^2 + Fpq … decrease in heterozygote frequencies– f(Aa) = 2pq - 2Fpq

119
Q

inbreeding depression

A

increased appearance of lethal and deleterious phenotypes as a result of inbreeding… increased numbers of homozygotes will lead to a greater proportion of affected individuals… inbreeding is harmful to fitness of populations

120
Q

migration (aka gene flow)

A

movement of some individuals from one population to another, resulting in a change in allelic frequency

121
Q

calculating allelic frequencies after migration

A

q’II = qIm + qII(1-m) [where q’II = little allele frequency in mixed population ; qI = little allele frequency in population 1 (migrant population) ; m = fraction of mixed population that came from the migrant population ; qII = little allele frequency in population 2] OR p’II = pIm + pII(1-m) [where p’II = big allele frequency in mixed population ; pI = big allele frequency in population 1 (migrant population) ; m = fraction of mixed population that came from the migrant population ; pII = big allele frequency in population 2] …. Δq = m(qI-qII) is the change in little allele frequency OR Δp = m(pI-pII) is the change in big allele frequency

122
Q

effects of migration

A

prevents genetic divergence between populations (reduces differences in allele frequencies between populations and tends to make populations more alike)… increased genetic variation within populations (spreads new alleles between different populations)

123
Q

mutation

A

sudden heritable change in genetic material, resulting in some new alleles/genetic variants… usually detrimental and recessive in nature… types: nonrecurrent (tends to only occur once) or recurrent (can occur in future generations, nonreversible or reversible)… does not have a large effect on allele frequencies… mutated allele is maintained in gene pool once it is enriched in population due to selection… slow accumulation of mutations is what provides genetic variability

124
Q

genetic drift

A

when population size is limited– gametes that randomly unite to form individuals of next generation carry only a sample of alleles present in parental gene pool, so proportions in sampled gametes can differ from those of parental generation due to random chance… sampling effects can lead to deviations from expected frequencies (sampling error)… can predict only the magnitude of change because it is a dispersive process

125
Q

genetic drift effects

A

changes allelic frequencies within a population… reduces genetic variation within a population (may lead to fixation of an allele)… increases genetic diversity between populations

126
Q

effective population size (Ne)

A

population of individuals that contribute genes to next generation… number of breeding adults

127
Q

causes of genetic drift

A
  1. founder effects– establishment of an isolated population by a small number of individuals (genes carried by descendants are derived from few alleles from founders)… 2. genetic bottleneck– develops when a population undergoes a drastic reduction in size (descendants will be genetically similar because they have alleles that were carried by a few survivors of bottleneck)

BIO 375 - Genetics (8 decks)

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