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evolution > envs lecture 5 > Flashcards

envs lecture 5 Flashcards

1
Q

what provides material that selection acts on

A

mutation and variation

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2
Q

what would happen without variation in phenotype

A

nothing for natural selection to act on

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3
Q

what provides new variation

A

mutation

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4
Q

chromosome

A

strings of DNA bases bound together by proteins

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5
Q

what is main structure in machinery of inheritance

A

chromosomes

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6
Q

what are proteins in chromosomes

A

histones

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7
Q

do all species have same number of chromosomes

A

no

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8
Q

locus

A

position on a chromosome

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9
Q

gene

A

physical unit of heredity

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10
Q

what is gene composed of

A

DNA

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11
Q

what is gene the code for

A

proteins and RNAs

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12
Q

what is gene used interchangeably with

A

locus

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13
Q

does a locus always code for protein

A

not always

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14
Q

is locus always part of a gene

A

not always

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15
Q

codons

A

sets of 3 DNA bases that are translated to AAs in protein-coding genes

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16
Q

synonymous codon/mutation

A

doesn’t change amino acid and thus protein

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17
Q

non-synonymous codon/mutation

A

changes amino acid, can cause sickle cell anemia etc.

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18
Q

allele

A

alternative forms of a gene

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19
Q

homozygotes

A

carry exact same form on both chromosomes

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20
Q

how many alleles for a given gene can an individual have

A

no more than two alleles

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21
Q

how many alleles for a given gene can a population have

A

many different alleles

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22
Q

what is genetic basis of variation in populations

A

population having many diff alleles for a given gene

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23
Q

central dogma

A

DNA –> RNA –> protein

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24
Q

what does dNA code for

A

codons

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25
Q

what are codons transcribed to

A

RNA

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26
Q

what is RNA translated to

A

proteins

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27
Q

SNP

A

single nucleotide polymorphism

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28
Q

what is SNP

A

single DNA base that defines alternative alleles at a locus

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29
Q

example of SNP

A

likeee 2 alleles of gene XYZ differ at a SNP at position 242

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30
Q

homologous chromosomes

A

pair of chromosomes

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31
Q

basically what is SNP

A

when a single base pair difference causes difference b/w two alleles

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32
Q

exon

A

segments of a gene that code for amino acids

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33
Q

introns

A

noncoding DNA segments in between exons

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34
Q

what is 1st step of protein synthesis

A

cell first transcribes DNA from genes into RNA (pre messenger RNA)

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35
Q

2nd step

A

pre mRNA is spliced, so parts of molecular are removed to form a mature mRNA

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36
Q

3rd step

A

mRNA translated into a string of AAs that make up a protein

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37
Q

what happens in genomes where this process happens

A

segments of gene that are spliced out b/c they don’t encode AAs are introns

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38
Q

what are regions that do encode for AAs

A

exons

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39
Q

purpose of introns?

A

variable, but we know they impact gene expression

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40
Q

how do introns impact gene expression

A

alternative splicing

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41
Q

alternative splicing

A

allows a single gene to encode for more than one protein

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42
Q

summary of chromosomes & machinery of inheritance

A

organisms have chromosomes, within which are found protein coding genes, which are composed of codons, which can be changed to form diff versions of the same gene called alleles

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43
Q

phneotype

A

observable characteristics of an organism

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44
Q

what does natural selection act on

A

phenotype

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45
Q

when does evolutionary change only occur

A

if phenotypes are heritable

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46
Q

genotype

A

unique genetic makeup of an organism

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47
Q

are genotype and phenotype completely linked

A

not necessarily; b/c phenotype can be influenced by environment as well as genetics

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48
Q

what happens if there’s no genetic variation and inheritance

A

no evolution

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49
Q

segregation

A

separation of alleles during meiosis so that each gamete carries only one allele for each locus

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50
Q

why is segregation important

A

all alleles have an equal change of being inherited in next gen

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51
Q

hardy weinberg equilibrium

A

HWE characterizes distributions of genotype frequencies in populations that are NOT EVOLVING

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52
Q

what happens if genotypic frequencies in the population we’re studying are not at HWE

A

we need to explain this pattern via one of many processes causing evolutionary change in populations

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53
Q

what does HWE provide

A

null model from which to understand process of genotypic & phenotypic evolution, based on what we expect due to chance alone

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54
Q

when a population is in HWE, what is needed for equilibrium to be reached

A

when segregation is the only factor that influences genotype frequencies

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55
Q

formula for genotype frequencies after one generation of random mating

A

p^2 + 2pq + q^2 = 1

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56
Q

what is p

A

frequency of homozygous genotypes (allele 1)

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57
Q

what is 2pq

A

frequency of heterozygous genotypes

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58
Q

what is q^2

A

frequency of homozygous genotypes (allele 2)

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59
Q

what is HWE

A

null model, reached under specific set of conditions

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60
Q

first HWE condition

A

mating is random

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61
Q

second HWE condition

A

population size is very large (inifinte)

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62
Q

3rd HWE condition

A

gene flow does not occur

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63
Q

4th HWE condition

A

mutation doesn’t occur [negligible anyway]

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64
Q

5th HWE condition

A

locus concerned is not under selection (no fitness difference b/w alleles)

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65
Q

why is this null model even useful

A

observed in natural populations; find it in nature when mating is random w/r to genotype at most loci in genome

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66
Q

so basically why is HWE interesting

A

deviations from HWE tell us that a locus is involved in an interesting evolutionary process

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67
Q

how to find frequency of A allele

A

add freq of homozygotes and half freq of heterozygote

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68
Q

a mechanism by which genetic variation is produced & inherited (i.e. evolution is allowed to occur)

A

recombination

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69
Q

recombination

A

occurs in meiosis & gamete production –> produces new genetic combos within a gamete

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70
Q

how does recombination occur

A

by independent assortment or crossing over

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71
Q

law of independent assortment / crossing over

A

the allele a gamete receives for one gene doesn’t influence the allele it gets for a different gene

72
Q

what does law of independent assortment produce

A

novel combos of alleles in gametes

73
Q

what two mechanisms can recombination occur through

A

independent assortment or crossing over

74
Q

what is crossing over

A

when homologous chromosomes swap segments of DNA

75
Q

what happens to loci in crossing over

A

loci on same chromosome can recombine by crossing over

76
Q

basically what is crossing over

A

process that involves genes linked on the same chromosome undergoing recombination

77
Q

what happens to chromosomes in meiosis

A

homologous chromosomes are aligned, crossing over occurs, exchanging pieces of the homologous chromosomes (which might be carrying different alleles)

78
Q

what does crossing over prodouce

A

both recombinant and non-recombinant chromatids

79
Q

what happens to recombinant ones

A

the ones resulted from exchanging pieces of chromosomes during crossing over

80
Q

what does process of crossing over do

A

produces new associations and combos of alleles in multiple genes on a given chromosome, thus increases genetic variation

81
Q

recombination & segregation

A

powerful tools that promote novel genetic combinations that can be inherited in future generations

82
Q

what do both recombination and segregation do

A

produce and promote novel genetic combos that are inherited by future generations

83
Q

recombination rate (r)

A

probability that recombination occurs between a given pair of loci

84
Q

what happens of two loci are on different chromosomes

A

r = 1/2

85
Q

if two loci are on the same chromosome

A

r < 1/2

86
Q

what happens of loci are on different chromosomes

A

50% chance that when an individual makes a gamete one of the chromosomes it carries will be from the mother and other from the father

87
Q

what happens of the loci are on the same chromosome

A

closer the loci are, smaller r

88
Q

what happens to loci right next to each other

A

r = 0

89
Q

linkage disequilibrium

A

alleles of multiple loci are found together more often than you would expect based on independent assortment

90
Q

another way to think about LD

A

allelic association

91
Q

what does LD suggest

A

different loci are physically linked on the same chromosome

92
Q

is LD actually the case

A

not necessarily (often isn’t)

93
Q

when does linkage disequilibrium occur

A

when recombination rate is low

94
Q

why does LD occur when recombination rate is low

A

b/c it acts to mix the association of alleles at different loci

95
Q

what happens to loci close together in linkage disequilibrium

A

loci closer together experience less recombination (lower r) and higher linkage

96
Q

what causes linkage disequilibrium

A

linkage disequilibrium can result from other processes besides physical proximity on a chromosome

97
Q

what else can cause LD

A

natural selection, genetic drift

98
Q

example of nat selection causing LD

A

epistasis

99
Q

epistasis

A

when the effect of an allele at one locus depends on the allele at a second locus

100
Q

when does selection promote linkage

A

when combos of alleles have high fitness

101
Q

example of LD in primrose

A

plants either have low anthers/high stigma or high anthers/low stigma; two traits are at linkage disequilibrium b/c specific combos have higher fitness

102
Q

gene mixing without inheritance

A

horizontal gene transfer (HGT)

103
Q

HGT

A

movement of DNA between individuals without sexual reproduction

104
Q

what is HGT common in

A

prokaryotes

105
Q

vertical gene transfer

A

how genetic variation is produced in sexually reproducing organisms

106
Q

why is HGT iimportatn

A

how antibiotic resistance is spread and transferred across bacteria

107
Q

bacterial transformation

A

spread of antibiotic resistance; donor cell releases DNA that is taken up by a recipient cell

108
Q

how is that variation ultimately produced

A

mutations

109
Q

mutation

A

ultimate source of genetic variation in all organisms

110
Q

what would happen w/o mutations

A

no variation, no evolution

111
Q

types of mutations

A

point mutation, structural mutation

112
Q

point mutation

A

single base pair mutation

113
Q

structural mutation

A

insertions/deletions (single to multiple bases), inversion (DNA segment), fusion/fission (chromosomes), whole genome amplification (all DNA in genome)

114
Q

what are point mutation

A

single nucleotide changes

115
Q

what can point mutations be

A

synonymous, nonsynonymous, can cause stop codon

116
Q

what do stop codons produce

A

pseudogenes (nonfunctional)

117
Q

ice fish

A

colorless blood b/c it lacks hemoglobin; either genes are deleted or rendered nonfunctional (point mutation) (pseudogenes)

118
Q

what are most mutations at 3rd codon position

A

synonymous

119
Q

what are all mutations at 2nd position

A

non-synonymous

120
Q

what is synonymous

A

don’t change AAs

121
Q

what are nonsynonymous

A

change AAs

122
Q

types of chromosomal mutation

A

deletion, duplication, inversion, fission, fusion,

123
Q

deletion

A

DNA segment is removed

124
Q

duplication

A

DNA segment is copied and inserted in the genome/chromosome

125
Q

inversion

A

chromosome segment is reversed

126
Q

fission

A

one chromosome breaks into two

127
Q

fusion

A

two chromosomes become 1

128
Q

what do fission/fusion do

A

alter number of chromosomes in the genome

129
Q

what is whole genome duplication

A

occurs when meiosis produces gametes that carry a diploid genome which then undergo fertilization

130
Q

which organisms have whole genome duplications?

A

common in plants; occurred deep in evolutionary history of many plant lineages

131
Q

whole genome duplication is important source of what

A

evolutionary novelty

132
Q

what does double the genes mean (WGD)

A

opportunity for new functions to evolve

133
Q

why is WGD important source of evolutionary novelty

A

b/c having double the number of genes provides opportunity for new functions to evolve

134
Q

is DNA replication accurate

A

extremely

135
Q

what do mistakes in DNA replication lead to

A

mutations

136
Q

how much of DNA bases are a mutant in humans

A

1 out of every 10^8 (100 million) bases

137
Q

given 3 billion base pairs, each gamete has how many mutations

A

approximately 30 mutations

138
Q

is mutation rate variable among tree of life

A

yeah

139
Q

who has more mutation rates

A

parasites and viruses have higher mutation rates than hosts

140
Q

why might it be advantageous to have high mutation rates

A

produces novel variation, allows them to evolve and keep evading hosts

141
Q

fitness

A

number of offspring an organism produces

142
Q

beneficial mutations

A

increase fitness

143
Q

are beneficial mutations rare or common

A

rare

144
Q

what are beneficial mutations acted on

A

acted on by natural selection

145
Q

what are deleterious mutations

A

decrease fitness

146
Q

are deleterious mutations rare or common

A

more common

147
Q

are deleterious mutations acted on or selected against

A

selected against

148
Q

pleiotropy

A

occurs when single mutation affects multiple traits

149
Q

what is currency of natural selection

A

fitness

150
Q

what do most genetic changes likely have

A

pleiotropic effects (side effects)

151
Q

do synonymous mutations have an effect on fitness

A

not really; almost no effect

152
Q

what do majority of mutations have

A

negative effects; deleterious

153
Q

are beneficial mutations common or rare

A

rare; very few mutations are beneficial

154
Q

germ line mutations

A

mutation in gamete (germ cell –> egg or sperm)

155
Q

are germ line mutations inherited

A

yes

156
Q

what are germ cells

A

egg or sperm

157
Q

what is gamete

A

germ cell; egg or sperm

158
Q

are somatic mutations inherited

A

no

159
Q

who does somatic mutations effect

A

the bearer

160
Q

somatic cell

A

body cell

161
Q

is mutation random

A

yes and no

162
Q

how is mutation not random

A

not random because certain types of mutations are favored

163
Q

what types of mutations are favored

A

transitions are more common than transversions, even though there are twice as many transversion mutations

164
Q

transitions

A

mutations between A and G or C and T (purine to purine, pyrimidine to pyrimidine)

165
Q

transversions

A

all other mutations

166
Q

how is mutation random

A

fitness effects of mutations are truly random

167
Q

how is fitness effects of mutations truly random

A

organism isn’t more likely to evolve beneficial mutations b/c of a strong selective pressure (but selection will act if a mutation is beneficial)

168
Q

when will selection act

A

if mutation is beneficial

169
Q

HOWEVER; what’s up w/ mutational hotspots

A

mutational hotspots may make adaptation more likely if a mutational hotspot lies within a locus w/ important function

170
Q

non genetic inheritence

A

epigenetics

171
Q

epigenetics

A

study of changes in expression of genes

172
Q

what is non genetic inheritance

A

form of inheritance that does not require changes to DNA

173
Q

what is expression

A

transcription of DNA into RNA; first step of formation of protein

174
Q

what can prevent genes from being expresed

A

methylation and histone modification of DNA

175
Q

can these methylation and histone modifications be inherited

A

yeah

176
Q

are these non genetic inheritance long term??

A

not rlly for long term evolutionary chage

evolution (11 decks)

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