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Genetics 380 > Genomes and Evolution > Flashcards

Genomes and Evolution Flashcards

1
Q

genomics

A

study of gene seq., mechanisms that regulate gene activity, interaction between genetic factors and btw. genetic and non-genetic factors, comparisons btwn species

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2
Q

genome

A

organism’s entire DNA/RNA; organisms’s entire collection of genes

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3
Q

genetic map

A

units are recombination frequency (Rf), centiMorgans (cM) or map units (m.u.); came first: only need to know seq. of 2 elements

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4
Q

physical maps

A

units are basepairs (bp) show distances btwn genes more clearly; made using enzymes to cut DNA into fragments inserting fragments into vectors and sequencing fragments; vectors bind certain set of PCR primers next to insertion site; overlapping clones = success

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5
Q

recombination frequency

A

diff in diff genders, ethnic groups, drug/chem. exposures; lower near centromere vs. telomere

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6
Q

sampling error

A

can cause genetic map to position genes improperly if the study had a small population

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7
Q

C Value Paradox

A

no relationship btwn genome size and organism complexity; more DNA does not mean more complex organism

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8
Q

C value

A

how much DNA that organism has in diploid cell

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9
Q

complex organism

A

protein diversity is key

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10
Q

eukaryotic genomes

A

contain genes and gene families

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11
Q

gene families

A

large duplications (segmental duplications) occurred during evolution w end result that some genes came from common ancestor but had time to diverge from each other through seq. changes that occurred after duplication

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12
Q

pseudogenes

A

mutation that renders some copies of gene families nonfunctional

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13
Q

homologs

A

gene related through evolution

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14
Q

orthologs

A

homologous genes found in two different species and evolved from common ancestor

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15
Q

paralogs

A

2 genes w/i single organism that are homologous and arose from duplication sometime in evolutionary past

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16
Q

globin gene family

A

carry oxygen

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17
Q

unique sequences

A

found only once in the genome; 30-75% of genome; protein coding genes or regulatory sequences (miRNAs other regulatory RNAs)

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18
Q

highly repetitive DNA

A

repeated sequences range from 5-300 bp; 5-45% of genome; up to 10,000 copies per genome; often found in heterochromatin at centromeres and telomeres

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19
Q

moderately repetitive DNA

A

150-300 bp; 1-30% of genome; 10-1000 copies per genome; genes for histone protein, some rRNA and some tRNAs

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20
Q

tandemly repeated sequences

A

back to back repeats w no intervening sequences

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21
Q

interspersed repeat sequences

A

scattered throughout the genome often due to action of transposable elements

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22
Q

short interspersed elements (SINEs)

A

approx. 200-300 bp; most common = Alu repeat (200-300 bp, several million copies per genome)

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23
Q

long interspersed elements (LINEs)

A

several thousand bp

24
Q

polymorphic

A

human DNA seq. is highly polymorphic; for any gene there are many diff specific versions of that gene’s seq. in the population

25
Q

allele

A

each different version of the gene’s sequence

26
Q

isoform

A

version of protein that has higher or lower level of activity than isoform made by most other people; made by alleles of a gene

27
Q

single nucleotide polymorphisms (SNPs)

A

single nucleotide position where some people have A, some C, some G, some T in that spot

28
Q

haplotype

A

SNPs that lie close together and are often transmitted together from parent to child

29
Q

insertion/deletion (I/D) polymorphisms

A

some people have certain stretch of bases and some do not

30
Q

copy number variations (CNVs)

A

some people have deletions and duplications that give either one copy or more than two copies of certain sequences

31
Q

transposable elements (transposons)

A

move from one place to another w/i the same cell’s DNA; cut and paste/copy and paste

32
Q

hybridization studies

A

show seq. similarity btwn. species; (1) DNA from one species is labelled then digested (2) fragmented DNA is denatured mixed w denatured DNA of 2nd species and DNAs are allowed to reanneal: more similar 2 sequences are more labeled fragments will bind to unlabeled species’ DNA; temp at which 2x stranded frags melt reflects how similar seqs. are to each other in 2 diff. species’ DNA (high temp to melt = more similar)

33
Q

closest genetic ancestor to humans

A

chimps based on hybridization studies

34
Q

tracing human migrations

A

determine gene alleles present in ancient bone samples shows trace migration and intermingling

35
Q

history of human females

A

mitochondrial DNA doesn’t undergo recombination the way DNA does so its easier to trace lineages w it (only reflects history of women)

36
Q

molecular clock

A

difference in mitochondrial DNA seq. between two lineages to gauge time at which 2 lineages diverged from common ancestor

37
Q

mitochondrial eve

A

one mitochondrial genotype that served as common ancestor for all currently living humans (120,000-220,000 years ago)

38
Q

3 mains groups

A

Neanderthals, homo sapiens, Denisovans

39
Q

mtDNA of Africans vs. non Africans

A

Africans are more diverse bc only small subpop. of humanoids migrated out of Africa; 2 major migrations out of Africa people setting in Asia and Europe and later migrations replaced them (killing etc.)

40
Q

modern human mtDNA

A

contains no evidence of Neanderthal contribution

41
Q

history of men

A

reflected in Y chromosome sequences; no recombination between X and Y chromosomes; all related males in uninterrupted line have same Y chromosome sequences

42
Q

smart X chromosome

A

X contains more genes critical for brain and intellectual development and contains several genes that influence sperm count and motility; early human females preferred more intelligent males for mating

43
Q

comparative genomics

A

reveals chromosomes rearrangements that have occurred during evolution

44
Q

collinearity (synteny)

A

order of gene that is preserved between species

45
Q

FADS gene

A

high activity allowed early humans to migrate away from water and sustain themselves by growing and gathering plants and hunting land-dwelling animals; didn’t need the gene after moving away

46
Q

microcephalin genes

A

6 different ones that encode a protein that contributes to brain size; mutations that reduce activity produce microcephaly (small heads)

47
Q

FOXP2 gene

A

encodes protein essential for speech; Neanderthals had FOXP2 more similar to modern humans than chimps

48
Q

HAR1 gene

A

encodes protein that fosters development of cerebral cortex; reduced diversity among human bc of strong selection for certain gene alleles

49
Q

lactose tolerance

A

due to dominant gain-of-function mutation that keeps LCT gene expressing lactase after weaning

50
Q

amylase gene

A

allows starch digestion; variation differs w respect to starch content of diet; more copies in farmers/hunter gatherers in dry climates than those who eat meat

51
Q

beta-globin gene

A

several mutations cause sickle cell and beta-thalassemia present in high frequencies in certain populations which protect against malaria; present in populations with roots in Africa and Asia

52
Q

skin color

A

different in different climates; tropical area = darker skin pigments to prevent skin cancer

53
Q

SLC24A5 gene

A

influences skin pigmentation

54
Q

lateral gene (horizontal) gene transfer

A

one species acquiring genes from another species in its environment; common in prokaryotes, protists etc for metabolic enzymes

55
Q

human genes from lateral gene transfer (occurred long ago)

A

3 hyaluronan synthases (from fungi) produce cell adhesion molecules that allows cells to signal w neighbors; fat mass and obesity associated gene (from marine algae); ABO blood type gene; 2 genes for amino acid synthesis; 15 genes for modifying macromolecules (methylation, phosphorylation); 13 genes for lipid metabolism; 5 w antioxidant activity; 7 w immune system function; several dozen from viruses

Genetics 380 (11 decks)

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