Genomes and Evolution

Question 1

genomics

Answer 1

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

Question 2

genome

Answer 2

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

Question 3

genetic map

Answer 3

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

Question 4

physical maps

Answer 4

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

Question 5

recombination frequency

Answer 5

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

Question 6

sampling error

Answer 6

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

Question 7

C Value Paradox

Answer 7

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

Question 8

C value

Answer 8

how much DNA that organism has in diploid cell

Question 9

complex organism

Answer 9

protein diversity is key

Question 10

eukaryotic genomes

Answer 10

contain genes and gene families

Question 11

gene families

Answer 11

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

Question 12

pseudogenes

Answer 12

mutation that renders some copies of gene families nonfunctional

Question 13

homologs

Answer 13

gene related through evolution

Question 14

orthologs

Answer 14

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

Question 15

paralogs

Answer 15

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

Question 16

globin gene family

Answer 16

carry oxygen

Question 17

unique sequences

Answer 17

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

Question 18

highly repetitive DNA

Answer 18

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

Question 19

moderately repetitive DNA

Answer 19

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

Question 20

tandemly repeated sequences

Answer 20

back to back repeats w no intervening sequences

Question 21

interspersed repeat sequences

Answer 21

scattered throughout the genome often due to action of transposable elements

Question 22

short interspersed elements (SINEs)

Answer 22

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

Question 23

long interspersed elements (LINEs)

Answer 23

several thousand bp

Question 24

polymorphic

Answer 24

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

Question 25

allele

Answer 25

each different version of the gene's sequence

Question 26

isoform

Answer 26

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

Question 27

single nucleotide polymorphisms (SNPs)

Answer 27

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

Question 28

haplotype

Answer 28

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

Question 29

insertion/deletion (I/D) polymorphisms

Answer 29

some people have certain stretch of bases and some do not

Question 30

copy number variations (CNVs)

Answer 30

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

Question 31

transposable elements (transposons)

Answer 31

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

Question 32

hybridization studies

Answer 32

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)

Question 33

closest genetic ancestor to humans

Answer 33

chimps based on hybridization studies

Question 34

tracing human migrations

Answer 34

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

Question 35

history of human females

Answer 35

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

Question 36

molecular clock

Answer 36

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

Question 37

mitochondrial eve

Answer 37

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

Question 38

3 mains groups

Answer 38

Neanderthals, homo sapiens, Denisovans

Question 39

mtDNA of Africans vs. non Africans

Answer 39

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.)

Question 40

modern human mtDNA

Answer 40

contains no evidence of Neanderthal contribution

Question 41

history of men

Answer 41

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

Question 42

smart X chromosome

Answer 42

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

Question 43

comparative genomics

Answer 43

reveals chromosomes rearrangements that have occurred during evolution

Question 44

collinearity (synteny)

Answer 44

order of gene that is preserved between species

Question 45

FADS gene

Answer 45

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

Question 46

microcephalin genes

Answer 46

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

Question 47

FOXP2 gene

Answer 47

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

Question 48

HAR1 gene

Answer 48

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

Question 49

lactose tolerance

Answer 49

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

Question 50

amylase gene

Answer 50

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

Question 51

beta-globin gene

Answer 51

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

Question 52

skin color

Answer 52

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

Question 53

SLC24A5 gene

Answer 53

influences skin pigmentation

Question 54

lateral gene (horizontal) gene transfer

Answer 54

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

Question 55

human genes from lateral gene transfer (occurred long ago)

Answer 55

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