Genomes and Evolution Flashcards
genomics
study of gene seq., mechanisms that regulate gene activity, interaction between genetic factors and btw. genetic and non-genetic factors, comparisons btwn species
genome
organism’s entire DNA/RNA; organisms’s entire collection of genes
genetic map
units are recombination frequency (Rf), centiMorgans (cM) or map units (m.u.); came first: only need to know seq. of 2 elements
physical maps
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
recombination frequency
diff in diff genders, ethnic groups, drug/chem. exposures; lower near centromere vs. telomere
sampling error
can cause genetic map to position genes improperly if the study had a small population
C Value Paradox
no relationship btwn genome size and organism complexity; more DNA does not mean more complex organism
C value
how much DNA that organism has in diploid cell
complex organism
protein diversity is key
eukaryotic genomes
contain genes and gene families
gene families
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
pseudogenes
mutation that renders some copies of gene families nonfunctional
homologs
gene related through evolution
orthologs
homologous genes found in two different species and evolved from common ancestor
paralogs
2 genes w/i single organism that are homologous and arose from duplication sometime in evolutionary past
globin gene family
carry oxygen
unique sequences
found only once in the genome; 30-75% of genome; protein coding genes or regulatory sequences (miRNAs other regulatory RNAs)
highly repetitive DNA
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
moderately repetitive DNA
150-300 bp; 1-30% of genome; 10-1000 copies per genome; genes for histone protein, some rRNA and some tRNAs
tandemly repeated sequences
back to back repeats w no intervening sequences
interspersed repeat sequences
scattered throughout the genome often due to action of transposable elements
short interspersed elements (SINEs)
approx. 200-300 bp; most common = Alu repeat (200-300 bp, several million copies per genome)
long interspersed elements (LINEs)
several thousand bp
polymorphic
human DNA seq. is highly polymorphic; for any gene there are many diff specific versions of that gene’s seq. in the population
allele
each different version of the gene’s sequence
isoform
version of protein that has higher or lower level of activity than isoform made by most other people; made by alleles of a gene
single nucleotide polymorphisms (SNPs)
single nucleotide position where some people have A, some C, some G, some T in that spot
haplotype
SNPs that lie close together and are often transmitted together from parent to child
insertion/deletion (I/D) polymorphisms
some people have certain stretch of bases and some do not
copy number variations (CNVs)
some people have deletions and duplications that give either one copy or more than two copies of certain sequences
transposable elements (transposons)
move from one place to another w/i the same cell’s DNA; cut and paste/copy and paste
hybridization studies
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)
closest genetic ancestor to humans
chimps based on hybridization studies
tracing human migrations
determine gene alleles present in ancient bone samples shows trace migration and intermingling
history of human females
mitochondrial DNA doesn’t undergo recombination the way DNA does so its easier to trace lineages w it (only reflects history of women)
molecular clock
difference in mitochondrial DNA seq. between two lineages to gauge time at which 2 lineages diverged from common ancestor
mitochondrial eve
one mitochondrial genotype that served as common ancestor for all currently living humans (120,000-220,000 years ago)
3 mains groups
Neanderthals, homo sapiens, Denisovans
mtDNA of Africans vs. non Africans
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.)
modern human mtDNA
contains no evidence of Neanderthal contribution
history of men
reflected in Y chromosome sequences; no recombination between X and Y chromosomes; all related males in uninterrupted line have same Y chromosome sequences
smart X chromosome
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
comparative genomics
reveals chromosomes rearrangements that have occurred during evolution
collinearity (synteny)
order of gene that is preserved between species
FADS gene
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
microcephalin genes
6 different ones that encode a protein that contributes to brain size; mutations that reduce activity produce microcephaly (small heads)
FOXP2 gene
encodes protein essential for speech; Neanderthals had FOXP2 more similar to modern humans than chimps
HAR1 gene
encodes protein that fosters development of cerebral cortex; reduced diversity among human bc of strong selection for certain gene alleles
lactose tolerance
due to dominant gain-of-function mutation that keeps LCT gene expressing lactase after weaning
amylase gene
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
beta-globin gene
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
skin color
different in different climates; tropical area = darker skin pigments to prevent skin cancer
SLC24A5 gene
influences skin pigmentation
lateral gene (horizontal) gene transfer
one species acquiring genes from another species in its environment; common in prokaryotes, protists etc for metabolic enzymes
human genes from lateral gene transfer (occurred long ago)
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
