BIOL 300 - Chapter 4

what is a genome?

complete set of genes in an organism

what is a transcriptome?

complete set of genes (in context) expressed in particular conditions

what is a proteome?

complete set of polypeptides encoded by entire genome, produced in other cells

what is an exome?

all the exons of a genome

what is an interactome?

all protein-protein interactions/number of indep protein complexes

what is the epigenome?

all the packaging tags on a chromosome

what is a linkage map?

maps genes on a chromosome based on linkage analysis and frequency of recombination between genetic markers -  shows genetic distance between loci

what is a restriction map?

type of linkage map that measures physical distance between DNA landmarks by size of DNA; can be generated using diff in recognition sites sites

what is a sequencing map?

ultimate map based on DNA sequence that’s constructed by genome sequencing (fragment sequencing and assembly)

What do recombination frequencies provide?

mapping information - not physical distance between genes

how does recombination frequency reflect mapping distance on a chromosome?

the farther away a gene on a linear chromosome, the more likely a crossover occurs between two genes

what is a restriction enzyme?

endonuclease that recognizes specific DNA sequences

what is a polymorphism?

coexistence of multiple alleles in a locus, which occur in a population with a frequency over 1% - usually neutral (ex - eye color)

what is the human genome project?

the first sequencing of the human genome - cost 2.7B, and took 13 years

how can polymorphic mutations be neutral?

seq change but not proteins, seq change protein but not function, or function changes without affecting viability/fertility (doesn’t impact fitness)

what is a deleterious mutation?

produces an abnormal protein that directly causes disease; usually has reduced fitness/inc selection pressure

where do most polymorphisms occur in higher organisms?

in noncoding genes, because because these regions are less subject to negative selection, which eliminates mutations detrimental to an individual's ability to reproduce

why do most polymorphisms not occur in coding regions/exons?

because these regions are under selective pressure to remain conserved (generally unchanged)

how are polymorphisms detected?

sequencing and gel electrophoresis

what is nonrepetitive DNA?

one copy of a DNA sequence in a monoploid genome - a good indicator for complexity

what is repetitive DNA?

more than one copy of a sequence in a monoploid genome - occurs in non-exon regions most frequently

what are the two types of repetitive DNA?

moderately and highly repetitive

what is moderately repetitive DNA?

short sequence repeated 10-1000 times - includes secondary pre-mRNA structures, transposons, genes for rRNA and tRNA

what are transposons?

mobile DNA sequences, often called "jumping genes," that can move to new locations within a genome and make copies of themselves, increasing genomic diversity - make up 45% of human genome, and make their own reverse transcriptase

what is highly repetitive DNA?

very short sequence repeated thousands of times - often tandem repeats (segments of DNA where short nucleotide sequences are repeated consecutively) such as satellite, minisatellite, microsatellite (smallest - 1-6bp repeated over)

what are SNPs?

single nucleotide polymorphisms - difference (deletion/insertion) of a single nucleotide in alleles of the same locus - they’re what make people unique

what can identifying SNPs be used for?

GWAS (genome-wide association study), building DNA profile/forensics, identify diseases, assessing parentage

what is GWAS?

genome-wide association study - genomes of pts and non pts can be scanned for SNPs to identify SNPs associated with different disorders

how can SNPs be used in the application of polymorphisms in genetics?

can be used as linkage markers, so physical locations can be characterized by where the SNPs are since every person has unique alleles at every polymorphic locus

how can STRs (short tandem repeats) be utilized?

parentage analysis (different people have different amounts of repeats at those sites) and forensics (probability of 2 unrelated people with same STR is low, so can be used to id individuals)

what do larger genomes typically contain more of in comparison to reglar-sized genomes?

repetitive DNA - of that, mostly transposons

what is uniparental inheritance?

genotype of one parent is inherited

why does non-mendelian inheritance occur?

because gene controlling trait is located on genome of an organelle

what organelles utilize maternal inheritance?

mitochondria and chloroplast

what is the rate that organelle DNA evolves at in comparison to nucleus DNA?

evolution occurs faster in animals, slower in plants - no recombination occurs

what are the characteristics of mtDNA (mitochondrial DNA)?

circular, genes mostly encode proteins, rRNA and tRNA, has several copies of DNA

what do sequence comparisons between mtDNA and ctDNA suggest?

common origin, and similar genome organization