Genetics Final

What accounts for most of the differences in genome size of eukaryotes?

repetitive DNA (transposable elements)

Approximately how much of the human genome is the Open Reading Frame?

2%

Approximately how much of the human genome is introns?

26%, more nucleotides in introns than in exons

Are genes found at high or low density in the human genome?

low density

Approximately how much of the human genome is unique non-coding sequences?

12%

Pseudogenes

former genes that have accumulated mutations and are nonfunctional (approx 30%), 70% are processed pseudogenes which is mRNA converted back to DNA and inserted at random into the genome

Approximately how much of the human genome is constitutive heterochromatin?

8%, always remain highly condensed and inaccessible to RNA polymerase

Approximately how much of the human genome is repetitive DNA?

50%, segmental duplications, simple sequence repeats, transposable elements (LINES, SINES, LTR retro transposons, DNA transposons)

segmental duplications

blocks of genomic sequences which have duplicated and moved to the same chromosome or a non-homologous chromosome, occur two or more places within the genome and share high level of sequence identity

simple sequence repeats

repeats of short sequences, basis for human identity testing

LTR retrotransposons

LTR of about 350 bps at each end of element, gag gene processes mRNA, pol gene makes reverse transcriptase that converts mRNA back to DNA allowing transposition, copy remains at original location after transposition (autonomous)

LINE

no LTR, pol encodes reverse transcriptase, autonomous, leave copy at original site

SINE

no LTR, no pol gene so no reverse transcriptase, nonautonomous as they rely on reverse transcriptase from LINE in order to transpose

DNA transposons

short inverted repeats at each end, autonomous contain single transposase gene that clips transposon DNA out of genome and reinserts at different location but non-autonomous rely on transposase from autonomous transposons to move

T or F: most repetitive DNA is inter-genetic (in introns).

T

ploidy

general term to describe number of chromosome sets

euploid

"true" ploidy = complete set(s) of chromosomes

diploid

2n, common ploidy of many plants & animals

haploid

n, common ploidy of many fungi

polyploid

general term for organisms with more than the common number of chromosome sets

triploid

(3n) 3 sets of chromosomes

tetraploid

(4n) four sets of chromosomes

monoploidy

only one set of chromosomes

autotetraploids (4n)

four chromosome sets that arose by self-doubling

How does autopolyploidy occur?

can occur naturally if S stage (replication) occurs but mitosis does not, also can be induced by treatment with colchicine which prevents anaphase

T or F- Polyploids are larger.

T

Why do autotetraploids have reduced fertility?

gametes are likely to be unbalanced for some chromosomes

What are methods to create sterile autotriploids?

cross a diploid and tetraploid of the same species, fertilize 1 egg by 2 sperm, fertilize diploid egg by 1 sperm

balanced gametes

have 1 copy of every chromosome in a set or 2 copies of every chromosome in a set

unbalanced gametes

have 1 copy of some chromosomes and 2 copies of other chromosomes

Are autotriploids sterile?

yes, due to problems with chromosome pairing in meiosis

allopolyploidy

a species with multiple sets of chromosomes derived from different but related species

how is polyploidization important in genome evolution?

polyploid formation results in duplicate copies of each gene which may evolve new functions due to accumulation of random mutation or may be lost/converted to pseudogenesalso polyploids can no longer breed with diploids so they become genetically isolated which can lead to speciation

Aneuploidy

not euploid, refers to loss or gain of PART of a chromosome set

monosomy

Chromosomal abnormality consisting of the absence of one chromosome from the normal diploid number, 2n-1

trisomy

a condition in which an extra copy of a chromosome is present in the cell nuclei, causing developmental abnormalities, 2n + 1

What occurs to produce aneuploid gametes?

nondisjunction during cell division

What syndrome is an example of the only viable monosomy?

turner syndrome

turner syndrome

monosomy of the X chromosome, no barr body formation, caused by fertilization of the n-1 gamete by a gamete with an X chromosome, lack of extra gene dosage from the inactivated X chromosome is the cause of observable phenotypes

what is a viable trisomy of sex chromosomes?

klinefelter syndrome (XXY), extra gene expression from inactivated X leads to feminization

What is a more common trisomy of autosomes?

trisomy-21 or down syndrome, phenotype explained by disruption of gene dosage

What are two ways chromosome mutations can occur?

after double stranded breaks or following crossovers between repetitive elements on chromosomes

T or F: Chromosome mutations generally cause a decrease in fertility during reproduction.

T

What is a single break deletion called?

terminal deletion

what is a double break deletion called?

internal deletion

deletion loop

the loop formed at meiosis by the pairing of a normal chromosome and a deletion-containing chromosome, contains the non-deleted region, cell is unbalanced for genes in deletion loop since only 1 copy (hemizygous)

duplication loop

contains the duplicated region of the DNA

duplications

additional gene copies may be detrimental (genetic imbalance) and reduce fertility

inversions

no genetic material lost (balanced), gene order is changed

pericentric inversion

inverted region includes centromere

paracentric inversion

inverted region does not include centromere

reciprocal translocation

parts of two non-homologous chromosomes trade places, no genes are lost just the order and location of genes are changed (T1/ T2 & N1/N2)

alternate segregation

normal chromosomes segregate together and gene balance is maintained, translocation chromosomes segregate together and gene balance is maintained

adjacent segregation

gametes unbalanced and likely non-viable, T1/N2 & N1/T2

population

group of individuals of the same species that can interbreed

gene pool

all of the alleles in the breeding members of a population at a particular point in time

genotype frequency

proportion of individuals in a population that are A/A or A/a or a/a

allele frequency

proportion of alleles in a population that are A vs a

p + q = 1

allele frequency equation

p2 + 2pq + q2 = 1

Hardy-Weinberg equation, genotype frequencies must total to 1

Hardy-Weinberg equilibrium

if no outside forces act on a population, genotype frequencies and allele frequencies will remain constant from generation to generation

hardy Weinberg assumptions

all individuals in LARGE population randomly interbreed (no bias in partner choice), individuals don't leave or join the population, no mutations occur, all individuals are equally fit, population is infinite

3 types of mating biases

isolation by distance, inbreeding, assortative mating

positive assortative mating

individuals with similar phenotypes mate preferentially, results in more homozygosity

negative assortative mating

individuals with different phenotypes mate preferentially, results in more heterozygosity

inbreeding

mating between closely related individuals, more homozygosity overall

Are small population more prone to inbreeding?

Yes

Mutations

random, occuring constantly, introduce new alleles into the gene pool (can be beneficial or detrimental depending on the environment/selection)

migration

gene flow, individuals who leave 1 population and join another introduce new alleles into the gene pool , has a greater effect on small populations than large ones

genetic drift

random change in allele frequencies that is much more impactful in small populations

fixation

a population has only one allele of a particular gene and the other allele is lost

founder effect

genetic drift that occurs after a small number of individuals colonize a new area

genetic bottleneck

sudden population decrease due to change in environment, emergence of new disease, habitat destruction

natural selection

acts on heritable features that an organism has, promotes adaptation

fitness

ability to survive and more importantly reproduce

absolute fitness

number of offspring per genotype

relative fitness

proportion of offspring produced by particular genotype relative to the most fit genotype

what are the evolutionary forces that change allele frequencies?

mutation, migration, genetic drift, natural selection

artificial selection

breeding done with human intervention

calculating genotype frequencies based on relative fitness

multiply relative fitness by genotype to get relative contribution to the gene pool in the next generation

selective sweep

a process in which one allele increases in a population due to positive selection, allele fixation

directional selection

changes allele frequency in population in one direction

balancing selection

changes allele frequency in population to maintain genetic diversity, heterozygote more fit (ex: sickle cell genes- HbA/HbS genotype has no anemia and few malarial parasites while people homozygous for HbA have no anemia but serious malarial infection)

what are the 4 likely fates of duplicated genes?

elimination by deletion event, pseudogenization, neofunctionalization, subfunctionalization

pseudogenization

enough mutations accumulate in one of the duplicates that it no longer makes functional protein

neofunctionalization

mutations allow a new function to evolve for the protein expressed from one of the duplicated genes, other genes retains original function

subfunctionalization

mutations in regulatory elements allow one copy to be regulated by one set of transcription factors, other copy regulated by different TFs

globin gene family

11 members of globin gene family that arose sequentially from an ancestral gene

alpha globin subfamily

two genes make functional alpha subunits of hemoglobin, expressed after birth, one pseudogene is present due to accumulated mutations (pseudogenization after duplication of alpha 1 gene)

beta globin subfamily

one gene makes functional beta subunits, one pseudogene occured after duplication

gamma globin genes

ONLY expressed in fetus, becomes beta after fetal life stage, subfunctionalization after duplication

T or F: There have been multiple Whole Genome Duplication events in the evolution of many species.

T

p + q = 1

allele frequency equation

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

genotype frequency equation