Genetics New Material

HOX genes

determine body plan; expressed in head-to-tail pattern

homeodomain protein

section of DNA that is similar in HOX genes across species; transcription factor that controls where and when genes are expressed

maternal genes

developmental genes that are transcribed in the mother; deposited in oocyte as RNA or protein

if zygote is treated with transcription-inhibiting drugs, which genes will be repressed?

zygotic genes only; not maternal

what is the sonic hedgehog pathway (Shh) and where is it found?

pathway that represses limb development; found in limb buds and feather precursors (chickens)

what causes polydactyly?

mutations in Shh regulatory elements that control when and where Shh is expressed

what is the relationship between maternal and zygotic genes?

maternal genes drive expression of zygotic genes (ex: Bicoid —> Hunchback)

silent/synonymous mutations

no change in amino acid sequence

missense/ substitution

amino acid is changed

conservative substitution

new amino acid has similar properties to the original

nonconservative substiution

new amino acid does not have similar properties to original

nonsense mutation

protein is cut short due to a premature stop codon

frameshift mutation

reading frame is shifted due to a single indel

base excision repair and what kind damage?

removes single base; can repair non-bulky damage, such as alkylation and oxidation

nucleotide excision repair and what kind damage?

removes chunk of DNA; can repair bulky damage, such as thymine dimers caused by UV and bulky adducts

mismatch repair and what kind damage?

replaces incorrectly placed bases; used in proofreading

non-homologous end-joining and what kind damage?

repairs double stranded breaks

homologous recombination and what kind damage?

repairs double stranded breaks

which is better and why: homologous recombination or non-homologous end-joining?

HR because it’s virtually error-free, but it can only occur during interphase of cell cycle

replication slippage and when it is more likely to occur?

DNA polymerase falls off double helix during DNA replication; highly repetitive sections

what mutation occurs when DNA polymerase falls off template strand?

deletion

what mutation occurs when DNA polymerase falls off newly synthesized strand?

insertion

fluctuation test procedure and purpose

1. grow multiple bacteria cultures in parallel

2. measure number of mutant cells in each culture and compare numbers

3. similar number of mutations = induced

4. varying number of mutations: spontaneous

Ames test procedure and purpose

1. soak a potential mutagen in a disc of filter paper

2. place soaked disc on a His- plate coated with His- bacterial cells

3. after 1 day, count number of colonies

4. this is the number of colonies that underwent reversion mutation from His- to His+ because of molecule

5. used to tell if a molecule is mutagenic

fragile X syndrome

trinucleotide repeat disease that can cause neurodevelopmental delay

What causes fragile X syndrome?

replication slippage

transposons

mobile genetic elements

autonomous transposable elements

can catalyze their own transposition because they produce their own transposase

insertion of a transposon into a gene can cause:

1. inactivation of gene

2. unstable mutant phenotype

3. chromosome breakage

In what regions are transposons usually found?

inverted repetitive regions because it helps their insertion into the genome

replicative transposition

transposon makes copy of itself that inserts into a new site of genome, but original stays at original site

conservative transposition

transposon is excised from original site and re-inserted in a completely new site of the genome

How do retrotransposons work?

they copy themselves via RNA intermediate and insert new transposon into a new site of genome

LTR

long terminal repeats that facilitate integration

LINE

autonomous retrotransposon that codes its own reverse transcriptase; they are long and have fewer copies

SINE

non-autonomous retrotransposon that does not code its own reverse transcriptase; they are short and have a higher copy number

What is the relationship between genome size and number LTR retrotransposons?

positive correlation

How were P elements discovered in Drosophila?

cross P strain (wild) male to a M strain (lab) female caused an infertile F1 because the lab female lacked piRNAs necessary to silence P element

piRNAs and where are they found?

short, single-stranded RNAs that silence P elements; deposited in oocyte (maternal genes)

ploidy

number of complete sets of chromosomes in an organism

euploid

normal ploidy (usually 2n or n)

polyploid

more than 2n

aneuploid

organism with incomplete set of chromosomes

How can polyploidy be caused during cytokinesis?

defects in microtubule polymerization

nondisjunction

unequal segregation of sister chromatids during meiosis that causes aneuploidy

nondisjunction at meiosis I =

two n + 1 gametes and two n-1 gametes

nondisjunction at meiosis II =

one n+1 and one n-1 gamete

Turner’s syndrome

XO; infertile and need estrogen replacement therapy

Klinefelter syndrome

XXY; lanky builds, mildly impaired IQ, and sterility

trisomy 21

extra copy of chromosome 21

gene-dosage effect

the relation between the number of copies of a gene and the amount of the gene’s product made

Why is aneuploidy deleterious?

interferes with the normal function of the genome

How does aneuploidy impact gene dosage compensation?

some genes may not be able to be fully compensated, especially autosomes

SNP

single base pair changes that may or may not affect the protein

microsatellites

variation at regions of repetitive DNA sequence

indels

insertions and deletions of one or more base pairs

p+q=1 usesd when

allele frequency

p²+2pq+q²=1 used when

genotype frequency

Conditions population must meet for Hardy Weinberg equilibrium

1. no mutation

2. random mating

3. no gene flow

4. no natural selection

5. very large population

which type of organisms are most genetically diverse?

unicellular eukaryotes

artificial selection

humans selectively breed organisms

How does the heterozygote advantage allow deleterious alleles to persist in a population?

ex: malaria resistance with one sickle-cell allele

how does polyploidy play a role in evolution?

more genes to mutate

how does gene duplication play a role in evolution?

more genes to mutation

horizontal DNA transfer

transfer of DNA between individual that is not inheritance from a mother or father

how does nonsynonymous substitution play a role in evolution?

more likely to change protein fuction

why do we observe more synonymous mutations

many nonsynonymous mutations are lethal and this not included in survivorship count