Genetics Exam 3

structural genes

encode a protein that is used for metabolism, biosynthesis, or cell structure

regulatory genes

can encode either RNA or proteins that affect transcription or translation of other genes

regulatory elements

not genes; DNA sequences that are not transcribed, but impact the expression of other genes (i.e. enhancers)

DNA-binding protein motifs (3)

helix-turn-helix, zinc fingers, leucine zipper

helix-turn-helix

located in bacterial regulatory proteins; two alpha helixes; binds in the major groove in DNA

zinc finger

located in eukaryotic regulatory proteins; loop of amino acids with zinc at the base; binds in the major groove in DNA

leucine zipper

located in eukaryotic TFs; helix of leucine and a basic arm; binds at two adjacent major grooves in DNA

operon

group of structural bacterial genes that are transcribed together; includes a single promoter and any other regulatory sequences; genes are transcribed as one large mRNA; (-) inducible

regulator gene

encodes regulator proteins; not part of the operon; different location than an operon, but will determine if it is being turned on/off; produces a repressor

regulator protein

binds to the operator and blocks the promoter

negative transcription control

the regulatory protein is a repressor (will stop transcription)

positive transcription control

the regulatory protein is an activator (will encourage transcription)

inducible transcription control

a small molecule that binds to the repressor and changes repressor conformation so the repressor can no longer bind to DNA; can turn on transcription

repressible transcription control

the transcription operon is not normally turned on; can be turned off by the repressor;

lac operon of E.coli

negative inducible operon; turned on only when lactose is present; the inducer = allolactose (need lacY and lacZ to get this); transcription is never completely shut down

genes responsible for transport and breakdown of lactose

permease - lacY

β -galactosidase - lacZ

transacetylase - lacA

mutations in the lac operon

structural gene, regulator gene, operator, promoter

structural gene mutations

affect only the ONE mutated gene

regulator gene mutations

may make transcription of all genes in the operon always on or always off (all the time or never); can be trans-acting; regulator protein normally binds to the operon and stops/prevents mutation

operator mutations

prevents the repressor from binding, allowing transcription all the time; located before structural genes where the repressor would normally bind and prevent transcription

promoter mutations

prevents the binding of RNAP and prevents transcription; in bacteria the RNAP would usually bind to the promoter and allow for transcription

catabolite repression

when glucose is present, genes that control the metabolism of other sugars are repressed (glucose is bacteria’s favorite sugar)

catabolite activator protein (CAP)

activates transcription of lac genes only when bound by cyclic-AMP (levels inversely proportionate to glucose levels); lots of glucose = not much CAP; lots of CAP = not much glucose

attenuation

premature termination of transcription; another way to add a 2nd layer of control; caused by 2º structures in the 5’ UTR (untranslated region); found in operons that code for enzymes involves in amino acid biosynthesis

Trp operon

a negative repressible operon; total reduction of transcription over 600-fold; the repressor and attenuator respond to different stimuli

why we have repression and attenuation

levels of expression; goal is being able to fully control what is happening, and this lets you turn transcription down significantly;

repression and attenuation and Trp operon

repressor responds to the free Trp; attenuation responds to the tRNA/amino acid that has Trp on it

antisense RNA

small complementary RNA molecules; binds to mRNA; prevents translation; similar to RNA interference

riboswitches

regulatory sequence of 5’ UTR of mRNA; attracts the regulatory protein and blocks ribosome binding

ribozymes

mRNAs that self-cleave when product is not needed; i.e. encoding ones of a sugar, enough sugar will bind and self-cleave

epigenetics

alterations to DNA and chromosome structure that are heritable but reversible; ability to change DNA/chromosome structure in ways that may impact phenotypes but not genotypes (ATGCs)

chromatin remodeling complexes

binds to DNA, repositions nucleosomes (where DNA is wrapped 2x around a histone), and exposes a TF to a binding site; the TFs and RNAP bind to DNA and initiate transcription

histone modification

acetyl transferase enzymes adds acetyl groups to histones; neutralizes so histones (+ charge) do not bind too tightly to DNA (- charge)

methylation (of histones)

can activate or repress transcription

deacetylases (of histones)

removes acetyl groups

transcription activator proteins (TAPs) and coactivators

binds to enhancers or regulatory promoters; coactivators interact with RAP and RNAP complex; both binds to regulatory promoter/enhancer to increase the rate of transcription at that site

repressors - transcriptional control

binds to regulatory promoters or silencer (to have a negative effect like enhancers); sometimes interact with RNAP to slow down or prevent TFs form binding; reduces the rate but does not completely stop the blocking

enhancers and silencers

sequences that bind activator or repressor proteins; DNA loops to allow interaction with the promoter region; stimulates multiple promoters in their vicinity; affects transcription at distant promoters; does not have to be right next to the promoter to interact with genes, and they are not limited to just one promoter

insulators

DNA sequences that limits “reaches” of (blocks) enhancers and silencers from affecting promoters; help to create neighborhoods of gene regulation

coordinated gene regulation

no operons in eukaryotes, but there are times when certain sets of genes must be turned on/off (i.e. metabolism); some groups of genes are activated by one stimulus (heat-shock proteins); the genes are not clustered and have common regulatory sequences in promoters

coordinated gene regulation - response elements

within gene regulatory sequences in promoters; allow one gene to be activated by multiple stimuli (turns on lots of genes at the same time); bound by TAPs

alternative splicing

different proteins in different tissues or times of development; i.e. fruit flies sex determination based on the tra protein

RNA stability

mRNA availability dictates the amount of translation; the stability time varies (based on the PolyA tail or other factors); degradation of the entire RNA begins with the shortening of the PolyA tail

RNA silencing

siRNAs and miRNAs inhibit transcription and translation; a way of controlling gene expression

RNA crosstalk

RNA molecules compete to bind miRNAs; RNA molecules may compete for binding of splicing (spliceosomes), stability, and translation-related proteins,

lncRNAs

long non-coding RNAs; act as “molecular decoys” to bind miRNAs so they don’t bind to their target mRNAs

translational and posttranslational control

depends on the availability of tRNA, ribosomes, elongation factors, and initiation factors; proteins can bind 5’ or 3’ UTR of mRNA and prevent ribosome binding; posttranslational modification may need to cleave to make 2

continuous characterisitics

typically polygenic; may be multifactorial; i.e. eye color

meristic characteristics

not continuous, but multifactorial; i.e. litter size in mice

threshold characteristics

only 2 phenotypes, but multifactorial; i.e. susceptibility to cancer/disease

heritability

inheriting a trait or not; the proportion of phenotypic variation caused by genetic factors (as opposed to environmental factors) within a defined group; does not indicate the degree to which a characteristic is genetically determined; varies based on the population examined and the environment

heritability is useful for (2)

predicting offspring phenotypes (i.e. dog breeding); predicting effects of selection

genotypic frequency

how often a genotype occurs in a population; i.e. f(TT)

phenotypic frequency

how often a phenotype occurs; i.e. how often plants are tall f(tall)

allelic frequency

how often a particular allele occurs in a population; i.e. f(T)

allelic frequency formula

(# of particular allele)/(total # of alleles in the population); p+q = 1; divide by 2N because each individual has 2 alleles

p = f(A) = (2nAA + nAa)/2N

q = f(a) = (2naa + nAa)/2N

calculating allelic frequencies for X-linked loci

women have 2 alleles, men have 1;

formula: p = f(X^A) = (2nXAXA + nXAXa = nXAY)/ (2n + n)

hardy weinberg law

if a population is large, randomly mates, and is not affected by mutation, migration, or natural selection, then the allelic frequencies stay constant/DO NOT CHANGE; works at individual loci, not the whole genome; genotypic frequencies are determined by allelic frequencies; reproduction alone does not cause evolution

hardy weinberg formula

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

p^2 = dominant allele (A)

q^2 = recessive allele (a)

2pq = heterozygotes (this frequency never exceeds 1/2)

when hardy-weinberg does not apply

non-random mating (affects only the traits that influence this) and inbreeding

positive assortative mating

non-random mating where like attracts like (i.e. tall person and tall person)

negative assortative mating

non-random mating where “opposites attract” (i.e. introvert and extrovert)

inbreeding

leads to a great decrease in heterozygotes; does not work well for humans/mammals; shows an increased probability of alleles identical by descent (in humans → low development)

somatic mutations

mutations occurring in somatic/body cells; passed to other associated cells (not entire organism)

germ line mutations

mutations occurring in the germ cells (sperm/egg); an organism that is conceived with these germ cells will carry the mutation

base substitution

one single base becomes another base

transition base substitution

purine replaced with purine (A with G) or pyrimidine replaced with pyrimidine (C with T)

transversion base substitution

when a purine is replaced with a pyrimidine (A→T) or a pyrimidine is replaced with a purine (C→G)

missense mutation

type of base substitution that changes the amino acid that is encoded

nonsense mutation

mutation where a codon that encoded an amino acid now encodes a premature stop codon

silent mutation

base substitution mutation where there is a change in DNA, and because of this change there is no impact on the encoded protein (i.e. TCA→TCC)

neutral mutation

base substitution where there is a single base substitution; the change to the amino acid encoded does NOT impact the protein; a type of missense mutation

insertion

mutation where nucleotides are added

deletion

mutation where nucleotides are deleted

frame shift mutation

mutation where nucleotides are added/deleted not in a multiple of 3; changes and shifts the entire reading frame; often time results in a premature stop codon

trinucleotide repeats

type of insertion; includes genetic anticipation, strand slippage, and uneven crossing over

uneven crossing over

incorrect lining up of homologous regions; one DNA molecule gets an insertion and one gets a deletion

strand slippage

repeats due to the strand not lining up properly; one DNA strand forms a small loop

genetic anticipation

at some point an individual gets more repeats of nucleotides than can be tolerated (i.e. Huntington’s disease); the next/subsequent generation gets more repeats and the diseases occur earlier onset and are more severe

forward mutation

mutation that alters the wild-type phenotype

reverse mutation

mutation that changes a mutant phenotype back to wild type; there is a strong selected pressure for producing old phenotypes

“loss of function”

recessive (both copies needed); where a protein loses its function or the ability to produce a protein all together

“gain of function”

dominant (one copy needed); where the protein either works in a new way or is produced at an inappropriate time/place

conditional mutations

mutations expressed only under certain conditions; useful for studying the functions of genes important for life; allows the study of mutations that are otherwise lethal; i.e. yeast, fruit flies

suppressor mutations

a second mutation that hides the effect of the first mutation

intragenic suppressor mutation

a mutation that happens within the same gene as the one being suppressed; i.e. if there is a reading frame shift, another nucleotide is added/deleted downstream and this restores the function of the gene

intergenic suppressor mutation

a mutation that occurs in a different gene that restores the wild-type phenotype in another gene; usually changes the way a protein is translated; i.e. changing so the tRNA carrying the correct amino acid identifies the mutant codon

mutation rate

tracks the frequency of change/new incidences from wild-type to mutant; varies by organism and gene; i.e. “how many mutations per cell cycle?”; “how many children born with this mutation in a given allele?”

mutation frequency

incidence of a mutation within a group of organisms; i.e. “how common do we find the mutation (overall incidence) in a population?”

3 factors that effect mutation rate

1. how often change happens in DNA (frequency)
2. the probability of repair
3. the probability of detecting/recognizing that it happened; phenotype=easy, but sequencing DNA to see=not easy

adaptive mutation

stressful environments (i.e. heat, pH) causes an increased mutation rate (in certain organisms)

spontaneous mutations

errors that occur during replication due to intrinsic factors; there is no specific cause; i.e. wobble and tautomeric shift

tautomeric shift

where the H+’s get rearranged; can incorporate into the next round of DNA

depurination

a type of spontaneous chemical change where a purine nucleotide (G or A) is lost and replaced with an incorrect nucleotide

deamination

a type of spontaneous chemical change where an amino group (-NH3) is lost from a base; of cytosine = uracil (error in DNA because there would be A pairing instead of G); of 5-methyl-cytosine = thymine

mutagens

environmental agents that increase mutation rates; they cannot be avoided but the risk can be reduced

chemical i.e. cigarette smoke

physical i.e. UV rays/sunlight

chemical mutagen: oxidative radicals

causes chemical changes in bases that results in mispairing; superoxide, hydrogen peroxide, and hydroxyl radicals can damage DNA

physical mutation: radiation

x-rays, gamma rays, cosmic rays; causes double strand breaks in the DNA; UV light - forms pyrimidine dimers; thymine dimers (thymine fused together); accumulating enough leads to skin cancer

ames test

classic test for mutagenicity; uses bacteria and colonies display what is mutagenic; only tells if there are mutagens or not

transposable elements

sequences of DNA that can move (mobile) around within a genome; aka transposons; often causes mutations by either inserting into another gene and disrupting it, or by promoting DNA rearrangements such as chromosome deletions, duplications, and inversions