UMN GCD 3022 Exam 3

repressors

proteins that inhibit/decrease transcription, bind to silencers

activators

proteins that increase transcription, bind to enhancers

transcription initiation

most common way to regulate gene expression is at this level

no

[transcription occurs: yes or no] repressor protein, no inducer

yes

[transcription occurs: yes or no] repressor protein, inducer

no

[transcription occurs: yes or no] activator protein, no inducer

yes

[transcription occurs: yes or no] activator protein, inducer

yes

[transcription occurs: yes or no] repressor protein, no corepressor

no

[transcription occurs: yes or no] repressor protein, corepressor

yes

[transcription occurs: yes or no] activator protein, no inhibitor

no

[transcription occurs: yes or no] activator protein, inhibitor

trans-effect

regulation occurs even though DNA segments are not physically adjacent

cis-effect

DNA sequence must be adjacent to the gene is regulates

catabolism

[catabolism or anabolism] typically inducible

anabolism

[catabolism or anabolism] typically repressible

translational repressors

inhibit translation

block the ribosome, stabilize mRNA secondary structure

how translational repressors inhibit translation

antisense RNA

regulate translation in prokaryotes via **

feedback inhibition

final produce in a pathway inhibits an enzyme that acts earlier in the pathway

allosteric

contains two different binding sites

catalytic site (of alleosteric enzyme)

binds to substrate

regulatory site (of alleosteric enzyme)

site that binds to final product of the pathway

transcription factors

proteins that influence the ability of RNA polyerase to transcribe genes

up-regulation

binding of a transcription factor to an enhancer increases the rate of transcription

down-regulation

binding of a transcription factor to a silencer decreases the rate of transcription

silencer

sequence of DNA that binds to a repressor

enhancer

sequence of DNA that binds to an activator

combinatorial control

control of transcription controlled by many factors

nucleosome arrangement (around promoters), DNA methylation

combinatorial control methods only in eukaryotes

bidirectional

orientation independent, can function in the forward or reversee orientation

true

[true or false] most regulatory transcription factors do not bind directly to RNA polymerase

TFIID, mediator

common protein complexes that communicate the effects of regulatory transcription factors

TFIID

general transcription factor that binds to TATA box and recruits RNA polymer to the promoter

mediator

protein complex that mediates between RNA pol ii and the regulatory transcription factors

yes

[transcription activated: yes or no] activator protein, coactivator protein, TFIID

no

[transcription activated: yes or no] repressor protein, TFIID

yes

[transcription activated: yes or no] activator protein interacts with mediator

no

[transcription activated: yes or no] repressor protein interacts with mediator

binding of effector molecule, protein-protein interactions, covalent modifications

common ways that the function of regulatory transcription factors can be affected

steroid hormone

secreted into bloodstream, taken up by cells, ultimate action: affect gene transcription

reposition or remove nucleotides

methods of chromatin remodeling (eukaryotes only!)

open conformation

more transcription

closed conformation

less transcription

acetylation, methylation, phosphorylation

methods of histone modification

NFR (nucleosome free region)

region around core promoter w/out nucleosomes

-1, +1

nucleosomes that flank the NFR

DNA methylation

methyl group added to a cytosine, common in some eukaryotes

CpG islands

inhibits binding of activator proteins, near promoters, unmethlated in housekeeping genes, methylated in tissue-specific genes

true

[true or false] DNA methylation is heritable

de novo methylation

specific genes are methylated in gametes

maintenance methylation

methylation pattern is maintained in resulting offspring

miRNA (microRNA)

hairpin structure, key role in regulation of gene expression esp during development

siRNA (short interfering RNA)

originate from 2 separate RNA molecules that come together to form dsRNA (double stranded), sometimes exogenous, key role in viral infections

RNAi benefits

new form of gene regulation, defense against viruses, silencing transposable elements

mutation

heritable change in genetic material, provide allelic variation, foundation for evolution, can be detrimental

gene mutation

[gene mutation or chromosomal change] affects one gene

chromosomal change

[gene mutation or chromosomal change] affects more than one gene

point mutation

change in a single base pair, involves base substitution

transition

change of a pyrimidine to another pyrimidine or a purine to another purine (2 to 2 or 1 to 1), more common

transversion

change of a pyrimidine to a purine or vise versa (2 to 1 or 1 to 2)

C, T

pyrimidines

A, G

purines

deletions/insertions

addition/deletion of short sequences of DNA

silent

[type of base substitution] no change in amino acids

missense

[type of base substitution] one amino acid changed, neutral or inhibitory effect

nonsense

[type of base substitution] many amino acids altered, inhibitory effect: change a codon to a stop codon

frameshift

involve the addition/deletion of nucleotides in multiples of one or two (but not three); shifts reading frame

germ-line mutation

occur in gametes

somatic mutations

occur directly in a body cell

genetic mosaic

individual with somatic cells that are genotypically different from each,other

wild-type

relatively prevalent genotype

reverse mutation (reversion)

changes a mutant allele back to wild-type

suppressor

a second mutation that affects the phenotypic expression of a first mutation

false

[true or false] suppressor mutations occur at the same site as the first mutation

position effect

expression of a gene altered because of its new location

spontaneous, induced

causes of mutations

mutagens

agents known to alter DNA

environmental agents, mutagens

induced mutations caused by

depurination, deamination, oxidative stress

spontaneous mutations caused by

depurination

removal of a purine from the DNA, can be repaired, occurs before replication

apurinic (AP) site

DNA site that is missing a purine base

false (25% chance)

[true or false] replication over an apurinic site cannot result in the correct sequence

deamination of cytosine

removal of an amino group to create uracil, can be repaired

deamination of 5-methylcytosine

removal of an amino group to create thymine, cannot be repaired

oxidative stress

imbalance between synthesis and destruction of ROS (reactive oxygen species)

ROS (reactive oxygen species)

generated by normal metabolism, used by immune system to kill invading cells

base modifiers, intercalcating agents, base analogs

types of chemical mutagens

base modifiers

covalently modify the structure of a nucleotide; cause base substitutions

alkylating agents

add methyl or ethyl groups to bases

intercalating agents

contain flat planar structures that intercalate themselves into the double helix; cause frameshifts

base analogs

become incorporated into daughter strands during DNA replications

ionizing or nonionizing radiation

physical mutagen types

ionizing radiation

causes single nicks or double strand breaks; creates free radicals; includes x-rays and gamma rays

nonionizing radiation

causes thymine dimers which cause mutations during DNA replication; includes UV light

mutation rate

likelihood that a gene will be altered by a new mutation; not constant

mutation frequency

total number of mutant genes divided by the total number of genes

Ames test

tests to see if an agent increases the reversion rate (His- to His+)

detection, removal, normal synthesis

DNA repair process

direct repair

enzyme recognizes incorrect alteration and directly converts it back to correct form

photolyase

repairs thymine dimers, uses light