Biochem - Gene Expression Transcription Flashcards
gene expression is primarily controlled at the level of _________ ___________
gene transcription
gene transcription is controlled by _____ and _______ regulatory elements
cis, trans
Stretches of DNA located near a gene - either immediately upstream, downstream, or inside an intron - that influence the expression of that gene. Cis regions often code for binding sites for one or more transposable factors
cis-acting elements
can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell (transcription factors)
trans-acting elements
most DNA-protein interactions are weak, non-_________, readily __________ bonds
covalent, reversible
DNA binding proteins contact several DNA bases to increase _________
specificity
many DNA binding proteins have specificity or ________ for multiple sequences
affinity
DNA binding proteins usually access the bases of DNA via the ________ __________
major groove
repressible operon, tryptophan binds to the repressor protein and enables it to repress gene transcription. (adjacent to initiation site)
trp operon
a protein that binds to the operator site of the trp operon and inhibits transcription (ligand activated)
trp repressor
bacteria have regulatory DNA sites called ___________ (O) that control many genes at an operon
operators
operators are bound by _________ that block RNA polymerase binding to the operator
repressors
controlled by ligand-inactivated repressor
lac operon
gene products allow use of lactose as energy source; 3 gene products are up-regulated in the presence of lactose because the lac repressor is ligand inactivated
lac operon
encodes B-galactosidase, cleaves lactose into glucose and galactose
lacZ
encodes the lactose permease, required for transport of lactose into the cell
lacY
encodes galactoside transacetylase, transfers acetyl group from acetyl-CoA (detoxification)
lacA
the lac operon is _________ and low-___________ dependent
lactose, glucose
high cAMP means there is low __________
glucose
LOW lactose concentrations: lac repressor protein binds to region of the promoter called operator; VERY LITTLE _________ produced
transcript
ADD lactose, then a stereoisomer, ____________, binds to the lac repressor protein, the lac repressor dissociates, RNA pol binds, transcription BEGINS
allolactose
lac operon has ___ regulatory sites
2
the __________ binding site of lac operon contains CRP + cAMP
activator
the __________ binding site of lac operon contains lac repressor
repressor
what structure is found between the activator and repressor binding sites
promoter
regulatory mechanism ensuring optimal substrate use. (for lac operon) = lactose present, low glucose = optimal transcription
catabolite repression
catabolite repression is achieved using the regulatory protein ______, which binds cAMP and becomes ligand activated
CRP
___________ is high when glucose is low, CRP binds this
cAMP
to get maximal expression of lac operon genes, _______ must be bound AND ______ _________ NOT bound
CRP, lac repressor
lactose intolerance means you have a ________ deficiency
lactase
lactose cannot be absorbed through the ________ wall unless it is _____________ digested to glucose and galactose
intestinal, enzymatically
X-gal
A chemical similar to lactose that turns dark blue when cleaved by beta-galactosidase (LAB)
in eukaryotes, the functional ground state is that expression is ______
off
the process of chemical changes to the DNA and histones that activate and inactivate gene expression (chromatin altered to allow transcription)
chromatin remodeling
in chromatin remodeling, core histones are either __________ or ___________
acetylated, methylated
acetylation of lysines by histone acetyltransferases (____) reduce the positive charge and decrease affinity of histones for _______
HATS, DNA
transcription by RNA Polymerase 2 requires __ classes of proteins
3
what 3 classes of proteins are required for transcription by RNA Poly 2
1) basal transcription factors
2) DNA-binding transactivators
3) Co-activators (and repressors) for protein-protein binding
eukaryotic gene expression is repressed by ________ chromatin structure
condensed
active transcription requires local ________ of chromatin to relieve repression
remodeling
dense chromatin structure
transcription off
loose chromatin structure
transcription on
how many types of chromatin remodeling were shown to us?
5
acetylation
methylation
ubiquination
sumoylation
phosphorylation
5 types chromatin remodeling (all post-translational mods)
vitamin _____ (chemical) binds vitamin D receptor (protein) resulting in ___________ with RXR (protein)
D3, dimerization
Produced in the skin by ultraviolet irradiation
Vitamin D3 (cholecalciferol)
proteins that bind to the cis sequences and direct the assembly of transcription complexes at the proper gene
trans factors
vitamin D receptor is a ______ ________, meaning it directs assembly of transcription complexes at the correct gene
trans factor
transcription factors bind at super specific _______ sequences
DNA
transcription factors have _________ motifs
conserved
zinc fingers
leucine zippers
helix-turn-helix
helix-loop-helix
examples of conserved motifs in transcription factors
vitamin D has a role in _________ of gene expression by using different _______-_________ factors
regulation, trans-acting
a regulatory protein that binds to a regulatory element in the DNA
trans acting factors
DNA sequences that bind regulatory proteins
cis elements
“Gene regulatory proteins that don’t bind to dna are called __________ and ___________ (proteins that bind other proteins)”
coactivators and corepressors
adding a methyl group to DNA, x inactivation in females is an example of this
DNA methylation
Inactivates transcription of DNA (decreases expression)
hypermethylation
increased gene expression
hypomethylation
important in eukaryotes; cellular and enzymatic reactions that inhibit the process by which polypeptides are synthesized on ribosomes
translational repression
in translational repression, if you phosphorylate initiation factors (___________ them)
inactivates
in translational repression, if ___________ bind to mRNA and initiation factors then it can stop ____________
proteins, translation
a phenomenon in which gene expression and phenotype depend on which parent the genes come from
gene imprinting
Compulsive eating; (expresses 1, 3; segment 2 not expressed)
DELETION OF PATERNAL
Prader-Willi Syndrome
aka happy puppet syndrome, mental retardation, seizures (expresses 2, 3; segment 1 not expressed)
DELETION OF MATERNAL
Angelman Syndrome
excess, ectopic agouti expression (yellow phenotype)
results in cancer, diabetes, obesity
LTR active
“pseudoagouti phenotype, ““normal”” agouti expression
results: lean, healthy, normal lifespan
LTR suppressed
the study of environmental influences on gene expression that occur without a DNA change
Epigenetics
transcription at the lactose (lac) operon is maximal in bacteria when?
The cAMP and lactose levels are both high within the cell.
a mechanism used to regulate transcription at a eukaryotic gene is?
protein-DNA interactions
