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Integrated Exam 2/9 > Biochem - Gene Expression Transcription > Flashcards

Biochem - Gene Expression Transcription Flashcards

1
Q

gene expression is primarily controlled at the level of _________ ___________

A

gene transcription

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2
Q

gene transcription is controlled by _____ and _______ regulatory elements

A

cis, trans

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3
Q

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

A

cis-acting elements

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4
Q

can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell (transcription factors)

A

trans-acting elements

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5
Q

most DNA-protein interactions are weak, non-_________, readily __________ bonds

A

covalent, reversible

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6
Q

DNA binding proteins contact several DNA bases to increase _________

A

specificity

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7
Q

many DNA binding proteins have specificity or ________ for multiple sequences

A

affinity

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8
Q

DNA binding proteins usually access the bases of DNA via the ________ __________

A

major groove

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9
Q

repressible operon, tryptophan binds to the repressor protein and enables it to repress gene transcription. (adjacent to initiation site)

A

trp operon

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10
Q

a protein that binds to the operator site of the trp operon and inhibits transcription (ligand activated)

A

trp repressor

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11
Q

bacteria have regulatory DNA sites called ___________ (O) that control many genes at an operon

A

operators

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12
Q

operators are bound by _________ that block RNA polymerase binding to the operator

A

repressors

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13
Q

controlled by ligand-inactivated repressor

A

lac operon

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14
Q

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

A

lac operon

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15
Q

encodes B-galactosidase, cleaves lactose into glucose and galactose

A

lacZ

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16
Q

encodes the lactose permease, required for transport of lactose into the cell

A

lacY

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17
Q

encodes galactoside transacetylase, transfers acetyl group from acetyl-CoA (detoxification)

A

lacA

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18
Q

the lac operon is _________ and low-___________ dependent

A

lactose, glucose

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19
Q

high cAMP means there is low __________

A

glucose

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20
Q

LOW lactose concentrations: lac repressor protein binds to region of the promoter called operator; VERY LITTLE _________ produced

A

transcript

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21
Q

ADD lactose, then a stereoisomer, ____________, binds to the lac repressor protein, the lac repressor dissociates, RNA pol binds, transcription BEGINS

A

allolactose

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22
Q

lac operon has ___ regulatory sites

A

2

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23
Q

the __________ binding site of lac operon contains CRP + cAMP

A

activator

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24
Q

the __________ binding site of lac operon contains lac repressor

A

repressor

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25
what structure is found between the activator and repressor binding sites
promoter
26
regulatory mechanism ensuring optimal substrate use. (for lac operon) = lactose present, low glucose = optimal transcription
catabolite repression
27
catabolite repression is achieved using the regulatory protein ______, which binds cAMP and becomes ligand activated
CRP
28
___________ is high when glucose is low, CRP binds this
cAMP
29
to get maximal expression of lac operon genes, _______ must be bound AND ______ _________ NOT bound
CRP, lac repressor
30
lactose intolerance means you have a ________ deficiency
lactase
31
lactose cannot be absorbed through the ________ wall unless it is _____________ digested to glucose and galactose
intestinal, enzymatically
32
X-gal
A chemical similar to lactose that turns dark blue when cleaved by beta-galactosidase (LAB)
33
in eukaryotes, the functional ground state is that expression is ______
off
34
the process of chemical changes to the DNA and histones that activate and inactivate gene expression (chromatin altered to allow transcription)
chromatin remodeling
35
in chromatin remodeling, core histones are either __________ or ___________
acetylated, methylated
36
acetylation of lysines by histone acetyltransferases (____) reduce the positive charge and decrease affinity of histones for _______
HATS, DNA
37
transcription by RNA Polymerase 2 requires __ classes of proteins
3
38
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
39
eukaryotic gene expression is repressed by ________ chromatin structure
condensed
40
active transcription requires local ________ of chromatin to relieve repression
remodeling
41
dense chromatin structure
transcription off
42
loose chromatin structure
transcription on
43
how many types of chromatin remodeling were shown to us?
5
44
acetylation methylation ubiquination sumoylation phosphorylation
5 types chromatin remodeling (all post-translational mods)
45
vitamin _____ (chemical) binds vitamin D receptor (protein) resulting in ___________ with RXR (protein)
D3, dimerization
46
Produced in the skin by ultraviolet irradiation
Vitamin D3 (cholecalciferol)
47
proteins that bind to the cis sequences and direct the assembly of transcription complexes at the proper gene
trans factors
48
vitamin D receptor is a ______ ________, meaning it directs assembly of transcription complexes at the correct gene
trans factor
49
transcription factors bind at super specific _______ sequences
DNA
50
transcription factors have _________ motifs
conserved
51
zinc fingers leucine zippers helix-turn-helix helix-loop-helix
examples of conserved motifs in transcription factors
52
vitamin D has a role in _________ of gene expression by using different _______-_________ factors
regulation, trans-acting
53
a regulatory protein that binds to a regulatory element in the DNA
trans acting factors
54
DNA sequences that bind regulatory proteins
cis elements
55
"Gene regulatory proteins that don't bind to dna are called __________ and ___________ (proteins that bind other proteins)"
coactivators and corepressors
56
adding a methyl group to DNA, x inactivation in females is an example of this
DNA methylation
57
Inactivates transcription of DNA (decreases expression)
hypermethylation
58
increased gene expression
hypomethylation
59
important in eukaryotes; cellular and enzymatic reactions that inhibit the process by which polypeptides are synthesized on ribosomes
translational repression
60
in translational repression, if you phosphorylate initiation factors (___________ them)
inactivates
61
in translational repression, if ___________ bind to mRNA and initiation factors then it can stop ____________
proteins, translation
62
a phenomenon in which gene expression and phenotype depend on which parent the genes come from
gene imprinting
63
Compulsive eating; (expresses 1, 3; segment 2 not expressed) DELETION OF PATERNAL
Prader-Willi Syndrome
64
aka happy puppet syndrome, mental retardation, seizures (expresses 2, 3; segment 1 not expressed) DELETION OF MATERNAL
Angelman Syndrome
65
excess, ectopic agouti expression (yellow phenotype) results in cancer, diabetes, obesity
LTR active
66
"pseudoagouti phenotype, ""normal"" agouti expression results: lean, healthy, normal lifespan
LTR suppressed
67
the study of environmental influences on gene expression that occur without a DNA change
Epigenetics
68
transcription at the lactose (lac) operon is maximal in bacteria when?
The cAMP and lactose levels are both high within the cell.
69
a mechanism used to regulate transcription at a eukaryotic gene is?
protein-DNA interactions

Integrated Exam 2/9 (11 decks)

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