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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
Q

what structure is found between the activator and repressor binding sites

A

promoter

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26
Q

regulatory mechanism ensuring optimal substrate use. (for lac operon) = lactose present, low glucose = optimal transcription

A

catabolite repression

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27
Q

catabolite repression is achieved using the regulatory protein ______, which binds cAMP and becomes ligand activated

A

CRP

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28
Q

___________ is high when glucose is low, CRP binds this

A

cAMP

29
Q

to get maximal expression of lac operon genes, _______ must be bound AND ______ _________ NOT bound

A

CRP, lac repressor

30
Q

lactose intolerance means you have a ________ deficiency

A

lactase

31
Q

lactose cannot be absorbed through the ________ wall unless it is _____________ digested to glucose and galactose

A

intestinal, enzymatically

32
Q

X-gal

A

A chemical similar to lactose that turns dark blue when cleaved by beta-galactosidase (LAB)

33
Q

in eukaryotes, the functional ground state is that expression is ______

A

off

34
Q

the process of chemical changes to the DNA and histones that activate and inactivate gene expression (chromatin altered to allow transcription)

A

chromatin remodeling

35
Q

in chromatin remodeling, core histones are either __________ or ___________

A

acetylated, methylated

36
Q

acetylation of lysines by histone acetyltransferases (____) reduce the positive charge and decrease affinity of histones for _______

A

HATS, DNA

37
Q

transcription by RNA Polymerase 2 requires __ classes of proteins

A

3

38
Q

what 3 classes of proteins are required for transcription by RNA Poly 2

A

1) basal transcription factors
2) DNA-binding transactivators
3) Co-activators (and repressors) for protein-protein binding

39
Q

eukaryotic gene expression is repressed by ________ chromatin structure

A

condensed

40
Q

active transcription requires local ________ of chromatin to relieve repression

A

remodeling

41
Q

dense chromatin structure

A

transcription off

42
Q

loose chromatin structure

A

transcription on

43
Q

how many types of chromatin remodeling were shown to us?

A

5

44
Q

acetylation
methylation
ubiquination
sumoylation
phosphorylation

A

5 types chromatin remodeling (all post-translational mods)

45
Q

vitamin _____ (chemical) binds vitamin D receptor (protein) resulting in ___________ with RXR (protein)

A

D3, dimerization

46
Q

Produced in the skin by ultraviolet irradiation

A

Vitamin D3 (cholecalciferol)

47
Q

proteins that bind to the cis sequences and direct the assembly of transcription complexes at the proper gene

A

trans factors

48
Q

vitamin D receptor is a ______ ________, meaning it directs assembly of transcription complexes at the correct gene

A

trans factor

49
Q

transcription factors bind at super specific _______ sequences

A

DNA

50
Q

transcription factors have _________ motifs

A

conserved

51
Q

zinc fingers
leucine zippers
helix-turn-helix
helix-loop-helix

A

examples of conserved motifs in transcription factors

52
Q

vitamin D has a role in _________ of gene expression by using different _______-_________ factors

A

regulation, trans-acting

53
Q

a regulatory protein that binds to a regulatory element in the DNA

A

trans acting factors

54
Q

DNA sequences that bind regulatory proteins

A

cis elements

55
Q

“Gene regulatory proteins that don’t bind to dna are called __________ and ___________ (proteins that bind other proteins)”

A

coactivators and corepressors

56
Q

adding a methyl group to DNA, x inactivation in females is an example of this

A

DNA methylation

57
Q

Inactivates transcription of DNA (decreases expression)

A

hypermethylation

58
Q

increased gene expression

A

hypomethylation

59
Q

important in eukaryotes; cellular and enzymatic reactions that inhibit the process by which polypeptides are synthesized on ribosomes

A

translational repression

60
Q

in translational repression, if you phosphorylate initiation factors (___________ them)

A

inactivates

61
Q

in translational repression, if ___________ bind to mRNA and initiation factors then it can stop ____________

A

proteins, translation

62
Q

a phenomenon in which gene expression and phenotype depend on which parent the genes come from

A

gene imprinting

63
Q

Compulsive eating; (expresses 1, 3; segment 2 not expressed)
DELETION OF PATERNAL

A

Prader-Willi Syndrome

64
Q

aka happy puppet syndrome, mental retardation, seizures (expresses 2, 3; segment 1 not expressed)
DELETION OF MATERNAL

A

Angelman Syndrome

65
Q

excess, ectopic agouti expression (yellow phenotype)

results in cancer, diabetes, obesity

A

LTR active

66
Q

“pseudoagouti phenotype, ““normal”” agouti expression

results: lean, healthy, normal lifespan

A

LTR suppressed

67
Q

the study of environmental influences on gene expression that occur without a DNA change

A

Epigenetics

68
Q

transcription at the lactose (lac) operon is maximal in bacteria when?

A

The cAMP and lactose levels are both high within the cell.

69
Q

a mechanism used to regulate transcription at a eukaryotic gene is?

A

protein-DNA interactions

Integrated Exam 2/9 (11 decks)

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