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Biochemistry > Transcription > Flashcards

Transcription Flashcards

1
Q

_____ is DNA-dependent synthesis of RNA (or the use of DNA as a template to the use of DNA as a template to synthesize RNA). Proceeds in the _____ direction.

A
  • transcription

- 5’ to 3’

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2
Q

_______ strand is read from 3’ to 5’ direction.

A
  • template (-)
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3
Q

_________ is the “coding strand”.

A
  • Nontemplate strand (“+”)
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4
Q

A ______ is a sequence of 20 – 200 bases “upstream” from a gene that serves as a recognition site for binding RNA polymerase.

A
  • promotor
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5
Q

By convention, the promoter occurs on the ________

A
  • nontemplate, or the coding strand.
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6
Q

Promotor contains regions rich in _______

A
  • A and T
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7
Q

____ base pairs separate more easily than ____ CG pairs

A
  • AT

- CG

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8
Q

Promoters are rich in ____ and _____

A
  • adenine

- thymine

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9
Q

AT pairs have ____ H bonds and CG pairs have ___ H bonds

A
  • 2

- 3

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10
Q

The closer the promoter corresponds to _______, the greater its “strength”.

A
  • consensus sequences
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11
Q

Strong promoters bind _______ more tightly, more frequently & more successfully, resulting in greater efficiency

A
  • RNA polymerase
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12
Q

Promoters can function in _____ specificity and _______ specificity

A
  • tissue/ organ (which express)

- developmental (when expressed)

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13
Q

______ is the enzyme that reads DNA to synthesize RNA

A
  • DNA polymerase
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14
Q

RNA polymerase contains

A
  1. Five polypeptides
  2. Core Enzymes
  3. Sigma Factor
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15
Q

____ does DNA binding.

A
  • B’
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16
Q

___ does catalytic site

A
  • B
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17
Q

___ does promotor binding, assembly and regulation

A
  • a
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18
Q

___ is the structural role known to restore activity of denatured RNA polymerase

A
  • w
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19
Q

___ promoter recognition (transiently binds to core enzyme to allow binding to correct strand & initiation site).

A
  • o factor
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20
Q

Three stages of transcription

A
  1. Initiation
  2. Elongation
  3. termination
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21
Q

Initiation Stages of transcription in prokaryotes

A
  • RNA polymerase binds to promoter, causing strand separation & unwinding
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22
Q

_____ continues as o factor falls away.

A
  • elongation
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23
Q

_______ in eukaryotes are an extreme example of active genes being transcribed many times

A
  • lampbrush chromosomes
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24
Q

_____ factor is an an ATP-dependent helicase (hexamer) that catalyzes the unwinding of RNA

A
  • Rho (p) factor
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25
Q

DNA duplex hybrids during ______ to promote termination of prokaryotic transcription.

A
  • transcription
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26
Q

______ attaches to transcript and follows RNA polymerase.

A
  • p factor
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27
Q

Hybrid duplex is unwound, RNA is detached when polymerase “stalls” at the _____ sequence.

A
  • terminator
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28
Q

The ______ is Poly A (consensus=AAUAAA) regions of (RNA) DNA that code for “hairpin” mRNA structures.

A
  • terminator
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29
Q

During termination of transcription in prokaryotes _____ and _____ fall away

A
  • mRNA

- polymerase

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30
Q

In eukaryotic transcription there are three different RNA polymerases and _____ can initiate transcription

A
  • none
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31
Q

In eukaryotic transcription ____ are more complex with more consensus sequences

A
  • complex
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32
Q

In _______ located in the located in nucleolus; transcribes large rRNA’s

A
  • RNA polymerase 1
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33
Q

In _____ located in nucleus; transcribes mRNA’s, snRNA’s

A
  • RNA polymerase 2
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34
Q

In _____ located in nucleus; transcribes tRNA’s, 5s rRNA’s

A
  • RNA polymerase 3
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35
Q

Eukaryotic RNA polymerases _____ initiate transcription

A
  • can not
36
Q

__ Box indicates transcription start site

A
  • TATA
37
Q

____ Box indicates “strong” promotor

A
  • CAAT
38
Q

___ Box indicates housekeeping gene

A
  • GC
39
Q

_________ are codes for proteins needed all the time

A
  • housekeeping genes
40
Q

In eukaryotic transcription ____ activates polymerase via _______ & transcription begins.

A
  • TFIIH

- phosphorylation

41
Q

An ______ is a short segment of DNA near eukaryotic promoters that bind transcription factors to enhance the level of transcription of certain genes.

A
  • enhancer
42
Q

Communication between enhancer regions and proteins bound at the promoter proceed through the multiprotein complex called ______

A
  • mediator
43
Q

Termination of transcription in eukaryotes

A
  • RNA polymerase 2 passes through TTATTT signals
  • pre mRNA carrying AAUAA signal is cleaved
  • A poly(A) tail is then added by poly(A) polymerase
44
Q

_______ is the addition of 100 – 250 adenylate residues (a “poly A tail”) to the 3’ end of mRNA transcripts after the “AAUAAA” termination sequence

A
  • Polyadenylation
45
Q

Function of Polyadenylation

A
  • Helps direct mRNA’s out of the nucleus to the cytoplasm.

- Protects 3’ end from exonuclease degradation; length of tail is related to “longevity of transcript”.

46
Q

rRNA’s & tRNA’s are encoded by _______

A
  • operons
47
Q

_______ do not require processing.

A
  • Prokaryotic mRNA’s
48
Q

Three types of mRNA processing in eukaryotes

A
  1. 5’ capping
  2. 3’-polyadenylation
  3. splicing
49
Q

_____ is the removal of introns and ligation of exons

A
  • splicing
50
Q

______ serves as a recognition site for ribosome attachment & prevents transcript degradation by exonucleases.

A
  • 5’ cap
51
Q

____ are coding regions

A
  • exons
52
Q

_______ is non-coding regions of pre-mRNA’s that must be excised and coding regions ligated together to form functional mRNA

A
  • mRNA splicing
53
Q

The snRNP pre-mRNA complex is called the _______

A
  • spliceosome
54
Q

snRNPs direct _____ formation and may catalyze _____

A
  • lariat

- splicing

55
Q

__________ recognize consensus splice sites (via RNA base pairing).

A
  • snRNPs, small nuclear ribo-nucleoproteins, or “snurps”
56
Q

Several snRNPs join together to form a “________”.

A
  • spliceosome
57
Q

Spliceosome cuts out _____ and attaches _____ ends together.

A
  • introns

- exons

58
Q

RNA splicing occurs in the ________

A
  • nucleus
59
Q

_____ provide cross-over recombination sites

A
  • introns
60
Q

______ correspond to different functional regions of a polypeptide

A
  • exons
61
Q

DNA binding proteins have ______ when genes are not transcribed unless an activator is present.

A
  • positive control

- activation and deactivation

62
Q

DNA binding proteins have

_____ when genes are always transcribed unless a repressor is present.

A
  • negative control
  • derepression (on)
  • repression (off)
63
Q

_____ are a unit of genetic function consisting of groups of genes with related functions where a single promoter and operator serve to control the expression of all genes in that unit together.

A
  • operon
64
Q

The _______ is a model system for investigating transcriptional regulation

A
  • lac operon
65
Q

Lac operon is consists of three genes and the promotor region

A
  1. lacZ
  2. lacY
  3. lacA
66
Q

When transcribed, the operon yields a ________ mRNA, one in which multiple coding sequences exist

A
  • polycistronic
67
Q

_______ phenotype is when all three genes are synthesized at high levels, even in the absence of inducer

A
  • Constitutive
68
Q

______ phenotype is when all three gene activities remain low, even after the addition of inducer

A
  • noninducible
69
Q

Mutations involving the two phenotypes of constitutive and noninducible are mapped to two locations

A
  1. lac O (operator)

2. lacI (repressor protein)

70
Q

______ is the true intracellular inducer

A
  • allolactose
71
Q

_____ is a synthetic inducer

A
  • IPTG
72
Q

Regulation by transcription factors is _______

A
  • combinatorial
73
Q

Summary of modes of gene regulation in eukaryotes

A
  1. Genomic control
  2. RNA processing (5’-capping, poly A tails, splicing).
  3. Regulation of nuclear RNA export out of nucleus.
  4. Translational control (message stability).
  5. Signal transduction.
74
Q

_______ inhibits RNA polymerase, silences expression.

A
  • Cytosine Methylation
75
Q

_______ promotes formation of euchromatin (i.e. uncoiling of supercoiled DNA); more accessible for transcription

A
  • Acetylation of histone lysines
76
Q

______ is condensed, darkly staining chromosomal DNA in nuclei.

A
  • Heterochromatin
77
Q

_______ is expanded, lightly staining chromosomal DNA in nuclei.

A
  • Euchromatin
78
Q

________ are associated with high transcriptional activity.

A
  • High levels of acetylation
79
Q

_______ and ______ are the enzymes responsible for adding or removing acetyl groups from specific lysine residues in histones.

A
  • Histone acetyltransferases and deacetylases
80
Q

_________ interact with acetylated lysine residues

A
  • Bromodomains
81
Q

__________ interact with methylated histones (especially at H3K4)

A
  • Chromodomains
82
Q

The relationship between histone modification patterns and activation or repression of genes is called _______

A
  • epigenetics
83
Q

_______ is a rare genetic disorder characterized by mental retardation and abnormalities of the head and facial and other areas. It is caused by mutations in the RSK2 gene (histone phosphorylation) and is inherited as a X-linked dominant genetic trait. Males are usually more severely affected than females.

A
  • Coffin-Lowry Syndrome
84
Q

________ is characterized by short stature, moderate to severe intellectual disability, distinctive facial features, and broad thumbs and 1st toes. It is caused by mutations in CREB-binding protein (histone acetylation)

A
  • Rubinstein-Taybi Syndrome
85
Q

____ is the cascade of processes by which an extracellular signal or stimulus (e.g. hormone, neurotransmitter, metabolite, light) is converted to some sort of physiological response.

A
  • signal transduction
86
Q

_______ produces cAMP.

cAMP activates ______.

A
  • Adenylate Cyclase

- Protein Kinase

Biochemistry (15 decks)

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