Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry 2 > gene expression > Flashcards

gene expression Flashcards

1
Q

upstream

A

before

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

downstream

A

after

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

RNA synthesis is catalyzed by

A

RNA pol using ssDNA as a template

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

core bacterial RNA polymerase

A

Core cannot directly interact with DNA - this function requires association of the core with a sigma factor
After initiation of transcription, sigma factor is released from RNAP holoenzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Strong promoters

A

Sigma factor makes sequence specific contacts with the promoter via the -10 and -35 regions
“Strength” of a promoter is dictated by affinity of sigma for these regions
Higher affinity = stronger promoter
Protein binding site is protected from DNAseI by protein binding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

does RNA pol require a primer

A

RNA pol can catalyze de novo synthesis of polynucleotides (does NOT require a primer)
5’ end of the transcript will carry a triphosphate from the first NTP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

RNAP uses ssDNA

A

RNAP maintains a region of ssDNA as it transcribes RNA

Transcription induces torsional stress, which is relieved by topoisomerases/gyrases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How are DNA replication and RNA transcription similar?

A

Both use ssDNA as template, template is always 3’ to 5’
Both make phosphodiester bonds RNApol uses NTPs DNApol uses dNTPs
Both synthesize nucleic acid 3’ to 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How are DNA replication and RNA transcription different?

A

RNApol starts at promoters, DNApol starts at origins of replication
But both have AT rich regions
DNA copies whole genome, RNA copies only discrete regions of genome
DNA ends with ds product, RNA ends with ss product

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

regulation of transcription in bacteria

A

Gene expression in bacteria is controlled by regulating whether or not a gene is expressed
Genes that work in common pathways are regulated together in units called operons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

polycistronic

A

A single mRNA is made that codes for multiple proteins: polycistronic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

operons

A

Operator and promoter are control regions (upstream of structural genes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

lacI

A

lacI = repressor protein

When lacI is bound to operator, transcription is off

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

lactose operon structural genes

A

lacZ, lacY, and lacA are structural genes: code for proteins needed to metabolize lactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

in vivo inducer

A

lactose is in vivo inducer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

in vitro inducer

A

IPTG is lactose analog

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

no lactose

A

Without lactose, a repressor prevents transcription of the structural genes
lacI gene codes for lacI repressor protein
This protein is made constitutively (ALWAYS)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

with lactose

A

With lactose, repressor binds lactose and releases the operator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

binding site for lac repressor protein

A

Many DNA binding sites have palindromic symmetry

The region from -5 to +21 is protected from DNAseI when lacI is bound

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what is required for full activation of lac operon

A

absence of glucose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

absence of glucose

A

Glucose is a preferred carbon source and will be used completely before lactose
“Catabolite repression”
An increase in cAMP signals the absence of glucose
cAMP binds CAP, which binds the promoter and stimulates transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

binding of CAP-cAMP induces,

A

DNA bending

Bending enhances RNAP holoenzyme binding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

arabinose operon (araBAD

A

Arabinose is a pentose that can be a carbon source
Its degradation requires 3 enzymes found in the araBAD operon
Transcription is regulated by both catabolite repression and arabinose-based induction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

araC gene

A

araC gene product binds arabinose and has a DNA binding domain
araC protein acts as BOTH an inducer and a repressor (depends on cellular conditions)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

araC with no arabinose

A

acts as a repressor
The operon has 3 binding sites for araC, araO1, araO2, and araI (really 2 half sites)
In absence of arabinose, araC protein forms a dimer that binds to araI1 and araO2
This keeps transcription of the operon off

26
Q

araC with arabinose

A

araC is an inducer
In presence of arabinose, araC releases the araO2 site and binds the araI2 site
araC-arabinose interacts with CAP-cAMP (when glucose is absent)
Together, this complex activates transcription

27
Q

Tryptophan (trp) operon

A

Codes for 5 proteins needed to synthesize tryptophan
Trp operon only transcribed when cellular trp levels are sufficiently low
Regulated by trp repressor, which binds trp
When trp repressor-trp complex is bound to the operator, the operon is off

28
Q

trp operon attenuation

A

Operon is also subject to attenuation, which allows transcription to be regulated based on amount of available trp in the cell

29
Q

in proks, how do translation and transcription occur

A

at the same time

30
Q

leader sequence

A

This allows aa concentration to regulate operon’s level of transcription
example of repressible negative regulation of gene expression
assumes 2 diff secondary structures

31
Q

2 structures of leader sequence of transcript

A

It trp levels are high, leader folds like a terminator, transcription STOPS (trp (the corepressor) binds trp repressor which blocks RNApol binding)
If trp levels are low, the leader folds like an anti-terminator, transcription continues

32
Q

attenuation: relatively high Trp levels

A

attenuation causing RNA pol to stop prematurely

Transcription = terminated

33
Q

attenuation: relatively low Trp levels

A

The transcript folds like an anti-terminator

Transcription continues

34
Q

Differences in transcription in eukaryotes

A

In euks, genomic DNA wraps around nucleosomes
Access of RNA pol to DNA is more complex
Euks have 3 RNA pols that transcribe different classes of genes
RNAPI transcribes ribosomal RNAs, RNAP II transcribes protein-coding genes, RNAP III transcribes tRNA genes, some ribosomal RNA genes, and other small RNAs
Regulation of transcription is more complicated in eukaryotes

35
Q

RNA pol II (yeast)

A

C terminal domain (CTD) is important in regulation

Alpha-amanitin is an RNAP II-specific inhibitor

36
Q

Promoters of eukaryotic protein-coding genes

A

TATA box (-25) is analogous to Pribnow box in proks
Strong promoters have a CAAT box located about -80
Housekeeping genes have GC boxes

37
Q

enhancers

A

Enhancers are positive regulators of gene transcription

They are bound by transcriptional activators

38
Q

silencers

A

Silencers are DNA sequences that act as negative regulators
They are bound by transcriptional repressors
Location with respect to transcription start site varies
Sequences are bidirectional - they function in either orientation

39
Q

response elements

A

sequences found in promoters that are responsible to cellular conditions
Response elements are bound by transcription factors that are activated by a particular cellular condition

40
Q

basal levels of transcription requires

A

a complex of general transcription factors plus RNAP II

41
Q

mediator

A

bridges transcription factors bound to enhances with the initiation complex
Mediator interacts with RNAPII-CTD and can activate or repress transcription

42
Q

DNA bending or looping

A

influences gene expression
DNA looping allows additional proteins to interact at the initiation site and either stabilize RNAP binding or destabilize RNAP binding

43
Q

access of transcription machinery to template strand

A

DNA is wrapped around nucleosomes (each nucleosome = 8 histone proteins)
For access, must move nucleosomes (chromatin-remodeling complexes) and/or must reduce affinity between DNA and histones (histone-modifying enzymes)

44
Q

chromatin-remodeling complexes

A

Contain proteins in SNF2 family of DEAD/H box-containing ATPases
3 complexes loosen DNA-nucleosome interactions by restructuring core octamers
This gives RNAP II and general transcription factors access to promoters

45
Q

histone-modifying enzymes

A

influence nucleosome-DNA affinity

46
Q

histone acetyltransferases (HATs)

A

add acetyl groups to histone tails
This separates DNA from nucleosomes (and promotes transcription)
TFIID has HAT activity

47
Q

methylation of histone tails

A

tightens DNA-nucleosome interactions (and represses transcription)

48
Q

histone modifications

A

Post-translational modifications to histone tails can selectively recruit proteins to chromatin
Proteins that cause compaction = repressed gene expression
Proteins that cause relaxation = activates gene expression

49
Q

important histone tail modifications

A

Lysine acetylation (HATs) and de-acetylation (HDACs)
Lysine methylation and de-methylation (methyltransferases)
Serine phosphorylation (kinases)
Lysine ubiquitination
Lysine sumolyation

50
Q

model of transcriptional regulation

A

Gene activation first requires altering nucleosomes to relieve the repressive state of chromatin, followed by interactions of RNAPII/GTFs with promoters
Transcriptional activators initiate the first step
Mediator then facilitates the second step by bridging distant transcriptional activators and GTFs/RNAPII

51
Q

DNA binding domains do what?

A

mediate interactions between proteins and DNA

52
Q

DNA binding domains examples (3)

A

Helix-turn-helix (HTH)
Zinc finger
Leucine zipper-basic region (leucine zipper is a dimerization domain; basic region binds DNA)

53
Q

helix-turn-helix motif

A

Alpha-helix fits into the major groove of B-form DNA
One of the helices binds DNA
It may recognize a specific sequence (direct readout) or a particular shape (indirect readout)
HTH proteins act as dimers

54
Q

Zn-finger motif

A

Zn is coordinated by Cys, His, or both
A single protein may have many zinc fingers
Each finger binds in the major groove of DNA

55
Q

Leucine zipper

A

basic region proteins

NOT a DNA binding domain, but is often found in DNA binding proteins

56
Q

capping of pre-mRNA

A

Guanylyl transferase catalyzes the addition of a guanylyl residue to the 5’ end of primary transcript (occurs co-transcriptionally)

57
Q

methylation of the 5’ end of pre-mRNA

A

This may facilitate later steps of pre-mRNA processing

58
Q

Splicing requires precise removal of introns

A

Essential sequences include the exon/intron junction and the branch site (located within the intron)

59
Q

snRNPs in spliceosomes

A

U1: targets 5’ splice
U2: targets branch
U4 to U6: targets 5’ splice, recruitment of branch point to 5’ splice site

60
Q

Spliceosome assembly

A

snRNPs (protein and RNA) interact with pre-mRNA to form the spliceosome
Splicing occurs co-transcriptionally

61
Q

Alternative splicing

A

creates multiple protein isoforms from the same gene

62
Q

DNA footprinting

A

methods to analyze protein–DNA complexes and to identify the position of the binding site

Biochemistry 2 (32 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions