Brainscape's Knowledge GenomeTM

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


See full index

bchm218 > module 4 > Flashcards

module 4 Flashcards

1
Q

what are the differences between the 7 rna synthesis factors? (i.e. mrna, trna, rrna)

A

mRNA; coding rna determines amino acid sequence of a protein
rRNA; present during translation
tRNA; present after translation
snRNA; gene regulation
snoRNA; processes rRNAs
miRNA; limit translation by binding to 3’end of target mRNA
lncRNA; regulatory RNAs

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

what is the different between transcription and dna replication?

A

transcription uses rNTPs as building blocks, does not require primers for initiation, selective, and only one strand is used as a template

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

what is similar between transcription and dna replication?

A

use template strand as blueprint to form polynulceotide, initiation-elongation termination steps, proceeds in 5’-3’ direction

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

what is the bacterial rna polymerase holoenzyme? (structure and function)

A

structure: five polypeptide subunit cores with 3 distinct subunits (B, B’, w) and two alpha subunits.

function: core associates with sigma coenzyme factor, acts as an initiator for transcription (dna binding selectivity)

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

what is the 3d clamp structure?

A

wraps around dna, channels within rna pol allows entry of different reaction component (rNTp entry, RNA exit, DNA entry)

function: pol moves down strand and forms a 17bp dna bubble for rNTPs to pair

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

describe the three steps of RNA synthesis

A
  1. three aspartic acid residues in rna pol active site that capture two mg+ ions
  2. one mg+ ion interacts with phosphate groups of rNTP and the other brings 3’-OH for nucleophilic attack (release PPi)
  3. hydrogen bonds between incoming rNTP and template DNA for alignment of active site
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is rna proofreading?

A

rna synthesizes 50-90 nucleotides per second, no built in centre

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

what is kinetic proofreading?

A

fraying is recognized by rna pol and stalls until pyrophosphorolysis reverses the reaction until correct rNTP is paired

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

what is nucleolytic proofreading?

A

pol reverses direction by a few nucleotides, endonuclease hydrolyzes the phosphodiester backbone to remove the incorrect base

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

describe the three phases of transcription

A
  1. initiation: pol binds to promoters upstream of transcriptional start site
  2. elongation: adds nucleotides to growing rna strand
  3. termination: release product of rna when its at the end of the transcriptional unit
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

describe the five steps of transcription

A
  1. binding of rna polymerase core to the dna promoter (assisted by sigma or transcriptional factors, closed complex)
  2. formation of transcription bubble (open complex)
  3. initiation
  4. elongation, promoter clears
  5. termination and recycling
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are the two types of sigma factors?

A

-35 and -10 regions: spacer between is 17-20 nucleotides for 2 turns of double helix, interaction site for sigma70

upstream promoter: between -40 and -60, bound by alpha subunit

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

what are the 7 steps of bacterial transcription?

A
  1. sigma factor binds to the promoter region (closed complex)
  2. the enzyme converts to open complex
  3. abortive initiation occurs; pol beings to transcribe but not all the way
  4. pol extends transcript beyond 10 nucleotides to create a stable rna
  5. elongation begins
  6. promoter sequence is cleared, sigma factor falls off pol
  7. pol is released when it encounters a termination sequence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are the differents between the three eukaryotic rna pols?

A

rna pol I: rRNA precursors, transcribe rRNAs

rna pol II: mRNA, protein coding genes

rna pol III: smaller functions RNAs (t and sn)

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

what is the TATA binding protein?

A

5’TATAAA sequence near -30 of promoter region, recruited through TAFs, external B sheets and loop stirrups in minor groove

function: initiation of all genes, inserts into alpha helices of major groove and bends dna to open to minor groove for hydrogen bonding

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

what are the two base pairs favoured in helical bending?

A

A-T base pairs, because they are more distorted for opening of the minor groove

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

what is electrophoretic mobility shift assay (EMSA)?

A

fragments of DNA are incubated with protein of interested (dark red band at top) and analyzed on nondenaturing polyacrylamide gel

dna covalently attaches radioactive phosphate groip at one end

free fragments (no protein) migrate more quickly the bottom (dark green bands)

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

what are the four steps of DNA footprinting?

A
  1. amplify and radiolabel one end of the dna
  2. add dna-binding proteins to aliquots of dna sample
  3. randomly cleave dna samples (expection: dna protected by protein)
  4. seperate samples by gel electrophoresis, film detects radioactive emissions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

result of dna footprinting?

A

Sp1 transcription factor is able to bind to two regions of a promoter (-42 and -21)

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

where does processing of pre mrna take place in eukaryotes vs prokaryotes?

A

eukaryotes; transcription/pre mrna takes place in nucleus and exits cytoplasm to be translated

prokaryotes: directly transcribed and translated by ribosomes, no place

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

what is 5’ capping?

A

prevents degradation when rna pol II synthesizes single stranded ribonucleic acids that are vulnerable to exos

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

what are the three components that help prevent mrna damage?

A

1-methyl-guanosine: prevents recognition of 5’ end by exos and mediates binding of mrna to ribosome

5-5’-triphosphate linkage: forms 5’ cap through condensation of GTP (guanylytransferase)

additional methyl groups: added at 2’OH of ribose sugars

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

what is 3’ polyadenylation? 3 steps

A
  1. pol II transcribes poly A addition site
  2. polyadenylation factors bind to poly A signal, initiating mRNA cleavage
  3. PAP synthesis the poly A tail, PABP protects the tail from degradation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what are splice sites?

A

determine whether an exon is included in the mature mRNA

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

what are introns?

A

alternative splicing for different protein products, certain exons are included

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what is pre mrna splicing?

A

introns are transcribed are are removed, exons join and form mature rna

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

what are the three meanings of the genetic code?

A

degenerate: one code, several codons have same meaning

robust: ability for single-base mutations with minimal consequences to protein

universal: amino acids and nucleotide bases have no chemical relationship

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

what are the five rules of the genetic code?

A
  1. it is non overlapping
  2. it does not contain pauses
  3. it is read in triplets
  4. it is read in linear fashion
  5. resistant to mutations
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

what do the three positions of the code do with mutations?

A
  1. amino acid change
  2. determines polar or hydrophobic amino acid
  3. no change at all
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

what are the four mutations of the genetic code?

A
  1. silent: no amino acid replacement
  2. missense: single base substitution, replaces one amino acid
  3. nonsense: results in termination codon
  4. nonstop: results in loss of stop codon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what is tRNA? (function and structure)

A

function: adaptor, recognizes specific codons within the mRNA sequences and covalently attaches the required amino acid to the polypeptide

structure: 73-93 nucleotide residues long, intramolecular base pairs fold in on itself

32
Q

what is the amino acid arm?

A

sequence CCA at 3’ terminus, amino acids attach, each carries specific A

33
Q

what is the anticodon arm?

A

base pairing between anticodon and codon of mrna, complementary (5’AUG with 5’ CAU)

34
Q

what is the difference between tRNA^Leu and Leu-tRNA^Leu

A

tRNALeu indicates uncharged, Leu-tRNALeu indicates charged.

35
Q

where does wobble base pairing occurs?

A

the third position of the mrna codon (5’ of anticodon)

36
Q

what are cricks four rules for wobble?

A
  1. first 2 bases correspond to tRNA anticodon
  2. when the first base is C or A tRNA only recognizes one codon, G or U tRNA can recognize 2 codons, I tRNA can recognize 3 codons
  3. different codons in first two bases require different tRNA
  4. minimum of 32, 1 for initiation, are needed for all 61 codons
37
Q

what is the ribosome? (structure and function)

A

function: place where interaction between trna and mrna occurs

structure: macromolecular complex of rrnas and r-proteins found in cytoplasm bound to endoplasmic reticulum

38
Q

what are the 60s and 40s functional centres of the ribosome?

A

60s: contains peptidyl transferase centre, catalyzes peptide bond formation between amino acids

40s: contains decoding centre, aminoacylated trnas read genetic code by base pairing

39
Q

what is the differences between a-site, p-site and e-site?

A

a-site: location of aminoacyl-trna binding

p-site: location of peptidyl-trna binding, growing polypeptide chain

e site: exit site occupied by the trna released

40
Q

what are the five steps of translation?

A
  1. initiator trna is charged with metionine
  2. translation initiates with assembly of mrna and aminoacylated trna on the small subunit (joins large unit to activate)
  3. polypeptide elongates with trna binding
  4. translation terminates at stop codon in mrna, releases mrna, dissociates ribosome subunits
  5. polypeptide folds following translation to form functional protein
41
Q

what are the three steps for initiation of translation?

A
  1. alignment of mrna on the small ribosomal subunit, IF-3 prevents premature assembly of ribosome
  2. association of trna with AUG codon in p-site, trna moves to ribosome by IF-2 and IF-1 blocks A site
  3. recruitment of large ribosomal subunit to form complex, IFs dissociate and consume GTP
42
Q

what is the shine dalgarno sequence? (location)

A

-initiation signal of 4-9 purine residues

-situated 8-13 nucleotides on the 5’ side of start codon

-recognized by 16s rrna of the 30s subunit

43
Q

what does polycistronic mrna mean?

A

has more than two genes that can be translated into proteins (bacterial, no eukaryotic)

44
Q

what are kozak sequences?

A

located near start codon, purine nucleotide, contact with Met-trna anticodon arm, circulate mrnas

45
Q

what is the function of the kozak sequence?

A

ensure mRNA processing is complete prior to translation, promote translational efficiency, and enable translational regulation of gene expression.

46
Q

what is a polysome?

A

single mrna transcript bound by multiple ribosomes

47
Q

what is trna fmet?

A

n-formylmethionine is incorporated after AUG initiation and this enzyme transfers the formyl group to the amino group of the methionyl part of tRNA, N group is blocked.

48
Q

what is trna met?

A

brings met residue at internal positions within growing polypeptide when there is an AUG codon (not initiator)

49
Q

what are the three steps of elongation?

A
  1. binding of aminoacyl-trna in the a site
  2. peptide bond formation between polypeptide in the p site and the amino acid in the a site
  3. translocation shifts the trnas and mrna by one codon
50
Q

what are the four steps of delivery of charged trnas?

A
  1. EF-Tu-GTP delivers charged trna to a site of active ribosome, two adenosine residues flip out in response to correct anticodon base pair
  2. hydrolysis of EF-Tu-GTP to EF-Tu-GDP + Pi creates energy
  3. accommodation; correct codon pairing, release EF-Tu-GDP
  4. EF-Tu-GDP recycles to EF-Tu-GTP through EF-Ts (exchange factors)
51
Q

what are the three steps of a peptidyl transferase reaction?

A
  1. transfer initiating N-formylmethionyl group from p site to a site
  2. nucleophilic attack of amino group on a site
  3. growing chain transfers to trna in a site, ribosome shifts, uncharged trna to e site, trna to p site
52
Q

what are the two antibiotics that interfere with translation?

A

aminonucleosides: bind to ribosomal a site and participate in bond formation but not translocation, halts protein synthesis (puromycin)

aminoglycosides: binds to small subunit and causes inappropriate flipping if a1492 and a1493 (gentamicin, streptomycin, and paromomycin)

53
Q

what causes translation termination?

A

RF-1 (UAG and UAA) and RF-2 (UGA and UAA) are release factors that recognize termination codons and bind to a site of ribosome , transfer polypeptide to water molecule

54
Q

how is lactose metabolized in e coli?

A

two regulatory regions (lacI and lacO) and three genes (lacZ, lacY, and lacA) that metabolize lactose

55
Q

what is the lac I region?

A

lac repressor protein (always expressed) that interacts with lacO to regulate transcription

56
Q

what is the lacO region?

A

lac operator, does not code for gene product, interacts with lacI to regulated transcription

57
Q

what is the lacZ gene?

A

B-galactosidase, catalyzes cleavage of lactose into components, metabolized further to generate ATP (enerZ)

58
Q

what is the lacY gene?

A

galactoside permease protein, inserts into bacterial plasma membrane and imports lactose into the cell (importY)

59
Q

what is the lacA gene?

A

thiogalactoside transacetylase, modifies toxic galactosidase that are removed from cell
(removA)

60
Q

what is the lac repressor function?

A

blocking gene transcription in absence of lactose, so bacteria doesn’t waste energy to produce protein products for lac operon (binded to for negative regulation)

61
Q

what is the lac repressor structure?

A

homotetrameric dna binding protein, 2 dimers, helix-turn-helix motif at n-terminus to bind to dna’s major groove

62
Q

what are the binding sites of lac operon?

A

inverted repeat of a dna sequence that binds to the repressor (always 1, but only 1 of the other two at a time)
1. O1 is 3’ of promoter region
2. O2 is in lacZ gene
3. O3 is 5’ of promoter region

63
Q

what is negative regulation of lac operon?

A

binding of the effector allolactose causes a conformational change in the lac repressor resulting in the dissociation of the repressor from the dna and a 1000 fold increase in the concentration of B-galactosidase

64
Q

what is positive regulation of lac operon?

A

in presence of glucose the lac operon is blocked by catabolite repression (inhibition of expression of genes required for the metabolism of other sugars in presence of glucose)

65
Q

what is the cAMP receptor protein?

A

activator, interacts with rna pol to enhance dna binding and transcriptional initiation, homodimer, subunits bind to cAMP

66
Q

what is inactivation and activation of cAMP?

A

inactivation: binding cAMP causes reduction of activator and inhibits expression

activation: cAMP binds activator (CRP) to binding region of DNA increasing expression

67
Q

glucose present, lactose present

A

repressor dissociates, low cAMP levels prevent CRP binding, rna pol initiates transcription

68
Q

glucose present, lactose absent

A

cAMP is low, cAMP-CRP does not bind to operon, repressor binds to operator, blocks rna pol preventing transcription

69
Q

glucose absent, lactose present

A

activator binds different molecule to dna and recruit rna pol for gene expression

70
Q

what is constitutive gene expression?

A

housekeeping genes, expressed constitutively, expression levels vary

71
Q

what is regulated gene expression?

A

genes undergo activation/repression, bind to dna sequences and facilitate/inhibit transcription

72
Q

what is dna looping?

A

distant regulation of a promoter occurs, activator binds to a DNA region distant from promoter, to make dna fold over in contact with transcriptional machinery

73
Q

what is post-transcriptional gene silencing?

A

genes are still transcribed but the resulting mRNAs are degraded before they can be translated into proteins

74
Q

what are the three steps for microrna expression and processing?

A
  1. mirnas are transcribed into sequences that can fold into hair-pin structures
  2. pri-mirnas are cleaved by nuclear endonuclease to produce 60 nucleotide long hairpins
  3. pre-mirnas bind to export receptor proteins, transported from nucleus to cytoplasm
75
Q

what are the four steps to gene silencing by sirna and mirna?

A
  1. pre-mrnas are cleaved by ribonuclease and incorporated into rna silencing complex
  2. mirrna unwinds and the unneeded strand is discarded
  3. needed strand is delivered to a particular mrna by argonaute protein
  4. mirna-mrna base pairing leads to argonaute-mediated degradation or translational repression followed by degradation

bchm218 (2 decks)

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