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MCB 265 > Topic 4 > Flashcards

Topic 4 Flashcards

1
Q

DNA is ….

A

inert

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2
Q

RNA is the….

A

heart of transcription

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3
Q

copied strand

A

coding strand

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4
Q

other strand

A

template strand

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5
Q

RNA builds

A

5’ to 3’

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6
Q

Which base is replaced in RNA and with what

A

T replaced with U

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7
Q

RNA polymerase core enzyme made up of …..

A

5 subunits: 2 alpha, 2 beta, w

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8
Q

RNA holoenzyme includes….

A

additional sigma unit

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9
Q

What does core enzyme do?

A

unwinds DNA and forms transcription bubble

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10
Q

What stops the RNA

A

transcriptional terminator

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11
Q

Intrinsic (rho-independent terminators)

A

Forms when RNA hairpin structures form, creating a U that pause RNAP then forces it off

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12
Q

RNAP

A

RNA polymerase

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13
Q

Rho-dependent terminators

A

protein called Rho that cause RNAP to dissociate after certain sequence

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14
Q

What initiates transcription

A

promoters

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15
Q

How do you is a promotor is activated

A

binding of sigma factors and regulatory proteins

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16
Q

housekeeping sigma factor

A

sigma70 or RpoD

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17
Q

Rpod

A

recognizes 2 sequences upstream of transcriptional start site, -35 and the Pibrew box

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18
Q

transcriptional start site

A

+1

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19
Q

Pribrew Box

A

~10 bp upstream of +1 site

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20
Q

Messenger RNA

A

converted to protein via translation

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21
Q

Transfer RNA

A

functional RNA used in translation

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22
Q

Ribosomal RNA

A

functional RNA used in translation

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23
Q

open reading frames (ORF)

A

sequences translated into proteins

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24
Q

untranslated regions (UTR)

A

parts of mRNA not translated

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25
Q

Polycistronic

A

encodes more than 1 polypeptide

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26
Q

Operons

A

cluster of genes with 1 promoter

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27
Q

Genes in an operon are…..

A

cotranscribed

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28
Q

5’ UTR

A

+1 to start codon of gene

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29
Q

ORF

A

start codon to stop codon

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30
Q

3’ UTR

A

stop codon to final transcribed residue, includes termination sequences

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31
Q

how is transcription different in eukaryotes (8)

A
  • 3 polymerase
  • more complex, 12+ subunits
  • requires transcription factors to bind DNA and recruit RNAP
  • do not use operons, each gene has own promoter
  • mRNA spliced to remove introns
  • 3’ polyadenylated and G cap at 5’
  • mRNA transcribed in nucleus, translated in cytoplasm
  • TATA box
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32
Q

Archea Transcription

less complex version of eukaryotic transcription

A
  • resembles RNA pol II
  • uses TATA box
  • uses operons
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33
Q

Protein Structure?

A
  • made of amino acids connected by peptide bonds (polypeptides)
  • run N—-> C
  • only get built at the C end
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34
Q

Name the 2 Rare Amino Acids

A
  1. Selenocysteine

2. Pyrrolysine

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35
Q

How are amino acids groups? Name the four groupings!

A
  • grouped based on R-groups!
    1. non-polar (hydrophobic)
    2. polar
    3. positively charged
    4. negatively charged
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36
Q

Primary structure of proteins?

A

chain of amino acids

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37
Q

Secondary structure of proteins

A

alpha helices and beta sheets

- formed by H bonding of peptide backbone

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38
Q

Tertiary structure of proteins

A

3D structure of protein

- many secondary structures arranged together

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39
Q

Quaternary structure of proteins

A

many polypeptides coming together

===> called multimeric proteins

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40
Q

what are subunits in proteins?

A

the individual peptide chains in multimeric proteins
Identical units: homomeric
Different: heteromeric

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41
Q

What are protein domains?

A
  • structural/functional segments in proteins

- can be small/large

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42
Q

Example of a protein domain?

A

Helix-turn-Helix (HTH) domains

  • bind DNA (DNA binding regulatory proteins)
  • found in many proteins of any Salmonella genome
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43
Q

what does tRNA do?

A
  • convert/translate the mRNA sequence into a protein sequence
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44
Q

Each tRNA has a specific ________ that binds a particular three-base codon.

A

anticodon

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45
Q

What are tRNA synthetases?

A
  • enzymes that ‘charge’ tRNAs (add amino acid to the CCA at the 3’ end)
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46
Q

How many base pairs in a codon?

A

3

keep going guys, we got this!!

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47
Q

T/F: The same tRNA can be used for two different codons.

A

True!

- some tRNAs work using the ‘wobble’ method by having a mismatch in the 3rd position

48
Q

the typical Start codon?

A

typically: AUG

ATG in DNA sequence

49
Q

alternative start codons?

A

GUG, UUG

these aren’t labelled on the codon table as start codons so we memorize them?? Uhh

50
Q

What is the start codon translated to in bacteria?

A

N-formylmethionine (fMet) using a special tRNA

51
Q

What are the ribosome subunits?

in prok.

A

large: 50S, small: 30S ===> total is the 70S ribosome

52
Q

What mainly carries out the functions of the ribosome?

A

rRNA! It also catalyzes peptide bond formation

53
Q

What are Shine - Dalgarno sequences?

A

the ribosome binding sites for translation initiation

54
Q

What is used for energy in translation?

A

GTP!!!!

55
Q

How does translation begin? (initiation)

A
  • the ribosome binding site (shine dalgarno) binds to 16S rRNA in a random 30S ribosomal unit
  • this helps robosome look for AUG codons (bona fide step start)
  • fMet tRNA binds + GTP used for energy ===> 50S subunit recruited
56
Q 
Translation Initiation
(dumbed down version)
A
  1. Shine Dalgarno finds random 30S small subunit for bon fide (which is just looking for AUG codon)
  2. fMet tRNA binds AUG and its ready to hunt down a 50S subunit
  3. 50S subunit found and bound –> ribosome is ready to translate!
57
Q

The three sites of the ribosome

A

EPA
A site: new tRNA enters
P site: where the growing peptide chain is
e: exittttt! uncharged tRNAs leave

58
Q

What is the order of steps in translation?

A
  1. Initiation
  2. Elongation
  3. Termination
59
Q

Translation Termination

A
  • ribosome encounters stop codon so a release factor binds and dissociates ribosome
60
Q

What are polysomes?

A

Many ribosomes on one transcript.

61
Q

Can RNA be translated while transcription is still ongoing?

A

Yup. This is coupled transcription/translation in prok.

62
Q

T/F Euk. ribosomes are smaller than prok. ribosomes.

A

False! They’re bigger –> 40S small, 60S large

63
Q

Differences between euk. and prok. translation

A
  • in euk. transcription/translation is NOT coupled
  • euk. mRNA only encodes one gene
  • 5’ cap recognized in euk.
  • euk. translation is slightly more complex/more regulation
64
Q

Chaperones

hint: ‘changing rooms’

A
  • help proteins to fold properly
  • have controlled environment for proteins to fold properly
  • use ATP hydrolysis!!!
65
Q

E. coli chaperones to know

A

DnaJ/DnaK, GroEL and GroES

- most abundant chaperones in E.coli cells

66
Q

Where are proteins synthesized in prokaryotes?

A

in the cytoplasm by ribosomes

67
Q

How are proteins transported outside the cell if they’re required elsewhere?
reminder: proteins are impermeable to membrane

A

translocase systems! they help move proteins across and into cytoplasmic membrane

68
Q

Two core secretion systems?

hint: sec tat

A
  1. Sec secretion system

2. twin arginine translocase (tat)

69
Q

Sec secretion system

A

secretes UNFOLDED proteins and then the protein folds once its at the place it needs to be

70
Q

Tat pathway

A

secretes FOLDED proteins

71
Q

Regulating Transcription Initiation?

A

control whether or not RNA polymerase binds a

promoter and initiates transcription

72
Q

Transcription Factors?

A
  • DNA binding regulatory factors

- dictate if RNA polymerase is able to regulate transcription at a given site

73
Q

Purposes of DNA binding domains?

A
  • dimerization
  • interacting with other proteins (RNA pol)
  • regulatory domain
74
Q

Activator

A

Transcription factors that promote transcription

75
Q

Repressor

A

transcription factors that inhibit transcription

76
Q

________ work by binding
DNA at promoter & recruiting
RNA polymerase (sigma factor)
to begin transcription

A

Activators

77
Q

__________ bind DNA &
prevent RNAP DNA binding or
transcriptional initiation after it
binds.

A

Repressor

78
Q

What does it mean to be regulated allosterically?

A

binding of an
effector activates or
inactivates protein

79
Q

Inducers

A

turn on activator proteins or inactivate repressors

80
Q

Co-repressors

A

activate repressor proteins

81
Q

Inducible System?

A

is one that is off by default, but

can be turned on

82
Q

Repressible System?

A

one that is on by default, but

can be turned off

83
Q

What is ArgR?

A

repressor protein that controls the expression of an arginine
biosynthesis operon

84
Q

Explain Arginine Biosynthesis?

A

Low arginine levels = ArgR isn’t bound by arginine, doesn’t bind DNA –> arginine is synthesized

High arginine levels = ArgR to bind
the Operator & prevent
transcription of this operon

85
Q

Lac operon?

A

Machinery for breaking down lactose

86
Q

LacI repressor protein

A

binds lac Operator prevents transcription

87
Q

Catabolite repression

A

microbes eat best nutrients first, shut off secondary nutrients until needed –> not wasting energy

88
Q

T/F: In the presence of glucose,
production of cAMP is
inhibited.

A

True!

89
Q

What is required for lac operon to be expressed? (2 important things)

A

lactose AND low glucose levels

90
Q

cAMP?

A

signalling molecule or second messenger

91
Q

Stringent Response

A

ppGpp (produced in response to amino acid starvation) shuts down protein synthesis & induces amino acid biosynthesis

92
Q

Quorum sensing?

A

sensing the local density of cells through secreting/detecting specific molecules

93
Q

Autoinducers?

A

Quorum sensing involves signalling molecules (form of chemical communication)

94
Q

Signal Transduction uses which two proteins:

A

Sensor Kinase and Response regulator

95
Q

Sensor Kinase?

A

-resides in cytoplasmic membrane. -Senses specific signal -> activates kinase activity -> adds phosphate to response regulator

96
Q

Response Regulator?

A
  • When phosphorylated, becomes active

- Binds DNA to regulate expression of target genes (activator and/or repressor

97
Q

Transcriptional Silencing?

A

very tightly shutting off

expression of genes by altering the genome structure at promoter regions

98
Q

Example of transcriptional silencer:

A

H-NS (E. coli, Salmonella,

other Gram-negative bacteria)

99
Q

Role of H-NS:

A

prevents binding & restructures
DNA to a rigid structure to prevent RNA
polymerase from binding the DNA

100
Q

H-NS binds to …

A

regions of genome with high AT%

101
Q

Counter-silencing?

A

DNA-binding activators bind specific silenced loci & reverse effects of H-NS (re-structure DNA and/or remove H-NS)
allow specific genes to be expressed

102
Q

Global Regulators?

A

regulate large numbers of different genes in response to a given signal or environmental cue

103
Q

Regulon?

A

complete set of genes controlled by a given regulator

104
Q

Transcriptional attenuation

A

regulation that involves prematurely

terminating mRNA synthesis

105
Q

Translation efficiency?

A

usually whether or not

RBS is free to be bound by the ribosome

106
Q

Two major RNA structures that “shut off ”

gene expression

A
  • Formation of a stem-loop structure involving RBS

- transcriptional terminator

106
Q

Two major RNA structures that “shut off ”

gene expression

A
  • Formation of a stem-loop structure involving RBS

- transcriptional terminator

107
Q

Ribonuclease (RNase)

A

degrade mRNA

108
Q

sRNA?

A
  • base-pair to target mRNA(s) to regulate half-life and/or translational initiation
  • affects RBS availability and/or RNase targeting
109
Q

Hfq?

A

RNA chaperone that binds to both RNAs to stabilize their interaction

110
Q

Riboswitches?

A
  • ligand-binding RNAs –> adopt intricate 3D structures that specifically bind a particular small molecule
  • allows riboswitches to sense their environment
111
Q

Mechanism of Riboswitches?

A

Aptamer binds ligand, changes base-pairing in
the 5’UTR of mRNA to affect formation of:

(i) A stem-loop that
sequesters the RBS (blocks translation)

(ii) a transcriptional terminator
that prevents transcription of the genes.

112
Q

Feedback inhibition?

A

An enzyme within a given biosynthetic pathway is sometimes inhibited by
the end product of that pathway

113
Q

Protein-Protein interaction?

A

one protein binds another to control its activity

114
Q

Post-translational modification

A

enzyme adds a chemical moiety to a specific amino acid residue of a
protein, which alters its activity (change activity, or turn it “on”/“off ”)

115
Q

Role of Proteases?

A

enzyme used for clearing away and recycling misfolded proteins

MCB 265 (6 decks)

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