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Microbio lecture > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

central dogma

A

dna-mrna-protein

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2
Q

Transcription

A

copying DNA to RNA

RNA polymerase

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3
Q

translation

A

decoding RNA to synthesize protein

Ribosome

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4
Q

Core polymerase =

A 
2 alpha (a) subunits + 1 beta (b) subunit + 1 beta-prime (b’) subunit + [1 omega (w) subunit (not required for transcription)]
B' subunit: houses Mg2+catalytic site
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5
Q

Sigma factors

A

guide RNA polymerase to beginn. of genes-to promoter

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6
Q

in e coli the sigma factor is

A

“housekeeping” sigma factor is RpoD s^70 (s=sigma symbol)

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7
Q

promoter

A
  • +1 nt

* promoter sequence generally (depends on sigma factor) at -10 and -35 nt

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8
Q

transcription begins

A
  • Typically with a purine (A, G)

* Sigma factor releases after first few bases are added (~9)

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9
Q

Transcription Elongation

A
  • Core RNAP synthesizes RNA ~45 bases per sec
  • Forms 17-bp transcription bubble
  • Energy for base addition comes release of pyrophosphate
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10
Q

Transcription Termination

• Rho-dependent termination

A
  • Rho – hexameric protein that binds to C-rich sequences in the open reading frame (ORF)
  • ATPase activity enables rho to move 5’ to 3’
  • RNAP pauses at termination site
  • Rho reaches RNAP and unwinds the RNA-DNA, releasing RNA and RNAP
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11
Q

Transcription Termination continued

• Rho-independent termination

A
  • Intrinsic termination
  • hairpin loop with GC-rich stem followed by poly-U
  • RNAP pauses at poly-U
  • U-A RNA-DNA hybrid is unstable
  • hairpin causes RNAP to leave DNA
  • NusA assists in RNAP pausing and hairpin formation
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12
Q

Rifamycin B binds to

A

b’ subunit near the Mg2+ active site and blocks the RNA exit channel. (antibiotics block transcription)

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13
Q

codons

A

nucleotides triplets that correspond to amino acids

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14
Q

Translation – The Ribosome

A

• Small subunit (30S) + large subunit (50S) = ribosome
(70S)
30S= 21 ribosomal proteins + 16S rRNA
50S=31 ribosomal proteins+ 5S rRNA + 23S rRNA

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15
Q

23S rRNA

A

ribozyme activity-peptidyltransferase

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16
Q

The ribosome has three binding sites for tRNA

A

E,P,A

17
Q

Initiation requires three initiation factors (IF)

A

IF1, IF2, IF3

18
Q

Translation – Elongation
1.
2.
3.

A

• Elongation factors (EF-Tu, EF-G) are complexed to GTP, which is used for energy
• 16 AA/sec
1. Aminoacyl-tRNA binds to the A site
• Bound to EF-Tu-GTP
2. Peptide bond forms between the new amino acid and growing peptide in position P
• 23S peptidyltransferase
3. Translocation - movement to the next codon
• EF-G-GTP

19
Q 
Translation – Termination
stops 
release
peptidyltransferase
rf3 enters
rrf
gtp hydrolysis
if3 binds
A
  • Stop codon moves into A site
  • Release factor RF1 or RF2 enters A site
  • Peptidyltransferase activity releases the peptide from tRNA in the P site
  • RF3 enters and triggers release of RF1 or RF2
  • Ribosome recycling factor (RRF) enters A site w/ EF-G GTP
  • GTP hydrolysis undocks the ribosomal subunits
  • IF3 binds 30S, preventing 50S from re-docking
20
Q

Streptomycin

A

binds to 30S subunit – interferes with codon-anticodon recognition site –results in mistranslated protein sequences

21
Q

Tetracycline

A

binds to 30S subunit and blocks aminoacyl-tRNA binding to the A site

22
Q

Chloramphenicol

A

inhibits peptidyltransferase activity of the 23S rRNA

23
Q

Erythromycin

A

binds to 23S rRNA and interferes with translocation

24
Q

Protein structure may be modified after translation

A

• N-formyl group may be removed by methionine deformylase (leaves a regular methionine)
•entire methionine may be removed by methionyl
aminopeptidase

25
Q

degrons

A

Proteins contain degradation signals

26
Q

N-terminal rule (protein degradation)

A
  • Leu, Phe, Trp, Tyr – short, 2 minute half-life
  • Asp, Glu, Cys – longer half-life
  • ClpS recognizes the N-terminal AA and presents protein to ClpAP protease
27
Q

Abnormally folded proteins are

A

recognized by proteases bc hydrophobic regions are exposed

  • Progressively degraded into smaller and smaller pieces
  • involve ATP-dependent endoproteases like Lon or ClpP
28
Q

cell envelope contains

How do they get to the specific locations?

A

proteins

  • Some proteins are secreted completely out of cell
  • Require special export systems
29
Q

Proteins meant for the inner membrane are

A

tagged with hydrophobic N-terminal signal sequences of 15-30 AA
Bound by the signal recognition particle (SRP)

30
Q

signal recognition particle (SRP)

A

pauses translation until its delivered to membrane

31
Q

Journeys through the outer membrane

A
  • Export out of the cell

* 7 secretion systems – classified based on their structure

32
Q

How many GTP molecules would it take to synthesize a

protein 100 amino acids in length?

A 
there are 99 bonds. 
GTPs 
1-initiation 
2-bond
1-termination
you do 99x2+1+1=200
33
Q

rna polymerase holoenzyme

A

core polymerase + sigma factor

34
Q

protein export to periplasm: general secretion pathway

A
  • Peptide completely translated in cytoplasm
  • protein wraps around SecB
  • SecB delivers the protein to SecA and SecYEG
  • SecA inserts the protein in SecYEG using ATP
  • LepB cleaves protein
  • protein must fold in periplasm

Microbio lecture (12 decks)

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