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Prokaryotic Gene Structure 2 Flashcards

transcription & translation (47 cards)

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1
Q

what are the 3 steps of transcription?

A
  1. initiation
  2. elongation/polymerisation
  3. termination
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2
Q

where in the cell does transcription occur?

A

cytoplasm

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3
Q

describe what happens in the initiation step of transcription (4)

A
  1. sigma factor recognises promoter & binds to TATA box (in promoter)
  2. binding signals rna polymerase coenzyme to attach & form holoenzyme
  3. weak TA bonds in TATA open & form open complex

different classes of sigma factor allows for regulated gene expr

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4
Q

describe what happens in the elongation step of transcription (4)

A
  1. RNA polymerase moves along DNA, create open complex as it moves
  2. template DNA strand used to make complementary mRNA as an RNA-DNA hybrid
  3. RNA synthesized in 5’ to 3’ direction using
    ribonucleoside triphosphates → pyrophosphate released
  4. transcription bubble moves @ 50 nucleotides per second

growing mRNA strand reads in 5’ - 3’ direction

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5
Q

describe what happens in the termination step of transcription (3)

A
  1. stops at termination signal
  2. mRNA & transcription bubble released
  3. post transcription modifications
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6
Q

what are the two types of bacterial mRNA transcripts?

A

monocistronic/monogenic
polycistronic/polygenic

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7
Q

what are the -35 and -10 consensus sequences?

A

another way to refer to the promoter in prokaryotes

(-10 is the TATA or pribnow box)

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8
Q

what does the promoter affect ito transcription and how does it do this? (3)

A

by influencing the affinity of RNA polymerase for a promoter

  • strong promoters tend to have unaltered consensus sequences
  • weak promoters = substitutions within promoter regions
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9
Q

what is the main part of RNA polymerase enzyme?

+ structure of this part

A

core enzyme - consists of 5 subunits & can’t bind DNA tightly or specifically

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10
Q

what is the holoenzyme? (3)

A

when the core enzyme is bound to a sigma factor, bind tightly to promoter at consensus sequences to form a closed promoter complex

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11
Q

how is the transcription bubble (open promoter complex formed)?

A

RNA polymerase holoenzymes unwinds DNA

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12
Q

what happens to the sigma factor when RNA polymerase starts moving in 3’ to 5’ direction @ 50 nucleotides per second?

A

it dissociates from the core enzyme

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13
Q

how are ribonucleotides added?

in transcription

A

via phosphodiester bonds at 3’ end of mRNA

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14
Q

what are terminators?

A

RNA sequences that signal that transcription must stop, causes core RNA polymerase to dissociate from template DNA

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15
Q

what are the two termination methods?

in transcription

A

rho-independent (intrinsic)
rho-dependent (extrinsic)

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16
Q

what are the steps of rho-independent (intrinsic) termination? (3)

in transcription

A
  1. formation of hairpin loop by U-rich sequence (6Us) & there are weak A-U bonds after the hairpin
  2. hairpin loop stalls RNA polymerase (stabilised by NusA protein)
  3. weak AU bonds can’t hold RNA-DNA hybrid together = RNA polymerase falls off DNA template
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17
Q

what are the steps of rho-dependent (extrinsic) termination? (3)

A
  1. RNA polymerase stalls at hairpin loop
  2. rho factor (p) binds to rut site on mRNA & moves to stalled RNA polymerase
  3. rho factor separates RNA polymerase from DNA-RNA hybrid

(rut = rho utilisation site)

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18
Q

what does actinomycin d do?

A

antibiotic
blocks elongation of bacterial RNA polymerase

Actin Delays Bacteria

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19
Q

what does α-β amanitin do?

Study These Flashcards
A

fungal toxins;
binds to & inhibits euk RNA pol II

Aminita Hits RNA pol II

20
Q

what does distamycin do?

Study These Flashcards
A

inhibits initiation of DNA transcription

Distamycin Dims DNA Transcription

21
Q

what does rifampicin do?

Study These Flashcards
A

antibiotic
inhibits initiation of DNA transcription
binds to beta subunit of RNA polymerase

22
Q

describe what happens in the initiation step of translation (2)

Study These Flashcards
A
  1. small ribosomal subunit binds to mRNA & tRNA
  2. binding of large ribosomal subunit (completes initiation)
23
Q

describe what happens in the elongation step of translation (3)

Study These Flashcards
A
  1. initiator tRNA docks at P-site
  2. A-site ready for incoming tRNA
  3. ribosomes catalyses peptide bond between aa (initiator leaves thru E-site)
    (repeat 3 steps)
24
Q

describe what happens in the termination step of translation (2)

Study These Flashcards
A
  • non-sense codons recognised by RF @ A-site
  • newly made polypeptide released from ribosome;
  • no complimentary stop anticodon (UAA, UAG, UGA)

RF = release factors
non-sense codons = stop codons

25
what is **code degeneracy**?
six diff codons can code for **a single amino acid**
26
what is **'wobble'** ?
base pairing at **3rd position** is **less precise** than at 1st & 2nd positions (tRNA can bind to more than one codon)
27
what is the direction of **protein synthesis**?
**N** terminal to **C** terminal
28
what about **protein synthesis in prokaryotes** can explain why bacteria can grow so fast?
multiple proteins can be made from **same mRNA** molecule & **ribosome** jumps **on transcript** as soon as **RNA emerges from RNA pol**
29
how is an amino acid matched with the correct codon? (2)
1. **aminoacylation** = aminoacyl-tRNA synthetase matches w tRNA by catalysing ATP-dep attachment of specific aa to 3' end of cognate tRNA 2. results in charged tRNA (aa-tRNA)
30
what is the function of the **A site** in the ribosome?
**acceptor site** attachment site for incoming **aminoacyl-tRNA**
31
what is the function of the **P site** in the ribosome?
**peptidyl site** occupied by tRNA **carrying the growing peptide chain**
32
what is the function of the **E site** in the ribosome?
**exit site** transiently occupied by **deacylated tRNA**
33
what does the **start codon** code for? (3) | name, what its used for, how its removed
**fMet-tRNAfMet**, a modified aa used to **initiate protein synthesis** (gets bound to P site) in bacteria and is **removed post-translationally**
34
what is normal **Met-tRNAMet** used for?
incorporation of Met for all other AUG codons
35
how is **30S ribosome subunit** formed (from initiation of translation)? (5)
**initiation factor proteins (IF) + GTP + N-fmet-tRNAfMet + mRNA + 16S rRNA**
36
which sequence is the **shine dalgarno sequence complementary to**?
**16S rRNA** sequence (UCCU core seq in E.coli) (allows proper alignment of ribosome on mRNA wrt start codon)
37
where does **shine dalgarno** lie on mRNA?
10 nucleotides upstream from AUG codons
38
how does **70S ribosome formation** take place?
**loss of IFs** → binding of **50S to 30S** **A site** now poised to accept incoming aminoacyl tRNA
39
what are the **3 steps** involved in **amino-acid addition**
**1. codon recognition 2. peptide bond formation 3. translocation**
40
what are the **stop codons**?
**UGA, UAA, UAG**
41
are stop codons read by tRNAs ?
no
42
what are **release factors**?
* **recognise stop** codon at A site, * causes **addition of water** molecule instead of aa, * allows **cleavage of tRNA carrier** from peptide chain
43
what happens in **translational coupling**?
each gene on polycistronic mRNA requires preceding gene to be translated first
44
how does translational coupling work?
as ribosome moves along **Gene 1**, ribosome causes **hairpin loop to unfold**, making **Gene 2's AUG codon available** for another ribosome to bind
45
what do **aminoglycosides** do?
**blocks** functioning of **initiation complex** & causes **misreading of mRNA**, used in treatment of TB
46
**tetracyclins**
**blocks** **tRNA binding to A site**
47
what is the difference between **bactericidal** and **bacteriostatic**?
bactericidal = kill bacteria bacteriostatic = stop from growing (allow immune system to kill)

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