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Genetics > Prokaryotic Gene Structure 2 > Flashcards

Prokaryotic Gene Structure 2 Flashcards

transcription & translation

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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?

A

fungal toxins;
binds to & inhibits euk RNA pol II

Aminita Hits RNA pol II

20
Q

what does distamycin do?

A

inhibits initiation of DNA transcription

Distamycin Dims DNA Transcription

21
Q

what does rifampicin do?

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)

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)

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)

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
Q

what is code degeneracy?

A

six diff codons can code for a single amino acid

26
Q

what is ‘wobble’ ?

A

base pairing at 3rd position is less precise than at 1st & 2nd positions (tRNA can bind to more than one codon)

27
Q

what is the direction of protein synthesis?

A

N terminal to C terminal

28
Q

what about protein synthesis in prokaryotes can explain why bacteria can grow so fast?

A

multiple proteins can be made from same mRNA molecule & ribosome jumps on transcript as soon as RNA emerges from RNA pol

29
Q

how is an amino acid matched with the correct codon? (2)

A
  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
Q

what is the function of the A site in the ribosome?

A

acceptor site

attachment site for incoming aminoacyl-tRNA

31
Q

what is the function of the P site in the ribosome?

A

peptidyl site

occupied by tRNA carrying the growing peptide chain

32
Q

what is the function of the E site in the ribosome?

A

exit site

transiently occupied by deacylated tRNA

33
Q

what does the start codon code for? (3)

name, what its used for, how its removed

A

fMet-tRNAfMet,

a modified aa used to initiate protein synthesis (gets bound to P site) in bacteria and is removed post-translationally

34
Q

what is normal Met-tRNAMet used for?

A

incorporation of Met for all other AUG codons

35
Q

how is 30S ribosome subunit formed (from initiation of translation)? (5)

A

initiation factor proteins (IF) + GTP + N-fmet-tRNAfMet + mRNA + 16S rRNA

36
Q

which sequence is the shine dalgarno sequence complementary to?

A

16S rRNA sequence (UCCU core seq in E.coli)
(allows proper alignment of ribosome on mRNA wrt start codon)

37
Q

where does shine dalgarno lie on mRNA?

A

10 nucleotides upstream from AUG codons

38
Q

how does 70S ribosome formation take place?

A

loss of IFs → binding of 50S to 30S
A site now poised to accept incoming aminoacyl tRNA

39
Q

what are the 3 steps involved in amino-acid addition

A

1. codon recognition
2. peptide bond formation
3. translocation

40
Q

what are the stop codons?

A

UGA, UAA, UAG

41
Q

are stop codons read by tRNAs ?

A

no

42
Q

what are release factors?

A
  • recognise stop codon at A site,
  • causes addition of water molecule instead of aa,
  • allows cleavage of tRNA carrier from peptide chain
43
Q

what happens in translational coupling?

A

each gene on polycistronic mRNA requires preceding gene to be translated first

44
Q

how does translational coupling work?

A

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
Q

what do aminoglycosides do?

A

blocks functioning of initiation complex & causes misreading of mRNA, used in treatment of TB

46
Q

tetracyclins

A

blocks tRNA binding to A site

47
Q

what is the difference between bactericidal and bacteriostatic?

A

bactericidal = kill bacteria
bacteriostatic = stop from growing (allow immune system to kill)

Genetics (14 decks)

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