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Molecular Genetics > Exam Two > Flashcards

Exam Two Flashcards

1
Q

DNA polymerase fails to incorporate a

A

ribonucleotide

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2
Q

Things that contribute to the complex structure of RNA

A
  • Base pairing
  • Base stacking
  • Hydrophobic interactions of bases
  • Repulsion of negatively charged phosphate groups
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3
Q

Things that will denature RNA

A
  • high temperature
  • hydrogen bonding reagents
  • methanol
  • decreased salt concentration
  • pH
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4
Q

The 2’ hydroxyl makes RNA susceptible to

A

Alkaline Hydrolysis

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5
Q

Three majors types of RNA

A

mRNA, tRNA, rRNA

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6
Q

mRNA function

A

template for protein synthesis

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7
Q

mRNA stability

A

Unstable, half life of three minutes

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8
Q

tRNA function

A

Adapter between mRNA and amino acids

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9
Q

tRNA stability

A

Stable

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10
Q

rRNA function

A

The heart of the ribosomes that synthesizes protein

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11
Q

rRNA subunits

A

5S, 16S, 23S (bacteria)

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12
Q

rRNA stability

A

Stable

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13
Q

Regulatory RNAs

A

Small RNAs that can be important for regulation by annealing to mRNAs

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14
Q

Catalytic RNAs

A

Ribozymes that can carry out enzymatic reactions that usually affect other RNAs (but not all)

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15
Q

Core Polymerase function

A
  • capable of performing the enzymatic function
  • interacts with a series of auxiliary proteins that provide regulation
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16
Q

Sigma Factor function

A

Required for recognition of the promoter

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17
Q

Characteristics of strong promoters

A
  • they match the consensus
  • frequent initiation = lots of gene product
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18
Q

Characteristics of weak promoters

A
  • they DO NOT match the consensus
  • infrequent initiation = low levels of product
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19
Q

Rho-Independent (Intrinsic) Termination

A
  • hairpin formation in RNA transcript assisted by NusA
  • Hairpin structure is recognized by RNA polymerase
  • Transcription stops and RNA is released
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20
Q

Rho-dependent Termination

A
  • Depends on coupling of transcription and translation of mRNA
  • RNA pol pauses to check ribosome progress
  • If ribosomes lag, Rho binds RNA and causes termination
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21
Q

A mutation in a gene in an operon can stop downstream genes from being transcribed. This mutation is said to be

A

Polar

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22
Q

What does sedimentation coefficient mean?

A

Measures how fast a molecule travels to the bottom of a centrifuge tube in a viscous solution. Depends on shape and density

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23
Q

Polymerase I subunits

A

14 protein subunits

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24
Q

Polymerase I function

A

Transcribes rRNAs (18S, 28S, 5.8S)

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25
Q

Polymerase II subunits

A

12 protein subunits

26
Q

Polymerase II function

A

Transcribes mRNAs and other small stable RNAs

27
Q

Polymerase III subunits

A

16 protein subunits

28
Q

Polymerase III function

A

Transcribes tRNAs, 5S rRNA and other small stable RNAs

29
Q

Transcription occurs where in eukaryotes

30
Q

Translation occurs where in eukaryotes

31
Q

5’ Capping overview

A
  • Modified guanine ribonucleotide added to 5’ end of mRNA
  • occurs immediately and prior to completion of transcription
32
Q

3 enzymes needed for 5’ Capping

A
  • RNA triphosphatase
  • Guanylyl transferase
  • Methyl transferase
33
Q

Functions of 5’ Capping

A
  • protection from RNases = more stability
  • Required for transport from nucleus
  • Enhances translatability
34
Q

Polyadenylation overview

A
  • Addition of adenine ribonucleotides to 3’ end of mRNA
  • can occur prior to completion of transcription
35
Q

Functions of polyadenylation

A
  • Protection from RNases = more stability
  • Required for efficient transport from nucleus
  • Enhances translatability
36
Q

Torpedo model of termination

A
  • RNase w 5’ to 3’ exonuclease activity loaded onto the uncapped end of the RNA transcript
  • Degrades RNA and interacts with the RNA polymerase to stop transcription
37
Q

Allosteric model of termination

A

Transfer of polyadenylation factors from tail causes a conformational change in the RNA polymerase to terminate transcription

38
Q

Spliceosome

A
  • Machinery that splices most primary mRNA transcripts
  • protein-RNA Complex
  • Ribozyme
39
Q

tRNA transcription in eukaryotes

A
  • transcribed by RNA polymerase III
  • promoter often located downstream from startsite
  • requires transcription factors
40
Q

Open Reading Frame Definition

A

Reading frame composed of a series of contiguous codons that encode amino acids

41
Q

Charging tRNA steps

A
  • adenylation of aa
  • transfer of adenylated aa to tRNA
42
Q

Ribosome small subunit

A
  • 30S
  • 16S rRNA
  • 21 Small Ribosomal Proteins (S1, S2… S21)
43
Q

Ribosome large subunit

A
  • 50S
  • 23S and 5S rRNAs
  • 34 large ribosomal proteins (L1, L2… L34)
44
Q

Wobble definition

A

The 3rd base in the codon (3’ end) base pairs w the 1st base in the anticodon (5’ end) can “wobble” with Inosine in the Wobble position

45
Q

Wobble base pairings

A
  • IC
  • IU
  • IA
  • GU
46
Q

Initiation (prokaryotes)

A

Ribosome, mRNA, charged tRNA come together into 70S initiation complex

47
Q

How is the reading frame in initiation (prokaryotes) set?

A

30S subunit binds to mRNA at the appropriate position based on 16S rRNA (shine dalgarno or RBS)

48
Q

Elongation (prokaryotes)

A
  • Delivery of correct aminoacyl tRNA to A site in ribosome
  • Peptide bond formation between incoming amino acid and the fMet
  • Movement of ribosome along mRNA for acceptance of next charged tRNA
49
Q

Translocation

A

Movement of the mRNA and tRNAs within the ribosome

50
Q

Translocation by EG-G (GTP)

A

binds to factor-binding site, straightens out, and pushes everything over

51
Q

How is ribosome fidelity maintained?

A
  1. H bonds in minor groove of codon- anticodon w 16S rRNA
  2. EF-Tu (GTP) must fit into factor binding center to induce GTP hydrolysis and release of tRNA
  3. Accommodation- aminoacyl-tRNA pivots into active site thus straining the codon-anticodon pairing
52
Q

Termination (prokaryotes)

A
  • Recognition of stop codons in mRNA
  • Release of peptide chain from tRNA at P site
  • Dissociation of ribosomal subunits, tRNA, mRNA
53
Q

Release factors and ribosome recycling factors are involved in what

A

Termination in Prokaryotes

54
Q

RF-1 and RF-2 function

A

stop codons, transfers chain to water and releases peptide

55
Q

RF-3 (GTP) function

A

assists release of RF-1 or RF-2

56
Q

Energy requirements for Translation

A
  • 1 ATP to charge tRNA
  • 1 GTP for EF-Tu to deliver aminoacyl0tRNA to ribosome
  • 1 GTP for EF-G to translocate ribosome
57
Q

Eukaryotic 40S subunit

A
  • 18S rRNA
  • 33 ribosomal proteins
58
Q

Eukaryotic 60S subunit

A
  • 28S, 5.8S, 5S rRNAs
  • 49 ribosomal proteins
59
Q

Kozak Sequence

A
  • Purine nucleotide 3 residues upstream of start codon and G residue immediately after start codon
  • Enhances translation by contact with initiator tRNA
60
Q

Aminoacyl tRNA synthetases attach

A

Amino Acids to tRNA

61
Q

Class I aminoacyl-tRNA synthetase characteristics

A
  • generally monomeric
  • aa initially attaches to 2’ OH of the ribonucleotide at the 3’ end of tRNA
62
Q

Class II aminoacyl-tRNA synthetase characteristics

A
  • generally dimeric or tetrameric
  • aa initially attaches to the 3’-OH of the ribonucleotide at the 3’ end of tRNA

Molecular Genetics (4 decks)

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