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Microbiology 201H > Topic #5 - Molecular Biology & Regulation > Flashcards

Topic #5 - Molecular Biology & Regulation Flashcards

1
Q

The Central Dogma

A

DNA → RNA → Proteins

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2
Q

Replication

A

DNA copying to more DNA

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3
Q

Transcription

A

DNA → RNA

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4
Q

Translation

A

RNA → Protein

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5
Q

Gene

A

A discrete segment of DNA

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6
Q

One Gene - One polypeptide

A

This one gene makes this one protein. Monocistronic mRNA

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7
Q

Introns (Pro vs. Euk)

A

Very Rare in Prokaryotes

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8
Q

Polycistronic mRNA

A

Prokaryotes Only

Related genes get grouped together to simplify common control over the group.

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9
Q

Ribose vs. Deoxyribose

A

RNA vs. DNA sugar - no oxygen in 2’ position of Deoxyribse

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10
Q

DNA Strand Polarity

A

5’→3’ polarity

Phosphate is connected from 3’ end of first to 5’ of the next

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11
Q

Tri-Phosphate addition of DNA bases

A

Adds new base to 3’ end

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12
Q

Stability of base pairing

A

G/C has 3 Hydrogen Bonds (∴ Stronger)

A/T has 2 Hydrogen Bonds

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13
Q

Phosphodiester backbone

A

Makes up outside of DNA Helix

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14
Q

Frequency of helical turns

A

1 turn/10 base bairs. About every 3.4 nm

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15
Q

Wide & Narrow grooves

A

Difference between helices changes. Asymmetrical helix helps with how certain proteins interact with the Minor Groove or the Major Groove

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16
Q

DNA Supercoiling

A

Done in Circular Chromosomes of Prokaryotes. Uses DNA Gyrase in Proks. Euk- Wrapped around nucleosomes

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17
Q

DNA Gyrase

A

Enzyme to supercoil DNA in Prokaryotes

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18
Q

Semi-Conservative DNA Replication

A

1 parental strand remains & 1 new strand

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19
Q

DNA pol III

A

Least abundant of the 3 pols, does the most work

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20
Q

DNA Synthesis from DNA Pols

A

Synthesizes from 5’→3’; Reads template 3’→5’

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21
Q

RNA Primase relationship with DNA

A

DNA Primase extends the RNA Primase into DNA primer of about 1-2 kilobases

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22
Q

Leading Strand

A

DNA synth reads from 3’→5’ so DNA pol can go from 5’→3’ easily

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23
Q

Lagging Strand

A

Reads from 5’→3’; can’t do read. Done in short 1-2 kilobase pieces

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24
Q

Okazaki Fragment

A

The fragments of DNA synthesized from discontinuous synthesis

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25
Q

DNA Helicase

A

Unzips strands at the fork

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26
Q

Single-Stranded Binding (SSB) Proteins

A

Protects nuclease degradation & shape loss

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27
Q

Topoisomerase

A

Changes shape, superhelical density, linkings to keep DNA straight. DNA Gyrase

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28
Q

DNA Pol I

A

Removes RNA primers. Has exonuclease activity from 5’→3’. Takes outer base pairs - cuts out RNA primers. Also replaces ribonuclueotides w/ deoxys

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29
Q

RNA Primer Removal

A
  1. DNA Pol I uses exonuclease activity from 5’→3’ to delete RNA primer
  2. Replaces Ribonucleotides with Deoxyribonucleotides
  3. DNA Ligase seals the deal - restoring Phosphodiester backbones
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30
Q

DNA Ligase

A

“Tape” - restores Phosphodiester backbone & connects fragments

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31
Q

Bidirectional Replication

A

oriC (Origin of Chromosome)→ Theta structure from Replication Fork → 2 strands. Next round starts before 1st round ends.

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32
Q

mRNA half-life

A

Short - minimize wasted molecules

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33
Q

tRNA

A

Amino Acid Gopher that transfers them to where they need to be

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34
Q

rRNA

A

Occurs in Ribosomes. Protein work-horses. S - affected by size & shape so change in shape makes subunit addition to ribosoms funky

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35
Q

RNA pol Reading

A

Reads DNA 3’→5’ because of the 5’→3’ polarity of synthesis. Needs the DNA template to work - not primer but promoter.

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36
Q

Bacterial RNA pol

A

Only 1 RNA pol - Core Enzyme made up of β, β’, α, ω & σ (Sigma subunits)
σs are not tightly bound to the enzyme

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37
Q

Holoenzymes

A

RNA pol in Bacteria - The Core Enzyme (RNA pol) + a Sigma subunit. This conjunction starts RNA transcription.

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38
Q

Sigma Subunits

A

E. Coli has 7 factors.
Different Sigma factors serve different purposes in different organisms and different numbers. i.e. Sigma-70 = 70 kilodaltons large

39
Q

Promoters of RNA transcription in Bacteria

A

Housekeeping Promoter - sigma-70

Pribnow Box (-10 bases from beginning)
-35 Sequence (-35 from beginning)
40
Q

Pribnow Box (-10 Region)

A

Centered 10 Nucleotides from the first nucleotide. Lots of A/T Pairs b/c weakness. Consensus: TATAAT ((NOT the TATA box))

41
Q

-35 Sequence

A

Consensus: TTGACA

Asymmetric like Pribnow

42
Q

Asymmetry of Recognition elements (-35 & -10)

A

Gives directionality of transcription - from 5’ to 3’ (go right)

43
Q

Eukaryotic RNA pols

A

3 types - More complicated

I, II, III.

44
Q

RNA pol I

A

Encodes rRNA genes (in the nucleolus)

45
Q

RNA pol II

A

Encodes mRNA genes (the least abundant pol)

46
Q

RNA pol III

A

Encodes tRNA genes

47
Q

pre-mRNA from RNA pol II

A

Directly from RNA pol II - requires processing first.

  1. Introns out, exons in
  2. 3’ poly-A tail (not by RNA pol)
  3. 5’ cap - Nucleotide w/weird linkage
48
Q

Termination of Bacterial RNA synth

A

Rho-Dependent & Intrinsic Terminators

49
Q

Rho-Dependent Terminators

A

Bacterial RNA synth

Needs the Rho protein to terminate (this is most common. Active complex)

50
Q

Intrinsic Terminators

A

Bacterial RNA synth

Stem-loop structure upstream of a run of U’s (U/A bonds are weaker). Better in test tubes - a rarer process.

51
Q

Archaean RNA synthesis

A

1 RNA pol - More complex than RNA pol from Bacteria; close to RNA pol II (euks).

52
Q

Protein Splicing in Archaeans

A

Very rare - but it happens.
Inteins & exeins - similar to introns & exons
Also happens in some lower eukaryotes

53
Q

mRNA Genetics

A

Uses 3 ribonucleotide codons

54
Q

mRNA Code & Codons

A

Code is degenerate ∴ Multiple codons can produce same amino acid.
AUG - the start codon - the Charlie Brown codon. Importance for proper reading frame.
UAA, UAG, UGA - Stop Codons

55
Q

Reading Frame

A

RNA needs to read in the correct order to produce the correct order & combination of polypeptides

56
Q

tRNA

A

Brings amino acids to protein synthesis reaction.

- Cognate Amino Acid attached by acid group

57
Q

tRNA polarity & charge

A

Polarity: reads 5’ to 3’

Charge from Aminoacylase - charging enzymes. These enzymes are super specific

58
Q

tRNA Nucleotide Modification

A

Adenine to Inosine happens at Anticodon 1. I can pair with anything but G at codon 3 - Wobble

59
Q

Base Pair Wobble

A

Relaxed rules of pairing - Specific for anticodon 1 (5’) and codon 3 (3’).
Part 2 of Wobble - G/U pairings allowed at positions 1 & 3

Reduces # of tRNA species - CCU, CCC, CCA can all use tRNA CGI

60
Q

Stop Codon Complexity

A

UGA, UAA, UAG

Needs 2 pieces of information to start translation with bacterial mRNA

  1. Shine-Delgarno Sequence
  2. Nearby AUG binding initiator tRNA that carries N-formylmethionine
61
Q

Shine-Delgarno Sequence

A

Sometimes called RBS - Ribosomal Binding Sequence.

Binds 16S rRNA near its 3’ end (in 30S subunit)

62
Q

AUG codon role in stopping

A

Binds tRNA with an N-formylmethionine

63
Q

50S Subunit with tRNA in translation

A

Joins the complex - makes a 70S ribosome

64
Q

Initiator tRNA location

A

In P site - the peptidyl site where peptides originate

65
Q

Next tRNA (for 2nd A.A.) location

A

A Site - Aminoacyl site - where tRNA has an attached aminoacylated amino acid.

66
Q

50S subunit in translation

A

Has ribozyme activity - RNA mediated catalysis. This forms the peptide bond in P site and in A site

67
Q

Translocation

A

Moves tRNA from A to P site - after a few turns this action will make a polypeptide

68
Q

Why GTP in Translation?

A

For Translocation (Pull the ribbon)

69
Q

Nonsense Codons

A

tRNA cannot translate them into anything. Translation stops.

70
Q

Release factors

A

Cleave protein from tRNA when its sitting doing nothing (from nonsense or stop codon)

71
Q

Ribosome of Translation dissociation

A

70S dissociates to 30S + 50S

72
Q

Bacteria - Uses multiple RBSs and AUG w/mRNA

A

Can utilize polycistronic mRNA - operons

73
Q

Methionine

A

Formyl group is lost after translation

74
Q

Polysome

A

Multiple ribosomes on one mRNA

75
Q

Archaean Ribosomes

A

Lack N-Formylmethionine (use plain methionine)

76
Q

Eukaryotic Ribosomes

A

Initiate scan with 5’ cap - need monocistronic mRNA

Lack N-Formylmethionine (use plain methionine)

77
Q

Stop Codon Complexity

A

UGA, UAA, UAG

Needs 2 pieces of information to start translation with bacterial mRNA

  1. Shine-Delgarno Sequence
  2. Nearby AUG binding initiator tRNA that carries N-formylmethionine
78
Q

Shine-Delgarno Sequence

A

Sometimes called RBS - Ribosomal Binding Sequence.

Binds 16S rRNA near its 3’ end (in 30S subunit)

79
Q

AUG codon role in stopping

A

Binds tRNA with an N-formylmethionine

80
Q

50S Subunit with tRNA in translation

A

Joins the complex - makes a 70S ribosome

81
Q

Initiator tRNA location

A

In P site - the peptidyl site where peptides originate

82
Q

Next tRNA (for 2nd A.A.) location

A

A Site - Aminoacyl site - where tRNA has an attached aminoacylated amino acid.

83
Q

50S subunit in translation

A

Has ribozyme activity - RNA mediated catalysis. This forms the peptide bond in P site and in A site

84
Q

Translocation

A

Moves tRNA from A to P site - after a few turns this action will make a polypeptide

85
Q

Why GTP in Translation?

A

For Translocation (Pull the ribbon)

86
Q

Nonsense Codons

A

tRNA cannot translate them into anything. Translation stops.

87
Q

Release factors

A

Cleave protein from tRNA when its sitting doing nothing (from nonsense or stop codon)

88
Q

Ribosome of Translation dissociation

A

70S dissociates to 30S + 50S

89
Q

Bacteria - Uses multiple RBSs and AUG w/mRNA

A

Can utilize polycistronic mRNA - operons

90
Q

Methionine

A

Formyl group is lost after translation

91
Q

Polysome

A

Multiple ribosomes on one mRNA

92
Q

Archaean Ribosomes

A

Lack N-Formylmethionine (use plain methionine)

93
Q

Eukaryotic Ribosomes

A

Initiate scan with 5’ cap - need monocistronic mRNA

Lack N-Formylmethionine (use plain methionine)

Microbiology 201H (5 decks)

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