Topic #5 - Molecular Biology & Regulation Flashcards
1
Q
The Central Dogma
A
DNA → RNA → Proteins
2
Q
Replication
A
DNA copying to more DNA
3
Q
Transcription
A
DNA → RNA
4
Q
Translation
A
RNA → Protein
5
Q
Gene
A
A discrete segment of DNA
6
Q
One Gene - One polypeptide
A
This one gene makes this one protein. Monocistronic mRNA
7
Q
Introns (Pro vs. Euk)
A
Very Rare in Prokaryotes
8
Q
Polycistronic mRNA
A
Prokaryotes Only
Related genes get grouped together to simplify common control over the group.
9
Q
Ribose vs. Deoxyribose
A
RNA vs. DNA sugar - no oxygen in 2’ position of Deoxyribse
10
Q
DNA Strand Polarity
A
5’→3’ polarity
Phosphate is connected from 3’ end of first to 5’ of the next
11
Q
Tri-Phosphate addition of DNA bases
A
Adds new base to 3’ end
12
Q
Stability of base pairing
A
G/C has 3 Hydrogen Bonds (∴ Stronger)
A/T has 2 Hydrogen Bonds
13
Q
Phosphodiester backbone
A
Makes up outside of DNA Helix
14
Q
Frequency of helical turns
A
1 turn/10 base bairs. About every 3.4 nm
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
16
Q
DNA Supercoiling
A
Done in Circular Chromosomes of Prokaryotes. Uses DNA Gyrase in Proks. Euk- Wrapped around nucleosomes
17
Q
DNA Gyrase
A
Enzyme to supercoil DNA in Prokaryotes
18
Q
Semi-Conservative DNA Replication
A
1 parental strand remains & 1 new strand
19
Q
DNA pol III
A
Least abundant of the 3 pols, does the most work
20
Q
DNA Synthesis from DNA Pols
A
Synthesizes from 5’→3’; Reads template 3’→5’
21
Q
RNA Primase relationship with DNA
A
DNA Primase extends the RNA Primase into DNA primer of about 1-2 kilobases
22
Q
Leading Strand
A
DNA synth reads from 3’→5’ so DNA pol can go from 5’→3’ easily
23
Q
Lagging Strand
A
Reads from 5’→3’; can’t do read. Done in short 1-2 kilobase pieces
24
Q
Okazaki Fragment
A
The fragments of DNA synthesized from discontinuous synthesis
25
DNA Helicase
Unzips strands at the fork
26
Single-Stranded Binding (SSB) Proteins
Protects nuclease degradation & shape loss
27
Topoisomerase
Changes shape, superhelical density, linkings to keep DNA straight. DNA Gyrase
28
DNA Pol I
Removes RNA primers. Has exonuclease activity from 5'→3'. Takes outer base pairs - cuts out RNA primers. Also replaces ribonuclueotides w/ deoxys
29
RNA Primer Removal
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
30
DNA Ligase
"Tape" - restores Phosphodiester backbone & connects fragments
31
Bidirectional Replication
oriC (Origin of Chromosome)→ Theta structure from Replication Fork → 2 strands. Next round starts before 1st round ends.
32
mRNA half-life
Short - minimize wasted molecules
33
tRNA
Amino Acid Gopher that transfers them to where they need to be
34
rRNA
Occurs in Ribosomes. Protein work-horses. S - affected by size & shape so change in shape makes subunit addition to ribosoms funky
35
RNA pol Reading
Reads DNA 3'→5' because of the 5'→3' polarity of synthesis. Needs the DNA template to work - not primer but promoter.
36
Bacterial RNA pol
Only 1 RNA pol - Core Enzyme made up of β, β', α, ω & σ (Sigma subunits)
σs are not tightly bound to the enzyme
37
Holoenzymes
RNA pol in Bacteria - The Core Enzyme (RNA pol) + a Sigma subunit. This conjunction starts RNA transcription.
38
Sigma Subunits
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
Promoters of RNA transcription in Bacteria
Housekeeping Promoter - sigma-70
```
Pribnow Box (-10 bases from beginning)
-35 Sequence (-35 from beginning)
```
40
Pribnow Box (-10 Region)
Centered 10 Nucleotides from the first nucleotide. Lots of A/T Pairs b/c weakness. Consensus: TATAAT ((NOT the TATA box))
41
-35 Sequence
Consensus: TTGACA
| Asymmetric like Pribnow
42
Asymmetry of Recognition elements (-35 & -10)
Gives directionality of transcription - from 5' to 3' (go right)
43
Eukaryotic RNA pols
3 types - More complicated
| I, II, III.
44
RNA pol I
Encodes rRNA genes (in the nucleolus)
45
RNA pol II
Encodes mRNA genes (the least abundant pol)
46
RNA pol III
Encodes tRNA genes
47
pre-mRNA from RNA pol II
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
Termination of Bacterial RNA synth
Rho-Dependent & Intrinsic Terminators
49
Rho-Dependent Terminators
Bacterial RNA synth
| Needs the Rho protein to terminate (this is most common. Active complex)
50
Intrinsic Terminators
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
Archaean RNA synthesis
1 RNA pol - More complex than RNA pol from Bacteria; close to RNA pol II (euks).
52
Protein Splicing in Archaeans
Very rare - but it happens.
Inteins & exeins - similar to introns & exons
Also happens in some lower eukaryotes
53
mRNA Genetics
Uses 3 ribonucleotide codons
54
mRNA Code & Codons
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
Reading Frame
RNA needs to read in the correct order to produce the correct order & combination of polypeptides
56
tRNA
Brings amino acids to protein synthesis reaction.
| - Cognate Amino Acid attached by acid group
57
tRNA polarity & charge
Polarity: reads 5' to 3'
| Charge from Aminoacylase - charging enzymes. These enzymes are super specific
58
tRNA Nucleotide Modification
Adenine to Inosine happens at Anticodon 1. I can pair with anything but G at codon 3 - Wobble
59
Base Pair Wobble
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
Stop Codon Complexity
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
Shine-Delgarno Sequence
Sometimes called RBS - Ribosomal Binding Sequence.
Binds 16S rRNA near its 3' end (in 30S subunit)
62
AUG codon role in stopping
Binds tRNA with an N-formylmethionine
63
50S Subunit with tRNA in translation
Joins the complex - makes a 70S ribosome
64
Initiator tRNA location
In P site - the peptidyl site where peptides originate
65
Next tRNA (for 2nd A.A.) location
A Site - Aminoacyl site - where tRNA has an attached aminoacylated amino acid.
66
50S subunit in translation
Has ribozyme activity - RNA mediated catalysis. This forms the peptide bond in P site and in A site
67
Translocation
Moves tRNA from A to P site - after a few turns this action will make a polypeptide
68
Why GTP in Translation?
For Translocation (Pull the ribbon)
69
Nonsense Codons
tRNA cannot translate them into anything. Translation stops.
70
Release factors
Cleave protein from tRNA when its sitting doing nothing (from nonsense or stop codon)
71
Ribosome of Translation dissociation
70S dissociates to 30S + 50S
72
Bacteria - Uses multiple RBSs and AUG w/mRNA
Can utilize polycistronic mRNA - operons
73
Methionine
Formyl group is lost after translation
74
Polysome
Multiple ribosomes on one mRNA
75
Archaean Ribosomes
Lack N-Formylmethionine (use plain methionine)
76
Eukaryotic Ribosomes
Initiate scan with 5' cap - need monocistronic mRNA
Lack N-Formylmethionine (use plain methionine)
77
Stop Codon Complexity
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
Shine-Delgarno Sequence
Sometimes called RBS - Ribosomal Binding Sequence.
Binds 16S rRNA near its 3' end (in 30S subunit)
79
AUG codon role in stopping
Binds tRNA with an N-formylmethionine
80
50S Subunit with tRNA in translation
Joins the complex - makes a 70S ribosome
81
Initiator tRNA location
In P site - the peptidyl site where peptides originate
82
Next tRNA (for 2nd A.A.) location
A Site - Aminoacyl site - where tRNA has an attached aminoacylated amino acid.
83
50S subunit in translation
Has ribozyme activity - RNA mediated catalysis. This forms the peptide bond in P site and in A site
84
Translocation
Moves tRNA from A to P site - after a few turns this action will make a polypeptide
85
Why GTP in Translation?
For Translocation (Pull the ribbon)
86
Nonsense Codons
tRNA cannot translate them into anything. Translation stops.
87
Release factors
Cleave protein from tRNA when its sitting doing nothing (from nonsense or stop codon)
88
Ribosome of Translation dissociation
70S dissociates to 30S + 50S
89
Bacteria - Uses multiple RBSs and AUG w/mRNA
Can utilize polycistronic mRNA - operons
90
Methionine
Formyl group is lost after translation
91
Polysome
Multiple ribosomes on one mRNA
92
Archaean Ribosomes
Lack N-Formylmethionine (use plain methionine)
93
Eukaryotic Ribosomes
Initiate scan with 5' cap - need monocistronic mRNA
Lack N-Formylmethionine (use plain methionine)
