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MBG 2040 > post midterm notes > Flashcards

post midterm notes Flashcards

1
Q

who first articulated the Central Dogma and when?

A

Francis Crick in 1958

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2
Q

what does DNA replication ensure?

A

that an exact copy of the species genetic info is passed from cell to cell during growth and from generation to generation

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3
Q

what happens if DNA fails to replicate itself?

A

the process for meiosis and mitosis would be halted.

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4
Q

true or false:

DNA replication is essential to life

A

true

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5
Q

who discovered the DNA structure?

A

J. Watson, F. Crick and M. Wilkins R. Franklin

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6
Q

how many base pairs are there per turn?

A

10

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7
Q

how many H-Bonds are there in G C pairs?

A

3

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8
Q

how many many Hbonds pair A and T?

A

2

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9
Q

what kind of base pairs does DNA have?

A

complementary

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10
Q

what is the most common form of DNA in living forms?

A

right-handed double helix (B-form DNA)

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11
Q

how many nm between stacked bases?

A

0.34nm

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12
Q

how many nm between helical turns?

A

3.4nm

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13
Q

how are DNA stands made by DNA polymerase?

A

5’-3’

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14
Q

what is left handed DNA?

A

Z-form DNA

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15
Q

what is A-form DNA

A
  • very compact form of DNA
  • not found in cells
  • only found in high salt concentrations
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16
Q

A linear, double-stranded DNA is 10,000 bp long (10 kb).

How many complete turns of the double helix are there?

A

1,000

10,000/10

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17
Q

A linear, double-stranded DNA is 10,000 bp long (10 kb).

What is the length of this molecule in μM?

A

3.4 x 1000 = 3400 nanometers or 3.4 micrometers

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18
Q

A linear, double-stranded DNA is 10,000 bp long (10 kb).

How many phosphorus atoms are there, assuming one phosphorus atom per nucleotide?

A

10,000 nucleotides per strand therefore 20,000 nucleotides total
20,000 phosphorous atoms

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19
Q

If there is 30% A in double-stranded DNA, how much G is there?What if the DNA was single-stranded?

A

20%

if single stranded, can’t tell composition of the rest

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20
Q

how many hydrogen bonds are there in the sequence, 5’ GATC 3’3’ CTAG 5’

A

10

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21
Q

Would G:C rich or A:T rich double-stranded DNA be more stable? Why?

A

G:C rich, more hydrogen bonds

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22
Q

true or false:

thermotropic microbes often have very highly rich G:C DNA

A

true:

need more hydrogen bonds to stay together in harsh environments

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23
Q

what were the 3 possibilities for DNA replication?

A

conservative replication
dispersive replication
semiconservative replication

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24
Q

what did Meselson and Stahl do?

A

proved that the semi-conservative model was the correct copying mechanism for DNA

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25
Q

what technique did Meselson and stahl use?

A

cesium chloride (CsCl) equilibrium-density gradient centrifugation to separate double-stranded DNA (dsDNA) molecules of different densities

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26
Q

how does cesium chloride (CsCl) equilibrium-density gradient centrifugation world?

A
  • permits separation of dsDNA based on density
  • heavier DNA (with 15N) sediments further down the CsCl gradient
  • lighter DNA (with 14N) migrates near the top of the CsCl gradient
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27
Q

which model of DNA replication applies to E. coli?

A

semiconservative

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28
Q

what is theta replication?

A

replication that occurs in most circular DNA

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29
Q

what is the product of theta replication?

A

2 circular DNA molecules

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30
Q

what are the 3 modes of DNA replication?

A

theta
rolling circle
linear chromosome

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31
Q

what is rolling circle replication?

A

specialized form of replication thatoccurs in the F factor and some viruses

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32
Q

is theta replication unidirectional or bidirectional?

A

bidirectional

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33
Q

is rolling circle replication unidirectional or bidirectional?

A

unidirectional

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34
Q

what are the products of rolling circle replication?

A

multiple circular DNA molecules

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35
Q

what is linear chromosome replication?

A

occurs in the linearchromosomes of eukaryotic cells

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36
Q

is linear chromosome replication unidirectional or bidirectional?.

A

bidirectional

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37
Q

what are the products of linear chromosome replication?

A

2 linear DNA molecules

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38
Q

true or false:

linear chromosome replication has 1 origin of replication

A

false:

multiple origins of replication

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39
Q

what mode of DNA replication do eukaryotic cells use?

A

linear chromosome replication

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40
Q

do origins of replication stay in the same spot after replication?

A

yes

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41
Q

what can use rolling circle replication?

A

small bacteria and viruses

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42
Q

what does DNA replication require?

A
  • Magnesium (Mg2+)
  • DNA dependent DNA polymerase
  • 4 deoxyribonucleoside triphosphates (dNTPs)
  • A template DNA to be copied
  • An RNA primer
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43
Q

what does an RNA primer provide?

A

the 3’-OH end to initiate DNA synthesis by DNA polymerase

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44
Q

true or false:

DNA is alwayssynthesized in the 5’ to 3’ direction

A

true

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45
Q

true or false:

Newly-synthesized DNA strand is complementary and anti-parallel tothe parent strand

A

true

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46
Q

Howard DNA strands held together?

A

by hydrogen bonds between complementary bases

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47
Q

A fragment of partially double-stranded DNA has the structure (5’ denotes the 5’ monophosphate; 3’ denotes the 3’ OH group),
5’ AGCTAGTTATTACG 3’
TCAATAAT
If this DNA was used as a template for replication, whichnucleotide would be incorporated first?

A

A

goes from 5’ to 3’
will extend to the left, right side will not extend anymore

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48
Q

where does chain cleavage lave the alpha phosphate group?

A

attached to 5’ or 3’ carbon

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49
Q

where is DNA synthesis continuous?

A

on the leading strand

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50
Q

where is DNA discontinued?

A

on the lagging strand

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51
Q

what are Okazaki fragments?

A

The short DNA fragments produced by discontinuousDNA synthesis

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52
Q

how many dnaA binding sites does E. coli have?

A

4

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53
Q

where does helices bind?

A

the strand that will express lagging strand synthesis

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54
Q

how does DNA helices unwind DNA?

A

in the 5’ to 3’ direction: travels on the lagging strand ahead of the replication machinery

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55
Q

what is unwound ss DNA coated with?

A

single-strand binding protein to keep DNA single-stranded

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56
Q

what does helicase-induced unwinding of the double helical DNA cause?

A

DNA ahead of the helicase to be overwound producing positive supercoils that would stop replication.

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57
Q

what nicks the DNA and releases the positive supercoils in bacteria?

A

specialized DNA topoisomerase II (DNA gyrase)

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58
Q

what does DNA primase synthesis?

A

short RNA primer that provides the 3’ OH end for DNA polymerase to begin DNA synthesis

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59
Q

how many DNA polymerase are there in E. coli?

A

5

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60
Q

what are the main DNA polymerases in E. coli?

A

I, III

Chromosomal DNA replication-replicative polymerases

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61
Q

what are DNA polymerase II, IV, V in E. coli?

A

DNA repair function

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62
Q

what are the activities of DNA polymerase I?

A
  • aids in removal of RNA primers
  • has 5’ to 3’ polymerase and 5’ to 3’ exonuclease activity
  • Proofreading: has 3’ to 5’ exonuclease activity
  • not highly processive; short tract synthesis
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63
Q

what are the Main activities on DNA polymerase III?

A
  • main replicative polymerase; highly processive
  • has 5’ to 3’ polymerase activity
  • lacks 5’ to 3’ exonuclease activity
  • Proofreading: has 3’ to 5’ exonuclease activity
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64
Q

what is the beta sliding clamp?

A

a ring-shaped polypeptide that encircles the DNA and interacts with DNA polymerase III to enhance processive DNA synthesis

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65
Q

What does ss DNA binding protein do?

A

keeps the unwound strand in an extended form for replication

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66
Q

what direction does all DNA synthesis occur in?

A

5’ to 3’

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67
Q

how fast is DNA synthesis in E. coli?

A

4000 base pairs added per second

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68
Q

what does the replication mechanism require?

A
  • topoisomerase
  • helicase
  • Single-strand DNA binding protein (SSB)
  • DNA primase
  • DNA polymerase III (plus βclamp)
  • DNA polymerase I
  • DNA ligase
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69
Q

what is the frequency for replicative polymerase?

A

30,000 nt/min

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70
Q

frequency of errors in replicative polymerase

A

1 error/ 10^10 nt added

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71
Q

describe eukaryote RNA primers and Okazaki fragments

A

shorter

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72
Q

when does DNA replication occur in eukaryotes?

A

S phase

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73
Q

what does Pol epsilon do in eukaryotes?

A

performs leading strand replication

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74
Q

what does Pol delta do in eukaryotes?

A

performs lagging strand replication

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75
Q

what does Pol alpha do in eukaryotes?

A

synthesizes has primase activity

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76
Q

true or false:

eukaryotes have Bidirectional replication from multiple origins of replication on each chromosome

A

true

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77
Q

what happens to the nucleosomes in eukaryotes?

A

need to be removed from parental DNA andproperly re-assembled on newly-synthesized DNA

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78
Q

describe telomeres in eukaryotes

A

shorten at each round of eukaryotic replication

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79
Q

true or false:

disassembly and Assembly of Nucleosomes is Tightly coupled and rapid during DNA synthesis

A

true

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80
Q

what is the telomere problem?

A

chromosome end will be degraded causing chromosome shortening during every round of replication

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81
Q

what does telomerase activity do in eukaryotes?

A

extends eukaryotic chromosome ends in replication

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82
Q

true or false:

telomerase does not resolve the terminal primer problem

A

false

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83
Q

true or false:

Most human somatic cells have high telomerase activity

A

false:

low

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84
Q

what are shorter telomeres associated with?

A

cellular senescence and death

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85
Q

what are diseases causing premature aging associated with?

A

short telomeres

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86
Q

true or false:

cancer cells have been found to have high telomerase activity

A

true:

thought to promote their growth

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87
Q

what are the 2 olecular biology techniques that are based upon fundamental knowledge of DNA replication?

A
  1. DNA sequencing

2. Polymerase chain reaction

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88
Q

what does DNA dependent RNA polymerase do?

A

moves along DNA to produce RNA

transcription

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89
Q

Describe what RNA contains

A
  • has a ribose sugar (bears an –OH group on its 2’ carbon)

- contains the base uracilin place of thymine

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90
Q

what kind of structure does RNA have?

A

tertiary structure

potential to be quaternary structure

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91
Q

what does structure in DNA affect?

A

how molecules bind to it

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92
Q

true or false:

transcription and translation happen at the same time in prokaryotes

A

true

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93
Q

true or false:

prokaryotes, the coding region of a gene is often a single, continuous unit

A

true

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94
Q

true or false:

tanscription, translation and mRNA degradation often occur at different times in prokaryote

A

false:

usually occurs simultaneously

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95
Q

what are exons?

A

protein coding segments

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96
Q

what are introns?

A

intervening (non-coding) segments

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97
Q

what happens when anscription and translation are not coupled-transcripts ?

A

made and processed in the nucleus and must be transported to the cytoplasm for translation

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98
Q

what is messenger RNA (mRNA)

A

intermediates that carry genetic information from DNA to the ribosomes

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99
Q

what is Transfer RNAs (tRNAs)

A

adaptors between amino acids and the codons in mRNA.

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100
Q

what is ribosomal RNAs (rRNAs)

A

structural and catalytic components of ribosomes

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101
Q

what is small nuclear RNAs (snRNAs and snoRNAs)

A

spliceosomes and rRNA, tRNA modification, respectively.

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102
Q

what are micro RNAs (miRNAs, siRNA and Crispr RNA)

A

short RNAs that block expression of complementary mRNAs

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103
Q

what is long noncoding RNAs

A

long RNAs that regulate gene transcription

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104
Q

who has a nucleus; eukaryotes or prokaryotes?

A

eukaryotes

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105
Q

which RNAs do not get made into proteins?

A

tRNAs, RNAs, nRNAs and snoRNAs, iRNAs, siRNA and Crispr RNA, long noncoding RNAs

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106
Q

what is the most frequent RNA in a cell?

A

ribosome (>80%)

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107
Q

what is the only kind of RNA that encodes proteins?

A

Messenger RNA (mRNA)

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108
Q

how is RNA synthesized?

A

in the 5’ to 3’ direction using the 3’ to 5’DNA template strand

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109
Q

true or false:

RNA and DNA strands are parallel

A

false:

antiparallel

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110
Q

how can transcription utilize the 3’ to 5’ template

A

either single strand of the double-stranded DNA (dsDNA), but always occurs in the 5’ to 3’ direction

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111
Q

true of false:

genes can overlap in 5’ to 3’ transcription

A

true

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112
Q

what is the DNA template?

A

4 ribonucleoside triphosphates (rNTPs)A, U, C, G

RNAn+ rNTP —> RNAn +1+ PPi

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113
Q

what does transcription use instead of deoxynucleoside triphosphate that are used in DNA replication?

A

ribonucleoside triphosphate

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114
Q 
A segment of mRNA has the sequence, 5’AUCCUGA 3’Which single-stranded DNA was it transcribed from?
A.5’ TAGGACT 3’
B.5’ UAGGACU 3’
C.3’ TAGGACT 5’
D.3’ UAGGACU 5’
E.More than one of the above
A

C.3’ TAGGACT 5’

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115
Q

what are some general features of RNA synthesis?

A
  • Similar to DNA Synthesis except
    –The precursors are ribonucleoside triphosphates (rNTPs)
    –Only one strand of DNA is used as a template.
    –RNA chains can be initiated de novo (no primer required)
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116
Q

how will RNA related to DNA?

A

complementary to the DNA template strand and identical to the DNA non-template strand

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117
Q

what is RNA synthesis catalyzed by?

A

RNA polymerases and proceeds in the 5’ to 3’ direction

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118
Q

what are the 3 stages of transcription?

A
  1. initiation
  2. elongation
  3. termination
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119
Q

describe initiation of transcription

A
  • RNA polymerase binds, unwinds and joins first 2 nucleotides.
  • initiation of RNA synthesis DOES NOT require a prime
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120
Q

describe elongation of transcription

A
  • complementary nucleotides continue to be added during the elongation process.
  • localized DNA unwinding ahead of RNA polymerase generates a “transcription bubble”.
  • transcription bubble moves with theRNA polymerase and the unwound DNA rewinds behind it
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121
Q

describe termination of transcription

A
  • stops when RNA polymerase reaches the “terminator”region of the gene
  • the newly-synthesized RNA together withRNA polymerase are released.
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122
Q

what are the 2 important sequence elements in a typical E. coli promoter?

A
  • the -35 element to which σfactor binds

- the -10 element, which due to it very A/T rich content is prone to unwinding

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123
Q

what do promoter recognition require in the initiation of transcription?

A

the RNA polymerase holoenzyme

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124
Q

what does the sigma factor recognize and bind to in the initiation of transcription?

A

the -35 element, thus positioningthe RNA polymerase at the promoterto begin transcription

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125
Q

what is the pribnow nob?

A
  • 35 sequence: 5’ TTGACA 3’

- 10 sequence: 5’ TATAAT 3’

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126
Q

where does transcription initiate?

A

about 5-9 base pairsdown from the end of the -10 sequence

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127
Q

what is the 5’ end of the RNA usually?

A

purine

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128
Q

when does elongation occur?

A

when Sigma factor is released and RNA polymerase begins to move along the 3’ to 5’ DNA template strand

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129
Q

what occurs as RNA polymerase moves along the DNA template?

A

A localized region of unwinding called the “transcription bubble”

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130
Q

what is removed by topoisomerases?

A

Positive supercoils formed in the double-stranded DNA ahead of the advancing RNA polymerase

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131
Q

true or false:

RNA polymerase has both helix unwinding and rewinding activities

A

true

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132
Q

what does Weak H-bonding at U:A residues allow?

A

mRNA release from DNA whenRNA polymerase pauses at terminator

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133
Q

what are Puffs in Drosophila polytene salivary chromosomes?

A

sites of localized unwinding due to gene transcription

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134
Q

true or false:

there are specific promoters for genes transcribed by Pol. I, Pol. II OR Pol. III

A

true

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135
Q

what do accessory proteins do in eukaryotes?

A

recognize each specific type of promoters (through interaction with DNA sequences) and recruit the appropriate polymerase to begin transcription

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136
Q

which has more complex promoters: eukaryotes or prokaryotes?

A

eukaryotes

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137
Q

what does eukaryotic initiation in the case of Pol II promoters involve?

A

step-wise assembly of general Transcription Factors of Pol. II (TFII A, B, D, E, F and H)

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138
Q

what does the preinitation complex do?

A

is sufficient to initiate transcription.

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139
Q

what does more complex transcriptional regulation involve?

A

a multi-subunit complex called “Mediator” that permits interactions with other activator proteins bound to upstream/downstream regulatory regions or enhancer sequences

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140
Q

what happens during elongation in eukaryotes?

A
  • many of the general transcription factors remain at the promoter providing for quick re-initiation with a new Pol. II.
  • an ~8 nucleotide “transcription bubble”is generated by RNA:DNA binding.
  • this together with DNA unwinding, ensures that the free RNA 3’-OH terminus is available for new rNTP addition.
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141
Q

what is alpha amanitin?

A

a molecules made from the death cap mushroom

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142
Q

what is alpha amanitin known as?

A

a known potent inhibitor RNA polymerase

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143
Q

what does termination in eukaryotes involve?

A
  • cleavage of the pre-mRNA and 5’ to 3’ degradation of the remaining RNA by the Rat1 exonuclease.
  • transcription terminates when Rat1 reaches RNA polymerase
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144
Q

describe the coding region in prokaryotes

A

coding region of a gene is not interrupted: the sequence of the gene is co-linear with the amino acid sequence of the protein

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145
Q

true or false:

the prokaryotic messenger RNA sequence corresponds to the gene from which it was transcribed

A

true

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146
Q

what is the Shine-Dalgarno sequence and what is it involved in?

A

5’ UAAGGAGGU 3’ is involved in the initiation of translation

147
Q

when was the presence of intron in eukaryotic genes discovered?

A

1970s

148
Q

what is required to form the mRNA that will be translated into a polypeptide?

A

the removal of introns along with additional RNA processing steps

149
Q

what are the 3 main processing steps in eukaryotic nuclear pre-mRNA?

A

A. addition of 7-methyl guanosine cap
B. addition of polyA tail
C. removal of introns

150
Q

describe A. addition of 7-methyl guanosine cap

A
  • Linked to pre-mRNA by a unique 5’-5’ phosphate linkage

- addition of 7-MG cap occurs early in the elongation process

151
Q

describe . Addition of PolyA tail

A
  • pre-mRNA is cleaved and then, a long string of “A” residues is added by Poly A polymerase
  • eukaryotic pre-mRNA is cleaved 11-30 nt following the 5’ AAUAAA 3’ sequence in the pre-mRNA.
  • Poly A polymerase adds a string of ~200 A residues at the cleaved end
152
Q

describe C. removal of introns

A
  • introns in pre-mRNA are removed by a specialized process called“RNA splicing”
  • removal of introns must be precise in order to properly fuse the 3’ end of one exon to the 5’ end of the next exon.
153
Q

what does every intro have?

A

two conserved sequences that are required for its removal

154
Q

what are the 2 conserved sequences that are required for an introns removals?

A

A. 5’ and 3’ splice sites: “GU and AG” sequences, respectively.
B. Intron Branch point: conserved “A” residue

155
Q

what is a spliceosome?

A
  • RNA/protein structure
  • Five small nuclear RNAs (snRNAs): designated U1, U2, U4, U5, and U6
  • The snRNAs associate with about 40 small proteins to form small nuclear ribonucleoproteins (snRNPs)
156
Q

what are the snRNPs that are assembled to form a complete spliceosome?

A

U1, U2, U4/6 and U5

157
Q

what does lariat formation involve?

A

a unique linkage between the 5’phosphate of the “G” and the2’ OH of the “A”

158
Q

how are introns of nuclear pre-mRNA transcript carried out?

A

by splicosomes

159
Q

how are introns of some rRNA precursors removed?

A

autocatalytically by reaction of the RNA molecule itself

160
Q

how are introns of tRNA precursors excised ?

A

by precise endonucleolytic cleavage and ligation reactions.

161
Q

how can 1 gene make many proteins?

A

presence of introns allows for alternative-modes of splicing and 3’ end processing that can generate protein diversity

162
Q

how many genes is it estimated that alternative processing occurs in for humans?

A

> 90%

163
Q

true or false:

genetic info is usually altered in the mRNA intermediary

A

false

164
Q

what are the 3 mechanisms that RNA editing can occur?

A
  • Changing the structures of individual bases (i.e., tRNAs, rRNAs).
  • Modification of mRNA by endogenous guide RNAs
  • Inserting or deleting uridine monophosphate residues
165
Q

what is an apoplipopotein?

A

blood proteins that carry lipids (fatand cholesterol) in the bloodstream

166
Q

what enzyme helps with RNA editing of ApoB?

A

Cytidine deaminase

167
Q

what does RNA editing f ApoB by the enzyme Cytidine deaminase do?

A

changes “C” to “U” converting a normal glutamine codon (CAA) to a termination codon (UAA), which truncates the protein and gives it a different function with respect to lipid binding

168
Q

what does the anticodon of the tRNA base pair bind with?

A

the codon of mRNA

169
Q

where is an amino acid covalently attached to?

A

the 3’ end of tRNA

170
Q

what do tRNAs often contain?

A

modified nucleotides through the action of tRNA modifying enzymes and they undergo processing events that remove small introns

171
Q

what are ribosomes composed of?

A

a large and a small subunit that are assembled from many different proteins and rRNAs

172
Q

what is a ribosome?

A

an “RNA machine” with key roles in protein synthesis, including the formation of peptide bonds between amino acids

173
Q

what is the nucleolus?

A

site of eukaryotic rRNA synthesis and ribosome assembly

174
Q

where does rRNA synthesis and ribosome assembly occur in prokaryotes?

A

in the cytoplasm

175
Q

what do enzymes do to rRNA transcripts?

A

modify and trim precursor rRNA transcripts to mature forms in the cell

176
Q

describe snRNAs

A
  • act complexes with proteins.

- play roles in post-transcriptional processing of RNA, such as splicing

177
Q

describe snoRNAs

A
  • act in complexes with proteins.

- guide the enzymatic chemical modifications of ribosomal RNAs, transfer RNAs and small nuclear RNAs

178
Q

describe small micro RNAs in eukaryotes

A
  • act as short (~22 nt), single-stranded RNAs that bind to complementary sequences in mRNA.
  • produced by cleavage of mRNAs, RNA transposons, and RNA viruses.
  • regulate and control gene expression in different ways
179
Q

describe small micro RNAs in prokaryotes

A
  • Crispr RNA- encoded by DNA sequences found in prokaryotic genomes.
  • Works in association with the prokaryotic Cas9 nuclease to cleave foreign DNA that might happen to enter a host cell (prevents incorporation of foreign DNA into the host genome
180
Q

where are long noncoding RNAs knows to function?

A

eukaryotic cells

181
Q

what is the signifiants of long noncoding RNAs?

A

about 80% of the mammalian genome consist of non-protein coding RNAs

182
Q

what is the function of long noncoding RNAs?

A
  • regulate and control gene expression at the level of transcription or translation by binding mRNA or sequestering micro-RNAs that control gene expression.
    OR
  • bind and recruit proteins involved in DNA modification
183
Q

what is sickle cell anemia caused by?

A

a single aminoacid change (Glu to Val) in one of the protein chains that make up hemoglobin in red blood cells

184
Q

what is an mRNA transcript?

A

the RNA copy of the template DNA strand of the gene

185
Q

what is the purpose of translation?

A

to decode the mRNA and make the functional protein product of the gene

186
Q

true of false:

Transcription, translation and mRNA degradation often occur simultaneously in prokaryotes

A

true

187
Q

where does transcription occur in eukaryotes?

A

the nucleus

188
Q

where does mRNA translation occur in eukaryotes?

A

the cytoplasm

189
Q

what do The sequence of base pair triplets in the coding region of a gene specify?

A

a colinear sequence of amino acids in its polypeptide product

190
Q

what did Beadle and Tatum: in the 1930s do?

A

through genetic analysis of nutritional mutants in the fungus Neurospora, they discovered that one gene encoded one discrete polypeptide

191
Q

what did Charles Yanofsky and colleagues: in the 1960s do?

A

through mutational/biochemical analysis, they discovered that the sequence of nucleotide triplets in the trpA gene of E. coli corresponded to the sequence of amino acids in the TrpA protein

192
Q

what are proteins made of?

A

polypeptides

193
Q

what is a polypeptide?

A

a long chain of amino acids

194
Q

what are amino acids made of?

A

a free amino group, a free carboxyl group, and a side group (R

195
Q

what are amino acids joined by?

A

peptide bonds

196
Q

what are peptide bonds?

A

The carboxyl group of one amino acid is covalently attached to the amino group of the next amino acid.

197
Q

describe primary structure of proteins

A

Linear arrangement of amino acids

198
Q

describe secondary structure of proteins

A

Determined by the spatial organization of amino acids

199
Q

describe tertiary structure of proteins

A

determined by the overall folding of the complete polypeptide

200
Q

describe quaternary structure of proteins

A

in some proteins, more than one polypeptide interacts to make a functional protein

201
Q

what is a singlet code?

A

since only 4 bases, only 4 codons specified…not enough for 20 amino acids

202
Q

what is a doublet code?

A

would specify only 42 = 16 possible codons… not enough for 20 amino acids

203
Q

what is a triplet code?

A

would specify, 43 = 64 possible codons… sufficient for synthesis of the 20 amino acids IF some amino acids were specified by more than one codon

204
Q

what kind of code is the genetic code?

A

triplet code

205
Q

what did arshall Nirenberg, Gobind Khorana, Philip Leder and colleagues play essential roles in?

A

deciphering the genetic code

206
Q

how was the genetic code deciphered?

A
  1. synthetic mRNAs of repeated sequence (homopolymers) were tested in vitro for protein synthesis: produced homopolypeptides
  2. Mixed mRNAs (random copolymers) were tested in same way: produced polypeptides with different amino acids.
207
Q

what did Nirenberg and Leder demonstrate in further experiments?

A

short mRNAs of known sequence stimulated the binding of ribosomes and the corresponding amino-acid bound tRNA

208
Q

true or false:

all Aino acids have 1 codon?

A

false:

some have more than one

209
Q

how many stop codons are there?

A

3

210
Q

how many start codons are there?

A

1

211
Q

why is there more than one codon for some amino acids?

A

Oftentimes, the base in the 3rd codon position can be changed and still specify the same amino acid: degeneracy

212
Q

true or false:

Base-pairing between mRNA codons and aminoacyl tRNAs is “anti-parallel”

A

true

213
Q

describe the wobble hypothesis

A
  • stringent base pairing between the codon in mRNA and the anti-codon intRNA only occurs for the first two bases of the codon
  • base-pairing at the third base of the codon is less stringent allowing “wobble”or flexibility at this position
214
Q

what does the wobble hypothesis explain?

A

how a single tRNA can respond to two or more codons

215
Q

what is at the wobble position?

A

ydrogen bondingand the non-standardbase-pairing

216
Q

what is inosine (I)?

A

a modified guanine/adenine derivative

217
Q

what are ribosomes made up of?

A

polypeptides (> 50) and ribosomal RNA (rRNA) molecules (3-4)

218
Q

what are macromolecules of translation made up of?

A
  • ribosomes
  • Amino-acid Activating Enzymes (20)
  • tRNA Molecules (40-60)
  • Soluble proteins
219
Q

what is a ribosome?

A

an “RNA machine” with key roles in protein synthesis, including the formation of peptide bonds between amino acids

220
Q

what are tRNAs?

A

adapters between amino acids and the codons in mRNA

221
Q

who and when was tRNA populated by?

A

Francis Crick in 1958

222
Q

what does he anticodon of the tRNA base pair with?

A

codon of mRNA

223
Q

where is the AA attached to tRNA?

A

covalently attached to the 3’ end

224
Q

how much tRNA synthetase does each ell contain?

A

1 for each amino acid

225
Q

what does tRNA synthetase catalyze?

A

formation of aminoacyl tRNA

226
Q

describe inititation f translation?

A
  • mRNA, large and small ribosomal subunits, initiation factors (IF1-3) and GTP are all required to form the initiation complex
  • 16S rRNA is a component of the 30S ribosomal (small) subunit
  • pairing between these sequences is involved in the formation of the mRNA/30S ribosomal subunit initiation complex
227
Q

what are the sites in the ribosome?

A

A - Aminoacyl site
P- Peptidyl site
E- Exit site

228
Q

what is the difference between the amino group of the methionine on the initiator tRNA in eukaryotes and prokaryotes?

A

is not formylated methionine in eukaryotes: simply MET

229
Q

what is there none of at the translation start site in eukaryotes?

A

no Shine-Dalgarno/AUG translation start site

230
Q

what do eukaryotes do to find the AUG initiation codon?

A

the initiation complex scans the 5’ end of the mRNA

231
Q

what does the Kozak sequence do in eukaryotes?

A

influences the efficiency of which AUG in the vicinity of the 5’ end is used to start translation

232
Q

what is the Kozak sequence?

A

at the 5’ end of the mRNA, the Kozak sequence is,5’- GCC (A or G) CC AUGG 3’

233
Q

what does the poly(A) tail of the eukaryotic mRNA interact with?

A

the mRNA 5’ cap structure via protein a cap-binding complex (CBC) to promote to promote translation initiation

234
Q

describe elongation of translation

A
  • An aminoacyl-tRNA binds to the A site of the ribosome
  • The amino acid is transferred from the tRNA in the P site to the tRNA in the A site by the formation of a peptide bond
  • The ribosome translocates along the mRNA to position the next codon in the A site.
  • This results in the polypeptide-tRNA being translocated from the A site to the P site
  • The uncharged tRNA is translocated from the P site to the E site and removed.
  • A new, aminoacyl-tRNA agains binds in the A site and the cycle is repeated
235
Q

when does termination of translation occur?

A

when a stop codon enters the A site of the ribosome.

236
Q

what are the stop codons?

A

UAA, UAG, and UGA.

237
Q

what happens when a stop codon is reached?

A
  • a release factor (RF) binds to the A site.
238
Q

what does release factor 1 recognize?

A

UAG and UAA

239
Q

what does relate factor 2 recognize?

A

UAA and UGA

240
Q

what did e discovery of ribosome structure permit?

A

detailed molecular analysis of how ribosomes work during protein synthesis

241
Q

what does chloromycetin inhibit?

A

formation of peptide bonds

242
Q

what does erythromycin inhibit?

A

translation of mRNA along ribosome

243
Q

what does neomycin inhibit?

A

interactions between tRNA and mRNA

244
Q

what does streptomycin inhibit?

A

initiation of translation

245
Q

what does tetracycline inhibit?

A

binding of tRNA to ribosome

246
Q

what does papomomycin inhibit?

A

validation of mRNA-tRNA match

247
Q

what do mRNA specialized mechanisms do?

A
  • eliminate mRNAs with nonsense mutations.
  • eliminate mRNAs in which a stalled ribosome cannot complete proper translation
  • eliminate mRNAs that are damaged by chemicals, unusual secondary structures, etc
248
Q

what do Molecular chaperones function to assist ?

A

proper foldingof newly-synthesized proteins and are often associatedwith the ribosome during translation.

249
Q

what are the steps of translation?

A
  1. polypeptide chain initiation
  2. chain elongation
  3. chain termination
250
Q

what is the Shine-Dalgarno sequence?

A

5’ AGGAGG 3’

251
Q

who helped with our understanding of how the ribosome works?

A

Venkatraman Ramakrishnan,
Thomas A. Steitz,
Ada E. Yonath

252
Q

what is Xeroderma pigmentosum?

A

lack of nucleotide excision repair of UV-induced lesions
(DNA repair pathway defect)
- develop skin cancer if pyrimidine dimers don’t get removed

253
Q

true or false:

changes in DNA structure and errors in replication dooccur

A

true:

just rare

254
Q

how is the vast majority of cellular DNA damage corrected?

A

by efficient DNA repair mechanisms.

255
Q

what happens what DNA damage is not corrected?

A

an inherited changein genetic informationmay occur and this is a “mutation”

256
Q

what is a mutation?

A
  • A heritable change in the sequence of an organism’s genetic material-the mutation may alter the phenotype of the organism.
  • The process by which genetic change occurs
257
Q

what is a mutant?

A

An organism that carries one or more mutations in its genetic material

258
Q

what do mutations occur in?

A

in all organisms with genetic material, from viruses to humans

259
Q

true or false:

Mutation is the source of all genetic variation.

A

true

260
Q

what happens during meiosis regarding mutations?

A

recombination between homologous chromosomes rearranges genetic variability into new gene combinations

261
Q

what is a somatic mutation?

A

occur in somatic cells; it will occur only in the descendants of that cell and will not be transmitted to the progeny.

262
Q

what is a germinal mutation?

A

occur in germ-line cells and will be transmitted through the gametes to the progeny.

263
Q

what were the original mutations that occurred in fruit trees?

A
  • somatic mosaics

- vegetative propagation allowed the somatic mutation to be perpetuate

264
Q

true or false:

somatic mutations can lead to cancer

A

true

265
Q

what is the expanding of nucleotide repeats known as?

A

“dynamic mutation” because the nucleotide repeat copynumber can expand or contract dramatically in each cell

266
Q

what occur at localized sites in DNA-often referred to as “point mutations”?

A
  1. Base substitution
  2. Frameshift mutation
  3. Tautomeric shifts
267
Q

what is gross chromosomal rearrangement?

A

A change in chromosomenumberor structure

268
Q

describe base substitution

A

replacing one base with another

269
Q

describe transition base substitution

A

replaces a pyrimidine with another pyrimidine or a purine for another purine

270
Q

describe transvehrsion base substitution

A

replaces a pyrimidine with a purine or a purine with a pyrimidine

271
Q

how many different base substitutions can occur in DNA?

A

12

272
Q

describe frameshift mutations

A

insertions or deletions of 1-2 base pairs alter the reading frame of the gene detail to the site of mutation

273
Q

true or false:

protein sequence is fairly similar after the frameshift mutation

A

false:

changes dramatically

274
Q

what is a tautomeric shift?

A

movement of H atoms from one position in a purine or pyrimidine base to another

275
Q

are tautomeric shifts common or rare?

A

rare:
can occur spontaneously during DNA replication where they alter DNA base pairing. Cause some spontaneous mutations
(A:C and G:T base pairs)

276
Q

when can bases form A-C and G-T base pairs?

A

When the bases are in their rare enol or imino states

277
Q

what is a G:C to A:T base pair change:?

A

transition mutation

278
Q

what are the normal forms of the DNA bases?

A

amino forms and keto forms

279
Q

what does the mechanism of expansion involve?

A

DNA replication

280
Q

what is a forward mutation?

A

a genetic alteration that changes the wild-type phenotype to mutant

281
Q

what is a reverse mutation?

A

changes the mutated site back to normal, hence reversing the mutant back to the wild-type phenotype

282
Q

what is a missense mutation?

A

a base substitution that results in an aminoacid change in the protein

283
Q

what is a nonsense mutation?

A

a base substitution that changes a sensecodon to one of the three nonsense (stop) codons (UAG, UGAor UAA)

284
Q

what is a silent mutation?

A

a base substitution at the 3rd codon position that changes the codon to one still specifying the same amino acid

285
Q

what is a neutral mutation?

A

a missense mutation in which the amino acid is changed to one of a similar chemical type

286
Q

what is a loss-of-function mutation?

A

he result of mutations that cause complete or partial loss of normal protein function

287
Q

what is a gain-of-function mutation?

A

the result of a mutation that causes the cell to produce a protein or gene product whose function is not normally present

288
Q

what is a conditional mutation?

A

expressed only under certain conditions (i.e., a temperature-sensitive mutation-only observed at elevated temps)

289
Q

what is a lethal mutation?

A

causes premature cell death

290
Q

what is a suppressor mutation?

A

a second site mutation that hides or suppresses the effect of the first mutation.

291
Q

true or false:

suppressor mutations can be within the same gene or different gene

A

true:
same - intragenic suppressor
different - intergenic suppressor

292
Q

true or false:

spontaneous mutations are frequent

A

false:
If we assume a typical gene is ~103nucleotide pairs, then the mutation rate varies from ~10–4to 10–7 per gene per generation

293
Q

how much can treatment of bacteria with mutagens increase mutation frequency?

A

> 1% per gene

294
Q

what are mutations that occur under normal circumstances a result of?

A

internal factors are called “spontaneous” mutations

295
Q

what are mutations that occur as a result of external factors called?

A

“induced” mutations

296
Q

what is most DNA damage caused by?

A

internal factors generated by normal metabolic processes

297
Q

true or false:

we have several dedicated DNA repair systems

A

true

298
Q

what does spontaneous DNA damage result from?

A
  • DNA replication errors
  • DNA replication pausing
  • Endogenous chemical reactions
299
Q

what are examples of DNA replication errors?

A
  • tautomeric shifts
  • wobble-induced base misfiring
  • strand slippage during replication
300
Q

describe how wobble-induced base misfiring occurs

A

flexibility in base-pairing (or wobble) can result in non-standard G-T and C-A base pairs, which lead to transition mutations

301
Q

what is strand slippage during replication?

A

occurs in repeated DNA sequences. Also, misalignments during recombination

302
Q

what is DNA replication pausing?

A
  • replication stalling at a DNA nick
  • unusual DNA structure or bulky lesion can generate broken DNA such as DNA ends or double-strand breaks (DSB), which can be lethal or mutagenic
303
Q

what are the 4 types of endogenous chemical reactions?

A
  1. depuration
  2. deamination
  3. oxidation
  4. alkylation
304
Q

what is depuration?

A

spontaneous loss of a purine base from a nucleotide through hydrolysis of the glycosidic bond
- generates transition or transversion mutations

305
Q

which is more frequent: loss of a purine or pyrimidine base?

A

loss of a purine

10,000 cell/day vs. 500 cell/day

306
Q

what is deamination?

A
  • spontaneous loss of -NH2 group of DNA base

- causes transition mutation

307
Q

what is oxidation?

A
  • endogenous reactive oxygen species (ROS) damage DNA

- Can produce oxidized bases, such as 8-oxoG, which frequently mispairs with C or Ato producetransversion mutations

308
Q

what is alkylation?

A

endogenous alkylating agents can add methyl groups to DNA bases
- produce transition mutations

309
Q

what mutagens induce DNA damage?

A
  • chemical agents

- radiation

310
Q

when were induced mutagens first discovered and by who?

A

1927 by Hermann Muller

311
Q

what did Muller’s experiment entail?

A

can induce mutations in the fruit fly Drosophila using X-rays: through studies of X-linked mutations.

312
Q

what are the categories of mutations caused by chemical agents?

A
  • mutagenic to both replicating and non replicating DNA

- mutagenic only to replicating DNA

313
Q

what are alkylating agents?

A
  • mutagens that great with DNA bases and add methyl or ethyl groups
  • directly or indirectly can induce transitions, transversions, frameshifts and chromosomal aberration
314
Q

what is nitrous acid?

A
  • deaminating agent.
  • Removes amino (–NH2) groups from DNA bases A, C and G.
  • Cause transition mutations
315
Q

what is hydroxyl amine?

A
  • hydroxylating agent
  • -hydroxylates the amino (-NH2) group of cytosine causingthe modified base to pair with adenine after replication
  • transition mutation
316
Q

what are the 2 common base analogs?

A
  • 5-bromouracil (5-BU) (resembles T)

- 2-aminopurine (2-AP) resembles A or G)

317
Q

what do base analogs do?

A

Incorporated into DNA during replication and when rare tautomers arise will eventually cause transition mutation

318
Q

describe acridines

A

ercalation of an Acridine dye causes frameshiftmutations during DNA replication

319
Q

what are the 2 main types of radiation that cause mutations?

A
  • Ultraviolet (UV) light induces mutations through excitation.
  • X-rays (and shorter wavelengths) induce mutations through ionization
320
Q

at peak sunlight, what does each human skin cell acquire?

A

4500 thymine dimers and UV-induced photoproducts per hour!

321
Q

what does ionizing radiation cause?

A

nicks and DSB in chromosomes

322
Q

what can faulty repair of DNA breaks by recombination cause?

A

gross chromosomal rearrangements such as deletions, duplications, inversions, and translocations

323
Q

NA is constantly being damaged by endogenous (mostly) and exogenous agents.-in spite of this, the rate of mutation in cell is remarkably low
why?

A

we have a number of very potent mechanisms for repairing DNA damage

324
Q

what are our DNA repair mechanisms?

A
  • Direct reversal of DNA damage
  • Excision repair (base excision and nucleotide excision)
  • Mismatch repair
  • Recombination
  • Translesion DNA polymerases (Error-prone repair)
325
Q

how does direct reversal of DNA damage work?

A
  1. Light-Dependent Repair: Direct repair of thymine dimers by the enzyme, photolyase (called, photoreactivation: only found in prokaryotes)
  2. Enzymatic removal of alkyl groups from DNA bases
  3. Ligation of single-stranded nicks in DNA.
326
Q

what are the 2 kinds of excision repair?

A
  • base excision repair

- nucleotide excision repair

327
Q

what are the common features of excision repair?

A
  • A DNA repair endonuclease or endonuclease-containing complex recognizes, binds to, and excises the damaged base or bases.
  • A DNA Polymerase fills in the gap, using the undamaged complementary strand of DNA as a template.
  • DNA ligase seals the break (nick) left by DNA polymerase
328
Q

how does base excision repair (BER) work?

A
  • a dedicated repair mechanism that specifically recognizes and repairsDNA bases damaged by deamination, alkylation or oxidation.
  • found in both prokaryotes and Eukaryotes
329
Q

how does nucleotide Excision Repair (NER) work?

A

NER acts to remove thymine dimersand other bulky forms of DNA damage

330
Q

what do mutations of human NER genes cause?

A

Xeroderma pigmentosum

331
Q

how does mismatch repair (MMP) work?

A
  • recognizes a mismatched base in the newly-replicated DNA strand through identification of the hemi-methylated GATC sequence
  • compares old and new strands based on methylation status of “A” in the sequence,
  • After detection, an exonuclease removes a portion of the newly-synthesized strand that includes the incorrect base.
  • DNA polymerase fills in the gap and ligase seals the nick
332
Q

wha do defects in the human mismatch repair result in?

A

cancer

333
Q

how much of colorectal and endometrial cancers are hereditary and cause by mutations in human mismatch repair genes?

A

10%

334
Q

what are the 2 types of recombination?

A
  • homologous recombination (HR)

- non-homologous end joining (NHEJ)

335
Q

how does homologous recombination work?

A
  • often occurs during or after DNA replication.
  • If one sister chromatid suffers a DSB, it can be repaired using the identical (unbroken) sister chromatid.
  • usually occurs in the S/G2 phases of the eukaryotic cell cycle
  • used to ensure proper chromosome separation (dysjunction )during meiosis
336
Q

how does non-homologous end joining work?

A
  • uses an entirely different set of proteins to repair DSB.

- available throughout the rest of the eukaryotic cell cycle

337
Q

what is Post-replication Recombination Repair?

A
  • involves pairing and strand exchanges between DNA duplexes
  • provides a mechanism for T:T to be by-passed so that replication can continue.
  • repairs double-stranded breaks in chromosomes
338
Q

what is the SOS response?

A

In the event that DNA is heavily damaged by mutagenic agents, a DNA damage response is activated

339
Q

true or false:

in bacterial cells, an increase in mutation = adaptation to environment

A

true

340
Q

what do pyrimidine dimers and other bulky DNA lesions block resulting in cell death if replication cannot continue?

A

replicative polymerases

341
Q

what are transposable elements?

A

segments of DNA capable of moving from one location in a chromosome to another, or even to a different chromosome

342
Q

what are the 3 categories of transposable elements?

A
  1. cut and paste transposons
  2. replicative transposons
  3. retrotranspons
343
Q

what are cut and paste transposons?

A

element is physically cut out of one site in a chromosome or plasmid and pasted into a new site

  • DNA transposon
  • excision and insertion catalyzed by a transposase
  • found in both prokaryotes and `eukaryotes
344
Q

what are replicative transposons?

A

element is replicated with one copy inserted ata new site and one remains at original site

  • DNA transposon
  • requires transposase
  • only found in prokaryotes
345
Q

what are retrotansposons?

A
  • DNA copy of element made by reversetranscription from its RNA and then inserted into a new chromosomal site
  • only found in eukaryotes
  • two kinds: Retrovirus-like elements and retroposons
346
Q

true or false:

Bacterial transposons move within and between chromosomes and plasmid

A

true

347
Q

what is a gene that encodes transposase?

A

a protein required for transposition to occur

348
Q

what are terminal inverted repeats?

A

identical, or nearly identical inverted sequences at both ends of element

349
Q

what are target site duplication?

A

short directly repeated sequences at both ends -result from staggered cleavage of the double-stranded DNA at the site of insertion

350
Q

what are the simplest bacterial transposons?

A

Insertion Sequences (IS elements)

351
Q

what are IS elements?

A
  • compactly organized and contain only genes whose products are involved in transposition.
  • inverted terminal repeats are found at the ends.
  • Some encode transposase
352
Q

what does insertion of an IS element cause?

A

traget site duplication

353
Q

what may happen when a particular IS element if found on both a plasmid and a chromosome?

A

homologous recombination may occur inserting the plasmid into the chromosome

354
Q

what is the R-determinant?

A

antibiotic resistance gene

355
Q

what is the RTF component?

A

resistance transfer factor

356
Q

when are composite transposons created?

A

when two IS elements insert near each other, “capturing” a DNA sequence

357
Q

what can IS element excision mobilize?

A

the captured DNA, which may mobilize antibiotic resistance genes

358
Q

where are replicative transposons found?

A

bacteria

359
Q

true or false:

Tn3 elements are larger than the simple IS element

A

true

360
Q

what do Tn3 elements often contain?

A

additional genes that are not involved in transpositio

361
Q

how were transposonsable elements discovered?

A

by analyzing genetic instabilities in maize

362
Q

what did Barbara McClintock do?

A

discovered transposons

363
Q

how much of our genome is made up by transposable elements?

A

44%

MBG 2040 (2 decks)

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