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Molecules, Cells and Organisms > The Central Dogma (11-21) > Flashcards

The Central Dogma (11-21) Flashcards

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1
Q

What are the base pairing rules for RNA synthesis?

A

C - G
A - U

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2
Q

How can cytosine produce uracil?

A

Cytosine can undergo spontaneous deamination to produce uracil

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3
Q

Why is the spontaneous deamination of cytosine an issue?

A

It can introduce mutations - DNA replication after deamination could replace a C-G base pair with U-A base pair (as C has become U)

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4
Q

Why is uracil not found in DNA?

A

In DNA any uracil is removed by uracil-DNA-glycosylase generating an abasic site, which is removed and repaired by DNA polymerases.

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5
Q

What are the 3 major classes of bacterial RNA?

A
  1. messenger RNA
  2. ribosomal RNA
  3. transfer RNA
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6
Q

What is the function of the 5’ promoter in bacterial transcription?

A

To attract and bind the RNA polymerase

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7
Q

Why does bacterial transcription and translation occur simultaneously?

A

Bacteria don’t have nuclei

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8
Q

What is the bacterial core RNA polymerase composed of?

A

α, β, β’ and ω subunits

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9
Q

What is the function of the sigma factor?

A

To bind to the core polymerase and direct it to a promoter - the addition of a sigma subunit converts it to a holoenzyme (complete functional enzyme)

E.coli has multiple sigma subunits which recognise different promoters - provide specificity

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10
Q

During bacterial transcription initiation why does the polymerase pull downstream DNA towards itself?

A

To scrunch the DNA until by chance the -10 region is open converting the closed promoter complex into an open promoter complex. Unlike the action of DNA helices it doesn’t require energy.

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11
Q

How does scrunching DNA during bacterial transcription affect the coiling of DNA?

A

downstream DNA becomes loser - negative supercoiling
upstream DNA becomes tighter - positive supercoiling

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12
Q

Does RNA polymerase require a primer?

A

No

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13
Q

When does the sigma factor disengage?

A

After 10 nucleotides of RNA synthesis - sigma factor is exposed and disengages ready for elongation

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14
Q

During bacterial elongation what are the characteristics of RNA polymerase?

A

highly processive
low fidelity - many errors

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15
Q

What happens if RNA polymerase mis-incorporates a ribonucleotide?

A

It hesitates, back-tracks, removes the nucleotide and then continues

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16
Q

Why is a high error rate of bacterial transcription tolerated?

A

If the transcript encodes a protein then most of the protein will be fine but a small subpopulation might be mutant - can probably be tolerated

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17
Q

What is Rho (p)-independent termination?

A

a terminator sequence in RNA recognised - as the RNA is being formed secondary structures start building (e.g. G-C base pairing forms a hairpin loop) here RNA pauses and dissociates due to weak base pairs

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18
Q

What is p-dependent termination?

A

requires p protein to break the RNA:DNA duplex in the transcription bubble - p protein is a hexameric helicase that binds C-rich G-poor sequence in the RNA and uses helicase activity to chase RNA pol, catches and disrupts the DNA:RNA hybrid releasing the RNA.

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19
Q

What is refampicin?

A

an inhibitor of prokaryotic transcription
inhibits RNA pol by binding tightly to the RNA exit channel - affecting initiation, preventing translation

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20
Q

Why doesn’t RNA polymerase require energy to open the helix?

A

When RNA pol binds to DNA it bends the DNA duplex so it can be opened more easily.

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21
Q

How are eukaryotic transcripts processed before being transported to the cytosol?

A

The primary transcript is:
1. capped at the 5’ end
2. spliced to remove introns
3. polyadenylated at the 3’end

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22
Q

How many RNA polymerases are there in eukaryotes?

A

3 - RNA polymerase I, II, III

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23
Q

RNA polymerases are complex compared to bacterial, what does this suggest about their mechanism of transcription?

A

The RNA polymerases differ greatly so have a different mechanism transcription.

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24
Q

What are general transcription factors in eukaryotic transcription?

A

Additional proteins required by eukaryotic RNA pols for initiation.

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25
Q

What are promoters in eukaryotic transcription?

A

A region of DNA upstream from a gene where relevant proteins bind to initiate transcription.

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26
Q

What are TATA box promoters?

A

Have an upstream sequence TATAAAA between -30 and -100 from the transcriptional start.

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27
Q

What are the shared homology of archaeal - eukaryotic transcription components?

A

Overall a similar process:
1. archaea have one RNA pol similar to eukaryotic pols
2. both have internal membranes
3. both have TATA box promoters
4. both transcribe tRNAs as individuals RNAs

suggests phylogenic relationship

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28
Q

What is the function of the TFIID complex in eukaryotic initiation?

A

TFIID guides RNA Pol II to its promoters

its large, has 11 TAF (TBP associated factors) and the TATA-box binding protein (TBP)

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29
Q

What does the TBP subunit of TFIID do?

A

Binds to the TATA box - causes DNA to bend and minor groove to widen

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30
Q

What does bound TBP do?

A

Recruits other transcription factors:

TFIIA binds TBP
TFIIB binds TBP

TFIIB recruits TFIIF, RNA Pol II, TFIIE and TFIIH - assemble around the promoter forming the basal transcription apparatus

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31
Q

What is the function of TFIIH in eukaryotic transcription?

A
  1. is a helicase - uses energy from ATP hydrolysis to locally unwind the DNA double helix
  2. is a kinase - phosphorylates the c’-terminal domain (CTD) of RNA Pol II, -ve charge changes its shape, releasing from TFs to start elongation
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32
Q

What happens during elongation in eukaryotic transcription?

A
  1. TFIIB, E and H dissociate from basal transcription apparatus
  2. RNA is synthesised
  3. RNA Pol II progresses, freeing the promoter and TFIIDA complex for further recruitment
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33
Q

What is α-amantin?

A

A potent inhibitor of RNA Pol II - binds tightly to the active site constraining the flexibility required to translocate DNA reducing rate of RNA production

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34
Q

What are enhancers?

A

Regulatory DNA sequences that increase the transcription levels of genes - promote high level expression

work over long distances
active in a tissue-specific manner

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35
Q

What is the DNA looping model?

A

Proteins bound to a distance enhancer interact with components of the transcription initiation complex, thus looping out the intervening DNA

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36
Q

How do enhancers react with RNA Pol II?

A

Mediator proteins act as a bridge between activator proteins that bind the enhancer control elements and the non-phosphorylated CTD of RNA Pol II (initiator state).

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37
Q

What provides the means of turning genes ‘on’ or ‘off’?

A

Enhancer/silencer elements

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38
Q

How do enhancers allow for cell-specific control of gene expression?

A

Activator proteins are required to bind enhancer control elements, transcription can only be enhanced if the appropriate activators are present .

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39
Q

How is eukaryotic transcription regulated by histones?

A

Histone acetylation

Acetylation of pertruding histone tails on nucleosomes neutralises the +ve charge on lysine - loosening its reaction with -ve DNA causing the nucleosome to unwind slightly. Loose chromatin structure permits transcription.

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40
Q

How are RNA Pol II transcripts modified?

A
  1. 5’ end is capped by a nucleotide triphosphate + methylation
  2. 3’ end is trimmed and a poly-A tail is added
  3. introns are removed by splicing
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41
Q

How is the 5’ cap added during RNA processing?

A

The 5’ mRNA triphosphate is modified:
one phosphate group removed, diphosphate left attacks the α-phosphate of GTP forming an unusual 5’-5’ triphosphate linkage

The N-7 of the terminal guanine is methylated to form cap 0, further methylations produce caps 1 and 2.

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42
Q

What is the function of the 5’ cap?

A

The 5’ cap looks like the 3’ end of RNA - resistant to 5’ exonucleases

Prolong half life of mRNAs
Enhance translation

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43
Q

How is the poly-A tail added during RNA processing?

A

The 3’ end of the primary transcript is cleaved by a specific exonuclease downstream of the motif AAUAAA

150-250 adenylate residues derived from ATP are added by polyA polymerase

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44
Q

Why is the poly-A tail important?

A

For the stability of mRNA - the tail is shortened overtime and when its short enough the mRNA is enzymatically degraded

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45
Q

What are the main differences between bacterial and eukaryotic transcription/translation?

A

Bacterial - mRNA molecules are translated while being transcribed and are generally not modified
Eukaryotic - mRNA precursors are processed and spliced in the nucleus then transported t the cytosol for translation

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46
Q

What are exons?

A

Nucleotide sequences that remain present in mature DNA

Covalently bonded during RNA splicing

Most less than ~1000 nucleotides long, many are ~100-200 long

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47
Q

What are introns?

A

Nucleotide sequences that are removed by RNA splicing

Possession is variable: histones have no introns (assume everything else does)

More DNA is devoted to introns than exons

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48
Q

What is R-loop analysis?

A

A laboratory technique used to analyse gene organisation - distinguish introns from exons

RNA-DNA hybridisation monitored by electron microscopy

Loops show displaced DNA

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49
Q

What are the 4 classes of introns?

A
  1. Group I: self-splicing, found in organelles (mitochondria, chloroplasts
  2. Group II: self-splicing, found in fungi/plants organelles
  3. Spliceosome-dependent
  4. Nuclear tRNA
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50
Q

What are the conserved features of introns?

A
  1. 5’ splice site
  2. 3’ splice site
  3. branch site (group II and spliceosomal introns)
51
Q

What did Thomas Cech’s work with the rDNA of Tetrahymena show about group I introns?

A

The Tetrahymena rDNA intron can self-splice in the absence of any protein - RNAs can have catalytic functions they can be ribozymes

52
Q

How is the splicing of group I introns performed?

A

Two sequential tranesterfication reactions - exchanging the R’’ group of an ester with the R’ group of an alcohol

53
Q

What does the co-factor do during the splicing of group I introns?

A

The 3’-OH of the co-factor (guanosine, GMP, GDP or GTP) acts as a nucleophile - attacks the phosphate at the 5’ splice site

54
Q

What attacks the 3’ splice site during the splicing of group I introns?

A

The 3’-OH of the upstream exon - becomes a nucleophile that attacks the 3’ splice site phosphate

55
Q

Why does the intron fold for splicing?

A

So the 5’ and 3’ splice sites are close - allows for efficient and accurate transesterfication reactions

56
Q

How does group II intron splicing differ from group I?

A

Group II introns carry their own co-factor
An internal nucleophile is used - the 2’-OH of the branch site adenine attacks the 5’ splice site phosphate forming a lariat structure

57
Q

What is the result of group II intron splicing?

A

Fusion of the upstream and downstream exons and release of the intron in its lariat form

58
Q

What are maturases?

A

Enzymes that improve the efficiency of intron splicing

59
Q

What is the intron-early hypothesis?

A

All 3 domain of life have introns so they must be of ancient origin - modern organisms maintain them so they must be useful/valuable

60
Q

What are homing endonucleases?

A

Enzymes that catalyse intron mobility - move intron from one location/organism to another

Introns may be parasitic nucleic acids that code for a protein which allows them to spread selfishly

61
Q

What is the role of the spliceosome in spliceosome dependant RNA splicing?

A

Inactive spliceosome assembles - bringing the splice sites close together

The spliceosome is then activated and provides a framework within which splicing occurs

62
Q

How is the tranesterfication reaction of spliceosome dependent RNA splicing made more efficient?

A

The branch site of adenine sits on a bulge, due to the base-pairing between U6 snRNA, U2 snRNA and the branch site, brining it close to the 5’ splice site

63
Q

What does the phosphylated C-terminal domain of the L’subunit of RNA Pol II recruit?

A
  1. capping factors
  2. 3’ end processing factors
  3. spliceosomes
64
Q

How is intron removal co-ordinated with transcription?

A

Spliceosomes are recruited by RNA Pol II - eukaryotic cell has control over the intron even if they are parasitic

65
Q

What is alternative splicing?

A

A mechanism that generates protein diversity - one gene is used to make more than one protein

66
Q

What happens if there are mutations in RNA splicing?

A

Mutations can destroy splice sites or create new splice sites - exons can be skipped or mis incorporated leading to genetic diseases

67
Q

What is the diamond code?

A

Proposed by George Gamow 1954, concluded that the genetic code is overlapping, degenerate and triplet - each amino acid fits directly into diamond shaped pockets within DNA grooves

68
Q

What did Sidney Brenner propose about the genetic code?

A

The code is written in a non-overlapping triplet style - if it were overlapping there would be constraints in the order of bases, some combinations would be impossible

69
Q

How was the triplet code experimentally determined?

A

In 1961 Crick and coworkers combined mutations of FC0 and showed that +3 or -3 restored the reading frame

70
Q

What are the subunits of a bacterial ribosome?

A

50S - catalyses the formation of peptide bonds to link amino acids
30S - provides a framework where tRNAs can be matched to codons

71
Q

What does an assembled bacterial ribosome consist of?

A

Assembled 70S ribosome -
E: tRNA exit site
P: peptide site
A: aminoacyl-tRNA site

72
Q

What are Svedberg units?

A

Unit for sedimentation rate - how fast a particle of given size and shape ‘settles’ at the bottom of a solution

  • not additive
73
Q

What is the Shine-Dalgarno sequence?

A

A short sequence dominated by purines - recruits the ribosome

74
Q

How is the bacterial ribosome S subunit kept inactive until mRNA and an initiating tRNA are available?

A

IF-1 blocks the A site

IF-3 prevents premature assembled of the ribosomal S and L subunit

75
Q

What is the function of initiation factors in bacterial translation initiation?

A

To co-ordinate ribosome assembly - resulting in a ribosome positioned around a specific initiator tRNA base-paired to a start codon in the P site

76
Q

How does bacterial translation elongation occur?

A
  1. EF-Tu guides the next aa-tRNA into the A site
  2. a peptide bonds is formed
  3. EF-G enters A site, ribosome moves one codon down, deacylated tRNA enters E site, dipeptide tRNA enters P site
  4. incoming tRNA displaces EF-G and the tRNA leaves the E site
77
Q

How is bacterial translation terminated?

A
  1. a release factor binds to the STOP codon
  2. the peptidyl-tRNA bond is cleaved, releasing the protein
  3. the mRNA-ribosome complex disassembles
78
Q

Why can many ribosomes travers a single bacterial mRNA?

A

Bacterial mRNAs are polycistronic - has multiple genes with a ribosome-binding site (S-D) required for each

79
Q

What provides the peptidyl transferase activity required for the formation of peptide bonds between aa?

A

Ribosomes - they are a giant catalytic ribozyme

80
Q

What does an assembled eukaryotic ribosome consist of?

A

Assembles 80S ribosome -
P: peptidyl site
A: aminoacyl-tRNA site

(no clearly defined E site)

81
Q

What are the subunits of a eukaryotic ribosome?

A

60S and 40S

82
Q

Why are eukaryotic mRNAs often circularised?

A

To facilitate the re-binding of ribosomes - if it falls off doesn’t have to diffused very far to rebind - efficient

83
Q

Eukaryotic mRNA doesn’t have a Shine-Dalgarno ribosome binding site, what does it do instead?

A

The small subunit of the ribosome scans the mRNA until it finds a translational start signal

84
Q

What happens after the multiple initiation factors assemble with the 40S subunit?

A

Binding of the charged initiator tRNA

Binding if the 5’cap of the mRNA to the S subunit

85
Q

How are secondary structures on eukaryotic mRNA unwound?

A

The helices activity of elF4A in the initiation complex

86
Q

What is the function of the kozak sequence?

A

A recognition sequence that signals to the ribosome that the next AUG is the initiator codon

87
Q

How is eukaryotic translational elongation carried out?

A
  1. an incoming aa-tRNA enters the A site, a peptide bond is formed
  2. eEF2 enters the A site - ribosomes translocates by one codon, deacylated tRNA leaves
  3. repeats
88
Q

How is eukaryotic translational termination carried out?

A

A single release factor, which recognises all 3 STOP codons, cleaves the peptidyl-tRNA bond, releasing the protein, ribosome disassociates

89
Q

What does the antibiotic puromycin do to protein synthesis?

A

Leads to premature termination - after puromycin added aa can’t be - it mimics charged tRNA enters the A site and transfers to the growing chain

90
Q

What does ricin do to protein synthesis?

A

Inhibits the translocation of elongation - protein synthesis ceases, cell dies

91
Q

What is covalent bonding?

A

Sharing of electron pair to complete outer shell

92
Q

Is there free rotation around a double covalent bond?

A

No - causes structure to become flat

93
Q

What is cis/trans isomerism?

A

Stereoisomers with the same formula but functional groups in different orientation - exists when there’s restricted rotation around a molecule
- Cis: same side (less stable)
- Trans: different sides

94
Q

What are 3 main points about covalent bonds?

A
  1. Covalent bonds are strong
  2. Give direction and shape
  3. Double bonds are stronger and have no rotation
95
Q

What are isomers?

A

Molecules that have the same molecular formula but different arrangements of atoms in space

96
Q

What are conformers?

A

Different arrangements of molecules due to rotating around particular bonds

Structures arising from bond rotation are called conformations

97
Q

What is stereoisomerism?

A

Isomers that differ in the orientation of groups attached to a chiral carbon (C with 4 different groups) - non superimposable

98
Q

What are the different glucose polymers and their properties?

A

Glycogen - fast breakdown of energy
Cellulose - fibre for structure
Starch - (amylose and amylopectin) breakdown for energy

99
Q

How are macromolecules stabilised?

A

Non-covalent bonds stabilisation rotations around covalent bonds

100
Q

Why are non-covalent interactions important in biology?

A

Non covalent bonds are:
individually weak
collectively strong
give flexibility
Important because e.g. membranes must be semi fluid, DNA strands must come apart

101
Q

How do polar covalent bonds form?

A

The unequal sharing of electrons due to electronegativity - the power of an atom to attract electrons to itself

102
Q

What are hydrogen bonds?

A

Dipole - dipole interaction
The electrostatic attraction between H bonded to a highly electronegative atom with a lone pair of electrons
Angled H bonds are weaker

103
Q

What are salt bridges?

A

Bonds between oppositely charges residues - charged amino acids make salt bridges (weak)

104
Q

What are Van der Waal’s bonds?

A

Weak electrostatic interaction between induces dipoles, induced by proximity - Van der Waal’s distance is the optimum distance, too close leads to repulsion

105
Q

What is at the N and C terminal of polypeptide chains?

A

N terminal: NH3+
C terminal: COO-

106
Q

Are amino acids stereoisomers?

A

Yes - the C has 4 different groups attached so its chiral

Forms two steriosimers D and L, only L is found in humans

107
Q

What is a zwitterion?

A

A molecule that contains an equal number of +ve and -ve function groups

At neutral pH amino acids are zwitterions - have no net charge (NH3+ and COO- balance)

108
Q

What is the physiological form of amino acids at high and low pH?

A

Low pH: positive charge, NH3+ and COOH - high conc of H+ pushes COO- to accept H+

High pH: negative charge, NH2 and COO-, low conc of H+ pushes NH3+ to loose H+

both forms can coexist

109
Q

What is the primary structure of proteins?

A

The sequence of amino acids

110
Q

What is the secondary structure of proteins?

A

The conformation of the protein backbone determined by hydrogen bonding between backbone atoms (no R groups)

111
Q

Why are peptide bonds planar?

A

Peptide bonds are partially double bonded

Leads to cis/trans isomers - cis leads to steric clashes so all are trans other then proline (due to its unusual ring structure)

112
Q

What are Phi and Psi angles?

A

Torsion (twisting) angles of the poly peptide backbone

Phi: right-handed rotation around Cα-N bond
Psi: right-handed rotation around Cα-C bond

113
Q

How is the α-helix secondary structure formed?

A

Backbone twists itself (right-handed) into a helix - C=O H bonds with N-H 4aa down

Side chains extend outwards and are not involved

DNA binding proteins are often α-helix to fit in the major grooves of DNA

114
Q

Describe the β-strand secondary structure:

A

β-strands hydrogen bonds with each other to form β-pleated sheets with alternating side chains

Parallel: one aa H bonds to 2 aa in adjacent strands
Anti-parallel: one aa H bonds to 1 aa in the adjacent strand

115
Q

What holds the protein tertiary structure together?

A

Salt bridges: interaction between opposite charges
Hydrogen bonds
Hydrophobic interactions: hydrophobic molecules clump together to exclude water
Disulphide bonds: covalent
Van der Waal’s forces: tight packing of side chains, no holes on proteins

116
Q

What is a motif?

A

Common elements that fit together

e.g. the combination of secondary structure elements ββ

117
Q

What is a protein domain?

A

A region of the polypeptide chain that folds independently forming a compact 3D structure made up of motifs

They give stability to aa chains and help support the extracellular matrix

118
Q

What is the quaternary structure of proteins?

A

Proteins made up of more than one polypeptide chain

e.g collagen - tight triple helix

119
Q

What is the conclusion for Anfinsen’s experiment?

A

Proteins adapt their native structure (fold) spontaneously

120
Q

What is the order of protein folding?

A
  1. Nucleation: hydrophobia regions condense (hydrophobic collapse) - short stretches of secondary structure
  2. Aggregation: motifs, domains - extensive secondary structure
  3. Compaction: tertiary structure is obtained
121
Q

What are chaperonins?

A

Enzymes that encase proteins are allow them to fold to their native shape inside

122
Q

How does the vast machinery in cells help to fold proteins?

A

The machinery doesn’t interfere with the inherent ability of a protein to fold (spontaneous) it just speed up the process and prevents incorrect bonding of side chains

123
Q

What is sickle cell anaemia?

A

A disease caused by protein misfolding - haemoglobin aggregates to form long chains that distort the shape of the cell

Molecules, Cells and Organisms (5 decks)

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