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protein synthesis - mechanisms Flashcards

1
Q

what is the role of dna in gene expression

A

1) encodes all genes in an organism

2) can be replicated as information to rna (ie to form proteins)

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2
Q

what is an important mediator in protein synthesis (translation)

A 
transfer RNA (tRNA)
also called aminoacyl-tRNA
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3
Q

what is the structure of tRNA molecules

A

single stranded
1 amino acid covalently bound to the 3’ end via the CCA (cytosine cytosine adenine) arm
anticodon loop contains the anticodon

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4
Q

what is the property of the amino acid in tRNA molecules and what does this mean

A

amino acylated

so bound to the nucleotide

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5
Q

what is the anticodon in tRNA

A
  • a base triplet

- template-recognition site (recognises codon on mRNA)

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6
Q

how do tRNAs bind to mRNAs

A
  • via their anticodon binding to codon on mRNA

- brings amino acid to right position in the genetic code for protein synthesis

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7
Q

why is the secondary structure of tRNA distinct

A
  • single stranded so folds back on itself
  • base pairs with itself by INTRAmolecular base pairing (bases in the sequence are self-complimentary)
  • to form anticodon loop
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8
Q

how is the amino acid in tRNA molecules amino-acylated

A
  • adenine is the last base of the CCA arm on tRNA
  • amino acid bound to the 3’ hydroxyl group of the terminal adenine via esterification
  • forms aminoacyl tRNA loaded with correct amino acid
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9
Q

we always read a genetic code in…

A

triplets

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10
Q

what is each amino acid on a base sequence encoded by

A

groups of 3 nucleobases (nucleotide codes) starting from a fixed point

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11
Q

what are base sequence triplets in dna/rna translated to

A 
correct corresponding amino acid
ie 
ABCDEFGHI
ABC = aa1 (amino acid 1)
DEF = aa2
GHI = aa3
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12
Q

what 3 properties does the genetic (triplet) code have

A

redundant
unambiguous
universal

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13
Q

what is meant by redundancy of the genetic code

A
  • only 20 amino acids make up most proteins
  • BUT 64 possible triplet codons (variants of 4 bases combined to triplet sequence = 64 possibilities) to code for those
  • SO several different triplet codon sequences can encode for the same amino acid
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14
Q

what is meant by unambiguity of the genetic code

A
  • each codon can only encode 1 specific amino acid (or START or STOP)

redundancy compensated for by every tRNA being v specific for its encoded amino acid

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15
Q

what is meant by universality of the genetic code

A
  • genetic code is universal

- all known living organisms use the same genetic code based on the same chemistry (common evolutionary ancestry)

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16
Q

what is scientific procedure is universality of the genetic code a fundamental concept for

A

genetic engineering

  • can take genes from one organisms and transfer it to another
  • the second organism still understands the code and is reprogrammed with the transferred gene
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17
Q

in a codon, what end is the

a) first base (1st position)
b) second base (2nd position)

A

a) 5’

b) 3’

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18
Q

what two codon tables do we have

A

1) translate mRNA into protein directly, has U instead of T

2) same genetic code as 1 but written for dna, T instead of U

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19
Q

what can be observed if we look at mitochondria

A
  • preferential codon usage
  • exceptions in standard codon codes
  • code in mitochondria different from universal genetic code
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20
Q

why is the code in mitochondria different from universal genetic code

A
  • derived from prokaryotes that have been taken up by the precursor eukaryotic cells
  • so have their own translation machinery and genes
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21
Q

other than mitochondria where else is preferential codon usage visible

A

for the nuclear genome

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22
Q

what codons are different in mitochondria compared to the standard code

A

1) UGA = stop code in standard, Trp in mito
2) AUA = Ile standard, Met in mito
3) AGA + AGG = Arg standard, stop in mito

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23
Q

what codons are shown in green in genetic code tables

A

preferential codon

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24
Q

what codons are shown in red in genetic code tables

A

low usage codons

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25
Q

what is a good example of species-specific differences in specific tRNA anti codon abundance for same amino acid

A

between homosapiens and yeast

  • same genetic code
  • different preferential codon usage (due to redundancy of genetic code)
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26
Q

so why would there be problems if we transfer a gene from human to yeast

A
  • yeast understands code
  • BUT takes longer to translate the protein
  • compensate for this in synthetic biology by optimisation process
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27
Q

how is translation initiated

A

1) mrna molecule
2) start codon (AUG/ATG)
3) codes for start amino acid methionine (Met)
4) this is a clear initiation signal

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28
Q

how is the mRNA binded to the ribosome to create the translation initiation sequence

A

1) purine-rich sequence at -10 position of mRNA seq
2) base pairs with rna molecule in the ribosome
3) rna rna base pairing binds the 2 together

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29
Q

what is the translation initiation sequence called

A

shine dalgarno sequence

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30
Q

what is a clear signal to the ribosome that protein translation needs to start

A

combination of the -10 initiation seq and +1 start codon

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31
Q

how do reading frames work

A
  • specified by start codon and strength of ribosome binding site
  • 3 reading frames are possible in a 4 letter encoded triplet decoded sequence (can start reading triplets from very 1st codon, 2nd codon or 3rd codon)
  • giving very distinct different amino acid sequences
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32
Q

what can a mutation lead to

A
  • reading frame shift
  • change protein codon sequence even though only 1 base changed
  • get completely different protein (ie in insertions and deletions not divisible by 3)
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33
Q

what does protein synthesis require

A

translation of nucleotide sequences into amino acid sequences

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34
Q

which enzymes load the correct tRNAs with the correct corresponding amino acid thus govern correct translation of the genetic code

A

aminoacyl-tRNA synthetases

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35
Q

which catalytic particles in the cell are responsible for translating tRNA into proteins by the use of tRNAs loaded w amino acids

A

ribosomes

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36
Q

what are prokaryotic ribosomes like

A

70s

  • 1 small 30s sub-unit
  • 1 large 50S sub-unit
  • sub-units are the secondary structures of the protein components of the ribosomal subunit
  • made up of large amount of structural ribosomal rna
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37
Q

what does the s correlate to in ribosome structure (ie 70s)

A
  • sedimentation coefficient in centrifugation
  • unit of sedimentation speed of ribosomal subunits
  • why 30s and 50s = 70s in combination (+ not 80)
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38
Q

what are ribosomes

A

hybrids of rna and protein called ribonucleoprotein particles

39
Q

what is contained in the site of peptide bond formation in ribosomes

A
  • only RNA
  • no protein
  • within 20Å
40
Q

proteins are synthesised by…

A

successive addition of amino acids (carried by tRNAs) to carboxyl terminus of previous amino acid
+ subsequent peptide bond formation

41
Q

what is the rate of and error rate of translation in e. coli what does this mean for protein synthesis

A
  • 40 amino acids/sec
  • 10^-4 = error in protein synthesis every 10,000 amino acids
  • good fidelity, high probability of synthesising correct protein, even for very long proteins
42
Q

what would it mean for protein synthesis if the error rate was 10^-2

A
  • 1 wrong amino acid every 100 amino acids incorporated (only get 36% of proteins without error)
  • okay for short proteins
  • not possible to synthesise 1000 amino acids without making a mistake
43
Q

what are the most important regions of a cloverleaf tRNA molecule

A

1) amino acid attachment site (cca arm) at top
2) anticodon loop containing anticodon at bottom
3) other loops containing strange/atypical nucleobases for structural recognition of the tRNA (ie DHU loop and TvC loop)

44
Q

how do tRNAs confer high fidelity

A
  • by its structural and base pairing features
  • INTRAmolecular base pairing
  • number of conserved features of base sequence
45
Q

what modified nucleosides / nucleobases are contained in tRNAs

A

1) methylinosine(mI)
2) dihydrouridine(UH2)
3) ribothymidine (T)
4) pseudouridine (ψ)
5) methylguanosine (mG)
6) dimethylguanosine (m2G)
7) inosine

46
Q

what are modified nucleosides / nucleobases important for

A
  • flexibility of codon binding possibilities for the anticodon
47
Q

what is the significance of INOSINE as a modified nucleoside

A
  • part of anticodon arm
  • can base pair with many different bases (C,A,U) compared to standard nucleobases
  • important for redundancy and wobble hypothesis
48
Q

what shape is tRNA likened to if looked at in a 3D way

A

L shape

  • CCA stem at one end of arm
  • anticodon at other
49
Q

how is the 3D L shape of tRNA formed

A
  • INTRAmolecular base pairing forms 3d structure, locks it in place and gives stability
50
Q

why are aminoacyl tRNA synthetases not called synthases

A

they require energy for this process of loading corresponding amino acids

51
Q

what do aminoacyl tRNA synthetases have to do

A

enzymes that attach amino acids to tRNAs
highly specific for each amino acid
read anticodon of tRNA they have to load and differentiate between amino acids with similar structure

52
Q

how can aminoacyl tRNA synthetases correct wrongly charged/attached tRNAs

A
  • proofreading function

- they hydrolyse and remove them

53
Q

how do aminoacyl tRNA synthetases attach amino acids to tRNA

A

aminoacylation

54
Q

explain the editing function of aminoacyl-tRNA synthetases (how it recognises the correct amino acid)

A
  • the synthetase enzyme has 2 sites; editing site and activation site
  • flexible CCA arm moves amino acid between the 2 sites
  • if amino acid fits into editing site = removed via hydrolysis
  • if amino acid only fits into activation site = attached to tRNA
55
Q

what is rRNA (ribosomal)

A

major structural component of each ribosomal subunit

56
Q

what is the structure of 16s rRNAs

A
  • extensive secondary structure
  • intramolecular base pairing leads to stem loop structures in the same molecule
  • x-ray crystallography determines 3d structure
57
Q

what 2 types of mRNA exist

A

1) polycistronic

2) monocistronic

58
Q

what is possible in ribosomes on prokaryotic mRNA but not eukaryotic

A

ribosome on prokaryotic dna initiates translation of a protein then reinitiates downstream again for another round of protein synthesis of a different protein
all proteins it synthesises are encoded on the same mRNA

59
Q

why cant ribosomes reinitiate translation in eukaryotic mRNA

A

every mRNA only encodes 1 protein

so each protein in genome coded for by a distinct mRNA

60
Q

how is the ribosome able to reinitiate translation in prokaryotes

A
  • prokaryotic mRNA contains multiple different reading frames for different proteins
  • structure = binding site -> start codon -> reading frame making protein alpha -> another binding site + start codon for protein beta etc
61
Q

what are polysomes

A
  • 2+ ribosomes translating mRNA sequence simultaneously
  • enable transcription and translation to occur simultaneously
  • mRNA nascent to dna its encoded by is synthesised and translation occurs at same time
  • specific to prokaryotes bc they dont have nuclei
62
Q

what is the shine dalgarno sequence

A
  • rna rna hybridisation between mRNA start seq and rRNA

- upstream of the start codon

63
Q

what site is present on mRNA in addition to the translation initiation site

A
  • site responsible for binding to ribosomes via interaction with 16S rRNA (UAAGGAGGU at -10 upstream of start codon)
  • mediate base pairing between rna of ribsome and mRNA
  • stabilises structure
  • allows initiation of translation
64
Q

where do prokaryotes show similarity in gene sequence

A

region upstream of start codon that pairs with the rna sequence in the ribosome

65
Q

what mediates initial assembly of the translation complex on mRNA

A

initiation factors

66
Q

what mediates the process of attaching an incoming amino acid to the growing polypeptide chain and proof reading

A

elongation factors (ensure high fidelity)

67
Q

which elongation factor is very important for translation

A

EF-Tu

  • binds to a tRNA
  • delivers aminoacyl-tRNA to the ribosome
68
Q

what 3 tRNA binding sites exist in prokaryotic dna and where

A

1) E site (exit site)
2) P site (site of peptide bond formation in ribosome)
3) A site (acceptor site = new tRNAs enter as ribosome moves along seq)
- they bridge across the 30s and 50s subunits

69
Q

how is the growing polypeptide chain (protein) extruded from the ribsome during translation and released from when translation is complete

A

through a tunnel which passes through the 50S subunit

70
Q

what is the action of initiation factor 1 in translation initiation (prokaryotes)

A

mediate assembly of 30S sub unit

71
Q

what is the action of initiation factor 2 in translation initiation (prokaryotes)

A

forms 30S initiation complex

by bringing the 1st tRNA (that recognises start codon + is amino acylated w methionine)

72
Q

what do initiation factors do following the formation of the 30s complex

A
  • 50s subunit assembled to 30s
  • forms 70s initiation complex
  • translation can start
    so translation initiation is assembly of fully functional ribosome made up of a small and large subunit on the mRNA which has to be translated
73
Q

how does translation occur on a ribosome

A

1) peptidyl-tRNA in P site
2) aminoacyl-tRNA binds in A site
3) new peptide bond formed as both sites occupied
4) translocation frees up A site
5) deacylated tRNA dissociates

74
Q

what does the elongation factor EF-G do

A

catalyses recycling of ribosome
ie once it has formed a peptide bond the ribosome moves along the mRNA to move the old tRNA into its P site and free up its A site the EF-G alters it shape so its ready to accept the next charged tRNA

75
Q

what do enzymes have for for energy and conformational change

A

GTP molecules

  • phosphorylate is to release energy (GDP + Pi)
  • both elongation factors have these
76
Q

what does EF-TU do

A

1) check for correct base pairing between codon + anticodon

2) brings new tRNA to catalyse formation of peptide bond

77
Q

what is the action of EF-Tu if base pairing is

a) incorrect
b) correct

A

a) rerelease of tRNA elongation factor compound from the ribosome
b) switch in EF-Tu turned on
- GTP hydrolysed to GDP and released releasing the tRNA amino acid complex for the action of the ribosome

78
Q

what is the wobble hypothesis

A
  • dictates allowed pairings at the 3rd base of the codon
  • tRNA has flexibility in 3rd base of codon (at 3’ end) to bind multiple codons and deliver the same amino acid
  • responsible for redundancy
79
Q

why does tRNA have this flexibility in its 3rd codon base

A

atypical nucleobases on 1st position of anticodon arm (‘wobble position’) have flexibility in binding (can bind multiple different nucleotides)

80
Q 
in bacteria what are the possible anticodon bases for the following wobble codon bases
U
C
A
G
A 
U = A,G, I
C = G, I
A = U, I
G = C, U
81
Q 
in eukaryotes what are the possible anticodon bases for the following wobble codon bases
U
C
A
G
A 
U = A,G, I
C = G, I
A = U 
G = C
82
Q

if the 1st base of the anticodon was
C, A, U, G, I
what would the 3rd base of the codon be

A 
C = G
A = U
U = A, G
G = U, C
I = U, C, A
83
Q

what is enabled if the first base of the anticodon is I

A
  • almost full flexibility of tRNA to bind (U C or A)
84
Q

explain why leucine is more complex in regards to its wobble flexibility

A
  • has 1 tRNA that can bind CUA, CUC, CUG, CUU codons because they only differ in the wobble base
  • but also has 2 additional codons (UUA, UUG) very different in initial bases
  • so a DIFFERENT trna also delivers leucine but recognises a different codon
85
Q

which antibiotics inhibit protein synthesis

A

1) streptomycin + other aminoglycosides
2) tetraccycline
3) chloramphenicol
4) cycloheximidine
5) erythromycin
6) puromycin

86
Q

how can antibiotics mediate killing in bacteria (prokaryotes only) by inhibiting protein synthesis

A

1) bc of 3d structural features = get into cell, into ribosome, bind ribosome in irreversible way that directly interferes with its function shutting its translation down
2) bind small or large ribosomal sub-unit depending on their chemical composition and structure

87
Q

what happens when antibiotics shut down protein translation

A
  • no longer synthesise proteins essential for survival

- cell dies

88
Q

how do streptomycin + other aminoglycosides inhibit protein synthesis

A
  • inhibit initiation
  • cause misreading of mRNA
  • pro only
89
Q

how does tetracycline inhibit protein synthesis

A
  • binds to 30s subunit
  • inhibits aminoacyl tRNA binding
  • pro only
90
Q

how does choramphenicol inhibit protein synthesis

A
  • inhibit peptidyl transferase activity of 50s

- pro only

91
Q

how does erythromycin inhibit protein synthesis

A
  • binds to 50s
  • inhibits translocation
  • pro only
92
Q

how does cycloheximidide inhibit protein synthesis

A
  • inhibit peptidyl transferase activity of 60s

- euk only

93
Q

how does puromycin inhibit protein synthesis

A
  • cause premature chain termination by acting as analogue of aminoacyl tRNA
  • pro + euk

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