L11 - Protein Synthesis Flashcards
(142 cards)
1
Q
What is the function of protein synthesis
A
To translate mRNA from the genome into protein using tRNA
2
Q
Four fundamental properties of the codon
A
Three bases encode an amino acid
The code is non overlapping
Code is degenerate - more than one amino acid codes for a protein
Code is read from a specific start point
3
Q
How many possible reading frames for an mRNA
A
3
4
Q
start codon
What AA does it encode
A
AUG
Methionine
5
Q
What are the three possible stop codons
A
UAA UAG UGA
6
Q
Describe the strucutre of a tRNA molecule
A
Anticodon loop - contains the anitocodon loop
3’ end carries the amino acid
D and T loops on either side
7
Q
Some nucleotides in the tRNA can be
A
Modified
8
Q
Name two modified nucleotides
A
Pseudouridine
Dihydrouridine
9
Q
How many possible modifications to nucleos with tRNA
What does this allow for
A
Over 50
Allows for specific interactions with the proteins
10
Q
Why isnt the codon:tRNA 1:1
A
Becuase wobble at position 3
Allows non Watson crick base pairing
Means that one anticodon (tRNA) is able to bind to more than one codon
11
Q
Describe one way in which a tRNA nucleotide can be modified
What can this nucleotide bind to
A
Adenine can be deaminated to create inosine
C U or A
12
Q
How many tRNAs do bacteria use
A
31 for 61 codons
13
Q
What is the function of aminoacyl tRNA synthases
A
Priming of the tRNAs
14
Q
Describe how the priming of the tRNAs is carried out
A
Addition of AMP onto the C terminus of the amino acid
Adenylated amino acid then to form the aa-tRNA
15
Q
Why is aa-tRNA described as being charged
A
Because the energy from the ATP hydrolysis is still contained within the ester linkage
16
Q
What two adaptors are required for proper translation
A
Synthase - which pairs the correct aa to the correct t-RNA
the tRNA which pairs to the correct codon within the ribosome
17
Q
How is synthase requires as an adaptor
A
Synthases are specific to the individual tRNAs
AAs have to fit into two pockets in the synthase (before and after the AMP is added)
18
Q
What is the role of peptidyl transferase
A
Enzyme which adds amino acids to the C’ termnius
19
Q
What is the ribosome made up from
A
50 ribosomal proteins
rRNAs
20
Q
What are the two ribosomal subunits - what occurs at each
A
LARGE - catalyses aa polymerisation (peptide formation)
SMALL - facilitates the interaction between tRNA and mRNA
21
Q
What are the 3 sites of the ribosome - what does each name stand for
A
A - aminoacyl tRNA
P - peptidyl transferase tRNA
E - exit site
22
Q
Where do charged tRNAs enter? Where do they exit
A
A site entry exit at the E site
23
Q
What is meant by the DNA code being non-overlapping
A
One triplet/codon is read at a time, followed by the next three bases (i.e. CGATTG –> CGA + TTG, CGATTG –> CGA + GAT TGX…)
24
Q
What is meant by the genetic code being degenerate
A
Some amino acid acids are specified by more than one different codon
25
How many different human codons are there
61
26
How many amino acids are there
20
27
What is meant by there being three possible reading frames
Within a codon there are three different points which can act as different starts points and determine different amino acid sequences
28
What is the universal start codon and what amino acid does it code for
Start codon AUG – Methionine/Met/M
29
If a protein starts with methionine, you can determine that that is the start codon, T or F
T
30
What is meant by the abbreviation ORF
Open reading frame
31
What are the three possible stop codons that signal the end of the ORF
UGA, UAG and UAA
32
What adapter molecule is required for translation
Transfer RNA (tRNA)
33
What is the name of the sequence in tRNA that binds to the mRNA codons
Anticodon loops
34
Which end of the tRNA strand contains the bound amino acid
The 3’ end
35
What accounts for the similar structure seen in all tRNA molecules
Internal base pairing
36
What is unique about the bases contained within tRNAs
The bases are highly modified to allows more specific interactions with the protein counterparts
37
There are over 50 possible modifications of the bases in tRNAs, what is meant by psi and D bases
psi corresponds to pseudouridine and D is dihydrouridine
38
How many different codons are there for serine, and how many different tRNAs
6 different codons but only 3 different tRNAs
39
What is meant by wobble base pairing and what does this achieve
Wobble bases occur at position 3 in the anticodon and allow the same anticodon to bind to more than one codon
40
How is wobble base pairing achieved
Modification of bases within the anticodon. Deamination of guanine creates inosine which can pair with uracil, cytosine or adenine
41
How are tRNAs with attached amino acids referred to
Aminoacyl-tRNAs or charged tRNAs
42
What is the name of the enzyme that catalyses the addition of an amino acid to a tRNA molecule
Aminoacyl-tRNA synthetase
43
Describe chemically, how amino acids are added to the 3’ end of the tRNA
Ester bond forms between the carboxyl group of the amino acid and the ribose group of the last nucleotide
44
Explain how the enzyme catalyses addition of an amino acid to the tRNA molecule
The aminoacyl-tRNA synthetase first primes the amino acid by the addition of an AMP to the C-terminus. It then uses the adenylated amino acid to form the aminoacyl tRNA
45
What is the other term used to describe aminoacyl tRNAs
Charged tRNA
46
New amino acids are added to the N-terminus of growing polypeptide chains, T or F
F – they are added to the C-terminus
47
Describe the composition of the ribosome in which protein synthesis/translation occurs in
The ribosome is composed of two different subunits. The complex consists of about 50 ribosomal proteins and several ribosomal RNAs (rRNAs)
48
What are the roles of the subunit in the ribosome
The large ribosomal subunit catalyses polymerisation and peptide elongation whereas the small subunit facilitates the tRNA/mRNA interactions
49
Describe how the process of translation is initiated
Initiator tRNA carrying methionine is loaded into the small ribosomal subunit with eIF-2. Met-charged tRNA is the only aminoacyl tRNA molecule capable of binding directly to the small ribosomal subunit and the only charged tRNA that can bind directly to the P site of the ribosome leading the A site vacant. Whilst the met-charged tRNA binds to the large ribosomal subunit, the small ribosomal subunit binds to the capped 5’ end of the mRNA and begins progressing along the strand until the met start codon AUG is reached. Once this AUG is reached the eIF’s dissociate and the large ribosomal subunit fully assembles
50
What is meant by the A site of the ribosome
Aminoacyl tRNA/activation site
51
What is meant by the P site of the ribosome
Peptidyl tRNA site
52
What is meant by the E site of the ribosome
Ejection/empty site
53
Describe the propagation of translation after the ribosome has fully assembled
Once this AUG has been reach and eIF’s have dissociated another aminoacyl tRNA bound to Elongation Factor-Tu binds to the vacant A site of the ribosome. If the anticodon of this aminoacyl tRNA doesn’t match the mRNA codon then this tRNA is ejected/falls off. Once the tRNA with the correct anticodon binds to the A site, EF-Tu hydrolyses its bound GTP and dissociates. The ribosome then catalyses formation of a peptide bond between the two amino acids. Following this the ribosome undergoes a conformational change that shifts the initiator tRNA into the E site of the ribosome. The now vacant P site is filled by the newly bound tRNA and EF-G binds to the ribosome. GTP hydrolysis by EF-G switches the ribosome back to being able to accept the next incoming rRNA. This process repeats until a stop codon is reached.
54
Describe the processes that occur during translation termination, after a stop codon is reached
Stop codons aren’t recognised by a tRNA molecule and thus don’t code for a corresponding amino acid. Once a stop codon is present in the A site of the ribosome, protein release factors bind to the site and terminate the polypeptide chain. Peptidyl transferase then catalyses the transfer of H2O to the C-terminus of the polypeptide chain resulting in the formation of a carbonyl group (COOH) and release of the protein from the ribosome. Release factors then move into the P site causing the ribosomal subunits to dissociate
55
What is the role of elongation factors in translation fidelity checking
Elongations promote translation and improve its accuracy
56
How specifically does elongation factor-1, EF-1 improve the accuracy of translation
After the anticodon has bound it causes two delays before the peptidyl transferase can act. Firstly it ensures that it must have hydrolysed its bound GTP and then it must have dissociated from the tRNA. These lags allow time for incorrect tRNAs to fall off.
57
Correct tRNAs once bound to the complimentary mRNA codon, don’t fall off, T or F
F – correct tRNAs do also fall off but at a much slower rate
58
How does codon-anticodon complementation impact GTP hydrolysis by EF-1
The hydrolysis of GTP by EF-1 occurs more rapidly if the codon and anticodon are correctly matched
59
What are the implication of translation in the absence of EF-1
There are more errors in the protein sequence
60
The large ribosomal complex contains the peptidyl transferase enzyme, T or F
T
61
Describe the localisation of the riboproteins and protein synthesising regions of the ribosome within its structure
Riboproteins are found on the surface of ribosomes whilst the protein synthesising regions are deep within the structure
62
What is meant by ribosomes being referred to as ribozymes
They are RNAs that act more like proteins/enzymes by catalysing reactions
63
Only the Met-tRNA with eIF-4A can bind to the P site of the small ribosomal subunit alone, T or F
F – met-tRNA is the only aminoacyl tRNA with eIF-2 bound that can bind the small ribosomal subunit alone
64
Explain how the action of eIF-4G and eIF-4E act as a checkpoint in translation
eIF-4E and eIF-4G only bind to mRNA that is capped and has a polyA tail. This acts as a checkpoint for broken mRNA
65
eIF-4G, eIF-4E, small ribosomal complex binds to the polyA tail of the mRNA strand, T or F
F – the complex binds the capped head of the mRNA
66
Release of eIF-2 initiates translation, T or F
T
67
Multiple ribosomes can bind to the same mRNA, T or F
T – this is referred to as a polysome
68
How far apart can ribosomes bind to RNA sequences
80 base pairs
69
What factors recognise stop codons and trigger dissociation of the ribosomal subunits
Release factors – molecular mimics that enter the A-site and cause dissociation
70
Folding of a protein begins immediately after leaving the ribosome, T or F
T
71
Why do proteins fold of their own accord
Proteins often contain hydrophobic regions which need to be hidden in the centre of the structure to achieve a low energy state
72
What is meant by a molten globule
A molten globule is the structure formed from the initial folding of the protein that achieves a roughly correct conformation
73
The amino acid sequence of proteins is thought to have evolved over time to promote formation of the molten globule, T or F
T
74
Correct folding is a multistep process that must occur in the correct order. What is the effect of an incorrect or out of sequence step
May reduce the energy state of the protein but blocks further folding and may lead to a dead end
75
Explain the link between protein misfolding and aggregation
Misfolding of proteins often leads to exposure of hydrophobic regions which is what causes aggregation
76
Name two of the major classes of molecular chaperones
Hsp60 and hsp70
77
What can be said about the expression of molecular chaperones at high temperatures
Expression of hsps is elevated when the temperature is raised above normal. This is because high temperatures can cause properly folded proteins to become misfolded
78
Which class of molecular chaperone acts directly on the proteins as they leave the ribosome and bind to hydrophobic residues
Hsp 70 class
79
What is the other mechanism of molecular chaperone action other than direct binding
Hsp60 class molecular chaperones put misfolded proteins into isolation. The hydrophobic entrance of hsp 60 binds to the protein and partially unfolds it. Then the GroES cap seals the protein inside for about 15 seconds to allow refolding
80
What is the benefit of isolating misfolded proteins
Stops them from interacting with other proteins in the cell
81
Monoubiquitination marks inappropriately folded proteins for degradation by the proteasome, T or F
F – this is the result of polyubiquitination
82
Give an example of a disease caused by a misfolded protein
Creutzfeldt–Jakob disease is caused by misfolded pathogenic proteins knowns as prions that enter the brain and convert normal proteins into misfolded ones. This seeds new cross-? filaments of protein aggregates.
83
What is meant by the DNA code being non-overlapping
One triplet/codon is read at a time, followed by the next three bases (i.e. CGATTG --> CGA + TTG, CGATTG --> CGA + GAT TGX…)
84
What is meant by the genetic code being degenerate
Some amino acid acids are specified by more than one different codon
85
How many different human codons are there
61
86
How many amino acids are there
20
87
What is meant by there being three possible reading frames
Within a codon there are three different points which can act as different starts points and determine different amino acid sequences
88
What is the universal start codon and what amino acid does it code for
Start codon AUG – Methionine/Met/M
89
If a protein starts with methionine, you can determine that that is the start codon, T or F
T
90
What is meant by the abbreviation ORF
Open reading frame
91
What are the three possible stop codons that signal the end of the ORF
UGA, UAG and UAA
92
What adapter molecule is required for translation
Transfer RNA (tRNA)
93
What is the name of the sequence in tRNA that binds to the mRNA codons
Anticodon loops
94
Which end of the tRNA strand contains the bound amino acid
The 3’ end
95
What accounts for the similar structure seen in all tRNA molecules
Internal base pairing
96
What is unique about the bases contained within tRNAs
The bases are highly modified to allows more specific interactions with the protein counterparts
97
There are over 50 possible modifications of the bases in tRNAs, what is meant by psi and D bases
psi corresponds to pseudouridine and D is dihydrouridine
98
How many different codons are there for serine, and how many different tRNAs
6 different codons but only 3 different tRNAs
99
What is meant by wobble base pairing and what does this achieve
Wobble bases occur at position 3 in the anticodon and allow the same anticodon to bind to more than one codon
100
How is wobble base pairing achieved
Modification of bases within the anticodon. Deamination of guanine creates inosine which can pair with uracil, cytosine or adenine
101
How are tRNAs with attached amino acids referred to
Aminoacyl-tRNAs or charged tRNAs
102
What is the name of the enzyme that catalyses the addition of an amino acid to a tRNA molecule
Aminoacyl-tRNA synthetase
103
Describe chemically, how amino acids are added to the 3’ end of the tRNA
Ester bond forms between the carboxyl group of the amino acid and the ribose group of the last nucleotide
104
Explain how the enzyme catalyses addition of an amino acid to the tRNA molecule
The aminoacyl-tRNA synthetase first primes the amino acid by the addition of an AMP to the C-terminus. It then uses the adenylated amino acid to form the aminoacyl tRNA
105
What is the other term used to describe aminoacyl tRNAs
Charged tRNA
106
New amino acids are added to the N-terminus of growing polypeptide chains, T or F
F – they are added to the C-terminus
107
Describe the composition of the ribosome in which protein synthesis/translation occurs in
The ribosome is composed of two different subunits. The complex consists of about 50 ribosomal proteins and several ribosomal RNAs (rRNAs)
108
What are the roles of the subunit in the ribosome
The large ribosomal subunit catalyses polymerisation and peptide elongation whereas the small subunit facilitates the tRNA/mRNA interactions
109
Describe how the process of translation is initiated
Initiator tRNA carrying methionine is loaded into the small ribosomal subunit with eIF-2. Met-charged tRNA is the only aminoacyl tRNA molecule capable of binding directly to the small ribosomal subunit and the only charged tRNA that can bind directly to the P site of the ribosome leading the A site vacant. Whilst the met-charged tRNA binds to the large ribosomal subunit, the small ribosomal subunit binds to the capped 5’ end of the mRNA and begins progressing along the strand until the met start codon AUG is reached. Once this AUG is reached the eIF’s dissociate and the large ribosomal subunit fully assembles
110
What is meant by the A site of the ribosome
Aminoacyl tRNA/activation site
111
What is meant by the P site of the ribosome
Peptidyl tRNA site
112
What is meant by the E site of the ribosome
Ejection/empty site
113
Describe the propagation of translation after the ribosome has fully assembled
Once this AUG has been reach and eIF’s have dissociated another aminoacyl tRNA bound to Elongation Factor-Tu binds to the vacant A site of the ribosome. If the anticodon of this aminoacyl tRNA doesn’t match the mRNA codon then this tRNA is ejected/falls off. Once the tRNA with the correct anticodon binds to the A site, EF-Tu hydrolyses its bound GTP and dissociates. The ribosome then catalyses formation of a peptide bond between the two amino acids. Following this the ribosome undergoes a conformational change that shifts the initiator tRNA into the E site of the ribosome. The now vacant P site is filled by the newly bound tRNA and EF-G binds to the ribosome. GTP hydrolysis by EF-G switches the ribosome back to being able to accept the next incoming rRNA. This process repeats until a stop codon is reached.
114
Describe the processes that occur during translation termination, after a stop codon is reached
Stop codons aren’t recognised by a tRNA molecule and thus don’t code for a corresponding amino acid. Once a stop codon is present in the A site of the ribosome, protein release factors bind to the site and terminate the polypeptide chain. Peptidyl transferase then catalyses the transfer of H2O to the C-terminus of the polypeptide chain resulting in the formation of a carbonyl group (COOH) and release of the protein from the ribosome. Release factors then move into the P site causing the ribosomal subunits to dissociate
115
What is the role of elongation factors in translation fidelity checking
Elongations promote translation and improve its accuracy
116
How specifically does elongation factor-1, EF-1 improve the accuracy of translation
After the anticodon has bound it causes two delays before the peptidyl transferase can act. Firstly it ensures that it must have hydrolysed its bound GTP and then it must have dissociated from the tRNA. These lags allow time for incorrect tRNAs to fall off.
117
Correct tRNAs once bound to the complimentary mRNA codon, don’t fall off, T or F
F – correct tRNAs do also fall off but at a much slower rate
118
How does codon-anticodon complementation impact GTP hydrolysis by EF-1
The hydrolysis of GTP by EF-1 occurs more rapidly if the codon and anticodon are correctly matched
119
What are the implication of translation in the absence of EF-1
There are more errors in the protein sequence
120
The large ribosomal complex contains the peptidyl transferase enzyme, T or F
T
121
Describe the localisation of the riboproteins and protein synthesising regions of the ribosome within its structure
Riboproteins are found on the surface of ribosomes whilst the protein synthesising regions are deep within the structure
122
What is meant by ribosomes being referred to as ribozymes
They are RNAs that act more like proteins/enzymes by catalysing reactions
123
Only the Met-tRNA with eIF-4A can bind to the P site of the small ribosomal subunit alone, T or F
F – met-tRNA is the only aminoacyl tRNA with eIF-2 bound that can bind the small ribosomal subunit alone
124
Explain how the action of eIF-4G and eIF-4E act as a checkpoint in translation
eIF-4E and eIF-4G only bind to mRNA that is capped and has a polyA tail. This acts as a checkpoint for broken mRNA
125
eIF-4G, eIF-4E, small ribosomal complex binds to the polyA tail of the mRNA strand, T or F
F – the complex binds the capped head of the mRNA
126
Release of eIF-2 initiates translation, T or F
T
127
Multiple ribosomes can bind to the same mRNA, T or F
T – this is referred to as a polysome
128
How far apart can ribosomes bind to RNA sequences
80 base pairs
129
What factors recognise stop codons and trigger dissociation of the ribosomal subunits
Release factors – molecular mimics that enter the A-site and cause dissociation
130
Folding of a protein begins immediately after leaving the ribosome, T or F
T
131
Why do proteins fold of their own accord
Proteins often contain hydrophobic regions which need to be hidden in the centre of the structure to achieve a low energy state
132
What is meant by a molten globule
A molten globule is the structure formed from the initial folding of the protein that achieves a roughly correct conformation
133
The amino acid sequence of proteins is thought to have evolved over time to promote formation of the molten globule, T or F
T
134
Correct folding is a multistep process that must occur in the correct order. What is the effect of an incorrect or out of sequence step
May reduce the energy state of the protein but blocks further folding and may lead to a dead end
135
Explain the link between protein misfolding and aggregation
Misfolding of proteins often leads to exposure of hydrophobic regions which is what causes aggregation
136
Name two of the major classes of molecular chaperones
Hsp60 and hsp70
137
What can be said about the expression of molecular chaperones at high temperatures
Expression of hsps is elevated when the temperature is raised above normal. This is because high temperatures can cause properly folded proteins to become misfolded
138
Which class of molecular chaperone acts directly on the proteins as they leave the ribosome and bind to hydrophobic residues
Hsp 70 class
139
What is the other mechanism of molecular chaperone action other than direct binding
Hsp60 class molecular chaperones put misfolded proteins into isolation. The hydrophobic entrance of hsp 60 binds to the protein and partially unfolds it. Then the GroES cap seals the protein inside for about 15 seconds to allow refolding
140
What is the benefit of isolating misfolded proteins
Stops them from interacting with other proteins in the cell
141
Monoubiquitination marks inappropriately folded proteins for degradation by the proteasome, T or F
F – this is the result of polyubiquitination
142
Give an example of a disease caused by a misfolded protein
Creutzfeldt–Jakob disease is caused by misfolded pathogenic proteins knowns as prions that enter the brain and convert normal proteins into misfolded ones. This seeds new cross-? filaments of protein aggregates.
