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BMS242 Cell and Molecular > L11 - Protein Synthesis > Flashcards

L11 - Protein Synthesis Flashcards

1
Q

What is the function of protein synthesis

A

To translate mRNA from the genome into protein using tRNA

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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

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3
Q

How many possible reading frames for an mRNA

A

3

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4
Q

start codon

What AA does it encode

A

AUG

Methionine

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5
Q

What are the three possible stop codons

A

UAA UAG UGA

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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

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7
Q

Some nucleotides in the tRNA can be

A

Modified

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8
Q

Name two modified nucleotides

A

Pseudouridine

Dihydrouridine

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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

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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

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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

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12
Q

How many tRNAs do bacteria use

A

31 for 61 codons

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13
Q

What is the function of aminoacyl tRNA synthases

A

Priming of the tRNAs

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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

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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

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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

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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)

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18
Q

What is the role of peptidyl transferase

A

Enzyme which adds amino acids to the C’ termnius

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19
Q

What is the ribosome made up from

A

50 ribosomal proteins

rRNAs

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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

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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

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22
Q

Where do charged tRNAs enter? Where do they exit

A

A site entry exit at the E site

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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…)

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24
Q

What is meant by the genetic code being degenerate

A

Some amino acid acids are specified by more than one different codon

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25
Q

How many different human codons are there

A

61

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26
Q

How many amino acids are there

A

20

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27
Q

What is meant by there being three possible reading frames

A

Within a codon there are three different points which can act as different starts points and determine different amino acid sequences

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28
Q

What is the universal start codon and what amino acid does it code for

A

Start codon AUG – Methionine/Met/M

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29
Q

If a protein starts with methionine, you can determine that that is the start codon, T or F

A

T

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30
Q

What is meant by the abbreviation ORF

A

Open reading frame

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31
Q

What are the three possible stop codons that signal the end of the ORF

A

UGA, UAG and UAA

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32
Q

What adapter molecule is required for translation

A

Transfer RNA (tRNA)

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33
Q

What is the name of the sequence in tRNA that binds to the mRNA codons

A

Anticodon loops

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34
Q

Which end of the tRNA strand contains the bound amino acid

A

The 3’ end

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35
Q

What accounts for the similar structure seen in all tRNA molecules

A

Internal base pairing

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36
Q

What is unique about the bases contained within tRNAs

A

The bases are highly modified to allows more specific interactions with the protein counterparts

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37
Q

There are over 50 possible modifications of the bases in tRNAs, what is meant by psi and D bases

A

psi corresponds to pseudouridine and D is dihydrouridine

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38
Q

How many different codons are there for serine, and how many different tRNAs

A

6 different codons but only 3 different tRNAs

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39
Q

What is meant by wobble base pairing and what does this achieve

A

Wobble bases occur at position 3 in the anticodon and allow the same anticodon to bind to more than one codon

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40
Q

How is wobble base pairing achieved

A

Modification of bases within the anticodon. Deamination of guanine creates inosine which can pair with uracil, cytosine or adenine

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41
Q

How are tRNAs with attached amino acids referred to

A

Aminoacyl-tRNAs or charged tRNAs

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42
Q

What is the name of the enzyme that catalyses the addition of an amino acid to a tRNA molecule

A

Aminoacyl-tRNA synthetase

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43
Q

Describe chemically, how amino acids are added to the 3’ end of the tRNA

A

Ester bond forms between the carboxyl group of the amino acid and the ribose group of the last nucleotide

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44
Q

Explain how the enzyme catalyses addition of an amino acid to the tRNA molecule

A

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

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45
Q

What is the other term used to describe aminoacyl tRNAs

A

Charged tRNA

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46
Q

New amino acids are added to the N-terminus of growing polypeptide chains, T or F

A

F – they are added to the C-terminus

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47
Q

Describe the composition of the ribosome in which protein synthesis/translation occurs in

A

The ribosome is composed of two different subunits. The complex consists of about 50 ribosomal proteins and several ribosomal RNAs (rRNAs)

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48
Q

What are the roles of the subunit in the ribosome

A

The large ribosomal subunit catalyses polymerisation and peptide elongation whereas the small subunit facilitates the tRNA/mRNA interactions

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49
Q

Describe how the process of translation is initiated

A

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

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50
Q

What is meant by the A site of the ribosome

A

Aminoacyl tRNA/activation site

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51
Q

What is meant by the P site of the ribosome

A

Peptidyl tRNA site

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52
Q

What is meant by the E site of the ribosome

A

Ejection/empty site

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53
Q

Describe the propagation of translation after the ribosome has fully assembled

A

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.

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54
Q

Describe the processes that occur during translation termination, after a stop codon is reached

A

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

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55
Q

What is the role of elongation factors in translation fidelity checking

A

Elongations promote translation and improve its accuracy

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56
Q

How specifically does elongation factor-1, EF-1 improve the accuracy of translation

A

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.

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57
Q

Correct tRNAs once bound to the complimentary mRNA codon, don’t fall off, T or F

A

F – correct tRNAs do also fall off but at a much slower rate

58
Q

How does codon-anticodon complementation impact GTP hydrolysis by EF-1

A

The hydrolysis of GTP by EF-1 occurs more rapidly if the codon and anticodon are correctly matched

59
Q

What are the implication of translation in the absence of EF-1

A

There are more errors in the protein sequence

60
Q

The large ribosomal complex contains the peptidyl transferase enzyme, T or F

A

T

61
Q

Describe the localisation of the riboproteins and protein synthesising regions of the ribosome within its structure

A

Riboproteins are found on the surface of ribosomes whilst the protein synthesising regions are deep within the structure

62
Q

What is meant by ribosomes being referred to as ribozymes

A

They are RNAs that act more like proteins/enzymes by catalysing reactions

63
Q

Only the Met-tRNA with eIF-4A can bind to the P site of the small ribosomal subunit alone, T or F

A

F – met-tRNA is the only aminoacyl tRNA with eIF-2 bound that can bind the small ribosomal subunit alone

64
Q

Explain how the action of eIF-4G and eIF-4E act as a checkpoint in translation

A

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
Q

eIF-4G, eIF-4E, small ribosomal complex binds to the polyA tail of the mRNA strand, T or F

A

F – the complex binds the capped head of the mRNA

66
Q

Release of eIF-2 initiates translation, T or F

A

T

67
Q

Multiple ribosomes can bind to the same mRNA, T or F

A

T – this is referred to as a polysome

68
Q

How far apart can ribosomes bind to RNA sequences

A

80 base pairs

69
Q

What factors recognise stop codons and trigger dissociation of the ribosomal subunits

A

Release factors – molecular mimics that enter the A-site and cause dissociation

70
Q

Folding of a protein begins immediately after leaving the ribosome, T or F

A

T

71
Q

Why do proteins fold of their own accord

A

Proteins often contain hydrophobic regions which need to be hidden in the centre of the structure to achieve a low energy state

72
Q

What is meant by a molten globule

A

A molten globule is the structure formed from the initial folding of the protein that achieves a roughly correct conformation

73
Q

The amino acid sequence of proteins is thought to have evolved over time to promote formation of the molten globule, T or F

A

T

74
Q

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

A

May reduce the energy state of the protein but blocks further folding and may lead to a dead end

75
Q

Explain the link between protein misfolding and aggregation

A

Misfolding of proteins often leads to exposure of hydrophobic regions which is what causes aggregation

76
Q

Name two of the major classes of molecular chaperones

A

Hsp60 and hsp70

77
Q

What can be said about the expression of molecular chaperones at high temperatures

A

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
Q

Which class of molecular chaperone acts directly on the proteins as they leave the ribosome and bind to hydrophobic residues

A

Hsp 70 class

79
Q

What is the other mechanism of molecular chaperone action other than direct binding

A

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
Q

What is the benefit of isolating misfolded proteins

A

Stops them from interacting with other proteins in the cell

81
Q

Monoubiquitination marks inappropriately folded proteins for degradation by the proteasome, T or F

A

F – this is the result of polyubiquitination

82
Q

Give an example of a disease caused by a misfolded protein

A

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
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…)

84
Q

What is meant by the genetic code being degenerate

A

Some amino acid acids are specified by more than one different codon

85
Q

How many different human codons are there

A

61

86
Q

How many amino acids are there

A

20

87
Q

What is meant by there being three possible reading frames

A

Within a codon there are three different points which can act as different starts points and determine different amino acid sequences

88
Q

What is the universal start codon and what amino acid does it code for

A

Start codon AUG – Methionine/Met/M

89
Q

If a protein starts with methionine, you can determine that that is the start codon, T or F

A

T

90
Q

What is meant by the abbreviation ORF

A

Open reading frame

91
Q

What are the three possible stop codons that signal the end of the ORF

A

UGA, UAG and UAA

92
Q

What adapter molecule is required for translation

A

Transfer RNA (tRNA)

93
Q

What is the name of the sequence in tRNA that binds to the mRNA codons

A

Anticodon loops

94
Q

Which end of the tRNA strand contains the bound amino acid

A

The 3’ end

95
Q

What accounts for the similar structure seen in all tRNA molecules

A

Internal base pairing

96
Q

What is unique about the bases contained within tRNAs

A

The bases are highly modified to allows more specific interactions with the protein counterparts

97
Q

There are over 50 possible modifications of the bases in tRNAs, what is meant by psi and D bases

A

psi corresponds to pseudouridine and D is dihydrouridine

98
Q

How many different codons are there for serine, and how many different tRNAs

A

6 different codons but only 3 different tRNAs

99
Q

What is meant by wobble base pairing and what does this achieve

A

Wobble bases occur at position 3 in the anticodon and allow the same anticodon to bind to more than one codon

100
Q

How is wobble base pairing achieved

A

Modification of bases within the anticodon. Deamination of guanine creates inosine which can pair with uracil, cytosine or adenine

101
Q

How are tRNAs with attached amino acids referred to

A

Aminoacyl-tRNAs or charged tRNAs

102
Q

What is the name of the enzyme that catalyses the addition of an amino acid to a tRNA molecule

A

Aminoacyl-tRNA synthetase

103
Q

Describe chemically, how amino acids are added to the 3’ end of the tRNA

A

Ester bond forms between the carboxyl group of the amino acid and the ribose group of the last nucleotide

104
Q

Explain how the enzyme catalyses addition of an amino acid to the tRNA molecule

A

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
Q

What is the other term used to describe aminoacyl tRNAs

A

Charged tRNA

106
Q

New amino acids are added to the N-terminus of growing polypeptide chains, T or F

A

F – they are added to the C-terminus

107
Q

Describe the composition of the ribosome in which protein synthesis/translation occurs in

A

The ribosome is composed of two different subunits. The complex consists of about 50 ribosomal proteins and several ribosomal RNAs (rRNAs)

108
Q

What are the roles of the subunit in the ribosome

A

The large ribosomal subunit catalyses polymerisation and peptide elongation whereas the small subunit facilitates the tRNA/mRNA interactions

109
Q

Describe how the process of translation is initiated

A

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
Q

What is meant by the A site of the ribosome

A

Aminoacyl tRNA/activation site

111
Q

What is meant by the P site of the ribosome

A

Peptidyl tRNA site

112
Q

What is meant by the E site of the ribosome

A

Ejection/empty site

113
Q

Describe the propagation of translation after the ribosome has fully assembled

A

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
Q

Describe the processes that occur during translation termination, after a stop codon is reached

A

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
Q

What is the role of elongation factors in translation fidelity checking

A

Elongations promote translation and improve its accuracy

116
Q

How specifically does elongation factor-1, EF-1 improve the accuracy of translation

A

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
Q

Correct tRNAs once bound to the complimentary mRNA codon, don’t fall off, T or F

A

F – correct tRNAs do also fall off but at a much slower rate

118
Q

How does codon-anticodon complementation impact GTP hydrolysis by EF-1

A

The hydrolysis of GTP by EF-1 occurs more rapidly if the codon and anticodon are correctly matched

119
Q

What are the implication of translation in the absence of EF-1

A

There are more errors in the protein sequence

120
Q

The large ribosomal complex contains the peptidyl transferase enzyme, T or F

A

T

121
Q

Describe the localisation of the riboproteins and protein synthesising regions of the ribosome within its structure

A

Riboproteins are found on the surface of ribosomes whilst the protein synthesising regions are deep within the structure

122
Q

What is meant by ribosomes being referred to as ribozymes

A

They are RNAs that act more like proteins/enzymes by catalysing reactions

123
Q

Only the Met-tRNA with eIF-4A can bind to the P site of the small ribosomal subunit alone, T or F

A

F – met-tRNA is the only aminoacyl tRNA with eIF-2 bound that can bind the small ribosomal subunit alone

124
Q

Explain how the action of eIF-4G and eIF-4E act as a checkpoint in translation

A

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
Q

eIF-4G, eIF-4E, small ribosomal complex binds to the polyA tail of the mRNA strand, T or F

A

F – the complex binds the capped head of the mRNA

126
Q

Release of eIF-2 initiates translation, T or F

A

T

127
Q

Multiple ribosomes can bind to the same mRNA, T or F

A

T – this is referred to as a polysome

128
Q

How far apart can ribosomes bind to RNA sequences

A

80 base pairs

129
Q

What factors recognise stop codons and trigger dissociation of the ribosomal subunits

A

Release factors – molecular mimics that enter the A-site and cause dissociation

130
Q

Folding of a protein begins immediately after leaving the ribosome, T or F

A

T

131
Q

Why do proteins fold of their own accord

A

Proteins often contain hydrophobic regions which need to be hidden in the centre of the structure to achieve a low energy state

132
Q

What is meant by a molten globule

A

A molten globule is the structure formed from the initial folding of the protein that achieves a roughly correct conformation

133
Q

The amino acid sequence of proteins is thought to have evolved over time to promote formation of the molten globule, T or F

A

T

134
Q

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

A

May reduce the energy state of the protein but blocks further folding and may lead to a dead end

135
Q

Explain the link between protein misfolding and aggregation

A

Misfolding of proteins often leads to exposure of hydrophobic regions which is what causes aggregation

136
Q

Name two of the major classes of molecular chaperones

A

Hsp60 and hsp70

137
Q

What can be said about the expression of molecular chaperones at high temperatures

A

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
Q

Which class of molecular chaperone acts directly on the proteins as they leave the ribosome and bind to hydrophobic residues

A

Hsp 70 class

139
Q

What is the other mechanism of molecular chaperone action other than direct binding

A

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
Q

What is the benefit of isolating misfolded proteins

A

Stops them from interacting with other proteins in the cell

141
Q

Monoubiquitination marks inappropriately folded proteins for degradation by the proteasome, T or F

A

F – this is the result of polyubiquitination

142
Q

Give an example of a disease caused by a misfolded protein

A

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.

BMS242 Cell and Molecular (26 decks)

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