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BIOC221 > Protein Translation, Targeting, Modification And Turnover > Flashcards

Protein Translation, Targeting, Modification And Turnover Flashcards

1
Q

Features of the genetic code in relation to translation

A

Non-overlapping
Universal (almost)
Highly degenerate- multiple codons code for one amino acid
Nonrandom

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2
Q

How many codons are there and what are the different types

A

64 codons- 61= amino acids, 3= stop codons

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3
Q

What must a ribosome do during translation to ensure it occurs as it should

A

Maintain correct reading frame

Start at the correct AUG

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4
Q

Features of tRNA (9)

A

Produced as a precursor
Mature tRNA 76-78 bases
Amino acid attaches to 3’OH
Anticodon binds to mRNA
Cloverleaf secondary structure- undergoes cleavage and bases are chemically modified for stabilisation and recognition
L shaped tertiary structure
Contain numerous modified bases (nearly 80 possible modifications)
Can recognise >1 codon due to the wobble base
Ensure fidelity of the genetic code

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5
Q

How is tRNA made

A

We have tRNA genes which are transcribed by RNA polymerase II which leads to the formation of the primary transcript. This undergoes cleavage to become secondary cloverleaf which has modifications to it

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6
Q

What is the wobble base pair

A

I can bp with U or C or A which allows a single tRNA to bind to multiple mRNA codons

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7
Q

What are aminoacyl tRNA synthetases (aaRS)

A

They couple each amino acid to its appropriate tRNA molecule

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8
Q

How does aaRS work

A

Catalyse formation of amino-acyl-tRNA via 2 step reaction which is ATP dependent- aa is adenylated, AMP attached to aa. Then aa is transferred from AMP to 3’OH on tRNA making aa activated and tRNA charged
Amino acid becomes activated and tRNA becomes charged
2 classes of enzymes
Each aaRS is specific for a single amino acid
Some aaRS have proof-reading activity
Each aaRS can recognise >1 tRNA (isoaccepting tRNAs)
Ensure fidelity of genetic code

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9
Q

An example of aminoacyl-tRNA synthetase proofreading

A

Ile and Val have similar structures so can both fit into synthetase active site
Only val fits in the editing hydrolysis site
Therefore, if valine binds in the active site it will be removed by the editing site so only ile will remain bound in the active site

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10
Q

What does it mean that aaRS can recognise >1 tRNA

A

Ala has 3 different tRNA which are specific for it
Only one ala aaRS can add alanine to all of its possible tRNAs
Therefore, it recognises all of them as they have a common feature on them which allows for this

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11
Q

Features of the ribosome

A

A site= aminoacyl site- where tRNA enters
P site= peptidyl tRNA site- where peptide is joined onto chain
E site= exit site- where tRNA exits
Made up of proteins (form scaffold) and rRNA (acts as catalyst
Nucleolus is ribosome-producing factory

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12
Q

Features of GTP binding proteins (G proteins)

A

Essential for protein synthesis
Catalyse hydrolysis of GTP-> GDP + Pi
GTP-bound and GDP- bound forms have different conformations and activities
GAP (GTPase activating protein) stimulates GTPase activity of GTP binding protein
GEF (guanine exchange factor) stimulates exchange of GTP for GDP-> GTP
GTP gamma S is a non-hydrolysable GTP analogue used to study G protein function

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13
Q

What initiates transcription in eukaryotes and what is the different functions of them

A

Eukaryotic initiation factors, Met-tRNAi(met) and tRNA are needed
Two eIFs are G proteins
Functions: binds to Met-tRNAi(met), binds to 5’cap and polyA binding proteins for RNA unwinding, binds to E site in 40S subunit, binds to A site in 40S subunit, binds to small subunit, binds to 43S preinitiation complex and binds to 60S subunit displacing other IFs

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14
Q

What is a Kozak consensus sequence

A

Sequences which start AUGs are commonly found in. Also recognised by small ribosomal subunit and helps with recognition of the correct AUG

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15
Q

Brief overview of how initiation of transcription occurs in eukaryotes

A

2 IFs are bound to the small subunit- each in the A and E sites
43S preinitiation complex forms by Met-tRNAi(met) binding to IF2GTP and binds into the P site
mRNA unwinds via helicase activity of IF on 5’ cap and polyABPs
Scanning for AUG in Kozak sequence
Met-tRNAi(met) anticodon binds to AUG codon= stimulation of GTPase activity= GTP-> GDP conformational change and tRNA can no longer bind as correct base pairing has occurred (48S initiation complex)
IF-GTP binds in A site and large ribosomal subunit is recruited
IFGTP-> IFGDP= conformational change and other factors dissociate
80S initiation complex formed ready for elongation= ribosome with Met-tRNAi(met) in P site and mRNA

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16
Q

Initiation of translation in prokaryotes

A

Co-transcriptional (occurs with transcription) on an operon- each gene having own start and stop codons where ribosome associates and dissociates for each gene. Each gene also has own shine delgarno
Requires IFs, fMet-tRNAf(met) and mRNA with no 5’cap
Shine-Dalgarno sequence in mRNA 5’UTR directs ribosome to start codon by binding to a complementary sequence in 16S rRNA
fMet-tRNAf(met) recognises initiation codon

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17
Q

What is required for elongation and the different functions

A

Eukaryotic elongation factors (EFs)
Binds to aa-tRNA(aa)
Binds in A site
Recycling EF used for binding to aa-tRNA(aa)
Process is same in prokaryotes and eukaryotes

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18
Q

What 3 things need to occur in elongation for translation to work

A

Decoding and proofreading- ribosome selects an aa-tRNA complex matching codon in the A-site
Formation of peptide bond- transpeptidation where peptidyl group of aa-tRNA(aa) in P-site is transferred to the aminoacyl group of aa-tRNA(aa) in A site, catalysed by 28S/23S rRNA
Translocation- movement along mRNA must occur by exactly 3 bases/ 1 codon, tRNA in A and P sites are transferred to P and E sites by binding to EFGTP

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19
Q

Decoding/ proofreading steps in elongation

A

aa-tRNA(aa) forms a complex with EFTuGTP
Anything that binds incorrectly to tRNA falls off. When correct bp-ing is achieved, stimulates GTPase activity of EF= changes in ribosome= GTPase activity in EF= shape change= can no longer bind to tRNA= tRNA falls off= correct tRNA in A site

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20
Q

How does peptide bond formation work in elongation

A

Amine group in new amino acid is nucleophile and attacks C-O-tRNA carbon
Causes OH-tRNA (3’OH) and new peptide bond formed on the aa-tRNA in the A site
Catalysed by ribosomal rRNA (ribozyme) in peptidyl transfer site by 23S rRNA- H bond forms between rRNA and aa to help hold everything in place for the reaction to occur

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21
Q

What happens after peptide bond formation in elongation

A

EFG/ eEF2 maintains correct reading frame so that mRNA can only move by 3 bases. EFG/eEF2 binds in A-site via molecular mimicry
GTP hydrolysis occurs-> GDP so EF2 unbinds. Leads to empty A site and next tRNA can bind in there. tRNA that was in A site is now in P site and tRNAi has left out of the E site

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22
Q

What is molecular mimicry

A

2 different molecules have the same shape so can bind in the same site (eg eEF2.GTP is mimic of tRNA eEF1a in ribosome- when binds in the same site= ribosome holds the 3 bases and when mRNA moves it can only move 3 bases along)

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23
Q

Fidelity in initiation

A

Ensuring tRNA connects to the right aa from aaRS
Met-tRNA-(met) binds in P site- done by IFs blocking A and E sites
Start at correct start codon- done by kozak sequence and correct codon-anticodon leading to release of G-protein initiation factor bound due to GTPase activity

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24
Q

What factors are involved in termination of translation

A

Eukaryotic release factors (eRFs)- eRF1 recognises all 3 stop conds (UAA, UAG, UGA), eRF3-GTP binds to eRF1 and assists termination, ABCE1 involved in ribosome recycling and displaces eRF3

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25
Q

How does termination of translation occur

A

RF1 recognises the stop codon in A site and enters via molecular mimicry. RF1 enables hydrolysis of ester bond between tRNA and aa to release polypeptide chain RF1 is bound to RF3-GTP and causes GTPase activity of RF3-GTP-> GDP as RF3 changes shape and comes off
ABCE1 then binds- has ATP hydrolysis activity and uses this to pull apart the ribosome complex- large subunit leaves, tRNAs fall off, initiation factors bind in the A and E sites putting the small subunit in same state as it was at the start of translation

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26
Q

Molecular mimicry in translation termination

A

eRF1 (RF) is a structural mimic of aa-tRNA(aa) so can bind in the A site
Domain 1 recognises stop codons= anticodon like site
GGQ motif has a 3aa sequence (glycine-glycine-glutamine) which hydrolyses reaction to break final aa-tRNA bond

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27
Q

How does the polypeptide release reaction work

A

H2O attacks carbon on C-O-tRNA creating OH-tRNA and COOH-protein

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28
Q

What are polysomes

A

Proteins are made on polyribosomes (polysomes) in eukaryotes= one mRNA with many ribosomes on it= multiple copies of protein from the same mRNA strand

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29
Q

Where does the polypeptide chain go after translation

A

Into the polypeptide tunnel
~10nm long and ~30aa fit into it
Slippery so that aas dont stick in the channel
Time taken to synthesis protein varies (sec-min_

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30
Q

Ways which translation can be inhibited

A

Inhibit of peptide bond formation
Premature termination- acts as RF1
Inhibition of translation by depurination of adenine in 28S rRNA inhibiting binding of eEF

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31
Q

How many protein coding genes in bacteria, animals and plants

A 
Bacteria= 4,300
Animals= 20,000
Plants= 27,000
32
Q

Three methods of protein transport and their features

A

Gated transport- pores in membrane, in and our of nucleus, controlled and reversible
Transmembrane transport- irreversible and requires translocon
Vesicular transport- packaged in lipid membranes, buds off one place and fuses with another place (endomembrane system or secretory pathway are other names), reversible, these proteins need to go to ER first

33
Q

Examples of proteins that enter the ER and transit the secretory pathway

A

Insulin (pancreatic B cells)
Spike protein encoded by mRNA COVID19 vaccine (many cell types)
Cystic fibrosis transmembrane receptor (epithelial cells)
Pro-opiomelanocortin (neurons)
Ricin (castor beans)

34
Q

Translocons in bacteria/ archaea and eukaryotes

A

SecYEG or YidC in bacteria/ archaea

Sec61 in eukaryotes- proteins go straight into ER lumen

35
Q

3 steps in protein translocation into the ER

A

Recognition of a targeting signal
Binding to the ER receptor
Translocation in a unidirectional channel

36
Q

What is an ER targeting sequence

A

N-terminal signal (lumenal and some transmembrane proteins) which form a hydrophobic a helix
Internal targeting signals (some transmembrane proteins)

37
Q

Features of the N-terminal ER targeting sequence

A

13-36 aa long
6-15 aa are rich in non-polar aas (eg Leucine rich) which fold into a hydrophobic a-helix
There is a basic aa in N-terminal region
This sequence drives formation of the a helix secondary structure and this structure is recognised by the SRP (not the sequence itself)

38
Q

How does recognition of the ER signal sequence work

A

Signal recognition particle (SRP)
Associated with ribosome, waits for the hydrophobic a-helix to come so it can bind and change shape
Pauses translation in the ribosome by binding in the A site
Composed of RNA (7S RNA, 300 nucleotides= structural component) and proteins (SRP#- number corresponds to the size of the protein in kDa)

39
Q

Roles of proteins in SRP

A

SRP54: M domain= methionine rich, non-polar, binding pocket for hydrophobic a-helix. NG domain= GTPase activity
SRP14: inhibits translation by binding in the A site, preventing elongation factors with tRNA and aa from binding in there

40
Q

Features of the SRP receptor

A

SRP receptor recognises SRP bound to a signal sequence
Allows for ribosome to associate with translocon which allows it to begin translation again
ER membrane protein
2 subunits: alpha subunit- peripheral (~70kDa, G protein) beta subunit- transmembrane (~30kDa)

41
Q

How does the SRP-receptor (SR) mechanism work

A

GTPase activity is required for protein import into ER
GTP(gamma)S non-hydrolysable GTP analogue will block translocation
SRP is initially GDP, binding with the ribosome causes exchange reaction= SRP-GTP (shape change in SRP occurs)
SR is initially GDP, binding to translocon causes exchange reaction= SR-GTP (shape change in SR occurs)
As both are GTP bound, the SRP and SR bind together and stimulate each other’s GTPase activity GTP-> GDP. As neither are GTP bound and both BDP bound, shape changes back and SRP/SR can no longer bind to each other and dissociate from ribosome. Ribosome is bound to translocon in ER membrane

42
Q

Features of the Sec61 translocon

A 
3 subunits:
Sec61 alpha: ~52kDa
Sec61 beta: ~10kDa
Sec61 gamma: ~8kDa
Makes interactions with ribosome so they stay associated
43
Q

What in the translocon ensures that proteins only go in the unidirectional location and that only the protein moves through (not other molecules like Ca leaving)

A

Pore ring= 6 hydrophobic aas. Closes tight around the protein so nothing else can fit through and opens just enough to let the protein through
Plug= alpha2-helix of Sec61a. Acts as a plug and is pushed out of the way by the incoming protein

44
Q

How does removal of the N-terminal signal work

A

First protein post-translational modification
Signal peptidase catalyses cleavage of sequence
Signal peptidase located in ER membrane and is associated with the translocon

45
Q

Features of protein translocation into the ER

A

Start transfer sequence= signal peptide= starts protein translocation
Stop transfer sequence= in transmembrane domain, can be multiple eg in CFTR gene- for transmembrane proteins that are meant to stay in the membrane. The stop sequence spans the membrane so that part of the protein is in the cell and part of it is out of the cell

46
Q

What are the post translational modifications in the secretory pathway

A

Signal peptide cleavage (first)
N-linked glycosylation and O-linked glycosylation (addition of sugars)
Disulfide bond formation (covalent bonds between cysteine)
Proline hydroxylation (modifying side chains)
Proprotein processing (cutting up)

47
Q

Features of modification by glycosylation

A

Addition of sugars (glycans, carbohydrates, saccharides) to amino acid side chains
Modified proteins= glycoproteins
Occurs in all cellular compartments (in different ways in different compartments)
Lipids and RNA can also be glycosylated
Disorders arise from glycosylation (over 100), mostly N-linked

48
Q

Where does glycosylation occur in N-linked

A

On the nitrogen in arginine sidechain

49
Q

How is a protein N-glycosylated

A

Synthesis of a 14 sugar lipid linked oligosaccharide precursor (composed of GlcNAC, mannose and glucose)
Transfer of oligosaccharide to protein- catalysed by oligosaccharyl transferase (OST), occurs between Asn-N and sugar-C, Asn-X-Ser/Thr consensus sequence (asparganine is recognised in this specific sequence by OST as it comes through translocon)
Addition of sugars is co-translocational= modification on unfolded protein coming out of the translocon
GlcNAC forms the glycosidic bond with N

50
Q

How does processing of the oligosaccharide chain work

A

14 chain in ER has sugars removed by glycosidase enzymes- removed as part of a process for protein folding
5 chain sugar via vesicular transport goes to golgi where ~200 glycosyl transferases add 1 sugar at a time to the chain. Up to 10 sugars can be added= different structures can be built on cells
~7000 different sugar structures= diversity

51
Q

Functional consequences of protein N-glycosylation and 2 examples (not in detail)

A

Contributes to protein folding and disulfide-bond formation in the ER, protein stability (longer half life) and protein function
Can also cause disorders- CDG (congenital disorders of glycosylation) eg ODT mutation= glysocylation not occurring properly or not at all
Cell surface expression of CFTR
Viral immune system evasion

52
Q

How is N-glycosylation required for cell surface expression of CFTR

A

There are two N-linked glycosylation sites in CFTR which are required for CFTR to get to the cell surface and important for surface expression
Mutation of one of these= decreased cell surface density
Mutation of both of these= even more decreased cell surface density
Similar effect to delta-F508 mutation (impacts folding and causes protein to not be able to fold properly)

53
Q

How does N-glycosylation link to virus immune system evasion

A

Spike proteins are highly glycosylated with different densities. The higher the glycan shield density, the harder it is for a human to induce an immune response to the protein and invasion by virus is strong
Sugars move around on the spike proteins
Vaccine of lower glycosylated density viruses allows good immune response

54
Q

Targeting of N-glycosylation and SARS-CoV-2

A

In vitro, targeting of N-glycosylation blocks SARS-CoV-2 variant infection
PNGase removes N-linked glycosylations
Endo H leaves one sugar on N-linked glycosylations
Shown to be effective as glycosylation is important for infection by SARS-CoV-2
OST inhibitor meant that spike without glycosylation was no longer able to bind to ACE2 and enter cell= needs sugars to bind to ACE2 and enter cells

55
Q

What is an SDS PAGE gel

A

Separates proteins by size (like electrophoresis separating DNA by size)

56
Q

Features of proprotein cleavage post-translational modification

A

Many secreted proteins produced as proproteins
Cleavage catalysed by proprotein convertase enzymes
Located throughout secretory pathway and secreted from the cell
Recognition sequence: (K/R)-(X)n-(K/R) (K= lysine, R= arginine, X= any aa, n= 0, 2, 4 or 6)
Different cell types have different enzymes
Single polypeptide chain generates different proteins in different cell types

57
Q

Different locations of the different proprotein convertase enzymes

A

Secreted
Secretory granules
Cell surface
Transgolgi network

58
Q

Example of proprotein cleavage for neuropeptide POMC

A

POMC cleaved by different proprotein convertases in different cell types to generate different products
Anterior lobe of pituitary: expresses PC1/3 (proprotein convertase 1/3) which generates 4 different neuro-peptides
Hypothalamus, skin, pars intermedia of pituitary: expresses PC1/3 and PC2 which generates 9 more products from the 4 produced above by PC1/3
Different POMC products have different functions

59
Q

Example of proprotein cleavage for insulin

A

2 cleavage sites in the proinsulin precursor (PC2 and PC1/3)
Disulfide bond formation between A and B chains occurs first
Cleavage of the sites one at a time to remove C peptide= active insulin with A and B still linked by disulfide bonds

60
Q

Example of proprotein cleavage for SARS-CoV-2

A

Cleavage of the protein is required for the virus infection
Furin= proprotein convertase enzyme
Without furin= attenuates pathogenesis and virus cant enter cells

61
Q

What mechanisms does a eukaryotic cell have for protein degradation

A

Autophagy and lysosomal protein degradation

Ubiquitin-proteasome system

62
Q

Features of lysosomal protein degradation

A

Lysosomes: packed with ~50 hydrolytic enzymes, pH 5= acidic which is pH enzymes work at (if they escape into cytosol will be inactive), non-selective degradation, activated by fasting, degrades 10-20% of cellular proteins and degrades organelles
Things enter via phagocytosis, endocytosis and autophagy (organelles)

63
Q

Features of ubiquitin-proteasome system and 2 parts

A

Occurs in cytosol
Degrades proteins from cytosol, nucleus and ER
Controls many cellular processes
2 parts; tagging protein for degradation (protein substrate, ubiquitin, E1, E2 and E3, ATP) and proteolysis (debiquinating enzyme, protein unfoldase, protease/ proteasome, ATP)

64
Q

Features of ubiquitin protein

A

76 aa monomeric protein= small (~7kDa)
C terminus= Gly76
Has Lys48
Added onto other proteins for them to be degraded

65
Q

3 steps in the ubiquitination pathway

A

E1 (ub activating enzyme) uses ATP and adds ub to E1 through a cysteine residue= thioester bond at gly76-cysteine
E2 (ub conjugating enzyme) catalyses transfer of Ub from E1 to E2= thioester bond at gly76-cysteine
E3 (ub ligase) catalyses transfer of Ub from E2 to lysine residue on substrate= isopeptide bond at gly76- Lys side chain on substrate

66
Q

Features of E1, E2 and E3

A

E1- 1 or 2 different types, activating enzyme, ATP dependent- Ub-AMP-> Ub-cysteine
E2- 30-50 different types, conjugating enzyme, can be needed for specificity if working in complex with E3
E3- >600 different types, Ub ligase, important for determining substrate specificity- recognises target proteins to be degraded, often works in complex with E2

67
Q

How are multiple Ub molecules added to a substrate (need atleast 4 for protein to be degraded)

A

Isopeptide between gly76-lysine side chain on protein
Isopeptide between lys48 of Ub1 and gly76 of Ub2
Isopepide between lys48 of Ub2 and gly76 of Ub3
Isopeptide between lys48 of Ub3 and gly76 of Ub4
= lys48 polyubiquitin chain (compact chain as Ubs all come close together when they bind together)

68
Q

Different signals that determine protein lifespan (determines recognition of substrates by an E3 enzyme)

A

Identity of residue at N-terminus of a protein
Phosphorylation
Oxidation
Subunit dissociation (hydrophobic surfaces)
Different E3/E2 combinations recognise different classes of substrates

69
Q

How does the N-end rule work

A

Targeting proteins for degradation based on residue at N-terminus, controls half-life
Peptidases and amidases control identity of N-terimus by removing methionine, the enzymes are activated in response to different signals
Specific E3 ligases (N-recognins) recognise destabilising residues at N-terminus

70
Q

Other roles of ubiquitin and what it means

A

Has multiple lysine residues that can form chains= multiple types of ubiquitin chains can form= different polyUb chains have different shapes and are recognised by different things= different functions

71
Q

Two parts of the proteasome and what they do

A

Caps on either end 19S- recognises polyUb protein, removes Ub chain and unfolds protein
Protease- responsible for proteolysis 20S= short peptides 4-25 aas long which are converted into aas by peptidases in cytosol
Is a 26S multisubunit complex
Can participate in antigen production (immunoproteasome)

72
Q

19S complex (cap) and how it works

A

~20 subunits (700kDa)= protein complex
Ub receptor recognises lys48 polyUb chains on target protein
Unfolding machinery unfolds the protein and pushes it into the protease
Deubiquitinating enzyme cleaves isopeptide bond between polyUb-protein and releases the Ub to be recycled

73
Q

How does protein unfolding in 19S complex work

A

Catalysed by AAA-ATPases (6 subunits), requires ATP as the energy is needed to pull proteins apart (pulls apart non-covalent bonds eg ionic or H bonds)
Unfolded protein fed into protease below
Non-hydrolysable ATP inhibits unfolding

74
Q

Features of the 20S proteasome (core particle)

A

Four ring core- each with 7 subunits
28 subunits (670kDa)= protein complex
Alpha subunits at either end- a1-7 and a’1-7- cover the pore in the middle of the complex
Beta subunits in middle- B1-7 and B’1-7 which act as proteases and perform peptide bond hydrolysis
Generates ~8 residue peptides

75
Q

What are the different beta catalytic subunits and where do they cleave

A

B1/B’1 cleaves after acidic residues
B2/B’2 cleaves after basic residues
B5/B’5 cleaves after hydrophobic residues
Hydrolysing peptide bonds
Is the reason why we generate protein residues of different lengths

76
Q

Bacterial protein degradation (process also used for some mitochondria)

A

Prokaryotes dont have Ub system- use a more simple multi-protein complex
ClpX ATPase forms 2 outer rings which unfolds and recognises proteins
ClpP protease forms 2 inner rings (6 subunits each) which undergo protein degradation
Other subunits provide substrate selection as dont have Ub tagging system (eg ClpS which is prokaryotic equivalent of N-end rule)

BIOC221 (5 decks)

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