Lecture 12 Flashcards
Multiple ribosomes can bind to the same mRNA, T or F
T – this is referred to as a polysome
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
What is the other term used to describe aminoacyl tRNAs
Charged tRNA
How many amino acids are there
20
What adapter molecule is required for translation
Transfer RNA (tRNA)
What is meant by the abbreviation ORF
Open reading frame
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
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. The small ribosomal subunit then 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
The large ribosomal complex contains the peptidyl transferase enzyme, T or F
T
What is meant by the P site of the ribosome
Peptidyl tRNA site
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
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.
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
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
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.
New amino acids are added to the N-terminus of growing polypeptide chains, T or F
F – they are added to the C-terminus
Which end of the tRNA strand contains the bound amino acid
The 3’ end
Release of eIF-2 initiates translation, T or F
T
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
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
How many different human codons are there
61
How far apart can ribosomes bind to RNA sequences
80 base pairs
Which class of molecular chaperone acts directly on the proteins as they leave the ribosome and bind to hydrophobic residues
Hsp 70 class
What is meant by the genetic code being degenerate
Some amino acid acids are specified by more than one different codon
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.
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
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
What accounts for the similar structure seen in all tRNA molecules
Internal base pairing
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
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
What is the benefit of isolating misfolded proteins
Stops them from interacting with other proteins in the cell
How many different codons are there for serine, and how many different tRNAs
6 different codons but only 3 different tRNAs
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
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)
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
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
How are tRNAs with attached amino acids referred to
Aminoacyl-tRNAs or charged tRNAs
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
What is meant by the E site of the ribosome
Ejection/empty site
Monoubiquitination marks inappropriately folded proteins for degradation by the proteasome, T or F
F – this is the result of polyubiquitination
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
What are the three possible stop codons that signal the end of the ORF
UGA, UAG and UAA
What is the role of elongation factors in translation fidelity checking
Elongations promote translation and improve its accuracy
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
What factors recognise stop codons and trigger dissociation of the ribosomal subunits
Release factors – molecular mimics that enter the A-site and cause dissociation
What is the name of the enzyme that catalyses the addition of an amino acid to a tRNA molecule
Aminoacyl-tRNA synthetase
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
What is meant by ribosomes being referred to as ribozymes
They are RNAs that act more like proteins/enzymes by catalysing reactions
Name two of the major classes of molecular chaperones
Hsp60 and hsp70
What is the universal start codon and what amino acid does it code for
Start codon AUG – Methionine/Met/M
What is unique about the bases contained within tRNAs
The bases are highly modified to allows more specific interactions with the protein counterparts
The amino acid sequence of proteins is thought to have evolved over time to promote formation of the molten globule, T or F
T
What is the name of the sequence in tRNA that binds to the mRNA codons
Anticodon loops
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
What is meant by the A site of the ribosome
Aminoacyl tRNA/activation site
What are the implication of translation in the absence of EF-1
There are more errors in the protein sequence
Explain the link between protein misfolding and aggregation
Misfolding of proteins often leads to exposure of hydrophobic regions which is what causes aggregation
Folding of a protein begins immediately after leaving the ribosome, T or F
T
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…)
If a protein starts with methionine, you can determine that that is the start codon, T or F
T
