From RNA to protein Flashcards
What carries the code from the genome to the ribosome?
mRNA
What makes proteins?
Ribosomes in the cytoplasm
What translates mRNA into proteins in the ribosome?
tRNA
When the protein comes out of the ribosome, what helps to fold the protein into the correct shape?
Chaperones
Who provided evidence that DNA carries genetic information and when?
Avery in 1944
Who figured out the DNA structure and when?
Waston, Crick and Franklin 1953
Who explained the genetic code and when?
Nirenberg, Ochoa and Khorana in 1966
What are the 4 ‘rules’ of the genetic code?
1) Non-overlapping
2) Degenerate
- Some amino acids are specified by MORE than ONE codon
3) Triplet code
- 3 bases encode an amino acid
- Invariable
4) Read from a fixed point (Start codon AUG = Methionine)
If there was no start codon, how many reading frames would mRNA have?
3
What is the start codon and which amino acid is specified?
Aug
Methionine
What are the stop codons in mRNA?
UAA
UAG
UGA
What is the ORF?
Open reading frame
The space between the start and stop codons
What is the structure of tRNA?
Clover-leaf: 3 loops joined together by base pairing WITHIN the tRNA
At one end - the ANTICODON loop
At the other end - Carries an amino acid
In a tRNA, where is the amino acid attached to?
The 3’ end
Is the nucleotide sequence of each tRNA the same?
No, they vary - even between the base pairs, which maintain the structure
How are some of the nucleotides altered in tRNA and why?
Altered by enzymes to form:
PseudoURIDINE and DihydroURIDINE
To increase the complexity of the molecule and allow more SPECIFIC, different interactions (H bonding) with different molecules
How many possible modifications are there that can be made to tRNA to increase specificity binding?
Over 50
What is ‘wobble-base pairing’ and what does this allow?
Position 3 can have non-Waston-Crick binding as the RNA is distorted in this position
Allows each tRNA to have more than one codon which it binds to - efficiency
In wobble base pairing, what can G in the CODON bind to? (bacteria)
C or U in the ANTICODON
In wobble base pairing, what can I in the ANTICODON bind to? (bacteria)
U, C or A
How can the anticodon in tRNA be modified?
A can be DEAMINATED to I (inosine)
How many tRNAs are there in bacteria for how many codons?
31 tRNAs for 61 codons
What must happen to the tRNA molecule before it gets to the ribosome?
What enzyme does this? How?
The tRNA must become charged with the RIGHT amino acid
Done by aminoacyl-tRNA synthetase - forms a HIGH ENERGY bond
How are tRNAs charged with the correct amino acid?
1) Aminoacyl-tRNA synthetase PRIMES the amino acid by adding AMP to the C-terminus (forming and adenylated amino acid)
- Phosphate bond has a HIGH energy, from the ATP hydrolysis to form AMP
2) Aminoacyl-tRNA synthetase then brings this into close contact with the 3’ end of the tRNA (-OH)
- ESTER linkage ( R1 - C - O - R2)
3) AMP drops off
- Energy from ATP hydrolysis is contained within the ester linkage
How are different amino acids the same/different to each other
They have the same backbone structure, with and amino end and a carboxyl end
They have different side chains
What is AMP?
Adenine, ribose sugar and a phosphate
Where does the energy, which is required for protein synthesis (in the ribosome) come from?
ATP hydrolysis, which forms an adenylated amino acid (amino acid + AMP)
This energy is then kept within the bond, in the ester linkage between the tRNA and the amino acid
What ensures that the correct amino acid is joined to the correct tRNA and therefor the translation from mRNA –> proteins is correct?
HOW?
2 adaptors, one after another:
1) The aminoacyl-tRNA synthase (pairs the right amino acid to tRNA molecule, with specific anticodon)
2) The tRNA itself (anticodon-codon matching)
- DIFFERENT synthases are specific to individual tRNAs
- The correct amino acid has the highest affinity for the pocket of its synthase - fits into it before and after AMP addition
- Other amino acids are excluded - do not have a complimentary surface to the binding pocket
How many synthases are there in the body? Why is this important?
20 different synthases
20 different amino acids
20 different tRNAs
As well as the correct amino acid, what has pockets in the synthase?
Nucleotides in the anticodon of tRNA
Acceptor stem of the tRNA
During protein synthesis, how are new amino acids joined to the growing poly peptide chain?
By the enzyme PEPTIDYL TRANSFERASE
What is the structure of the ribosome? (pockets, subunits)
What does each subunit do?
Large subunit - catalyses polymerisation (contains peptidyl transferase)
Small subunit - facilitates the tRNA/mRNA interaction at the anticodon
Has 3 pocket which bind to tRNA:
1) A - Where CHARGED tRNAs enter
2) P - Where amino acid is attached to the pp chain
3) E - Where the UNCHARGED tRNA leaves the ribosome
Where do the 2 ribosomal subunits come together on mRNA?
At the 5’ end
How many tRNAs are in the ribosome at any given time?
2
What happens at the P site in the ribosome?
The HIGH ENERGY bond (which is between the tRNA at the P site and the last amino acid on the growing chain) is broken and a new LOW ENERGY bond is formed between the amino acid on the growing chain and the amino acid on the tRNA at site A
Catalysed by peptidyl transferase
What do elongation factors improve in translation?
Accuracy and efficiency (movement in the forwards direction)
What does EF-1 do?
How does it do this?
Slows down translation to prevent errors in the protein sequence - allows incorrect codon/anticodon matched to be released:w
1) EF-1 binds to GTP and aminoacylated tRNA
2) Aminoacylated rRNA into the A site of the ribosome
3) EF-1 prevents peptidyl transferase from working (before it works, GTP must hydrolyse into GDP, by EF-1 and then it must dissociate from the ribosome
4) GTP hydrolysis occurs when there is a correct codon/anticodon match. If not, EF-1 and aminoacyl tRNA dissociates from the ribosome
What type of enzyme is peptidyl transferase?
What is this?
How was this discovered?
A RIBOZYME
An RNA which catalyses a reaction
- Discovered as ALL the proteins sit on the SURFACE of the ribosome, BUT peptidyl transferase sits INSIDE the ribosome
- Showed that PT is not a protein
What is the structure on mRNA as it comes out of the nucleus and why?
Poly A tail (which is bound by poly-A binding proteins) is bound by eIF-4G and eIF-4E, which also bind the cap at the 5’ end - forms a loop
This is to ensure BOTH ends of the mRNA is intact before protein synthesis occurs
What are eIFs?
Eukaryotic initiation factors
How is transcription initiated?
1) Small subunit of the ribosome is held in place by methionine tRNA and eIF2 - forming a complex
2) This complex binds to the cap and associated initiation factors (eIF-4G and eIF-4E) on the mRNA
3) Small subunit can move away from the cap and begin to find the start codon (AUG) - ATP facilitates each movement to AUG
4) When find AUG - methionine mRNA forms base pairs
5) This signals for the release of EIF and the binding of the large subunit - forming a stable complex
6) Protein synthesis can start
MANY ribosomes do this on one loop of DNA
What are the ONLY things which can bind to the small subunit of the ribosome?
Methionine tRNA and eIF2
Where does methionine tRNA bind to the small subunit when initiating transcription?
Directly to the P site - leaving the A site vacant so that a tRNA can come in
What is needed to facilitate the movement of the small ribosomal subunit to the start site, when the large subunit is not present?
ATP
How far apart on one loop of mRNA are ribosomes?
80 nucleotides apart - many on one loop of DNA
What are stop codons recognised by?
How does this cause dissociation of the ribosome?
Release factors, which look like charged tRNAs and enter the A site (molecular mimicry)
Addition of water to the growing polypeptide chain instead of an amino acid
What about proteins is important for function?
Structure
What happens to proteins as they are formed?
What does this form
Fold rapidly by putting the hydrophobic side chains in the middle - to achieve a lower energy state
Fold into roughly the correct configuration - forming a MOLTEN GLOBULE
What is thought to help the formation of a molten globule?
The amino acid sequence - contains information about folding but doesn’t play a direct part in the function of the protein
What type of process is the folding of a protein?
Why is it important that the right steps occur in the right order?
A highly regulated multistep process
Important that the steps occur in the right order because and incorrect step by reduce the energy state but BLOCK further folding - leading to a DEAD END
Forms an UNFOLDED protein which may have hydrophobic regions on the outside and can cause aggregation
What 2 things can miss-folded proteins (with hydrophobic regions on the outside) do?
1) Interact with the hydrophobic regions of other proteins and lead to AGGREGATION
2) Penetrate into correctly folded proteins, find their hydrophobic regions and unfold them
Do protein aggregates occur naturally?
Yes
What are aggregates?
The conjugation of miss-folded proteins which are protease resistant and eventually lead to cell death
What are prions?
Miss-folded proteins which cause a chain reaction and convert normal proteins into aggregated by unfolding them - are infectious
What diseases are characterised by prions?
Degenerative neurodegenerative diseases:
- Huntingtons
- Alzheimers
- CJD (by eating infected meat)
How do prions cause neurodegenerative disease?
Enter the brain and form amyloid plaques, which are made up of cross-beta fillaments
What do molecular chaperones do?
Assist folding and can reverse incorrect folding steps
If proteins come to a ‘dead end’ and cannot be unfolded, what happens?
They are degraded by proteases
Why are molecular chaperones called ‘heat shock proteins’?
Because their expression is elevated when the temperature is above normal
Heat causes mature (properly folded) proteins to unfold
When do hsp work?
Both when the cell is at normal temperature - to assist folding of new proteins
And when the temperature of the cell is elevated - as mature proteins begin to unfold
What do hsp70 proteins do?
Work directly on proteins as they exit the ribosome
Bind to exposed hydrophobic amino acids and prevents them from binding together - allowing the proteins to fold properly
What do hsp60 proteins do?
How do they work?
Create an isolation chamber for the miss-folded proteins to go into and attempt to fold correctly:
1) Hydrophobic entrance binds to hydrophobic parts on the protein - slightly unfolds it
2) Protein falls into the chamber (which has a hydrophillic surface)
3) GroES cap seals the protein inside for about 15 seconds
4) GroES cap is removed when ATP is hydrolysed
5) Multiple rounds may be needed to correctly fold the protein
What fraction of newly synthesised proteins are incorrectly folded and digested in the proteasome?
1/3
What marks incorrectly folded proteins for degradation?
POLYubiquitination
