4. Protein in Synthesis Flashcards
At which end on the tRNA is the specific amino acid attached to?
3’ end
what are anti-codons?
tRNA triplet nucleotide sequence that are complimentary to the mRNA codons
How are some tRNA able to read more than one codon?
first base of anti codon is not squeezed/constrained as it would be in a DNA double helix and can wobble making other base pairings possible i.e. wobble base pairing
What allows tRNA to recognise up to 3 different codons?
adenosine to inosine conversion at the wobble position of the anticodon
What does aminoacyl tRNA synthetases do?
charges each tRNA by specific enzyme that recognises both tRNA and amino acid
What are the steps for tRNA charging?
- amino acid adenylation
- transfer of the amino acid to the free 3’ OH of tRNA
Are the new amino acids attached on the amino or carboxyl terminus of the growing polypeptide chain?
the new amino acids is added to the carboxyl end (peptide bond)
what are ribosomes and function
- very large protein RNA complexes
- bind both the mRNA and amino acid charged tRNAs to decode information in the mRNA into a polypeptide sequence of amino acids
what is critical to rRNA function
- 2/3 of molceular weight for ribosome
- form complex and defined secondary structure
- required for most ribosomes function
- x-ray crystallography show no proteins are proximal to catalytic site to participate
- 23S rRNA (prokaryotes) act as a peptidyl transferase ribozyme
- sequence mutagenesis studies of 23SrRNA show its function is correctly position the incoming charged tRNA to allow spontaneous formation of peptide bond
What is the start codon?
AUG (codes for methionine)
How does ribosome recognise the correct AUG as the start codon?
various initiation factors (IF) participate in this process
16S rRNA base-pairing leads to:
- small ribosomal s/u recognition
- large ribosomal s/u recruitment and formation of the 70S initiation complex
How do variations in S-D sequence (Shine delgarno) affect translation?
affects translation initiation effciency
Describe eukaryotic ribosomes
the 5’ cap is recognised leading to recruitment of
- 40S small ribosome s/u
- initiator tRNA(met)
initiator complex scans in a 5’ to 3’ direction until AUG
- eLF2 & other factors dissociate
- large ribosmal subunit binds (eLF5 assisted)
Step 1 of elongation phase of translation
Charged tRNA enters A-site
- specificity dictated by codon-anticodon base pairing
Step2 of elongation phase of translation
new peptide bond formation (between adjacent amino acids in P & A sites)
Step 3 of elongation phase of translation
ribosome translocates along mRNA to next codon
Step 4 of elongation phase of translation
bound tRNA move to next site
As next charged tRNA enters A-site the E-site occupants departs the ribosome
can the A- and E- site be simultaneously occupied?
No
Through what is the elongation phase governed?
elongation factors (EFs)
- EF-Ts exchanges GDP from EF-Tu for fresh GTP allowing it to recruit more charged tRNAs to the A-site
- EF-Tu binds to charged tRNAs and delivers them to the A-site. This requires energy from GTP hydrolysis to GDP
What does ribosomal translocation along mRNA require?
energy from GTP hydrolysis mediated by EF-G
- also needed fri migration of tRNAs
EF-G binding causes bound tRNAs to exist partially bound to both sites (A&P or P&E)
GTP hydrolysis completes the translocation
Describe termination of translation
- no tRNAs can recognise a stop codon in the A site. the stop sign is recognised by a“release factor (RF)”
- RFs activate the peptidyl transferase of the ribosome to hydrolyse the bond between the completed polypeptide chain and the tRNA in the p-site
- Further RFs (RF3 and ribosome recyclicing factor (RRF)’ dissociate RF 1/2 and the small/large ribosomal s/u’s
How many ribosomes can translate a single mRNA at the same time?
more than 1 this is called a polysome in eukaryotes
How are polysomes formed?
5’ cap binding protein (eIF4) interacts with PABP at the 3’end of mRNA with translating ribosomes with intervals around the mRNA
what is PABP
poly A binding protein
How long are the intervals of ribosomes on a polysome
100bp
Does the mRNA in bacteria have to be extensively processed?
No. can be transcribed and translated (coupled) in cytoplasm
- even as mRNA appears it is immidiately recognized by ribosomes
What types of bonds contribute to protein structure?
- non covalent bonds
- covalent disulphide bonds (2 Cys chains)
Describe secondary structure of proteins
interactions between the amino acid (mostly H bonds) resulting in an array of regular sub structures (alpha helix, beta strands)
describe the tertiary structure of proteins
overal 3D structure describes spatial arrangement of secondary strcural elements
How does the alpha helix structure form
right handed coiled conformation in which the NH group of amino acid (of peptide backbone) forms H bond with CO group of an amino acid 4 residues earlier
How are beta sheets formed?
- polypeptide exists in stretched conformation
- peptide backbone forms H bonds between NH and CO
- peptide chains have polarity and can run parallel or anti-parallel to each other
- arrangement of beta strands forms a beta sheet
Why do polypeptides spontaneously fold into protein structure?
amino side chains (allows hydrophobic on inside and hydrophilic outside)
When are cofactors incoperated into protein structure?
At the beginning of folding (noncovalent interactions) of polypeptide
When are post translational covalent modifications done
during folding after cofactors, they are covalent modifications by glycosylation, phosphorylation, acetylation etc
- required for protein activity or recruitment
What are chaperons
- proteins within the cell that assist with appropriate folding of proteins
- prevents misfolding (rather than actively direct correct folding)
- can delay any foldings
- can rescue misfolded proteins to correct conformation
When are proteins more likely to unfold/denature?
when temparture increases, so more Hsps are produced
What are Hsps?
Heat Shock proteins
Descrive how heat shock protein 70 (hsp70) prevents misfolding
- hsp70-ATP loosly binds to hydrophobic patches
- peptide binding induces intrinsic ATPase activity
- hsp70ADP associates with unfolded protein and prevent aggregration
- nucleotide exchange factors replace ADP with ATP
- hsp70 releases unfolded protein
How does groEL/Hsp60 rescue misfolded proteins
- proteins with exposed hydrophobic regions bind to neck of groEL
- binding and ATP cause confromational change that releases misfolded protein into lumen to be folded
- hydrolysis of ATP releases GroES cap and correct folded protein
What does proteasome do
degrades unneeded and misfolded proteins
Describe strcuture of proteasome in eukaryotes
has 19S regulartory particle (alpha subunit) and 20 S core particle (active beta subunits)
How are proteins targeted by protesome
through poly-ubiquitination
What is ubiquitin
76 amino acid highly conserved polypeptide found in all cells that when attached to a condemned protein
What enzymes does ubiquitnation of condemned proteins require
- E1, E2, E3
What does E1 ubiquitin do
activating enzyme that hydrokyses ATP to attach itself to and thus activate ubiquitin
What does E 2 do
recognise E1 ubiquitin complex and transfers complex to itself
what does E3 do?
ligase enzyme binds the condemned protein substrates and an E2 ubiquitin complex
- allows E2 to transfer ubiquitin to protein to be destroyed
What happens to the folding ability the older the protein is
the more likely it is to fold incorrectly and end up digested by proteasome or aggregate
What can signal sequences do?
specific sequences can direct proteins to correct sub cellular location. For example targets proteins for export
What can phosphorylation status of an enzyme dictate
dictates activity. regulates whether enzyme is active or not
How is glycogen metabolism in the liver regulated by phosphorylation?
- singal to stop storing glucose as glycogen, and to mobilise is processed through protein kinase A
- phosphorylation of glycogen synthase inactivates glycogen production
- wheras phosphorylation of glycogen phosphorylase causes its activation (leading to glycogen breakdown/glucose production)
