21: Translation Flashcards
What direction are proteins made?
N->C direction
What is a codon?
3 letter base code for each amino acid (3^4 bases = 64 codons total) 3 stop and 61 AA coding including Met for start
What are the key features of the genetic code?
- almost completely universal
- non-overlapping
- no gaps
- redundancy of some codons coding for same amino acid
Why is the genetic code non-overlapping?
significant restrictions on what amino acid residues could follow each other
Where is redundancy common?
3rd codon position
What are the allowed Wobble pairs at the 3rd codon position?
5’ anti codon base, 3’ codon base:
C, G
A, U
U, A/G
G, U/C
I, U/C/A
What is the I anticodon base?
example of modified tRNA; modified A by deamination; smaller = more leniency
AA found less frequently…
have fewer codons
Why is Tryptophan found less frequent?
large and bulky
What are the stop codons?
UAA
UAG
UGA
similar codons are…
functionally related with similar structure (same charge) bc then a change in mutation will have a lesser effect = increase chance of functional protein in the case of a single base mutation
1st or 3rd base change
How was genetic code determined?
put same repeated code in a mixture and see translated amino acid
missense, silent, nonsense, mutation?
frameshift?
missense - change 1 base=new AA
silent - change 1 base = same AA
nonsense - change 1 base = stop codon
frameshift - insert or delete 1-2 bases affecting everything downstream
When are mutations problematic?
loss of function, gain of function
What are examples of loss of function?
missense mutation in important AA residue
nonsense or frameshift causing shortened or different protein
mutation leading to loss of structural integrity, stability, may degrade
What are examples of gain of function?
permanent ON of oncogene (loss of control)
new function that are toxic to cell
Current example of gain of function?
delta variant of covid have special jackknife function to help virus fuse with cell membrane more efficiently = more infectious
What are the important components of tRNA?
acceptor stem attaches to amino acid on 3’ end
anitcodon binds to mRNA
each tRNA has a specific amino acid that it binds to depending on anticodon
What are the structural characteristics of tRNA?
2ndary structure clover leaf, with double helical structure
highly modified and fairly stable
looks like an L in 3D structure
2 key single stranded region: 3’ acceptor site + anticodon
also has D loop and T loop
Why is there only 1 type of Phe tRNA?
GAA anticodon
bc can do wobble
What are the mechanics of wobble?
5’ end of anticodon (1st position) and 3’ end of mRNA (3rd position) are the wobble position
What Is the purpose of amino acyl tRNA synthetases? What is a characteristic?
enzyme that charges tRNA with an amino acid and some have proofreading function
there is at least one synthetase for each amino acid (highly specific)
couples the 3’ end of tRNA to its correct amino acid, recognizing anticodon
What does the structure of tRNA + amino acid look like?
adenine of tRNA covalent bond ligation to carboxyl group of amino acid
What are the steps of the Aminoacytl-tRNA synthetase reaction to put an amino acid onto a tRNA?
- amino acid reacts with ATP to form an aminoacyl-adenylate (aminoacyl-AMP) - energy translation
- activated AA reacts with tRNA to make aminoacyl-tRNA (high energy) inside the aminoacyl tRNA synthetase active site AMP released
Where does peptide bond formation energy come from?
high energy ester bond between tRNA (A) and O of carboxyl of AA
- indirectly from ATP
What is a ribosome similar to?
spliceosome (rRNA and protein scaffolding complex)
rRNA component interact with tRNA and mRNA
What are the components of ribosome structure?
small subunit and large subunit (majority of tRNA is bound in large subunit)
exit site, peptidyl site, aminoacyl site
What is the ribosome purpose?
catalyses protein synthesis rxn of mRNA and tRNA to make peptide bonds between AA brought to ribosome by tRNA
What is a difference between initiation of translation in bacteria vs eukaryotes?
start with f-Met (special Met) in bacteria and normal Met in eukaryotes
What are the steps of eukaryotic elongation in translation?
- incoming aminoacyl-tRNA binds to A site of ribosome requiring BP between tRNA anti codon and codon of mRNA template
- new aminoacyl-tRNA gets ligated to previous amino acid in the P site through peptide bond from **ester bond energy **(charge removed from new AA-tRNA)
- large ribosome subunit moves over (conformational change) so that old tRNA is in E site and new is in P site
- small subunit moves forward (towards 3’ end of mRNA) to align with large subunit
- spent tRNA leaves E site
Where does translation occur?
cytoplasm
What direction does translation occur interns of the mRNA?
5’ to 3’
Where does specificity come from in translation?
aminoacyl tRNA synthetase
requirement of BP in A site of ribosome of anticodon and codon
How is translation initiated in eukaryotes?
remember eukaryotes have circularized mRNA
- initiation factors bind to 5’ cap and poly A tail proteins
- initiation factors recruit small subunit of ribosome at the cap
- normal Met binds to P site of small ribo subunit with initiation factors bound
- small subunit moves 5’ to 3’ to find 1st AUG
- initiation factors dissociates and large ribo subunit attaches
- aminoacyl-tRNA binds to A site
How is translation initiated in prokaryotes?
- ribosomes recognize internal ribosome binding sites consensus sequence found upstream of each functional AUG in front of each open reading frame of each protein
RBS is the shine-dalgarno sequence before 1st start codon which is the reverse complement sequence in rRNA
What are the steps of prokaryotic elongation?
- elongation factor Tu is tRNA carrier, brings tRNA to ribosome
- if anticodon matches, EF-Tu hydrolyzes GTP and dissociates from ribosome leaving aminoacyl-tRNA in A site
but
- if tRNA anti codon is mismated, the amino acyl tRNA dissociates before EF-ty hydrolyzes GTP
(sampling processes)
what is an energy difference between prokaryotes and eukaryotes in translation?
GTP required for prokaryotes
How is translation terminated in prokaryotes?
- specific termination factors called release factors recognize stop codon in A site when no matching tRNA is found for stop codon
- RF causes ribosome to transfer the peptide group to water and releases the peptide chain
- GTP hydrolysis by another RF allows first RF to dissociate
- mRNA dissociates from ribosome
Why is more mistakes tolerable in translation?
replication - DNA issue = mRNA issue = protein issue
mistakes least tolerate
protein level mistakes only affect proteins
what are targets of antibiotics?
inhibitors of protein synthesis (eukaryotes and prokaryotic translation)
What happens to proteins after translation?
folding and modification of protein
what are the characteristics f 1º, 2º, 3º, and 4º protein structures?
1º amino acid sequence
2º alpha helices, B sheets and coils
3º 3D folding
4º complex with other proteins
What are the 3 protein folding pathways?
- folds on its own
- Heat shock proteins help spontaneous folding
- chaperone proteins help proteins fold (15%)
What are the characteristics of a chaperone protein?
- uses ATP
- lid opens and inserts polypeptide
- large protein
- reducing environment
- found in all cells
- many are HSPs
ribosome catalyzes the formation of a peptide bond between the…
amino group of incoming AA + tRNA and C terminus of previous AA
what is the mechanism for chaperone proteins?
nascent protein energy from ribosome are met by ribosome associated chaperones (trigger factor TF in E. coli and nascent chain associated complex NAC in euk)
when are heat shock proteins always present?
high temperature
What are prions? What do they cause?
infectious agent caused by misfolded protein
causes transmissible spongiform encephalopathies (TSE)s called prion disease
What is the prion mechanism in mad cow disease?
- major prion protein (PrP) is found in NS mainly and can exist in 2 forms: PrPc or PrPsc (disease)
- regular form interacts with PrPsc causing different protein folding/3º structure = disease
- mainly a-helices in PrPc converted to B-sheets in PrPsc
Why does a protein do from disordered un folded state to ordered folded state if this goes against entropy? What determines U or F favoured?
must be energetically favourable to be folded
∆G determine which state is favoured - must be negative
∆G = ∆H - T∆S
What is ∆G if enthalpy - energy - is -ve and entropy is +ve?
enthalpically and entropically favoured , spontaneous (exergonic) at all temperatures (ex. fire)
What is ∆G if enthalpy is -ve and entropy is -ve?
enthalphically favoured spontaneous only if temp is lower
What is ∆G if enthalpy is +ve and entropy is +ve?
entropically favoured (endothermic)
spontaneous if high temp
What is ∆G if enthalpy is +ve and entropy is -ve?
always nonspontanous (endergonic)
How do enthalpy and entropy relate to protein folding?
entropy (disorder of water) makes folding a favourable rxn when ordered water in hyptophobic core is removed and made disordered - hydrophobic effect
enthalpy is forming and breaking bonds
side chains of the amino acids determine the — of proteins
shape and properties and function
The expression of the correct genes is essential for…
growth and differentiation
How are proteins modified post translation?
phosphate group added by kinase (usually activating protein) and removed by phosphatase (usually deactivating protein)
What are the advantages and disadvantages of proteins modified post translation?
adv: quick compared to transcription. and translation
disadvantage: make protein whether needed or not
How is insulin regulated with proteins modified post translation?
preinsulin Is S-shaped protein connected by disulphide bonds
hold of protein gets cleaved off = active insulin
- quick response to blood sugar changes
