Translation Flashcards
why is the central dogma a simplification
- Central dogma is a simplification due to the regulatory links which can pass information back, where proteins and RNA interact of DNA and control information
just after transcription takes place what is happening
- RNA has left the nucleus with PolyA tail and 5’cap
- Genetic data is transcribed to a readable format
- And now it can be translated to a useable format
where does translation occur
occurs on large complexes called the ribosome
what does translation use
Translation involves 4 things
- MRNA
- TRNA
- Ribosome 30S and 50s
- RRNA – ribosomal RNA
what does tRNA do
tRNA coverts mRNA to amino acids
what does rRNA do
rRNA catalyses the attachment of each new amino acid to the growing chain
what is the ribosome made out of
ribosome is made out of..
- 60% RNA
- 40% protein
A codon is …
three bases pairs that code for one amino acid
where do you start the reading frame
- you start the reading frame from the first codon this is AUG
- this defines the sequence that is read and the protein that is made
how many possible reading frames are there
- there are 6 possible reading frames – there are 3 on one strand and 3 on the other strand
what is a frame shift mutations
- frame shifting mutations – any mutation that removes 1 or 2 bases leads to frame shift
what direction do you read protein sequences from
- protein sequences always written from N terminal, analogous to 5’- with a protein sequence you start with the N terminal – always read from N-terminus to C terminius (5’-3’)
what are degerneacy
this is the fact that there is more than one codon per amino acid
what is a codon usage bias
- there is a codon usage basis – certain codons that are used for one amino acid that are more common than other
what are the stop codons and what do they do
- some are STOP codons these mark the end of a protein
- these are UAA, UGA, UAG
why are there 64 possible combinations but only 20 amino acids
because of the degenerative nature of the genetic code - wobbling in tRNA allows degeneracy to happen
what shape does tRNA have
has an l shaped 3D fold
what are the different ends of a tRNA molecule
- one end is of the molecule is attached to a specific amino acid –this is catalysed by aminoacyl tRNA transferase
- the other end has three exposed bases – the anti-codon this is the loop at the bottom, this is complementary to one codon
what does aminoacyl tRNA do
- aminoacyl tRNA synthetase catalyses and error checks
how is the tRNA held together
shape of tRNA held together by hydrogen bonds between complimentary pairs
why do tRNAs have a wobble
- not enough tRNAs for all 64 codons therefore tRNAs have wobble – mainly G-U or I (I is a modified base)
- Therefore wobble at 3rd position
- this means that the base in the 3rd position does not have one base but two so form example the codon could have bases C and U present therefore the 3rd base in a tRNA can be used for multiple codons
describe the ribosome
- Synthesised from rRNA in the nucleoli with the nucleus
- Prokaryotic 70s – 50s (large) and 30s (small)subunits (consists of the large and small subunits
- Eukaryotic 60s (large subunit) and 40s (small) subunits
- Difference in structures allow for drug specific
- There are 3 distinct tRNA binding sites
- They conduct the binding to appropriate codons and building of the peptide chain
what are the 3 tRNA binding sites in the ribosome
A site (aminoacyl-tRNA binding site) P site - (peptide-tRNA binding site) E site (exit site)
what does A site do
binds to aminoacyl tRNA ( a tRNA bound to an amino acid)
what does P site do
binds a peptidyl tRNA (a tRNA bound to the peptide being synthesised)
What does E site do
binds a free tRNA before it exits the ribosome
what are the parts of the translation process
- initiation
- elongation
- termination
- protein tagging
what are the requirements of the initiation process and how does imitation work
(STEP 1)
Requirements
- small ribosome bound with initiation factor proteins– IF1, IF2, IF3 bind to the small subunit
- start codon AUG is what the initatior binds to
- initiation tRNA (bound to methionine)
- forms initiation complex on mRNA
how it works
- small ribosomal sunlit is separated from the large subunit by the IF1 and IF3 imitation factors
- binds to the purine rich region of the mRNA which is called the shine dalgarno sequence this is upstream to the AUG codon
- the shine dalgarno sequence is then base paired to a complementary sequence on the 16S rRNA (component of the small subunit)
- this alignment ensures the start codon is in the right position of the ribosome
- another imitation factor IF2 brings in the initiator tRNA to bind to the start codon carrying a specific amino acid
- large subunit binds to the complex and the imitation reaction is released, this requires GTP to be hydrolysed in order to release energy
describe the 5’-UTR
- regulates translation
- Structure can prevent efficient ribosome loading/ mask the start site
- Other proteins temperature can affect RNA structure
What does UTR stand for
- UTR – untranslated region – this is the portion of mRNA that is located between the first nucleotide that is transcribed and the start codon of the coding region
what does IRES stand for
internal ribosome entry site
where is IRES found
- Found in viruses – RNA not capped but still needs to be translated
- Not all translation starts from the CAP
- IRES – first found in viral RNA but is present in some eukaryotic genes
describe elongation (STEP 2)
- the initiator tRNA is at the P site
- a new tRNA that is charged with a specific amino acid comes along and binds to the next codon in the A site
- peptide bond is formed between the amino acid
- where the initiator tRNA releases its amino acid adjacent to the adjacent new tRNA that now has two amino acids linked together
- initiator tRNA is now uncharged so it moves to the E site where it exists
- the tRNA with the amino acid sequence shifts to the P site
- the next tRNA comes to the A site and the process continues building up the amino acid sequence
- this is called elongation
describe termination
- ribosome reaches the stop codon of mRNA
- release factors binds to the stop codon and this cleaves the bond between tRNA and the polypeptide
- this releases the polypeptide from the ribosomes
what are the 3 stop codons
UAA, UAG, UGA
Describe protein targeting
- You can target a protein using a unique address
- Membrane and excreted proteins are inserted into the ER
- Nuclear proteins maintain address label where others lose it, so that if the nucleus disappears and goes into the cytoplasm and hen the nucleus reforms in new cells it can go back into the nucleus
why does protein targeting happen
- Eukaryotic cell is made of multi-compartments
describe the process of protein targeting
- Ribosome binds to the transporter so the protein is placed straight into the ER
- Recognised by the transporter and pushing the protein into the ER
why can antibiotics target a bacteria without harming host cells
this is because bacteria has different RNA polymerase and therefore it has different ribosome subunits compared to eukaryotes this means that antibiotics can target the bacteria without harming the host cells
what to bacterial antibiotics do
- prevent bacterial transcription
what are the types of bacterial antibiotics
- Rifamycin - inhibitor of RNA polymerase
- Streptolydigin
- Microcin j25
- CBR703
what are translation antibiotic types
chlorophenicol (50s inhibitor)
erythromycin (50s inhibitor)
tetracyclines (30s inhibitor)
streptomycin (30s inhibitor)
what does chlorophenicol do
binds to 5OS portion and inhibits the formation of peptide bonds
what does erythromycin do
binds to the 5OS portion prevents translocation movement of the ribosome along mRNA
what does tetracyclines do
they interfere with the attachment of tRNA to mRNA
what does streptomycin do
changes the shape of the 30S portion causes code on the mRNA to be read incorrectly
what does mitochondria have
- Have their own transcription and translation system for some mitochondrial proteins
- This resembles that of an alpha proteobacteria
describe the different types of viral hijaking
- Viruses are unable to replicated without taking over the host machinery – they have develop viral proteins to allow this to occur
- Viral mRNA may not be capped therefore there is an abundance IRES, to get ribosomes to bind to them
- IRES is an entry site within mRNA allowing translocation to be initiated in an end- independent manner
- Some viruses completely take over host machinery and stop non-viral activity such as picornaviruses – these have a collection of enzymes that do this
describe viruses that take over the whole host machinery and stop non viral activity
- Dephosphorylate eIF4E biding protein – binds to eIF4E therefore inhibits
- Protease – this cleaves eIF – 4G
- Protease (2A and 3c) this cleaves Poly-A binding protein
- Proteases (2A and 3C) also cleave transcription factors
- Aim to stop host gene expression
what are the post translational modifications
Mechanisms
- Phosphorylation
- Glycosylation
- Lipidation – attaching lipid molecules
- Cleavage of peptide bonds
- Formation of disulphide bonds from cysteine residues
where do the post translational modifications occur
- Occurs on the side chains of the polypeptide – C terminus and N terminus
