Translation Flashcards
- How many possible combinations of nucleotides are there?
- Nucleotides are read __ to __
- Protein is synthesized from __ to __
- 64
- 5’ to 3’
- N terminus to C terminus (amino terminal end to carboxyl terminal end)
- If you see ATG as a start codon, what does that mean?
- AUG codes for?
- 3 stop codons?
- When counting how many amino acids the protein encodes __ counts, but __ does not
- That its DNA
- Methinonine
- UGA, UAA, UAG
- AUG counts, but stop codon does not (remember dont start counting from the beginning, start counting once you encounter AUG)
- Missense mutation?
- Nonsense mutation?
- Insertion/deletion mutation vs. frameshift?
- Splice site mutation?
- Mutation results in a different codon, but one with similar properties
- Changes amino acid to a stop codon
- Insertion/deletion is when its a multiple of 3; frameshift is when insertion/deletion is not a multiple of 3
- Changes in nucleotides involved in splicing RNA
- What is a trinucleotide repeat expansion mutation?
2. 2 locations where this can happen and what it would do
- Repeats of the 3 nucleotides keep occuring until it becomes unstable
- Coding region= a faulty protein; can become prone to aggregation (Huntingtons disease)
5’-3’ UTR: doesnt affect protein sequence, but affects ability of that transcript to be translated (mytonic dystrophy)
~trinucleotide repeat expansion can cause anticipation (2 alleles during crossover in meiosis but one parent has very long gamete that it gives child)
- Where is the amino acid attachment site on tRNA?
- What is anticodon?
- Example question: What is the anticodon of the tRNA that delivers AUG?
- CCA- 3’ terminus
- Specific 3 nucleotide sequence that base pairs with the mRNA (antiparallel binding)
- 5’ CAU 3’ (because 3’ UAC 5’)
Each amino acid requires at least one specific tRNA
- What are aminoacyl-tRNA synthetases?
- What is important to know about tRNA charging?
- Enzymes that attach amino acids to the corresponding tRNA (they recognize ALL the tRNAs that correspond to that amino acid); also have proofreading and editing activities
- Energy is required
- What is the template for translation?
- What part of the cell translates the message on an mRNA molecule into a specific protein?
- 3 important sites on a ribosome important for function and what happens at each?
- Which one is only on prokaryotic ribosomes?
- mRNA
- Ribosomes (80S = 60S + 40S; 70S = 50S + 30S)
- A site- binds incoming aminoacyl-tRNA
P site- binds peptidyl-tRNA which carries the chain of amino acids that have already been synthesized
E site- exit, contains empty tRNA - E site
- Proteins that are translated on ribosomes that are on ER opposed to free in the cytosol are destined for?
- These proteins are commonly referred to as ___ and many of them go where?
- Post-translational modifications and/or subcellular compartmentalization
- Secretory proteins and many exit the cell
4 high energy bonds are required for each amino acid that is added (which is very energy expensive) what steps require energy?
Charging the tRNA = 2 high energy bonds
Binding aminoacyl-tRNA to the a site = 1 GTP
Moving the ribosome to the next codon (translocation) = 1 GTP
Wobble hypothesis allows tRNA to do what?
Recognize more than one codon
In prokaryotes, translation can begin before transcription is complete. Why cant eukaryotes do this?
Because the 5’ cap has to be associated with mRNA and in the cytosol (preparation for transcription)
- PROKARYOTIC translation:
Initiation is potentiated by shine-delgarno sequence; small ribosomal subunit contains a sequence ____ that allows for correct alignment of small ribosomal subunit with the AUG start codon - EUKARYOTIC translation: small ribosomal subunit recognizes ___ and scanning along the mRNA until first AUG is found
- Because of this mechanism of scanning, eukaryotes are monocistronic and prokaryotes are polycistronic..why?
- complementary to shine-delgarno sequence
- 5’ cap structure
- Prokaryotes are poly because initiation process can begin in the interior of the mRNA (as long as shine-delgarno and AUG start codon is present)
Next step in translation is the initiator tRNA binds the small ribosomal subunit. How is this step different between prokaryotes and eukaryotes?
Prokaryotes: initiator tRNA is bound to a formylated methionine (aldehyde)
Eukaryotes: initiator tRNA is bound to a methionine
- What completes the initiation process?
- Initiator tRNA occupies the __ site and the subsequent tRNAs enter in the __ site
- Initiation requires __ and energy from __
- The large ribosomal subunit joining the initiation complex
- P; A
- Initiation factors and energy from GTP (different than the 4 high energy bonds needed for each amino acid)
- Polypeptide chain is elongated by adding amino acids to what end?
- Peptidyltransferase forms what and is a component of?
- Carboxyl end (this forms peptide bonds)
2. Forms peptide bonds and is component of the large ribosomal subunit
- What is happening in translocation?
- What happens at each site during translocation?
- Does translocation require elongation factors and GTP?
- Ribosome moves 3 nucleotides to the next codon to be translated
- Uncharged tRNA is moved into the E site, Peptidyl-tRNA is moved into the P site, A site becomes opened up for the next aminoacyl-tRNA
- Yes
Termination:
- What site does the stop codon appear at?
- Termination release factors promote release of what?
- How many release factors do prokaryotes have? Eukaryotes?
- A site
- Promote release of tRNA from mRNA
- Pro=3, Eu=1
- What is a polysome/polyribosome?
- Multiple ribosomes on a single mRNA molecule that can be in different stages of protein synthesis (these can be present in prokaryotes and eukaryotes even though eukaryotes are monocistronic)
Give brief role of the following prokaryotic translational inhibitors:
- Puromycin
- Tetracycline
- Streptomycin
- Erythromycin
- Chloramphenicol
- Kills elongation of growing polypeptide chain (mimics charged tRNA)
- Blocks ribosomal movement forward
- Changes the ability to initiate
- Inhibits translocation
- Inhibits transfer or amino acids from P site to A site (stops peptide bond formation)
Rifamycin is a DNA dependent RNA polymerase.. what does that mean?
It means it reads DNA and makes RNA
Similar to RNA pol III which is what makes transcript
- Name two prokaryotic translational inhibitors of DNA replication
- Other important prokaryotic translational inhibitors to be aware of inhibit what?
- Quinolones and nitroimidazoles
2. Protein synthesis
Diphtheria and Pseudomonas are toxins that do what?
Inactivate eEF-2 (eukaryotic elongation factor 2), preventing translocation
Two general types of proteins are cytoplasmic proteins and secretory proteins:
- What must happen in order for a protein to be considered a secretory protein?
- Cytoplasmic proteins can be destined for different locations in the cell. What do they contain for correct localization?
- They are associated with ribosomes on ER (not free ribosomes in the cytoplasm)
- Specific localization signals
Model for translation of secretory proteins (general path)
Signal peptide gets recognized by signal recognition particles in the cell and binds to it. This stalls out the ribosome temporarily (so no longer doing translation) and that causes the ribosome to associate with a signal recognition particle receptor. The receptor helps the ribosome and the small peptide produced associate with a pore in the ER. Ribosome stays in association with the pore and translocates into the ER.
Then the signal gets cleaved off and polypeptide gets produced and eventually becomes a folded protein
Post translational modifications:
- What do molecular chaperones do?
- Trimming- inactive precursors can be trimmed later to their active form - one reason why this would need to happen?
- In trimming, what is being trimmed?
- They are proteins that help other proteins fold correctly (during translation and/or after)
- If an enzyme needs to be localized properly prior to becoming active
- Trimming is removal of signal peptide sequence
Covalent post-translational modifications:
- Phosphorylation: when is it used?
- Glycosylation: addition of sugar residues- what are the two types?
- Hydroxylation: important for?
- To regulate metabolic pathways and enzyme activity
- O linked or N linked (based on type of amino acid that the sugar moiety is being added to)
- Cross linking of collagen fibers
- Certain proteins are targeted for the lysosome as a post translational modification ..why?
- Name a kind of enzyme that needs to go to lysosome for degradation
- Proteins designated for the lysosome are ____ where?
- Lysosomes digest many different macromolecules so if protein with macromolecules that need to be degraded was not sent to lysosome, macromolecules will accumulate and form inclusions
- Hydrolytic enzymes
- Phosphorylated at specific mannose residues
- When proteins that are outside of the cell need to be degraded, where do they go? Inside?
- Brief walkthrough of protein degradation inside the cell?
- Proteins outside of the cell go to lysosome, proteins inside of the cell go to proteosomes
- Protein gets recognized as damaged and gets tagged by Ubiquitin molecule. Once 4 ubiquitin has tagged the molecule, it will drag the protein into the proteosome (and ubiquitin will be released to be used again)
