Lecture 1.11 Flashcards
(25 cards)
Why is the genetic code considered degenerate?
There are multiple codons for some amino acids, thus there are more codes than it needs
-61 codons for 20 amino acids
What is wobble base pairing?
5’ position of the anticodon tolerates mismatches or non-standard base pairing
Nonsense mutation
Change an amino acid to a stop codon
- terminates protein prematurely
- almost always alters protein function
missense mutation
Change an amino acid due to a base change
- allows protein synthesis
- doesn’t always alter protein function
What are two sources of specificity in formation of aminoacyl-tRNAs?
- high specificity
- tRNA synthetases have editing activity (hydrolyase)
What are three peptide binding sites in a ribosome and what is their function?
E-site: things exit the ribosome
P-site: growing polypeptide chain located here (also where the intiation complex attaches)
A-site: incoming tRNAs bind here
What are the general steps in translation initiation?
- protein synthesis initiates at AUG (met) codon
- specialized methionine tRNA binds to small subunit of ribosome (in the P-site)
- small subunit binds to cap of mRNA and treks along until it encounters the first AUG codon
- eIFs dissociate and large subunit binds
- aminoacyl-tRNA binds to A site and first peptide bond forms
Steps of elongation
- nascent polypeptide in P-site and a new aminoacyl-tRNA binds to the A-site
- New peptide bond is formed by peptidyl transferase (ribozyme) and conformationals change causes the tRNA to move to the E- and P- sites
steps of termination?
- stop codons mar the end of translation
- release factors bind to ribosomes wit top codon in A-site
- release factor causes peptidyl transferase to hydrolyze the last amino acid releasing the completed protein and resulting in disassociation of the ribosome
- release factors are proteins that are shaped like a tRNA
How much energy is utilized to synthesize a peptide bond in a protein?
4 high energy bonds per every new peptide bond
Where is the energy needed to synthesize a peptide bond consumed in the cell?
- 2 phosphate bonds cleaved from ATP –> AMP to charge the tRNA (put amino acid on tRNA)
- 1 phosphate bond cleaved from GTP –> GDP to dissociate the initiation factors and allow the large ribosomal subunit to bind to the initiation complex
- 1 phosphate bond cleaved from GTP–> GDP to translocate the mRNA and tRNA
suppressor
mutated tRNA
- Nonsense suppressor: mutated anticodon complements terminator sequence (can inhibit effects of nonsense mutation
- Frameshift suppressor: anticodon contains 4 residues and can insert an amino acid and restore a frame sift mutation
What differences in initiation of translation allow prokaryotes but not eukaryotes to have polycistronic mRNA?
- Prokaryotic ribosomes can bind at any ribosome-binding site (rbs - which is upstream from AUG) on the mRNA and start protein translation of multiple proteins in a single mRNA
- Eukaryotic ribosomes must attached at the 5’ cap
What is RNA editing ?
the modification of RNA after synthesis: modification of bases to change “meaning” of message
-molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase.
what is nonsense-mediated mRNA decay?
a pathway that acts on transcripts right after splicing to degrade RNAs containing nonsense mutations
-a surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons.
How are expression of ferritin and transferrin receptor regulated? (ferritin stores iron and transferrin help cells take up iron)
- regulated by translational repression and mRNA stability
- low iron levels = aconitase binds to both ferritin and transferrin receptor mRNA –> thus inhibiting ferritin and stabilizing transferrin
- high iron levels = aconitase binds iron and realeases both messages –> thus increasing translation of ferritin and destabilizing transferrin
What is the function of molecular chaperones in cells?
to help proteins fold properly and reach their final conformation
- require ATP hydrolysis to function
What is the role of ubiquitin in protein turnover?
a small, highly conserved protein that is used as a signal for protein degradation
1) activated by E1
2) E1 binds to ubiquitin ligase complex (E2 & E3)
3) E3 binds to target protein
4) ubiquitin gets transferred to nitrogen termianl of protein
hsp70-like chaperone
binds to hydrophobic patches on proteins (as they are prevalent if protein is improperly folded) and “slows” the initial folding
hsp60-like chaperone
bind incorrectly folded proteins and creates a hydrophobic chamber ( a favorable environment for folding)
Proteosome
protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases
genetic code
- has three residue words in a non-overlapping syntax
- encodes 20 amino acids including 1 star codon and 3 stop codons
- no punctuation
- all nucleic acids have 3 reading frames
Open reading frame
series of codons without stop codons
- reading frame that can be translated in a protein because it is long enough
tRNA
short RNAs containing three step loops that form an L shaped structure
- 3’ end is linke to an amino acid and the anticodn loop base pairs with corresponding codon
