C39:The Genetic Code (Translation)
What general features do all tRNAs have in common?
They are single-stranded RNAs, usually L-shaped, have an acceptor stem and anticodon loop, and mature tRNAs have many modified bases to facilitate or limit base pairing.
Where are the A,P,&E sites in a translating ribosome?
A:Aminoacyl- 3' end, binds incoming tRNA
P:Peptidyl- middle of the 30S subunit, holds growing peptide chain
E:Exit- towards 5' end, holds deacylated tRNA before release.
What is Dicer and how does it apply to RISC?
What is the general role of Coenzyme-A?
Carrier of Acyl groups, known for being used in Fatty Acid Metabolism, Citric Acid Cycle, and Cholesterol synthesis.
Where does the electron transport chain undergo its processes.
The mitochondria.
How is an amino acid activated?
the amino acid reacts with ATP to form aminoacyl adenylate AKA AMP (this reaction produces pyrophosphate) , AMP is then transferred to the appropriate tRNA and both are catalyzed by aminoacyl-tRNA synthetase.
What is the significance of the Shine-Dalgarno sequence?
It is a Cis-acting element in protein synthesis, 16S rRNA interacts with this sequence on mRNA for initiating translation. It is centered ~10 nucleotides upstream of the AUG codon, this is in the untranslated region of the mRNA, it's made up of As & Gs.
What are the key differences between siRNA and miRNA?
miRNA: single-stranded, endogenous, is cleaved from Pol 2 and sometimes Pol 3
Which Amino Acid is oxidized to form disulfide bonds that contribute to protein tertiary structure?
Cysteine: it has a sulfhydryl group in its side chain.
What are the 3 enzymatic activities and their corresponding enzymes that occur in the mitochondrial matrix when dealing with the pyruvate dehydrogenase complex?
1. E1 : Pyruvate dehydrogenase component
2. E2 : dihydrolipoyl transacetylase
3. E3 : dihydrolipoyl dehydrogenase
What is Wobble? (other than a popular line dance at Black Weddings)
A phenomenon that some tRNAs can read more than one codon, The 1st base of anticodon sets the number of codons can be read.
C/A: one codon
U/G: two codons
I: three codons
Describe the three main elongation factors for translation elongation.
EF-Tu(GTP): Delivers AA-tRNAs to the A site on the ribosome
EF-Ts : reactivates/resets EF-Tu
EF-G: Promotes Translocation, binds near A site, interacting with large subunit and that binding promotes GTP hydrolysis, this moves the tRNA to the P site.
What is cDNA and why is it used in bacterial expression systems?
Is the DNA version of the mature RNA. It is an intron-free template.
It increases efficiency, bacteria don't have the enzymes required to break down Eukaryotic mRNA.
Breaks down glucose to extract 2 ATP and create intermediates for the other metabolic pathways.
->Pyruvate & NADH
How are metabolic pathways generically controlled?
1. The amount of an enzyme that catalyzes the pathway reactions
2. The catalytic activity of that enzyme
3. The accessibility of the substrate that the enzyme acts on
Why can co-transcriptional translation occur in bacteria?
Both processes (translation and transcription) happen in the cytoplasm which make for close proximity of the operational machinery. The direction of translation also matches the direction of mRNA production.
Stop Codons (UGA, UAA, UAG)
Release Factors (RF1, RF2, RF3*)
EF-G
Ribosome Release Factor (RRF)
What are the two components of CRISPR and how do they work?
2. Cas Protein: has two lobes; REC lobe- binds to duplex formed by sgRNA and target DNA, NUC lobe- contains two nucleases that do a double strand break in the target.
What is the purpose of the pentose phosphate pathway?
To produce NADPH ( a crucial reducing agent)
and Ribose-5-Phosphate ( precursor for the synthesis of nucleotides)
What type of inhibitor only binds to the ES complex and lowers Vmax and Km?
uncompetitive inhibitors: doesn't bind to the free enzyme, stabilizes the complex
Using the genetic code decipher this sequence:
5'-TAC GGA TTC GCA TGG-3'
Hint: this is in DNA, change it to mRNA first.
mRNA: 5'-AUG CCU AAG CGU ACC-3'
AA Sequence: Met-Pro-Lys-Arg-Thr
Explain the Transferrin-Ferritin system's role in translation regulation.
Transferrin: Iron Transporter in Blood
Ferritin: intracellular Iron storage protein
IRE-binding protein (IRE-BP) binds mRNA in the absence of Iron.
No/Low Iron level: IRE-BP binds the IRE, blocking translation of the gene
High Iron: IRE-BP instead binds Iron and doesn't bind to IRE: translation occurs/continues.
Explain what goes into the reaction tubes during Sanger sequencing.
Template DNA, Labeled Primer, DNA Polymerase, all four dNTPS, and a small amount of one of the 2',3'-dideoxy Analog of one of the dNTPS.
What are the biochemical Properties of Histone H3?
Metabolic Pathways use these common carriers, what do each carry?
ATP, FAD, NADPH, NAD+, CoA
ATP: carries phosphate
NAD+ : carries electrons in oxidation reactions, (2e-, 1H+)
FAD : carries e- in oxidation reactions (2e-,2H+)
NADPH : carries e- in reduction reactions
CoA : carries 2 carbon units