Transcription
____ is the enzyme that catalyzes the synthesis of RNA in prokaryotic transcription
Bonus points if you can give both names
Name the 4 classes of amino acids.
1. Hydrophobic/ non-polar
2. Hydrophilic/ polar
3. Acidic side groups
4. Basic side groups
What are the 3 stop codons?
UGA, UAA, UAG
Why are dideoxy-nucleotides referred to as terminators?
There is no hydroxyl group in the molecular structure of dideoxyribose so it cannot form a phosphodiester bond
In which direction do the DNA samples migrate in the gel (flow of current)
From the cathode(-) to anode(+)
State 2 differences between DNA polymerase and RNA polymerase.
1. DNA polymerase produces DNA polymers, RNA polymerase produces RNA polymers
2. DNA polymerase has an error correction function, RNA does not
3. DNA polymerase requires a primer to polymerize, RNA does not
What are the 3 critical translation sites at the ribosome?
1. E- Exit site
2. P- peptidyl transfer site
3. A- acceptor site
What are the types of DNA mutations? List their components.
1. Point Mutations (one base replaced with another)
-transition
-transversion
2. Indel mutations
-insertion
-deletion
The shortest bands are the DNA products _____(closest or farthest) to the primer and these travel _____ (slowest or fastest) on the gel
1. Closest
2. Fastest
How do the bands in the gel differ between males and females?
Female DNA will be shown as one thick band
Male DNA will be shown as two thinner bands
E. coli has two different mechanisms that cause termination. What are they?
1. Rho-independent
2.Rho-dependent
Determine the anticodon and amino acid for 5'-CUU-3'
3'-GAA-5' ; leu
What are the types of coding region mutations?
1. Silent
2. Missense
3. Nonsense
4. Frameshift
What does Dideoxy sequencing do?
Uses DNA polymerase to replicate new DNA from a template
DNA migration in an agarose gel is a function of: (4)
1. Strength of the electrical field
2. Buffer
3. Density of agarose gel
4. Size of the DNA molecules
What are the 5 steps by which the introns are spliced out in an mRNA transcript?
1. SNRPs assemble at intron to form spliceosome
2. Intron is cut at the exon/GU junction
3. 5' end of intron covalently bonds to internal 'A' to form lariat
4. 3' end of intron is cut, releasing complete intron
5. Exons are covalently joined
What is a potential consequence of redundancy in codons?
a protein produced by different organisms may be identical in amino acid sequence, but the DNA sequence at the gene level may be very different
What are the types of single-base position mutations? Give a short description of each.
1. Depurination
-Complete removal of a purine --> apurinic site
2. Deamination
-Loss of amino group from C -->changes C to U
3. Tautomeric shift
-Short lived shift or alteration in base structure
4. Oxidative damage
-Produce reactive oxygen species (ROSs)
What are the 4 separate reactions according to the principle of Sanger Sequencing?
How are these reactions recognized on a gel?
One reaction for each of the four types of ddNTPs: A, T, G, or C
All four reactions run side by side on a gel
Explain how electrophoresis works
Electrophoresis uses an electrical field to separate molecules based on differential migration through the gel based on molecule size.
State if each feature is true of a prokaryote, eukaryote or both.
1. Ribosomes bind to the 5' end of the transcript as soon as it emerges from the transcription bubble
2. Termination of transcription requires an enzyme to cut the transcript between two short sequence signals
3. Employs a polymerase that produces an RNA polymer from a DNA template
4. Primary transcript includes introns and exons
5. The polymerase used has a 'built in' component (sigma) that binds to the promoter
1. Prokaryote
2. Eukaryote
3. Both
4. Eukaryote
5. Prokaryote
Determine the amino acids for the following sequence and determine the functional class
I=hydrophobic II=hydrophilic III=acidic IV=basic
5'ATG/TTC/CTG/TCC/TTC/CCC/ACC/ACC/AAG/ACC/TAC/TTC3'
NH2-met(I)-phe(I)-leu(I)-ser(II)-phe(I)-pro(I)-thr(II)-thr(II)-lys(IV)-thr(II)-tyr(II)-phe(I)-COOH
Consider 5'-ATG/GGA/CTA/GAT/ACC-3'
Which kind of mutation is the following (silent, missense, nonsense, or frameshift)?
1. 5'-ATG/[C]GA/CTA/GAT/ACC-3'
2. 5'-ATG/GGA/CTA/[A]GA/TAC/C-3'
3. 5'-ATG/GG[T]/CTA/GAT/ACC-3'
1. Missense
2. Frameshift
3. Silent
If a researcher made a mistake during his/her dideoxy-C reaction sequencing by including a high concentration of the terminator and a low concentration of the regular deoxy-C triphosphate nucleotides, what would be the result?
Only the C lane would be affected because the base in question comes from a 'dideoxy-C' reaction. The presence of high concentration of terminator will lead to the early termination, so there would only be one initial band in column ddCTP because it was terminated
List the loading dye components and their functions
1. Bromphenol Blue: allows the samples to be seen when loading the gel
2. Glycerol: increases the density of the samples causing them to sink into the wells for loading
3. DNA stain: allows DNA sample to be visualized by UV light