Metabolism
What are the net reactants and products for the Ebden-Meyerhof pathway of glycolysis?
Glucose + 2ADP + 2Pi + 2 NAd+ → 2 pyruvate + 2 ATP + 2 NADH + 2 H+
The trp operon is an example of what kind of system?
Negative control of a repressible gene
In a newly replicating strand of DNA, to what part of the last nucleotide is the next nucleotide added?
The new nucleotide is added to the free 3’ OH group
Why is transcriptional and translational coupling possible in bacterial cells but not within eukaryotic cells?
Eukaryotic cells have a nucleus
In gel electrophoresis, what is the purpose of the DNA marker?
It allows us to comparatively label the rest of our bands with an approximate size
How many intermediate carbon molecules of the citric acid cycle contain only four carbons (excluding carbons in CoA)?
Five (Succinyl-CoA, Succinate, Fumarate, Malate, Oxaloacetate)
What activates RecA in the SOS repair response?
ssDNA (single-stranded DNA)
After DNA Polymerase I adds in bases on the lagging strand, which enzyme catalyzes the reaction to connect the gap?
DNA Ligase
What aspect of the DNA template being transcribed helps Rho-independent termination to occur?
The series of U residues downstream of the pause site
When doing Illumina sequencing, what role does the computer have for us?
Both captures pictures, and more importantly, aligns similar sequences to form the entire sequence
Give one example of a final electron acceptor for anaerobic respiration.
Possible answers include: NO3-, SO42-, CO2, Fe3+, SeO42-
If during an Ames test, the compound we are testing gives rise to more colonies than the control plate, what does this result mean?
The compound being tested is mutagenic
Which type of topoisomerase changes the supercoiling of DNA by a factor of 2?
Type II
What does the 30S small ribosomal subunit scan for in order to find to the mRNA?
Ribosomal Binding Site (rbs), or Shine-Dalgarno sequence
Why is it necessary to add an additional base to the 5’ end of a designed primer that is to be cloned into a plasmid vector?
The restriction endonuclease normally needs an extra base to “sit on” in order for the chemistry to occur.
DOUBLE BONUS: The main purpose of fermentation is to oxidize what, and why?
NADH; to replenish the supply of NAD+ for glycolysis to occur and continue to make ATP
In the lac operon system, what combination of glucose and lactose would lead to the following result: CAP-cAMP protein bound to the CAP- binding site, repressor bound to operator?
No glucose, no lactose
In the Meselson-Stahl Experiment, why was only one band seen after the first division, but two bands were seen after the second division?
First Division: each replicated strand had one new and one old (old is N15, new is N14). Second Division: two strands are 50% new , two strand are 100% new
If this is the mRNA product (5’ UGUAAGUC 3’ ), what would the original antisense DNA sequence have been, written in the conventional 5’ to 3’ manner?
5’ GACTTACA 3’
What aspect of a PCR system is used to actually select for the area of DNA that the scientist desires to amplify?
DNA primers (designed by the scientist)
If a beta subunit of the ATP synthase complex is in the βDP conformation, what conformation will it be in next?
The βTP conformation
What does it mean for bacterial cells to be “competent?”
They will more easily take up exogenous DNA from the environment
Why must the lagging strand synthesis occur discontinuously?
Okazaki fragments; DNA polymerase III must work in a 5’ to 3’ direction, and it cannot start further down than from where the helicase has unwinded
DOUBLE BONUS: What is codon usage? Why is this a reason that a synonymous mutation could end up not being a truly silent mutation?
Different codons have different amounts of tRNA’s in the cell. A synonymous mutation could code for a tRNA that is less abundant and thus there could be a noticeable scarcity of a particular amino acid
How does the way we design a primer for PCR allow us to insert the amplified segment into a plasmid vector?
By adding restriction endonuclease sites, they can be cleaved into sticky ends and added to the plasmid