Central Dogma
What are the start and stop codons?
+100 points: What amino acid is coded for by the start codon?
+100 more points: What is the first amino acid in each of the 3 domains?
Start: AUG
Stop: UAG, UAA, UGA
Bacteria: N-formylmethionine (fMet)
Archaea: methionine (Met)
Eukarya: methionine (Met)
The I gene associated with the trp operon codes for what (be specific)?
+100 points: what molecule this bind to?
+100 more points: what is this complex called (general term)
inactive repressor protein
tryptophan
aporepressor (protein) + corepressor (trp) = holorepressor (active)
How many methods of bacterial genetic recombination are you expected to know? What are their names?
+100 points: briefly describe each type
3: Transformation, Transduction, Conjugation
What is a phage?
+100 points: what is phage short for?
Bacteriophage: a virus that only infects bacteria
Name one of the big 3 teratogenic human viruses.
+100 points: name all 3
Cytomegalovirus
Herpes simplex virus type I and II
Rubella
In which direction are nucleic acid strands synthesized?
+100 points: why?
5' to 3'
I can't explain it as beautifully as can the explanation I found online. I'll show you!!
Feedback inhibition is a regulatory technique of: anabolic metabolism, catabolic metabolism, both, or neither?
+100 points: how? (defend your response)
Anabolic! :D
End product builds up and represses constitutive expression of anabolic enzymes (by activating the repressor protein).
What is specialized transduction?
Prophage excises itself but takes a bit of bacterial DNA with it (similar to Hfr reverting to F'). Then lytic cycle! When the phage infects a new host, it may enter the lysogenic cycle again, integrating the original bacterial DNA along with it.
Argue in support or in favor of the statement: phages cannot infect humans and are of no concern to us
Prophage exotoxins (botulism, cholera, scarlet fever, etc.)
:( Not fun.
+100 points if I hear the word "lysogen."
What are the two main capsid shapes and what do they look like?
+100 points: what is the name of the special "most stable" subtype and what does it look like?
Polyhedral (polyhedron, many-sided figure)
Helical (I think of it like a slinky. It spirals and forms a tube around the nucleic acid.)
Icosahedral (D20)
What are the 3 ribosome sites in order?
In order as new codons are being read: nucleotide enters A site, moves to P site, and is released at the E site. APE
What are the genes in the lac operon and what do they code for?
+100 points per protein: what do these proteins do?
lacZ: β-galactosidase (aka lactase, hydrolyzes lactose)
lacY: permease (transports lactose into the cell)
lacA: transacetylase (transfers acetyl group from acetyl-CoA to β-galactosidase)
At what point in the lytic cycle could there be an error that leads to bacterial genetic recombination? What is this type of recombination called? How does it happen?
Maturation. Transformation. Host DNA is packaged into capsid instead of viral DNA. When this "phage" eventually infects a new host cell, the inserted DNA may recombine with the chromosome.
At what point do the lytic and lysogenic cycles overlap/intersect?
After penetration/before biosynthesis.
If the prophage excises from the bacterial chromosome, the virus may then enter the biosynthesis phase of the lytic cycle.
How do the phases of animal virus replication differ from the phases of phage replication?
Animal virus replication: Attachment, Penetration, Uncoating, Biosynthesis, Maturation, Release
Phage replication (lytic cycle): no uncoating phase, otherwise the same
What is pre-mRNA and where is it found?
In eukaryotes, DNA is first directly transcribed into pre-mRNA, which is processed (5' cap and 3' poly-A tail, introns spliced out) into mRNA, which can then exit the nucleus.
The lac operon in a bacterial cell has a faulty lacZ gene. How does this impact the metabolic regulation of the operon?
lacZ is essential to the breakdown of lactose. Without it, no lactose is broken down, no ATP is generated, the operon stays on, and we waste so much energy. ;_; And probably RIP unless we find more glucose.
An F- cell has become an F' cell, but no conjugation has occurred. What is a plausible explanation?
Basically any explanation including transduction or transformation.
Mutagens? Maybe 100 points for an entertaining suggestion. (But no, that will absolutely not be an acceptable answer on the exam.)
What are plaques? How do they relate to phages?
Phages on a lawn of bacteria: "reverse colony" of no growth = bacterial inhibition = viral growth!!
What family of RNA viruses can cause cancer? How?
Retroviridae can reverse transcribe DNA from their RNA and then act in much the same way as oncogenic DNA viruses: integration of DNA, contact inhibition suppressors, etc.
What are the enzymes that are needed for DNA replication (to the extent we've covered)? In order.
Helicase, Primase/RNA Polymerase, DNA Polymerase III, DNA Polymerase I (exonuclease), Ligase
slides and video differ
A spontaneous mutation impacts a regulator mechanism. How may this positively, neutrally, or negatively impact the cell? Pick one possibility and describe a detailed scenario and outcome.
No silent mutations. Be more creative.
So many possibilities!! Maybe it changes a regulatory gene, promoter, or operator? Maybe it changes the allosteric site of the key enzyme in a feedback inhibition loop. :)
E. coli is a beneficial human gut bacteria, but we hear about dangerous outbreaks of it all the time. How do you consolidate those two conflicting facts? How would you explain it to a layperson?
In general, E. coli is a beneficial gut bacteria. However, E. coli O157:H7 acquired
Shiga toxin!! D:
via genetic recombination with Shigella. Presumably through transduction according to the interwebs.
Viruses have a unique taxonomy apart from cellular life. What are the 3 most important taxonomic criteria?
Host Organism(s)
Particle Morphology
Genome Type
What are syncytia and how are they formed?
giant, multinucleate cells caused by fusion of adjacent cells (e.g. paramyxoviruses)