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Replication
Transcription
Translation
Gene Regulation
Molecular Structures
100
What are the general functions of DNA Polymerase I, II and III?
DNA Pol I removes RNA primers and replaces with DNA, DNA Pol II repairs damaged DNA, DNA Pol III synthesizes DNA
100
Which DNA strand is identical (with the exception of T and U) to the newly synthesized RNA strand?
The coding strand (Remember: Coding = Copy)
100
What are the three stop codons?
UAA, UGA, and UAG
100
What process does DNA methylation inhibit?
Transcription
100
What is the key difference between a ribose and deoxyribose sugar?
Ribose has a 2' hydroxyl group, deoxyribose does not.
200
In which direction does DNA polymerase remove mistakes?
In 3' --> 5' direction
200
What are the three major modifications made to eukaryotic messenger RNA?
Addition of 5' G-cap, addition of 3' poly-A tail, splicing (removal of introns)
200
How many ATP are used per peptide bond?
4 ATP
200
Why is the promoter region larger for eukaryotes than prokaryotes?
Eukaryotes are more complex, and therefore need more gene regulation.
200
Which bases are purines? Which are pyrimidines?
Adenine and guanine are purines, cytosine and thymine are pyrimidines.
300
In a replication bubble, how do you determine which is the leading strand?
The leading strand is being synthesized in the same direction that helicase is unzipping. (Remember, strands must be antiparallel)
300
What are eukaryotic RNA polymerase I, II and III responsible for making?
RNA Polymerase I makes tRNA, RNA Polymerase II makes mRNA and RNA Polymerase III makes rRNA.
300
Why can't eukaryotes have polycistronic mRNA?
Ribosome locates 5' cap, there are no Shine Dalgarno sequences. Eukaryotes are too complex, need too much regulation to have polycistronic mRNA.
300
What is the fastest form of gene regulation?
Feedback inhibition
300
What is the structure of a nucleotide?
A phosphate, a ribose sugar, and a base
400
What is the function of topoisomerase in replication?
Prevents supercoiling by breaking two strands, passing one strand through the other, and religating.
400
In what conditions would the lac operon be transcribed? Why?
When levels of glucose are low and levels of lactose are high. Allolactose (present in high lactose conditions) binds the repressor, causing it to fall off. When glucose is low, cAMP can be formed to allow binding of the CAP protein that recruits RNA polymerase.
400
What enzyme charges the tRNA? What enzyme links the two amino acids together? What enzyme moves the ribosome?
Aminoacetyl tRNA synthetase, peptidyl transferase, translocase
400
Explain how eukaryotic transcription can be regulated by silencers or enhancers that are far from the start site of transcription.
Because eukaryotic DNA is highly compact, so enhancers/silencers can be right next to the start site (even though they may be very far away linearly).
400
In an RNA nucleotide, what is attached to each of the carbons in the ribose sugar?
1' C is attached to a base, 2' and 3' have a hydroxyl group, 4' is attached to the 5' C which is attached to a phosphate.
500
What are benefits and downfalls to D-loop synthesis?
Solves lagging strand problem, but only works for small genomes. Because it leaves half the genome single stranded, it is very fragile and unstable.
500
How does a rho independent terminator work?
Terminating stem loop folds back and interacts with RNA polymerase, causing it to pause. Lots of A's and T's on the DNA being transcribed have only 2 hydrogen bonds, which causes the RNA to fall off, along with RNA polymerase.
500
Why do ribosomes exist in both the rough ER and the cytosol? How do ribosomes know where to bring the mRNA?
Rough ER ribosomes can ship newly synthesized proteins elsewhere. If the mRNA has a signal peptide, it binds to a signal recognition particle (SRP), pausing translation, and docks the mRNA, corresponding peptide and ribosome to docking proteins on the rough ER, where translation can continue.
500
Explain how methylation can lead to mutation.
Cytosine is methylated as a form of regulation. Both methylation and deamination can occur to produce thymine instead of cytosine.
500
What is the structure of a histone and how does it relate to its function?
8 histone subunits, 2 sets of 4 different subunits, H2A, H2B, H3 and H4. This octomer is positively charged, which allows about 200 bp of negatively charged DNA to wrap around it.