Section J Practice Questions

Some questions may not be exactly the same, but have the same concept covered as the given question

What are the components of a Deoxyribonucleotide?

1. Deoxyribonucleoside

2. Phosphate

3. Nitrogenous Base

Which base is found in DNA, but not RNA?

Thymine (T) is found in DNA, not RNA

RNA has Uracil (U) instead

If given a percentage of a specific base as making up part of somethings DNA, how can you figure out how much each base or base pair makes up of the total DNA?

In any double helical DNA, A=T and C=G

If given A, you can find T

If given C, you can find G

Describe the three-dimensional structure of DNA.

1. Consists of two antiparallel chains in a right-handed double-helical arrangement

2. Complementary base pairs are formed by H-bonding between chains in the helix

3. Base pairs are stacked perpendicular to the long axis of the double helix

4. Offset pairing of the two strands create a major and minor groove

Describe the fundamental rules of DNA replication.

1. Semi-Conservative and requires a template

2. Proceeds in 5’—>3’ direction and is Semi-Discontinuous

3. Requires an enzyme with two unique active sites (each catalyzing a different reaction)

4. Synthesis of the Leading and Lagging Strands by DNA Polymerase III are coordinated and dependent on each other; requires RNA Primers

5. Begins at a location known as an Origin

6. Involves both polymerizing Deoxyribonucleotides and RNA Primers

What is the function of DNA Gyrase during DNA Replication?

Relieves topological stress introduced by strand separation ahead of the replication forks

What is the function of DnaB Helicase during DNA Replication?

Migrates along ssDNA in the 5’—>3’ direction and unwinds DNA

What is the function of Single-Stranded DNA-Binding Protein (SSB) during DNA Replication?

Stabilizes the separated strands after unwinding by Helicase

What is the mechanism of action for the drug Acyclovir?

Inhibits the DNA Polymerase of the Herpes Simplex Virus (antiviral)

What is the mechanism of action for the drug Etoposide?

Inhibits Topoisomerase II (DNA Gyrase), thereby inhibiting DNA strand separation and the relief of topological stress ahead of the replication forks (cancer drug)

What is the mechanism of action for the drug 5-Fluorouracil?

Inhibits Thymidylate Synthase, an enzyme required for DNA Synthesis (cancer drug)

What is the mechanism of action for the drug Doxorubicin?

Intercalates / inserts itself into DNA, causing breaks and hindering replication (cancer drug)

During transcription, the α-phosphate group of an incoming ribonucleotide triphosphate is added to which moiety of the growing RNA polymer?

Ribose at the 3’ end

What is the relationship between the base sequence of transcribed RNA and the template strand of DNA?

Base sequence of transcribed RNA is identical to the NONtemplate DNA sequence

NONtemplate (coding) sequence is complementary to the template sequence

What are the steps of transcription initiation after E.coli RNA Polymerase binds to a promoter? 

1. Polymerase binds to promoter

2. Closed Complex forms

3. Open Complex forms

4. Transcription is initiated

5. Promoter Clearance

What are some examples of compounds used to inhibit bacterial RNA Polymerase?

How each of them do so?

Do they also function in eukaryotic RNA Polymerases?

Rifampin — prevents the promoter clearance step of transcription; does NOT inhibit RNA Polymerase in eukaryotes

Actinomycin D — inhibits RNA elongation in both bacteria AND eukaryotes

How does Alpha-Amanitin disrupt transcription?

Does it do so in bacteria or animals?

Where does it come from?

Disrupts transcription by blocking Pol II and (at higher conc.) Pol III

Does so in ANIMAL cells only, NOT BACTERIA (or of the mushroom it comes from)

Comes from the death cap mushroom, Amanita phalloides

What three enzymes are components of the 5’-cap synthesizing complex for eukaryotic mRNAs?

What do each of them do in the complex?

1. Phosphohydrolase — emoves the terminal phosphate from the 5′ triphosphate end of the nascent RNA

2. Guanylyl Transferase — adds a GMP moiety (in a 5′–5′ triphosphate linkage) to form the “cap.”

3. Methyl Transferase — methylates the guanine at the N7 position to form the mature m⁷G cap

What is the function of Polyadenylate Polymerase?

Catalyzes the addition of A residues to the free 3’-OH group (addition of PolyA tail) by the reaction:

RNA + nATP —> RNA-(AMP)n + nPPi

What is removed from the RNA primary transcript in order to produce mRNA?

Introns

What two processes involve the formation of a Lariat structure?

1. Splicing of Group II Introns

2. Splicing of Spliceosome Introns

What is Alternative Splicing in Differential RNA Processing?

Process in which a particular exon may or may not be incorporated into the mature mRNA transcript (could be removed along with the introns by the Spliceosome at 3’ splice sites)

What does it mean that the genetic code is “degenerate”?

Certain AAs can be specified by more than one codon, but each codon only specificies one AA

What is the “Wobble” Hypothesis?

The third base of most codons pair loosely with the corresponding anticodon base; one tRNA molecule may recognize more than one codon

Describe the main characteristics of mature tRNAs.

1. Relatively small (73 to 93 nucleotide residues)

2. Consist of a single strand of RNA folded into a precise 3D structure

3. All have very similar 3D structures as well

What are important characteristics to know about Aminoacyl-tRNA Synthetases?

1. Hydrolyze ATP into AMP and 2Pi

2. Forms a reactive adenylate intermediate (aminoacyl-AMP) and a pyrophosphate

3. Specific for ONE AA

4. Has two classes (one initially attaches an AA to the 3’—OH end, other initially attaches an AA to the 2’—OH)

5. Correct attachment of an AA to its tRNA constitutes the Second Genetic Code

What is a significant difference between bacteria and eukaryotes in initiation of translation?

Bacteria — base-pairing between mRNA and an rRNA determines which start codon to use (guides 5’AUG codon to correct position)

Eukaryotes — small subunit begins scanning the mRNA at the 5’ cap until it reaches the first start codon (until first AUG codon is encountered)

What role do these four reaction mechanisms have in the proofreading step of Bacterial Cell Elongation?

• Phosphorylation from ATP

• Peptide Bond Formation

• Adenylylation

• GTP Hydrolysis

Phosphorylation from ATP — ensure right AA is attached to the tRNA (activates AA and allows editing)

Peptide Bond Formation — final commitment step once accuracy has been confirmed

Adenylylation — ensure right AA is attached to the tRNA (forms intermediate; checkpoint)

GTP Hydrolysis — ensures right tRNA is selected by the ribosome

How many nucleoside triphosphates (or their equivalents) are hydrolyzed into nucleoside diphosphates in order to make one peptide bond during the initiation and elongation phases of protein synthesis?

At least 4

What is the mechanism of action of Streptomycin?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits initiation by distorting the 30S structure and preventing the initiation complex formation

Prokaryotes only

What is the mechanism of action of Tetracycline?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits elongation by blocking the A site and preventing the binding of the aminoacyl-tRNAs

Prokaryotes only

What is the mechanism of action of Chloramphenicol?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits elongation by blocking peptidyl transfer

Prokaryotes only

What is the mechanism of action of Cycloheximide?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits elongation by binding to the E site in 60S and halting translocation

Eukaryotes only

What is the mechanism of action of Diphtheria Toxin?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits protein synthesis by inactivating eEF2 through ADP-ribosylation

Eukaryotes only

What is the mechanism of action of Ricin?

Does it work on Prokaryotes, Eukaryotes, or both?

Inhibits protein synthesis by inactivating the 60S subunit through depurination of the 28S rRNA

Eukaryotes only

What is the mechanism of action of Puromycin?

Does it work on Prokaryotes, Eukaryotes, or both?

Terminates polypeptide synthesis by binding to the A site and producing peptidylpuromycin that is released from the ribosome