Molecular Biology II

Question 1

Describe the process and direction of DNA and RNA synthesis.

Answer 1

DNA and RNA are synthesized in 5’ –> 3’ direction. 5’ end of incoming nucleotide bears the triphosphate (energy source for bond). Triphosphate bond is the target of a 3’ hydroxyl attack (p.69)

Question 2

In which direction is mRNA read?

Answer 2

5’ –> 3’ (p.69)

Question 3

In which direction does protein synthesis occur?

Answer 3

N terminus to C terminus (p.69)

Question 4

Name and describe the three types of RNA.

Answer 4

rRNA –> most abundant type; mRNA –> longest type; tRNA –> smallest type (p.70)

Question 5

What are the mRNA start codons and what do they code for?

Answer 5

AUG (rarely GUG); codes for methionine in eukaryotes and formylmethionine (f-met) in prokaryotes (p.70)

Question 6

What are the mRNA stop codons?

Answer 6

UGA, UAG, UAA (p.70)

Question 7

What is the role of the promoter in regulation of gene expression?

Answer 7

An AT rich upstream sequence with TATA and CAAT boxes where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus. Mutations dramatically reduce amount of gene transcribed (p.70)

Question 8

What is the function of enhancers and silencers in gene expression and where are they located?

Answer 8

Enhancers bind transcription factors while silencers are sites where negative regulators (repressors) bind. They both can be located close to, far from, or within an intron of the gene whose expression is being regulated (p.70)

Question 9

Describe the functions of Eukaryotic RNA polymerases.

Answer 9

RNA Pol I: makes rRNA; RNA Pol II: makes mRNA; RNA Pol III: makes tRNA. These polymerases have no proofreading function but can initiate chains. RNA Pol II opens DNA at promoter sites (p.70)

Question 10

How can a-amanitin (in deathcap mushrooms) cause hepatotoxicity?

Answer 10

By inhibiting RNA Pol II.

Question 11

Describe the function of prokaryotic RNA polymerase.

Answer 11

A multisubunit complex composed of only 1 RNA polymerase. This complex makes all three kinds of RNA (p.70)

Question 12

Where does eukaryotic RNA processing occur and what is the initial transcript called?

Answer 12

Initial transcript is called heterogeneous nuclear RNA (hnRNA). When destined for translation, it is called pre-mRNA where it undergoes processing inside the nucleus. Only processed RNA is transported out of the nucleus (p.71)

Question 13

What is the product of eukaryotic RNA processing and what three steps are required?

Answer 13

Occurs after transcription; 1.) capping of 5’ end (addition of 7-methylguanosine cap); 2.) polyadenylation on 3’ end (~200 As); 3.) splicing out of introns. Capped, tailed, spliced transcript is then mRNA (p.71)

Question 14

List the steps of pre-mRNA splicing.

Answer 14

1.) primary transcript combines with snRNPs and other proteins to form a spliceosome; 2.) Lariat (looped) intermediate is generated; 3.) Lariat is released to remove the intron and join 2 exons (p.71)

Question 15

In what condition do patients make antibodies to splicosomal snRNPs?

Answer 15

SLE; lupus (p.71)

Question 16

How does pre-mRNA splicing play a role in b-thalassemia mutations?

Answer 16

Different exons can be combined by alternative splicing makes unique proteins in different tissues and is the cause of b-thalassemia mutations (p.71)

Question 17

Describe the basic structure of a tRNA molecule.

Answer 17

Secondary structure in clover leaf form with anticodon end opposite to 3’ aminoacyl end. All tRNAs have CCA at 3’ end along with a number of chemically modified bases. Amino acids are covalently bound to the 3’ end of the tRNA (p.72)

Question 18

How is a tRNA molecule charged with an amino acid?

Answer 18

Aminoacyl tRNA synthetases, specific to each amino acid use ATP to scrutinize amino acid before and after it binds to tRNA. If incorrect, the bond is hydrolyzed. Amino acid tRNA bond has the energy for formation of a peptide bond (p.72)

Question 19

What happens when a tRNA is mischarged?

Answer 19

Mischarged tRNAs read the usual codon but insert the wrong amino acid (p.72)

Question 20

What is responsible for the accuracy of amino acid selection in protein synthesis?

Answer 20

Aminoacyl- tRNA synthetase and binding of charged tRNA to the codon (p.72)

Question 21

What is the mechanism of action of Tetracyclines?

Answer 21

Binds the 30s subunit, preventing attachment of aminoacyl-tRNA (p.72)

Question 22

How is eukaryotic protein synthesis initiated?

Answer 22

GTP hydorlysis activates initiation factors to help assemble the 40s ribosomal subunit with initiator tRNA. Initiation factors are released when the mRNA and ribosomal subunit assemble within the complex (p.73)

Question 23

What is the difference between ribosomal subunits in eukaryotes and prokaryotes?

Answer 23

Eukaryotes: 40s + 60s –> 80s Prokaryotes: 30s + 50s –> 70s (p.73)

Question 24

What is the role of ATP and GTP in initiation of protein synthesis?

Answer 24

ATP: tRNA activation, charging GTP: tRNA translocation (p.73)

Question 25

Describe the three steps of elongation in protein synthesis.

Answer 25

1.) aminoacyl- tRNA binds to A site; 2.) Ribosomal rRNA “ribozyme” catalyzes peptide bond formation and transfers the growing polypeptide to the amino acid in the A site; 3.) Ribosome advances 3 nucleotides towards 3’ end of mRNA, moving peptidyl tRNA to the P site (p.73)