Molecular Bio Exam 3

DNA Backbone Damage

What is depurination? What is the mutagen? What does it result in? What is the rate?

When the bond between the sugar group and the purine base of a nucleotide is broken, the mutagen is water. Results in an abasic site, which is a location in DNA or RNA that has lost its nitrogenous base, leaving only the sugar-phosphate backbone. About 18,000 bases per genome per day.

DNA Structural Distortion

What are pyrimidine dimers? How are they formed? On which pyrimidines do they occur? What do they result in? UV radiation with a wavelength of ~260 nm is very harmful. Why?

They are cyclobutane rings formed by UV light. Usually thymine-thymine, but they can also be thymine-cytosine. This distorts DNA's double-helix shape. Because this is peak absorption for nucleic acids in DNA and RNA.

Direct Reversal of DNA Damage

What is photoreactivation? Is the enzyme responsible present in many organisms?

T-T dimer repair by DNA photolyase. This enzyme is not present in mammals, only in less complex creatures.

What is lesion bypass? How does it happen?

A cellular mechanism in which high-fidelity DNA polymerases are switched out for error-prone DNA polymerases. Happens through TLS (trans lesion synthesis).

Single Base Changes

What is alkylation? What is the mutagen? What removes the methyl group?

Alkylation is the addition of a methyl group to oxygen on guanine; the mutagen is nitrosamines. DNA methyltransferase removes the methyl group, and is then trashed.

What is DNA mismatch repair? What recognizes these mismatches? What directs the repair machinery where to cut?

The correction of mistakes from DNA replication that are not repaired by proofreading. MutSa and MutLa recognize these mismatches. RFC and PCNA direct the repair machinery to cut.

What are motifs of secondary RNA structures?

Motif = a 3D structure that does something

• Bulges - Nucleotides without a binding partner

• Hairpin loop - found at the end of the stem where no bonds are present

• Internal loops - occur when two bases do not pair

What are the two types of different base pairing in RNA helices

1. Noncanonical base pairs

2. Base triples

What are the 3 main parts of tRNA and what do they do? What is the actual shape of tRNA in real life?

1. The T loop recognizes the ribosome

2. The D loop allows the correct amino acids to be added

3. The anticodon site binds to the mRNA

• L-shaped

What two things aid in RNA folding?

1. Binding proteins - bind to RNAs to limit the types of structures that can form

2. RNA chaperones - allow messed-up RNAs to unfold and fix the structure

What are the 3 main sections of amino acids?

1. amino group

2. carboxyl group

3. side chain

What are peptide bonds and where do they form? What are amino acids called when they’re in a peptide chain?

Peptide bonds bind amino acids together in peptide chains and form between the N of the amino group and the C of the carboxyl group. They are called residues.

When is the codon methionine usually cleaved?

During or after translation.