Lecture 18: Exam III

What is processivity, and what is it in reference to?

The ability for DNA polymerase to stay bound to the template strand of DNA, particularly at the phosphate backbone and the minor groove of the DNA strand. This binding is independent of the sequence of nucleotides

The 5’ exonuclease is composed of amino acids __*() - () in DNA polymerase I*__

1-323

What is the name of the thermophile whose heat-resistant DNA polymerase is central to the functionality of PCR tests?

Thermus aquaticus (Taq)

What are the three steps of PCR?

T-cycling / amplicon generation / amplification

The inner ring of the sliding clamp is __ - charged and forms __ with DNA backbone

positively / salt bridges

What does the analogy “biochemical shift work” refer to?

Exchanging of DNA polymerase molecules throughout a full genome replication

What is the role of DNA ligase?

* Stitches together okazaki fragments after primer replaced and filled in
* Blunt or cohesive ends - forms phosphodiester bond

What are exogenous influences which DNA ligase repairs?

* Radiation and certain chemicals (i.e. BaP’s)
* UV and IR light

What are endogenous influences which DNA ligase repairs?

* Hydrolysis, oxidation, alkylation
* Mismatch of DNA bases
* Free radicals

What are the levels of organization of DNA compaction into chromosomes?

DNA double helix → wrapped around nucleosomes/histones → nucleosomes are coiled into chromatin fiber → condensation of chromatin → chromosome

What is OriC?

Origin of replication in bacterial chromosome

Characteristics of histones:

Basic- rich in arginine and lysine

What triggers DNA polymerase to let go of the lagging strand once it has reached the end of what it can synthesize?

Gamma complex disassembles the beta 2 sliding clamp once it encounters the primase-generated RNA primer

The “ter” termination locus is rich in () bps and has () bound

GT / Tus protein is bound