BIOL 300: Principles of Genetics - DNA Replication

Flashcards covering DNA replication, DNA Polymerase III structure and function, plasmids, episomes, bacterial conjugation (F+/F- and Hfr/F-), and Agrobacterium-mediated transgenic plant infection.

Processivity (DNA Polymerase III)

How many nucleotides are incorporated into a daughter strand without the polymerase falling off.

Fidelity (DNA Polymerase III)

How accurate the polymerase incorporates base pairs.

Palm (DNA Polymerase III)

The part of the DNA Polymerase III's DNA binding domain that provides the catalytic active site.

Fingers (DNA Polymerase III)

The part of the DNA Polymerase III's DNA binding domain that positions the template in the active site.

Thumb (DNA Polymerase III)

The part of the DNA Polymerase III's DNA binding domain that binds DNA as it exits, contributing to processivity.

Exonuclease activity (DNA Polymerase III)

Resides in an independent domain with its own catalytic site (3’->5’ exonuclease) for proofreading.

Dimerizing subunit (τ)

Links the two core enzymes of DNA Polymerase III Holoenzyme.

Clamp (β)

Holds the catalytic core of DNA Polymerase III on the DNA template.

Clamp loader (γ complex)

A complex consisting of 5 proteins that opens the beta clamp to attach it to the DNA strand.

DNA Helicase

An enzyme that unwinds DNA at the replication fork, consuming 1 ATP/bp of melting.

DNA Gyrase

An enzyme that releases strain on the DNA molecule during replication.

Single Stranded Binding Proteins (SSBP)

Proteins that keep single-stranded DNA from re-annealing; binding is cooperative.

DNA Primase

Synthesizes a short stretch of RNA primer, which provides the 3’OH needed by DNA polymerase.

DNA Polymerase III

The primary enzyme that synthesizes most of the new DNA (5’->3’ polymerase activity) and has 3’->5’ proofreading exonuclease activity.

DNA Polymerase I

An enzyme that removes RNA primers with its 5’->3’ exonuclease activity.

DNA Ligase

An enzyme that seals Okazaki fragments on the lagging strand.

Leading Strand

The DNA template strand where nucleotides are added continuously during replication.

Lagging Strand

The DNA template strand where nucleotides are added discontinuously, forming Okazaki fragments.

Semiconservative Replication

A replication process where two copies of DNA are produced, each containing one original strand and one newly synthesized strand.

Plasmid

A small circular, double-stranded DNA molecule that replicates independently of the host chromosome.

Episome

A plasmid that has the ability to integrate into the host chromosome.

F+ cell

A bacterial cell that contains a complete F plasmid and acts as a donor in conjugation.

F- cell

A bacterial cell that does not contain the F plasmid and acts as an acceptor in conjugation.

F' cell

A bacterial cell that contains part of the F plasmid or an F plasmid with other bacterial genes, acting as a donor.

Hfr cell

A bacterial cell that contains the F plasmid integrated into its bacterial genome, acting as a donor with high frequency recombination.

Pili (pilus)

Hollow, hair-like projections on the surface of some bacteria (traA product) that initiate conjugation.

TraI (Relaxase)

An enzyme that nicks the oriT region of the F plasmid and forms a covalent bond with the 5' end of the nick during conjugation.

oriT

The origin of transfer on an F plasmid, where TraY binds and TraI nicks to initiate DNA transfer during conjugation.

Agrobacterium

A bacterial species known for causing tumor formation in plants by transferring its T-DNA.

Acetosyringone

A plant-wounding hormone that activates the VirA receptor in Agrobacterium.

VirA

A receptor in Agrobacterium that is activated by acetosyringone, which then activates VirG.

VirG-PO4

A phosphorylated transcription factor in Agrobacterium that binds to and activates virB, C, D, E, F promoters.

VirD

Proteins encoded by the Agrobacterium virulence region that act as endonuclease to initiate nicks at correct locations of the T-DNA.

VirE

A protein in Agrobacterium that encodes a single-stranded binding protein (SSBP) which binds to excised T-DNA to form a 'T-complex'.

T-DNA

A specific region of the Ti plasmid that contains genes which, upon transfer to a plant cell, generate a transformed tumor state and synthesize opines.

Ti Plasmid

The tumor-inducing plasmid found in Agrobacterium, responsible for plant tumor formation.

Opines

Unusual amino acid derivatives synthesized by transformed plant cells, serving as a specific source of nitrogen and carbon for Agrobacterium.