DNA Replication (Video) - Vocabulary

Vocabulary flashcards covering key terms from the DNA Replication lecture video.

Semiconservative replication

Each daughter DNA molecule contains one old strand (template) and one new strand.

Origin of replication

The specific DNA sequence where replication loops are initiated; AT-rich region. Prokaryotes have one, eukaryotes have multiple

Replication fork

Points where parent DNA is unwound and strands are separated for replication, which proceeds in both directions with both strands replicated simultaneously

Leading strand

Synthesized continuously 5' to 3' in the same direction the replication fork moves.

Lagging strand

Synthesis proceeds in the opposite direction of the replication fork’s movement. Synthesized discontinuously using Okazaki fragments, which will be spliced together by DNA ligase

Okazaki fragment

Short DNA fragment synthesized on the lagging strand. These fragments eventually have the RNA primer removed and replaced with DNA by DNA Pol I, and DNA ligase seals the nick

Semi-discontinuous replication

DNA replication moves bidirectionally, with the leading strand synthesized continuously and the lagging strand synthesized discontinuously, both in the 5’ to 3’ direction

DNA polymerase

Enzyme that catalyzes DNA synthesis using a phosphoryl group transfer reaction, where the 3’-OH of the nucleotide at the 3’ end of the strand attacks the a-P on the incoming dNTP. Mg2+ is used for stability.

3’ → 5’ exonuclease proofreading

Capability of some DNA polymerases to remove a newly added nucleotide, improving accuracy 10² to 10³ times, leaving an error rate of around one error in every 10⁶ to 10⁸ bases

RNA primer

Short RNA segment providing a free 3′-OH to start DNA synthesis.

Telomere

Chromosomal “caps” of repetitive protective DNA sequences at chromosome ends. They prevent coding sequence shortening, and the triggering of repair mechanisms that could result in end-to-end chromosomal joining

Telomerase

Carries RNA template for creating caps; germ cells, immune cells, and stem cells have these enzymes. Cancer cells and senescence may also have this enzymatic activity

DNA polymerase I

Abundant but slow E. coli polymerase involved in primer removal and cleanup; has 5'→3' exonuclease and 3'→5' proofreading.

DNA polymerase II

E. coli polymerase mainly for DNA repair with 3’ to 5’ exonuclease proofreading

DNA polymerase III

Main replication enzyme in E. coli; high processivity and 3’ to 5’ proofreading.

DNA polymerase IV and V

E. coli polymerase involved in an unusual form of DNA repair with no proofreading capabilities and low progressivity

5′ to 3′ exonuclease activity

Activity that removes RNA primers and performs nick translation.

E. coli DNA Pol III

includes 16 subunits:

a-subunit for polymerization

ε subunit for 3’ to 5’ proofreading

θ subunit, which associates a with ε to form a core pol

X and gamma bind to clamp-loading complex

B subunits as sliding DNA clamps, keeping pol bound to DNA

Helicases

enzymes that move along DNA and separate strands

Topoisomerases

relieve topological stress created by strand separation

DNA-binding proteins

stabilize separated strands

Primases

synthesize short segments of RNA to serve as primers

DNA Pol I

removes and replaces RNA primers

DNA ligases

seal nicks in the DNA backbone following removal and replacement of an RNA primer

DNA synthesis stages

Initiation: includes appropriate sequences motifs for relevant proteins to bind

Elongation: RNA primer begins process, and dNTPs are added through unwinding of strands and cuts as needed

Termination: replication forks meet and are halted

Proteins acting at the replication fork

SSB (binding to single-strand DNA), DnaB helicase (DNA unwinding), DnaG primase (RNA primer synthesis), DNA Pol III (new strand elongation), DNA Pol I (filling gaps; excision of primers), DNA ligase (ligation), DNA gyrase (topoisomerase, supercoiling)

DNA polymerase E

synthesizes the leading strand with high processivity; has 3’ to 5’ proofreading

DNA polymerase delta

synthesizes the lagging strand; has 3’ to 5’ proofreading

DNA polymerase a

DNA polymerase/ primase that synthesizes RNA primers and extends them to initiate Okazaki fragment synthesis; no proofreading

Proliferating cell nuclear antigen (PCNA)

analogous to the B subunit; forms a circular clamp to enhance the processivity of two polymerases by keeping them on the strand