DNA Structure / Replication (Week 2)

Wound, gut

DNA replication in adulthood is present in (1) __ healing and (2) lumen of the __

helix, nucleosome, histone, 30, 750, chromosome

DNA structure

double __ → Beads on string (__ = have __ octamers)→ __ nm fiber → highly condensed __ nm fiber → __ tight coiling of fiber

Histones

Regulate chromatin architecture and has protein tails that determine structure and gene expression

Nucleosomes

 Use mechanisms to package and store DNA

Nucleoside, nucleotide

A __ is a nitrogenous base + sugar

A __ is a nitrogenous base + sugar + phosphate group

DNTP, phosphodiester, 3’

__ (deoxyribonucleoside triphosphate) establishes a __ bond of DNA at the _’ end of primer strand

S phase

Phase of cell cycle where DNA replication takes place

Meselson and Stahl’s Experiment

Researchers found through centrifugation if E coli in nitrogen isotopes that DNA replication is semiconservative

Theta Replication

Single origin of replication form the replication fork, bi-directional (i.e. circular DNA, E. coli)

Rolling-Circle Replication

Single origin of replication, no replication fork (i.e. Virus, F factor)

Initiation (bacterial DNA)

Occurs only at at 245 base pairs in oriC (single origin replicon)

Helicase

Unwinds hydrogen bonds of DNA, in front separated and behind annealed

Gyrase (topoisomerase)

Removes supercoiling ahead of replication fork

Single-stranded binding proteins (SSB)

Prevent single-stranded DNA from annealing and meeting together

RNA primers, 3’-OH

__ __ are an existing group of RNA nucleotides with _’-__ group where nucleotide can be added

Elongation

Carried out by DNA polymerase III (proofreads 3’ to 5’)

DNA polymerase I

Removes RNA primers in exchange for nucleotides in new strand

DNA Ligase

Connects fragments after RNA primers are removed

Termination

When replication fork meets, or done by specific protein (replication stage)

DNA polymerase II

Involved in repair and restart of stalled replication forks for bacterial replication, not as important polymerase

Initiation (eukaryotic DNA)

• Each chromosome has numerous origins

• At each DNA unwinds and makes a replication bubble

• DNA synthesis occurs on both strands and bubbles eventually fuse

• Bidirectional has net product of 2 linear DNA molecules

3’ 5’ 3’

Requirements of eukaryotic replication

• Template strand

• Raw materials (DNTPs, nucleotides)

• Enzymes and other proteins

• DNA polymerase adding nucleotides to _’ end of growing strand, replication must go from _’ → _’ (for both leading + lagging)

Lagging strand

Undergoes discontinuous DNA replication with Okazaki fragments

Leading strand

Undergoes continuous replication of DNA

Poly alpha

Initiates DNA replication by extending RNA-DNA primers

Poly delta

 Synthesizes lagging strand and is involved in DNA repair

Poly epsilon

Synthesizes leading strand and participates in DNA repair

Poly gamma

Replicates and repairs mitochondrial DNA

Poly beta

 Involved in base excision repair of nuclear DNA

Telomerase, germ, cancer

__ extends the DNA, filling in gap due to removal of RNA primer

• Only found in __ cells (eggs, sperm) and __ cells

DNA, telomeres, shorten, apoptosis

__ is extended each time it’s copied → we don’t have circular ends → __ (ends of chromosomes) __ as cells divide → Aging of cell and then __

Reverse transcriptase

Telomeres also function as a __ __ (enzyme) acting without DNA template