Bio 305 - Ch 7.1-7.4: DNA Structure and Replication

Bacteriophages (phages)

Viruses that infect bacteria

Deoxynucleotide monophosphates (dNMPs)

N can be any of the nucleotide bases. dAMP, dGMP, dCMP, dTMP

Deoxynucleotide triphosphates (dNTPs)

Free (reactive) DNA nucleotides in their triphosphate configurations. dATP, dGTP, dCTP, dTTP

Sugar phosphate backbone

Alternating sugar (deoxyribose or ribose) and phosphate molecule pattern

Base stacking

Slight rotation of adjacent base pairs around the axis of symmetry - giving the double helix

Major groove

Approx 12 A wide. Created by base pair stacking making two grooves, partially exposing nucleotides for regulatory proteins to access.

Minor groove

Approx 6 A wide. Created by base pair stacking making two grooves, partially exposing nucleotides for regulatory proteins to access.

Semiconservative DNA replication

Correct model. Each new strand contains one original parent strand and one new daughter

Conservative DNA replication

Incorrect model. One daughter duplex contains the two strands of the parental molecule and the other has two new daughters

Dispersive DNA replication

Incorrect model. Each strand has a mix of parent and daughter strands

Bidirectional movement for DNA replication

DNA replication synthesizes DNA in both directions from a single origin of replication

Origin of replication

Specific start sequence

Replication bubble

Region of replication with replication forks on each end, origin of replication in the middle, and leading and lagging strands in each half of the bubble

Consensus sequences

Comparisons of evolutionarily conserved sequences within and among related species can lead to the identification of them. Similar functions, length, and pattern of base pairs. Not identical, defined by nucleotides that occur most often at particular positions in the sequence. Not unique to DNA replication

Helicase

Protein that breaks H bonds to separate the DNA strands and unwinds the double helix ahead of advancing DNA replication

Single-stranded binding protein (SSB)

Unwound strands bound by this which prevents them from reforming a DNA duplex (open for DNA synthesis)

Primase

Specialized RNA polymerase that synthesizes the RNA primer during DNA replication. Operate in the initial stages of archaeal and eukaryotic DNA replication

RNA primer

Short, single stranded RNA segment synthesis by primase. 3’ end of RNA primer is used by DNA polymerase to begin synthesis of DNA. Temporary

DNA Polymerase III

Synthesizes DNA, starts at 3’ OH end of RNA primer. Enzymes with identical function found in archaea and eukaryotes

Replisome

Large molecular machine located at the replication fork that coordinates multiple reaction steps during DNA replication. Includes two molecules of DNA polymerase III that lead continuous and discontinuous strands

Leading strand

Continuously synthesizes strand

Lagging strand

Runs opposite to the direction of movement of the replication fork. Okazaki fragments

Okazaki fragments

Ligated together to make a continuous strand

DNA polymerase I

Removes nucleotides of RNA primer and replaces them with DNA nucleotides. Begins with 5’ nucleotide and goes in the 3’ direction

5’ to 3’ exonuclease activity

DNA polymerase I removes the 5’ most nucleotide from the RNA primer

5’ to 3’ polymerase activity

DNA polymerase I then fills the created gap with correct DNA nucleotide

DNA Ligase

Forms the phosphodiester bond to join the gap created by the Okazaki fragments

Sliding clamp

Encircles DNA polymerases and drives it forward

DNA proofreading

Most DNA polymerase can stop and revers replication to remove incorrect base and replace it. 3’ to 5’ exonuclease activity

DNA Topoisomerases

Enzyme that relaxes DNA supercoiling by controlled strand nicking and rejoining

Telomeres

Bases at ends of chromosomes that act as a buffer to replication loss. Shorten with age

Telomerase RNA component (TERC)

Protect against chromosome shrinking in germ cells (and other select cells)

Telomerase RNA

RNA portion of telomerase enzyme that provides a template for synthesis of the repeating sequence of the telomere

T loop

Formed during DNA replication of a telomeric repeat sequence. Protects the telomere from enzymatic degradation by joining with protein complex “shelterin”

Shelterin

Protects telomere from damage

Hayflick limit

Apoptosis induced by telomere shortening associated with this (hayflick limit) - apparent life span of a cell after so many DNA replications