Genetics Chapter 11

• double helix
• nucleotides
• four bases
• hydrogen bonding between bases
• A-T & C-G
• antiparallel alignment

one strand is original mother helix and the other strand is the daughter 

• signle origin of replication
• synthesis of new daughter strand is bidirectional

origin of replication in bacterial chromosomes

• AT-rich region 
• DnaA box (4-5)
• GTAC methylation site

• DnaA proteins bind to all 4-5 DnaA boxes 
• stimulates the cooperative binding of an additional 20-40 DnaA proteins to form a large complex

• HU
• IHF

• the tension caused from the wrapping of DNA around the DnaA complex causes the AT-rich region to separate
• after DnaA and DnaC proteins recruit DNA helicase to bind to site and being strand separation withing the OriC

• helicase opens helix
• DNA gryase alleviates supercoiling
• polymerase III synthesizes leading strand
• primase synthesizes RNA primer
• polymerase III elongates primer; prodcues okazaki fragments
• polymerase I excises RNA primer; fills gaps
• DNA ligase links Okazaki fragments to form continuous strand

covalently attaches nucleotides in daughter strand

• pol I and pol III: normal DNA replication
• pol II, IV, and V: DNA repair and replication of damaged DNA

• single subunit
• fills in small regions wehre RNA primers were located

• 10 subunits
• responsible for most DNA replication 

enxyme that has many subunits to it

• unable to initiate DNA synthesis by linking together two individual nucleotides (primase needed)
• works only in 5' to 3' direction (no bidirectional synthesis)

lagging

• RNA primers removed by DNA polymerase I (5'-3')
• polymerase I fills in this region with newly synthesized DNA
• DNA ligase covalently bonds to last nucleotide made by polymerase I and the first nucleotide in the next new DNA fragment

processive

• opposite OriC are termination sequences (ter sequences)
• T1 ter and T2 ter sequences work alternatively 
• DNA ligase covalently links the two daughter strands, creating two circular, double stranded molecules
• topoisomerases break DNA strands and then rejoin them after strands have become unlocked

• T1- allows advncement of clockwise-moving forks, but prevents the movement of counter clockwise-moving forks
• T2- permits the advancement of counter clockwise-moving forks, but prevents the advancement of clockwise-moving forks

DNA helicase and primase

primosome and two DNA polymerase holoenzymes

term used to describe two DNA polymerase holoenzymes that move as a unit toward the replication fork

• hydroen bonds between correct partners are more stable
• induced fit phenomenon 
• enzymatic removal of mismatch at 3' end of newly made strand (exonucleases)

polymerase less likely to catalyze bonds between nucleotides if there are mismatched bases

• identify and remove mismatched nucleotides
• occurs in 3' to 5' direction
• reduces error rate to 1 in 100 million

• replication must be coordinated with cell division
• mechanisms must regulate initiation of replication

• insufficient amount of DnaA peoteins to bind to all the DnaA boxes within the OriC 
• prevents premature replication

• involves the temporary lack of adenine methylation in the GATC sites within OriC 
• enzyme DAM (DNA adenine methyltransferase) methylates all the GATC sites in the newly replicated strands of DNA
• replication does not occur until after it has become fully methylated
• methyl group on parent strand but not daughter strand (hemimethylated)

• not as well understoood
• common enzymes with prokaryotic replication 
• appears to be substantially more complex 

• multiple origins of replication
• ARS elements (Autonomously Replicating Sequences)
• origin of recognition complex (ORC)

• occurs bidirectionally from many origins of replication
• during S phase
• forks eventually meet and complete process 

• Autonomously Replicating Sequences
• ~50 base pairs
• the high percentage of A and T bases in this sequence
• consensus sequence ATTTAT (A or G) TTTA
• ^ where replication bubble begins

• 6 subunit protein complex that acts as the initiator of eukaryotic replication when it binds to the ARS in the G₁ phase 
• licensing factors bind to MCM
• MCM helicase (minichromosome maintenence) must coat DNA for replication to begin

• DNA polymerase delta generates flap
• flap endonuclease cuts the flap off

• needed for DNA replication
• occurs in the S phase of cell cycle
• histones are assembled into octamer structures and associate with newly made DNA very near the replication fork
• each daughter strand contains a random mixture of new and old octamers

complex of telomeric sequences within the DNA and the special proteins that bind to it

• moderately repetitive tandem arraw with a 3' overhauling region (12-16 nucleotides)
• many G's and T's
• are a problem when it comes to replication because they have more hydrogen bonds
• incomplete ends because the polymerase will not connect two nucleotides

• telomerase recognizes teomeric sequences at the ends of chromosomes and synthesize additional repeats of telemetric sequences
• contains both proteins and RNA 
• RNA sequence functions as a template allowing the attachment of a series of 6-nucleotide sequences

• ribonucleoprotein
• a single RNA molecule is called TERC (telomeric RNA component)
• its protein comoponent is TERT (telomere reverse transcriptase)

• reverse transcriptase 
• sythesizes DNA from an RNA template 
• only found in a few somatic cells