NOTES: CH 16 (part 2) DNA Replication and Repair

NOTES: CH 16 (part 2) – DNA Replication and Repair ● During DNA replication, base-pairing enables existing (“parental”) DNA strands to serve as temp...
Author: Leslie Stokes
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NOTES: CH 16 (part 2) – DNA Replication and Repair

● During DNA replication, base-pairing enables existing (“parental”) DNA strands to serve as templates for new (“daughter”) complementary strands

● Watson and Crick proposed that during DNA replication: 1) the 2 DNA strands separate; 2) each strand is a template for assembling a complementary strand; 3) nucleotides line up singly along the template strand (A-T, G-C); 4) ENZYMES link the nucleotides together at their sugar-phosphate groups.

● Watson and Crick’s proposed model is a SEMICONSERVATIVE model (each of the 2 daughter molecules will have 1 old or CONSERVED strand from the parent molecule and 1 newly created strand)

● DNA replication begins at special sites called ORIGINS OF REPLICATION. -DNA double helix opens at the origin & replication “forks” spread in both directions away from the central initiation site creating a REPLICATION BUBBLE.

-100’s to 1000’s of replication origins form in eukaryotic chromosomes, which eventually fuse forming 2 continuous DNA molecules

“Unzipping” the parent DNA strands: ● 2 types of proteins involved with separation of

parental DNA strands: *HELICASES: enzymes that catalyze the unwinding of parental DNA double helix to expose template

*single-strand binding proteins: keep the separated strands apart & stabilize unwound DNA until new strands can be made

Elongating the new DNA strands: -new nucleotides align themselves along templates of old DNA strands according to base-pairing rules (A-T, G-C)

DNA polymerases catalyze synthesis of new DNA strand:

-DNA polymerases link the nucleotides to growing strand. -new strands grow in the 5’ to 3’ direction; new nucleotides are added only to the 3’ end of the growing strand

What is the source of energy that drives the synthesis of the new DNA strands? ● Nucleoside triphosphates (nucleotides with 3 phosphate groups linked to the 5’ carbon of the sugar) provides energy for DNA synthesis: -nucleoside triphosphate loses 2 phosphates -exergonic hydrolysis of these phosphate bonds drives the endergonic synthesis of DNA; it provides the energy to form new covalent linkages between nucleotides

Now, back to…

DNA polymerase can only add on the 3' end!

*RECALL:

DNA strands run in opposite directions; DNA polymerase can elongate strands only in the 5’ to 3’ direction

● this problem is solved by continuous synthesis of 1 strand (LEADING STRAND) and…discontinuous synthesis of the complementary strand (LAGGING STRAND)

● the LAGGING STRAND is produced as a series of short fragments (“Okazaki” fragments) which are synthesized in the 5’ to 3’ direction and then linked together by the enzyme DNA ligase.

● Before new DNA strands can form, there must be small pre-existing PRIMERS to start the addition of new nucleotides -a primer is a short RNA segment that is complementary to a DNA segment

-primers are polymerized by primase enzyme

*only 1 primer is necessary for replication of the leading strand, but many primers are necessary to replicate the lagging strand *an RNA primer must initiate the synthesis of each Okazaki fragment!  *DNA polymerase removes the RNA primer and replaces it with DNA nucleotides

Hydrogen Bonds Breaking!

Enzymes proofread DNA during its replication and repair damage to existing DNA

 MISMATCH REPAIR: corrects mistakes (mismatched bases) that occur when DNA is being copied *one form of colon cancer is due to a defect in one of the proteins involved in this type of DNA repair

 NUCLEOTIDE EXCISION REPAIR: corrects accidental changes that occur in existing DNA -an enzyme (nuclease) cuts out damaged segment of DNA -the enzymes DNA polymerase and ligase fill in the resulting gaps *xeroderma pigmentosum is caused by an inherited defect in an excision-repair enzyme

What about the 5’ ends of long DNA molecules?

 DNA polymerase can only add nucleotides to the 3’ end of a preexisting polynucleotide…  The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands;  As a result, repeated rounds of replication produce shorter and shorter DNA molecules

Solutions to the problem:  Prokaryotes avoid this problem by having circular DNA molecules…but what about eukaryotes?  The answer is…TELOMERES!

TELOMERES:  special nucleotide sequences at the end of eukaryotic chromosomal DNA molecules;  do not contain genes;  contain multiple repetitions of one short nucleotide sequence  example: in humans, TTAGGG.  # of repeats varies between 100 and 1,000.

TELOMERES:  expendable, noncoding sequences;  they protect an organism’s genes from being eroded through successive rounds of DNA replication.  a special enzyme, TELOMERASE, catalyzes the lengthening of telomeres

Things that make you go hmmmm…  telomerase is NOT present in most cells of multicellular organisms (like ourselves!)…this means  the DNA of dividing somatic cells tends to be shorter in older individuals (older tissues / cells);  thus, telomeres may be a limiting factor in the life span of certain tissues and even the organism as a whole…  telomerase has been found, however, in somatic cells that are cancerous!

A note about chromatin packing…

A note about chromatin packing…