Ch. 15 DNA & Gene: Synthesis And Repair

radioactive viruses with either S or P infected E.coli cells. If genes consist of DNA, then radioactive protein should only be found in capsids outside the infected cells, while DNA should be located in cells.

consist of deoxyribose sugar, phosphate group, and nitrogenous base. These link together into polymer when a hydroxyl group on 3' carbon on one deoxyribose and the phosphate group attached 5' carbon of another deoxyribose are joined by a covalent linkage called phosphodiester bond.

has a backbone made up of sugar and phosphate groups of deoxyribonucleotide monomers and series of bases that project from the backbone. Each strand of DNA has a directionality: one end has an exposed hydroxyl group on 3' carbon while the other has an exposed phosphate group on 5' carbon. Therefore they have distinctly different 3' and 5' end.

1) complementary base pairing and 2) hydrophobic interactions between bases inside the helix.

semiconservative: if parental strands are separated, each one could be a template for new daughter strand. conservative: bases of both strands are temporarily turned out from helix, they could serve as template for synthesis of entirely new double helix at once. dispersive: if double helix were cut at frequent intervals and DNA is synthesized in short sections.

any enzyme that catalyzes synthesis of DNA from deoxyribonucleotide triphosphate.

5' to 3' direction.

monomer used by DNA polymerase to polymerize DNA. Consists of the sugar deoxyribose, a base, and three phosphate group. They have high potential energy because of the spaced phosphate group, and this makes the subsequent formation of phosphodiester bonds in a growing DNA strand exergonic as two of the phosphate are cleaved off.

site on a chromosome at which DNA replication begins.

Y-shaped region where the parental DNA double helix is separated into single strand and copied.

it occurs in both directions at the same time.

breaks H bonds between base pairs in their location and opens the double helix there. this reaction causes the two strands of DNA to separate at the replication fork.

a protein that attaches to separate strands of DNA during replication, preventing them from re-forming a double helix. These attach to the separated strands to prevent them from snapping back into a double helix.

enzyme that cuts DNA, allows it unwind, and rejoins it ahead of the advancing replication fork.

1) works only in 5' to 3' direction along a single-stranded template and 2) requires a 3' end to extend from.

the single-stranded template dictates which deoxyribonucleotide should be added next.

the 3' end is supplied with a primer, and RNA strand about a dozen nucleotides long that forms complementary base pairs with DNA template strand. This provides DNA polymerase with 3' hydroxyl group that can be linked to a deoxyribonucleotide to form a phosphodiester bond.

an enzyme that synthesizes as a short stretch of RNA to use as a primer during DNA replication. 1 type of RNA polymerase

an enzyme that catalyzes the synthesis of RNA ribonucleotides using a DNA template.

Part of DNA polymerase forms a ring that surrounds DNA and another part grips the strand. Deoxyribonucleotide addition is catalyzed at an active site in a groove between enzyme's thumb and finger.

The strand that is synthesized toward replication fork is called leading strand because its synthesis proceeds continuously in direction of moving replication fork. After an RNA primer is in its place, DNA polymerase moves along adding nucleotides to 3' end of that strand. The enzyme moves into replication fork, which is unwound ahead of it. The lagging strand is done in segments though because of its opposite direction.

must be synthesized in a direction that runs away from moving replication fork.

primase synthesizes new RNA primers for lagging strands as the moving replication fork opens single-stranded regions of DNA, and that DNA polymerase uses these primers to synthesize short lagging strand DNA fragments, and these are eventually linked together into a continuous strand.

short segments of DNA produced during replication of lagging strand template. The Okazaki fragments are eventually linked together to produce the lagging strand in newly synthesized DNA.

DNA polymerase attaches to 3' end of an Okazaki fragment. As it moves in 5' to 3' direction, it removes the RNA primer ahead of it and replaces the ribonucleotides with deoxyribonucleotides. Once the RNA primer is removed and replaced by DNA, an enzyme called DNA ligase catalyzes the formation of phosphodiester bond between adjacent fragments.

Helicase catalyzes the breaking of H bonds between base pairs to open the double helix, SSBPs stabilizes single stranded DNA, and topoisomerase breaks and rejoins DNA to double helix to relieve twisting forces caused by the opening of the helix.

Primase catalyzes the synthesis of RNA primer, then DNA polymerase III extends the leading strand, and the sliding clamp holds DNA polymerase in place during strand extension.

Primase catalyzes the synthesis of RNA primer on an Okazaki fragment, DNA polymerase III extends an Okazaki fragment, the sliding clamp holds DNA polymerase in place during strand extension, DNA polymerase I removes the RNA primer and replaces it with DNA, and DNA ligase catalyzes the joining of Okazaki fragments into a continuous strand.

region at the end of a eukaryotic chromosome.

when replication fork reaches end, a DNA polymerase synthesizes the leading strand all the way to end of DNA template, as a result leading strand synthesis results in double-stranded copy of DNA model. On lagging strand, primase adds an RNA primer close to end of chromosome. DNA polymerase synthesizes the final fragment of lagging strand, an enzyme that degrades ribonucleotides removes the primer. DNA polymerase is unable to add DNA near the end of chromosome because it can't synthesize DNA without a primer. As a result, single stranded DNA that is left stay single stranded.

enzyme that adds DNA to ends on chromosomes to prevent their shortening by standard DNA synthesis; catalyzes DNA synthesis guided by an RNA template that is part of enzyme.

1. unreplicated segment at 3' end of template for lagging strand forms a single-stranded "overhang." 2. telomerase binds to overhanging single-stranded DNA and uses portion of RNA within telomerase as a template for DNA synthesis. DNA is synthesized from 3' OH of single strand. 3. Telomerase shifts down the newly synthesized DNA and catalyzes another addition of same short sequence of end of strand. This step is repeated. 4. Once overhang of parental strand is lengthened, standard enzymes of DNA synthesis use it as a template to synthesize a complementary strand. The resulting addition of a double-stranded DNA to end of a chromosome counteracts any shortening of lagging strand.

The idea that chromosomes get shorter and shorter in cells without telomerase led to hypothesis that number of cell division is possible for somatic cell is limited by initial length of telomeres.

1) correct base pairs are the most energetically favorable. 2) correct are pairs have a shape distinct from incorrect base pairs.

DNA polymerase's active site can discriminate between these shapes and will add a new nucleotide only when previous base pair is correct. DNA polymerase pauses when it detects a misaligned base pair and exonuclease activity of DNA polymerase III e subunit then removes the mismatched nucleotide.

ability of DNA polymerase to recognize and remove an incorrect deoxyribonucleotide. This is important mechanism for achieving accuracy in DNA synthesis.

type of DNA repair used to correct mismatched base pairs in DNA that result in mistakes from DNA synthesis.

proteins that are like a copy editor who corrects error that DNA polymerase didn't catch.

type of DNA repair that removes a damaged region in one strand of DNA and replaces it with the correct sequence using the undamaged strand as a template. This removes thymine dimers causes by UV light that distorts the DNA helix, and replaces the damaged DNA strand with correct newly synthesized DNA.

a DNA sequence that is expressed to form a function product; either RNA or polypeptide.

ligase.

each new DNA double helix consists of one old DNA strand and one new DNA strand.

helicase.

replication fork and replication bubbles.

DNA polymerase can assemble DNA only in the 5' to 3' direction.

RNA primer complementary to a pre-existing DNA strand.

template.

both leading and lagging strand synthesis would be incomplete.

The new DNA strand is synthesized in 5' to 3' direction ; the template strand is read in 3' to 5' direction.

the deoxyribonucleotide triphosphate substrates.

leading strand is synthesized in same direction as the movement of replication fork, and the lagging strand is synthesized in opposite direction.

both leading and lagging strands.

leading: made continuously, only one primer needed, daughter strand elongates toward replication fork. lagging: made in segments, multiple primers needed, and daughter strand elongates away from replication fork. both strands: synthesized in 5' to 3' direction.

telomerase is involved in adding DNA to end of lagging strand.

used predominantly on lagging strand because this strand is synthesized in numerous small fragments.

Telomere length is more important in determining cell division because all cells with longer telomeres divided more times that cells with shorter telomeres, regardless of donor age.

proofreading mechanism of DNA polymerase wasn't working properly.

there are several proteins involved in nucleotide excision repair process.

a higher than normal rate of DNA synthesis errors.

breaks H bonds between bases, and binds at replication fork.

breaks covalent bonds in DNA backbone, and binds ahead of the replication fork.

binds after replication fork, and prevents H bonds between bases.