BIOL Chapter 15

daughter DNA

replication fork

origin of replication. Both leading and lagging strand. Bacterial chromosomes form a single replication bubble, but eukaroytes can form several along each chromosome

DNA polymerase

primase

Okazaki fragments

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

leading strand.

Both leading and lagging strands, but spaced differently

The leading strand would continue to be synthesized, but lagging strand synthesis would be halted. DNA ligase seals the gaps between Okazaki fragments

Eukaryotes contain linear chromosomes and therefore require telomerase to prevent loss of the ends of the chromosomes

a higher-than-normal rate of DNA synthesis errors. Without this proofreading function, incorrect nucleotides would be inserted about once every 100,000 bases instead of once every 10,000,000 bases.

breaks H-bonds between bases binds at replication fork

bind ahead of the replication fork breaks covalent bonds in DNA backbone

prevents H-bonds between bases, binds after replication fork

Nucleotides at the ends of the DNA strands are lost when DNA replicates.

Their cells do not produce telomerase.

regions of DNA at the end of chromosomes which do not code for making proteins

The cells in a developing embryo.

an enzyme that regulates the assembly of DNA at the ends of chromosomes

Cells with short telomeres can no longer divide, so damaged tissues cannot be repaired.

Find a way to turn off the gene for making telomerase in cancer cells, since the cells would stop dividing when the telomeres were gone.

3' ; continuously

Virus enter hosts cell, caspid (the exterior protein coat) doesnt, new virus particles created directed by genes, and the new generation burst from host cell

-Proteins contain sulfur, not phosphorous -DNA has phosphorus, not sulfur

This finding would indicate that the virus injected both DNA and protein into the cell, revealing nothing about which of these molecules was the genetic material.

starts on a phosphate phosphate group attached

sugar strand/ OH tail

The parental strands of DNA separate, each one is used as a template for the synthesis of a new daughter strand. Each new daughter DNA molecule is one old and one new strand.

DNA Polymerase

DNA Helicase

Topoisomerase II

DNA Polymerase

Single-stranded binding proteins

Polymerizes DNA monomers into DNA. Catalyzes DNA synthesis

5' -> 3' because deoxyribonucleotides can only be added to the 3' end of a growing DNA chain (bcs thats the end w the free OH group)

dNTP

deoxyribonucleoside triphosphates (N standing for any of the four bases in DNA) have close phosphate groups for high enough potential energy to form phosphodiester bonds in growing dna strand exergonic when the phosphates are cleaved

eukaryotes- multiple along each chromosome prokaryotes-one origin, one replication bubble

y shaped region where the parental DNA double helix is separated into single strands and copied

breaks down the hydrogen bonds between the base pairs in the location and opens the double helix there

attach to the separated strands to prevent them from snapping back into the double helix

goes ahead of replication fork and prevents twisting of DNA before fork by cutting DNA and allowing it to unwind and rejoins it

1. works only in the 5' -> 3' direction 2.requires a 3' end to extend form

an RNA strand about a dozen nucleotides long that forms complementary base pairs with the DNA template strand.

the primer provides DNA polymerase with a 3' hydroxyl group that can be added to a deoxyribonucleiotide to form a phophodiester bond

primase sytnehsizes the short stretch of RNA

a class of enzymes catalyzing the polymerization of riboonucleotides into RNA. Unlike DNA polymerases, primase and other RNA polymerases do not require a primer to begin synthesis

this surrounds the DNA, and another part grips the DNA strans in a way similar to hand classping rope. deoxyribo nucleotides additions catalyzed at an active site in a groove between the enzymes "thumb and fingers"

strand of DNA synthesized TOWARD replication fork; aka continuous strand

easy, primers put in place, DNA polymerase moces along, addinf deoxyribonucleotides to the 3' end of thaat strand. The enzyme moves into the replication fork, which is unwound ahead of it.

Helicase, topoisomerase, single-strand DNA-binding proteins, primase, and DNA polymerase are all required for leading-strand synthesis. If any one of these proteins is nonfunctional, DNA replication will not occur.

discontinuous strand; runs away from replication fork. as the fork moves, it exposes gaps of single-stranded template DNA

short DNA fragments produced during replication of lagging-stranf template. eventually link to gether to produce that lagging strand in newly synthesized DNA

removes the RNA primer ahead of it and replaces the ribonucleotides with deoxyribonucleotides

Once RNA primer is remove and replaces by DNA, this enzyme catalyzes the formation of a phosphodiester bond between adjacent fragments

The leading strand would be continuous if either DNA polymerase I or DNA ligase were defective. However, on the lagging strand, if (a) DNA polymerase I were defective, there would be many unjoined Okazaki fragments that begin with RNA primers (because DNA polymerase I works to remove these primers); and if (b) ligase were defective, the lagging strand would have Okazaki fragments without RNA primers but with nicks separating each fragment (because ligase works to join Okazaki fragments).

macromolecular machine that copies DNA: includes DNA polymerse, helicase, primase, and other enzymes

Leading- Extends the leading Strand, Lagging- Removes RNA Primer and replaces it with DNA

Holds DNA polymerase in place during strand extension in leading-strand and lagging-strnd synthesis

in lagging strand synthesis, removes the RNA primer and replaces it with DNA

Catalyzes the joining of okazaki fragments into a continuous strand

Leasing-catlyzes syntheisis of RNA primer. Lagging same but on okazaki fragment

(1) DNA polymerase adds nucleotides only to the free 3? -OH on a strand. Primase synthesizes a short RNA sequence—a primer—that provides the free 3? end necessary for DNA polymerase to start working. (2) The need to begin DNA synthesis many times on the lagging strand requires many new primers. Since bacterial DNA polymerase I is used to remove primers, it is required predominantly on the primer-rich lagging strand.

end of eukaryotic chromosome

if they did, the linear chromosome would be destroyed bcs 50-100 would be destroyed in every replication

catalyzes the synthesis of DNA from an RNA template that it contains.

telemorase

telemorase

okay so like telomerase attaches to the strand of unreplicated DNA (that would have been unmatched )with its predetremined RNA and free nucleotides attach to its overhanging parts and the backboneand each other, extending the DNA strand then it goes into regular synthesis and the regular enzymes catalyze a complementary strand

the unreplicated segment of the telomere at the 3' end of the template for the lagging strand forms a single-stranded overhang, telomerase binds to overhanging section of the single-stranded parental DNA, uses portion of RNA held in telomerase as a template, DNA synthesized from 3' OH of the single strand, Telomerase shifts down the newly synthesized DNA and catalyzes another additions of the same short DNA sequence to the end of the strand. Repeated. Once overhang of parental extended, standard enzymes of DNA synthesis use it as template to create complimentary strand

(positively correlated) cells with initially longer telomeres had more divisions before cell division ceased

Telomere length is important, and donor age makes little difference. The figure shows a strong relationship between telomere length and cell divisions but a weak relationship between age and cell divisions.

(1) Telomerase is needed only to replicate the ends of a linear DNA. Because bacterial DNAs are circular, they lack ends and don't require telomerase. (2) Since telomerase works by extending one strand of DNA without any external template and because DNA synthesis requires a template, telomerase must contain an internal template to allow it to extend a DNA chain.

about one mistake per billion deoxyribonucleotides. eggs have rougly 12 billion replicated to create trillions of cells. if more than 1 - 2 problems happened in each cell divisions, gene would be deadly and riddles with errors

Correct base pairs are entergetically favor specific pairs, and they have a shape distict from incorect base pairs. (cant fit like a puzzle piece if the dont match, it would make the backbone bugle, noticably) it would notice the difference and replace it

final error correction after DNA synthesis complete. remove section of DNA with incorrect base, resynthesize missing DNA using older strand as template (the older strand has chemical marks to allow distinguish between old and new in bacteria). copy editor who corrects errors writer- DNA polymerase didnt catch

an example of DNA damage repair in which UV ray damage fixed. a damaged DNA strand would develop a bond between adjacent pyrimidine bases within the same strand, (thymine dimer) creates a kink in DNA structure. enzymes excise a stretch of nucleotides including the damage, and replace them in 5' -> 3' direction according to complementary strand, and re link the DNA with DNA ligase

Humans super sensitive to UV light, DNA damage from UV rays not repaired properly, DNA synthesis doesn't occur with that DNA so the radioactive nucleotides never incorporate. 1000 to 2000x more likely to develop skin cancer than those with nucleotide excision repair systems bcs mutation rate increases when DNA damage unrepaired

Radioactive nucleotide is incorporated into DNA in this study anytime there's DNA synthesis. Nucleotide excision repair requires DNA synthesis. Increasing UV doses cause increasing DNA damage and therefore corresponding increases in incorporation of radioactive nucleotides.

(1) The mutation rate would rise because differences in base-pair stability and shape make it possible for DNA polymerase to distinguish correct from incorrect base pairs during DNA replication. (2) The enzymes that remove the dimer and surrounding DNA are specific to nucleotide excision repair. DNA polymerase and DNA ligase work in both nucleotide excision repair and normal DNA synthesis.