BIOL Chapter 15

DNA Polymerase II

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

mistake rate

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

primer

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

helicase

breaks H-bonds between bases binds at replication fork

DNA helicase

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

telemorase

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

What is the energy input for the endergonic reaction of DNA synthesis?

dNTP

After replication is complete, the new DNAs, called ---- are identical to each other.

daughter DNA

Telomeres

end of eukaryotic chromosome

Replisome

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

Replication fork

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

A mutation that prevented DNA ligase from functioning would result in what effect on DNA synthesis? See Section 15.3

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

Which of the following has the greatest potential as a cancer treatment?

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.

Xeroderma pigmentosum (XP)

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

Which strand of DNA is synthesized toward the middle of the replication bubble? See Section 15.3

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

Primase

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

Which of the following problems during DNA replication is being illustrated with the kids in the video?

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

_ are the short sections of DNA that are synthesized on the lagging strand of the replicating DNA.

Okazaki fragments

DNA Ligase,

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

DNA Polymerase

Polymerizes DNA monomers into DNA. Catalyzes DNA synthesis

The leading strand is the daughter strand that has its _ end pointed towards the replication fork and is therefore synthesized _ .

3' ; continuously

DNA polymerases can only work in one direction, which is?

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)

DNA Ligase

Catalyzes the joining of okazaki fragments into a continuous strand

How is the aging process linked to telomeres?

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

Separates the Double Stranded DNA

DNA Helicase

Attaches DNA nucleotides to an RNA primer

DNA Polymerase

Proofreads the growing DNA strands and replaces mismatched nucleotides

DNA Polymerase

The enzyme that can replicate DNA is called ___

DNA polymerase

Is donor age or telemore length more important in determining how many divisoins a cell will undergo

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.

Which cells are most likely to have the gene for making telomerase switched on?

The cells in a developing embryo.

Why does increasing doses of UV light cause increasing amounts of radioactive nucleotide to be incorporated in DNA

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.

Prevents Strands of DNA from rejoining after being unwound

Single-stranded binding proteins

Which of the following is NOT true about naked mole rats?

Their cells do not produce telomerase.

what would it have meant if both raidoactive DNA and protein were in the pellet?

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.

How do viruses work?

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

RNA polymerase

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

A mutation that knocked out the proofreading function of DNA polymerase would result in __________. See Section 15.

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.

Many enzymes are named for the substrate on which they work, either to build or disassemble molecules. Also, enzyme names often end in "-ase." For example, lactase is the enzyme that breaks down lactose. With a name like "telomerase," we can deduce that telomerase is probably:

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

nucleotide excision repair

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

Single-strand DNA binding proteins SSBPs

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

topoisomerase

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

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

lagging strand

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

leading strand synthesis

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.

origin of replication

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

mismatch repair proteins

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

Topoismerase

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

why do they not get destroyed?

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

DNA Polymerase I

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

The new DNA strand that grows continuously in the 5' to 3' direction is called the _

leading strand.

simplified telomerase

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

A DNA replication bubble forms at a specific sequence of bases called the ___________. See Section 15.3

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

single-strand binding protein

prevents H-bonds between bases, binds after replication fork

The enzyme that synthesizes RNA primers for use in DNA replication is _______________. See Section 15.3 ( page 321) .

primase

how is primer added?

primase sytnehsizes the short stretch of RNA

What are telomeres?

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

As DNA polymerse i attaches to the 3' end of an ozaki fragment, as DNA moves in 5' ->3' direction, it _

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

During DNA replication, an open section of DNA, in which a DNA polymerase can replicate DNA, is called a _

replication fork

okazaki fragments

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

what do primers do?

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

extra telomerase

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

Part of DNA polymerase forms a ring- a sliding clamp like a ziploc bag

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"

Relieves Stress on the replication fork caused by unwinding

Topoisomerase II

Explain function of primase and why DNA polymerase I is used predominately in lagging strand in bacteria

(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.

Why do bacterial cells not need telomerase? Why does telomerase have a built-in template?

(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.

1. predict how the mutation rate would be affected if all base pairs had the same shape and degree of stability 2. State which enzymes are specific for nucleotide excision repair and which work in both normal DNA replication and in DNA repair

(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.

telomere legnth prdicts the number of divisions before cells stop dividing

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

biochemical facts

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

What restrictions control how synthesis occurs on both template strands of DNA

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

RNA primers must be present on which strand during DNA synthesis? See Section 15.3 ( page 321) .

Both leading and lagging strands, but spaced differently

What allows DNA polymerases to pick the right deoxyribonuceotides?

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

What kinds of organisms require telomerase? See Section 15.4

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

What would happen if the hings introduced above didnt funtion?

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.

Sliding Clamp

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

What would a strand look like if DNA polymerase I were defective or DNA ligase where defective

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).

Semiconservative replication

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.

5' end

starts on a phosphate phosphate group attached

leading strand

strand of DNA synthesized TOWARD replication fork; aka continuous strand

3' end

sugar strand/ OH tail

adds DNA onto end of chromosomes to prevent it from growing shorter

telemorase

extends repeated sequences in the 5'_. 3- direction to provide room for primase to add RNA primer to lagging-strand template and stop it from shortening

telemorase