Fig. 16-1

DNA is the genetic material Since Ancient Greece, people have speculated about how we inherit traits from our parents Early in the 20th century, one of the biggest questions in biology was this: What kinds of molecules determine what traits we get from our parents, and how? Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig (a) Rosalind Franklin (b) Franklin’s X-ray diffraction photograph of DNA

Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA was a double helix The X-ray images also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig. 16-7a Hydrogen bond 3 end 5 end 3.4 nm 0.34 nm 3 end 5 end (b) Partial chemical structure(a) Key features of DNA structure 1 nm

Fig. 16-7b (c) Space-filling model

Watson and Crick built models of a double helix to conform to the X-rays and chemistry of DNA Franklin had concluded that there were two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Watson and Crick reasoned that the pairing was more specific, dictated by the base structures They determined that adenine (A) paired only with thymine (T), and guanine (G) paired only with cytosine (C) The Watson-Crick model explains Chargaff’s rules: in any organism the amount of A = T, and the amount of G = C Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Summary DNA is made of antiparellel strands  One runs 5’ to 3’, the other 3’ to 5’  DNA can only be built from 5’ to 3’ (we’ll get into this in a few slides) DNA base pairs:  A with T  C with G DNA structure, like a ladder  Sugar phosphate backbone (rails of ladder)  Nitrogenous bases are the steps of the ladder

The Basic Principle: Base Pairing to a Template Strand Since the two strands of DNA are complementary (one kind of base only pairs with one other kind of base), each strand acts as a template for building a new strand in replication In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig A T G C TA TA G C (a) Parent molecule

Fig A T G C TA TA G C A T G C T A T A G C (a) Parent molecule (b) Separation of strands

Fig A T G C TA TA G C (a) Parent molecule AT GC T A T A GC (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand (b) Separation of strands A T G C TA TA G C A T G C T A T A G C What is the sequence of nitrogenous bases that is complementary to the strand “AAGTAC”?

DNA Replication: A Closer Look The copying of DNA is remarkable in its speed and accuracy More than a dozen enzymes and other proteins participate in DNA replication Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Getting Started Replication begins at special sites called origins of replication, where the two DNA strands are separated, opening up a replication “bubble” A eukaryotic chromosome may have hundreds or even thousands of origins of replication; a prokaryotic chromosome has only one Replication proceeds in both directions from each origin, until the entire molecule is copied Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig b 0.25 µm Origin of replicationDouble-stranded DNA molecule Parental (template) strand Daughter (new) strand Bubble Replication fork Two daughter DNA molecules (b) Origins of replication in eukaryotes Eukaryotic DNA replication

At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating Helicases are enzymes that untwist the double helix at the replication forks Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template  The DNA would naturally want to twist in on itself, and this protein prohibits that Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig Topoisomerase Helicase Primase Single-strand binding proteins RNA primer

DNA polymerases cannot initiate (begin) synthesis of a polynucleotide; they can only add nucleotides to the 3 end of another nucleotide.  In other words, they can’t start from scratch, so they need a PRIMER The initial nucleotide strand is a short RNA primer Have you ever painted something with primer? What is it used for? Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

An enzyme called primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand Since it is made of RNA, the primer has U’s instead of T’s Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Synthesizing a New DNA Strand Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork Most DNA polymerases require a primer and a DNA template strand The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells – that’s fast! Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Antiparallel Elongation The antiparallel structure of the double helix (two strands oriented in opposite directions) affects replication DNA polymerases add nucleotides only to the free 3  end of a growing strand; therefore, a new DNA strand can elongate only in the 5  to  3  direction Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig a Overview Leading strand Lagging strand Origin of replication Primer Overall directions of replication

Fig b Origin of replication RNA primer “Sliding clamp” DNA pol III Parental DNA

To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Animation: Lagging Strand Animation: Lagging Strand

Fig a Overview Origin of replication Leading strand Lagging strand Overall directions of replication 1 2

Fig b1 Template strand

Fig b2 Template strand RNA primer DNA Polymerase III Adds nucleotides to the primer, forming an Okazaki fragment

Fig b3 Template strand RNA primer Okazaki fragment DNA Polymerase III Adds nucleotides to the primer, forming an Okazaki fragment

Fig b4 Template strand RNA primer Okazaki fragment DNA Polymerase III Adds nucleotides to the primer, forming an Okazaki fragment

Fig b5 Template strand RNA primer Okazaki fragment DNA Polymerase III DNA Polymerase I Replaces the primer with DNA, adding to the 3’ end of the fragment Adds nucleotides to the primer, forming an Okazaki fragment

Fig b6 Template strand RNA primer Okazaki fragment Overall direction of replication DNA Polymerase III Adds nucleotides to the primer, forming an Okazaki fragment DNA Polymerase I Replaces the primer with DNA, adding to the 3’ end of the fragment DNA ligase Binds the fragments together

Table 16-1

Fig Overview Origin of replication Leading strand Lagging strand Overall directions of replication Leading strand Lagging strand Helicase Parental DNA DNA pol III PrimerPrimase DNA ligase DNA pol III DNA pol I Single-strand binding protein

Mutations Sometimes, during DNA replication, the wrong nucleotide is attached (an A to a G, or a T to a C). Sometimes a nucleotide fails to attach, and the new strand is missing a letter. When the new strand has different letters than the parent strand that was attached in the same place, we call that a mutation. Mutations change the instructions that DNA gives for making proteins. Sometimes the new protein works better, but usually it works worse.

What are mutations? Parent DNA strands: 5’ GTTAGCAT 3’ 3’ CAATCGTA 5’ Normal replicated DNA strand: 5’ GTTAGCAT 3’ 3’ CAATCGTA 5’ Mutated replicated DNA strands: 5’ GTTAACAT 3’5’ GTTAGGCAT 3’ 3’ CAATTATA 5’ 3’ CAATCCGTA 5’

Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides In mismatch repair of DNA, repair enzymes correct errors in base pairing (e.g. if C is paired with A) DNA can be damaged by chemicals, radioactive emissions, X-rays, UV light, and certain molecules (in cigarette smoke for example) In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig Nuclease DNA polymerase DNA ligase

What might happen if you had a mutation in the part of your DNA that tells your ribosomes how to make DNA repair enzymes or nuclease?

Replicating the Ends of DNA Molecules Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes After replication, the primers fall off and there is no way to complete the 5’ end of the daughter strand, so it becomes shorter. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Fig Ends of parental DNA strands Leading strand Lagging strand Last fragment Previous fragment Parental strand RNA primer Removal of primers and replacement with DNA where a 3 end is available Second round of replication New leading strand New lagging strand Further rounds of replication Shorter and shorter daughter molecules

Eukaryotic chromosomal DNA molecules have at their ends repetitive, noncoding nucleotide sequences called telomeres (TTAGGGTTAGGGTTAGGG repeated) When the DNA shortens, it is the repetitive telomere part that gets shorter, not the important genes Many scientists are researching telomeres and how the length of the telomere is related to aging and cancer Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Once the chromosome has divided enough times that there is no telomere left on the end, there are problems during mitosis that lead to apoptosis (programmed cell death). If cells with no telomeres did not die, you would lose important genes as the chromosomes got shorter and shorter, and your chromosomes would start to stick together.

Fig µm

If chromosomes of gamete cells (eggs and sperm) became shorter after every cell division, important genes would eventually be missing from the gametes they produce An enzyme called telomerase catalyzes the lengthening of telomeres in gametes and other cells (like embryonic stem cells, hair cells, etc.) that need to divide many times. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

The shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions. (REMEMBER: every time your cell replicates its DNA and divides, there is a risk of mutations) There is evidence of telomerase activity in cancer cells, which may allow cancer cells to continue dividing forever without losing their telomeres. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Your genome is like a cookbook All of your cells contain the whole genome (the entire cookbook). Your genome contains genes (recipes) for all of the proteins your body knows how to make: histones, DNA polymerases, other enzymes, ALL of them. Even though all the cells have the whole cookbook, each cell does not make all the recipes all the time. Signals from inside and outside the cell can turn the recipes on and off, so your cell only makes the proteins it needs

So… a blood cell turns different genes on (makes different recipes) than a muscle cell We’re making the recipe for hemoglobin right now! (our hemoglobin genes are turned on right now) We’re making the recipe for ATP synthase right now! (our ATP synthase genes are turned on right now)

ALL of your cells have all the genes, but they don’t all use them. For example, all your cells have the gene (recipe) for making telomerase, but it’s turned off in most of them. All your cells have the genes that cause apoptosis (programmed cell death), but they’re turned off until the cell is damaged or loses too big a section of its telomeres.