General Biology (Ch. 16)
Topoisomerase
Corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands.
Erwin Chargaff
Analyzed the base content of DNA and found that the amount of adenine equaled and amount of thymine and the amount of guanine equals the amount of cytosine.
Single-strand binding proteins
Bind to and stabilize single-stranded DNA.
Define antiparallel and distinguish between the leading strand and the lagging strand.
DNA is composed of 2 antiparallel strands. The leading strand is in the 3'5' direction and continuously synthesized (DNA polymerase synthesizes the copied strand continuously by moving in the complementary 5' to 3' direction) The lagging strand is in the 5'3' direction and is discontinuously synthesized.
Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair.
DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides. • In mismatch repair of DNA, repair enzymes correct errors in base pairing. • DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes. • In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA.
Helicases
Enzymes that untwist the double helix at the replication forks.
Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3' end. Describe the significance of Okazaki fragments.
The lagging strand is synthesized in a series of short fragments called okazaki fragments. Each okazaki fragment is bonded covalently by DNA ligase to the others to create a continuous strand. Each fragment requires a primer. These small fragments are generated by the polymerase making a small 5' to 3' fragment inside the replication bubble as it opens. Then all the little fragments are joined together.
Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of the research of Rosalind Franklin.
They used Rosalind Franklin's experiments with X-ray and came up with the concept of the double helix
Explain what energy source drives the polymerization of DNA.
When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced creates a phosphodiester bond that attaches the remaining phosphate to the growing chain.
DNA Ligase
binds together okazaki fragments
Primer and Primase
creates free 3' ends for polymerase to attach and being to synthesize
Describe the structure of DNA. Explain the base-pairing rule and describe its significance.
• A double-helix with two outer sugar-phosphate backbones, with the nitrogenous bases paired in the molecule's interior. • 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.
Explain the role of DNA polymerases in replication.
• 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.
Alfred Hershey and Martha Chase
• In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2 • To determine this, they designed an experiment showing that only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection. • They concluded that the injected DNA of the phage provides the genetic information.
Describe the process of DNA replication, including the role of the origins of replication and replication forks.
• Replication begins at particular sites called origins of replication, where the two DNA strands are separated, opening up a replication "bubble" • Replication proceeds in both directions from each origin, until the entire molecule is copied. At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating.
Describe the semiconservative model of replication and the significance of the experiments of Matthew Meselson and Franklin Stahl.
• Watson and Crick's semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or "conserved" from the parent molecule) and one newly made strand. • Experiments by Matthew Meselson and Franklin Stahl supported the semiconservative model. • They labeled the nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were labeled with a lighter isotope. • The first replication produced a band of hybrid DNA, eliminating the conservative model. • A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model.