Class Notes (807,339)
Canada (492,708)
Biology (6,676)
Lecture 12

Biology 1202B Lecture 12: DNA Structure, Replication, and Organization

10 Pages
Unlock Document

Western University
Biology 1202B
Patrick Mc Donald

Chapter 12: DNA Structure, Replication, and Organization Chapter Introduction • DNA damage and contamination • Double helix of DNA is subject to breakages • Inappropriate cross-linking • Chemical modification of individual bases • Living cells can prevent or repair most DNA damage • Post-mortem degradation can be extensive • Cold temperatures preserve aDNA well (ancient DNA) • Miescher: Nuclein - Deoxyribonucleic acid, DNA • 1952: Scientists recognize that the hereditary molecule was DNA • 3-D Model of DNA: Watson, Crick - Understand key processes in cells for the first time in terms of the structure and interaction of molecules 12.1 Establishing DNA as the Hereditary Molecule • Because there are 20 amino acids and only 4 bases, there is more information in a string of amino acids than in a string of nucleotides of the same length • Many scientists believed that proteins were the most likely candidates for the hereditary molecules because of the intensive information for coding (20 types of amino acids) - More than nucleic acids (4 different nitrogenous bases) 12.1a Experiments Began When Griffith Found a Substance That Could Genetically Transform Pneumonia Bacteria • S - Smooth strain - Polysaccharide capsule surrounding each cell and forms colonies that appear smooth and glossy • S strain into mice - Virulent (highly infective, pathogenic) - Caused pneumonia and killed the mice in a day or two • R - Rough strain - No polysaccharide capsule and forms colonies with a non-shiny, rough appearance • R stain into mice - avirulent (not infective, nonpathogenic) - Mice lived • S strain was the capsule responsible for virulence • Molecules released when S cells were killed could change living nonvirulent R cells genetically to the virulent S form Transforming principle and the process of genetic change transformation - The conversion of R • bacteria to S bacteria • Injected living R bacteria along with health-killed S bacteria 12.1b Avery and His Coworkers Identified DNA as the Molecule That Transforms Avirulent Rough Streptococcus to the Virulent Smooth Form • Avery, Macleod, McCarty - Experiment to identify chemical nature of transforming principle • Change the avirulent rough form of streptococcus bacteria into the infective smooth form • Heat to kill virulent S bacteria and then treated the macromolecules extracted from the cells with the enzymes that break down each of the three main candidate molecules for the hereditary material - Protein, DNA, RNA • Destroyed DNA - No transformation occurred 12.1c Hershey and Chase Found the Final Evidence Establishing DNA as the Hereditary Molecule • Hershey and Chase studied the infection of the bacterium Escherichia coli by bacteriophage T2 • Escherichia coli - Normally found in intestines of mammals • Bacteriophages (phages): A virus that infects bacteria • Virus: An infectious agent that contains either DNA or RNA surrounded by a protein coat - Cannot reproduce except in a host cell • Virus infects cell - It can use the cell's resources to produce more virus particles • Phage replication cycle (lytic cycle) begins when a phage attaches to the surface of a bacterium • Infected cells begin producing progeny phages • T2 phage that Hershey and Chase studied consists of only a core of DNA surrounded by proteins - Most viruses are not much more than DNA or RNA surrounded by a protein coat • Two batches of phages - Added T2 to E. coli growing in the presence of either the radioactive isotope of sulfur (35S) or the radioactive isotope of phosphorus (32P) • Progeny phages produced in the S35 had labelled proteins and unlabelled DNA because sulfur is a component of proteins but not of DNA • Phages produced in 32P had labelled DNA and unlabelled proteins because phosphorus is a component of DNA but not of proteins • Only the protein will be labelled with 35S and only the DNA will be labelled with 32P • Infected separate cultures of E. coli with two types of labelled phages • Mixed bacteria in a blender • Infected bacteria with phages that contained labelled protein coats - no radioactivity • Radioactivity: The giving off of particles of matter and energy by decaying nuclei • The genetic material of the phage was DNA not protein • Established that DNA, not proteins, carries genetic information • Transformation: The conversion of the hereditary type of a cell by the uptake of DNA released by the breakdown of another cell 12.2 DNA Structure • Watson and Crick discovered the structure of DNA 12.2a Watson and Crick Brought Together Information from Several Sources to Work Out DNA Structure • Base pairing rules: A-T and G-C • DNA contains 4 different nucleotides • Each nucleotide consists of: o 5-carbon sugar deoxyribose o A phosphate group o One of 4 nitrogenous bases: Adenine (A), guanine (G), thymine (T), and cytosine C o Adenine and Guanine are purines o Thymine and cytosine are pyrimidines o Chargaff rule - Number of purines equals the number of pyrimidines - The amount of adenine equals the amount of thymine - The amount of guanine equals the amount of cytosine • DNA contains nucleotides joined to form a polynucleotide chain • Deoxyribose sugars linked by phosphate groups in an alternating sugar-phosphate-sugar- phosphate pattern, forming a sugar-phosphate backbone • Sugar-phosphate backbone: Structure in a polynucleotide chain that is formed when deoxyribose sugars are linked by phosphate groups in an alternating sugar-phosphate-sugar-phosphate pattern • Each phosphate group = "bridge" between the 3' carbon of one sugar and the 5' carbon of the next sugar • Entire linkage, including the bridging phosphate group = Phosphodiester bond • Phosphodiester bond: The linkage of nucleotides in polynucleotide chains by a bridging phosphate group between the '5 carbon of one sugar and the 3' carbon of the next sugar in line • The two ends of the polynucleotide chain of DNA are not the same - they have polarity o At one end, a phosphate group is bound to the 5' carbon of a deoxyribose sugar o At the other end, a hydroxyl group is bonded to the 3' carbon of the deoxyribose sugar o The two ends are called the 5' end and the 3' end o Hydroxyl group: Group consisting of an oxygen atom linked to a hydrogen atom on one side and to a carbon chain on the other side • Watson and Crick used research data of others in their analysis with work using x-ray diffraction • X-ray diffraction: Method for deducting the position of atoms in a molecule • The X-shaped pattern of spots (dashed lines)was correctly interpreted by Franklin to indicate the DNA has a helical structure similar to a spiral staircase 12.2b The New Model Proposed That Two Polynucleotide Chains Wind into a DNA Double Helix • Watson and Crick took the analysis of Wilkin's and Franklin's X-ray data and Chargaff's chemical analysis and proposed the famous double-helix model for DNA • The 2 polynucleotide chains of the double helix are antiparallel - Have opposite polarity in that they run in opposite directions • Double-helix model: Model of DNA consisting of two complementary sugar-phosphate backbones • 2 sugar-phosphate backbones are separated by a regular distance o Bases extend to fill this central space o Purine and pyrimidine pair are exactly wide enough to fill the space between the backbone chains o Complementary base-pairing: Feature of DNA in which the specific purine-pyrimidine base pairs A-T (adenine-thymine) and G-C (guanine-cytosine) occur to bridge the two sugar- phosphate backbones o Antiparallel: Refers to strands of DNA that run in opposite directions • DNA sequence preserved by covalent bonds between the molecules in a DNA double helix 12.3 DNA Replication • Complementary base-pairing explains how DNA replicates • The semi-conservative model meaning that one of the strands is new while the other (which served as template) is old • Semiconservative Replication: The process of DNA replication in which the two parental strands separate and each serves as a template for the synthesis of new progeny double-stranded DNA molecules 12.3a Meselson and Stahl Showed That DNA Replication is Semiconservative • Meselson and Stahl distinguished parental DNA molecules from newly synthesized DNA • Used nonradioactive "heavy" nitrogen isotope to tag the parental DNA Heavy isotope - N-15, has one more neutron in its nucleus than the normal N-14 isotope • • Results were compatible with only the semiconservative replication model (shown in diagram -->) 12.3b DNA Polymerases are the Primary Enzymes of DNA Replication • During replication - Complementary polynucleotide chains are assembled from individual deoxyribonucleotides by enzymes known as DNA polymerases • DNA polymerases: An enzyme that assembles complementary nucleotide chains during replication • More than one kind of DNA polymerase is required for DNA replication in all cells • Deoxyribonucleoside triphosphates are the substrates for the polymerization reaction catalyzed by DNA polymerases • Nucleoside triphosphate = nitrogenous base linked to a sugar - in turn linked to a chain of three phosphate groups • Ex. Nucleoside triphosphate - ATP produced in cellular respiration o Sugar is ribose, making ATP a ribonucleoside triphosphate o DNA replication deoxyribonucleoside triphosphates have sugar deoxyribose rather than the sugar ribose • 4 different deoxyribonuleoside triphosphates are used for DNA replication • Each DNA strand has two distinct ends: o The 5' end has an exposed phosphate group attached to the 5' carbon of the sugar o The 3' end has an exposed hydroxyl group attached to the 3' carbon of the sugar o Antiparallel nature - The 5' end of one strand is opposite the 3' end of the other o DNA polymerase can add a nucleotide ONLY to the 3' end of an existing nucleotide chain o 3' -OH group is always exposed at its "newest" end; the "oldest" end of the new chain has an exposed 5' phosphate o DNA polymerases are therefore said to assemble nucleotide chains in the 5' to 3' direction o The template strand is "read" in the 3' to 5' direction • Polymerases share a shape that resemble a partially closed human right hand in which the template DNA lies over the "palm" in a groove formed by the "fingers" and "thumb" • Palm domain is related among the polymerases of bacteria, archaea, and eukaryotes • The finger and thumb domains are difference sequences in each of these three types of organisms • Sliding DNA clamp: A protein that encircles the DNA and binds to the DNA polymerase to tether the enzyme to the template, thereby making replication more efficient o Without it the enzyme would detach from the template after only a few dozen polymerizations • Key molecular events of DNA replication: o The two strands of the DNA molecule unwind for replication to occur o DNA polymerase can add nucleotides only to an existing chain o The overall direction of new synthesis is in the 5' to 3' direction, which is a direction antiparallel to that of the template strand o Nucleotides enter into a newly synthesized chain according to the A-T and G-C complementary base-pairing rules 12.3c Helicases Unwind DNA for New DNA Synthesis, and Other Proteins Stabilize the DNA at the Replication Fork • Unwinding of the DNA for replication occurs at a small, specific sequence in the bacterial chromosome known as the origin of replication • Origin of Replication: A specific region at which replication of a bacterial chromosome commences • Specific proteins bind and promote the binding of DNA helicase DNA helicase: An enzyme that catalyzes the unwinding of DNA template strands • • Unwinds the DNA strands and the unwinding produces a Y-shaped structure • Replication fork: The region of DNA synthesis where the parental strands separate and two new daughter strands elongate • Consists of the two unwound template strands transitioning to double-helical DNA • Single-stranded binding proteins coat the exposed single-stranded DNA segments • Stabilize the DNA and keep the two strands from pairing back together • SSBs: Protein that coats single-stranded segments of DNA, stabilizing the DNA for the replication process • In the cell, the twisting of DNA during replication is relieved by topoisomerase • Topoisomerase: An enzyme that relieves the over twisting and strain of DNA ahead of the replication fork o Cuts the DNA ahead of the replication fork, turns the DNA on one side of the break in the opposite direction of the twisting force, and rejoins the two strands 12.3d RNA Primers Provide the Starting Point for DNA Polymerase to Begin Synthesizing a New DNA Chain • Primer: A short nucleotide chain made of RNA that is laid down as the first series of nucleotides in a new DNA strand or made of DNA for use in the polymerase chain reaction (pCR) o Allows a new strand of DNA to begin when there is no existing strand in place o Primer is synthesized by the enzyme primase o Primase: An enzyme that assembles the primer for a new DNA strand during DNA replication o Primase leaves the template and DNA polymerase takes over o Extending RNA primer with DNA nucleotides as it synthesizes the new DNA chain o RNA primers are removed and replaced with DNA later in replication 12.3e One New DNA Strand is Synthesized Continuously; the Other, Discontinuously • DNA polymerases synthesize a new DNA strand on a template strand in the 5' -> 3' direction • Top template strand - new DNA is synthesized continuously in the direction of unwinding of the double helix • Bottom template strand runs in the opposite direction - DNA polymerase has to copy it in the direction opposite to the unwinding direction • The new DNA is polymerised in the direction opposite to the unwinding by the polymerases making this strand in short lengths that are synthesized in the direction opposite to that of DNA unwinding • Discontinuous replication: Replication in which a DNA strand is formed in short lengths that are synthesized in the direction opposite to DNA unwinding • Short lengths produced by discontinuous replication are covalently linked into a single continuous polynucleotide chain • Short lengths = Okazaki fragments: Relatively short segments of DNA synthesized on the lagging strand at a replication fork • New strand synthesized in the direction of DNA unwinding: Leading strand: A DNA strand assembled in the direction of DNA unwinding - Template for that strand is the leading strand template: The "old" DNA used as a template for synthesis of "new"
More Less

Related notes for Biology 1202B

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.