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MOLECULAR GENETICS DNA What is the significance of DNA? Why is it so important? • Because it is universal. It is the genetic material for all forms of life. • It points to a common evolutionary origin of all living things. • Why is it relevant in your life today? The knowledge of DNA have changed our lives drastically. From forensics to the biotechnology industry, in agriculture and in medicine to name just a few areas. Where is DNA and what does it do? • DNA is packed in the chromosomes and the chromosomes are in the nucleus of all eukaryotic cells. What is DNA’s function? DNA’s function is to store and transfer genetic information from one generation to the next. To do this we need mitosis and meiosis so we can copy our own DNA and pass it on. What kind of information is encoded in DNA? • Instructions of how to make proteins. What does DNA look like? • DNA is a nucleic acid. • Nucleic acids are made up of nucleotides. ( remember that a nucleotide consists of three parts: a 5 carbon sugar, a phosphate group and a nitrogen base) DNA looks like a twisted staircase. The handrails or sides are also called its backbone and are made up of sugars and phosphate groups connected to each other. The paired bases made up the rungs of the ladder connecting the two strands. – The structure of DNA • Consists of two nucleotide strands wrapped around each other in a double helix Figure 10.3C Twist •DNA and RNA are polymers of nucleotides – DNA is a nucleic acid • Made of long chains of nucleotide monomers Sugar-phosphate backbone Phosphate group A C Nitrogenous base A Sugar DNA nucleotide C Nitrogenous base (A, G, C, or T) Phosphate group O H3C O T T O P O CH2 O– G C HC O C N N C H O Thymine (T) O C H G H C HC CH H Sugar (deoxyribose) T T DNA nucleotide Figure 10.2A DNA polynucleotide Fig. 16.5 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings – DNA has four kinds of nitrogenous bases • A, T, C, and G A pairs with T and H O H3C H C H N H N C N C C C C H O Thymine (T) Cytosine (C) Pyrimidines Figure 10.2B N H H H C H C N G pairs with C N H O N H O C C N C C N H C N N H N C C N H Adenine (A) Guanine (G) Purines H C N H C C N H H – RNA is also a nucleic acid • But has a slightly different sugar • And has U instead of T Nitrogenous base (A, G, C, or U) O Phosphate group H O O P N C C H O CH2 N H O Uracil (U) O– O C H H C H C C H O Figure 10.2C, D C C OH Sugar (ribose) Key Hydrogen atom Carbon atom Nitrogen atom Oxygen atom Phosphorus atom A little history… • In April 1953, James Watson and Francis Crick – published a model for the structure of deoxyribonucleic acid or DNA. – won the Nobel prize for it • Your genetic material is the DNA you inherited from your parents. • Nucleic acids are unique – direct their own replication. • The resemblance of offspring to their parents – depends on the precise replication of DNA – transmission from one generation to the next. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The Search for Genetic Material • Once Thomas Morgan’s group showed that genes are located on chromosomes, the two constituents of chromosomes - proteins and DNA - were the candidates for the genetic material. • Until the 1940s, abundance and variety of proteins seemed to indicate that proteins were the genetic material. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Early 1900”s everyone “knew” that the genetic material was protein. In 1928 Fred Griffith trying to produce a vaccine against pneumonia made scientist doubt . • Griffith said that protein was not the genetic material because heat denatures proteins and in his experiments heat did not denatured the genetic material • Still nobody knew what was the genetic material • Griffith called this phenomenon transformation, a change in genotype and phenotype due to the assimilation of a foreign substance (now known to be DNA) by a cell. Fig. 16.1 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 1944, Oswald Avery, McCarty and MacLeod announced that the transforming substance was DNA. • Still, many biologists were skeptical. – this reflected a belief that the genes of bacteria could not be similar in composition and function to those humans. – Avery confirmed Griffith discovery and that the genetic material was a nucleotide and not a protein THE STRUCTURE OF THE GENETIC MATERIAL • Experiments showed that DNA is the genetic material – The Hershey-Chase experiment showed that certain viruses reprogram host cells • To produce more viruses by injecting their DNA Head DNA Tail Tail fiber Figure 10.1A What did Hershey and Chase do? • They showed that the genetic material of a virus is DNA. • They separated the protein coat and the DNA of the virus (a phage known as T2) and tagged it with a radioactive isotope and then traced it. The protein coat remained outside and only the DNA when inside the bacteria. • In 1952, Alfred Hershey and Martha Chase showed that DNA was the genetic material of the phage T2.( a phage is a virus that attacks bacteria) • The T2 phage (the virus), consisting almost entirely of DNA and protein, attacks Escherichia coli (E. coli), a common intestinal bacteria of mammals. • This phage can quickly turn an E. coli cell into a T2-producing factory that releases phages when the cell ruptures. Fig. 16.2a Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings – The Hershey-Chase experiment Phage Radioactive protein Bacterium Empty protein shell Radioactivity in liquid Phage DNA DNA Batch 1 Radioactive protein Centrifuge Pellet 1 Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. 2 Agitate in a blender to separate phages outside the bacteria from the cells and their contents. 3 Centrifuge the mixture so bacteria form a pellet at the bottom of the test tube. 4 Measure the radioactivity in the pellet and the liquid. Radioactive DNA Batch 2 Radioactive DNA Centrifuge Pellet Figure 10.1B Radioactivity in pellet Chargaff’s Rules • By 1947, Erwin Chargaff already knew that DNA was a polymer of nucleotides consisting of a nitrogenous base, deoxyribose ( a sugar), and a phosphate group. By 1947 Chargaff had developed rules saying that The bases could be adenine (A), thymine (T), guanine (G), or cytosine (C). Chargaff rule: A always pairs with T and C always pairs with G • In any one species, the four bases are found in characteristic, but not necessarily equal, ratios. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • He found a regular ratio of nucleotide bases which are known as Chargaff’s rules. • The number of adenines was approximately equal to the number of thymines (%T = %A). • The number of guanines was approximately equal to the number of cytosines (%G = %C). – Human DNA is 30.9% adenine, 29.4% thymine, 19.9% guanine and 19.8% cytosine. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings By 1950 DNA was accepted by scientists as the genetic material but nobody knew its structure • Many scientists wanted to be the first to discover it Race for the Prize • By the beginnings of the 1950’s, the race was on to move from the structure of a single DNA strand to the three-dimensional structure of DNA. – Among the scientists working on the problem were Linus Pauling, in California, and Maurice Wilkins and Rosalind Franklin, in London. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The story of DNA :The social nature of science • • • • • • • In 1951 James Watson went to Europe (after completing his PhD) and met Crick. Francis Crick was a graduate student working in hemoglobin in Cambridge, England. They talked about DNA Crick and Watson teamed up to work on the structure of DNA. Watson went to London to hear a lecture by Rosalind Franklin on DNA. She and Maurice Wilkins were authorities on X-ray diffraction and had been working on the DNA structure on the same lab. R.Franklin made observations about her X ray diffraction of DNA. Watson didn’t understand about X-ray crystallography so he didn’t get much out of Franklin’s lecture. Rosalind Franklin was a well know physical chemist because of her previous work on carbon fiber technology. She was invited to King’s College in London to set up an Xray diffraction lab. She was not told of Wilkins interest in her DNA work. Wilkins did not know about Franklin. He treated her as a lab technician or a secretary, attacked her behind her back. Watson and Crick made a model of DNA that was all wrong because they did not have Franklin’s information. Watson believed that the sugar-phosphate backbone was on the inside and the bases sticking out. Franklin knew it was on the inside. The story continues…. • In December 1952 Watson and Crick learned that Linus Pauling was working on DNA structure. They asked Pauling for a copy of his paper and Pauling sent one to Watson. They also got the information from Chargaff about the bases A-t ans C-G. • Wilkins allowed Crick to get Franklin’s information from her lab’s annual report without asking Franklin. He gave Franklin’s X ray pictures to Crick. • They learned all the positions and measurements from Franklin’s picture and build a model in which everything fit except the bases. • Examining Chargaff rules they build an accurate model of DNA in March 1953. • When Watson and Crick wrote their results in a scientific journal Franklin was given no credit • Franklin died in 1958 (breast cancer) without ever knowing her data was used to figure the structure of DNA. • Franklin’s failure was due to her social isolation because Watson and Crick had many contacts in her lab, lots of friends and people supporting and consulting with them. •DNA is a double-stranded helix – James Watson and Francis Crick • Worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin Figure 10.3A, B • Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA. – In this technique, X-rays are diffracted as they passed through aligned fibers of purified DNA. – The diffraction pattern can be used to deduce the threedimensional shape of molecules. • James Watson learned from their research that DNA was helical in shape and he deduced the width of the helix and the spacing of bases. Fig. 16.4 Watson and Crick • James Watson and his colleague Francis Crick began to work on a model of DNA with two strands, the double helix. They decided on a helix shape after seeing Franklin’s X ray. • They build their model to scale to conform to the X ray data. Using molecular models made of wire, they first tried to place the sugar-phosphate chains on the inside.. However, this did not fit the X-ray measurements and other information on the chemistry of DNA. In 1953 Watson and Crick won the Nobel prize for discovering the structure of DNA The Molecule Comes Together • The key breakthrough came when Watson put the sugar-phosphate chain on the outside and the nitrogen bases on the inside of the double helix. – The sugar-phosphate chains of each strand are like the side ropes of a rope ladder. – Pairs of nitrogen bases, one from each strand, form rungs. – The ladder forms a twist every ten bases. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • The nitrogenous bases are paired in specific combinations: adenine with thymine and guanine with cytosine. • Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data. – A purine-purine pair would be too wide and a pyrimidinepyrimidine pairing would be too short. – Only a pyrimidinepurine pairing would produce the 2-nm diameter indicated by the X-ray data. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • In addition, Watson and Crick determined that chemical side groups off the nitrogen bases would form hydrogen bonds, connecting the two strands. – Based on details of their structure, adenine would form two hydrogen bonds only with thymine and guanine would form three hydrogen bonds only with cytosine. – This finding explained Chargaff’s rules. Fig. 16.6 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings – The structure of DNA • Consists of two nucleotide strands wrapped around each other in a double helix Figure 10.3C Twist Fig. 16.5 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Protein synthesis DNA RNA protein What type of chemical bonds hold the DNA molecule together? • The sugar-phosphates are joined by covalent bonds which are strong • The base pairs that form the rungs of the ladder are hydrogen bonds. • Hydrogen bonds are easily broken which is good when the DNA molecule is going to replicate. Replication • When? Replication occurs during the “S” phase of the cell cycle • It requires lots of enzymes • Ex: enzymes unwinds the double helix breaks the hydrogen bonds between the paired bases and other enzymes separate the two strands and add new nucleotides. • The main team of enzymes are the DNA polymerases Form Predicts Function • The specific pairing of nitrogenous bases in DNA was the flash of inspiration that led Watson and Crick to the correct double helix. • The possible mechanism for the next step, the accurate replication of DNA, was clear to Watson and Crick from their double helix model. • In a second paper Watson and Crick published their hypothesis for how DNA replicates. – Essentially, because each strand is complementary to each other, each can form a template when separated. – The order of bases on one strand can be used to add in complementary bases and therefore duplicate the pairs of bases exactly. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings – DNA replication is a complex process • Due in part to the fact that some of the helical DNA molecule must untwist G C A T G C C G A T T A A C G T C G C C A A T A A Figure 10.4B G G T G C G T T G C C G C T A A A A G T T T A C T T A Replication is Relatively Fast and Very Accurate • It takes E. coli less than an hour to copy 5 million base pairs in its chromosome and divide to form two identical daughter cells. • A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few hours. • This process is remarkably accurate, with only one error per billion nucleotides. • More than a dozen enzymes and other proteins participate in DNA replication. Enzymes: Helicase, DNA polymerase and ligase • Helicase: Is the enzyme that untwists the double helix at the replication forks • DNA polymerase: is the enzyme that adds nucleotides to the existing chain. It catalizes the elongation of the new DNA strand. It also does proof-reading to remove mistakes. • Ligase: a linking enzyme. It bonds fragments, like glue DNA REPLICATION • DNA replication depends on base pairing – DNA replication starts with the separation of DNA strands (done by an enzyme) – Then enzymes use each strand as a template to assemble new nucleotides into complementary strands.( DNA polymerase and ligase) A with T C with G A T A T A T A T A T C G C G C G C G C G G C G C G C G C A T A T A T A T T A T A T A T A Parental molecule of DNA Figure 10.4A C A Nucleotides Both parental strands serve as templates Two identical daughter molecules of DNA • When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new complimentary strand. – One at a time, nucleotides line up along the template strand according to the base-pairing rules. – The nucleotides are linked to form new strands. Each strand serves as a template (blueprint) for the synthesis of a new strand • DNA polymerase can only work in one direction so each new molecule is made up of an old and a new strand. • Since DNA is a very long molecule replication occurs simultaneously at many sites called replication forks the enzyme ligase joins them Errors • Errors are made frequently during replication. DNA polymerase may skip a nucleotide or add an extra one or put one in the wrong place. • Very few errors remain because a system of enzymes ( repair nuclease) that detect and repair the errors. • Those errors that remain are called MUTATIONS • Watson and Crick’s model, semiconservative replication, predicts that when a double helix replicates each of the daughter molecules will have one old strand and one newly made strand. • Other competing models, the conservative model and the dispersive model, were also proposed. Fig. 16.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA, eliminating the conservative model. • A second replication produced both light and hybrid DNA, eliminating the dispersive model and supporting the semiconservative model. Fig. 16.9 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings – Each strand of the double helix • Is oriented in the opposite direction 5 end P 3 end HO 5 4 3 2 2 1 A T 1 5 P P C G P P G C P P T OH 3 end Figure 10.5B 3 4 A P 5 end – Using the enzyme DNA polymerase • The cell synthesizes one daughter strand as a continuous piece – The other strand is synthesized as a series of short pieces • Which are then connected by the enzyme DNA ligase DNA polymerase molecule 5 3 3 5 Daughter strand synthesized continuously Parental DNA 3 5 5 3 DNA ligase Figure 10.5C Overall direction of replication Daughter strand synthesized in pieces Protein synthesis DNA RNA protein THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN • The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits • The information constituting an organism’s genotype – Is carried in its sequence of its DNA bases • A particular gene, a linear sequence of many nucleotides – Specifies a polypeptide • Genetic information written in codons is translated into amino acid sequences – The “words” of the DNA “language” • Are triplets of bases called codons – The codons in a gene • Specify the amino acid sequence of a polypeptide DNA molecule Gene 1 Gene 2 Gene 3 DNA strand A A A C C G G C A A A A Transcription U U U G G C C G U U U U RNA Codon Translation Polypeptide Figure 10.7 Amino acid • The genetic code is the Rosetta stone of life – Nearly all organisms • Use exactly the same genetic code Second base U U C UUU Phe UUC UCU UCC UUA UCA UUG Leu CUU C CUC First base CUA CUG A Leu GUA GUG Figure 10.8A UGA Stop A UGG Trp CCU CAU His CAC CGU CGC CAA CAG Gln CGA CGG AAU Asn AAC U AGU Ser AGC C AAA AGA A AGG Arg G U GGU C GGC Gly GGA A CCC CCA CCG ACA ACC Pro Thr AAG GAU GCU GCC Val UAC UGU Cys U UGC C UAA Stop AUA GUC G Ser Tyr UAG Stop ACU ACC GUU UAU G UCG AUU AUC Ile Met or AUG start A GCA GCG GAC Ala Lys Asp GAA GAG Glu GGG G U C Arg A G G – An exercise in translating the genetic code Strand to be transcribed T A C T T C A A A A T C A T G A A G T T T T A G U A G DNA Transcription A U G A A G U U U RNA Start condon Stop condon Translation Figure 10.8B Polypeptide Met Lys Phe • Transcription produces genetic messages in the form of RNA – A close-up view of transcription RNA nucleotides RNA polymerase T C C A A U A T T A C C A T A G G T Direction of transcription Figure 10.9A Newly made RNA Template Strand of DNA – In the nucleus, the DNA helix unzips • And RNA nucleotides line up along one strand of the DNA, following the base pairing rules – As the single-stranded messenger RNA (mRNA) peels away from the gene • The DNA strands rejoin – Transcription of a gene RNA polymerase DNA of gene Promoter DNA Terminator DNA 1 Initiation 2 Elongation 3 Termination Completed RNA Figure 10.9B Area shown In Figure 10.9A Growing RNA RNA polymerase • Eukaryotic RNA is processed before leaving the nucleus – Noncoding segments called introns are spliced out • And a cap and a tail are added to the ends Exon Intron Exon Intron Exon DNA Cap RNA transcript with cap and tail Transcription Addition of cap and tail Introns removed Tail Exons spliced together mRNA Coding sequence Nucleus Cytoplasm Figure 10.10 • Transfer RNA molecules serve as interpreters during translation – Translation • Takes place in the cytoplasm – A ribosome attaches to the mRNA • And translates its message into a specific polypeptide aided by transfer RNAs (tRNAs) Amino acid attachment site Hydrogen bond RNA polynucleotide chain Figure 10.11A Anticodon • Ribosomes build polypeptides – A ribosome consists of two subunits • Each made up of proteins and a kind of RNA called ribosomal RNA tRNA molecules Growing polypeptide Large subunit mRNA Figure 10.12A Small subunit – The subunits of a ribosome • Hold the tRNA and mRNA close together during translation tRNA-binding sites Large subunit Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNAbinding site mRNA Small subunit Codons Figure 10.12B, C • An initiation codon marks the start of an mRNA message Start of genetic message End Figure 10.13A – mRNA, a specific tRNA, and the ribosome subunits • Assemble during initiation Met Met Large ribosomal subunit Initiator tRNA P site U A C A U G U A C A U G Start codon 1 mRNA Figure 10.13B A site Small ribosomal subunit 2 • Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation – Once initiation is complete • Amino acids are added one by one to the first amino acid – Each addition of an amino acid • Occurs in a three-step elongation process Amino acid Polypeptide P site A site Anticodon mRNA Codons 1 Codon recognition mRNA movement Stop codon 2 Peptide bond formation New Peptide bond Figure 10.14 3 Translocation – The mRNA moves a codon at a time • And a tRNA with a complementary anticodon pairs with each codon, adding its amino acid to the peptide chain – Elongation continues • Until a stop codon reaches the ribosome’s A site, terminating translation • Review: The flow of genetic information in the cell is DNARNAprotein – The sequence of codons in DNA, via the sequence of codons • Spells out the primary structure of a polypeptide – Summary of transcription and translation DNA Transcription 1 mRNA is transcribed from a DNA template. mRNA RNA polymerase Amino acid 2 Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. Translation Enzyme ATP tRNA Large ribosomal subunit Initiator tRNA Start Codon mRNA Anticodon 3 Initiation of polypeptide synthesis The mRNA, the first tRNA, and the ribosomal subunits come together. Small ribosomal subunit New peptide bond forming 4 Elongation Growing polypeptide A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time. Codons mRNA Polypeptide 5 Termination The ribosome recognizes a stop codon. The poly-peptide is terminated and released. Figure 10.15 Stop codon • Mutations can change the meaning of genes – Mutations are changes in the DNA base sequence caused by errors in DNA replication or recombination, or by mutagens Normal hemoglobin DNA C T T mRNA A T G U A C mRNA G Figure 10.16A Mutant hemoglobin DNA A A Normal hemoglobin Sickle-cell hemoglobin Glu Val – Substituting, inserting, or deleting nucleotides alters a gene • With varying effects on the organism Normal gene A U G A A G U U U G G C G C A mRNA Met Protein Lys Phe Gly Ala Base substitution A U G A A G U U U A G C G C A Met Lys Phe Ser Ala U Missing Base deletion A U G A A G U U G G C G C A U Figure 10.16B Met Lys Leu Ala His MICROBIAL GENETICS • Viral DNA may become part of the host chromosome – Viruses • Can be regarded as genes packaged in protein – When phage DNA enters a lytic cycle inside a bacterium • It is replicated, transcribed, and translated – The new viral DNA and protein molecules • Then assemble into new phages, which burst from the host cell – In the lysogenic cycle • Phage DNA inserts into the host chromosome and is passed on to generations of daughter cells – Much later • It may initiate phage production The AIDS virus makes DNA on an RNA template – HIV, the AIDS virus • Is a retrovirus Envelope Glycoprotein Protein coat RNA (two identical strands) Reverse transcriptase Figure 10.21A – Inside a cell, HIV uses its RNA as a template for making DNA • To insert into a host chromosome Viral RNA CYTOPLASM 1 RNA strand NUCLEUS Chromosomal DNA 2 Doublestranded DNA 3 Provirus DNA 4 Viral RNA and proteins 5 RNA 6 Figure 10.21B • 10.22 Bacteria can transfer DNA in three ways – Bacteria can transfer genes from cell to cell by one of three processes • Transformation, transduction, or conjugation Mating bridge DNA enters cell Fragment of DNA from another bacterial cell Bacterial chromosome (DNA) Figure 10.22A–C Phage Phage Fragment of DNA from another bacterial cell (former phage host) Sex pili Donor cell (“male”) Recipient cell (“female”) – Once new DNA gets into a bacterial cell • Part of it may then integrate into the recipient’s chromosome Donated DNA Figure 10.22D Recipient cell’s chromosome Crossovers Degraded DNA Recombinant chromosome • Bacterial plasmids can serve as carriers for gene transfer – Plasmids • Are small circular DNA molecules separate from the bacterial chromosome – Plasmids can serve as carriers • For the transfer of genes F factor (plasmid) F factor (integrated) Male (donor) cell Origin of F replication Bacterial chromosome F factor starts replication and transfer of chromosome Male (donor) cell Bacterial chromosome F factor starts replication and transfer Only part of the chromosome transfers Plasmid completes transfer and circularizes Plasmids Recombination can occur Cell now male Figure 10.23A–C Colorized TEM 2,000 Recipient cell