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THE NUCLEIC ACIDS © 2007 Paul Billiet ODWS Day 5 – Nucleic Acids Do Now: Draw a picture of an amino acid. Label all parts. Draw a picture of the condensation reaction between two amino acids forming a peptide bond What influences the folding of protein? 2-3 sentences Homework: Flashcards 26-32. Packet pgs. 15-17. Exit Ticket 1. The complex structure of proteins can be explained in terms of four levels of structure, primary, secondary, tertiary and quaternary. (a) Primary structure involves the sequence of amino acids that are bonded together to form a polypeptide. State the name of the linkage that bonds the amino acids together. (b) Beta pleated sheets are an example of secondary structure. State one other example. (c) Tertiary structure in globular proteins involves the folding of polypeptides. State one type of bond that stabilizes the tertiary structure. 2. Which is not a primary function of protein molecules? A. Hormones B. Energy storage C. Transport D. Structure Proteins classified by function CATALYTIC: enzymes STORAGE: ovalbumen (in eggs), casein (in milk), zein (in maize) TRANSPORT: haemoglobin COMMUNICATION: hormones (eg insulin) and neurotransmitters CONTRACTILE: actin, myosin, dynein (in microtubules) PROTECTIVE: Immunoglobulin, fibrinogen, blood clotting factors TOXINS: snake venom STRUCTURAL: cell membrane proteins, keratin (hair), collagen Friedrich Miescher in 1869 Isolated what he called nuclein from the nuclei of pus cells Nuclein was shown to have acidic properties, hence it became called nucleic acid © 2007 Paul Billiet ODWS Two types of nucleic acid are found Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) © 2007 Paul Billiet ODWS The distribution of nucleic acids in the eukaryotic cell DNA is found in the nucleus with small amounts in mitochondria and chloroplasts RNA is found throughout the cell Ribosomes, tRNA, mRNA, etc. © 2007 Paul Billiet ODWS DNA as genetic material: The circumstantial evidence 1. 2. 3. 4. Present in all cells and virtually restricted to the nucleus The amount of DNA in somatic cells (body cells) of any given species is constant (like the number of chromosomes) The DNA content of gametes (sex cells) is half that of somatic cells. In cases of polyploidy (multiple sets of chromosomes) the DNA content increases by a proportional factor The mutagenic effect of UV light peaks at 253.7nm. The peak for the absorption of UV light by DNA © 2007 Paul Billiet ODWS Introduction The amino acid sequence of a polypeptide is programmed by a gene. A gene consists of regions of DNA, a polymer of nucleic acids. DNA (and their genes) is passed by the mechanisms of inheritance. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 1. Nucleic acids store and transmit hereditary information There are two types of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). DNA provides direction for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Organisms Each inherit DNA from their parents. DNA molecule is very long and usually consists of hundreds to thousands of genes. When a cell reproduces itself by dividing, its DNA is copied and passed to the next generation of cells. While DNA has the information for all the cell’s activities, it is not directly involved in the day to day operations of the cell. Proteins are responsible for implementing the instructions contained in DNA. Each gene along a DNA molecule directs the synthesis of a specific type of messenger RNA molecule (mRNA). The mRNA interacts with the protein-synthesizing machinery to direct the ordering of amino acids in a polypeptide. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The flow of genetic information is from DNA -> RNA -> protein. Protein synthesis occurs in cellular structures called ribosomes. In eukaryotes, DNA is located in the nucleus, but most ribosomes are in the cytoplasm with mRNA as an intermediary. Fig. 5.28 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 2. A nucleic acid strand is a polymer of nucleotides Nucleic acids are polymers of monomers called nucleotides. Each nucleotide consists of three parts: a nitrogen base, a pentose sugar, and a phosphate group. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.29 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Mnemonics CUT the Py(rimidines) (pie is a circle) Many years AGo, it was important 2 get PUR(ine) water NUCLEIC ACID STRUCTURE Nucleic acids are polynucleotides Their building blocks are nucleotides © 2007 Paul Billiet ODWS NUCLEOTIDE STRUCTURE PHOSPATE SUGAR Ribose or Deoxyribose BASE PURINES Adenine (A) Cytocine (C) Guanine(G) Thymine (T) Uracil (U) NUCLEOTIDE © 2007 Paul Billiet ODWS PYRIMIDINES Ribose is a pentose C5 O C1 C4 C3 © 2007 Paul Billiet ODWS C2 Spot the difference DEOXYRIBOSE RIBOSE CH2OH O C H H H C OH © 2007 Paul Billiet ODWS OH CH2OH C C H H OH O C H H C C C OH OH H H Nucleic Acids The subunits of Nucleic Acids are called: Nucleotides These are small molecules that are made out of THREE even smaller molecules: 5 Carbon Sugar Phosphate Group Nitrogenous Base 5 Carbon Sugar Phosphate Group Nitogenous Base Nucleic Acids Nitrogenous Bases A nucleotide can have one of five different bases attached: Adenine Thymine Guanine Cytosine Uracil The nitrogen bases, rings of carbon and nitrogen, come in two types: purines and pyrimidines. Pyrimidines have a single six-membered ring. The three different pyrimidines, cytosine (C), thymine (T), and uracil (U) differ in atoms attached to the ring. Purine have a six-membered ring joined to a fivemembered ring. The two purines are adenine (A) and guanine (G). Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The pentose joined to the nitrogen base is ribose in nucleotides of RNA and deoxyribose in DNA. The only difference between the sugars is the lack of an oxygen atom on carbon two in deoxyribose. The combination of a pentose and nucleic acid is a nucleoside. The addition of a phosphate group creates a nucleoside monophosphate or nucleotide. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Polynucleotides are synthesized by connecting the sugars of one nucleotide to the phosphate of the next with a phosphodiester link. This creates a repeating backbone of sugarphosphate units with the nitrogen bases as appendages. The sequence of nitrogen bases along a DNA or mRNA polymer is unique for each gene. Genes are normally hundreds to thousands of nucleotides long. The number of possible combinations of the four DNA bases is limitless. The linear order of bases in a gene specifies the order of amino acids - the primary structure of a protein. The primary structure in turn determines threedimensional conformation and function. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Nucleic Acids Complementary Base Pairing IN DNA there are FOUR Bases. Because DNA is double stranded the nitrogenous bases pair with each other. Adenine Pairs with Thymine Guanine Pairs with Cytosine IN RNA there are FOUR Bases Because RNA is made from DNA it also goes through base pairing with other bases Adenine Pairs with Uracil Guanine Pairs with Cytosine Nucleic Acids Another name for a Nucleic Acid is a polynucleotide. Examples of Polynucleotides in the cell DNA and RNA Characteristic DNA RNA Type of Sugar Deoxyribose Ribose Nitrogenous Bases Adenine, Thymine, Guanine, Cytosine Adenine, Uracil, Guanine , Cytosine Number of Strands 2 1 Location in the Cell Nucleus Cytoplasm Nucleic Acids RN A DN A THE SUGAR-PHOSPHATE BACKBONE The nucleotides are all orientated in the same direction The phosphate group joins the 3rd Carbon of one sugar to the 5th Carbon of the next in line. P P P P P P © 2007 Paul Billiet ODWS P G ADDING IN THE BASES P C The bases are attached to the 1st Carbon Their order is important It determines the genetic information of the molecule P C P A P T P © 2007 Paul Billiet ODWS T DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDE The sister strands of the DNA molecule run in opposite directions (antiparallel) They are joined by the bases Each base is paired with a specific partner: A is always paired with T G is always paired with C Purine with Pyrimidine This the sister strands are complementary but not identical The bases are joined by hydrogen bonds, individually weak but collectively strong © 2007 Paul Billiet ODWS Hydrogen bonds P DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDE G C P P C G P P A with T….TWO G with C….THREE C G P P A T P P T A P P © 2007 Paul Billiet ODWS T A P Erwin Chargaff’s Data (1950-51) Wilkins & Franklin (1952): X-ray crystallography © Norman Collection on the History of Molecular Biology in Novato, CA Purines & Pyrimidines Adenine Guanine © 2007 Paul Billiet ODWS Thymine Cytosine Watson & Crick Base pairing © 2007 Paul Billiet ODWS • Pairs pairs are held together by hydrogen bonds • The two strings of DNA have to run anti-parallel in order to line up the pairs Cytosine Guanine Thymine Adenine The Double Helix (1953) © Dr Kalju Kahn USBC Chemistry and Biochemistry Public Domain image 3. Inheritance is based on replication of the DNA double helix An RNA molecule is single polynucleotide chain. DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a double helix. The double helix was first proposed as the structure of DNA in 1953 by James Watson and Francis Crick. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The sugar-phosphate backbones of the two polynucleotides are on the outside of the helix. Pairs of nitrogenous bases, one from each strand, connect the polynucleotide chains with hydrogen bonds. Most DNA molecules have thousands to millions of base pairs. Fig. 5.30 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Because of their shapes, only some bases are compatible with each other. Adenine (A) always pairs with thymine (T) and guanine (G) with cytosine (C). With these base-pairing rules, if we know the sequence of bases on one strand, we know the sequence on the opposite strand. The two strands are complementary. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings During preparations for cell division each of the strands serves as a template to order nucleotides into a new complementary strand. This results in two identical copies of the original double-stranded DNA molecule. The copies are then distributed to the daughter cells. This mechanism ensures that the genetic information is transmitted whenever a cell reproduces. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Quick Check – Hands Up! Which substance is a base found in RNA? A. Ribose B. Thymine C. Adenosine D. Uracil Quick Check – Hands Up! Which base is connected to its complementary base in a base pair by three hydrogen bonds? A. Uracil B. Thymine C. Guanine D. Adenine Quick Check – Hands Up! Which molecule is found in both DNA and RNA? A. Ribose B. Uracil C. Phosphate D. Amino acid Pair Share and Write – 2 Minutes State the type of bonds that (i) connect base pairs in a DNA molecule. (1) (ii) link DNA nucleotides into a single strand. (1) Think Aloud (b) Distinguish between DNA and RNA nucleotides by giving two differences in the chemical structure of the molecules. (2) 4. We can use DNA and proteins as tape measures of evolution Genes (DNA) and their products (proteins) document the hereditary background of an organism. Because DNA molecules are passed from parents to offspring, siblings have greater similarity than do unrelated individuals of the same species. This argument can be extended to develop a molecular genealogy between species. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Two species that appear to be closely-related based on fossil and molecular evidence should also be more similar in DNA and protein sequences than are more distantly related species. In fact, the sequence of amino acids in hemoglobin molecules differ by only one amino acid between humans and gorilla. More distantly related species have more differences. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings CHAPTER 16 THE MOLECULE BASIS OF INHERITANCE Section B: DNA Replication and Repair Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Introduction 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. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 1. During DNA replication, base pairing enables existing DNA strands to serve as templates for new strands 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 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. Fig. 16.7 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 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. Fig. 16.8 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Experiments in the late 1950s by Matthew Meselson and Franklin Stahl supported the semiconservative model, proposed by Watson and Crick, over the other two models. In their experiments, they labeled the nucleotides of the old strands with a heavy isotope of nitrogen (15N) while any new nucleotides would be indicated by a lighter isotope (14N). Replicated strands could be separated by density in a centrifuge. Each model: the semi-conservative model, the conservative model, and the dispersive model, made specific predictions on the density of replicated DNA strands. 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 2. A large team of enzymes and other proteins carries out DNA replication It takes E. coli less than an hour to copy each of the 5 million base pairs in its single 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. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The replication of a DNA molecule begins at special sites, origins of replication. In bacteria, this is a single specific sequence of nucleotides that is recognized by the replication enzymes. These enzymes separate the strands, forming a replication “bubble”. Replication proceeds in both directions until the entire molecule is copied. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings In eukaryotes, there may be hundreds or thousands of origin sites per chromosome. At the origin sites, the DNA strands separate forming a replication “bubble” with replication forks at each end. The replication bubbles elongate as the DNA is replicated and eventually fuse. Fig. 16.10 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings DNA polymerases catalyze the elongation of new DNA at a replication fork. As nucleotides align with complementary bases along the template strand, they are added to the growing end of the new strand by the polymerase. The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells. The raw nucleotides are nucleoside triphosphates. Each has a nitrogen base, deoxyribose, and a triphosphate tail. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings As each nucleotide is added, the last two phosphate groups are hydrolyzed to form pyrophosphate. Fig. 16.11 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The strands in the double helix are antiparallel. The sugar-phosphate backbones run in opposite directions. Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose. The 5’ -> 3’ direction of one strand runs counter to the 3’ -> 5’ direction of the other strand. Fig. 16.12 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand. A new DNA strand can only elongate in the 5’->3’ direction. This creates a problem at the replication fork because one parental strand is oriented 3’->5’ into the fork, while the other antiparallel parental strand is oriented 5’->3’ into the fork. At the replication fork, one parental strand (3’-> 5’ into the fork), the leading strand, can be used by polymerases as a template for a continuous complimentary strand. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The other parental strand (5’->3’ into the fork), the lagging strand, is copied away from the fork in short segments (Okazaki fragments). Okazaki fragments, each about 100-200 nucleotides, are joined by DNA ligase to form the sugar-phosphate backbone of a single DNA strand. Fig. 16.13 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings DNA polymerases cannot initiate synthesis of a polynucleotide because they can only add nucleotides to the end of an existing chain that is base-paired with the template strand. To start a new chain requires a primer, a short segment of RNA. The primer is about 10 nucleotides long in eukaryotes. Primase, an RNA polymerase, links ribonucleotides that are complementary to the DNA template into the primer. RNA polymerases can start an RNA chain from a single template strand. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings After formation of the primer, DNA polymerases can add deoxyribonucleotides to the 3’ end of the ribonucleotide chain. Another DNA polymerase later replaces the primer ribonucleotides with deoxyribonucleotides complimentary to the template. Fig. 16.14 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Returning to the original problem at the replication fork, the leading strand requires the formation of only a single primer as the replication fork continues to separate. The lagging strand requires formation of a new primer as the replication fork progresses. After the primer is formed, DNA polymerase can add new nucleotides away from the fork until it runs into the previous Okazaki fragment. The primers are converted to DNA before DNA ligase joins the fragments together. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings In addition to primase, DNA polymerases, and DNA ligases, several other proteins have prominent roles in DNA synthesis. A helicase untwists and separates the template DNA strands at the replication fork. Single-strand binding proteins keep the unpaired template strands apart during replication. Fig. 16.15 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings To summarize, at the replication fork, the leading stand is copied continuously into the fork from a single primer. The lagging strand is copied away from the fork in short segments, each requiring a new primer. Fig. 16.16 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Quick Check – Hands Up! What are Okazaki fragments? A. Short lengths of RNA primase attached to the DNA during replication B. Short sections of DNA formed during DNA replication C. Nucleotides added by DNA polymerase I in the same direction as the replication fork D. Sections of RNA removed by DNA polymerase III and replaced with DNA Quick Check – Hands Up! Which enzyme catalyzes the elongation of the leading strand? [Source: image from W K Purves, et al., (2003) Life: The Science of Biology, 4, Sinauer Associates (www.sinauer.com) and W H Freeman (www.whfreeman.com)] A. B. C. D. RNA polymerase Helicase DNA polymerase Ligase