The Structure and Function of DNA Chapter 10 The Structure and Function of DNA Laura Coronado Bio 10 Chapter 10

Biology and Society: Tracking a Killer The influenza virus is one of the deadliest pathogens in the world. Each year in the United States, over 20,000 people die from influenza infection. In the flu of 1918–1919, about 40 million people died worldwide. Vaccines against the flu are the best way to protect public health. Because flu viruses mutate quickly, new vaccines must be created every year. Laura Coronado Bio 10 Chapter 10

DNA: STRUCTURE AND REPLICATION Was known to be a chemical in cells by the end of the nineteenth century Has the capacity to store genetic information Can be copied and passed from generation to generation DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Phosphate group Nitrogenous base Nitrogenous base (can be A, G, C, or T) Sugar Nucleotide Thymine (T) DNA double helix Phosphate group Figure 10.1 The chemical structure of a DNA polynucleotide. Sugar (deoxyribose) DNA nucleotide Polynucleotide Sugar-phosphate backbone Laura Coronado Bio 10 Chapter 10 Figure 10.1

Discovery of the Double Helix James Watson and Francis Crick determined that DNA is a double helix. Rosalind Franklin collected the X-ray crystallography data. Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Figure 10.3b Discoverers of the double helix. X-ray image of DNA Rosalind Franklin Laura Coronado Bio 10 Chapter 10 Figure 10.3b

Laura Coronado Bio 10 Chapter 10 DNA Structure DNA is like a rope ladder twisted into a spiral. The ropes at the sides represent the sugar-phosphate backbones. Each wooden rung represents a pair of bases connected by hydrogen bonds. The four nucleotides found in DNA differ in their nitrogenous bases. These bases are: Thymine (T), Cytosine (C), Adenine (A) & Guanine (G) RNA has uracil (U) in place of thymine. DNA bases pair in a complementary fashion: Adenine (A) pairs with thymine (T) Cytosine (C) pairs with guanine (G) Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Figure 10.4 A rope-ladder model of a double helix. Twist Laura Coronado Bio 10 Chapter 10 Figure 10.4

Laura Coronado Bio 10 Chapter 10 Hydrogen bond Figure 10.5 Three representatives of DNA. (a) Ribbon model (b) Atomic model (c) Computer model Laura Coronado Bio 10 Chapter 10 Figure 10.5

Laura Coronado Bio 10 Chapter 10 DNA Replication When a cell reproduces, a complete copy of the DNA must pass from one generation to the next. Watson and Crick’s model for DNA suggested that DNA replicates by a template mechanism. DNA replication in eukaryotes: Begins at specific sites on a double helix Proceeds in both directions Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Parental (old) DNA molecule Daughter (new) strand Figure 10.6 DNA replication Daughter DNA molecules (double helices) Laura Coronado Bio 10 Chapter 10 Figure 10.6

Laura Coronado Bio 10 Chapter 10 DNA Polymerases Are enzymes Make the covalent bonds between the nucleotides of a new DNA strand Are involved in repairing damaged DNA DNA can be damaged by ultraviolet light. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Origin of replication Origin of replication Parental strands Origin of replication Parental strand Daughter strand Figure 10.7 Multiple "bubbles" in replicating DNA. Bubble Two daughter DNA molecules Laura Coronado Bio 10 Chapter 10 Figure 10.7

THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN DNA functions as the inherited directions for a cell or organism. An organism’s genotype is its genetic makeup, the sequence of nucleotide bases in DNA. The phenotype is the organism’s physical traits, which arise from the actions of a wide variety of proteins. DNA specifies the synthesis of proteins in two stages: Transcription, the transfer of genetic information from DNA into an RNA molecule Translation, the transfer of information from RNA into a protein Transcription and translation are how genes control: The structures & the activities of cells Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Nucleus DNA TRANSCRIPTION RNA Figure 10.8 The flow of genetic information in a eukaryotic cell. (Step 3) TRANSLATION Protein Cytoplasm Laura Coronado Bio 10 Chapter 10 Figure 10.8-3

Overview - The Big Picture The function of a gene is to dictate the production of a polypeptide. In DNA, it is the linear sequence of nucleotide bases. A typical gene consists of thousands of nucleotides. A single DNA molecule may contain thousands of genes. When DNA is transcribed, the result is an RNA molecule. RNA is then translated into a sequence of amino acids in a polypeptide. A protein may consist of two or more different polypeptides. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 The RNA message is translated into a polypeptide by using a codon is a triplet of bases, which codes for one amino acid. The genetic code is: The set of rules relating nucleotide sequence to amino acid sequence Shared by all organisms There are 64 codons: 61 code for amino acids 3 are stop codons, indicating the end of a polypeptide Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Gene 1 DNA molecule Gene 2 Gene 3 DNA strand TRANSCRIPTION Figure 10.10 Transcription of DNA and translation of codons. RNA TRANSLATION Codon Polypeptide Amino acid Laura Coronado Bio 10 Chapter 10 Figure 10.10

Laura Coronado Bio 10 Chapter 10 Second base of RNA codon Phenylalanine (Phe) Tyrosine (Tyr) Cysteine (Cys) Serine (Ser) Stop Stop Leucine (Leu) Stop Tryptophan (Trp) Histidine (His) Leucine (Leu) Proline (Pro) Arginine (Arg) Glutamine (Gln) First base of RNA codon Third base of RNA codon Asparagine (Asn) Serine (Ser) Isoleucine (Ile) Threonine (Thr) Figure 10.11 The dictionary of the genetic code, listed by RNA codons. Lysine (Lys) Arginine (Arg) Met or start Aspartic acid (Asp) Valine (Val) Alanine (Ala) Glycine (Gly) Glutamic acid (Glu) Laura Coronado Bio 10 Chapter 10 Figure 10.11

Transcription: From DNA to RNA Makes RNA from a DNA template Uses a process that resembles DNA replication Substitutes uracil (U) for thymine (T) RNA nucleotides are linked by RNA polymerase. The “start transcribing” signal is a nucleotide sequence called a promoter. The first phase of transcription is initiation, in which: RNA polymerase attaches to the promoter RNA synthesis begins Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 RNA Elongation During the second phase of transcription, called elongation: The RNA grows longer The RNA strand peels away from the DNA template During the third phase of transcription, called termination: RNA polymerase reaches a sequence of DNA bases called a terminator Polymerase detaches from the RNA The DNA strands rejoin Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 RNA polymerase DNA of gene Promoter DNA Initiation Terminator DNA RNA Area shown in part (a) at left Elongation RNA nucleotides RNA polymerase Termination Growing RNA Figure 10.13 Transcription Newly made RNA Completed RNA Direction of transcription Template strand of DNA RNA polymerase (a) A close-up view of transcription (b) Transcription of a gene Laura Coronado Bio 10 Chapter 10 Figure 10.13

Laura Coronado Bio 10 Chapter 10 Figure 10.12 Mice expressing a foreign gene. Laura Coronado Bio 10 Chapter 10 Figure 10.12

The Processing of Eukaryotic RNA After transcription: Eukaryotic cells process RNA Prokaryotic cells do not RNA processing includes: Adding a cap and tail Removing introns Splicing exons together to form messenger RNA (mRNA) Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Intron Exon Intron Exon Exon DNA Transcription Addition of cap and tail Cap RNA transcript with cap and tail Tail Introns removed Exons spliced together mRNA Coding sequence Nucleus Figure 10.14 The production of messenger RNA (mRNA) in a eukaryotic cell. Cytoplasm Laura Coronado Bio 10 Chapter 10 Figure 10.14

Translation: The Players Translation is the conversion from the nucleic acid language to the protein language. Translation requires: Messenger RNA (mRNA) ATP Enzymes Ribosomes Transfer RNA (tRNA) Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Transfer RNA (tRNA) Transfer RNA (tRNA): Acts as a molecular interpreter Carries amino acids Matches amino acids with codons in mRNA using anticodons Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Amino acid attachment site Hydrogen bond RNA polynucleotide chain Figure 10.15 The structure of tRNA Anticodon tRNA (simplified representation) tRNA polynucleotide (ribbon model) Laura Coronado Bio 10 Chapter 10 Figure 10.15

Laura Coronado Bio 10 Chapter 10 Ribosomes Ribosomes are organelles that: Coordinate the functions of mRNA and tRNA Are made of two protein subunits Contain ribosomal RNA (rRNA) A fully assembled ribosome holds tRNA and mRNA for use in translation. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Next amino acid to be added to polypeptide tRNA binding sites Growing polypeptide P site A site Ribosome tRNA Large subunit mRNA binding site mRNA Small subunit Figure 10.16 The ribosome. Codons (a) A simplified diagram of a ribosome (b) The “players” of translation Laura Coronado Bio 10 Chapter 10 Figure 10.16

Translation: The Process Translation is divided into three phases: Initiation Elongation Termination Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Initiation Initiation brings together: mRNA The first amino acid, Met, with its attached tRNA Two subunits of the ribosome The mRNA molecule has a cap and tail that help it bind to the ribosome. Initiation occurs in two steps: First, an mRNA molecule binds to a small ribosomal subunit, then an initiator tRNA binds to the start codon. Second, a large ribosomal subunit binds, creating a functional ribosome. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Cap Start of genetic message Figure 10.17 A molecule of mRNA. End Tail Laura Coronado Bio 10 Chapter 10 Figure 10.17

Laura Coronado Bio 10 Chapter 10 Met Large ribosomal subunit Initiator tRNA P site A site mRNA Figure 10.18 The initiation of translation Start codon Small ribosomal subunit Laura Coronado Bio 10 Chapter 10 Figure 10.18

Laura Coronado Bio 10 Chapter 10 Elongation Elongation occurs in three steps. Step 1, codon recognition: the anticodon of an incoming tRNA pairs with the mRNA codon at the A site of the ribosome. Step 2, peptide bond formation: The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site The ribosome catalyzes the bond formation between the two amino acids Step 3, translocation: The P site tRNA leaves the ribosome The tRNA carrying the polypeptide moves from the A to the P site Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Termination Elongation continues until: The ribosome reaches a stop codon The completed polypeptide is freed The ribosome splits into its subunits Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Amino acid Polypeptide P site mRNA Anticodon A site Codons Codon recognition ELONGATION Stop codon Peptide bond formation New peptide bond Figure 10.19 The elongation of a polypeptide. (Step 4) mRNA movement Translocation Laura Coronado Bio 10 Chapter 10 Figure 10.19-4

Review: DNA RNA Protein In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein in the cytoplasm. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 RNA polymerase Transcription Polypeptide Nucleus DNA mRNA Stop codon Intron RNA processing Cap Termination Tail mRNA Intron Anticodon Amino acid Ribosomal subunits Codon tRNA Figure 10.20 A summary of transcription and translation. (Step 6) Enzyme Elongation ATP Initiation of translation Amino acid attachment Laura Coronado Bio 10 Chapter 10 Figure 10.20-6

Laura Coronado Bio 10 Chapter 10 As it is made, a polypeptide: Coils and folds Assumes a three-dimensional shape, its tertiary structure Several polypeptides may come together, forming a protein with quaternary structure. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Mutations A mutation is any change in the nucleotide sequence of DNA. Mutations can change the amino acids in a protein. Mutations can involve: Large regions of a chromosome Just a single nucleotide pair, as occurs in sickle cell anemia Mutations within a gene can occur as a result of: Base substitution, the replacement of one base by another Nucleotide deletion, the loss of a nucleotide Nucleotide insertion, the addition of a nucleotide Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Insertions and deletions can: Change the reading frame of the genetic message Lead to disastrous effects Have beneficial effects Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Normal hemoglobin DNA Mutant hemoglobin DNA mRNA mRNA Figure 10.21 The molecular basis of sickle-cell disease. Normal hemoglobin Sickle-cell hemoglobin Laura Coronado Bio 10 Chapter 10 Figure 10.21

Laura Coronado Bio 10 Chapter 10 Mutagens Mutations may result from: Errors in DNA replication Physical or chemical agents called mutagens Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection. Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 mRNA and protein from a normal gene (a) Base substitution Deleted Figure 10.22 Three types of mutations and their effects. (b) Nucleotide deletion Inserted (c) Nucleotide insertion Laura Coronado Bio 10 Chapter 10 Figure 10.22

VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS Viruses exhibit some, but not all, characteristics of living organisms. Viruses: Possess genetic material in the form of nucleic acids Are not cellular and cannot reproduce on their own. Bacteriophages, or phages, are viruses that attack bacteria. DNA Protein coat Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Head Bacteriophage (200 nm tall) Tail Tail fiber Figure 10.25 Bacteriophages (viruses) infecting a bacterial cell. DNA of virus Bacterial cell Colorized TEM Laura Coronado Bio 10 Chapter 10 Figure 10.25

Bacteriophages Reproduction Phages have two reproductive cycles. (1) In the lytic cycle: Many copies of the phage are made within the bacterial cell, and then The bacterium lyses (breaks open) (2) In the lysogenic cycle: The phage DNA inserts into the bacterial chromosome and The bacterium reproduces normally, copying the phage at each cell division Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Phage Phage attaches to cell. Phage DNA Bacterial chromosome (DNA) Cell lyses, releasing phages. Phage injects DNA Many cell divisions Occasionally a prophage may leave the bacterial chromosome. LYTIC CYCLE LYSOGENIC CYCLE Phages assemble Phage DNA circularizes. Lysogenic bacterium reproduces normally, replicating the prophage at each cell division. Figure 10.26 Alternative phage reproductive cycles. (Step 2) Prophage OR New phage DNA and proteins are synthesized. Phage DNA is inserted into the bacterial chromosome. Laura Coronado Bio 10 Chapter 10 Figure 10.26-2

Laura Coronado Bio 10 Chapter 10 Plant Viruses Viruses that infect plants can: Stunt growth Diminish plant yields Spread throughout the entire plant Viral plant diseases: Have no cure Are prevented by producing plants that resist viral infection, controversial Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 RNA Protein Figure 10.27 Tobacco mosaic virus Tobacco mosaic virus Laura Coronado Bio 10 Chapter 10 Figure 10.27

Laura Coronado Bio 10 Chapter 10 Animal Viruses Viruses that infect animals are: Common causes of disease May have RNA or DNA genomes Some animal viruses steal a bit of host cell membrane as a protective envelope. Membranous envelope Protein spike RNA Figure 10.28 An influenza virus. Protein coat Laura Coronado Bio 10 Chapter 10

Viral Reproductive Cycle The reproductive cycle of an enveloped RNA virus can be broken into seven steps. Entry Uncoating RNA Synthesis Protein Synthesis RNA Synthesis (other strand) Assembly Exit Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Virus Protein spike Viral RNA (genome) Protein coat Envelope Plasma membrane of host cell Entry Uncoating Viral RNA (genome) RNA synthesis by viral enzyme Protein synthesis RNA synthesis (other strand) mRNA Template New viral genome Assembly New viral proteins Figure 10.29 The reproductive cycle of an enveloped virus. Exit Laura Coronado Bio 10 Chapter 10 Figure 10.29

Laura Coronado Bio 10 Chapter 10 Mumps virus Protein spike Envelope Figure 10.29c The reproductive cycle of an enveloped virus. Colorized TEM Laura Coronado Bio 10 Chapter 10 Figure 10.29c

The Process of Science: Do Flu Vaccines Protect the Elderly? Observation: Vaccination rates among the elderly rose from 15% in 1980 to 65% in 1996. Question: Do flu vaccines decrease the mortality rate among those elderly people who receive them? Hypothesis: Elderly people who were immunized would have fewer hospital stays and deaths during the winter after vaccination. Laura Coronado Bio 10 Chapter 10

The Process of Science: Do Flu Vaccines Protect the Elderly? Experiment: Tens of thousands of people over the age of 65 were followed during the ten flu seasons of the 1990s. Results: People who were vaccinated had a: 27% less chance of being hospitalized during the next flu season and 48% less chance of dying Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 HIV, the AIDS Virus HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule. Retroviruses use the enzyme reverse transcriptase to synthesize DNA on an RNA template. HIV steals a bit of host cell membrane as a protective envelope. The behavior of HIV nucleic acid in an infected cell can be broken into six steps. AIDS (acquired immune deficiency syndrome) is: Caused by HIV infection and Treated with drugs that interfere with the reproduction of the virus Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Envelope Surface protein Protein coat RNA (two identical strands) Figure 10.31 HIV, the AIDS virus. Reverse transcriptase Laura Coronado Bio 10 Chapter 10 Figure 10.31

HIV (red dots) infecting Reverse transcriptase Viral RNA Cytoplasm Nucleus DNA strand Chromosomal DNA Provirus Double stranded DNA Viral RNA and proteins RNA SEM Figure 10.32 The behavior of HIV nucleic acid in an infected cell. HIV (red dots) infecting a white blood cell Laura Coronado Bio 10 Chapter 10 Figure 10.32

Laura Coronado Bio 10 Chapter 10 Thymine (T) Figure 10.33 AZT and the T nucleotide. Part of a T nucleotide AZT Laura Coronado Bio 10 Chapter 10 Figure 10.33

Laura Coronado Bio 10 Chapter 10 Viroids and Prions Two classes of pathogens are smaller than viruses: Viroids are small circular RNA molecules that do not encode proteins Prions are misfolded proteins that somehow convert normal proteins to the misfolded prion version Prions are responsible for neurodegenerative diseases including: Mad cow disease Scrapie in sheep and goats Chronic wasting disease in deer and elk Creutzfeldt-Jakob disease in humans Laura Coronado Bio 10 Chapter 10

Evolution Connection: Emerging Viruses Emerging viruses are viruses that have: Appeared suddenly or Have only recently come to the attention of science Figure 10.35 Rounding up ducks in Vietnam to help prevent the spread of the Avian flu virus. Laura Coronado Bio 10 Chapter 10 Figure 10.35

Evolution Connection: Emerging Viruses Avian flu: Infects birds Infected 18 people in 1997 Since has spread to Europe and Africa infecting 300 people and killing 200 of them If avian flu mutates to a form that can easily spread between people, the potential for a major human outbreak is significant. New viruses can arise by: Mutation of existing viruses Spread to new host species Laura Coronado Bio 10 Chapter 10

Laura Coronado Bio 10 Chapter 10 Figure 10.UN7 Summary: Mutations Laura Coronado Bio 10 Chapter 10 Figure 10.UN7