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Molecular Biology of the Gene Chapter 10

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In 2002, 5 million people worldwide were newly infected with HIV Because all organisms use the same genetic code, scientists can make a plant glow like a firefly

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The loss of a single nucleotide from a 1,000- nucleotide gene can completely destroy the genes function Many viruses have genes that are not made of DNA

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AIDS is one of the most challenging health problems facing the world today BIOLOGY AND SOCIETY: SABOTAGING HIV Infection by HIV can cause AIDS

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The drug AZT (3-azido-3deoxythymidine or Azidothymidine/Zidovudine) is effective at preventing the spread of HIV Thymine (T) AZT Part of a T nucleotide

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DNA THE STRUCTURE AND REPLICATION OF DNA Was known as 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

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DNA and RNA are nucleic acids DNA and RNA: Polymers of Nucleotides They consist of chemical units called nucleotides The nucleotides are joined by a sugar- phosphate backbone

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Phosphate groupNitrogenous base Sugar Nucleotide Polynucleotide Sugar-phosphate backbone Nitrogenous base (A,G,C, or T) Thymine (T) Phosphate group Sugar (deoxyribose) DNA nucleotide

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The four nucleotides found in DNA Differ in their nitrogenous bases Are thymine (T), cytosine (C), adenine (A), and guanine (G) RNA has uracil (U) in place of thymine

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James Watson and Francis Crick determined that DNA is a double helix Watson and Cricks Discovery of the Double Helix James Watson and Francis Crick

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James D. Watson and Francis Crick: DNA characteristics Ability to replicate itself Encode information Control the destiny and function of each cell Structure should change as a result of mutation; it should be flexible to minor changes

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Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA Rosalind Franklin collected the X-ray crystallography data (b) Rosalind Franklin

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The model of DNA is like a rope ladder twisted into a spiral Twist

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Detailed representations of DNA Notice that the bases pair in a complementary fashion Hydrogen bond (a)(b)(c)

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When a cell or organism reproduces, a complete set of genetic instructions must pass from one generation to the next DNA Replication

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Watson and Cricks model for DNA suggested that DNA replicated by a template mechanism Parental (old) DNA molecule Daughter (new) strand Daughter DNA molecule (double helices)

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Watson-Crick: DNA replication depends on specific base pairing

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Semiconservative replication H-bonds break, parent strands separate Enzymes use each parent strand as template to assemble new strands

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DNA can be damaged by ultraviolet light The enzymes and proteins involved in replication can repair the damage

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DNA replication DNA replication requires more than a dozen enzymes and proteins to work together Rate of nucleotide addition ~ 50 per second in mammals ~ 500 per second in bacteria

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DNA replication begins at specific sites Two daughter DNA molecules Bubble Origin of replication Parental strand Daughter strand

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DNA replication Begins at specific sites on a double helix Proceeds in both directions Origin of replication Origin of replication Origin of replication Parental strand Daughter strand Bubble Two daughter DNA molecules

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3 end 5 end Each strand of the double helix is oriented in the opposite direction

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Parental DNA DNA ligase DNA polymerase molecule 3 3 3 3 3 3 5 5 5 5 5 5 Overall direction of replication daughter strand synthesized continuously daughter strand synthesized in pieces DNA polymerases: -link nucleotides in the new DNA strand - adds nucleotides only in the 5 3 direction DNA ligase - links up the short segments (or Osazaki fragments) of newly synthesized DNA Helicase Helicase: -Unwinds DNA double helix

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DNA replication is very accurate; one in 10,000 nucleotides are incorrectly paired DNA polymerases also proofread the newly synthesized DNA DNA polymerases and DNA ligase repair DNA damaged by harmful radiations (UV or X-rays) or toxic chemicals in the environment After proofreading and repair, one in a billion nucleotides are incorrectly paired

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DNA functions as the inherited directions for a cell or organism The flow of genetic information is from: DNA to RNA to PROTEIN How are these directions carried out?

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How an organisms DNA genotype produces its phenotype The information of an organisms genotype is carried in its sequence of bases The genotype is expressed as proteins, which provide the molecular basis of phenotypic traits DNA does not directly synthesize proteins, but passes on specific information for protein synthesis via the RNA to the cytoplasm

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A specific gene specifies a polypeptide DNA is transcribed into RNA, which is translated into the polypeptide TRANSCRIPTION TRANSLATION DNA mRNA Protein Nucleus Nuclear membrane Cytoplasm tRNA Ribosomes (rRNA)

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DNA are a small number of large immobile molecules that change little during their lifetime RNA are small, highly mobile and short lived TRANSCRIPTION TRANSLATION DNA mRNA Protein tRNA Ribosomes (rRNA)

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The one geneone protein hypothesis states that the function of an individual gene is to dictate the production of a specific protein One gene one polypeptide hypothesis

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The information, or language, in DNA is ultimately translated into the language of polypeptides From nucleotide sequence to amino acid sequence: an overview

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DNA molecule Gene 1 Gene 2 Gene 3 DNA strand TRANSCRIPTION mRNA TRANSLATION Polypeptide Amino acid Codon

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An exercise in translating the genetic code _____________________ T A C T T C A A A A T C A T G A A G T T T T A G DNA helix transcribed strand What is the sequence of bases in the mRNA?

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Transcribed strand DNA mRNA Polypeptide Transcription Translation Stop codon Start codon An exercise in translating the genetic code

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Genetic information written in codons is translated in amino acid sequences Four different nucleotides code for twenty amino acids The words of the DNA language are triplets of bases called codons The DNA code is - universal (applies to all species, almost) - degenerate (redundant) - unambiguous - non-overlapping

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The genetic code

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Cracking the genetic code Marshal Nirenberg and Heinrich Matthaei (1961) Artificial mRNA poly U poly phenylalanine poly A poly lysine poly C poly proline etc. 61 of 64 triplets code for amino acids AUG is the start codon and codes for methionine UAA, UAG and UGA are stop codons

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The genetic code is shared by all organisms

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Decoding the DNA Part I: TRANSCRIPTION: TRANSCRIPTION TRANSLATION DNA mRNA Protein Nucleus Nuclear membrane Cytoplasm tRNA Ribosomes (rRNA)

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Transcription: From DNA to RNA In transcription Genetic information is transferred from DNA to RNA An mRNA (messenger RNA) molecule is transcribed from a DNA template

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The start transcribing signal is a nucleotide sequence called a promoter Initiation of Transcription The first phase of transcription is initiation RNA polymerase attaches to the promoter RNA synthesis begins

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The second phase of transcription is elongation RNA Elongation The RNA grows longer

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The third phase of transcription is termination Termination of Transcription RNA polymerase reaches a sequence of DNA bases called a terminator

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Transcription of an entire gene RNA polymerase DNA of gene Promoter DNA Initiation Terminator DNA mRNA Elongation Termination Growing mRNA Completed mRNA RNA polymerase

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RNA polymerase RNA nucleotides Newly made mRNA Direction of transcription Template strand of DNA A close-up view of transcription

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Overview of transcription: Initiation - RNA polymerase binds to promoter sequence Elongation - mRNA synthesis continues, RNA peels off from DNA Termination - RNA polymerase reaches termination sequence - RNA polymerase detaches from DNA strand and mRNA strand

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The eukaryotic cell processes the mRNA after transcription The Processing of Eukaryotic RNA

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RNA processing includes Adding a cap (G) and tail (poly A) Removing introns Splicing exons together DNA RNA transcript with cap and tail mRNA Exon Intron Exon Intron Exon Cap Introns removed Tail Exons spliced together Coding sequence Nucleus Cytoplasm Transcription Addition of cap and tail

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Decoding the DNA Part II: TRANSLATION: TRANSCRIPTION TRANSLATION DNA mRNA Protein Nucleus Nuclear membrane Cytoplasm tRNA Ribosomes (rRNA)

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Key players in translation: - Messenger RNA - Transfer RNAs - Ribosomes (amino acids, ATP, specific enzymes and protein factors)

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mRNA Messenger RNA (mRNA) Is the first ingredient for translation

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tRNA Transfer RNA (tRNA) Acts as a molecular interpreter Carries amino acids Matches amino acids with codons in mRNA using anticodons Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon

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Hydrogen bond RNA polynucleotide chain Anticodon Amino acid attachment site Structure of transfer RNA CCA 5 3

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Transfer RNAs

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Ribosomes Are organelles that actually make polypeptides Are made up of two protein subunits Contain ribosomal RNA (rRNA) tRNA binding sites P site A site P A Large subunit mRNA binding site Small subunit

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A fully assembled ribosome holds tRNA and mRNA for use in translation Next amino acid to be added to polypeptide Growing polypeptide mRNA tRNA

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Translation is divided into three phases Translation: The Process Initiation Elongation Termination

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The first phase brings together Initiation The mRNA The first amino acid with its attached tRNA The two subunits of the ribosome

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An mRNA molecule has a cap and tail that help it bind to the ribosome Start of genetic message G cap End Poly A tail

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The process of initiation Met Initiator tRNA mRNA Large ribosomal subunit Start codon Small ribosomal subunit Initiation P site A site 1 2

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Step 1, codon recognition Elongation The anticodon of an incoming tRNA pairs with the mRNA codon Step 2, peptide bond formation The ribosome catalyzes bond formation between amino acids Step 3, translocation A tRNA leaves the P site of the ribosome The ribosome moves down the mRNA

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Polypeptide Amino acid P site Anticodon mRNA A site Codons Elongation 2 3 Translocation Codon recognition Peptide bond formation The process of elongation mRNA movement New peptide bond 1

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Elongation continues until the ribosome reaches a stop codon Termination

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Overview of translation: Initiation - mRNA attaches to small subunit of ribosome - initiator tRNA carrying methionine binds to start codon - large subunit of ribosome binds to small subunit such that the initiator tRNA fits to the P site Elongation - codon recognition by specific tRNA that enters the A site - peptide bond formation between amino acids at P and A site - translocation: ribosome moves along mRNA, tRNA with attached polypeptide moves from A to P site Termination - stop codon reaches A site - release factor binds to A site - polypeptide detaches from ribosome

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The flow of genetic information in a cell Review: DNA RNA Protein

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1 2 3 4 Amino acid attachment 5 Elongation Initiation of translation 6 Termination Transcription RNA processing RNA Polymerase Nucleus DNA RNA transcript Intron Tail Intron mRNA CAP tRNA Enzyme Amino acid Ribosomal subunits Anticodon Codon Stop codon 1 4

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In eukaryotic cells Transcription occurs in the nucleus Translation occurs in the cytoplasm Transcription and translation Are the processes whereby genes control the structures and activities of cells

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A mutation Mutations Is any change in the nucleotide sequence of DNA Normal hemoglobin Sickle-cell hemoglobin Glu Val Normal hemoglobin DNA Mutant hemoglobin DNA mRNA

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Mutations may result from Mutagens Errors in DNA replication Physical or chemical agents called mutagens

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Mutations within a gene Types of Mutations Can be divided into two general categories Can result in changes in the amino acids in proteins mRNA Protein MetLysPheGlyAla (a) Base substitution MetLysPheSerAla

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Insertions and deletions Can have disastrous effects Change the reading frame of the genetic message MetLysLeuAlaHis (b) Nucleotide deletion mRNA Protein MetLysPheGlyAla

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1.SILENT MUTATION: when substitution of one base for another leads to no change in the amino acids Mutation at position 12 in DNA: C A DNA template strand 3------TAC ACC GAG GGA CTA ATT------5 Transcription 5------AUG UGG CUC CCU GAU UAA------3 mRNA Translation Peptide Met Trp Leu Pro Asp Stop CCG codes for Proline, as does CCU, CCA and CCC Result: no change in amino acid sequence GGC CCG

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The genetic code is degenerate

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2. MISSENSE MUTATION: a base change that results in the substitution of one amino acid for another in the protein Mutation at position 14 in the DNA: T A 3------TAC ACC GAG GGC CAA ATT------5 5------AUG UGG CUC CCG GUU UAA------3 Transcription Translation Met Trp Leu Pro Val Stop Result: Amino acid change at position 5: Asp Val Peptide mRNA DNA template strand CTA GAU

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Sickle Cell Anemia

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3. NONSENSE MUTATION: a base substitution that causes a chain terminator (stop) codon to form in the mRNA Mutation at position 5 in DNA: C T 3------TAC ATC GAG GGC CTA ATT------5 5------AUG UAG CUC CCG GAU UAA------3 Transcription Translation Met Stop mRNA Result: Only one amino acid translated; no protein made Peptide DNA template strand ACC UGG

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4. FRAMESHIFT MUTATION: single base insertions or deletions into the DNA that shifts the reading frame of the genetic code Mutation by insertion of T between bases 6 and 7 in DNA 3------TAC ACC GAG GGC CTA ATT------5 T Translation Transcription 5------AUG UGG ACU CCC GGA UUA A------3 Met Trp Thr Pro Gly Leu --- mRNA Peptide Result: All amino acids changed beyond insertion DNA template strand DNA template strand

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Neutral mutations: occur in sequences of DNA in the non-coding regions that have no apparent function Mutation is the only way new alleles are produced. Thus, they play a key role in the evolution of life forms

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Although mutations are often harmful They are the source of the rich diversity of genes in the living world They contribute to the process of evolution by natural selection

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Viruses sit on the fence between life and non-life VIRUSES: GENES IN PACKAGES They exhibit some but not all characteristics of living organisms

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Bacteriophages, or phages Bacteriophages Attack bacteria Head Tail Tail fiber DNA of virus Bacterial cell

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Phages have two reproductive cycles Phage DNA 1 2 3 4 Phage DNA circularizes New phage DNA and proteins are sythesized 5 Phage DNA inserts into the bacterial chromosome by recombination Cell lyses, releasing phages 6 Lysogenic bacterium reproduces normally, replicating the prophage at each cell division 7 Occasionally a prophage may leave the bacterial chromosome Bacterial chromosome (DNA) Lytic cycle Lysogenic cycle Prophage Many cell divisions

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Viruses that infect plants Plant Viruses Can stunt growth and diminish plant yields Can spread throughout the entire plant Protein RNA Genetic engineering methods Have been used to create virus-resistant plants

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Virus studies help establish molecular genetics Animal Viruses Molecular genetics helps us understand viruses Membranous envelope RNA Protein coat Protein spike

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VIRUS Entry 1 2 3 4 Uncoating RNA synthesis by viral enzyme 5 RNA synthesis (other strand) Protein synthesis 6 Assembly 7 Exit Viral RNA (genome) Protein spike Protein coat Envelope Plasma membrane of host cell mRNA New viral proteins Template New viral genome The reproductive cycle of an enveloped virus

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HIV is a retrovirus HIV, the AIDS Virus A retrovirus is an RNA virus that reproduces by means of a DNA molecule It copies its RNA to DNA using reverse transcriptase Envelope Protein Protein coat RNA (two identical strands) Reverse transcriptase HIV

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1 2 3 4 5 6 DNA strand Viral RNA Reverse transcriptase Cytoplasm Double- stranded DNA Chromosomal DNA Provirus DNA Viral RNA and proteins Nucleus The behavior of HIV nucleic acid in an infected cell How HIV reproduces inside a cell

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AIDS is Acquired immune deficiency syndrome The disease caused by HIV infection Treated with the drug AZT HIV infecting a white blood cell

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Many new viruses have emerged in recent years EVOLUTION CONNECTION: EMERGING VIRUSES HIV Ebola Hantavirus (a) Ebola virus (b) Hantavirus

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How do new viruses arise? Mutation of existing viruses Spread to new host species

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DNA and RNA: Polymers of Nucleotides SUMMARY OF KEY CONCEPTS DNA Polynucleotide Nitrogenous base Phosphate group Nucleotide Sugar

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DNA Replication Parental DNA molecule Identical daughter DNA molecules

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Translation: The Players Large ribosomal subunit Amino acid mRNA tRNA Anticodon Codons Small ribosomal subunit

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