1. Chapter 10 Molecular Biology of the Gene

2. Sabotage Inside Our Cells Viruses are biological saboteurs – Hijack the genetic material of host cells in order to reproduce themselves – May remain permanently dormant in the body Viruses share some characteristics of living organisms but are not generally considered alive – Genetic material composed of nucleic acid – Not cellular – Cannot reproduce on their own First understanding of DNA based on viruses

3. THE STRUCTURE OF THE GENETIC MATERIAL 10.1 Experiments showed that DNA is the genetic material "Transforming factor" postulated in 1928 by Frederick Griffith Hershey-Chase experiments in 1952 determined that the heredity material was DNA not protein – Studied the simple bacteriophage T2 – Showed that the virus injects its DNA into host cells and reprograms them to produce more viruses

4. LE 10-1a Head Tail Tail fiber DNA 300,000 

5. LE 10-1b Phage Bacterium DNA Radioactive protein Empty protein shell Radioactivity in liquid Phage DNA Pellet Centrifuge Pellet Radioactivity in pellet Radioactive DNA Batch 2 Radioactive DNA Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. Measure the radioactivity in the pellet and the liquid. Agitate in a blender to separate phages outside the bacteria from the cells and their contents. Centrifuge the mixture so bacteria form a pellet at the bottom of the test tube. Batch 1 Radioactive protein

6. LE 10-1c Phage attaches to bacterial cell. Phage injects DNA. Phage DNA directs host cell to make more phage DNA and protein parts. New phages assemble. Cell lyses and releases new phages. Animation: Phage T2 Reproductive Cycle Animation: Phage T2 Reproductive Cycle Animation: Hershey-Chase Experiment Animation: Hershey-Chase Experiment

7. 10.2 DNA and RNA are polymers of nucleotides Nucleic acids are polynucleotides made of long chains of nucleotide monomers – Nitrogenous bases Single-ring pyrimidines: thymine (T), cytosine (C) Double-ring purines: adenine (A), guanine (G) – Sugar-phosphate backbone

8. DNA and RNA are identical except for two things – Nitrogenous bases DNA: A, C, G, T RNA: A, G, C, U – Sugars DNA: deoxyribose RNA: ribose Animation: DNA and RNA Structure Animation: DNA and RNA Structure

9. LE 10-2a Sugar-phosphate backbone Phosphate group Nitrogenous base Sugar DNA nucleotide DNA polynucleotide DNA nucleotide Sugar (deoxyribose) Thymine (T) Nitrogenous base (A, G, C, or T) Phosphate group A C T G T T G T C A

10. LE 10-2b Thymine (T) Cytosine (C) Pyrimidines Adenine (A) Purines Guanine (G)

11. Phosphate group Nitrogenous base (A, G, C, or U) Sugar (ribose) Uracil (U)

12. LE 10-2d Key Hydrogen atom Phosphorus atom Carbon atom Nitrogen atom Oxygen atom

13. 10.3 DNA is a double-stranded helix James Watson and Francis Crick worked out the three-dimensional structure of DNA, based on X-ray crystallography by Rosalind Franklin DNA consists of two polynucleotide strands wrapped around each other in a double helix – Sugar-phosphate backbones are on the outside and nitrogenous bases on the inside Animation: DNA Double Helix Animation: DNA Double Helix

16. – Each base pairs with a complementary partner A with T, and G with C – Hydrogen bonds between the bases hold the strands together The Watson-Crick model of DNA suggested a molecular explanation for genetic inheritance

17. LE 10-3d Hydrogen bond Base pair Ribbon model Partial chemical structure Computer model G C TA A T T A C C G G G C T T T T A A A A GC A T A C T G CG A T

18. DNA REPLICATION 10.4 DNA replication depends on specific base pairing The Watson-Crick model of DNA structure suggested a mechanism for its replication – DNA strands separate – Enzymes use each strand as a template to assemble new nucleotides into complementary strands The mechanism of DNA replication is semiconservative – Each new double helix consists of one old and one new strand

19. LE 10-4a Parental molecule of DNA Both parental strands serve as templates Two identical daughter molecules of DNA T Nucleotides CG A GC A A T T A A A A C C C T T G G A C A A A A A A CC C CG T G T T T T G T T T G G Animation: DNA Replication Overview Animation: DNA Replication Overview

20. LE 10-4b G C T A A T G G C C T T A A C C G G G G C C G G G C C C T T T T T C A A A A A G T G C A T T T T A A A A

21. 10.5 DNA replication: A closer look DNA replication begins at specific sites (origins of replication) on the double helix – Proteins attach and separate the strands – Replication proceeds in both directions, creating replication bubbles Parent strands open, daughter strands elongate – Replication occurs simultaneously at many sites

22. LE 10-5a Origin of replication Bubble Parental strand Daughter strand Two daughter DNA molecules

23. DNA's sugar-phosphate backbones are oriented in opposite directions – The enzyme DNA polymerase adds nucleotides at only the 3’ end One daughter strand is synthesized as a continuous piece The other strand is synthesized as a series of short pieces The two strands are connected by the enzyme DNA ligase

24. LE 10-5b 3 end 5 end 3 end P 4 A T C G HO OH P 1 3 2 5 P P P P C G P P A T P 4 3 1 2 5

25. LE 10-5c DNA polymerase molecule Parental DNA Daughter strand synthesized continuously Daughter strand synthesized In pieces 3 5 3 5 5 3 3 5 DNA ligase Overall direction of replication Animation: Origins of Replication Animation: Origins of Replication Animation: Leading Strand Animation: Leading Strand Animation: Lagging Strand Animation: Lagging Strand Animation: DNA Replication Review Animation: DNA Replication Review

26. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN 10.6 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 DNA bases A particular gene—a linear sequence of many nucleotides—specifies a particular polypeptide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

27. The flow of genetic information 1.Transcription of the genetic information in DNA into RNA 2.Translation of RNA into the polypeptide Beadle-Tatum one gene-one enzyme hypothesis – Studies of inherited metabolic disorders in mold suggested that phenotype is expressed through proteins – A gene dictates production of a specific enzyme – The hypothesis has been restated to one gene- one polypeptide

28. 10.7 Genetic information written in codons is translated into amino acid sequences Genetic information flows from DNA to RNA to protein Nucleotide monomers represent letters in an alphabet that can form words in a language – Triplet code Three-letter words (codons) Each word codes for one amino acid in a polypeptide

29. LE 10-7a DNA molecule Gene 1 Gene 2 Gene 3 AAA AA C C GGC C C GG G UUU UU U U AA DNA strand Transcription RNA Translation Polypeptide Amino acid Codon

30. 10.8 The genetic code is the Rosetta stone of life The genetic code specifies the correspondence between RNA codons and amino acids in proteins – Includes start and stop codons – Redundant but not ambiguous Nearly all organisms use exactly the same genetic code

32. LE 10-8b Strand to be transcribed Transcription DNA T A G T A C T T T T A A AAG C G C T T T A A A A G U RNA Translation Start codon A A UU G UU A G Stop codon Phe Lys MetPolypeptide

33. 10.9 Transcription produces genetic messages in the form of RNA One DNA strand serves as a template for the new RNA strand RNA polymerase constructs the RNA strand in a multistep process – Initiation RNA polymerase attaches to the promotor Synthesis starts

34. Elongation: – RNA synthesis continues – RNA strand peels away from DNA template – DNA strands come back together in transcribed region Termination – RNA polymerase reaches a terminator sequence at the end of the gene – Polymerase detaches

35. LE 10-9a RNA polymerase RNA nucleotides Template strand of DNA Direction of transcription Newly made RNA T A A CC A C T C CA A U T T G G U G T T A A C C U A C G G T A

36. LE 10-9b RNA polymerase Initiation Promoter DNA Terminator DNA Area shown In Figure 10.9A Initiation Elongation Termination Growing RNA Completed RNA RNA polymerase DNA of gene

37. 10.10 Eukaryotic RNA is processed before leaving the nucleus The RNA that encodes an amino acid sequence is messenger RNA (mRNA) In prokaryotes, transcription and translation both occur in the cytoplasm In eukaryotes, RNA transcribed in the nucleus is processed before moving to the cytoplasm for translation

38. RNA Splicing – Noncoding segments called introns are cut out – Remaining exons are joined to form a continuous coding sequence – A cap and a tail are added to the ends

39. LE 10-10 Exon Intron Cap DNA RNA transcript with cap and tail mRNA Coding sequence Nucleus Cytoplasm Exons spliced together Tail Introns removed Transcription Addition of cap and tail

40. 10.11 Transfer RNA molecules serve as interpreters during translation Transfer RNA (tRNA) molecules match the right amino acid to the correct codon tRNA is a twisted and folded single strand of RNA – Anticodon loop at one end recognizes a particular mRNA codon by base pairing – Amino acid attachment site is at the other end Each amino acid is joined to the correct tRNA by a specific enzyme

41. LE 10-11a Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon Amino acid attachment site

43. 10.12 Ribosomes build polypeptides A ribosome consists of two subunits – Each is made up of proteins and ribosomal RNA (rRNA) The subunits of a ribosome – Hold the tRNA and mRNA close together in binding sites during translation – Allow amino acids to be connected into a polypeptide chain

44. tRNA-binding sites Large subunit Small subunit mRNA binding site tRNA molecules Growing polypeptide Large subunit Small subunit mRNA

45. LE 10-12c Growing polypeptide mRNA Codons tRNA Next amino acid to be added to polypeptide

46. 10.13 An initiation codon marks the start of an mRNA message The initiation phase of translation – Brings together mRNA, a specific tRNA, and the two subunits of a ribosome – Establishes exactly where translation will begin Ensures that mRNA codes are translated in the correct sequence

47. Initiation is a two-step process – Step 1 mRNA binds to a small ribosomal subunit Initiator tRNA, carrying the amino acid Met, binds to the start codon – Step 2 A large ribosomal subunit binds to the small one, forming a functional ribosome Initiator tRNA fits into one binding site; the other is vacant for the next tRNA

48. LE 10-13b C Initiator tRNA Met P site mRNA Start codon Small ribosomal subunit A site Large Ribosomal subunit C A U A AU U G A G U Start of genetic message End

49. 10.14 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 in a three-step elongation process 1.Codon recognition 2.Peptide bond formation 3.Translocation Elongation continues until a stop codon reaches the ribosome's A site, terminating translation

50. LE 10-14 Polypeptide P site mRNA A site Codons Anticodon Amino acid Condon recognition Peptide bond formation New peptide bond Translocation Stop codon mRNA movement Animation: Translation Animation: Translation

51. 10.15 Review: The flow of genetic information in the cell is DNA  RNA  protein The sequence of codons in DNA, via the sequence of codons in RNA, spells out the primary structure of a polypeptide 1.Transcription of mRNA from a DNA template 2.Attachment of amino acid to tRNA 3.Initiation of polypeptide synthesis 4.Elongation 5.Termination

52. 10.16 Mutations can change the meaning of genes Mutation: any change in the nucleotide sequence of DNA – Caused by errors in DNA replication or recombination, or by mutagens – Can involve large regions of a chromosome or a single base pair – Can cause many genetic diseases, such as sickle-cell disease

53. LE 10-16a Normal hemoglobin DNA mRNA C T T AA G Normal hemoglobin Glu mRNA C G A Sickle-cell hemoglobin Val Mutant hemoglobin DNA A T U

54. Two general categories of genetic mutations – Base substitutions replace one base with another Most are harmful but may occasionally have no effect or be beneficial – Base insertions or deletions alter the reading frame Result is most likely a nonfunctioning polypeptide Mutagenesis caused by spontaneous error or a physical or chemical mutagen

55. LE 10-16b Normal gene Base substitution Protein mRNA Base deletion Missing Met Lys PheGlyAla Phe Ala Ser LeuHis A A A A A AAA A A AAA A U U U U U U UU UUUUG G GGG GGG G C C CC G GG GG CC U

56. MICROBIAL GENETICS 10.17 Viral DNA may become part of the host chromosome Viruses are infectious particles consisting of nucleic acid enclosed in a protein capsid Viruses depend on their host cells for the replication, transcription, and translation of their nucleic acid – DNA enters host bacterium, circularizes, and enters one of two pathways

57. – Lytic cycle Host produces more viruses Host cell lyses (breaks open) to release new viruses

58. – Lysogenic cycle Phage DNA inserted by recombination into the host chromosome; is now a prophage Prophages replicated each time host cell divides; passed on to generations of daughter cells Does not destroy host Environmental signal may trigger switch from lysogenic to lytic cycle

59. Phage Phage DNA Attaches to cell Cell lyses, releasing phages Phage injects DNA Lytic cycle Phages assemble Phage DNA circularizes New phage DNA and proteins are synthesized Bacterial chromosome OR Lysogenic cycle Prophage Many cell divisions Lysogenic bacterium repro- duces normally, replicating the prophage at each cell division Phage DNA inserts into the bacterial chromosome by recombination Animation: Simplified Viral Reproductive Cycle Animation: Simplified Viral Reproductive Cycle Animation: Phage T4 Lytic Cycle Animation: Phage T4 Lytic Cycle Animation: Phage Lambda Lysogenic and Lytic Cycles Animation: Phage Lambda Lysogenic and Lytic Cycles

60. CONNECTION 10.18 Many viruses cause disease in animals Structure of a virus that invades animal cells – Genetic material may be RNA (examples: flu, HIV) or DNA (examples: hepatitis, herpes) – Protein coat – Sometimes a membranous envelope with glycoprotein spikes The envelope helps the virus enter and leave the host cell during its reproductive cycle

61. VIRUS Viral RNA (genome) Glycoprotein spike Protein coat Envelope Entry Plasma membrane of host cell Uncoating Viral RNA (genome) RNA synthesis by viral enzyme RNA synthesis (other strand) Template mRNA Protein synthesis New viral proteins New viral genome Assembly Exit Membranous envelope RNA Protein coat Glycoprotein spike

62. CONNECTION 10.19 Plant viruses are serious agricultural pests Most plant viruses – Have RNA genomes – Enter their hosts via wounds in the plant's outer layers – May spread throughout the plant through plasmodesmata There is no cure for most plant viruses

63. LE 10-19 RNAProtein

64. CONNECTION 10.20 Emerging viruses threaten human health Emerging viruses have appeared suddenly or have recently come to the attention of scientists – Examples: HIV, SARS, Ebola, West Nile Processes contributing to emergence – Mutation – Contact between species – Spread from isolated populations

67. 10.21 The AIDS virus makes DNA on an RNA template HIV, the AIDS virus, is a retrovirus – Flow of genetic information is RNA _ DNA – Inside a cell, HIV uses its RNA as a template for making DNA – The enzyme reverse transcriptase catalyzes reverse transcription Animation: HIV Reproductive Cycle Animation: HIV Reproductive Cycle

68. LE 10-21a Envelope Glycoprotein Protein coat RNA (two identical strands) Reverse transcriptase

69. LE 10-21b Viral RNA DNA strand Double- stranded DNA Viral RNA and proteins C YTOPLASM N UCLEUS Chromosomal DNA Provirus DNA RNA

70. 10.22 Bacteria can transfer DNA in three ways Bacteria can transfer genes from cell to cell by one of three processes – Transformation: the uptake of foreign DNA from the surrounding environment – Transduction: transfer of bacterial genes by a phage – Conjugation: union of two bacterial cells and the transfer of DNA between them

71. LE 10-22a DNA enters cell Fragment of DNA from another bacterial cell Bacterial chromosome (DNA)

72. LE 10-22b Phage Fragment of DNA from another bacterial cell (former phage host)

73. LE 10-22c Mating bridge Recipient cell (“female”) Sex pili Donor cell (“male”)

74. Once new DNA is in a bacterial cell, part of it may integrate into the recipient's chromosome – Occurs by crossing over between the two molecules – Leaves the recipient with a recombinant chromosome

75. LE 10-22d Donated DNACrossoversDegraded DNA Recombinant chromosome Recipient cell’s chromosome

76. 10.23 Bacterial plasmids can serve as carriers for gene transfer The F factor is a piece of bacterial DNA – Carries genes for things needed for conjugation – Contains an origin of replication – Can transfer chromosomal DNA by integrating into the donor bacterium's chromosome or entering the cell as a plasmid

77. F factor (integrated) Male (donor) cell Origin of F replication Bacterial chromosome F factor starts replication and transfer of chromosome Recipient cell Only part of the chromosome transfers Recombination can occur Cell now male Plasmid completes transfer and circularizes F factor starts replication and transfer Bacterial chromosome Male (donor) cell F factor (plasmid)

78. Plasmids – Small circular DNA molecules separate from the bacterial chromosome – Can serve as carriers for the transfer of genes Plasmids Colorized TEM 2,000 