1. © 2010 Pearson Education, Inc. DNA: STRUCTURE DNA: Deoxyribonucleic acid 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

2. © 2010 Pearson Education, Inc. DNA and RNA Structure DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. Watch these(nucleotides) https://youtu.be/NNASRkIU5Fw https://youtu.be/NNASRkIU5Fw

3. © 2010 Pearson Education, Inc. The structure of DNA and RNA Genetic material of living organisms is either DNA or RNA. DNA – Deoxyribonucleic acid RNA – Ribonucleic acid Genes are lengths of DNA that code for particular proteins.

4. © 2010 Pearson Education, Inc. DNA and RNA are polynucleotides Both DNA and RNA are polynucleotides. They are made up of smaller molecules called nucleotides. DNA is made of two polynucleotide strands: RNA is made of a single polynucleotide strand:

5. © 2010 Pearson Education, Inc. Structure of a nucleotide A nucleotide is made of 3 components: A Pentose sugar This is a 5 carbon sugar The sugar in DNA is deoxyribose. The sugar in RNA is ribose.

6. © 2010 Pearson Education, Inc. Structure of a nucleotide A Phosphate group Phosphate groups are important because they link the sugar on one nucleotide onto the phosphate of the next nucleotide to make a polynucleotide.

7. © 2010 Pearson Education, Inc. Structure of a nucleotide A Nitogenous base In DNA the four bases are: Thymine Adenine Cytosine Guanine In RNA the four bases are: Uracil Adenine Cytosine Guanine

8. © 2010 Pearson Education, Inc. Nitrogenous bases – Two types Pyramidines Thymine - T Cytosine - C Uracil - U Purines Adenine - A Guanine - G

9. © 2010 Pearson Education, Inc. Adenine

10. © 2010 Pearson Education, Inc. Guanine

11. © 2010 Pearson Education, Inc.

12. Sugar phosphate bonds (backbone of DNA) Nucleotides are connected to each other via the phosphate on one nucleotide and the sugar on the next nucleotide A Polynucleotide

13. © 2010 Pearson Education, Inc. Sugar-phosphate backbone Phosphate group Nitrogenous base DNA nucleotide Nucleotide Thymine (T) Sugar Polynucleotide DNA double helix Sugar (deoxyribose) Phosphate group Nitrogenous base (can be A, G, C, or T) Figure 10.1

14. © 2010 Pearson Education, Inc. Polynucleotide Phosphate group Nucleotide Sugar DNA Nitrogenous base Nitrogenous base Number of strands Sugar DNA RNA Ribose Deoxy- ribose CGATCGAT CGAUCGAU 1 2 Figure 10.UN3

15. © 2010 Pearson Education, Inc. 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.

16. © 2010 Pearson Education, Inc. Watson and Crick’s Discovery of the Double Helix James Watson and Francis Crick determined that DNA is a double helix.

17. © 2010 Pearson Education, Inc. The model of 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.

18. © 2010 Pearson Education, Inc. Twist Figure 10.4

19. © 2010 Pearson Education, Inc. DNA bases pair in a complementary fashion: Adenine (A) pairs with thymine (T) Cytosine (C) pairs with guanine (G)

20. © 2010 Pearson Education, Inc. (c) Computer model (b) Atomic model (a) Ribbon model Hydrogen bond Figure 10.5 5’ 3’ 5’ 3’

21. © 2010 Pearson Education, Inc. Check out the 5’ and 3’ binding sites!

22. © 2010 Pearson Education, Inc. James Watson (L) and Francis Crick (R), and the model they built of the structure of DNA

23. © 2010 Pearson Education, Inc. Base pairing The Nitrogenous Bases pair up with other bases. For example the bases of one strand of DNA base pair with the bases on the opposite strand of the DNA.

24. © 2010 Pearson Education, Inc. Double helix

25. © 2010 Pearson Education, Inc.

27. The Rule: Adenine always base pairs with Thymine (or Uracil if RNA) Cytosine always base pairs with Guanine. This is beacuse there is exactly enough room for one purine and one pyramide base between the two polynucleotide strands of DNA.

28. © 2010 Pearson Education, Inc. Complementary base pairing PurinesPyramidines Adenine Thymine AdenineUracil GuanineCytosine

29. © 2010 Pearson Education, Inc. Nature of the Genetic Material Property 1 - it must contain, in a stable form, information encoding the organism’s structure, function, development and reproduction Property 2 - it must replicate accurately so progeny cells have the same genetic makeup Property 3 - it must be capable of some variation (mutation) to permit evolution

30. © 2010 Pearson Education, Inc. Replication of DNA and Chromosomes Speed of DNA replication: 3,000 nucleotides/min in human 30,000 nucleotides/min in E.coli Accuracy of DNA replication: Very precise (1 error/1,000,000,000 nt)

31. © 2010 Pearson Education, Inc.

34. Meselson and Stahl (1958)

35. © 2010 Pearson Education, Inc. 35 DNA Replication https://youtu.be/FBmO _rmXxIw https://youtu.be/FBmO _rmXxIw https://youtu.be/FBmO _rmXxIw copyright cmassengale

36. © 2010 Pearson Education, Inc. 36 Replication Facts DNA has to be copied before a cell divides DNA is copied during the S or synthesis phase of interphase New cells will need identical DNA strands copyright cmassengale

37. © 2010 Pearson Education, Inc. 37 Synthesis Phase (S phase) S phase during interphase of the cell cycle Nucleus of eukaryotes Mitosis -prophase -metaphase -anaphase -telophase G1G1 G2G2 S phase interphase DNA replication takes place in the S phase. copyright cmassengale

38. © 2010 Pearson Education, Inc. 38 DNA Replication Begins at Origins of Replication Two strands open forming Replication Forks (Y-shaped region) New strands grow at the forks ReplicationFork Parental DNA Molecule 3’ 5’ 3’ 5’ copyright cmassengale

39. © 2010 Pearson Education, Inc. 39 DNA Replication As the 2 DNA strands open at the origin, Replication Bubbles form Prokaryotes (bacteria) have a single bubble Eukaryotic chromosomes have MANY bubbles Bubbles copyright cmassengale

40. © 2010 Pearson Education, Inc. 40 DNA Replication Enzyme Helicase unwinds and separates the 2 DNA strands by breaking the weak hydrogen bonds Single-Strand Binding Proteins(SSB) Single-Strand Binding Proteins(SSB) attach and keep the 2 DNA strands separated and untwisted copyright cmassengale

41. © 2010 Pearson Education, Inc. 41 DNA Replication Enzyme SSB relieve stressDNA molecule Enzyme SSB attaches to the 2 forks of the bubble to relieve stress on the DNA molecule as it separates Enzyme DNA Enzyme copyright cmassengale

42. © 2010 Pearson Education, Inc. 42 DNA Replication Before RNA primers Before new DNA strands can form, there must be RNA primers present to start the addition of new nucleotides Primase Primase is the enzyme that synthesizes the RNA Primer DNA polymerase can then add the new nucleotides copyright cmassengale

43. © 2010 Pearson Education, Inc. 43copyright cmassengale

44. © 2010 Pearson Education, Inc. 44 DNA Replication DNA polymerase can only add nucleotides to the 3’ end of the DNA This causes the NEW strand to be built in a 5’ to 3’ direction RNAPrimer DNA Polymerase Nucleotide 5’ 3’ Direction of Replication copyright cmassengale

45. © 2010 Pearson Education, Inc. 45 Remember HOW the Carbons Are Numbered! O O=P-O OPhosphate Group Group N Nitrogenous base (A, G, C, or T) (A, G, C, or T) CH2 O C1C1 C4C4 C3C3 C2C2 5 Sugar Sugar(deoxyribose) copyright cmassengale

46. © 2010 Pearson Education, Inc. 46 Remember the Strands are Antiparallel P P P O O O 1 2 3 4 5 5 3 3 5 P P P O O O 1 2 3 4 5 5 3 5 3 G C TA copyright cmassengale

47. © 2010 Pearson Education, Inc. 47 Synthesis of the New DNA Strands The Leading Strand single strand The Leading Strand is synthesized as a single strand from the point of origin toward the opening replication fork RNAPrimer DNA Polymerase Nucleotides 3’5’ copyright cmassengale

48. © 2010 Pearson Education, Inc. 48 Synthesis of the New DNA Strands The Lagging Strand is discontinuously The Lagging Strand is synthesized discontinuously against overall direction of replication This strand is made in MANY short segments It is replicated from the replication fork toward the origin RNA Primer Leading Strand DNA Polymerase 5’5’ 5’ 3’ Lagging Strand 5’ 3’ copyright cmassengale

49. © 2010 Pearson Education, Inc. 49 Lagging Strand Segments Okazaki Fragments - lagging strand Okazaki Fragments - series of short segments on the lagging strand Must be joined together by an enzyme Lagging Strand RNAPrimerDNAPolymerase 3’ 5’ Okazaki Fragment copyright cmassengale

50. © 2010 Pearson Education, Inc. 50 Joining of Okazaki Fragments The enzyme Ligase joins the Okazaki fragments together to make one strand Lagging Strand Okazaki Fragment 2 DNA ligase DNA ligase Okazaki Fragment 1 5’ 3’ copyright cmassengale

51. © 2010 Pearson Education, Inc. 51 Replication of Strands Replication Fork Point of Origin copyright cmassengale

52. © 2010 Pearson Education, Inc. 52 Proofreading New DNA DNA polymerase initially makes about 1 in 10,000 base pairing errors Enzymes proofread and correct these mistakes The new error rate for DNA that has been proofread is 1 in 1 billion base pairing errors copyright cmassengale

53. © 2010 Pearson Education, Inc. 53 Semiconservative Model of Replication Idea presented by Watson & Crick The The two strands of the parental molecule separate, and each acts as a template for a new complementary strand New DNA consists of 1 PARENTAL (original) and 1 NEW strand of DNA Parental DNA DNA Template New DNA copyright cmassengale

54. © 2010 Pearson Education, Inc. 54 DNA Damage & Repair Chemicals & ultraviolet radiation damage the DNA in our body cells Cells must continuously repair DAMAGED DNA Excision repair occurs when any of over 50 repair enzymes remove damaged parts of DNA DNA polymerase and DNA ligase replace and bond the new nucleotides together copyright cmassengale

55. © 2010 Pearson Education, Inc. 55 Question: What would be the complementary DNA strand for the following DNA sequence? DNA 5’-CGTATG- 3’ copyright cmassengale

56. © 2010 Pearson Education, Inc. 56 Answer: DNA 5’-CGTATG- 3’ DNA 3’-GCATAC- 5’ copyright cmassengale

57. © 2010 Pearson Education, Inc. Lectures by Chris C. Romero, updated by Edward J. Zalisko PowerPoint ® Lectures for Campbell Essential Biology, Fourth Edition – Eric Simon, Jane Reece, and Jean Dickey Campbell Essential Biology with Physiology, Third Edition – Eric Simon, Jane Reece, and Jean Dickey Protein Synthesis https://youtu.be/h3b9ArupXZg

58. © 2010 Pearson Education, Inc. 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

59. © 2010 Pearson Education, Inc. TRANSLATION Protein RNA TRANSCRIPTION DNA Cytoplasm Nucleus Figure 10.8-3

60. © 2010 Pearson Education, Inc. The function of a gene is to dictate the production of a polypeptide. A protein may consist of two or more different polypeptides. Genetic information in DNA is: Transcribed into RNA, then Translated into polypeptides

61. © 2010 Pearson Education, Inc. What is the language of nucleic acids? 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.

62. © 2010 Pearson Education, Inc. What are the rules for translating the RNA message into a polypeptide? A codon is a triplet of bases, which codes for one amino acid.

63. © 2010 Pearson Education, Inc. The Genetic Code The genetic code is: The set of rules relating nucleotide sequence to amino acid sequence Shared by all organisms Of the 64 triplets: 61 code for amino acids 3 are stop codons, indicating the end of a polypeptide

64. © 2010 Pearson Education, Inc. TRANSLATION Amino acid RNA TRANSCRIPTION DNA strand Polypeptide Codon Gene 1 Gene 3 Gene 2 DNA molecule Figure 10.10

65. © 2010 Pearson Education, Inc. Second base of RNA codon First base of RNA codon Phenylalanine (Phe) Leucine (Leu) Cysteine (Cys) Leucine (Leu) Isoleucine (Ile) Valine (Val) Met or start Serine (Ser) Proline (Pro) Threonine (Thr) Tyrosine (Tyr) Histidine (His) Glutamine (Gln) Asparagine (Asn) Alanine (Ala) Stop Glutamic acid (Glu) Aspartic acid (Asp) Lysine (Lys) Arginine (Arg) Tryptophan (Trp) Arginine (Arg) Serine (Ser) Glycine (Gly) Third base of RNA codon Figure 10.11

66. © 2010 Pearson Education, Inc. Transcription: From DNA to RNA Transcription: 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.

67. © 2010 Pearson Education, Inc. Initiation of Transcription 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

68. © 2010 Pearson Education, Inc. RNA Elongation During the second phase of transcription, called elongation: The RNA grows longer The RNA strand peels away from the DNA template

69. © 2010 Pearson Education, Inc. Termination of Transcription 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

70. © 2010 Pearson Education, Inc. 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)

71. © 2010 Pearson Education, Inc. Newly made RNA RNA nucleotides RNA polymerase Template strand of DNA Direction of transcription (a) A close-up view of transcription (b) Transcription of a gene RNA polymerase Completed RNA Growing RNA Termination Elongation Initiation Terminator DNA Area shown in part (a) at left RNA Promoter DNA RNA polymerase DNA of gene Figure 10.13

72. © 2010 Pearson Education, Inc. Translation: The Players Translation is the conversion from the nucleic acid language to the protein language. Messenger RNA (mRNA) Translation requires: mRNA ATP Enzymes Ribosomes Transfer RNA (tRNA)

73. © 2010 Pearson Education, Inc. Transcription Addition of cap and tail Coding sequence mRNA DNA Cytoplasm Nucleus Exons spliced together Introns removed Tail Cap RNA transcript with cap and tail Exon Intron Figure 10.14

74. © 2010 Pearson Education, Inc. Transfer RNA (tRNA) Transfer RNA (tRNA): Acts as a molecular interpreter Carries amino acids Matches amino acids with codons in mRNA using anticodons

75. © 2010 Pearson Education, Inc. tRNA polynucleotide (ribbon model) RNA polynucleotide chain Anticodon Hydrogen bond Amino acid attachment site tRNA (simplified representation) Figure 10.15

76. © 2010 Pearson Education, Inc. Ribosomes Ribosomes are organelles that: Coordinate the functions of mRNA and tRNA Are made of two protein subunits Contain ribosomal RNA (rRNA)

77. © 2010 Pearson Education, Inc. Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA tRNA binding sites Codons Ribosome (b) The “players” of translation (a) A simplified diagram of a ribosome Large subunit Small subunit P site mRNA binding site A site Figure 10.16

78. © 2010 Pearson Education, Inc. Translation: The Process Translation is divided into three phases: Initiation Elongation Termination

79. © 2010 Pearson Education, Inc. 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.

80. © 2010 Pearson Education, Inc. Start of genetic message Tail End Cap Figure 10.17

81. © 2010 Pearson Education, Inc. 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.

82. © 2010 Pearson Education, Inc. Initiator tRNA mRNA Start codon Met P site Small ribosomal subunit A site Large ribosomal subunit Figure 10.18

83. © 2010 Pearson Education, Inc. 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

84. © 2010 Pearson Education, Inc. Step 3, translocation: The P site tRNA leaves the ribosome The tRNA carrying the polypeptide moves from the A to the P site

85. © 2010 Pearson Education, Inc. New peptide bond Stop codon mRNA movement mRNA P site Translocation Peptide bond formation Polypeptide ELONGATION Codon recognition A site Codons Anticodon Amino acid Figure 10.19-4

86. © 2010 Pearson Education, Inc. Termination Elongation continues until: The ribosome reaches a stop codon The completed polypeptide is freed The ribosome splits into its subunits

87. © 2010 Pearson Education, Inc. Review: DNA  RNA  Protein In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein in the cytoplasm.

88. © 2010 Pearson Education, Inc. Transcription RNA polymerase mRNA DNA Intron Nucleus mRNA Intron Tail Cap RNA processing tRNA Amino acid attachment Enzyme ATP Initiation of translation Ribosomal subunits Elongation Anticodon Codon Termination Polypeptide Stop codon Figure 10.20-6

89. © 2010 Pearson Education, Inc. 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.

90. © 2010 Pearson Education, Inc. 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

91. © 2010 Pearson Education, Inc. Types of Mutations 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

92. © 2010 Pearson Education, Inc. Normal hemoglobin DNA mRNA Normal hemoglobin Mutant hemoglobin DNA mRNA Sickle-cell hemoglobin Figure 10.21

93. © 2010 Pearson Education, Inc. Insertions and deletions can: Change the reading frame of the genetic message Lead to disastrous effects

94. © 2010 Pearson Education, Inc. Mutagens Mutations may result from: Errors in DNA replication Physical or chemical agents called mutagens

95. © 2010 Pearson Education, Inc. Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection.

96. © 2010 Pearson Education, Inc. mRNA and protein from a normal gene Deleted (a) Base substitution Inserted (b) Nucleotide deletion (c) Nucleotide insertion Figure 10.22

97. © 2010 Pearson Education, Inc. 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.

98. © 2010 Pearson Education, Inc. Bacterial cell Head Tail fiber DNA of virus Bacteriophage (200 nm tall) Colorized TEM Figure 10.25

99. © 2010 Pearson Education, Inc. Plant Viruses Viruses that infect plants can: Stunt growth Diminish plant yields Spread throughout the entire plant

100. © 2010 Pearson Education, Inc. Viral plant diseases: Have no cure Are best prevented by producing plants that resist viral infection

101. © 2010 Pearson Education, Inc. 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.

102. © 2010 Pearson Education, Inc. Protein coat RNA Protein spike Membranous envelope Figure 10.28

103. © 2010 Pearson Education, Inc. Protein spike Envelope Mumps virus Colorized TEM Figure 10.29c

104. © 2010 Pearson Education, Inc. 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.

105. © 2010 Pearson Education, Inc. Envelope Reverse transcriptase Surface protein Protein coat RNA (two identical strands) Figure 10.31

106. © 2010 Pearson Education, Inc. 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

107. © 2010 Pearson Education, Inc. 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

108. © 2010 Pearson Education, Inc. 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.

109. © 2010 Pearson Education, Inc. Protein coat RNA Protein spike Membranous envelope Figure 10.28

110. © 2010 Pearson Education, Inc. New viruses can arise by: Mutation of existing viruses Spread to new host species