1. DNA: part II Making sense out of the message Dr. Wilson Muse Schoolcraft college

2. Cytoplasm Nucleus DNA Transcription RNA Translation Protein

3. 10.7 Genetic information written in codons is translated into amino acid sequences –The sequence of nucleotides in DNA provides a code for constructing a protein –Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence –Transcription rewrites the DNA code into RNA, using the same nucleotide “ language ” –Each “ word ” is a codon, consisting of three nucleotides –Translation involves switching from the nucleotide “ language ” to amino acid “ language ” –Each amino acid is specified by a codon –64 codons are possible –Some amino acids have more than one possible codon

4. Polypeptide Translation Transcription Gene 1 DNA molecule DNA strand Codon Amino acid Gene 2 Gene 3 RNA The Central Dogma

5. Polypeptide Translation Transcription DNA strand Codon Amino acid RNA

6. 10.8 The genetic code is the Rosetta Stone of life –Characteristics of the genetic code –Triplet: Three nucleotides specify one amino acid –61 codons correspond to amino acids –AUG codes for methionine and signals the start of transcription –3 “ stop ” codons signal the end of translation

7. 10.8 The genetic code is the Rosetta stone of life –Redundant: More than one codon for some amino acids –Unambiguous: Any codon for one amino acid does not code for any other amino acid –Does not contain spacers or punctuation: Codons are adjacent to each other with no gaps in between –Nearly universal

8. First base Third base Second base

9. Genetic code circular form Can see the redundant codons note the third nucleotide in each codon

10. Strand to be transcribed DNA

11. Strand to be transcribed DNA Start codon RNA Transcription Stop codon

12. Strand to be transcribed DNA Start codon RNA Transcription Stop codon Polypeptide Translation Met Lys Phe

13. Review Transcription is making RNA from DNA template RNA polymerase synthesizes 5’ to 3’ mRNA can be processed leaves nucleus to be translated

14. RNA polymerase Newly made RNA Direction of transcription Template strand of DNA RNA nucleotides

15. Terminator DNA DNA of gene RNA polymerase Initiation Promoter DNA 1 Elongation 2 Area shown in Figure 10.9A Termination 3 Growing RNA polymerase Completed RNA

16. 10.10 Eukaryotic RNA is processed before leaving the nucleus –Eukaryotic mRNA has interrupting sequences called introns, separating the coding regions called exons –Eukaryotic mRNA undergoes processing before leaving the nucleus –Cap added to 5 ’ end: single guanine nucleotide –Tail added to 3 ’ end: Poly-A tail of 50 – 250 adenines –RNA splicing: removal of introns and joining of exons to produce a continuous coding sequence

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

18. 10.11 Transfer RNA molecules serve as interpreters during translation –Transfer RNA (tRNA) molecules match an amino acid to its corresponding mRNA codon –tRNA structure allows it to convert one language to the other –An amino acid attachment site allows each tRNA to carry a specific amino acid –An anticodon allows the tRNA to bind to a specific mRNA codon, complementary in sequence –A pairs with U, G pairs with C

19. Anticodon Amino acid attachment site RNA polynucleotide chain Hydrogen bond

21. 10.12 Ribosomes build polypeptides –Translation occurs on the surface of the ribosome –Ribosomes have two subunits: small and large –Each subunit is composed of ribosomal RNAs and proteins –Ribosomal subunits come together during translation –Ribosomes have binding sites for mRNA and tRNAs

22. tRNA molecules Growing polypeptide Large subunit Small subunit mRNA

23. tRNA-binding sites Large subunit Small subunit mRNA binding site

24. mRNA Next amino acid to be added to polypeptide Growing polypeptide Codons tRNA

25. 10.13 An initiation codon marks the start of an mRNA message –Initiation brings together the components needed to begin RNA synthesis –Initiation occurs in two steps § mRNA binds to a small ribosomal subunit, and the first tRNA binds to mRNA at the start codon –The start codon reads AUG and codes for methionine –The first tRNA has the anticodon UAC § A large ribosomal subunit joins the small subunit, allowing the ribosome to function –The first tRNA occupies the P site, which will hold the growing peptide chain –The A site is available to receive the next tRNA

26. Start of genetic message End

27. Small ribosomal subunit Start codon P site mRNA A site Large ribosomal subunit Initiator tRNA Met 2 1

28. 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation –Elongation is the addition of amino acids to the polypeptide chain –Each cycle of elongation has three steps § Codon recognition: next tRNA binds to the mRNA at the A site § Peptide bond formation: joining of the new amino acid to the chain –Amino acids on the tRNA at the P site are attached by a covalent bond to the amino acid on the tRNA at the A site

29. § Translocation: tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation = UAG, UGA, UAA

30. –Termination –The completed polypeptide is released –The ribosomal subunits separate –mRNA is released and can be translated again 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation Animation: Translation

31. Polypeptide A site 1 Codon recognition Codons Amino acid Anticodon P site mRNA 2 Peptide bond formation 3 Translocation New peptide bond Stop codon mRNA movement

32. 10.15 Review: The flow of genetic information in the cell is DNA  RNA  protein –Does translation represent: –DNA  RNA or RNA  protein? –Where does the information for producing a protein originate: –DNA or RNA? –Which one has a linear sequence of codons: –rRNA, mRNA, or tRNA? –Which one directly influences the phenotype: –DNA, RNA, or protein?

33. Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. mRNA is transcribed from a DNA template. 2 1 RNA polymerase Amino acid DNA Transcription mRNA tRNA ATP Translation Enzyme 3 The mRNA, the first tRNA, and the ribo- somal sub-units come together. Initiator tRNA Large ribosomal subunit Anticodon Initiation of polypeptide synthesis Small ribosomal subunit mRNA Start Codon New peptide bond forming Growing polypeptide 4 A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time. Elongation Codons mRNA Polypeptide 5 The ribosome recognizes a stop codon. The poly- peptide is terminated and released. Termination Stop codon

34. mRNA is transcribed from a DNA template. RNA polymerase Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. Amino acid DNA Transcription mRNA tRNA ATP Translation Enzyme The mRNA, the first tRNA, and the ribosomal sub-units come together. Initiator tRNA Large ribosomal subunit Anticodon Initiation of polypeptide synthesis Small ribosomal subunit mRNA Start Codon 1 2 3

35. New peptide bond forming Growing polypeptide 4 A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time. Elongation Codons mRNA Polypeptide 5 The ribosome recognizes a stop codon. The polypeptide is terminated and released. Termination Stop codon

36. 10.16 Mutations can change the meaning of genes –A mutation is a change in the nucleotide sequence of DNA –Base substitutions: replacement of one nucleotide with another –Effect depends on whether there is an amino acid change that alters the function of the protein –Deletions or insertions –Alter the reading frame of the mRNA, so that nucleotides are grouped into different codons –Lead to significant changes in amino acid sequence downstream of mutation –Cause a nonfunctional polypeptide to be produced

37. 10.16 Mutations can change the meaning of genes –Mutations can be –Spontaneous: due to errors in DNA replication or recombination –Induced by mutagens –High-energy radiation –Chemicals

38. Normal hemoglobin DNAMutant hemoglobin DNA Sickle-cell hemoglobin Normal hemoglobin mRNA ValGlu

39. Normal gene Protein Base substitution Base deletion Missing mRNA Met Lys Phe Ser Ala Met Lys Phe Gly Ala Met Lys Leu Ala His

40. Gene Mutations Point Mutations – changes in one or a few nucleotides –Substitution THE FAT CAT ATE THE RAT THE FAT HAT ATE THE RAT –Insertion THE FAT CAT ATE THE RAT THE FAT CAT XLW ATE THE RAT –Deletion THE FAT CAT ATE THE RAT THE FAT ATE THE RAT

41. Gene Mutations Frameshift Mutations – shifts the reading frame of the genetic message so that the protein may not be able to perform its function. –Insertion THE FAT CAT ATE THE RAT THE FAT HCA TAT ETH ERA T –Deletion THE FAT CAT ATE THE RAT TEF ATC ATA TET GER AT H H

42. Chromosome Mutations Changes in number and structure of entire chromosomes Original Chromosome ABC * DEF DeletionAC * DEF DuplicationABBC * DEF InversionAED * CBF TranslocationABC * JKL GHI * DEF

43. Significance of Mutations Most are neutral Eye color Birth marks Some are harmful Sickle Cell Anemia Down Syndrome Some are beneficial Sickle Cell Anemia to Malaria Immunity to HIV

44. What Causes Mutations? There are two ways in which DNA can become mutated: –Mutations can be inherited. Parent to child –Mutations can be acquired. Environmental damage Mistakes when DNA is copied

45. How should you feel about mutations? Without mutation, there would be no evolution. Mutations can lead to problems, (skin cancer), but genetic diversity and adaptation are probably worth the risk.

46. MICROBIAL GENETICS How did scientists learn all this stuff?

47. 10.17 Viral DNA may become part of the host chromosome –Viruses have two types of reproductive cycles –Lytic cycle –Viral particles are produced using host cell components –The host cell lyses, and viruses are released

48. Bacterial chromosome Phage injects DNA Phage Phage DNA Attaches to cell Phage DNA circularizes Lytic cycle New phage DNA and proteins are synthesized Phages assemble Cell lyses, releasing phages 1 2 3 4

49. 10.17 Viral DNA may become part of the host chromosome –Viruses have two types of reproductive cycles –Lysogenic cycle –Viral DNA is inserted into the host chromosome by recombination –Viral DNA is duplicated along with the host chromosome during each cell division –The inserted phage DNA is called a prophage –Most prophage genes are inactive –Environmental signals can cause a switch to the lytic cycle Animation: Phage T4 Lytic Cycle Animation: Phage Lambda Lysogenic and Lytic Cycles

50. Bacterial chromosome Phage injects DNA Phage Phage DNA Attaches to cell 2 1 3 Phage DNA circularizes Lytic cycle 4 New phage DNA and proteins are synthesized Phages assemble Cell lyses, releasing phages 6 5 7 Phage DNA inserts into the bacterial chromosome by recombination Lysogenic bacterium reproduces normally, replicating the prophage at each cell division Prophage Lysogenic cycle Many cell divisions OR

51. Bacterial chromosome Phage injects DNA Phage DNA circularizes Phage DNA inserts into the bacterial chromosome by recombination Lysogenic bacterium reproduces normally, replicating the prophage at each cell division Prophage Lysogenic cycle Many cell divisions 5 7 6 2 Phage Phage DNA Attaches to cell 1

52. 10.18 CONNECTION: Many viruses cause disease in animals and plants –Some animal viruses reproduce in the cell nucleus –Most plant viruses are RNA viruses –They breach the outer protective layer of the plant –They spread from cell to cell through plasmodesmata –Infection can spread to other plants by animals, humans, or farming practices Animation: Simplified Viral Reproductive Cycle

53. Plasma membrane of host cell VIRUS Entry Uncoating Viral RNA (genome) Viral RNA (genome) 2 1 3 Membranous envelope Protein coat Glycoprotein spike RNA synthesis by viral enzyme Template RNA synthesis (other strand) Protein synthesis mRNA 4 5 6 New viral genome New viral proteins Assembly 7 Exit

54. Plasma membrane of host cell VIRUS Entry Viral RNA (genome) Viral RNA (genome) 2 Membranous envelope Protein coat Glycoprotein spike Uncoating RNA synthesis by viral enzyme 3 1

55. Template RNA synthesis (other strand) Protein synthesis New viral genome mRNA New viral proteins Assembly Exit 4 5 6 7

56. 10.19 : Emerging viruses threaten human health –Examples of emerging viruses –HIV –Ebola virus –West Nile virus –RNA coronavirus causing severe acute respiratory syndrome (SARS) –Avian flu virus

57. 10.20 The AIDS virus makes DNA on an RNA template –AIDS is caused by HIV, human immunodeficiency virus –HIV is a retrovirus, containing –Two copies of its RNA genome –Reverse transcriptase, an enzyme that produces DNA from an RNA template - RNA viruses can be highly mutable

58. –HIV duplication –Reverse transcriptase uses RNA to produce one DNA strand –Reverse transcriptase produces the complementary DNA strand –Viral DNA enters the nucleus and integrates into the chromosome, becoming a provirus –Provirus DNA is used to produce mRNA –mRNA is translated to produce viral proteins –Viral particles are assembled and leave the host cell 10.20 The AIDS virus makes DNA on an RNA template Animation: HIV Reproductive Cycle

59. Reverse transcriptase RNA (two identical strands) Protein coat Glycoprotein Envelope

60. Double- stranded DNA Viral RNA and proteins DNA strand Viral RNA N UCLEUS C YTOPLASM Chromosomal DNA Provirus DNA RNA 2 1 5 3 4 6

61. 10.23 Bacterial plasmids can serve as carriers for gene transfer –Plasmids are small circular DNA molecules that are separate from the bacterial chromosome –F factor is involved in conjugation –When integrated into the chromosome, transfers bacterial genes from donor to recipient –When separate, transfers F-factor plasmid –R plasmids transfer genes for antibiotic resistance by conjugation Workhorses in recombinant DNA technology

62. Male (donor) cell Bacterial chromosome F factor starts replication and transfer F factor (plasmid) Plasmid completes transfer and circularizes Cell now male

63. Plasmids

64. DNA enters cell Bacterial chromosome (DNA) Fragment of DNA from another bacterial cell Genetic Recombination: Homologous recombination

65. Donated DNA Recipient cell’s chromosome Crossovers Recombinant chromosome Degraded DNA Recombination can lead to gene sharing

66. Disease without nucleic acids: Prions Prions (pre - ons) - are proteins that are misfolded and can corrupt their properfolded counterparts to misfold One bad apple..........

67. Prion proteins play roles in some of our cells Properly folded Improperly folded and infective

68. Wrap up and Review All living things encode their genes as either DNA or RNA RNA acts as an intermediate to the formation of proteins The genetic code allows us to predict protein sequence from DNA/RNA sequence

69. Sugar- phosphate backbone Deoxy- ribose Ribose Nucleotide Sugar Phosphate group DNA Nitrogenous base Nitrogenous base Polynucleotide DNA RNA Sugar CGATCGAT CGAUCGAU

70. Codons Growing polypeptide Amino acid tRNA Anticodon Large ribosomal subunit mRNA Small ribosomal subunit

71. comes in three kinds called RNA (d) (e) (f) is performed by organelles called use amino-acid-bearing molecules called (h) molecules are components of one or more polymers made from monomers called is performed by enzyme called is a polymer made from monomers called DNA (a) (b) (c) Protein (g) (i)

72. § Compare and contrast the structures of DNA and RNA § Describe how DNA replicates § Explain how a protein is produced § Distinguish between the functions of mRNA, tRNA, and rRNA in translation § Determine DNA, RNA, and protein sequences when given any complementary sequence You should now be able to:

73. § Distinguish between exons and introns and describe the steps in RNA processing that lead to a mature mRNA § Explain the relationship between DNA genotype and the action of proteins in influencing phenotype § Distinguish between the effects of base substitution and insertion or deletion mutations You should now be able to:

74. § Distinguish between lytic and lysogenic viral reproductive cycles and describe how RNA viruses are duplicated within a host cell § Explain how an emerging virus can become a threat to human health § Identify three methods of transfer for bacterial genes § Distinguish between viroids and prions § Describe the effects of transferring plasmids from donor to recipient cells You should now be able to: