Chapter 10

1. Chapter 10 0 Molecular Biology of the Gene: (Molecular Genetics)

2. 1. Nucleic Acid Structure Sugar-phosphate backbone Phosphate group Nitrogenous base A A Sugar Nitrogenous base(A, G, C, or T) Phosphategroup C C DNA nucleotide O H H3C C C N O C C T CH2 H T O P N O O O– Thymine (T) O C C H H H H G G C C H O Sugar(deoxyribose) T T DNA nucleotide DNA polynucleotide • DNA and RNA are polymers of nucleotides • DNA is a nucleic acid • Made of long chains of nucleotide monomers

3. H H H H O N N O C H C H H3C C C H N N N C C N C N N C H H C C C C C C C C C C H O H N N N O H N N H N N H H H H H Adenine (A) Guanine (G) Thymine (T) Cytosine (C) Purines Pyrimidines • DNA has four kinds of nitrogenous bases • A, T, C, and G

4. Nitrogenous base (A, G, C, or U) Key Hydrogen atom O Phosphategroup Carbon atom C H Nitrogen atom H N C Oxygen atom O C C Phosphorus atom H O P O CH2 O N Uracil (U) O– O C C H H H H C C OH O Sugar(ribose) • RNA is also a nucleic acid • But has a slightly different sugar • And has U instead of T

5. DNA is a double-stranded helix • James Watson and Francis Crick • Worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin

6. Twist • The structure of DNA • Consists of two polynucleotide strands wrapped around each other in a double helix

7. G C O T A OH P Hydrogen bond –O O A T OH O H2C A T Basepair O CH2 O O C G P O O– –O C G O P O H2C O O C T G A O CH2 C G O O P O O– – O O P O H2C O O G C A T O CH2 O O A T P O – O O– O P A T O O H2C O A T A T CH2 O OH O O– P G C HO O T A Partial chemical structure Ribbon model Computer model • Hydrogen bonds between bases • Hold the strands together • Each base pairs with a complementary partner • A with T, and G with C

8. T A T T A A T A T A G C G G G C C C G C C C G G G C G C C A A T A T A A T T A T T T A A A T Both parental strands serve as templates Two identical daughtermolecules of DNA Parental moleculeof DNA 2. DNA REPLICATION • DNA replication depends on specific base pairing • DNA replication • Starts with the separation of DNA strands • Then enzymes use each strand as a template • To assemble new nucleotides into complementary strands Nucleotides

9. G C T A G C G C A T T A C G A T C G G C C G G C C C G G A C A T A T G T A T T G T T A A A A A C T T T A • DNA replication is a complex process, which occurs during “S” Phase of the eukaryotic cell cycle. • Due in part to the fact that some of the helical DNA molecule must untwist Replication Fork

10. Parental strand Origin of replication Daughter strand Bubble Two daughter DNA molecules • DNA replication: A closer look • DNA replication • Begins at specific sites on the double helix

11. At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating Helicases are enzymes that untwist the double helix at the replication forks Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

12. 5 end 3 end P HO 5 4 2 3 A T 3 1 1 4 2 5 P P C G P P G C P P A T OH P 3 end 5 end • Each strand of the double helix • Is oriented in the opposite direction

13. DNA polymerase molecule 3 5 Daughter strandsynthesizedcontinuously Parental DNA 5 3 Daughter strandsynthesizedin pieces 3 5 5 3 DNA ligase Overall direction of replication • Using the enzyme DNA polymerase • The cell synthesizes one daughter strand as a continuous piece • The other strand is synthesized as a series of short pieces • Which are then connected by the enzyme DNA ligase

14. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN • 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 its DNA bases • A particular gene, a linear sequence of many nucleotides • Specifies a polypeptide

15. DNA Transcription RNA Translation Protein Figure 10.6A 3. Gene Transcription • The DNA of the gene is transcribed into RNA • Which is translated into the polypeptide

16. Genetic information written in codons is translated into amino acid sequences • The “words” of the DNA “language” • Are triplets of bases called codons • The codons in a gene • Specify the amino acid sequence of a polypeptide

17. DNA molecule Gene 1 Gene 2 Gene 3 DNA strand A A A C A C G G A A C A Transcription U U U G U G C C U U G U RNA Codon Translation Polypeptide Amino acid

18. The genetic code is the Rosetta stone of life • Nearly all organisms • Use exactly the same genetic code

19. Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Transcription G U U U A G A U A A G U RNA Startcondon Stopcondon Translation Met Polypeptide Lys Phe • An exercise in translating the genetic code

20. RNA nucleotides RNA polymerase A C C A T T A U T C T G U G A C A U C C A C C A G A T T T A G G Direction of transcription Template Strand of DNA Newly made RNA • Transcription produces genetic messages in the form of RNA • A close-up view of transcription

21. In the nucleus, the DNA helix unzips • And RNA nucleotides line up along one strand of the DNA, following the base pairing rules • As the single-stranded messenger RNA (mRNA) peels away from the gene • The DNA strands rejoin

22. RNA polymerase DNA of gene Promoter DNA Terminator DNA Area shown In Figure 10.9A Growing RNA Completed RNA RNA polymerase Figure 10.9B • Transcription of a gene 1 Initiation 2 Elongation 3 Termination

23. Exon Intron Exon Intron Exon DNA Transcription Addition of cap and tail Cap RNA transcript with cap and tail Introns removed Tail Exons spliced together mRNA Coding sequence Nucleus Cytoplasm • Eukaryotic RNA is processed before leaving the nucleus • Noncoding segments called introns are spliced out • And a cap and a tail are added to the ends

24. 4. Translation: Gene to Protein • Transfer RNA molecules serve as interpreters during translation • Translation • Takes place in the cytoplasm

25. 0 Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon • A ribosome attaches to the mRNA • And translates its message into a specific polypeptide aided by transfer RNAs (tRNAs)

26. Amino acid attachment site Anticodon • Each tRNA molecule • Is a folded molecule bearing a base triplet called an anticodon on one end • A specific amino acid • Is attached to the other end

27. tRNAmolecules Growingpolypeptide Largesubunit mRNA Small subunit • Ribosomes build polypeptides • A ribosome consists of two subunits • Each made up of proteins and a kind of RNA called ribosomal RNA

28. The subunits of a ribosome • Hold the tRNA and mRNA close together during translation tRNA-binding sites Largesubunit Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA-binding site mRNA Smallsubunit Codons

29. Start of genetic message End • An initiation codon marks the start of an mRNA message

30. Large ribosomalsubunit Met Met Initiator tRNA P site A site U C U A C A A U G AUG Startcodon Small ribosomalsubunit mRNA 1 2 • mRNA, a specific tRNA, and the ribosome subunits • Assemble during initiation

31. 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 to the first amino acid

32. 1 Codon recognition 2 Peptide bondformation Translocation 3 • Each addition of an amino acid • Occurs in a three-step elongation process Aminoacid Polypeptide P site A site Anticodon mRNA Codons mRNAmovement Stopcodon New Peptidebond

33. The mRNA moves a codon at a time • And a tRNA with a complementary anticodon pairs with each codon, adding its amino acid to the peptide chain

34. Elongation continues • Until a stop codon reaches the ribosome’s A site, terminating translation

35. Review: The flow of genetic information in the cell is DNARNAprotein • The sequence of codons in DNA, via the sequence of codons • Spells out the primary structure of a polypeptide

36. 1     mRNA is transcribed from a DNA template. 2      Each amino acidattaches to its propertRNA with the help of aspecific enzyme and ATP. 3       Initiation ofpolypeptide synthesis The mRNA, the first tRNA, and the ribosomal subunits come together. 4 Elongation A succession of tRNAsadd their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time. 5 Termination The ribosome recognizes a stop codon. The poly-peptide is terminated and released. • Summary of transcription and translation DNA Transcription mRNA RNApolymerase Amino acid Translation Enzyme ATP tRNA Anticodon Largeribosomal subunit InitiatortRNA Start Codon Smallribosomal subunit mRNA New peptidebond forming Growingpolypeptide Codons mRNA Polypeptide Stop codon

37. Normal hemoglobin DNA Mutant hemoglobin DNA C A T T T C mRNA mRNA G A A G U A Normal hemoglobin Sickle-cell hemoglobin Glu Val • Mutations can change the meaning of genes • Mutations are changes in the DNA base sequence • Caused by errors in DNA replication or recombination, or by mutagens

38. 1. Point Mutations a. A gene mutation is a change that takes place within a single gene. Point mutations are mutations that involved one base pair and may include ... substitutions, insertions or deletions of nucleotides. The sentence below contains all three-letter words but has experienced a mutation. Can you find the mutation? THE IGR EDC ATA TET HEB IGB ADR AT What kind of mutation did you find? Now what does the sentence say?

39. Normal gene U G C U U C A G A A U G A G G mRNA Met Lys Gly Protein Phe Ala Base substitution A A G A U G C A U G A G U U C Lys Met Phe Ser Ala Missing U Base deletion G G C G A C A U A U G A G U U Lys Ala His Met Leu • Substituting, inserting, or deleting nucleotides alters a gene • With varying effects on the organism

40. MICROBIAL GENETICS • Viral DNA may become part of the host chromosome • Viruses • Can be regarded as genes packaged in protein

41. When phage DNA enters a lytic cycle inside a bacterium • It is replicated, transcribed, and translated • The new viral DNA and protein molecules • Then assemble into new phages, which burst from the host cell

42. In the lysogenic cycle • Phage DNA inserts into the host chromosome and is passed on to generations of daughter cells • Much later • It may initiate phage production

43. Phage Attachesto cell Bacterialchromosome Phage DNA Cell lyses,releasing phages Phage injects DNA Many celldivisions Lytic cycle Lysogenic cycle Phages assemble Lysogenic bacterium reproducesnormally, replicating the prophageat each cell division Phage DNAcircularizes Prophage OR Phage DNA inserts into the bacterialchromosome by recombination New phage DNA andproteins are synthesized • Phage reproductive cycles 1 7 2 4 3 5 6

44. Membranousenvelope RNA Protein coat Glycoprotein spike CONNECTION • Many viruses cause disease in animals • Many viruses cause disease • When they invade animal or plant cells • Many, such as flu viruses • Have RNA, rather than DNA, as their genetic material

45. 1 Entry 2 Uncoating RNA synthesisby viral enzyme 3 RNA synthesis(other strand) 4 Proteinsynthesis 5 6 Assembly • Some animal viruses • Steal a bit of host cell membrane as a protective envelope • Can remain latent in the host’s body for long periods Glycoprotein spike VIRUS Protein coat Viral RNA(genome) Envelope Plasma membraneof host cell Viral RNA(genome) mRNA Template New viralgenome Newviral proteins Exit 7

46. RNA Protein CONNECTION • Plant viruses are serious agricultural pests • Most plant viruses • Have RNA genomes • Enter their hosts via wounds in the plant’s outer layers

47. Colorized TEM 370,000 Colorized TEM 50,000 CONNECTION • Emerging viruses threaten human health

48. Envelope Glycoprotein Protein coat RNA (two identical strands) Reverse transcriptase • The AIDS virus makes DNA on an RNA template • HIV, the AIDS virus • Is a retrovirus

49. Viral RNA CYTOPLASM NUCLEUS Chromosomal DNA RNAstrand Double-strandedDNA Provirus DNA Viral RNAand proteins RNA • Inside a cell, HIV uses its RNA as a template for making DNA • To insert into a host chromosome 1 2 3 4 5 6

50. Mating bridge DNA enters cell Phage Phage Fragment of DNAfrom anotherbacterial cell Fragment of DNA fromanotherbacterial cell(former phagehost) Sex pili Bacterial chromosome (DNA) Recipient cell(“female”) Donor cell(“male”) • Bacteria can transfer DNA in three ways • Bacteria can transfer genes from cell to cell by one of three processes • Transformation, transduction, or conjugation