The Structure and Function of DNA

1. The Structure and Function of DNA Chapter 10 Part II

2. Figure 10.10

3. The Genetic Code • Set of rules relating nucleotide sequence to amino acid sequence - redundancy of the code but no ambiguity • In 1961 an American biochemist Marshall Nierenberg synthesized an artificial RNA molecule - linked together RNA nucleotides having uracil as their base - UUU always coded for phenylalanine

4. Translate the sequence CCAUUUACG Figure 10.11

5. Universality of the Code • The genetic code is shared by all organisms - from the simplest bacteria to the most complex plants and animals - genes can be transcribed and translated after transfer from one species to another

6. Researchers incorporated a gene from a firefly into the DNA of a tobacco plant • The gene codes for the firefly enzyme that produces a glow Figure 10.12

7. Transcription: From DNA to RNA • Transcription – transfer of genetic information from DNA to RNA - an RNA molecule is transcribed from a DNA template • As with replication the 2 DNA strands must first separate - but only one strand serves as a template - RNA nucleotides take their places one at a time along the DNA template strand by forming hydrogen bonds - the RNA nucleotides are linked by the transcription enzyme RNA polymerase

8. RNA nucleotides base-pair one by one with DNA bases on the DNA template strand • The enzyme RNA polymerase links the RNA nucleotides into an RNA chain Fig 10.13a

9. Transcription of an Entire Gene • Special DNA nucleotide sequences inform the RNA polymerase - where to start & where to stop the transcribing process • Initiation of Transcription – the first phase, transcription starts - the ‘start transcribing’ signal, is a nucleotide sequence called a promoter - RNA polymerase attaches to the promoter - RNA synthesis begins - for any gene the promotor dictates which of the 2 strands is to be transcribed

10. RNA Elongation – the second phase of transcription, the RNA strand grows longer - as RNA synthesis continues, the RNA strand separates from its DNA template - allows the separated DNA strands to recombine • Termination of Transcription – the third phase, termination, transcription stops - special sequence of bases in the DNA template, the terminator, signals the end of the gene - at this point, the RNA polymerase detaches from the RNA molecule and the gene

11. Figure 10.13a,b

12. The Processing of Eukaryotic DNA • Prokaryotic cells lack nuclei – RNA transcribed from a gene functions immediately - the messenger molecule, mRNA is translated into protein • Eukaryotic cells have nuclei – localizes transcription in the nucleus - also modifies, or processes, the RNA transcripts before the mRNA moves to the cytoplasm for translation

13. RNA Processing • Addition of a cap and tail – extra nucleotides added to the ends of the RNA transcript - protects the RNA from attack by cellular enzymes - help ribosomes recognize the RNA as mRNA • Removing introns – noncoding stretches of nucleotides are removed - introns are interspersed between the nucleotides that code for amino acids - the coding regions, or exons, are parts of the gene that are expressed

14. RNA splicing –occurs before the RNA leaves the nucleus - introns are removed, and the exons are joined to produce an mRNA molecule • RNA splicing plays a significant role in humans - allows approximately 25,000 genes to produce many 1000s more polypeptides - this is accomplished by varying the exons that are included in the final mRNA

15. Figure 10.14

16. Translation: The Players • Is the conversion from the nucleic acid language to the protein language • First important player is the mRNA produced by transcription - the machinery used to translate mRNA requires enzymes and energy, such as _____ - also requires 2 important players: ribosomes and another kind of RNA called transfer RNA (tRNA)

17. Transfer RNA (tRNA) • Acts as a molecular interpreter - translates the 3-letter word (codon) of nucleic acids to a one-letter word (amino acid) of proteins - tRNA matches amino acids with codons in mRNA using anticodons • To accomplish translation, tRNA molecules must carry out 2 distinct functions: 1) pick up the appropriate amino acids from the cytoplasm 2) recognize the appropriate codons in the mRNA

18. A tRNA molecule is made of a single strand of RNA – polynucleotide chain of ~80 nucleotides - chain twists and folds forming several double-stranded regions where short stretches of RNA base-pair - one end of the folded molecule is a special triplet of bases, anticodon - anticodon triplet is complementary to a codon triplet on the mRNA - during translation, the anticodon on the tRNA molecule recognizes its codon on the mRNA (base-pairing rules) - at the other end of the tRNA molecule is a site where an amino acid can attach

19. Structure of a tRNA Polynucleotide • A twisted ‘rope’ – appendages are the nitrogenous bases • 3-nucleotide segment at one end (purple) - site where an amino acid will attach • 3-base anticodon at the bottom of the molecule will base-pair with its codon Figure 10.15

20. Ribosomes • Organelles that coordinate the function of making a polypeptide – consist of 2 subunits - each subunit is made up of proteins and ribosomal RNA (rRNA) - an assembled ribososme has a binding site for mRNA on its small subunit and - 2 binding sites for tRNA on its large subunit, the - P site, holds the tRNA carrying the growing polypeptide chain, the - A site, holds a tRNA carrying the next amino acid to be added to the chain

21. Figure 10.16a

22. A ribosome holds one molecule of mRNA, 2 molecules of tRNA • Subunits act like a vise, holding the tRNA and mRNA molecules close together • The ribosome can then connect the amino acid from the A site tRNA to the growing polypeptide Figure 10.16b

23. Translation: The Process • Translation can be divided into the same 3 phases as transcription: - Initiation - Elongation - Termination

24. Initiation • The first phase brings together: - The mRNA - The first amino acid with its attached tRNA - The two subunits of the ribosome • Nucleotide sequences at either end of the mRNA are not part of the message - but, along with the cap and tail help the mRNA bind to the ribosome - determines where translation will begin so - the mRNA codons will be translated into the correct sequence of amino acids

25. A Molecule of mRNA • Pink ends are nucleotides that are not part of the message • Along with the cap and tail help the mRNA attach to the ribosome but are not translated • Initiation of translation occurs in 2 steps Figure 10.17

26. 1. mRNA binds to the small subunit; a special initiator tRNA binds to the start codon, the initiator tRNA carries Met; its anticodon UAC binds to the start codon, AUG 2. The large ribosomal subunit binds to the small one, creating a functional ribosome; the initiator tRNA fits into the P site on the ribosome Figure 10.18

27. Elongation • Once initiation is complete, amino acids are added one by one to the first amino acid • Each addition occurs in a 3-step elongation process Step 1 – Codon recognition Step 2 – Peptide bond formation Step 3 – Translocation

28. Step 1, codon recognition – the anticodon of an incoming tRNA carrying its amino acid, pairs with the mRNA codon in 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 bond formation; now the chain has one more amino acid • Step 3, translocation – the P site tRNA now leaves the ribosome, and - the ribosome moves the remaining tRNA, carrying the growing polypeptide to the P site - the mRNA and tRNA move as a unit which brings into the A site the next mRNA codon

29. Figure 10.19

30. Termination • Elongation continues until a stop codon reaches the ribosome’s A site - stop codons: UAA, UAG, UGA • Completed polypeptide, typically several 100 amino acids long, is released, and the ribosome splits into its subunits

31. Review: DNARNAProtein • Is the flow of genetic information in the cell • In eukaryotic cells, transcription – the stage from DNA to RNA, occurs in the nucleus, and - the mRNA is processed before it enters the cytoplasm • Translation is rapid – a single ribosome can make an average-sized polypeptide in less than a minute - as it is made a polypeptide coils and folds, assuming a 3-dimensional or tertiary shape - several polypeptides may come together, forming a protein with a quaternary structure

32. Figure 10.20

33. Transcription and Translation • Are the processes whereby genes control the structures and activites of cells, or - the way the genotype produces the phenotype • Originates with the information in a gene - a specific linear sequence of nucleotides in DNA - the gene serves as a template for the transcription of a complementary sequence of nucleotides in mRNA - mRNA specifies the linear sequence in which amino acids appear in a polypeptide, and - the proteins that form determine the appearance and capabilities of the cell and organism

34. Mutations • A mutation is any change in the nucleotide sequence of DNA - occasionally a base substitution leads to an improved protein or - one with new capabilities that enhance the success of the mutant organism and its descendants - more often, mutations are harmful

35. The molecular basis of sickle-cell disease: the sickle-cell allele differs by only one nucleotide. The difference changes the mRNA codon from one that codes for glutamate (Glu) to one that codes for valine (Val) Fig 10.21

36. Types of Mutations • Within a gene can be divided into 2 general categories: base substitutions and base insertions or deletions • Base substitution – replacement of one base, or nucleotide, by another; can result in - no change in the protein, redundancy of the genetic code - a change in the amino acid coding (missense and nonsense mutations) which might be crucial to the life of the organism

37. Missense Mutations Figure 10.22a

38. Insertions and deletions – often have disastrous effects - mRNA is read as a series of nucleotide triplets during translation, adding or subtracting nucleotides may alter the reading frame - all the nucleotides ‘downstream’ will be regrouped into different codons - the altered polypeptide is likely to be nonfunctional

39. Figure 10.22b

40. Mutagens • Mutagenesis, the creation of mutations, can occur in a number of ways - errors during DNA replication or recombination are called spontaneous mutations (de novo) - physical or chemical agents called mutagens - most common physical mutagen is high-energy radiation, such as X-rays and UV light) - chemical mutagens are of various types, one type consists of chemicals that are similar to normal DNA bases

41. Many mutagens can act as carcinogens – cancer causing agents - UV light and smoking: lifestyle practices can help • Although mutations are often harmful – they can be useful both in nature and in the lab - they are the source of the rich diversity of genes in the living world - they contribute to the process of evolution by natural selection

42. Mutations are the ultimate source of diversity of life Fig 10.23

43. Viruses: Genes in Packages • Viruses sit on the fence between life and nonlife - they exhibit some, but not all characteristics of living organisms - viruses have genes and a highly organized structure - but are not able to reproduce on their own - a virus can survive only by infecting a living cell with genetic material that directs the host cell’s molecular machinery to make more viruses

44. Adenovirus: infects the human respiratory system, consists of DNA enclosed in a protein shell. At each vertex of the polyhedron is a protein spike, helps the virus attach to a cell Fig 10.24

45. Bacteriophages • Or phages – attack bacteria • Once they infect a bacterium, most phages enter a reproductive cycle, the lytic cycle - after many copies of the phage are produced the bacterium lyses (breaks open) - some also reproduce by the lysogenic cycle: viral DNA replication occurs without phage production or the death of the cell

46. The phage consists of a molecule of DNA enclosed within a protein structure; tail fibers bend when they touch the cell surface – the tail is a hollow rod enclosed in a springlike sheath, as the fibers bend, the spring compresses, the bottom of the rod punctures the membrane Fig 10.25

47. Figure 10.26

48. Plant Viruses • Can stunt growth and diminish crop yields – most have RNA rather than DNA - many, like the tobacco mosaic virus are rod-shaped with a sprial arrangement of proteins surrounding the nucleic acid - a virus must get past the plant’s outer protective layer of cells and so a weak plant is more susceptible to infection - infected plants may pass viruses to their offspring - there is no cure for most viral plant diseases • Genetic engineering methods have been used to create virus-resistant plants

49. Tobacco mosaic virus – the rod-shaped virus has RNA as its genetic material; Fig 10.27

50. Animal Viruses • Viruses that infect animals are common causes of disease