DNA Structure, Function, and Engineering Page /14/2018 Dr. Amjid Iqbal 1

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1 DNA Structure, Function, and Engineering Page /14/2018 Dr. Amjid Iqbal 1

2 Background Organisms exhibit striking similarity at the molecular level. The structures and metabolic activities of all cells rely on a common set of molecules that including amino acids, carbohydrates, lipids and nucleotides, as well as their polymeric forms. Nucleotides: (building block of nucleic acid ) are Involved in nearly every facet of cellular life. Specifically, they participate in oxidation reduction, energy transfer, intracellular signaling, and biosynthesis reaction. 2/14/2018 Dr. Amjid Iqbal 2

3 Introduction Their polymers, The nucleic acids DNA and RNA, are the primary players in the storage and decoding of genetic information. Perform structural and catalytic roles in cells (it and their polymers). 2/14/2018 Dr. Amjid Iqbal 3

4 Focus of this Chapter Structure of Nucleotides (Monomers) Structure of Nucleic acids (DNA and RNA)- Polymer How these molecules carry biological information 2/14/2018 Dr. Amjid Iqbal 4

5 Nucleotides There are eight common varieties of nucleotides 2/14/2018 Dr. Amjid Iqbal 5

6 Each nucleotide composed of a nitrogen base linked to sugar to which at least one phosphate group is attached Base PO 4 Nucleoside Sugar 2/14/2018 Dr. Amjid Iqbal 6

7 NUCLEOTIDE STRUCTURE PHOSPHATE SUGAR Ribose or Deoxyribose Nitrogenous Base PURINES Adenine (A) Guanine(G) PYRIMIDINES Cytocine (C) Thymine (T) Uracil (U) NUCLEOTIDE 2/14/2018 Dr. Amjid Iqbal 7

8 Nucleotides 2/14/2018 Dr. Amjid Iqbal 8

9 Nitrogenous Bases Purines: The most common are Adenine (A) and Guanine (G). Form bonds to a five carbon sugar (a pentose) via their N9 atoms (β 1 N9). Pyrimidine: The major are Cytosine (C) and Uracil (U) and Thymine (T). Form bonds to a five carbon sugar (a pentose) via their N1 atoms (β1 N1). 2/14/2018 Dr. Amjid Iqbal 9

10 Nitrogenous Bases (planar, aromatic and heterocylic) 2 purine bases Adenine: A Guanine: G A G Bases Pyrimidines Purines C T U 2 pyrimidine bases (in DNA) Cytosine: C Thymine: T or Uracil: U (in RNA, instead of Thymine) 2/14/2018 Dr. Amjid Iqbal 10

11 Nitrogenous Bases 2/14/2018 Dr. Amjid Iqbal 11

12 Ribose-Sugar carbons numbered: 1,2,3,4,5 DNA: 2 Deoxyribose or just deoxyribose /14/2018 Dr. Amjid Iqbal 12

13 Spot the difference HOCH 2 O OH HOCH 2 O OH OH OH OH (no O) ribose deoxyribose 2/14/2018 Dr. Amjid Iqbal 13

14 Nucleotides In ribonucleotide or deoxyribonucleotide, one or more phosphate groups are bonded to C3 or atom C5 of the pentose to form 3 - nucleotide or 5 -nucleotide Nucleotides most commonly contain one to three phosphate groups at the C5ʹ position and are called nucleoside monophosphates, diphosphates, and triphosphates. 2/14/2018 Dr. Amjid Iqbal 14

15 Example of a Nucleotide NH 2 N O - O P O - O O CH 2 O N OH deoxyctyidine monophosphate (dcmp) 2/14/2018 Dr. Amjid Iqbal 15

16 Nucleotides Figure 3-1: chemical structure of nucleotides. (a) A 5 ʹ ribonucleotide and (b) 3ʹ deoxyribonucleotide. The purine or pyrimidine base is linked to C1ʹ of the pentose and at least one phosphate (red) is also attached. A nucleoside consists only of a base and a pentose. 2/14/2018 Dr. Amjid Iqbal 16

17 Nucleoside When the phosphate groups is absent, the compound is known as nucleoside 2/14/2018 Dr. Amjid Iqbal 17

18 2/14/2018 Dr. Amjid Iqbal 18

19 Nucleotides 2/14/2018 Dr. Amjid Iqbal 19

20 Nucleotides in DNA and RNA Ribonucleotides are components of RNA (Ribonucleic acid). Deoxyribonucleotides are components DNA (Deoxyribonucleic acid). of Free Nucleotides, which are anionic, are almost always associated with the counterion Mg 2+ in cells. 2/14/2018 Dr. Amjid Iqbal 20

21 Nucleotides Participate in Metabolic Reactions Adenosine Triphosphate (ATP): a nucleotide containing adenine, ribose, and a triphosphate group. ATP is often mistakenly referred to as an energy storage molecule, but it is more accurately termed an energy carrier orenergy transfer agent. 2/14/2018 Dr. Amjid Iqbal 21

22 2/14/2018 Dr. Amjid Iqbal 22

23 1- Nucleotides The process of photosynthesis or the breakdown of metabolic fuels such as carbohydrates and fatty acids leads to the formation of ATP from Adenosine Diphosphate (ADP): 2/14/2018 Dr. Amjid Iqbal 23

24 1- Nucleotides The Chemical Potential Energy of ATP is made available when it transfers one (or two) of its phosphate groups to another molecule. This process can be represented by the reverse of the preceding reaction, namely the hydrolysis of ATP toadp. Starch synthesis in plants proceeds by repeated additions of glucose units donated by ADP Glucose (Fig. 3 2). 2/14/2018 Dr. Amjid Iqbal 24

25 1- Nucleotides Figure 3-2: ADP glucose. In this nucleotide derivative, glucose (blue) is attached to adenosine (black) by a diphosphate group (red) 2/14/2018 Dr. Amjid Iqbal 25

26 Introduction to Nucleic Acid Structure Nucleotides can be joined to each other to form the polymers that familiar as DNA & RNA 2/14/2018 Dr. Amjid Iqbal 26

27 Polymerise Nucleotides Phosphates of polynucleotides are acidic, so at physiological ph, nucleic acids are polyanions. nucleotides can be linked phosphates linked to 2 pentoses phosphodiester linkages Link PO 4 at 5 end to 3 OH of next nucleotide Each nucleotide in polynucleotide is known as nucleotide residue 2/14/2018 Dr. Amjid Iqbal 27

28 The 5ʹ end: is the terminal residue whose C5ʹ is not linked to another nucleotide. The 3ʹ end: is the terminal residue whose C3ʹ is not linked to another nucleotide. By convention, the sequence of nucleotide residues in a nucleic acid is written, left to right, from The 5ʹ end to The 3ʹ end. 2/14/2018 Dr. Amjid Iqbal 28

29 Nucleic Acids are Polymers of Nucleotides (a) Figure 3-3: Chemical structure of nucleic acid. Nucleic acid contains information in the form of its sequence of residues 2/14/2018 Dr. Amjid Iqbal 29

30 Nucleic Acids are Polymers of Nucleotides (b) Figure 3-3: Chemical structure of nucleic acid. (b) schematic representation of paucg. A vertical denotes a ribose residue, the attached base is indicated by a single letter, and a diagonal line flanking an optional p represents a phosphodiester bond. The atom numbers for the ribose residue may be omitted. The equivalent representation of d(patcg) differs only by the absence of the 2ʹ-OH group and the the replacement of U by T. 2/14/2018 Dr. Amjid Iqbal 30

31 Chargaff's Rules Describe the Base Composition of DNA: Although there appear to be no rules governing the nucleotide composition of typical RNA molecules, DNA has equal numbers of adenine and thymine (A = T) and equal numbers of guanine and cytosine residues (G C). Chargaff's Rules: are the relationships between the numbers of base residues (A / T, G / C) and were discovered in the late 1940s by Erwin Chargaff. 2/14/2018 Dr. Amjid Iqbal 31

32 Erwin Chargaff s Data 2/14/2018 Dr. Amjid Iqbal Paul Billiet ODWS

33 DNA Forms a Double Helix 2/14/2018 Dr. Amjid Iqbal 33

34 2 Introduction to Nucleic Acid Structure: B DNA Forms a Double Helix: The determination of the structure of DNA by James Watson and Francis Crick in 1953 is often said to mark the birth of Modern Molecular Biology. The Watson Crick structure of DNA not only provided a model of what is arguable the central molecule of life, it also suggested the molecular mechanism of heredity. 2/14/2018 Dr. Amjid Iqbal 34

35 Watson-Crick Model of DNA 2/14/2018 Dr. Amjid Iqbal 35

36 DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDE The sister strands of the DNA molecule run in opposite directions (antiparallel) They are joined by the bases Each base is paired with a specific partner: A is always paired with T G is always paired with C Purine with Pyrimidine Thus the sister strands are complementary but not identical The bases are joined by hydrogen bonds, individually weak but collectively strong. 2/14/2018 Dr. Amjid Iqbal 36

37 Hydrogen bonds Bases occupy the core of helix and sugar-phosphate chains run along periphery, minimizing the repulsions between phosphate groups P P P G C C C G G P P P P A T P P T A P 2016 Paul Billiet ODWS 2/14/2018 Dr. Amjid Iqbal 37 P T A P

38 Double Helix of DNA 2/14/2018 Dr. Amjid Iqbal 38

39 DNA Forms a Double Helix: Figure 3-6: Three Dimensional structure of DNA. The repeating helix is based on the structure of the self complementary dodecamer d(cgcgaattcgcg) determined by Richard Dickerson and Horace Drew. The view in this ball and - stick model is perpendicular to the helix axis. The sugar phosphate backbones (blue, with green ribbon outlines) wind around the periphery of the molecule. The bases (red) form hydrogen bonded pairs that occupy the core. H atoms have been omitted for clarity. The two strands run in opposite directions. 2/14/2018 Dr. Amjid Iqbal 39

40 The Double Helix Two polynucleotide chains wind around a common axis to form double helix 2 anti-parallel strands Major and minor grooves 2/14/2018 Dr. Amjid Iqbal 40

41 Each base is hydrogen bonded to a base in opposite strand to form base Pairing A T basepair 2 h-bonds G C basepair 3 h-bonds 2 anti-parallel DNA strands 2/14/2018 Dr. Amjid Iqbal 41

42 Complementary Base Pairs Watson-Crick structure can accommodate only two types of base pairs. Each A must pair with T and each G must pair with C. These hydrogen bonding interactions, known as complementary base pairing 2/14/2018 Dr. Amjid Iqbal 42

43 Figure 3 8: Complementary base pairing in DNA. Adenine in one strand pairs with thymine in the other strand by forming hydrogen (dashed Similarly, specific bonds lines). guanine pairs with cytosine. This base pairing between polynucleotide chains is responsible for the double strand nature of DNA. 2/14/2018 Dr. Amjid Iqbal 43

44 The DNA Double Helix Watson-Crick structure can accommodate any sequence of bases on one polynucleotide strand if the opposite strand has complementary base 2/14/2018 Dr. Amjid Iqbal 44

45 Learning Check Each DNA strand can act as a template for the synthesis of its complementary strand and hence hereditary information is encoded -A-G-T-C-C-A-A-T-G-C- 2/14/2018 Dr. Amjid Iqbal 45

46 Solution NA1 -A-G-T-C-C-A-A-T-G-C- -T-C-A-G-G-T-T-A-C-G- 2/14/2018 Dr. Amjid Iqbal 46

47 Size of DNA Most DNA molecules are extremely large in size. In organism s genome, its unique DNA contents are allocated among several chromosomes Each chromosome has separate DNA molecule 2/14/2018 Dr. Amjid Iqbal 47

48 Diploid and haploid Organisms which contain two equivalent set of chromosomes (one set from each parent) called diploid. For example human are diploid contain 46 chromosomes per cell, their haploid number is 23. 2/14/2018 Dr. Amjid Iqbal 48

49 Base Pair Length of DNA molecules are described in term of bp or Kb Length of DNA in Viruses is about 5kb while largest mammalian contain DNA well over 250,000 kb DNA double helix forms coils and loops when it is packaged inside the cell. 2/14/2018 Dr. Amjid Iqbal 49

50 RNA is a Single Stranded Nucleic Acid Single stranded DNA is rare, mainly heredity material of viruses RNA form compact structure Base pairing occurs intra-molecularly give stem-loop structures. 2/14/2018 Dr. Amjid Iqbal 50

51 2 Introduction to Nucleic Acid Structure: B DNA Forms a Double Helix. Figure 3 9: Formation of a stem loop structure. Base pairing between complementary sequence within an RNA strand allows the polynucleotide to fold back on itself. RNA 2/14/2018 Dr. Amjid Iqbal 51

52 Type of RNA 1 - Ribosomal RNA (rrna): integral part of ribosomes (very abundant) 2 - Transfer RNA (trna): carries activated amino acids to ribosomes. 3 - Messenger RNA (mrna): endcodes sequences of amino acids in proteins. 4 - Catalytic RNA (Ribozymes): catalzye cleavage of specific RNA species. 2/14/2018 Dr. Amjid Iqbal 52

53 RNA vs. DNA DNA Double stranded Deoxyribose sugar Bases: C,G A,T RNA Single stranded Ribose sugar Bases: C,G,A,U Both contain a sugar, phosphate, and base. 2/14/2018 Dr. Amjid Iqbal 53

54 3 Overview of Nucleic Acid Function 2/14/2018 Dr. Amjid Iqbal 54

55 DNA Carries Genetic Information in the form of its sequence of nucleotides. 2/14/2018 Dr. Amjid Iqbal 55

56 DNA Replication When a cell divide, two strands of DNA separate. Each strand acts like a template for the assembly of its complementary strand Every progeny cell contain a complete DNA molecule. Each DNA molecule consists of one parental strand and one daughter strand 2/14/2018 Dr. Amjid Iqbal 56

57 DNA Unwinds G-C G C A-T A T C-G C G T-A T A 2/14/2018 Dr. Amjid Iqbal 57

58 DNA Copied with Base Pairs Two copies of original DNA strand G-C A-T C-G T-A G-C A-T C-G G-A Daughter strands are synthesized by the stepwise polymerization of nucleotides at pair with bases on the parental strands 2/14/2018 Dr. Amjid Iqbal 58

59 Figure 3 11: DNA replication. Each strand of parental DNA (blue) acts as a template for the synthesis of a complementary daughter strand (red). Thus, the resulting double stranded molecules are identical. 2/14/2018 Dr. Amjid Iqbal 59

60 Genes Direct Protein Synthesis There is specific connection between genes and enzymes, one gene one enzyme (protein) theory The link between DNA and enzymes (nearly all of which are proteins) is RNA. 2/14/2018 Dr. Amjid Iqbal 60

61 cell Gene nucleus chromosome DNA gene 2/14/2018 Dr. Amjid Iqbal 61

62 Protein Synthesis Overview Two processes are required: 1. Transcription: DNA > mrna DNA of gene transcribed to produce RNA molecule 2. Translation: mrna > protein RNA sequence is then translated into corresponding sequence of amino acids to form protein 2/14/2018 Dr. Amjid Iqbal 62

63 Transcription and Translation: An Overview (aka the Central Dogma) DNA RNA Protein Transcription Translation 2/14/2018 Dr. Amjid Iqbal 63

64 Transcription 2/14/2018 Dr. Amjid Iqbal 64

65 Transcription: DNA > mrna Process of making messenger RNA (mrna) from a DNA template to take the DNA info outside of the nucleus mrna makes its way to ribosome, an organelle that is itself composed of RNA (called rrna) 2/14/2018 Dr. Amjid Iqbal 65

66 Now you try Based on the DNA template, create the matching mrna strand: DNA: mrna: C T A T G C A A A C T A T A G G A U A C G U U U G A U A U C Check: Are there any T s in your mrna? There shouldn t be!!! 2/14/2018 Dr. Amjid Iqbal 66

67 Transcription Try it! What RNA strand will be made from the following DNA sequence? TCTCCACGA 2/14/2018 Dr. Amjid Iqbal 67

68 Step One: Transcription Try it! What RNA strand will be made from the following DNA sequence? TCTCCACGA AGAGGUGCU 2/14/2018 Dr. Amjid Iqbal 68

69 Transcription is done what now? Now we have mature mrna transcribed from the cell s DNA. It is leaving the nucleus through a nuclear pore. Once in the cytoplasm, it finds a ribosome so that translation can begin. We know how mrna is made, but how do we read the code? 2/14/2018 Dr. Amjid Iqbal 69

70 Translation: mrna > protein Process of making proteins from information on mrna mrna travels out of nucleus to the ribosome, which reads the mrna as a series of 3 letter words called codons 2/14/2018 Dr. Amjid Iqbal 70

71 Translation At ribosome, each set of three nucleotides in mrna (codon) make pairs with three complementary nucleotide of small RNA called trna 2/14/2018 Dr. Amjid Iqbal 71

72 trna Transfer RNA Bound to one amino acid on one end Anticodon on the other end complements mrna codon 2/14/2018 Dr. Amjid Iqbal 72

73 Codon: 3-base code on mrna that codes for a specific amino acid Ex. CGU = alanine GUU = valine The sequence of bases in DNA tell mrna what order amino acids must join together to make a particular protein. 2/14/2018 Dr. Amjid Iqbal 73

74 Figure 3 13: Translation. 2/14/2018 Dr. Amjid Iqbal 74

75 Each trna molecule is attached to its corresponding amino acid. Ribosome catalyzes the joining of amino acids, which are monomers of proteins. Amino acids added to the growing protein chain according to the order in which trna molecules bind to mrna 2/14/2018 Dr. Amjid Iqbal 75

76 Since nucleotide sequence of mrna reflects the sequence of nucleotides in the gene, DNA directs the protein synthesis. 2/14/2018 Dr. Amjid Iqbal 76

77 Gene Direct Protein Synthesis 2/14/2018 Dr. Amjid Iqbal 77

78 2/14/2018 Dr. Amjid Iqbal 78

79 RECAP: 1. DNA is transcribed into mrna in the nucleus. 2. The mrna leaves the nucleus and enters the cytoplasm. 3. The protein is translated from the mrna sequence using trna and amino acids. 2/14/2018 Dr. Amjid Iqbal 79

80 These transfers of biological information are summarized in the so called central dogma of molecular biology formulated by Crick in /14/2018 Dr. Amjid Iqbal 80

81 Mutation Alterations to the genetic material of an organism, result in protein with altered structures and functions. Genomics The study of the genome s size and gene content Transcriptomics Study of gene expression 2/14/2018 Dr. Amjid Iqbal 81

82 Gene Expression which focus on set of mrna molecules (transcriptome), that is transcribed from DNA Proteomics Study of proteins produced as a result of transcription and translation 2/14/2018 Dr. Amjid Iqbal 82

83 End of Chapter 2/14/2018 Dr. Amjid Iqbal 83