What Mad Pursuit (1988, Ch.5) Francis Crick (1916 ) British molecular Biologist 12 BIOLOGY, CH 1

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2 Almost all aspects of life are engineered at the molecular level, and without understanding molecules we can only have a very sketchy understanding of life itself. What Mad Pursuit (1988, Ch.5) Francis Crick (1916 ) British molecular Biologist 2

3 There are new fields in biological science: Genomics the study of the genome (an organism s entire DNA sequence) Proteomics the study of the structure and function of proteins Bioinformatics the science of managing and analysing biological data using advanced computing techniques. 3

4 THE NATURE OF MATTER Matter has mass and takes up space. Matter is composed of atoms. Atoms are made up of a nucleus which contains protons (+) and neutrons (0). Electrons (-) spin around the nucleus in paths called orbitals. An atom is neutral if electrons = protons The number of protons defines an element. 4

5 ORGANIC CHEMICALS Carbon is found in all compounds (except water) that make up living things on Earth. Organic compounds are complex carbon-containing compounds such as: Carbohydrates Lipids (fats & oils) Proteins Nucleic acids (DNA, RNA) Carbon dioxide is not complex and is grouped with inorganic compounds. 5

6 OTHER ELEMENTS Besides carbon, there are many other elements that are essential for making organic compounds: Oxygen (O), Hydrogen (H) Nitrogen (N), Phosphorus (P) Iron (Fe), Calcium (Ca) Sodium (Na), Potassium (K) Magnesium (Mg), and many others in very small quantities 6

7 ISOTOPES Some atoms of an element can have more neutrons in their nucleus than others. Such atoms are called isotopes of the element eg. Carbon-14 The nucleus of the isotope is unstable and breaks apart giving off energy, which we call radiation. When this happens we say that the element decays. By giving off radiation, atoms reach a more stable state. Radioactive isotopes are useful tools in the study of many areas of science, including biochemical reactions and medical research (Biobox 1.1, pg 6) because their presence can be detected by the radiation they release. 7

8 ISOTOPES 8

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11 Review Questions Set 1 11

12 Chemical Bonds The number and arrangement of electrons in an atom s outer shell determine its chemical behaviour or reactivity. Outer shell electrons are called valence electrons. 12

13 Chemical Bonds Atoms accept, give away or share their valence electrons with other atoms, thereby achieving chemical stability. Compounds are stable combinations of atoms of different elements that are held together by chemical bonds. The nature of the bonds differs according to the type of atoms involved. 13

14 Ionic Compounds 14

15 Electrolytes Salts are ionic compounds that dissolve in water as the bonds holding the ions together weaken and break, releasing them. These particles in solution are called electrolytes. 15

16 Molecular Compounds Instead of losing or gaining electrons, atoms of non-metals combine with other non-metal atoms by sharing pairs of valence electrons, thus forming molecular compounds. The bonds holding the atoms in these molecules together are covalent bonds. Ionic and Covalent bonding animation 16

17 Molecular Compounds - water In the water molecule, oxygen and the two hydrogens share outer electrons. Oxygen now has 8 outer electrons (stable) Each hydrogen now has 2 outer electrons (stable) 17

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19 Review Questions Set 2 19

20 Acids, Bases and Buffers An acid is a substance that produces hydrogen ions (H + ) in solution. The acidity of a solution is measured by its ph. The lower the ph, the more acidic the solution. A buffer is a substance that can react with an acid or a base and maintain a steady ph. 20

21 From Jacaranda Biology 3&4 21

22 Water Opposites attract About 75-85% of a cell by weight is water. Most reactions occur in a watery medium. Many organisms live in water. Water molecules are polar and form hydrogen bonds with each other. More substances dissolve in water than in any other substance. Polar substances dissolve in water and are Hydrophilic (water loving). Non-polar substances (eg. Oil, petrol) do not dissolve in water and are Hydrophobic. Most gases dissolve in water. 22

23 Properties of Water 23

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25 Review Questions Set 3 25

26 BIOLOGICAL MACROMOLECULES Macromolecules are large molecules involved in many processes in the cell. The four main groups of macromolecules are: PROTEINS NUCLEIC ACIDS CARBOHYDRATES LIPIDS (fats and oils) Each of the macromolecules is made up of smaller components. 26

27 BIOLOGICAL MACROMOLECULES 27

28 MACRO- MOLECULE MAIN ELEMENTS SUBUNITS CARBOHYDRATE C, H, O Saccharides EXAMPLE Glucose, starch, cellulose, sucrose LIPID C, H, O Fatty acids Vegetable oil PROTEIN C, H, O, N Amino acids enzymes NUCLEIC ACID C, H, O, N, P Nucleotides DNA, RNA 28

29 Functional groups in Hydrocarbons 29

30 Review Questions Set 4 30

31 Polymerisation 31

32 Review Questions Set 5 32

33 Carbohydrates Each molecule consists of carbon, hydrogen and oxygen atoms in the ratio of 1:2:1, giving the general formula for carbohydrates of nch 2 O. Carbohydrates are classified as: monosaccharides (eg. glucose) disaccharides (eg. sucrose) and polysaccharides (eg. cellulose) Run Molworks 33

34 From Jacaranda Biology 3&4 34

35 Make models of glucose Carbohydrates Join 2 glucose molecules at 1,4 to show cellulose bonds, and at 1,6 to show starch & glycogen Demonstrate condensation Make ribose models 35

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37 Carbohydrates 37

38 From Jacaranda Biology 3&4 38

39 From Jacaranda Biology 3&4 39

40 Carbohydrates Organisms use carbohydrates as an energy source (eg. starch and glycogen) and for structural components (eg. cellulose and chitin). Most animals do not have the enzymes to break down cellulose in their diet, but have to rely on bacteria in their gut to do it for them. Carbohydrate molecules can combine with other atoms or groups to form important compounds, eg. glycoproteins, which are a combination of carbohydrate and protein molecules. 40

41 Review Questions Set 6 41

42 Lipids Lipids are a diverse group of molecules and include: fats and oils, terpenes, waxes, phospholipids, glycolipids and steroids whose various functions relate to their hydrophobic nature. 42

43 Lipids In cells, lipids have three important functions: 1 energy storage they have twice the amount of energy as carbohydrates 2 structural component of membranes 3 specific biological functions, such as the transmission of chemical signals both within and between cells (hormones). 43

44 Lipids The fats and oils of plants and animals are typically composed of triglyceride molecules three fatty acid chains attached to a glycerol backbone. GLYCEROL 44

45 Lipids 45

46 Lipids in the membranes of cells Phospholipids form when a phosphate group is added to the glycerol backbone rather than a third fatty acid chain. Glycolipids form when a carbohydrate group attaches to the glycerol backbone rather than a third fatty acid chain. They are vital for communication and detect, and bind with, signalling molecules. Cholesterol is a component of cell membranes and of myelin sheaths around nerve cells. It belongs to the group of lipids collectively known as steroids. 46

47 Steroids From Jacaranda Biology 3&4 47

48 Review Questions Set 7 48

49 Proteins Virtually everything a cell is or does depends on the proteins it contains. Keratin is a protein found in your hair, feathers of birds, the rattle of a rattlesnake and the spines of an echidna. The whole set of proteins produced by a cell is called its proteome and the study of proteomes is proteomics. 49

50 Proteins Proteins are large complex molecules and are the most important molecules in living organisms. As enzymes they control the thousands of chemical reactions that maintain life processes. This diversity of proteins can be explained by the way their subunits, the 20 amino acids, are sequenced in various combinations (like arranging 20 kinds of beads in different ways to make different necklaces of different lengths and the necklace chains can then be arranged differently in loops and folds to give each its characteristic features). 50

51 Proteins 51

52 Proteins - amino acids Amino acids are small molecules that have the same basic structure: a central carbon atom a hydrogen atom a carboxyl acid group (COO - ) an amine group (NH 3 + ) and an R group. It is the difference in the R group that distinguishes one amino acid from another and gives them their particular chemical properties. There are only 20 different amino acids found in the proteins of living organisms 52

53 Proteins - amino acids Some of the R groups are non-polar, some are polar and others are charged. Run Molworks 53

54 Isomerisation in amino acids 54

55 Proteins - structure Primary structure DNA determines the sequence of amino acids in the polypeptide. Secondary structure various parts of the polypeptide undergo coiling and folding due to interactions between the various amino acids that are present. Hydrogen bonding Ionic bonding Disulfide bridges Hydrophobic Interactions (van der Waals interactions) Tight coils are known as α-helices and the folding forms β-sheets. 55

56 Proteins structure: α-helix 56

57 Proteins structure: β-sheet 57

58 Proteins - structure Tertiary structure R groups attract similar R groups. This causes the polypeptide chains to become folded, coiled or twisted into the protein s functional shape or conformation. Protein molecules with the same sequence of amino acids will fold into the same shape. A change to just one amino acid will alter the shape of the protein molecule and it may not function properly. 58

59 Proteins - structure 59

60 Proteins - structure Quaternary structure Many large, complex protein molecules consist of two or more polypeptide chains. Haemoglobin, for example, which carries oxygen in the blood, consists of four polypeptide chains. A variety of bonds holds the polypeptide chains together and gives the overall shape to the molecule. Run Cn3D Program 60

61 From Jacaranda Biology 3&4 61

62 Protein binding site 62

63 Proteins - structure The function of protein molecules may change as a result of a number of factors: misreading the DNA code for proteins high temperatures strong salty solutions or very acidic or alkaline conditions (ph). These conditions can denature or change the shape of the protein molecules. 63

64 Review Questions Set 8 64

65 Review Questions set 9 65

66 Nucleic Acids Nucleic acids store information in a chemical code that directs the machinery of the cell to produce proteins. Nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are large, linear polymers. A molecule of DNA is composed of two long strands of subunits called nucleotides, wound around each other to form the familiar double helix. RNA is usually composed of a single chain of nucleotides and forms a single strand. 66

67 Nucleic Acids - Nucleotides A nucleotide has three chemical parts: a five carbon sugar (ribose in RNA and deoxyribose in DNA) a negatively charged phosphate group an organic nitrogen-containing compound called a base 67

68 Nucleic Acids - Bases There are four kinds of nitrogenous bases in DNA: adenine (A) thymine (T) guanine (G) cytosine (C). 68

69 Nucleic Acids - Nucleotides In each nucleotide strand, the sugar molecule of one nucleotide binds to the phosphate group of the next nucleotide, leaving the nitrogenous base sticking out from each sugar and opposite the nitrogenous base of the second strand. Hydrogen bonds between the opposing pairs of nitrogenous bases hold the double helix together, much like the rungs of a twisted ladder or a spiral staircase. 69

70 Nucleic Acids - Nucleotides The bonding of the nitrogen bases does not happen by chance: A bonds with T and C bonds with G, giving rise to the base-pairing rule. also refer to SRAM on Nucleic Acids 70

71 Nucleic Acids DNA vs RNA The difference between the deoxyribose sugar of the DNA and the ribose sugar of RNA is that ribose has one more oxygen atom. The nitrogenous base thymine is replaced by the base uracil (U) in RNA. 71

72 Nucleic Acids DNA code The code carried by the DNA is organised in triplets (three nucleotides) that determine the order in which the amino acids are sequenced and this determines which protein is formed. Each cell of our body has over a metre in length of DNA, twisted and coiled into 46 chromosomes that have more than three billion base pairs (bp). The parts of the DNA that code for proteins are called genes. The total set of genes that each cell of an organism has is called its genome. The study of these sets of genes and the way they interact with each other is called genomics. 72

73 Nucleic Acids function of RNA RNA has many functions in producing proteins. The information on genes in the DNA that codes for making proteins is transferred to messenger RNA (mrna). The mrna molecule carries the code out of the nucleus and into the cytoplasm. This is where the protein-making factories (ribosomes) are located. The ribosomes read the mrna code three nucleotides at a time (in codons). The ribosomes are composed of ribosomal RNA (rrna) and protein. The incoming amino acids are attached to transfer RNA (trna) molecules. Each trna molecule has an anticodon that will bind with a complementary codon on mrna. This is how the ribosomes know the correct amino acid to add to a growing protein chain. 73

74 DNA Interactive View and discuss some of the sections within THEMES DNA Molecule 74

75 DNA and PROTEIN molecules have specific structure Molecular Specificity There is interaction between molecules The shape of a molecule determines its function Binding sites have specificity 75

76 Review questions set 10 76

77 Challenge question 1 77

78 Challenge question 2 78

79 From Jacaranda Biology 3&4 79

80 GTAC Summary Slides covering all biomolecules. s/teacher_access_resources/making%20b iomacromolecules/index.html 80

81 Visual Summary 81

82 At the end of the chapter do the following activities: Matchup (on text CD) Self-test (on text CD) Biotech Game 82

83 What is this? Clue: Parrot s name is Polly POLYUNSATURATED 83

84 What is this? Clue: Parrot s name is Polly POLYSACCHARIDE 84

85 What is this? Clue: Parrot s name is Polly POLYNOMIAL 85

86 What is this? Clue: Parrot s name is Polly POLYGON 86