Chapter 2 Molecules of Life

2.

5. Electron Orbitals Volumes of space that surround the nucleus Electrons move in orbitals

15. Fig. 3.3

19. Isotope

26. Fig. 3.8

40. pH scaleAcidicNeutralBasic

46. Chemistry:Macromolecules

49. More on Macromolecules Polymer: a molecule made of MANY chains of a similar subunit Monomer: a single molecule that is the BASIC building block of a macromolecule Monomers can combine to form a polymer View animation on Polymer formation http://science.nhmccd.edu/biol/dehydrat/dehydrat.html

50. Dehydration Synthesis The process of FORMING a macromolecule Forms a COVALENT bond between two subunits: A hydroxyl (OH) group is removed from one subunit A hydrogen (H) is removed from the other subunit

52. Carbohydrates Contain C, H, O atoms (1:2:1 ratio) # Carbon atoms = # Oxygen atoms Hydrophilic Excellent for energy storage Why?? The C-H bonds store energy. When an organism requires an energy source, C-H bonds are the ones most often broken. This results in the release of stored energy. Comprise 1-2% of a cells mass 2 types: simple carbohydrates complex carbohydrates

53. Simple Carbohydrates Monosaccharide Simple sugar Consists of one subunit; smallest carbs Ex. Glucose (C6H12O6) Also, fructose, ribose, deoxyribose See Figure 3.29 Disaccharide Result of linkage of two monosaccharides Ex. Sucrose, lactose, maltose See Figure 3.30

54. Complex Carbohydrates Polysaccharides Long chain polymers of sugars The body converts soluble sugars into insoluble forms (polysaccharides). These polysaccharides are then deposited throughout the body in specific storage areas. Preferred form of energy storage Plants: starch = glucose polysaccharide that plants use to store energy Animals: glycogen = highly insoluble macromolecule formed of glucose and polysaccharides that serves as stored energy Celluose = indigestible b/c we lack enzymes to break it down = fiber; synthesized by plants for cell wall constructionCelluose = indigestible b/c we lack enzymes to break it down = fiber; synthesized by plants for cell wall construction

55. Lipids Contain C, H, and O Hydrophobic (held together by non-polar covalent bonds) Used as long term storage Contains MORE energy-rich C-H bonds than carbs

56. LipidsI. Triglycerides (Fat)

57. Lipids, continuedTriglycerides Saturated Fatty acids with ALL internal carbon atoms forming covalent bonds with two hydrogen atoms Animal source Solid at room temperature and body temp (37C) Unsaturated Fats with fatty acids that have double bonds between 1 or more pairs of carbon atoms Plant source Kink imparts a 30� bend: Liquid at room temperature Low melting point When we eat fat, lipase digests the fat and breaks it down to the 3 individual fatty acids The longer the fatty acid chain, the HIGHER the melting temp I.E. Butter � is a saturated triglyceride (composed of different saturated triglycerides). That is why it melts slowly, not all at once! Different triglycerides melt at different temps. Unsaturated fats melt at lower temps than saturated (> irregular the shape of unsat = lower melting point); as unsat increases, MP reduces Solid at RT b/c they pack very well � they are straight like sticks, whereas unsaturated is liquid at RT b/c the kinks imparted by the double bonds make them pack less efficientlyWhen we eat fat, lipase digests the fat and breaks it down to the 3 individual fatty acids The longer the fatty acid chain, the HIGHER the melting temp I.E. Butter � is a saturated triglyceride (composed of different saturated triglycerides). That is why it melts slowly, not all at once! Different triglycerides melt at different temps. Unsaturated fats melt at lower temps than saturated (> irregular the shape of unsat = lower melting point); as unsat increases, MP reduces Solid at RT b/c they pack very well � they are straight like sticks, whereas unsaturated is liquid at RT b/c the kinks imparted by the double bonds make them pack less efficiently

58. Why are unsaturated fats good while saturated fats are bad for your health? The C C bond in unsaturated fats creates a negative charge that causes the fat molecules to repel each other rather than stick together (as they do in long chain saturated fats).

59. Hydrogenation Example: Margarine Margarine is formed from heating oil (unsaturated triglycerides) in the presence of a metal catalyst (aluminum) and hydrogen. That environment breaks the C C and replaces it with two hydrogen atoms producing very hard, saturated fats. Chemists vary the degree of time that hydrogenation occurs resulting in a product that is soft and spreadable (partially hydrogenated). N.B. Margarine is 10-50% trans fatty acids = BAD Margarine has been found to be contaminated with aluminum. Al is a causative agent in AD Catalyst = something that facilitates a chemical reaction without itself being used up AD = Alzheimer�s DiseaseCatalyst = something that facilitates a chemical reaction without itself being used up AD = Alzheimer�s Disease

60. What is a trans-fatty acid? Trans fatty acids have hydrogen atoms on opposite sides of the double bonded carbons Cis fatty acids have hydrogen atoms that on the same side with each other The enzymes that metabolize fat can only metabolize cis fatty acids

61. Butter is a saturated triglyceride.Why does butter soften as it melts, why doesn�t it instantly melt? Because the fatty acid chains that come off the glycerol backbone differ. Each different fatty acid has a different melting point.

62. Common fats Saturated Palmitic acid Unsaturated Omega-3 Palmitic acod Myristic acid = id�d from nutmeg; found in N-terminus of plasma mem associated cytoplasmic proteinsPalmitic acod Myristic acid = id�d from nutmeg; found in N-terminus of plasma mem associated cytoplasmic proteins

63. Types of Lipids Per gram, Fat has twice the energy as carbsPer gram, Fat has twice the energy as carbs

66. Protein Comprises 10-30% cell mass Functional roles (enzymes) and structural roles (collagen, keratin) All proteins are a long polymer chain of amino acid subunits small molecules, 20 total all 20 have a basic structure of a central carbon atom to which the 4 following are attached: hydrogen atom amino group (-NH2) carboxyl group (-COOH) an �R� group Collagen = cartilage, bones, tendons Keratin = feathers of birdsCollagen = cartilage, bones, tendons Keratin = feathers of birds

67. Amino Acids

68. How to make a protein Link specific amino acids together in a particular order Peptide bond = covalent bond that links 2 amino acids together Polypeptides = long chains of amino acids liked by peptide bonds

69. Protein Structure Structure determines function What determines protein structure?

70. Primary Structure of Protein The sequence of amino acids of a polypeptide chain

71. Initial folding of the polypeptide chain caused by formation of hydrogen bonds Can result in sheets (Beta sheets) or coils (alpha helices) of polypeptides Because some AAs are polar and some are nonpolar, a polypeptide folds in solution: nonpolar regions are forced together (forced by the polar groups and their attraction to water resulting in the polar groups repulsion of nonpolar amino acids)

72. Tertiary Structure of a Protein A folded and twisted molecule Repulsion by water forces nonpolar amino acids towards the interior leaving polar amino acids exposed to the exterior

73. Quaternary Structure of a Protein Spatial arrangement of several component polypeptide chains

74. Denaturation What influences how a polypeptide folds in solution?

75. Nucleic Acids Long polymers of nucleotides that serve as information storage devices of cells Nucleotides have 3 components: A five carbon sugar A phosphate group (PO4) An organic nitrogen-containing base

76. Nucleic Acids DNA and RNA DNA (deoxyribonucleic acid) Possible nucleotides: Adenine, Guanine, Cytosine, THYMINE Structure: 2 nucleotide strands = double helix RNA (ribonucleic acid) Possible nucleotides: Adenine, Guanine, Cytosine, URACIL Long, single strand How do nucleic acids function as information storage devices? Each nucleotide serves as a letter and each nucleic acid has different nucleotides (letters)