BIOLOGY 189 Foundations of Life Science Spring 2004

1. BIOLOGY 189Foundations of Life ScienceSpring 2004 Chapter 3 The Molecules of Cells

2. Introduction • Ability to spin a web is genetically programmed … • But so are the properties of the silk produced • Structure of silk proteins are determined by DNA

3. Introduction • Structure determines function • Elasticity results from coiling and uncoiling of silk fibers • 5 times stronger than steel • Industrial applications • Surgical thread • Fishing line • Bulletproof vests

4. Introduction • Spider DNA and spider silk represent two of the four classes of molecules in living organisms • Carbohydrates • Lipids • Proteins • Nucleic acids • A nearly infinite variety of molecules can be made from these four simple classes

5. 1) Organic Compounds • Next to water, compounds containing carbon are the most abundant in an organism • Organic compounds – compounds synthesized by cells and containing carbon • Large diversity of organic compounds, over 2M described. Diversity stems from… • Carbon’s ability to form 4 covalent bonds • Molecules composed only of carbon and hydrogen are called hydrocarbons

6. Carbon atoms with attached hydrogen atoms can bond together in chains of various lengths • - Lengths and shapes determine function • - Carbon skeleton – the chain of carbon atoms in organic molecules • - Carbon skeletons may or may not be branched, and may / not have multiple bonds • - Isomers – same molecular formula, but different structure

7. 1) Organic Compounds • Carbon skeletons may be arranged in rings • Ball and stick (3D) models are vastly different from the structural formulas Ethane Cyclohexane

8. 2) Functional Groups • Functional groups – groups of atoms that usually participate in chemical reactions • Give a compound some of its unique properties • Four common types in biological systems. All are polar due to O or N. Therefore they are usually hydrophilic (water-loving) and soluble • Hydroxyl – appendage to C skeleton • Carbonyl – add a C to the C skeleton • Carboxyl – add a C to the C skeleton • Amino - appendage to C skeleton

9. 2) Functional Groups

10. 3) Macromolecules • Macromolecules – gigantic biological molecules • Carbohydrates • Proteins • Lipids • Nucleic acids • Polymers – large molecules consisting of many identical or similar molecular subunits strung together in a chain • Monomers – the units that serve as the building blocks of polymers

11. 3) Macromolecules • Immense diversity of polymers, and all are made from a list of 40-50 common monomers. Alphabet example • Examples: 20 amino acids, 4 nucleotides • Arrangement / sequence is the key to diversity • Dehydration synthesis – process by which cells link monomers to form polymers • Hydrolysis – process by which polymers are broken into monomers

12. 3) Macromolecules

13. 4) Carbohydrates • Carbohydrate – class of molecules ranging from small sugar monomers to very long polymers • Monosaccharide – carbohydrate monomer • The molecular formula of a monosaccharide is usually a multiple of CH2O. Glucose= C6H12O6 • Monosaccharides possess several hydroxyl groups and a carbonyl group

14. 4) Carbohydrates • Glucose and fructose are isomers and… • This gives these monomers different properties. • Example: Fructose tastes considerably sweeter than glucose

15. 4) Carbohydrates • C skeleton can vary from 3 to 7 carbons • Pentoses – 5 C • Hexoses – 6 C • Some monosaccharides switch between linear and ring forms in an aqueous solution • Monosaccharides are the main fuel for cellular work. Cells also use C skeletons

16. 4) Carbohydrates • Disaccharide – a double sugar constructed by a cell, from two monosaccharides. Occurs via dehydration synthesis • Sucrose (table sugar) is made from 1 glucose and 1 fructose

17. 4) Carbohydrates • The chemical structure of a compound determines its shape, which determines how well it fits into a taste receptor • Compounds that bind more tightly to a sweet receptor are perceived as being sweeter • Artificial sweeteners may bind to other types of taste receptors, leaving an aftertaste

18. 4) Carbohydrates • Polysaccharides – polymers of a few hundred to a few thousand monosaccharides linked together by dehydration synthesis • Starch – storage polysaccharide in plant roots, ect. that consists entirely of glucose monomers. Coiled / helical • Cells can break starch down as needed to obtain glucose. This is done via hydrolysis in the digestive system • Potatoes, grains, corn and rice are good sources

19. 4) Carbohydrates • Animals store excess sugar in the form of glycogen • Glycogen – polysaccharide identical to starch, but extensively branched • Stored as granules in liver and muscle cells. These cells hydrolyze glycogen to release glucose • Our digestive system hydrolyzes glycogen in the meat we eat

20. 4) Carbohydrates • The most abundant organic compound on Earth is cellulose • Cellulose – polysaccharide resembling starch and glycogen, but forms unbranched fibrils supported by hydrogen bonds • Forms plant cell walls; major component of wood • Cannot be hydrolyzed by most animals. Fiber or roughage. Requires microorganisms (cows / termites)

21. 5) Lipids • Lipids – diverse compounds consisting of C and H atoms linked by nonpolar covalent bonds • Lipids do not include polymers. Exception among macromolecules • Lipids are hydrophobic (water fearing). Insoluble in water and aren’t attracted to water • Example: Salad dressing. Oil is a type of lipid. It separates from vinegar (mostly water) • Also…

22. 5) Lipids • The feathers of waterfowl are water resistant!! • “Like water off a duck’s back”

23. 5) Lipids • Fat – large lipid made from two types of smaller molecules: • glycerol • fatty acids • The main function of fat is energy storage. • One gram of fat contains twice the energy of a gram of starch. • 9 calories per gram of fat • 4 calories per gram of carbohydrate or protein

24. 5) Lipids • Glycerol – alcohol with 3 carbons, each with a hydroxyl group • Fatty acid – molecule consisting of a carboxyl group and a carbon chain with about 15 other carbons. Nonpolar and therefore hydrophobic • Fatty acids link to glycerol via dehydration synthesis • Triglyceride – synonym for fat. Three fatty acid chains linked to glycerol.

25. 5) Lipids • Fatty acid chains are often different • Unsaturated – fatty acids and fats with double bonds. • Double bonds cause kinks in the carbon chain and prevent the maximum number of H atoms from bonding • Saturated – single bonds, maximum H atoms

26. 5) Lipids • Kinks prevent molecules from packing tightly together and solidifying at room temperature • Oils are unsaturated fats (corn, vegetable, olive oil). Plant fats are unsaturated • Margarine and some vegetable oils are hydrogenated • Animal fats are saturated (butter and lard) • Health risk (atherosclerosis) due to plaque build-up

27. 5) Lipids • There are other lipids of importance • Phospholipids – major component of cell membranes. Structurally similar to fats but… • only have two fatty acid tails • contain phosphorous

28. 5) Lipids • Waxes – consist of one fatty acid linked to an alcohol • More hydrophobic than fats • Natural protective coating • Fruits • Insects • Plants

29. 5) Lipids • Steroids – lipids with a carbon skeleton of four fused rings • Cholesterol is a common steroid found in animal cells • Starting material for other steroids (sex hormones) • Too much leads to atherosclerosis • Anabolic steroids pose health risks • Mood swings • Cardiovascular problems • Decrease in natural testosterone

30. 6) Proteins • Protein – biological polymer constructed from amino acid monomers • Extremely diverse and important molecules • Tens of thousands of different proteins in the human body • Each has a specific function

31. 6) Proteins • Seven classes of proteins. Different structures for different functions • Structural – spider silk, mammal hair, fibers of tendons and ligaments • Contractile - work with structural proteins, provide muscle movement • Storage - ovalbumin (egg whites), source of AAs for developing embryo • Defensive – antibodies, fight infections • Transport - hemoglobin, carries oxygen around the body • Signal - hormones, chemical messengers that coordinate body activities • Enzymes – catalysts – change rate of chemical reactions without being used up in the process. Most important class of proteins. Suffix -ase

32. 6) Proteins • Protein diversity is based on different arrangements of 20 universal amino acids • Amino acid – has an amino group, a carboxyl group and an R group • R group – variable part of an amino acid • R groups can be polar (hydrophilic) or nonpolar (hydrophobic). This will determine an AA’s properties

33. 6) Proteins • Cells link amino acids by dehydration synthesis • Peptide bond – connects the carboxyl group of one AA to the amino-group of a second AA • Multiple AAs connected in a chain • Dipeptide • Polypeptide, can be thousands of monomers or more! • Peptide bonds are cleaved by hydrolysis

34. 6) Proteins • Protein shape determines function • Ribbon model of lysozyme, an enzyme in tears and WBCs • Lysozyme has a globular shape with a groove • Groove fits over surface molecule on bacteria. Lysozyme recognizes target as bacteria, and destroys!

35. 6) Proteins • Space –filling model of lysozyme • Denaturation – unraveling of polypeptide chain, usually due to • Extreme temperature • Change in pH • Change in salinity • Denaturation alters the specific shape of a protein • As a result the protein loses it’s function (fried egg ex.)

36. 6) Proteins • Four levels of structure determining a protein’s specific shape • Primary (1°) structure • Secondary (2°) structure • Tertiary (3°) structure • Quaternary (4°) structure • Transthyretin example. Transport protein in blood • It’s primary structure consists of 4 polypeptide chains, each 127 AAs long • Altering hemoglobin’s AA sequence by one AA causes sickle-cell disease

37. 6) Proteins • Secondary structure of transthyretin consists of… • Alpha helix – coiling of a polypeptide chain • Pleated sheet – folding of a polypeptide chain • These patterns are maintained by H bonds

38. 6) Proteins • Tertiary structure – overall 3D shape of protein • Two shapes • Globular – helix and sheet • Fibrous - helical • Globular proteins in aqueous solutions are folded so that hydrophobic R groups are on the inside

39. 6) Proteins • Quaternary structure – overall shape or structure resulting from the bonding interactions among multiple polypeptide chains (subunits) • Transthyretin has 4 identical subunits • Hemoglobin has 4 subunits of 2 different types

40. 7) Nucleic Acids • Nucleic acids – polymers that serve as blueprints for proteins • DNA – deoxyribonucleic acid. Inherited from parents • RNA – ribonucleic acid • Genes – specific stretches of DNA molecules that program AA sequences (1° structure) of proteins • Genes ultimately determine the 3D structure of proteins, and thus, their function

41. 7) Nucleic Acids • DNA works in conjunction with RNA • Information from DNA is transcribed into RNA • This information is translated into the 1° structure of proteins • More on this later in the course!

42. 7) Nucleic Acids • Nucleotides – monomers that make up nucleic acids • 3 parts • Pentose (5-C sugar) • Phosphate group • Nitrogenous base • DNA nitrogenous bases • Adenine (A) • Thymine (T) • Cytosine (C) • Guanine (G) • Same for RNA, except Uracil (U) instead of Thymine

43. 7) Nucleic Acids • Polynucleotide – polymer formed from nucleotide monomers via dehydration synthesis • To form a polynucleotide the phosphate group of one nucleotide bonds to the sugar of the next monomer • The result is a repeating sugar-phosphate backbone

44. 7) Nucleic Acids • DNA forms a double helix, RNA is a single polynucleotide • Double helix – two polynucleotide strands wrapped around each other • Nitrogenous bases protrude into the center of the helix from the sugar-phosphate backbone • Nitrogenous bases pair up via H bonds • A pairs with T • C pairs with G

45. 7) Nucleic Acids