Exploring Biochemistry Basics: Bonds, Water, Carbon, and Macromolecules

1. Biochemistry Chapters 2-5

2. Ch. 2 Chemistry Review • Know chemistry vocabulary (review packet) • Difference between types of bonds and how many bonds elements form (CHNOPS) • hydrogen (weak bonds between molecules) • ionic (lose electron) • covalent (share electrons) • polar v. nonpolar molecules

3. Ch. 3 Water • polar molecule...results in “v” shape • know properties of water (cohesion, adhesion, surface tension) • high heat capacity • solid less dense than liquid (ice floats) • know differences between solution, solute, solvent, aqueous solution; hydrophilic and hydrophobic • Water is an excellent solvent. • Ionic and polar substances dissolve easily in water • nonpolar substances do not dissolve in water • Acids, bases, pH and buffers **Think about all of these concepts in terms of living systems. How do all of these concepts allow a living organism to function? or cause an organism to not function successfully?

4. Ch. 4I <3 Carbon! • Carbon is the most important element in living things. “Carbon-based life forms” • Carbon has the ability to make 4 bonds...resulting in incredible versatility in bonding with other elements (it can make large, complex molecules) • Hydrocarbons (carbon and hydrogen only)--fossil fuels • Isomers (structural v. geometric) • Structural- differ in covalent arrangement of atoms • Geometric- differ in spatial arrangements • Enantiomer- mirror images • can form branches, chains and rings

5. Macromolecules • polymer--long molecule made of smaller building blocks • carbohydrates, proteins, nucleic acids. **lipids** • monomer--building blocks that make up polymers • synthesis of polymers • dehydration reactions--covalent bonds between molecules with the loss of a water molecule • breakdown of polymers • hydrolysis--molecules are broken using water (reverse of dehydration rxn) • enzymes: macromolecules that speed up chemical reactions

6. Biological Molecules • Functional Groups--chemical groups attached to carbon skeleton that determine function and unique properties of large molecules • Figure 4.9 • testosterone vs. estradiol

7. Functional Groups • Each has specific chemical properties, when attaches to larger molecule it gives those properties to that molecule • A single molecule may contain many different functional groups • Determines molecular shape and reactivity • Hydroxyl (-OH) • Alcohols • Polar • Hydrogen bond with water • Carbs, proteins, nucleic acids and lipids

8. Carbonyl (-CO) • ketones and aldehydes • Component of sugars • Carbohydrates, nucleic acids • Carboxyl (-COOH) • important part of amino acids • organic acids (ie. vinegar) • Proteins, lipids • Amino (-NH2) • important part of amino acids • Basic (H+ acceptor) • Proteins, nucleic acids

9. Sulfhydryl (-SH) • present in certain amino acids (methionine and cysteine) • Forms disulfide bridge (protein structure) • proteins • Phosphate (-OPO3) • part of cellular energy sources (ATP, ADP) • Acidic • Nucleic acids • Methyl (-CH3) • part of DNA molecules (gene expression) • proteins

10. Carbohydrates • Have the general formula CnH2nOn • Functions • Source of stored energy • Used to transport energy • Structural molecules • Used as building blocks for other macromolecules • Recognition or signaling molecules that trigger specific responses

11. Monosaccharide: simple sugar • Pentose sugar (5 carbon) C5H10O5 • Ribose, deoxyribose • Hexose sugar (6 carbon) C6H12O6 • Glucose**, fructose, galactose (isomers) • Fructose—”fruit sugar”, very sweet! • Example of how arrangement of carbon atoms change molecule properties

12. Polysaccharide: polymer of monosaccharides • Formed by glycosidic linkages (covalent bond that results from dehydration reaction—lose H2O) • “sugar bond” • Sucrose (glucose + fructose)—disaccharide • Used in carbohydrate transport • Lactose (glucose + galactose)—disaccharide • Milk sugar • Some individuals are missing the enzyme to break down this sugar…”lactose intolerance”

13. Starch (glucose+ glucose+ glucose….) • Storage polysaccharide (plants) • Molecules broken by hydrolysis for energy • Long chain of alpha-glucose molecules • Glycogen-- highly branched polymer of alpha-glucose • Storage polysaccharide (animals) in liver and muscles • “animal starch” • Cellulose—unbranched polymer of beta-glucose • Structural polysaccharide (plant cell wall) • Not easily broken down by most organisms • Herbivores have special bacteria to do this • Chitin (modified glucose chain) • Structural material found in arthropods (insects) and fungi • Makes up exoskeletons

14. Lipids • Group of molecules that are insoluble in water • Hydrophobic • May be storage fats, oils, steroids, or waxes • Important component of cell membranes • Phospholipids (phosphate attached to glycerol) • 2 FA instead of 3 • Polar and nonpolar ends of molecule (hydrophilic and hydrophobic regions) • Phosphate hydrophilic • Serve as a long-term form of energy storage • Very efficient molecule for storage

15. Made of two components: • Fatty acid “tail of molecule” • Long chain hydrocarbons with carboxyl group • Chain is usually 14-20 carbons long • Glycerol “head of molecule” • Three –OH groups (hydroxyl) • alcohol • Holds molecule together • FA and glycerol held together by an “ester linkage” • Carboxyl + Hydroxyl

16. “Triglyceride”- one glycerol plus 3 FA (basic fat/oil) • Saturated FA • No double bonds (carbon atoms) • Maximum number of hydrogens • Solid at room temperature (animal fats-- butter) • Unsaturated FA • One or more double/triple bonds (carbon atoms) • Liquid at room temperature (plant fats--oils) • Monounsaturated (one double/triple bond) • Polyunsaturated (more than one double/triple bond) • “trans fats” partially hydrogenated unsaturated fats . Created by adding hydrogen and breaking double/triple bonds (health risks)

17. Waxes • Alcohol + unsaturated oil • Steriods • 4 carbon rings • Attached functional groups make them unique (testosterone vs. estrogen) • Ex. Cholesterol (component of cell membranes and precursor to other steriods)

18. Nucleic Acids • DNA and RNA • Genetic information inherited from parents • RNA used in protein synthesis • Polymers of nucleotides • Sugar, phosphate, nitrogenous base

19. Proteins • Every dynamic function of an organism depends on proteins! • Functions include: (Fig. 5.15) • Transport (hemoglobin) • Structure (collagen) • Enzymes (trypsin) • Movement (myosin) • Defensive (immunoglobin) • Hormones (insulin) • Storage (caesin)

20. Proteins are made of monomers called amino acids. • 20 amino acids exist in nature (fig. 5.16) • Each has an amino and carboxyl group • Chains of amino acids are called polypeptides • Amino acids are linked together with a peptide bond • Each polypeptide has an amino group at one end and a carboxyl group at the other • The unique properties and structure are determined by the side groups of the amino acid (unique to each a.a.)

21. Protein Structure • A polypeptide chain becomes a protein once it has undergone modification and folding (3-dimensional) • The 3-D structure is determined by the unique sequence of amino acids. (each protein is folded uniquely) • Four Levels (fig. 5.20) • Primary—chain of a.a. (not folded) • Secondary—H-bonds form between a.a. (making helix or pleated sheet) • Tertiary– 3-D shape formed from reactions between a.a. side chains (sulfide bridges) • Quaternary– multiple polypeptides (chains) linked together in 3-D structure

22. Denaturing Proteins exposed to excessive heat, pH changes, chemical, or other environmental changes may change their shape and become ineffective (misshapen)