1. UNIT II - BIOCHEMISTRY Hillis ~ Ch 2,3 Dual Campbell ~ Ch 2,3,6 Big Campbell ~ Ch 2-5 Baby Campbell ~ Ch 2,3

2. I. THE MOLECULES OF LIFE Molecules are formed when two or more ______________ come together to form covalent bonds.  Created when electrons are ________________  Single Covalent Bond  Double Covalent Bond  Triple Covalent Bond  Very __________________  Non-polar Covalent Bond   Polar Covalent Bond 

3. II. WATER Water o Properties due to ________________  Defined as  Properties of Water  Ability to form hydrogen “bonds”  “Stickiness”  Cohesion  Surface Tension  Adhesion  Capillary Action

4. II. WATER, cont  Regulation of Temperature  High specific heat  High heat of vaporization  Density of “solid” water ____ density of liquid water  Solvent of Life   “Water-loving”  Polar molecules “pull apart” ionic compounds & other polar molecules   “Water-hating”  Non-ionic and non-polar substances are repelled by water

5. II. WATER, cont  Dissociation of Water  Rare, but measurable phenomenon   In aqueous solution at 25˚C, [H + ] + [OH - ] = 1x10 -14  Neutral solution → [H + ] = [OH - ]  [H + ] =  pH = Provides a means for a compressed measurement of [H + ]  -log 10 [H + ]  Acid – Substance that dissolves in water to ____________ [H + ]  [H + ] ____ 1 x 10 -7 ; pH ____ 7  Base - Substance that dissolves in water to ____________ [H + ]  [H + ] ____ 1 x 10 -7 ; pH ____ 7  pH of Water =

6. II. WATER, cont  Buffers  Maintain a constant pH by donating, accepting H +  Bicarbonate Buffer System  Very important buffer system in blood  pH of blood = _________

7. III. ORGANIC CHEMISTRY Carbon o Atomic Number of C   _____ valence electrons o Hydrocarbons o Isomer

8. III. ORGANIC CHEMISTRY, cont Functional GroupStructureCharacteristics Hydroxyl Very polar; forms “ –ols” Carbonyl Carboxyl Acts as an acid; donates H + to solution Amino Acts as a base; removes H + from solution

9. III. ORGANIC CHEMISTRY, cont Functional GroupStructureCharacteristics Sulfhydryl Important in stabilizing protein structure; forms disulfide bridges Phosphate Gives molecule negative charge; react with water to release energy Methyl Affects the expression of DNA

10. Functional Group ID

11. IV. THE BIOMOLECULES Most are ______________ made up of single units called ______________ Four Main Groups 

12. IV. BIOMOLECULES, cont Dehydration Synthesis oAlso called ________________________ o Reaction that occurs to build polymers o Forms ________________ bond between 2 monomers o ____________lost as waste product o Requires energy input, enzymes

13. IV. BIOMOLECULES, cont Hydrolysis o“________________________” oCovalent bonds between monomers broken Releases energy; reaction accelerated with enzymes

14. V. PROTEINS Important part of virtually all cell structures, processes, reactions Amino Acids – Proteins are large polymers made up of amino acid monomers. All amino acids have the same basic structure:  Amino group  Carboxyl group  Carbon known as alpha carbon  R group → variable component; gives each amino acid its unique properties. Determines whether amino acid is classified as polar, non- polar, acidic, or basic.

15. V. PROTEINS, cont

18. Amino Acid → Protein oDehydration synthesis results in formation of a peptide bond oPolypeptide – many amino acids covalently bonded together

19. V. PROTEINS, cont Protein Conformation oProtein’s shape is related to its function. Generally, a protein must recognize/bind to another molecule to carry out its function. oDenaturation - A change in a protein’s shape. Results in a loss of protein’s ability to carry out function. o Four levels of protein structure  Primary  Secondary  Tertiary  Quaternary

20. V. PROTEINS Protein Structure  Primary

21. V. PROTEINS Protein Structure, cont  Secondary – Coiling of polypeptide chain due to formation of H-bonds between H of amino end of one aa and OH of carboxyl end of another aa  Alpha helix – Created from H-bonds forming within one pp chain  Beta pleated sheet – H-bonds form between aa in parallel pp chains

22. V. PROTEINS Protein Structure, cont  Tertiary  Involves interactions between R groups of amino acids.  Helps to give each protein its unique shape.

23. V. PROTEINS Protein Structure, cont  Quaternary  Proteins that are formed from interactions between 2 or more polypeptide chains folded together  Examples include hemoglobin, collagen, chlorophyll

24. V. PROTEINS Protein Structure, cont

26. V. PROTEINS Protein Function

27. V. PROTEINS Protein Function, cont

28. Cell Communication

29. V. PROTEINS Protein Function, cont Enzymes oBiological catalysts that act by lowering activation energy; that is, the amount of energy needed to get the reaction going oOnly catalyze reactions that would normally occur

30. V. PROTEINS Enzymes

31. V. PROTEINS Enzymes, cont oRecycled – not used up or changed by the reaction oTemperature and pH sensitive oSubstrate specific oMay require a co-factor or co-enzyme to be functional

32. V. PROTEINS Enzymes, cont oInduced Fit  As enzyme envelops substrate, a slight change takes place in bond angles, orientation of atoms.  Allows chemical rxns to occur more readily oInhibition of Enzyme Function  Competitive inhibitor – mimics normal substrate  Non-competitive inhibitor – attaches to another part of enzyme; changes shape of active site

33. V. PROTEINS Enzymes, cont oRegulation of Enzyme Function  Allosteric Regulation  Binding of a molecule to enzyme that affects function of protein at another site  May act as activators or inhibitors

34. V. PROTEINS Enzymes, cont o Regulation, cont  Feedback Inhibition  As end product is synthesized and accumulates, enzyme is inactivated → switches off metabolic pathway

35. VI. CARBOHYDRATES Provide fuel, act as building material Generally, formula is a multiple of Contain Monomer = monosaccharides Monosaccharides – usually found as ringed structures o Pentoses  Ribose  Deoxyribose

36. VI. CARBOHYDRATES, cont o Hexoses  Glucose  Fructose  Galactose

37. VI. CARBOHYDRATES, cont Disaccharides o Formed by o Example  Sucrose  Lactose  Maltose

38. VI. CARBOHYDRATES, cont Polysaccharides o Many monosaccharides covalently bonded together through dehydration synthesis o Two main groups  Energy Storage Polysaccharides  Starch  Plants store glucose as starch in cell structures called plastids.  Humans have enzymes to hydrolyze starch to glucose monomers.  Glycogen  Storage form of glucose in animals.  More highly-branched than starch.  In humans, found mainly in liver, muscle cells

39. VI. CARBOHYDRATES, cont  Structural polysaccharides  Cellulose  Polymer of glucose.   Chitin  Found in arthropod exoskeleton, cell walls of ____________

40. VII. LIPIDS Very diverse group Not true polymers Four groups 

41. VII. LIPIDS, cont Fats& Oils oComposed of glycerol + 3 fatty acids oGlycerol = 3-C alcohol oFatty acids – long hydrocarbon chains ending with carboxyl group oAKA triglycerides oUsed for energy storage

42. VII. LIPIDS, cont  Saturated Fats  Contain all single bonds  “Saturated with hydrogens”  Typically from animal source  Solid at room temp.  Associated with greater health risk.  Unsaturated Fats  Contain double bonds  Fewer H-atoms  Produces “kinked” hydrocarbon chain  Typically from plant source, liquid at room temp.

43. VII. LIPIDS, cont Phospholipids  2 fatty acids, each attached to carboxyl group of glycerol.  Negatively-charged phosphate group is attached to 3 rd carboxyl  Partially polar and partially non-polar  Found in all cell membranes.

44. VII. LIPIDS, cont Steroids  Consist of 4-rings with different functional groups attached  Cholesterol  Found in animal cell membranes  Precursor for sex hormones

45. VII. LIPIDS, cont Waxes  Very hydrophobic  Used as coating, lubricant

46. VIII. NUCLEIC ACIDS Nucleic acid group includes DNA, RNA, ATP Monomers = __________________  Composed of  Pentose   Phosphate group  Nitrogen base Polymers formed through ____________________________  Phosphate group of one nucleotide covalently binds to sugar of next

47. VIII. NUCLEIC ACIDS, cont  Nitrogen Bases  Pyrimidines   Purines 

48. VIII. NUCLEIC ACIDS, cont DNA