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

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 

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

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

II. WATER, cont  Dissociation of Water  Rare, but measurable phenomenon   In aqueous solution at 25˚C, [H + ] + [OH - ] = 1x  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 ; pH ____ 7  Base - Substance that dissolves in water to ____________ [H + ]  [H + ] ____ 1 x ; pH ____ 7  pH of Water =

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

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

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

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

Functional Group ID

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

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

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

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.

V. PROTEINS, cont

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

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

V. PROTEINS Protein Structure  Primary

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

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

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

V. PROTEINS Protein Structure, cont

V. PROTEINS Protein Function

V. PROTEINS Protein Function, cont

Cell Communication

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

V. PROTEINS Enzymes

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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

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

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

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

VIII. NUCLEIC ACIDS, cont DNA