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UNIT II - BIOCHEMISTRY Big Campbell ~ Ch 2-5 Baby Campbell ~ Ch 2-3 I. CHEMICAL BASIS OF LIFE • Elements o Cannot be broken down without losing characteristic properties o Six elements in greatest concentration in living things are Sulfur Phosphorus Oxygen Nitrogen Carbon Hydrogen o Defined by Atomic # which is = #of protons and the #of electrons in most cases I. CHEMICAL BASIS OF LIFE, cont • Atoms o Smallest unit of matter that retains properties of that element Protons (+); found in nucleus Neutrons (neutral); found in nucleus Electrons (-); found in electron clouds. o Atomic Mass = p + n o Isotopes – when an atom has a different atomic mass, Ex: C12, C13, C14 I. CHEMICAL BASIS OF LIFE, cont • Chemical Bonds o Chemical behavior of atom determined by valence electrons o Atoms interact with other atoms to complete their valence shells, either by transferring or sharing electrons I. CHEMICAL BASIS OF LIFE, cont • Types of Chemical Bonds o Ionic – Results when one atom has a much stronger attraction for electrons than another; one atom has a greater electronegativity. Electron(s) are transferred resulting in formation of ions. Bond forms due to charge attraction. Strength is dependent on environment I. CHEMICAL BASIS OF LIFE, cont o Covalent Bonds – More stable; results from sharing a pair of valence electrons. Forms a molecule. One pair of electrons shared = single covalent bond; two pair of electrons shared = double covalent bond. Non-polar covalent bond – formed when electronegativity of atoms is the same Polar covalent bond – formed when one atom is more electronegative; unequal sharing of electrons results in slight charges at either end of molecule II. WATER • Properties of Water Due to its Polarity o Hydrogen “bonds” II. WATER o “Stickiness” Cohesion Surface Tension Adhesion Capillary Action II. WATER, cont o Regulation of Temperature High specific heat High heat of vaporization o Density of “solid” water _<_ density of liquid water II. WATER, cont o Solvent of Life Hydrophilic “Water-loving” Polar molecules “pull apart” ionic compounds & other polar molecules Hydrophobic “Water-hating” Non-ionic and non-polar substances are repelled by water II. WATER, cont • Dissociation of Water o Rare, but measurable phenomenon o (2)H2O → H3O+ + OH- → H+ + OHo In aqueous solution at 25˚C, total conc of [H+] [OH-] = 1x10-14 Neutral solution → [H+] = [OH-]; therefore [H+] = 1 x 10-7 o pH = Provides a means for a compressed measurement of [H+] -log10[H+] o Acid – Substance that dissolves in water to __increase_ [H+] [H+] _>___ 1 x 10-7; pH __<__ 7 o Base - Substance that dissolves in water to _decrease_ [H+] [H+] _<___ 1 x 10-7; pH _>_ 7 o pH of Water = 7 II. WATER, cont o Buffers Maintain a constant pH by donating, accepting H+ Bicarbonate Buffer System Very important buffer system in blood pH of blood = _7.4_ III. ORGANIC CHEMISTRY – THE STUDY OF CARBON • Atomic Structure of C o Atomic Number of C = 6 6 protons 6 electrons __4___ valence electrons o Hydrocarbon – composed on only C-H; impt in fossil fuels. Hydrophobic o Isomer – compounds with the same #of elements/atoms, but a different structural arrangement. See Ex… Four Ways Carbon skeletons can vary III. ORGANIC CHEMISTRY, cont Functional Group Hydroxyl Structure Characteristics -OH may be written as HO- Very polar; forms “ –ols” (alcohols) C=O, also written -CO Ketone – if carbonyl group is within the carbon skeleton Carbonyl Aldehydes – if carbonyl group is at the end of the carbon skeleton. Carboxyl -COOH; c alled carboxylic acids Acts as an acid; donates H+ to solution III. ORGANIC CHEMISTRY, cont Functional Group Structure -NH2; called amines Acts as a base; removes H+ from solution -SH; called thiols Important in stabilizing protein structure; forms disulfide bridges Amino Sulfhydryl Characteristics Phosphate Methyl -OPO3; known as organic phosphates Gives molecule negative charge; react with water to release energy -CH3 Affects the expression of DNA IV. THE BIOMOLECULES • Most are polymers made up of single units called monomers • Four Main Groups CARBOHYDRATES LIPIDS PROTEINS NUCLEIC ACIDS IV. BIOMOLECULES, cont • Dehydration Synthesis o o o o o Also called _CONDENSATION REACTION__ Reaction that occurs to build polymers Forms __COVALENT_ bond between 2 monomers _WATER_lost as waste product Requires energy input, enzymes IV. BIOMOLECULES, cont • Hydrolysis o “__WATER BREAKING/SPLITTING_” o Covalent bonds between monomers broken Releases energy; reaction accelerated with enzymes V. CARBOHYDRATES • • • • • Provide fuel, act as building material Generally, formula is a multiple of CH2O Contain carbonyl group & multiple hydroxyl groups Monomer = monosaccharides Monosaccharides – usually found as ringed structures o Pentoses Ribose Deoxyribose V. CARBOHYDRATES, cont o Hexoses Glucose Fructose Galactose V. CARBOHYDRATES, cont • Disaccharides o 2 monosaccharides covalently bonded together through dehydration synthesis o Example Sucrose Lactose Maltose V. 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 V. CARBOHYDRATES, cont Structural polysaccharides Cellulose – polymer of glucose. Every other glucose is upside down – forms parallel strands of glucose molecules held together with H-bonds V. CARBOHYDRATES, cont Structural polysaccharides • Chitin – found in arthropod exoskeleton, cell walls of fungi VI. LIPIDS • • • • • Very diverse group Non-polar, hydrophobic molecules Hydro_phobic__ Not true polymers Four groups Fats & oils phospholipids steroids waxes VI. LIPIDS, cont • Fats& Oils o Composed of glycerol + 3 fatty acids o Glycerol = 3-C alcohol o Fatty acids – long hydrocarbon chains ending with carboxyl group o AKA triglycerides o Used for energy storage VI. LIPIDS, cont Saturated fats – “Saturated with hydrogens”; contain all single bonds. Typically from animal source, solid at room temp. Associated with greater health risk. Unsaturated fats – Contain double bonds, fewer Hatoms. Results in “kinked” hydrocarbon chain. Typically from plant source, liquid at room temp. Fats, cont. • Saturated fat • Unsaturated fat VI. LIPIDS, cont • Phospholipids 2 fatty acids attached first 2carboxyl groups of glycerol. Negatively-charged phosphate group is attached to 3rd carboxyl Partially polar and partially non-polar Found in all cell membranes. Phospholipid, cont. VI. LIPIDS, cont • Waxes – One fatty acid attached to an alcohol. Very hydrophobic. Used as coating, lubricant • Steroids – Consist of 4-rings with different functional groups attached. o Cholesterol – steroid found in animal cell membranes; precursor for sex hormones Steroids, cont. VII. 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: o o o o 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, nonpolar, acidic, or basic. VII. PROTEINS, cont VII. PROTEINS, cont VII. PROTEINS, cont VII. PROTEINS, cont • Amino Acid → Protein o Dehydration synthesis results in formation of a peptide bond o Polypeptide – many amino acids covalently bonded together VII. PROTEINS, cont • Protein Conformation o Protein’s shape is related to its function. Generally, a protein must recognize/bind to another molecule to carry out its function. o Denaturation - 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 VII. PROTEINS, cont Primary – Sequence of amino acids VII. PROTEINS, 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 VII. PROTEINS, cont Tertiary - Involves interactions between R groups of amino acids. Helps to give each protein its unique shape. VII. PROTEINS, cont Quaternary – Proteins that are formed from interactions between 2 or more polypeptide chains folded together. Examples include hemoglobin, collagen, chlorophyll VII. PROTEINS, cont • Enzymes o Biological catalysts that act by lowering activation energy; that is, the amount of energy needed to get the reaction going o Only catalyze reactions that would normally occur o Recycled – not used up or changed by the reaction o Temperature and pH sensitive o Substrate specific VII. PROTEINS, cont o Induced fit – As enzyme envelops substrate, a slight change takes place in bond angles, orientation of atoms. Allows chemical rxns to occur more readily o Inhibition of Enzyme Function Competitive inhibitor – mimics normal substrate Non-competitive inhibitor – attaches to another part of enzyme; changes shape of active site VII. PROTEINS, cont o Regulation of enzyme function Allosteric Regulation – binding of a molecule to enzyme that affects function of protein at another site Feedback Inhibition – as end product is synthesized and accumulates, enzyme is inactivated → switches off metabolic pathway VIII. NUCLEIC ACIDS • Nucleic acid group includes DNA, RNA, ATP • Monomers = _NUCLEOTIDES_ Composed of Pentose deoxyribose (DNA) ribose (RNA) Phosphate group Nitrogen base • Polymers formed through _dehydration synthesis__ Phosphate group of one nucleotide covalently binds to sugar of next VIII. NUCLEIC ACIDS, cont Nitrogen Bases Pyrimidines – Single-ringed structure Thymine Cytosine Uracil Purines – Doubleringed structure Adenine Guanine VIII. NUCLEIC ACIDS, cont • DNA