BIOLOGY 22 MODULE 1 Chemical Basis of Life v2.

.0 Levels of Organization biological functions are ultimately based on the properties of atoms and molecules o Subatomic particles neutrons, electrons, protons o Atoms o Compounds o Complexes of compounds o Organelles bodies within cells that perform specific functions o Cell Specific combination of organelles Can metabolize and reproduce Least elaborate living structure Significance of Chemistry/Physics in Biology o Biology based on chemistry o Chemistry based on physics Important Concept in Chemistry o Matter, Atoms, Atomic Structure Matter anything that has mass and occupies space (e.g. solid, liquid, gas, plasma) Atomic Theory Dalton All matter is made of atoms All atoms are made of subatomic particles Atoms units of matter Bohr proposed structure of atom (similar to solar system) Parts of atoms Nucleus Proton Neutron Electron in an electron cloud Important concepts Electrons are arranged in shells according to energy levels Filled innermost shell 2 electrons Filled outermost shell 8 electrons Same number of valence = similar chemical behaviors

Elements Pure substances made of one kind of atom Cannot be decomposed Compounds / Molecules Chemical reaction processes where atoms combine/break with other atoms Molecule two or more atoms, may be same atoms (e.g. H2) Compound molecule containing at least 2 kinds of atoms (e.g. H2O) Chemical Bonds Ionic Bond One atom gains electrons, one atom loses electrons Bond strength = 5-10 kcal/mol Cations atom that loses electrons (+) Anions atom that gains electrons (-) Covalent Bond Two or more atoms share electrons Electrons behave as if they belong to each atom Bond strength = 50-100 kcal/mol Types Nonpolar covalent e.g. H2 Atoms of the same element Equal sharing No charge Does not mix with polar covalent bonded molecules Polar covalent e.g. H2O Atoms of different elements Unequal sharing One of the shared electrons tends to get pulled towards one element Resulting molecule has a positive and negative end Greater pull = more electronegative atom Hydrogen Bond Formed between water molecules Slightly positive end of one molecule is attracted to slightly negative end of another molecule Bond strength = 3-5 kcal/mol Stabilize DNA Represented by dotted line 2

Van der Waals Forces e.g. antigen-antibody, insect on ceiling Occur where electron clouds overlap, creating weak attraction Bond strength = 1-2 kcal/mol o Free Radicals Molecules containing atom with a single unpaired electron in outer shell Steals electrons from other atoms, creating more free radicals from donor molecules Can do harm by disrupting biomolecule structure Represented by a dot next to atomic symbol o Chemical Reactions Synthesis reaction e.g. glucose glycogen; amino acids proteins A+B AB Anabolism Decomposition reaction e.g. fats glycerol + fatty acids AB A+B Catabolism Exchange reaction Double displacement AB + CD AC + BD Reversible reaction End product can revert to the original combining reactants Inorganic Compounds ionically bonded molecules required for biological functions; NO CARBON o Water Abundance Most abundant in biosphere 75% of earths surface 60% of RBC 75% of muscle 92% of blood plasma 65-75% in living organisms (average) 58% in humans Structure Tetrahedral Polar covalent bond of H and O Hydrogen bond between H2O molecules Ice = crystalline structure

Properties Water molecules are highly dipolar Excellent solvent + suspending medium Participant in many chemical reactions Lubricant Water molecules are cohesive Molecules tend to stick together Highest surface tension due to H bonds Water molecules are adhesive Molecules tend to stick to surfaces Capillary action drawn into small channels Water expands when it crystallizes Water reaches highest density at 4C Ice is less dense than water floats Allows for organisms to live in ponds/lakes during winter Water has a high specific heat Absorbs and releases heat very slowly Maintains temperature in oceans Water has a high heat of vaporization Needing a lot of heat to convert from liquid to gas Water has neutral pH Functions Needed for life to exist Raw material in photosynthesis basis of life Major component in hydrological cycle cycling of matter and nutrients, dissipates energy Acids and Bases Acids Substances that give off H+ in solutions Proton donors pH < 7 Bases Substances that give off OH- in solutions Proton acceptors pH > 7 pH Degree of acidity or alkalinity based on concentration of H+ in solution pH = -log [H+]

Buffer systems e.g. carbonate-bicarbonate system in blood Mechanisms that maintain homeostatic pH values React with strong acids/bases, replace them with weak acids/bases o Salts Yield neither H+ nor OHDo not affect pH Formed by reaction of acid and base o Trace Elements elements occurring in nature and needed in smaller amounts in biological systems Magnesium chlorophyll, enzymes Iodine thyroxin Iron hemoglobin Calcium bone Sodium nerve impulse Chlorine digestive chemicals, photosynthesis Potassium nerve impulse Organic Compounds / Biomolecules very complex molecules responsible for living properties exclusive distribution in living/previously living matter o Chemical composition principal bonds = C-C and C-H o Unique/Exclusive Properties of Carbon Carbon is versatile Can form as many as 4 covalent bonds with other atoms Carbon can be joined into various structures Rings e.g. benzene Linear chains that vary in length and location of double bonds e.g. butane Branches e.g. isobutane 2D structures 3D structures o Properties of Organic Compounds Can react with various other compounds to form different molecules Large size, do not dissolve easily (nonpolar) Useful materials for body structure Carbon + covalent bonds = good source of energy C-C bonds are shorter and more stable at different temperature C-C = shortest bond known Stability of life exists in extreme environments

Functional Groups groups to atoms attached to C backbone; where most chemical reactions happen (break C-C, transfer groups) Group Name Characteristics H-C-H Hydrocarbon = insoluble in H2O = nonpolar = does not form H bonds = shared electrons -OH Hydroxyl = soluble in H2O = forms H bonds = in alcohols, sugars -C= O Carbonyl = forms H bonds = in sugars = C=O + H = aldehyde = C=O w/o H = ketone -COOH Carboxyl = forms H bonds = acid = ionized to COO= in lipids -NH2 Amino = forms H bonds = base = ionized to NH3+ -PO4 Phosphate = very soluble = forms H bonds = always ionized HS Sulfhydryl = forms weak H bonds = HS + HS S-S = in polypeptides Isomers Definition Molecules with same elemental ratios occur in different spatial arrangements/structures Biological molecules = amazing variety of forms Types Structural isomers e.g. nitrogenous bases (A T C G) Differ in arrangement of covalent bonds Geometric isomers Always involve arrangement around a double bond Trans different sides of double bond Cis same side of double bond Important in enzymes Enantiomers Isomeric forms that form when carbon is bonded to 4 different functional groups Form a 3D tetrahedron 6

Carbohydrates Definition Consists of C, H, O O, H in a 2:1 ratio Formula = Cx(H2O)y Functional groups hydroxyl, carbonyl Bonds glycosidic Classification Monosaccharides simple sugars Monomers building blocks of carbohydrates 3 carbons = triose 4 carbons = tetrose 5 carbons = pentose ribose, deoxyribose 6 carbons = hexose most abundant glucose, fructose, galactose, etc. Disaccharides from dehydrations synthesis of 2 monosaccharides Maltose (malt sugar) = glucose + fructose Sucrose (cane sugar) = glucose + fructose Lactose (milk sugar) = glucose + galactose Oligosaccharides 8-12 monomer units cell membrane Polysaccharides more than 20 monomer units (e.g. dextrines) Glycogen 100s or 1000s of glucose units Animal starch Highly branched Unstable, metabolizable, decomposable Starch Principal storage product in plant Moderately branched Unstable, decomposable Cellulose 2000 glucose units Plant cell wall Unbranched Very stable Digested by cellulose Chitin Tough structural nitrogenous polysaccharide Exoskeleton of insects, cell wall of fungi

Glycosaminoglycans Structural polysaccharide Major C H O in connective tissue matrix Fibers e.g. hemicelluloses, pectins, gums, mucilages Stable, unbranched Dietary fiber vehicle for toxin elimination Gives feeling of fullness Lowers risk of cancer / cardiovascular disease, obesity, etc. Mechanisms Condensation reaction Formation of carbohydrates by removal of H2O Dehydration synthesis Hydrolysis Breaking of carbohydrates by addition of H2O Polymerization Series of dehydration synthesis of simple sugars resulting in polysaccharides Functions Structural building blocks of DNA and RNA deoxyribose and ribose Energy rich molecules glycogen Major component in connective tissue matrix glycosaminoglycans o Lipids Definition and structure Large organic compounds that are insoluble in water but soluble in organic solvents (e.g. ether, chloroform, alcohol) Glycerol 3C alcohol with 3OH Backbone of lipid Fatty acids Building blocks C H O in chains Have a terminal carboxylic group confers acidity Formic acid formalin Acetic acid Propionic acid Butyric acid butanol Functional groups carboxyl Bonds ester bonds

Classification Simple lipids triglyceride (fats) 3 fatty acids + glycerol bonded with ester bond Saturated fats no double bond (linear) Animal origin except for coconut oil Solid at room temperature Raise cholesterol level Unsaturated fats w/ double bond (bent) Plant origin Liquid at room temperature MUFA monosaturated fatty acid single double bond PUFA polysaturated fatty acid more than 1 double bond (healthier) Lower cholesterol level Trans fatty acids e.g. margarine, spreads, dairy, etc. MUFA/PUFA undergo partial hydrogenation removal of double bonds Product = similar to saturated acid Complex lipids fatty acids + glycerol + additional group Phospholipids e.g. lecithin Glycerol + 2 fatty acids + phosphate Cell membrane Also in brain cells and nerves Sphingolipids Myelin sheath Waxes Alcohol + 1 fatty acid H2O repellent, cell wall protection Steroids lipids without fatty acid tail Skeleton of 4 interlocking C rings e.g. vitamin D, cholesterol, sex hormones, ecdysone Mechanisms Esterification removal of H2O formation of fats Ester bond holds fats together Glyoxidic cycle conversion of fatty acids to glucose

Functions Fats Energy storage 2x more than glycogen Cushioning and protection of organs Insulation adipose tissue Phospholipids Diffusion through cell membrane Sphingolipids Impulse conduction Waxes Water repellent Cell wall protection in mycobacteria Steroids Message transmission Membrane fluidity o Proteins Definition and Structure Biomolecules made out of amino acids Amino acids C center + H + COOH + NH2 + R group Unique properties from R group 21 known amino acids Essential amino acids cannot be easily produced by body acquired through diet Nonessential amino acids can be produced by body glycine simplest amino acid cysteine gives toughness to proteins (S) Diversity of proteins from various combinations of amino acids Functional groups carbonyl, amino, sulfhydryl, others Bonds peptide bonds Structural Organization Primary structure e.g. ribonuclease (124 amino acids) In ribosomes Linear sequence of 40-1000 amino acids Joined by peptide bonds Not functional

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Secondary structure Binding of primary structures Hydrophilic end attracted to aqueous surface of molecule Hydrophobic end attracted to non-aqueous center of molecule Joined by H bonds Helical structure alpha helix Sheet structure beta pleated sheet Not functional Tertiary structure Globular (3D) structure Joined by numerous bonds Hydrophobic Van der Waals forces H bonds Ionic bonds C+ attracts electrons Covalent bonds between HS Functional Most proteins are tertiary Quaternary structure Two or more polypeptide chains join into one molecule Numerous bonds (same as tertiary) hemoglobin 2 alpha helix + 2 beta pleated sheet collagen 3 chains of fibrous protein Mechanisms Protein synthesis/translation Creation of protein in ribosomes from mRNA Involves removal of H2O Molecular Techniques Immunoprecipitation determine structure of protein constituents Gel electrophoresis differentiation of complex proteins Denaturation Proteins sensitive to heat, pH, electricity, pressure, etc. Denaturation environmental factors disruption of bonds unfolding of protein loss of 3D conformation loss of function

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Types and Functions Protein Type Catalytic speed up chem rxn Storage

Transport

Contractile muscle function Protective immune function

Toxins Hormones regulation

Structural support/strength

Examples = enzymes = ovalbumin = casein = seed protein = hemoglobin = myoglobin hemoglobin in muscle tissue (enhanced) = albumin transport fatty acids = actin = myosin = antibodies = fibrinogen in blood clotting = thrombin in blood clotting = hemotoxin = neurotoxin = insulin = ACTH = GH = collagen most abundant = elastin = glycoproteins = keratin hair, nails

Enzymology Enzyme Biological catalysts that speed up chemical reactions Lower activation energy Activation energy energy needed to start a reaction Low activation energy reaction starts easily Methods to lower activation energy Increasing temperature increased collision of molecules DISADVANTAGE: denaturation Use of a catalyst Nature of enzymes Enzyme protein with active sites produces enzyme-substrate complex Enzyme action VERY SPECIFIC Models Lock and key model Simple binding of substrate to enzyme Abandoned implication that enzyme never changes 12

Induced fit model Enzyme alters shape to better accommodate substrate Enzyme dynamic More acceped Enzymes function with: Cofactors - minerals Coenzymes vitamins + nucleic acid Important factors in enzyme function Temperature 38C peak function pH peak depending on enzyme R groups Charge of substrate Reversibility Enzymes form complexes with substrate but retain their identity after the reaction Enzymes may detach from substrate Nucleic Acids Definition First isolated by Meischer from pus cell nuclei Secret to life (NOT PROTEIN) Polymer of nucleotides Functional groups hydroxyl, carbonyl, phosphate Bonds phosphodiester bonds Structure Pentose sugar component deoxyribose / ribose Phosphate group Nitrogenous bases Purines adenine, guanine Pyrimidines cytosine, thymine, uracil Structures Nucleoside structure = nitrogenous base + sugar Nucleotide structure = nitrogenous base + sugar + phosphate group Derivatives of Nucleotides Energy carrier molecules ADP, ATP High energy phosphate bonds + pentose sugar + nitrogenous base Adenine in adenosine Cofactors and coenzymes NAD, FAD Signaling molecules endocrine function 13

Nucleic acids Polymer of nucleotides Storage of biological information Structure Outside sugar + phosphate backbone bonded by phosphodiester bond Inside specific nitrogen base pairs stablized by hydrogen bond Chargaffs Rule Adenine to thymine Guanine to cytosine Types DNA deoxyribonucleic acid Deoxyribose sugar Adenine, thymine, guanine, cytosine Double alpha-helix RNA ribonucleic acid Ribose sugar Adenine, uracil, guanine, cytosine Single strand Central Dogma of Biology DNA transcribed to mRNA in nucleus mRNA translated to protein in rough endoplasmic reticulum DNA replicated to DNA in nucleus

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