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BIOLOGY 22 MODULE 1 Chemical Basis of Life v2.

.0 y 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 3

 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 4

 Mechanisms that maintain homeostatic pH values  React with strong acids/bases, replace them with weak acids/bases Salts  Yield neither H+ nor OH Do 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 o o Functional Groups groups to atoms attached to C backbone; where most chemical reactions happen (break C-C, transfer groups) 5

Group H-C-H

Name Hydrocarbon



-C= O










Characteristics = insoluble in H2O = nonpolar = does not form H bonds = shared electrons = soluble in H2O = forms H bonds = in alcohols, sugars = forms H bonds = in sugars = C=O + H = aldehyde = C=O w/o H = ketone = forms H bonds = acid = ionized to COO= in lipids = forms H bonds = base = ionized to NH3+ = very soluble = forms H bonds = always ionized = 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 Carbohydrates  Definition 6

 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 7

 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

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) 8

 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 9


 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

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

 Secondary structure  Binding of primary structures 10

 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

Types and Functions Protein Type Catalytic speed up chem rxn

Examples = enzymes 11



Contractile muscle function Protective immune function

Toxins Hormones regulation

Structural support/strength

= 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 enzymesubstrate complex  Enzyme action VERY SPECIFIC  Models  Lock and key model Simple binding of substrate to enzyme Abandoned implication that enzyme never changes  Induced fit model Enzyme alters shape to better accommodate substrate Enzyme dynamic 12

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  Nucleic acids  Polymer of nucleotides  Storage of biological information  Structure 13

 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