Chemistry of Life : Organic Compounds

Organic Compounds Covalently bonded C atoms form the backbone of molecule >5M organic compounds have been identified, including macromolecules(proteins) constructed from modular subnits (Amino Acids)

Properties of Carbon Form 4 covalent bonds Strong single bond, double bond, triple bond Hydrocarbon(only hydrogen & carbon) Unbranched, branched, ring

Molecular Shapes Shapes determine biological properties & function C atoms link to 1 another, produce 3D shapes because Carbons 4 covalent bonds do not form in a single plane Freedom rotation around C-C bond assume variety shapes, depends degree of rotation

Isomers Same components link >1 pattern Same molecular formulas but different structure & properties Usually 1 biological active, another dont 2 types Structural isomers: Formula same, arrangement different Stereoisomers Geometrial isomerism: Spatial arrangement different. E.g. Cis Trans Optical isomerism : (Enantiomers=Mirror image) cant superimposed, enzyme can react

with 1 only Epimers : Occur when stereoisomers occur in a single carbon E.g. : 2 formula, same structural formula except there is isomerism on a single carbon.

Functional Groups Hydrocarbon lack distinct charged regions, insoluble in water, cluster together(hydrophobic interactions) Groups that determine types of chemical reactions and associations Readily form associations (Ionic, H bond) Polar & Ionic functional groups are hydrophilic ~Associate with H2 O molecules Methyl Group (R-CH3) : Non-polar Hydroxyl Group (R-OH) : Polar ~ Strong electronegative O2 atom Carbonyl Group : C atom has double bond with O2 atom Aldehyde (R-CHO) ; Ketone (R-CO-R)

Carboxyl Group (R-COOH) Ionized & form (R-COO-) Constituents of Amino Acids & fatty acids. Amino Group (R-NH2 ) Ionized & form R-NH3 + Components of amino acids & nucleic acids Phosphate Group (R-O-P(O)(OH)2 Can release H+ ion Components of nucleic acids & certain lipids Sulfhydryl Group (R-SH) found in thiols(cysteine) ;Important in proteins

Making and Breaking Polymers Can be broken by hydrolysis reactions and mad by condensation reactions

 Carbohydrates (C, H & O) Ratio 1C:2H:1O (CH2 O)n Sugar, starches (energy sources) Cellulose (Structural component of plants) Monosaccharides 3-7 C OH group bonded to each C except 1 C bonded to O atom forming aldehyde/ketone Trioses: glyceraldehyde, dihydroxyacetone Pentoses: ribose, deoxyribose Hexoses: glucose, fructose, galactose ~Ring Form ~Ring Form

Glucose (C6 H12O6) ~Aldehyde : Store energy, maintain blood glucose level Fructose ~ Ketone Glucose & Fructose are structural isomers Galactose & Glucose Different atom arrangement to asymmetrical C atom 4 Isomers of Glucose Different orientation of OH group attached to C 1, important when glucose rings join to form polymers -glucose : OH group on opposite of CH2 OH side group -glucose : OH group on CH2OH side group, same side as plane of ring

Can be divided to aldoses, ketoses Disaccharides 2 monosaccharide rings joined by glycosidic linkage Consisting central O covalently bonded to 2 Carbons, 1 in each ring Maltose (Malt Sugar) : 2 covalently linkage -glucose units Sucrose (Table Sugar): 1 glucose + 1 fructose Lactose (Milk Sugar) : 1 glucose + 1 galactose Polysaccharides

 Macromolecues, repeating units of simple sugar, usually glucose Starches: Energy storage in plants Consist -glucose 2 forms : amylose(unbranched chain), amylopectin(branched chain) Store starch as granules in amyloplasts Glycogen: Energy storage in animals More extensively branched & H2 O soluble Cellulose: Structural polysaccharide in plants (fibre) Many joined glucose molecules, most abundant carbohydrate Some microorganisms digest cellulose to glucose Human lack enzymes to hydrolyze Carbohydrates with Special Roles Amino sugars : Galactosamine & Glucosamine Present in cartilage Chitin : Component of external skeletons of arthropods Glycoproteins : Functional proteins secreted by cells Glycolipids : Recognition compounds on surfaces of animal cells Lipids Soluble in organic solvent, insoluble in polar solvent Mainly C & H, few O functional groups Biological important groups : fats, phospholipids, carotenoids, steroids & waxes Used for : Energy storage, structural components of cell membranes, important hormones Triacylglycerol (Fats) Most abundant lipids, reserve fuel storage, glycerol joined to 3 fatty acids Glycerol 3 carbon alcohol with 3 OH group Fatty Acid 1-4 linkage

 Long unbranched hydrocarbon chain with COOH group at the end Making & Breaking a Triacylglycerol Molecule Form from condensation reactions(ester linkage) 1st reaction yields monoacylgylcerol (monoglyceride) 2nd reaction yields diacylglycerol 3rd reaction yields triacylglycerol (diglyceride) (triglyceride)

Break when triacylglycerols are hydrolyzed to produce fatty acids & gylcerol Saturated & Unsaturated Fatty Acids Saturated : Max. no. of H atom, found in animal fat, solid vegetable shortening, solid due to van der Waals interaction Unsaturated : 1 or >1 C atom joined by double bond, liquid, double bond produces a bend prevents close alignment with adjavent chain limiting van der Waals interactions Monounsaturated Fatty Acids: 1 double bond, oleic acid Polyunsaturated Fatty Acids: >1 double bond, linoleic acid Trans Fats Hydrogenate or partially hydrogenate cooking oils Naturally-occuring unsaturated fatty acids: Cis configuration Artificial hydrogenation: Trans configuration Solid at r.t. Increases risk of cardiovascular disease Animal store fats at adipose cells ~ cushions vital orangs, insulates the body Phospholipids Amphipathic lipids: hydrophilic end & hydrophobic end Hydrophilic head consists glycerol molecule, phosphate group, organic group(choline) Hydrophobic tail consists 2 fatty acids Its properties cause it to form lipid bilayers in aqueous solution Basic component of cell membrane Carotenoids Orange, yellow plant pigments; insoluble in water, oil consistency; function in photosynthesis,

consists 5 C hydrocarbon monomers(Isoprene units) Animals convert carotenoids to Vitamin A which convert to visual pigment Retinal Proteins Macromolecules ~Composed amino acid, consist 1 or >1 polypeptide chains Most enzymes are proteins a.a. in proteins~letters of protein alphabet. Each protein~ 2 a.a. combine to form dipeptide >2 a.a. combine to form dipeptide Protein Class Enzyme Structural protein Storage protein Functions and examples Catalyse specific chemical reactions Strengthen and protect cells and tissues Store nutrients; particularly abundant in eggs (Ovalbumin in egg white and seeds: Zein in corn kernels) Transport specific substances between cells (Hemoglobin transport O2 in red blood cells), (Move substances across cell membranes: ions, glucose, amino acids) Protein hormones(Insulin), Control expression of specific genes Participate in cellular movements(Actin & myosin essential for muscle contraction) Defend against foreign invaders(Antibodies play role in immune system)

Transport protein

Regulatory protein Motile protein

Protective protein

Collagen: Strengthen animal tissues Amino Acid Subunit of proteins Have NH2 & COOH group bonded to C

In solution form is neutral pH due to dipolar ions COOH donates proton become H+ NH2 accepts proton becomes NH3 + Amino Acids in Proteins 20 a.a. found in most protein; identified by variable side chain(R group) bonded to C

 Grouped by properties of side chain Nonpolar side chains are hydrophobic Polar side chains are hydrophilic Carboxyl side chains are acidic Acidic or alkaline depends on acception/donation of H+ ion Some proteins have additional a.a. Essential Amino Acid Amino acids that animal cant synthesize sufficient amount, must be obtain from diet; differs from species 9 Essential amino acid: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, histidine Peptide Bonds Bonds between carboxyl group and amino nitrogen group of a.a. Covalent carbon-to-nitrogen bond links 2 a.a. long sentence made of a.a. letters Almost infinite variety of protein molecules is possible, differes in numbers, types, sequences Amino Acid Sequence Determines Conformation In vitro: Polypeptide folds into normal, functional conformation In vivo: Protein (Molecular chaperones): mediate the folding of other protein molecules; Thought to make folding process efficient, prevent partially folded proteins from becoming inappropriately aggregated Stereochemistry of Amino Acids Proteins are assembled from L-amino acids (few D-amino acids occur in nature) Classified as , , according the carbon that bears the nitrogen Enzyme Accelerate chemical reactions Protein Shape Twist or folded form specific conformation (3D shape) Some form long fibers; globular proteins folded into spherical shapes

 Its function determined by its conformation Enzymes shape allows it to catalyze specific chemical reaction Protein hormones shape allows it to combine with receptors on its target cell Four Levels of Protein Organization Primary Structure Sequence of a.a. in a polypeptide chain; specific by instructions in a gene Ex: Glucagon, small polypeptide made of 29a.a. Represented in a linear(beads-on-astring) NH3+ & COO- at each end Secondary Structure May occur on same polypeptide chain -helix H bond between O2 & H Fibrous, elastic protein -pleated sheet H bond between regions of polypeptide chains Strong, flexible, not elastic Tertiary Structure 3D shape of 1 polypeptide chain Determine by 4 factors involving R groups of same polypeptide chain 3 Weak interactions: H bond, ionic bond, hydrophobic interactions Strong covalent bond: disulfide bridges between sulfhydryl groups of 2 cysteines Quaternary Structure 3D structure of >1 polypeptide chains Biologically active molecule 2 chains & 2 chains

Hemoglobin (Globular protein): 4 polypeptide chains Collagen (Fibrous protein): 3 polypeptide chains Protein Conformation Determines Function Determines biological activity

 Many proteins >1 globular domains, each with its own function Can be disrupted by change in a.a sequence Sickle Cell anemia Denaturation of protein Structure disordered & unfolds when: heated, pH change, certain chemical Loss of normal function; reversible Misfolded Proteins in Human Diseases Serious diseases occur: Mad cow disease (Misfolded proteins called prions), Alzheimers disease & Huntingtons disease Steroid Consist C atom arranged in 4 attached rings, side chain distinguish from 1 another Synthesized from isoprene units Ex: Cholesterol, bile salts, reproductive hormones, cortisol & other hormones secreted by adrenal cortex Plant cell membranes contain molecules similar to cholesterol Chemical Mediators Used for communication or internal regulation Produced by modification of fatty acids removed from phospholipid Lipid chemical mediators: Prostaglandins & certain hormones results in change in protein conformation

Dextrorotatory, D (+) & Lexoratory, L (-) sugar: mirror image L-sugar less abundant Calculate Stereoisomers N chiral center = 2n stereoisomer Aldose 2n-2, ketose 2n-3 n=number of chiral C atom Amino acid (Can acidic & alkaline) form polyamide/polypeptide Ester (Polyester)