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Biological Molecules Organic Chemistry & Functional Groups Organic Compounds Carbon-based molecules Second most abundant type of compound found in organisms Over 2 million known organic compounds Properties of organic compounds depend on its size, shape, and type of functional group attached to it What is a Functional Group? Atoms, such as nitrogen, oxygen, phosphate and sulfur covalently bonded to a carbon backbone They are groups that change both the structure and behavior of a molecule, i.e., solubility, reactivity with other molecules They help chemists and biochemists classify different molecules found in living organisms Functional groups containing nitrogen or oxygen are polar and therefore hydrophylic and thus water-soluble Functional Groups in Biological Molecules GROUP Methyl Hydroxyl STRUCTURAL FORMULA H -C-H H - OH COMMON LOCATION fats, oils, waxes sugars, other alcohols H Aldehyde -C sugars OH Ketone -C=O sugars, hormones O Carboxyl -C sugars, fats, amino acids OH Functional Groups in Biological Molecules GROUP Amino STRUCTURAL FORMULA H H -N or - N - H H H COMMON LOCATION amino acids, proteins Phosphate O- O - P - OO DNA, RNA, ATP, lipids Sulfhydryl -S-H proteins Five Classes of Chemical Reactions in Biological Systems Five Classes of Reactions 1. 2. 3. 4. 5. Functional-group transfer Electron transfer Rearrangement Condensation (dehydration) Cleavage (hydrolysis) 1. Functional-Group Transfer one molecule gives up a functional group, which another molecule accepts seen in metabolic reactions, ex., glycolysis 2. Electron Transfer one or more electrons stripped from one molecule are donated to another molecule seen in metabolic reactions, ex., Kreb’s cycle, glycolysis 3. Rearrangement a juggling of internal bonds converts one type of organic compound into another seen in many metabolic pathways ex., glycolysis, Kreb’s cycle, etc. 4. Condensation (Dehydration) through covalent bonding, two molecules combine to form a larger molecule many successive condensation reactions leads to polymerization cells undergo condensation reactions to produce complex carbohydrates, lipids and proteins Polymerization & Condensation/Dehydration Reactions 5. Cleavage (Hydrolysis) a molecule splits into two smaller ones hydrolysis, is a very common biological cleavage. It is like condensation in reverse cells hydrolyze large polymers like starch and proteins, then use the released subunits as building blocks or energy sources Hydrolysis/Cleavage Reactions Carbohydrates Carbohydrates a simple sugar or a molecule composed of two or more sugar units can be used as either an immediate energy source, stored energy source or structural material 3 classes are: 1) monosaccharides, 2) oligosaccharides, 3) polysaccharides Monosaccharides Simplest carbohydrates Also called simple sugars Suffix - ose Glucose, Fructose, Galactose (hexoses) Ribose (pentose) Empirical formula is generally CH2O Usually form ring structures in aqueous solution functional groups include: hydroxyl and aldehyde or ketone Aldehyde vs. Keytone ISOMERS both have chemical formula of C6H12O6 Glucose Ring Structures Oligosaccharide Is a short chain of two or more covalently bonded sugar units Two or more monosaccharides join by dehydration reactions Disaccharide = two sugars – lactose - milk sugar (glucose + galactose) – sucrose - fruit sugar (glucose + fructose) – maltose - beer, seeds (glucose + glucose) Sucrose Dehydration Reaction in Maltose Formation Complex Carbohydrates Polysaccharides straight or branched chain of hundreds or thousands of the same or different sugar units (monomers) glucose-based polysaccharides: – starch - plant energy storage – cellulose - plant structural form – glycogen - animal energy storage Polymers of Glucose Fats & Lipids Five Classes of Lipids Fatty Acids Triglycerides Phospholipids Waxes Sterols Fatty Acids Contains a carbon backbone of up to 36 carbon atoms Contains a carboxyl group at one end Can be saturated (only single bonds) Can be unsaturated (may have one or more double or triple bonds) Saturated are solid at room temperature Unsaturated are liquid Saturated vs. Unsaturated Fatty Acids Saturated & Unsaturated Fatty Acids Trans Fatty Acids Increases the « bad » LDL cholesterol (low-density lipoprotein) and decreases the good HDL (highdensity lipoprotein) Suggested that you should not consume more than 2 g of trans fat/day in a 2000 kcal/day diet Myristic Acid – a Saturated fatty-acid Elaidic Acid - a Trans- fatty acid Oleic Acid in olive oil – cis-fatty acid O OH O O OH OH Other Effects of Trans Fats Cancer Type 2 diabetes Obesity Liver Dysfunction Ovulatory Infertility What if Trans fats are not labelled? add up the values for saturated, polyunsaturated and monounsaturated fats. If the number is less than the "Total fats" shown on the label, the unaccounted is trans fat. Triglycerides Composed of a glycerol molecule and three fatty acids Body’s most abundant lipid & best source of energy FAT!!! Adipose tissue contains high concentrations of triglycerides Condensation Reaction in Triglycerides Phospholipids Main component of cell membrane Hydrophilic head - glycerol + phosphate Hydrophobic tail - 2 fatty acids Phospholipid WAXES Waxes Long-chain fatty acids linked to an alcohol or carbon rings Very water repellent Paraffin Wax Breathing in paraffin candle wax may be carcinogenic Bee’s Wax Sterols/Steroids No fatty acid tails! Backbone of 4 fused carbon rings Sterols differ functional group types and positions Examples: cholesterol and hormones Cholesterol Anabolic Steroids Synthetic variants of testosterone Overdosing causes: • • • • Mood swings Liver damage leading to cancer High blood pressure Shrinks testicles, reduces sex drive & causes infertility & breast enlargement in men • Disrupts menstral cycle & leads to male characteristics in females • Stunts growth & stops bone growth in teens Proteins Silk Proteins Protein Biological polymer constructed from amino acid monomers Tens of thousands of proteins found in the human body Each protein has its unique threedimensional structure that corresponds to a specific function Seven classes of proteins Classes of Proteins Protein Structural – silk, hair, fibers, ligaments Contractile – muscle Storage – ovalbumin Defensive – antibodies Transport – hemoglobin, membrane Signal – certain hormones Enzymes - catalyst Protein Shape Consists of one or more polypeptide chains Either globular or fibrous in shape Can be denatured (unraveled) by heat, changes in salt concentration and pH Basic Structure of an Amino Acid Water vs. Fat-Soluble Amino Acids Peptide-Bond Formation Structural Levels Primary 1° Secondary 2° Tertiary 3° Quaternary 4° Primary Structure Amino acid sequence Secondary Structure Either alpha helix or pleated sheet Patterns maintained by hydrogen bonding between the –N-H groups and – C=O groups Tertiary Structure Globular – contain mixture of -helix and pleated sheets Fibrous – almost entirely helical Maintained by hydrogen bonding and ionic bonding between R groups of the amino acids. Quaternary Structure Results from bonding interactions between different polypeptides or subunits Quaternary Structure of Collagen Ribbon vs. Space-filling Models of Proteins Enzymes Enzymes in General speed up metabolic reactions that would normally take years to undergo by lowering the “activation energy” needed for a reaction to occur are named by adding the suffix “ase” to part of the name of the substrate (ex. sucrase) Enzymes Decrease the Activation Energy Mexican Jumping Bean analogy for energy of activation (EA) and the role of enzymes Characteristics of Enzymes Do not make any reaction occur that would not normally occur naturally Do not get used up during the reaction Can work both in the forward and reverse directions of a reaction Are highly selective to specific substrates Induced-Fit Model Enzymes have specifically shaped “active sites” on their surfaces that interact with the substrate(s) As the substrate enters this active site it induces the enzyme to change shape so that the active site fits even more snugly around the substrate (clasping handshake) This “induced-fit” strains the pre-existing bonds within the substrate(s) and promotes the formation of new bonds (in products) The role of sucrase in sucrose cleavage Hexokinase is an enzyme that catalyzes the ATPdependent phosphorylation of glucose to glucose-6phosphate. This is the first step and the first rate-limiting step the glycolytic pathway Induced-Fit Model of Hexokinase Factors Affecting Enzyme Activity Temperature - causes denaturation of the secondary & tertiary structures of the enzyme, hence changing the shape of the active site, therefore destroying enzymatic action pH - same as above Salinity - same as above Effect of Temperature on Different Enzymes Allosteric Control allo - different steric - structure enzymes can be activated or inhibited when a specific substance combines with them at a site other than the active site or within the active site Enzyme Inhibitors Feedback Inhibition When an end product accumulates, some of the excess product binds to an enzyme molecule, hence acting as an allosteric inhibitor and therefore blocking the production of more product Coenzymes A coenzyme can alter the shape of the enzyme’s active site allowing a better fit with its substrate they can also serve as transfer agents of atoms, electrons, H+ ions or functional groups. Nucleic Acids What is the problem with the figure of the double helix?