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Chapter 3 Biochemistry 1 Why study carbon? • All living things are made of cells • Cells are… – ~72% water – ~3% salts – ~25% carbon compounds • • • • Carbohydrates Proteins Lipids Nucleic acids 2 Carbon Chemistry • Organic chemistry -study of carbon compounds • Carbon atoms can form diverse molecules by bonding to four other atoms • Carbon has four valence electrons and may form single, double, triple, or quadruple bonds 3 • The electron configuration of carbon gives it covalent compatibility with many different elements Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C 4 Hydrocarbons • Hydrocarbons are molecules consisting of only carbon and hydrogen • Hydrocarbons are found in many of a cell’s organic molecules 5 H H H H H (a) Length C H H H C C C C H H H H Propane H H Ethane H (b) Branching H H H H H C C C H H H H C H H C H H C C C H H H H H Butane (c) Double bonds H isobutane H H H H C C C C H H H H H H C (d) Rings H C C C C H C C H H H H Cyclohexane C H H C H 1-Butene H H H H H C H H 2-Butene H H C C C C H C Benzene 6 Functional Groups • Functional groups are the parts of molecules involved in chemical reactions • They Are the chemically reactive Female lion groups of atoms within an organic molecule • Give organic molecules distinctive chemical properties Male lion Estradiol OH CH3 HO OH CH3 CH3 O Testosterone 7 • Six functional groups are important in the chemistry of life – Hydroxyl – in alcohols, sugar – Carbonyl – in sugars, amino acids, nucleotide bases – Carboxyl – in amino acids, fatty acids; acts as an acid and releases H+ – Amino – in amino acids; acts as a weak base – Sulfhydryl – in amino acid cysteine; helps stabilize protein structure – Phosphate – in ATP, nucleotides, proteins, phospholipids; acidic; 8 Some important functional groups of organic compounds FUNCTIONAL GROUP HYDROXYL CARBONYL O OH (may be written HO STRUCTURE CARBOXYL C C OH ) In a hydroxyl group (— OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) O The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH). 9 • Some important functional groups of organic compounds AMINO SULFHYDRYL H N H The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. PHOSPHATE O SH (may be written HS ) O P OH OH The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). 10 Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures 11 Macromolecules •Most macromolecules are polymers, built from monomers • Four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids – Lipids 12 • A polymer – Is a long molecule consisting of many similar building blocks called monomers – Specific monomers make up each macromolecule – E.g. amino acids are the monomers for proteins 13 How are organic compounds built? • Enzymes (proteins) are needed to make metabolic reactions proceed much faster than they would on their own. 14 The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis HO 1 2 3 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 H HO 3 H 2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer 15 The Synthesis and Breakdown of Polymers • Polymers can disassemble by a cleavage reaction -Hydrolysis (addition of water molecules) HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H H H 2O HO H (b) Hydrolysis of a polymer 16 Carbohydrates • Serve as fuel and building material • Include both sugars and their polymers (starch, cellulose, etc.) 17 Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 18 • Examples of monosaccharides Triose sugars Pentose sugars (C3H6O3) (C5H10O5) Aldoses H C O H O H C C H O C H C OH H C OH H C OH H C OH H C OH HO C H C OH H H C OH H Glyceraldehyde H Ribose H H H C OH H HO C H C OH HO C H H C OH H C OH H C OH H C OH H H Glucose Galactose H C OH C O H C OH C O O C OH H C OH HO H H C OH H C OH Dihydroxyacetone H C OH H C OH H C OH H H O H H C OH C Ketoses Hexose sugars (C6H12O6) Ribulose C H H Fructose 19 • Monosaccharides – May be linear – Can form rings H H HO H H H O 1C 2 6CH C OH C H C OH 3 4 5 C 6 C OH OH 2OH 5C H 4C OH 3 H OH C H 6CH O H 2C OH H 1C H O H 4C OH 2OH 5C H OH 3C H CH2OH O H H 1C 2C OH OH 6 H 5 4 HO H OH 3 H O H 1 2 OH OH H (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. 20 • Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage 21 (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. H (b) Dehydration reaction H in the synthesis of O sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. CH2OH CH2OH O H OH H H H H OH HO H OH H 2O H O H Glucose CH2OH H O H HO H 2O O H H OHOH H HO H O H H OH O H CH2OH H 1–4 1 glycosidic linkage HO OH H Fructose H O H H O H H OH OH Maltose H H 4 O CH2OH O H OH Glucose Glucose CH2O H O H O H H H OH CH2OH CH2OH H HO H O H O H OH H 1–2 H glycosidic 1 linkage O CH2OH O 2 H HO H CH2OH OH H Sucrose 22 Polysaccharides • Polysaccharides (complex carbohydrates) – Are polymers of sugars – Serve many roles in organisms 23 Storage Polysaccharides Chloroplast Starch • Starch – Is a polymer consisting entirely of glucose monomers – Is the major storage form of glucose in plants 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide 24 • Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m Glycogen (b) Glycogen: an animal polysaccharide 25 Structural Polysaccharides • Cellulose – Is a polymer of glucose – Its bonding arrangement stabilizes the chains and make it resist being digested 26 – Has different glycosidic linkages than starch H 4 H O CH2O H O HO H H H O H H H O H glucose O C H H O H C H C H C O H H O H O H O H C C CH2O H O H O H H H 4 H O O H H O H 1 H glucose (a) and glucose ring structures H O CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H H O O H 1 O 4 O H O CH2O H O O H O O H O O O H H H (b) Starch: 1– 4 linkage of glucose monomers CH2O H O O H 1 O H O O H O O CH2O CH2O O O H H H H (c) Cellulose: 1– 4 linkage of glucose monomers O H 27 – Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH 2 2OH H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. 28 • Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process 29 • Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods – Can be used as surgical thread – Has a nitrogen group CH2O H O OH H H OH H OH H H NH C O CH3 (b) Chitin forms the exoskeleton (a) The structure of the of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 30 Lipids • Lipids are a diverse group of hydrophobic molecules • Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic 31 Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids – Vary in the length and number and locations of double bonds they contain 32 • Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds Stearic acid (a) Saturated fat and fatty acid 33 • Unsaturated fatty acids – Have one or more double bonds Oleic acid (b) Unsaturated fat and fatty acid cis double bond causes bending 34 • Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid 35 • Phospholipid structure – Consists of a hydrophilic “head” and hydrophobic “tails” CH2 CH2 O O P O– + N(CH3)3 Choline Phosphate O CH2 CH O O C O C CH2 Glycerol O Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol 36 • The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail 37 Sterols • Sterols (steroids) – Are lipids characterized by a carbon skeleton consisting of four fused rings 38 • One steroid, cholesterol – Is found in cell membranes – Is a precursor for some hormones H 3C CH3 CH3 CH3 CH3 HO 39 Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids 40 • An overview of protein functions 41 • Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H 2O Fructose H O 4 Products are released. 3 Substrate is converted to products. 42 Enzymes vs catalyst 43 Polypeptides • Polypeptides – Are polymers (chains) of amino acids • A protein – Consists of one or more polypeptides 44 • Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups 45 Twenty Amino Acids • 20 different amino acids make up proteins CH3 CH3 H H3N+ C CH3 O H3N+ C H Glycine (Gly) O– C H3N C H + O– C CH2 O H3N C H Valine (Val) Alanine (Ala) CH CH3 CH3 O CH3 CH3 C + O– CH2 O C H Leucine (Leu) H3C H3N + O– CH C O C H Isoleucine (Ile) O– Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H CH2 O H3N+ C O– Methionine (Met) C H CH2 O C O– Phenylalanine (Phe) H3N+ C H O C H2C CH2 H2 N C O C H O– Tryptophan (Trp) Proline (Pro) 46 O– OH OH Polar H3N + CH2 C O C H CH H3N O– Serine (Ser) C + O C H3N O– H + CH2 C H O C CH2 H3N O– C + O C H Electrically charged H3N + C + O– O– O NH3+ NH2 C CH2 C CH2 CH2 CH2 CH2 CH2 CH2 O H O– H3N + CH2 C O C H O– H3N + CH2 C H Aspartic acid (Asp) O– + CH2 C O C H O– Glutamine (Gln) Asparagine (Asn) C C C H3N Basic O C CH2 O H Acidic –O CH2 H3N Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH2 O Glutamic acid (Glu) O– Lysine (Lys) NH2+ H3N + CH2 O C NH+ H3N + CH2 C H NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) 47 Amino Acid Polymers • Amino acids – Are linked by peptide bonds 48 Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions 49 Four Levels of Protein Structure • Primary structure – Is the unique sequence of amino acids in a polypeptide +H 3N Amino end Amino acid subunits Gly ProThrGly Thr Gly Glu Cys LysSeu LeuPro Met Val Lys Val Leu Asp AlaVal ArgGly Ser Pro Ala Glu Lle Asp Thr Lys Ser Lys TrpTyr Leu Ala Gly lle Ser Pro Phe His Glu AlaThrPhe Val Asn His Ala Glu Val Thr Asp Tyr Arg Ser Arg Gly Pro lle Ala Ala Leu Leu Ser Pro SerTyr Tyr Ser Thr Thr Ala Val Val Glu Thr ProLys Asn c o o– Carboxyl end 50 • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet pleated sheet Amino acid subunits O H H C C N C N H R R C C N O H H C C R N H C H R O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H C O N H N C H C H R R C R R O H H C C N C C N OH H R R R O O H H C C N O H O H H C C N C C N OH H R O C H H N HC N H C N H C N C H H C O C O R R C R O C H H NH C N C H O C R R C C O R H C N HC N H O C H helix 51 • Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hyrdogen bond CH22 CH O H O H 3C CH CH3 H 3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+-O C CH2 Ionic bond 52 • Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains Iron Heme Chains Hemoglobin 53 Review of Protein Structure +H 3N Amino end Amino acid subunits helix 54 What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Temperature, pH, etc. affect protein structure 55 •Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Normal protein Denatured protein Renaturation 56 The Protein-Folding Problem • Most proteins – Probably go through several intermediate states on their way to a stable conformation – Denaturated proteins no longer work in their unfolded condition – Proteins may be denaturated by extreme changes in pH or temperature 57 Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin 58 Normal hemoglobin Primary structure Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Val His Leu Thr Pro Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Val Glu structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures QuaternaryHemoglobin A structure Function Sickle-cell hemoglobin . . . Primary Quaternary structure Function 10 m ... Exposed hydrophobic region subunit 10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape. 59 Nucleotides • Consist of sugar, phosphate group, and nitrogen-containing bases • ATP – adenosine triphosphate contains 3 phosphate groups; important source of energy • Coenzymes – enzyme helpers that accept hydrogen atoms and electrons 60 Nucleic Acids • Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 61 The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 62 Deoxyribonucleic Acid • DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells 63 DNA Functions – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA DNA (translation) 1 Synthesis of mRNA in the nucleus NUCLEUS 2 Movement of mRNA into cytoplasm via nuclear pore mRNA CYTOPLASM mRNA Ribosome 3 Synthesis of protein Polypeptide Amino acids 64 The Structure of Nucleic Acids 5’ end • Nucleic acids – Exist as polymers called polynucleotides 5’C O 3’C O O 5’C O 3’C (a) Polynucleotide, or nucleic acid OH 3’ end 65 • Each polynucleotide – Consists of monomers called nucleotides – Sugar + phosphate + nitrogen base Nucleoside Nitrogenous base O O P 5’C O CH2 O O Phosphate group 3’C Pentose sugar (b) Nucleotide 66 67