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Chapter 3

Chapter 3. Biochemistry. Why study carbon?. All living things are made of cells Cells are… ~72% water ~3% salts ~25% carbon compounds Carbohydrates Proteins Lipids Nucleic acids. Carbon Chemistry. Organic chemistry - study of carbon compounds

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Chapter 3

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  1. Chapter 3 Biochemistry

  2. Why study carbon? • All living things are made of cells • Cells are… • ~72% water • ~3% salts • ~25% carbon compounds • Carbohydrates • Proteins • Lipids • Nucleic acids

  3. 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

  4. Carbon (valence = 4) Nitrogen (valence = 3) Hydrogen (valence = 1) Oxygen (valence = 2) O H N C • The electron configuration of carbon gives it covalent compatibility with many different elements

  5. Hydrocarbons • Hydrocarbons are molecules consisting of only carbon and hydrogen • Hydrocarbons are found in many of a cell’s organic molecules

  6. H H C H C C C H C H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length H Ethane Propane H H H H H H H H H H H C C C C C C C C H H H H (b) Branching Butane isobutane H H H H C H (c) Double bonds H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Cyclohexane Benzene

  7. OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Functional Groups • Functional groups are the parts of molecules involved in chemical reactions • They Are the chemically reactive groups of atoms within an organic molecule • Give organic molecules distinctive chemical properties

  8. 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;

  9. FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O O OH C C OH (may be written HO ) 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–.) STRUCTURE 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).  Some important functional groups of organic compounds

  10. AMINO SULFHYDRYL PHOSPHATE O H SH N P OH O (may be written HS ) H OH 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). The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. • Some important functional groups of organic compounds

  11. Macromolecules • Are large molecules composed of smaller molecules • Are complex in their structures

  12. Macromolecules • Most macromolecules are polymers, built from monomers • Four classes of life’s organic molecules are polymers • Carbohydrates • Proteins • Nucleic acids • Lipids

  13. 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

  14. How are organic compounds built? • Enzymes (proteins) are needed to make metabolic reactions proceed much faster than they would on their own.

  15. 1 HO H 3 2 H HO Unlinked monomer Short polymer Dehydration removes a watermolecule, forming a new bond H2O 1 2 3 4 HO H Longer polymer (a) Dehydration reaction in the synthesis of a polymer The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis

  16. 1 3 HO 4 2 H Hydrolysis adds a watermolecule, breaking a bond H2O 1 2 H HO 3 H HO (b) Hydrolysis of a polymer The Synthesis and Breakdown of Polymers • Polymers can disassemble by a cleavage reaction -Hydrolysis (addition of water molecules)

  17. Carbohydrates • Serve as fuel and building material • Include both sugars and their polymers (starch, cellulose, etc.)

  18. Sugars • Monosaccharides • Are the simplest sugars • Can be used for fuel • Can be converted into other organic molecules • Can be combined into polymers

  19. Triose sugars(C3H6O3) Pentose sugars(C5H10O5) Hexose sugars(C6H12O6) H H H H O O O O C C C C H C OH H C OH H C OH H C OH H C OH H C OH HO C H HO C H Aldoses H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H C OH H C OH H Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O HO C H H C OH H C OH Ketoses H C OH H C OH H Dihydroxyacetone H C OH H C OH H C OH H Ribulose H Fructose • Examples of monosaccharides

  20. O H 1 C 6CH2OH 6CH2OH 2 CH2OH H C OH 5C H 5C O O 6 3 H O H H H H H 5 HO C H HOH H HOH 4 4C 1 C 1C 4C 4 1 OH H H H C OH O HO OH 3 2 OH OH 5 OH 2 C C 3 C 2C 3 OH H C H OH 6 H H OH OH H C 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. • Monosaccharides • May be linear • Can form rings

  21. Disaccharides • Consist of two monosaccharides • Are joined by a glycosidic linkage

  22. (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H 1–4glycosidiclinkage HOH HOH HOH HOH 4 1 H H H H OH OH O H OH HO HO OH O H H H H OH OH OH OH H2O Glucose Maltose Glucose CH2OH CH2OH CH2OH CH2OH O O O O 1–2glycosidiclinkage H H H H H HOH HOH H 2 1 H OH H HO H HO H Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring. (b) HO H O O HO CH2OH CH2OH OH H OH H H H OH OH H2O Glucose Sucrose Fructose

  23. Polysaccharides • Polysaccharides (complex carbohydrates) • Are polymers of sugars • Serve many roles in organisms

  24. Chloroplast Starch 1 m Amylose Amylopectin (a) Starch: a plant polysaccharide Storage Polysaccharides • Starch • Is a polymer consisting entirely of glucose monomers • Is the major storage form of glucose in plants

  25. Giycogen granules Mitochondria 0.5 m Glycogen (b) Glycogen: an animal polysaccharide • Glycogen • Consists of glucose monomers • Is the major storage form of glucose in animals

  26. Structural Polysaccharides • Cellulose • Is a polymer of glucose • Its bonding arrangement stabilizes the chains and make it resist being digested

  27. H O CH2OH C CH2OH OH OH H C H O O H H H H HO OH OH C H 4 4 1 H H HO OH HO OH H H C OH OH H OH H C H OH  glucose C  glucose H (a)  and  glucose ring structures CH2OH CH2OH CH2OH CH2OH O O O O OH OH OH OH 1 4 4 4 1 1 1 HO O O O O OH OH OH OH (b) Starch: 1– 4 linkage of  glucose monomers OH CH2OH OH CH2OH O O OH OH O O OH OH HO OH 4 O 1 O O CH2OH CH2OH OH OH (c) Cellulose: 1– 4 linkage of  glucose monomers • Has different glycosidic linkages than starch

  28. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. Cellulose microfibrils in a plant cell wall Microfibril Cell walls  0.5 m Plant cells OH OH CH2OH CH2OH O O O O OH OH OH OH O O O O O OH CH2OH OH CH2OH Cellulose molecules CH2OH OH CH2OH OH O O O O OH OH OH OH Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. O O O O O OH CH2OH OH CH2OH CH2OH CH2OH OH OH O O O O OH OH OH OH O O O A cellulose molecule is an unbranched  glucose polymer. O O OH CH2OH OH CH2OH • Glucose monomer • Is a major component of the tough walls that enclose plant cells

  29. Cellulose is difficult to digest • Cows have microbes in their stomachs to facilitate this process

  30. CH2OH O OH H H OH H H H NH O C CH3 OH (b) Chitin forms the exoskeleton of arthropods. This cicada 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. (a) The structure of the chitin monomer. • Chitin, another important structural polysaccharide • Is found in the exoskeleton of arthropods • Can be used as surgical thread • Has a nitrogen group

  31. 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

  32. 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

  33. Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds Stearic acid (a) Saturated fat and fatty acid

  34. Oleic acid cis double bond causes bending (b) Unsaturated fat and fatty acid • Unsaturated fatty acids • Have one or more double bonds

  35. Phospholipids • Have only two fatty acids • Have a phosphate group instead of a third fatty acid

  36. + CH2 Choline N(CH3)3 CH2 O Phosphate Hydrophilic head – P O O O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails Hydrophobic tails (c) Phospholipid symbol (b) Space-filling model (a) Structural formula • Phospholipid structure • Consists of a hydrophilic “head” and hydrophobic “tails”

  37. WATER Hydrophilic head WATER Hydrophobic tail • The structure of phospholipids • Results in a bilayer arrangement found in cell membranes

  38. Sterols • Sterols (steroids) • Are lipids characterized by a carbon skeleton consisting of four fused rings

  39. H3C CH3 CH3 CH3 CH3 HO • One steroid, cholesterol • Is found in cell membranes • Is a precursor for some hormones

  40. 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

  41. An overview of protein functions

  42. Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. • Enzymes • Are a type of protein that acts as a catalyst, speeding up chemical reactions

  43. Enzymes vs catalyst

  44. Polypeptides • Polypeptides • Are polymers (chains) of amino acids • A protein • Consists of one or more polypeptides

  45. Amino acids • Are organic molecules possessing both carboxyl and amino groups • Differ in their properties due to differing side chains, called R groups

  46. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ H3N+ H3N+ H3N+ C H3N+ C C C C C C C C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 H2N C C CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Twenty Amino Acids • 20 different amino acids make up proteins

  47. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ C C C C C C C C C C C C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O H3N+ H3N+ CH2 CH2 C CH2 C C C O O– H3N+ O– CH2 C CH2 C H O H H3N+ O– C C CH2 H O O– H3N+ C C H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp)

  48. Amino Acid Polymers • Amino acids • Are linked by peptide bonds

  49. Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions

  50. Amino acid subunits +H3NAmino end Pro Thr Gly Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Four Levels of Protein Structure • Primary structure • Is the unique sequence of amino acids in a polypeptide

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