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CHAPTER 5: THE STRUCTURE & FUNCTION OF LARGE BIOLOGICAL MOLECULES Overview: The Molecules of Life • All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids • Within cells, small organic molecules are joined together to form larger molecules • Macromolecules are large molecules composed of thousands of covalently connected atoms • Molecular structure and function are inseparable Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Monomers •Small organic •Used for building blocks of polymers •Connects with condensation reaction (dehydration synthesis) Polymers Macromolecules •Long molecules of •Giant molecules monomers •2 or more polymers •With many identical or bonded together similar blocks linked by covalent bonds ie. amino acid peptide polypeptide protein smaller larger Lipids do not have monomers and polymers Dehydration Synthesis (Condensation Reaction) Hydrolysis Make polymers Breakdown polymers Monomers Polymers Polymers Monomers A + B AB AB A + B + + H2O + H2O + • Enzymes are macromolecules that speed up these processes Fig. 5-2 HO 1 2 3 H Short polymer HO Unlinked monomer Dehydration removes a water molecule, forming a new bond HO 2 1 H 3 H2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 (b) Hydrolysis of a polymer H H H2O HO H I. Carbohydrates • Fuel (short-term energy) and building material (structure) • Include simple sugars (fructose) and polymers (starch) • Ratio of 1 carbon: 2 hydrogen: 1 oxygen or CH2O • monosaccharide disaccharide polysaccharide • Monosaccharides = monomers (eg. glucose, ribose) • Polysaccharides: Storage (plants-starch, animals-glycogen) Structure (plant-cellulose, arthropod-chitin) Differ in position & orientation of glycosidic linkage • The structure and classification of some monosaccharides • Monosaccharides are classified by • The location of the carbonyl group (C=O) • Aldose (end) or Ketose (middle) • The number of carbons in the carbon skeleton Linear and ring forms of glucose Monosaccharide + monosaccharide = disaccharide Covalent bond = glycosidic linkage Carbohydrate synthesis Cellulose vs. Starch (storage polysaccharides) Two Forms of Glucose: glucose & glucose Cellulose vs. Starch (storage polysaccharides • Starch = glucose monomers • Cellulose = glucose monomers • Storage polysaccharides of plants (starch) and animals (glycogen) Starch is stored in chloroplasts; Glycogen stored in liver and muscle cells • Structural polysaccharides: cellulose (cell wall of plants) & chitin (exoskeleton of arthropods and cell walls of fungi) • Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in cellulose – Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose • Many herbivores, from cows to termites, have symbiotic relationships with these microbes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Sample FRQ- Short Response Acidic Mammalian Chitinase (AMCase) activity (nmol/ml/hour) of subject at different pH values (Paoletti et al.2007) •Predict and explain where in the human body AMCase is most likely to be found. •Identify what types of food an individual that lacks properly functioning AMCase would have difficulty digesting. •Pose an evolutionary explanation for the AMCase secretions in humans. Lipids are a diverse group of hydrophobic molecules • Lipids are the one class of large biological molecules that do not form polymers • The unifying feature of lipids is having little or no affinity for water • Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds • The most biologically important lipids are fats, phospholipids, and steroids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings II. Lipids A.Fats (triglyceride): store energy – Glycerol + 3 Fatty Acids (joined by ester linkage) – saturated, unsaturated, polyunsaturated B.Steroids: cholesterol and hormones C.Phospholipids: lipid bilayer of cell membrane – hydrophilic head, hydrophobic tails Hydrophilic head Hydrophobic tail Saturated Unsaturated Polyunsaturated “saturated” with H Have some C=C, result in kinks In animals In plants Solid at room temp. Liquid at room temp. Eg. butter, lard Eg. corn oil, olive oil • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits • Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen • Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds • These trans fats may contribute more than saturated fats to cardiovascular disease Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings • The major function of fats is energy storage • Humans and other mammals store their fat in adipose cells • Adipose tissue also cushions vital organs and insulates the body Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings • Steroids are lipids characterized by a carbon skeleton consisting of four fused rings • Cholesterol, an important steroid, is a component in animal cell membranes Cholesterol, a steroid The structure of a phospholipid Hydrophobic/hydrophilic interactions make a phospholipid bilayer III. Proteins • “Proteios” = first or primary • 50% dry weight of cells • Contains: C, H, O, N, S Myoglobin protein Protein Functions (+ examples) • Enzymes (lactase) • Defense (antibodies) • Storage (milk protein = casein) • Transport (hemoglobin) • Hormones (insulin) • Receptors • Movement (motor proteins) • Structure (keratin) Overview of protein functions Overview of protein functions • Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions • Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-16 Substrate (sucrose) Glucose OH Fructose HO Enzyme (sucrase) H2O Four Levels of Protein Structure • Primary – Amino acid (AA) sequence – 20 different AA’s – peptide bonds link AA’s Amino Acid • R group = side chains • Properties: • hydrophobic • hydrophilic • ionic (acids & bases) • “amino” : -NH2 • “acid” : -COOH • Amino acids are linked by peptide bonds • A polypeptide is a polymer of amino acids • Polypeptides range in length from a few to more than a thousand monomers • Each polypeptide has a unique linear sequence of amino acids Four Levels of Protein Structure (continued) 2.Secondary – Gains 3-D shape (folds, coils) by H-bonding – Alpha (α) helix, Beta (β) pleated sheet Four Levels of Protein Structure (continued) 3.Tertiary – Bonding between side chains (R groups) of amino acids – H bonds, ionic bonds, disulfide bridges, van der Waals interactions Four Levels of Protein Structure (continued) 4.Quaternary – 2+ polypeptides bond together – R groups of polypeptide chains held together with H bonds, ionic bonds, disulfide bridges, van der Waals interactions amino acids polypeptides protein Chaperonins assist in proper folding of proteins • Protein structure and function are sensitive to chemical and physical conditions • Unfolds or denatures if pH and temperature are not optimal change in structure = change in function IV. Nucleic Acids Function: store hereditary info DNA RNA • Double-stranded helix • N-bases: A, G, C, Thymine • Stores hereditary info • Longer/larger • Sugar: deoxyribose • Single-stranded • N-bases: A, G, C, Uracil • Carry info from DNA to ribosomes • tRNA, rRNA, mRNA, RNAi • Sugar: ribose Fig. 5-26-3 DNA Information flow in a cell: DNA RNA protein 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Polypeptide Amino acids Nucleotides: monomer of DNA/RNA Nucleotide = Sugar + Phosphate + Nitrogen Base Polynucleotide or nucleic acid = Polymer Nucleotide phosphate Nitrogen base 5-C sugar Purines A–T G–C Pyrimidines •Adenine •Guanine •Cytosine •Thymine (DNA) •Uracil (RNA) •Double ring •Single ring Nucleotide Polymers • Nucleotide polymers are linked together to build a polynucleotide • Adjacent nucleotides are joined by covalent phosphodiester bonds that form between the –OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next – These links create a backbone of sugarphosphate units with nitrogenous bases as appendages • The sequence of bases along a DNA or mRNA polymer is unique for each gene Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The DNA Double Helix • A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix • In the DNA double helix, the two backbones run in opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel • One DNA molecule includes many genes • The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-28 5' end 3' end Sugar-phosphate backbones Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 3' end 5' end New strands 5' end 3' end 5' end 3' end Fig. 5-UN9 You should now be able to: 1. List, describe, explain the formation of, and give examples of the four major classes of molecules 2. Distinguish between mono, di, and polysaccharides 3. Distinguish between saturated and unsaturated fats and between cis and trans fat molecules 4. Describe the four levels of protein structure and explain how the function of a protein can be affected by a small change 5. Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, the 5 end and 3 end of a nucleotide Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings