Proteins, Carbohydrates, and Lipids PDF

3 Proteins, Carbohydrates, and Lipids © Oxford University Press Chapter 3 Proteins, Carbohydrates, and Lipids Key Concepts 3.1 Macromolecules Characterize Living Things 3.2 Proteins Are Polymers with Highly Variable Structures...

3 Proteins, Carbohydrates, and Lipids © Oxford University Press Chapter 3 Proteins, Carbohydrates, and Lipids Key Concepts 3.1 Macromolecules Characterize Living Things 3.2 Proteins Are Polymers with Highly Variable Structures 3.3 Carbohydrates Are Made from Simple Sugars 3.4 Lipids Are Defined by Their Insolubility in Water © Oxford University Press Chapter 3 Proteins, Carbohydrates, and Lipids (IL 1) Investigating LIFE introduction Weaving a Web Spider silk is composed of proteins and is extremely strong. The protein molecules in different types of silk have different structural characteristics and functions. Q&A: What are practical uses for spider silk? (See slides 10-11, and 79.) © Oxford University Press Table 2.3 Some Electronegativities © Oxford University Press Concept 2.2 Atoms Bond to Form Molecules (8) Nonpolar covalent bond: Electrons are shared equally (atoms have similar electronegativity). Polar covalent bond: One atom has greater electronegativity, so electrons are drawn more to that nucleus. A molecule with a polar bond has a slightly negative charge on one end and a slightly positive charge on the other. © Oxford University Press © Oxford University Press Concept 3.1 Macromolecules Characterize Living Things (1) Molecules that make up organisms: Proteins Carbohydrates Lipids Nucleic acids All except lipids are polymers of smaller molecules called monomers. © Oxford University Press Figure 3.3 Substances Found in Living Tissues Concept 3.1 Macromolecules Characterize Living Things (2) Macromolecules: Polymers containing thousands or more atoms. (Large lipids are also treated as macromolecules.) Macromolecule function depends on the properties of functional groups. Each group has specific properties, such as polarity. A single macromolecule may contain many different functional groups. © Oxford University Press Figure 3.1 Some Functional Groups Important to Living Systems © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (8) Acids release hydrogen ions (H+) in water: HCl → H+ + Cl– H+ concentration is increased; the solution is acidic. H+ ions can attach to other molecules and change their properties. © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (9) Biological acids have a carboxyl group: —COOH → —COO– + H+ Weak acids: Not all the acid molecules dissociate into ions (e.g., acetic acid CH3COOH). Strong acids, such as hydrochloric acid (HCl), dissociate completely. © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (10) Bases accept H+ ions. NaOH is a strong base. NaOH → Na+ + OH– OH– + H+ → H2O Weak bases include bicarbonate ion (HCO3–), ammonia (NH3), and compounds with amino groups (-NH2). © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (11) Acid–base reactions may be reversible: CH3COOH  CH3COO– + H+ Ionization of strong acids and bases is irreversible. Ionization of weak acids and bases is somewhat reversible. © Oxford University Press © Oxford University Press  Nonpolar. Important in interacting with other nonpolar molecules and in energy transfer. © Oxford University Press Figure 3.6 A Disulfide Bridge © Oxford University Press Concept 3.1 Macromolecules Characterize Living Things (3) Isomers: Molecules with the same chemical formula, but the atoms are arranged differently. Structural isomers differ in how atoms are joined cis-trans isomers: different orientation around a double bond Optical isomers: mirror images © Oxford University Press Figure 3.2 Isomers Concept 3.1 Macromolecules Characterize Living Things (1) Molecules that make up organisms: – Proteins – Carbohydrates – Lipids – Nucleic acids All except lipids are polymers of smaller molecules called monomers. Concept 3.1 Macromolecules Characterize Living Things (6) Condensation reactions: energy is used to make covalent bonds between monomers to make a polymer; a water molecule is removed. Hydrolysis reactions: polymers are broken down into monomers; energy is released and water is consumed. © Oxford University Press Figure 3.4 Condensation and Hydrolysis of Polymers (Part 1) Figure 3.4 Condensation and Hydrolysis of Polymers (Part 2) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (1) Proteins consist of one or more polypeptide chains—single, unbranched chains of amino acids. The chains are folded into specific 3-D shapes as defined by the sequence of amino acids. Proteins have diverse functions. © Oxford University Press Table 3.1 Proteins and Their Functions Concept 3.2 Proteins Are Polymers with Highly Variable Structures (2) Amino acids have carboxyl and amino groups— they function as both acid and base. Side chains or R-groups also have functional groups. Amino acids are grouped based on the side chains. The α carbon is asymmetrical; amino acids can be optical isomers: D- and L-amino acids. © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (13) pH: negative log of the molar concentration of free H+ ions in the solution: pH = –log[H+] H+ concentration of pure water is 10–7 M, its pH = 7. Lower pH numbers mean higher H+ concentration, or greater acidity. © Oxford University Press Figure 3.5 An Amino Acid Low pH H+ H+ H+ H + H+ H+ H+ + H+ H H+ H+ H+ H+ H H+ neutral 2 High pH H+ © Oxford University Press Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life (14) pH influences rates of biological reactions and can change the 3-D structure of biological molecules, which impacts function. Organisms use many mechanisms to minimize change in pH in their cells and tissues. © Oxford University Press Figure 2.13 Hydrophilic and Hydrophobic Some functional groups of amino acid side chains  Hydrophylic side chains Hydrophobic side chains Figure 3-2 University © Oxford Molecular Press Biology of the Cell (© Garland Science 2008) Table 3.2 The Twenty Amino Acids (Part 1) Table 3.2 The Twenty Amino Acids (Part 2) Table 3.2 The Twenty Amino Acids (Part 3) Table 3.2 The Twenty Amino Acids (Part 4) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (3) Cysteine: The terminal —SH group can react with another cysteine side chain to form a disulfide bridge, or disulfide bond (—S—S—). These are important in protein folding but most cysteines in a protein are not involved in disulfide bridges. © Oxford University Press Figure 3.6 A Disulfide Bridge Concept 3.2 Proteins Are Polymers with Highly Variable Structures (4) Oligopeptides, or peptides: short polymers of 20 or fewer amino acids. Polypeptides: longer polymers. Amino acids bond together covalently in a condensation reaction by peptide linkages (peptide bonds). © Oxford University Press Figure 3.7 Peptide Bond Formation Concept 3.2 Proteins Are Polymers with Highly Variable Structures (5) Primary structure of a protein: the sequence of amino acids. Properties of side chain functional groups determine how the protein can twist and fold; determines secondary and tertiary structure. The number of different proteins that can be made from 20 amino acids is enormous! © Oxford University Press Figure 3.8 The Four Levels of Protein Structure (Part 1) PRIMARY STRUCTURE Figure 3-1 Molecular Biology of the Cell (© Garland Science 2008)  (no rotation) Figure 3-3a Molecular Biology of the Cell (© Garland Science 2008) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (6) Secondary structure: α helix—right-handed coil resulting from hydrogen bonding between N–H groups and C=O groups. β pleated sheet—two or more polypeptide chains are aligned; hydrogen bonds form between the chains. © Oxford University Press Figure 3.8 The Four Levels of Protein Structure (Part 2) δ+ δ- δ+ δ- δ+ δ- δ+ δ- δ+ δ- δ+ δ- δ+ δ+ δ- δ- δ+ δ- δ+ δ-  Alpha helix is the most common type of helix Figure 3-7a,b,c Molecular Biology of the Cell (© Garland Science 2008) https://www.open.edu/openlearn/scien...-section-1.3.1. Figure 3.9 Left- and Right-Handed Helices α helix is right-handed coil Figure 3-11 Molecular Biology of the Cell (© Garland Science 2008) Figure 3-5 Molecular Biology of the Cell (© Garland Science 2008) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (7) Tertiary structure: Folding results in the specific 3-D shape. Determined by interactions between R-groups (disulfide bonds, hydrogen bonds, etc). The outer surfaces present functional groups that can interact with other molecules. © Oxford University Press Figure 3.8 The Four Levels of Protein Structure (Part 3)  van der Waals interactions © Oxford University Press Figure 3.10 Three Representations of Lysozyme Domain is a three-dimensional protein structure, a region of a polypeptide chain, that folds independently from the rest. It has often special function (catalytic domain, transmembrane domain, ATP-binding domain, DNA binding zinc finger domain …) Proteins can comprise a single domain or a combination of domains (multi-domain proteins). Figure 3-15 Molecular Biology of the Cell (© Garland Science 2008) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (9) Many proteins have two or more polypeptide chains, or subunits. Quaternary structure results from interaction of subunits by hydrophobic interactions, van der Waals forces, ionic attractions, and hydrogen bonds. Each subunit has its own unique tertiary structure. © Oxford University Press Figure 3.8 The Four Levels of Protein Structure (Part 4) Figure 3.12 Quaternary Structure of a Protein Concept 3.2 Proteins Are Polymers with Highly Variable Structures (10) Proteins bind noncovalently with specific molecules. Specificity is determined by: Shape—there must be a general “fit” between the protein and the other molecule. Chemistry—surface R groups interact with other molecules via ionic, hydrophobic, or hydrogen bonds. © Oxford University Press Figure 3.13 Noncovalent Interactions between Proteins and Other Molecules ionic bond van der Waals forces H bond MONOMERS Figure 2-32 Molecular Biology of the Cell (© Garland Science 2008) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (8) If a protein is heated, secondary and tertiary structure (and quaternary structure) break down; the protein is said to be denatured. When cooled, some proteins return to normal tertiary structure, demonstrating that the information to specify protein shape is in the primary structure. Figure 3.11A (1) Primary Structure Specifies Tertiary Structure (1) (Experiment) Denaturation Irreversible Reversible  Reversible denaturation by high concentration of urea (polar substance) © Oxford University Press Figure 3-6a Molecular Biology of the Cell (© Garland Science 2008) Concept 3.2 Proteins Are Polymers with Highly Variable Structures (11) Conditions that affect secondary and tertiary structure: High temperature pH changes High concentrations of polar molecules Nonpolar substances, via hydrophobic interactions © Oxford University Press  Denaturation by High temperature: Rapid molecular movements break H-bonds and hydrophobic interactions. pH changes: change the charged R groups disrupting the ionic bonds High concentrations of polar molecules: can disrupt the H bonds Nonpolar substances: via disruption of hydrophobic interactions © Oxford University Press Concept 3.2 Proteins Are Polymers with Highly Variable Structures (12) Protein shape can change as a result of: Interaction with other molecules—for example, an enzyme changes shape when it comes into contact with a reactant. Covalent modification—addition of a chemical group, such as a phosphate, to an amino acid. © Oxford University Press Figure 3.14 Protein Structure Can Change Figure 3.14 Protein Structure Can Change Substrate Ligand Inhibitor … MODIFICATION Phosphate group Phosphoprylation Acetyl group Acetylation Methyl group Methylation … … Concept 3.2 Proteins Are Polymers with Highly Variable Structures (13) Proteins can bind to the wrong molecules after denaturation or when they are newly made and still unfolded. Chaperones are proteins that help prevent this. Chaperones, such as heat shock proteins, surround a denatured protein and allow it to refold. © Oxford University Press Figure 3.15 Molecular Chaperones Protect Proteins from Inappropriate Binding Some newly synthetised proteins need this help (during or after synthesis) to avoid misfolding and aggregation. Concept 3.3 Carbohydrates Are Made from Simple Sugars (1) Carbohydrates: (C1H2O1)n. Sources of stored energy Used to transport stored energy Carbon skeletons for many other molecules Form extracellular structures such as cell walls © Oxford University Press Concept 3.3 Carbohydrates Are Made from Simple Sugars (2) Monosaccharides: Simple sugars. Disaccharides: Two simple sugars linked by covalent bonds. Oligosaccharides: 3 to 20 monosaccharides. Polysaccharides: Hundreds or thousands of monosaccharides. © Oxford University Press Concept 3.3 Carbohydrates Are Made from Simple Sugars (3) All cells use glucose as an energy source. Exists as a straight chain or ring form (more stable). Ring form exists as α- or β-glucose, which can interconvert. © Oxford University Press Concept 3.3 Carbohydrates Are Made from Simple Sugars (4) Monosaccharides: Pentoses: five-carbon sugars; includes ribose and deoxyribose in RNA and DNA Hexoses: six-carbon sugars; some are structural isomers. © Oxford University Press Figure 3.17 Monosaccharides Are Simple Sugars  Monosaccharides bind together in condensation reactions to form glycosidic bonds to form disaccharides © Oxford University Press  Oligosaccharides: several (3-20) monosaccharides linked by glycosidic bonds; often covalently bonded to proteins and lipids on cell surfaces, where they serve as recognition signals outside cell ABO blood types https://en.wikipedia.org/wiki/ABO_blood_group_system#/media/File:ABO_blood_group_diagram.svg  Polysaccharides are large polymers of monosaccharides connected by glycosidic bonds; some are branched. Cellulose: very stable, good for structural components Starch: storage of glucose in plants Glycogen: storage of glucose in animals © Oxford University Press Figure 3.19 Representative Polysaccharides (Part 1) Starch and glycogen Figure 3.19 Representative Polysaccharides (Part 3) Concept 3.3 Carbohydrates Are Made from Simple Sugars (7) Carbohydrates can be modified by the addition of functional groups to form: Sugar phosphates Amino sugars Chitin © Oxford University Press Figure 3.20 Chemically Modified Carbohydrates https://en.wikipedia.org/wiki/Mushroom#/media/File:Amanita_muscaria_(fly_agaric).JPG Concept 3.4 Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons; insoluble in water. If close together, weak but additive van der Waals forces hold them together in aggregates. © Oxford University Press https://testoil.com/program-management/water-in-oil/ Concept 3.4 Lipids Are Defined by Their Insolubility in Water (2) Types of lipids: Fats and oils store energy. Phospholipids—structural role in cell membranes. Carotenoids and chlorophylls—capture light energy in plants. Steroids and modified fatty acids—hormones and vitamins. Waxes © Oxford University Press Concept 3.4 Lipids Are Defined by Their Insolubility in Water (3) Animal fat—thermal insulation. Lipid coating around nerves provides electrical insulation. Oil and wax on skin, fur, and feathers repel water and slows evaporation. © Oxford University Press Concept 3.4 Lipids Are Defined by Their Insolubility in Water (4) Fats and oils are triglycerides: three fatty acids plus glycerol. Fatty acid: Nonpolar hydrocarbon chain with a polar carboxyl group. Carboxyls bond with hydroxyls of glycerol in ester linkages (condensation reactions). © Oxford University Press Figure 3.21 Synthesis of a Triglyceride  Saturated fatty acid: No double bonds between carbons—it is saturated with H atoms (animal fats; solid at room temperature). Unsaturated fatty acid: One or more double bonds in the carbon chain result in kinks that prevent packing (plant oils; liquid at room © Oxford University Press temperature). Concept 3.4 Lipids Are Defined by Their Insolubility in Water (6) Double bonds in naturally occurring unsaturated fats are cis (H atoms are on the same side). Trans fats: H atoms are on opposite sides of the C=C bond (trans). Trans fats result from hydrogenation of vegetable oils to produce a saturated fat (e.g. for margerine), but some of the cis bonds convert to trans. Trans fats may contribute to heart disease and stroke. © Oxford University Press © Oxford University Press Concept 3.4 Lipids Are Defined by Their Insolubility in Water (7) Polyunsaturated fatty acids has a backbone with two or more carbon–carbon double bonds. Omega-3 fatty acids protect against heart disease and stroke. The first C=C bond is at position 3 in the fatty acid chain. © Oxford University Press Concept 3.4 Lipids Are Defined by Their Insolubility in Water (8) Phospholipids: Fatty acids bound to glycerol; a phosphate group replaces one fatty acid. They are amphipathic: “Head” is a phosphate group—hydrophilic. “Tails” are fatty acid chains—hydrophobic. © Oxford University Press Figure 3.23 Phospholipids (Part 1) Concept 3.4 Lipids Are Defined by Their Insolubility in Water (9) Bilayer: In water, phospholipids line up with the hydrophobic tails together and the phosphate heads facing outward. Biological membranes have this kind of phospholipid bilayer structure. In animals, phospholipids and proteins form lipoproteins which transport lipids such as cholesterol in the blood. © Oxford University Press Figure 3.23 Phospholipids (Part 2) Figure 3.23 Phospholipids (Part 3) Concept 3.4 Lipids Are Defined by Their Insolubility in Water (10) Carotenoids: light-absorbing pigments, e.g., β- carotene traps light energy for photosynthesis. In humans, β-carotene breaks down into Vitamin A. Steroids: Multiple rings share carbons. Cholesterol is important in membranes; other steroids are hormones. Waxes: long-chain alcohol bound to an unsaturated fatty acid. © Oxford University Press Figure 3.24 More Lipids Chapter 3 Proteins, Carbohydrates, and Lipids (IL 2) Investigating LIFE conclusion Q&A: What are practical uses of spider silk? Composite silkworm–spider silk is now available in industrial quantities. Applications include surgical sutures, bullet- proof vests, and textiles. © Oxford University Press  Thank you for your attention! © Oxford University Press