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Chapter 3

Chapter 3.odt

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University of Toronto Mississauga
Fiona Rawle

Chapter 3 Key Concepts • Proteins are made of amino acids.Amino acids vary in structure and function. • The structure of a protein can be analyzed at four levels: (1) Amino acid sequence (2) Substructures called a-helices and b-pleated sheets (3) Interactions between amino acids that dictate a protein’s overall shape (4) Combinations of individual proteins that make up larger, multiunit molecules • In cells, most proteins are enzymes that function as catalysts. What Do Proteins Do? • The diverse functions of proteins include: defense, movement, catalysis, signalling, structure, and transport. Early Origin-of-Life Experiments Could the first steps of chemical evolution have occurred on ancient Earth? • To find out, Stanley Miller combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source. • The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids. • In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions. The Structure of AminoAcids • All proteins are made from just 21 amino acids. • All amino acids have a central carbon atom that bonds to NH2, COOH, H, and a variable side chain. • In water (pH7), the amino and carboxyl groups ionize to NH3+ and COO–, respectively—this helps amino acids stay in solution and makes them more reactive. The Nature of Side Chains • The 21 amino acids differ only in the variable side chain or R-group attached to the central carbon • R-groups differ in their size, shape, reactivity, and interactions with water. 1. Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water 2. Polar R-groups: Form hydrogen bonds; readily dissolve in water • Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms. WhatAre Isomers? Isomers are molecules with the same molecular formula but different structures. Isomers include the following: 1. Structural isomers: Differ in the order which their atoms are attached 2. Geometric isomers: Differ in the arrangement of atoms around a double bond 3. Optical isomers: Differ in the arrangement of atoms, or groups, around a carbon atom that has four different groups attached Condensation and Hydrolysis Reactions • Amino acids polymerize to form proteins. Polymerization reactions require energy and are not spontaneous. • Monomers polymerize through condensation reactions, which release a water molecule. In the reverse reaction, hydrolysis, water reacts with a polymer to release a monomer. • In the prebiotic soup, hydrolysis would predominate over condensation because it is energetically favorable. However, polymers on mineral particles such as clay or mud are protected from hydrolysis. The Peptide Bond • Condensation reactions bond the carboxyl group of one amino acid to the amino group of another toform a peptide bond. • Apolypeptide is flexible and has directionality (the N-terminus has a free amino group and the C-terminus has a free carboxyl group), and its side chains extend out from the backbone. What Do Proteins Look Like? • Proteins are diverse in size and shape, as well as in the chemical properties of their amino acids. • Proteins have four basic levels of structure: primary, secondary, tertiary, and quaternary. Primary Structure • Aprotein’s primary structure is its unique sequence of amino acids. • Because the amino acid R-groups affect a polypeptide’s properties and function, just a single amino acid change can radically alter protein function. Secondary Structure • Secondary structure results in part from hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another.A polypeptide must bend to allow this hydrogen bonding—thus, a-helices or b-pleated sheets are formed. • Secondary structure depends on the primary structure—some amino acids are more likely to be involved in α-helices; while others, in β-pleated sheets. • Secondary Structure increases stability by way of the large number of hydrogen bonds. Tertiary Structure • The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide. • R-group interactions include hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds. • Hydrogen bonds can form between hydrogen atoms and the carboxyl group in the peptide- bonded backbone, and between hydrogen atoms and at
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