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Chapter 3

Chapter 3: Proteins, Carbohydrates, and Lipids

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Boston University
CAS BI 108
Francis Monette

BI108 Chapter 3 Notes: Proteins, Carbohydrates, and Lipids 3.1: Molecules that Characterize Living Things (1) Proteins, (2) carbohydrates, (3) lipids, (4) nucleic acids; with the exception of lipids, these molecules are polymers constructed by covalent bonding of monomers Proteins: formed from different combinations of 20 amino acids Carbohydrates: giant molecules linking together monosaccharides to form polysaccharides NucleicAcids: formed from four kinds of nucleotides linked together in long chains Lipids: large structures formed from set of molecules (noncovalent forces maintain interactions between lipid monomers Macromolecules: polymers w/mw exceeding 1000; lipids not technically, but treated as such Functional groups give specific properties to biological molecules Functional Groups: certain groups of atoms that occur frequently in biological molecules; help determine shape of macromolecule/how it interacts Isomers have different arrangements of the same atoms • Isomers: molecules that have the same chemical formula, but atoms arranged different • Structural Isomers: differ in how atoms are joined together • Cis-trans: double bond between two carbon atoms, where carbons share two pairs of e’s; identifies which side of double bond functional groups found Cis: same side, trans: opposite sides • Optical Isomers: when carbon has four different atoms/groups attached to it; mirror image; asymmetric isomer The structures of macromolecules reflect their functions • In all living organisms; biochemical unity reflects evolution of all life from a common ancestor, by descent with modifications • Macromolecules perform many functions (energy storage, structural support, catalysis); only nucleic acids specialize in info storage and transmission Most macromolecules are formed by condensation and broken down by hydrolysis • Condensation reactions: (dehydration) formation of covalent bonds between monomers (loss of water); polymers form when water removed and energy added • Hydrolysis: breakdown of polymers into their monomers; water reacts with the covalent bond and splits into H and OH; releases energy 3.2: Chemical Structures and Functions of Proteins Diverse roles: structural support, catalysis, transport, regulation, defense, movement; *however, they do not provide energy storage or info storage 1 BI108 Chapter 3 Notes: Proteins, Carbohydrates, and Lipids Proteins: polymers made up of 20 amino acids; consist of one or more polypeptide chains (unbranched polymers of amino acids) Variation in sequence of amino acids allows for vast diversity in structure/function Amino acids are the building blocks of proteins AminoAcid: carboxyl functional group and amino functional group attached to α carbon along with side chain and R group; α carbon is asymmetrical • Can exist as optical isomers: D-amino acids (right) and L-amino acids (left) • L-amino acids commonly found in proteins of most organisms; “signature of life” • Simultaneously acids and bases: + - + Carboxyl loses H : COOH  COO + H Amino Group gains H : NH + H 2 NH + 3 Side chain (R-groups) contain functional groups that determine shape and function • Ionized (electrically charged) side chain: hydrophilic • Polar side chains: hydrophilic • Non-polar side chain: hydrophobic • Cysteine: has —SH group, can react with another cysteine side to form disulfide bridge (covalent bond); determine how it folds • Glycine: single hydrogen atom (small, fits into interior of protein) • Proline: lacks hydrogen and forms covalent bond with hydrocarbon side chain; ring structure Peptide linkages form the backbone of a protein Peptide Linkage: carboxyl of one amino acid reacts with amino group of another; condensation reaction Reactive groups: carboxyl and amino groups on α carbon C=O-negative, N-H-positive The primary structure of a protein is its amino acid sequence Primary Structure: precise sequence of amino acid in polypeptide chain; 20 amino acids, 2 linked amino acids: 20x20= 400 dipeptides • Sequence of amino acids in polypeptide chain determines final shape The secondary structure of a protein requires hydrogen bonding Secondary Structure: regular, repeated spatial patterns in different regions of a polypeptide chain • 2 types of secondary structure (determined by hydrogen bonding between amino acids): α helix and β pleated sheet • α helix: right-handed coil that turns, result of C=O (neg) and N-H (pos) • β pleated sheet: formed from two or more polypeptide chains that are completely extended/aligned; C=O and N-H groups stabilize • Hydrogen bonds stabilize 2 BI108 Chapter 3 Notes: Proteins, Carbohydrates, and Lipids The tertiary structure of a protein is formed by bending and folding Tertiary Structure: polypeptide chain bent at sites and folded back and forth; macromolecules 3D shape Interactions between R-groups and environment determine tertiary structure • Hydrogen bonds between side chains stabilize folds in proteins • Close interactions between hydrophobic side chains stabilized by van der Waals forces • Ionic attractions form between positively and negatively charged side chains, forming salt bridges • Secondary and tertiary structure derive from primary structure • If protein is heated, heat energy will disrupt weak interactions, causing secondary and tertiary to break down, protein is then denatured The quaternary structure of a protein consists of subunits Quaternary Structure: results from way subunits (two or more polypeptide chains) bind together and interact; i.e. the number/kind of polypeptide subunits Weak nature of forces permits small changes in quaternary structure to aid proteins function (carry oxygen in red blood cells) Shape and surface chemistry contribute to protein function Shapes/structures allow sites on exposed surface to bind (noncovalently) to other molecules • Shape: a give molecule will not bind to a protein unless there is a “fit” between their 3D shapes • Chemistry: many important functions involve interactions between surface R groups and other molecules Environmental conditions affect protein structure 3D structures determined by weak forces, so influenced by environment; do not break covalent bonds, but disrupt weaker noncovalent interactions that determine secondary, tertiary, and quaternary structure: • Increase in temperature: break hydrogen bonds/hydrophobic interactions • Alterations in pH: change pattern of ionization of carboxyl and amino groups in R
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