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Chapter 3

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CAS BI 108
Francis Monette

Proteins, Carbohydrates, and Lipids 1. Large molecules (aka macromolecules, all contain carbon – organic compounds, and they are held together covalently) a. Proteins, Carbohydrates, Lipids, Nucleic acids i. Lipids form large structures from a limited set of smaller molecules, but in this case, noncovalent forces maintain the interactions between the lipid forces b. Polymers – constructed by covalent bonding of smaller molecules called monomers (lot of monomers make a macromolecule) i. Consist of proteins, carbohydrates, and nucleic acids (all macromolecules) 1. Proteins are formed from different combinations of 20 amino acids 2. Carbohydrates can form giant molecules by linking together chemically similar sugar monomers to form polysaccharides 3. Nucleic acids are form from four kinds of nucleotide monomers linked together in long chains 2. Functional Groups a. -Attached on paper- 3. Isomers - Molecules that have the same chemical formula (same kinds and numbers of atoms) but with the atoms arranged differently a. Structural Isomers i. Differ in how their atoms are joined together. b. cis-trans isomers i. usually involve a double bond between two carbon atoms 1. same side = cis 2. opposite side = trans c. Optical isomers i. Occur when a carbon atom has four different atoms or groups of atoms attached to it ii. Mirror image of each other iii. Unable to “fit” each other 4. Function and structure of macromolecules a. Other polymers can have a part in other roles but ONLY nucleic acids specialize in information storage and transmission i. Nucleic acids function as hereditary material, carrying the traits of both species and individuals from generations ii. Our body has mostly protein followed by nucleic acids followed by carbohydrates and then lipids b. Macromolecules sometimes fold and have certain features to make them water-soluble, capable of intimate interactions with other molecules, provide strength and rigidity (hair) and proteins in muscles contract to result in movement c. Monomers are broken down through condensation aka dehydration (removal of water) to create polymers i. Condensation is the result of a formation of covalent bonds between monomers; where every covalent bond is, a molecule of water is released ii. Polymers + H O 2 monomers’covalent bonds release water + energy d. Polymers are broken down into monomers through the hydrolysis reaction (the absorption of water through polymers) i. The water breaks down the covalent bond and the water molecule splits into two ions (H and OH) which become end parts 5. Proteins a. Proteins and their functions i. Category Function Enzymes Speed up reactions Structural proteins Provide physical stability and movement Defensive proteins Recognize and respond to nonself substances ii. Category Function Signaling proteins Control physiological processes Receptor proteins Receive and respond to chemical signals Membrane transporters Regulate passage of substances across the cellular membrane Storage proteins Store amino acids for later use Transport proteins Bind and carry substances within the organism All proteins are polymers made up of 20 amino acids in different proportions and sequences iii. Proteins consist of one or more polypeptide chains – unbranched polymers of covalently linked amino acids b. Amino acids are the building blocks of protein i. Each amino acid has both a carboxyl functional group and an amino functional group attached to the same carbon atom called the α carbon which is also connected to a hydrogen atom and a side chain ii. Amino acids can exist as optical isomers called D-amino acids and L-amino acids. (d= dextro and l=levo) Only L- amino acids are found readily iii. At the pH level of 7, carboxyl and amino groups are ionized in that carboxyl lost an H and amino gained an H iv. Amino acids are acids and bases v. 20 amino acids found in living organisms are grouped and distinguished by their side chains: 1. 5 amino acids have ionized side chains which are hydrophilic 2. 5 amino acids have polar side chains and are hydrophilic 3. 7 amino acids have nonpolar side chains and are hydrophobic 4. 3 amino acids, cysteine, glycine, and proline are special cases a. Cysteine which usually has a –SH side group can react with another cysteine side chain in an oxidation reaction to form a covalent bond. Such a bond called disulfide bridge (–S-S-) determines how a polypeptide folds b. Glycine consists of a single hydrogen atom and is hydrophobic c. Proline lacks a hydrogen and instead, forms a covalent bond with the hydrocarbon side chain resulting in a ring structure. i. Proline is found where a protein bends or loops and is hydrophobic c. Backbone of protein α i. When amino acids polymerize, the carboxyl and amino groups attached to the carbon are the reactive groups ii. The carboxyl group reacts with the amino group of another undergoing a condensation reaction that forms a peptide linkage 1. Apeptide linkage begins with the amino group of the first amino acid added to the chain and is known as the N terminus. The end of the peptide linkage is the carboxyl group of the last amino acid. This is the C terminus. This C – N linkage cannot rotate freely and so limits the folding of the polypeptide chain. The oxygen bound to the carbon (C=O) in the carboxyl group carries a slight negative charge whereas the hydrogen bound to the nitrogen (N-H) in the amino group is slightly positive. This difference in charges favors hydrogen bonding within and between molecules of the protein iii. The primary structure is made of the same repeating sequence –N-C-C- where N is from amino group, C from a carboxyl and another C from the alpha carbon. iv. The secondary structure consists of regular repeated spatial patterns in different regions of a polypeptide chain. 1. Two types of secondary structures a. The alpha helix is a right-handed coil that turns in the same direction as a screw i. T Both secondary and tertiary h structures are derived from e primary structure R groups extend outward from the peptide backbone of the helix ii. The coiling results from hydrogen bonds that form between the (+) hydrogen of the N-H and the (-) oxygen of the C=O b. The beta pleated sheets i. Formed from two or more polypeptide chains that are almost completely extended and aligned. The sheet is stabilized by hydrogen bonds between the N-H groups on one chain and the C=O groups on the other. v. The tertiary structure 1. The definitive 3-D shape that fold and bend in specific places, exposing and hiding certain surfaces a. The protein’s exposed surfaces present functional groups capable of interacting with other molecules in the cell such as proteins, nucleic acids, carbohydrates, and lipid structures 2. Caused by the interactions between the R-group in amino-acid side chains and the R-group in the environment 3. Covalent disulfide bridges can form between specific cysteine side chains holding a folded polypeptide in place 4. Hydrogen bonds between side chains also stabilize folds in proteins 5. Hydrophobic side chains can aggregate together in the interior of the protein, away from water, folding the polypeptide in the process. 6. Ionic attractions can form between positively and negatively charged side chains, forming salt bridges between amino acids. This occurs between + and – charged amino acids vi. If heat is added to protein, the secondary and tertiary structures will break down and the protein will be denatured vii. The quaternary structure 1. Hydrophobic interactions, van der Waals, hydrogen bonding, and ionic attractions help hold the subunits together to form a hemoglobin molecule. 2. Because the bonds are weak, the cell is allowed to do its job a. Example: hemoglobin: once an O binds2 the four subunits shift to fit the molecule. d. What contributes to protein function i. Shape (and they can change!) 1. Molecules can only bind if their 3D shapes match or fit into each other 2. Shapes of proteins change when: a. Proteins interact with other molecules b. Proteins undergo covalent modifications i. Example is when a charged phosphate group is added to a nonpolar R group which causes the amino acid to become more hydrophilic and to move to the outer surface altering the shape around the amino acid area ii. Chemistry 1. Exposed R groups permit chemical interactions with other substances. There are three types of interactions: ionic, hydrophobic, or hydrogen bonding. e. The environment can affect protein structure i. High temperatures can cause rapid molecular movements and a break in hydrogen bonds and hydrophobic interactions ii. Alterations in pH can change the pattern of ionization of exposed carboxyl and amino groups in the R groups of amino acids, disrupting the pattern of ionic attractions and repulsions iii. High concentrations of polar substances can disrupt the hydrogen bonding that is crucial to protein structure. Example is urea which causes protein denaturation. iv. Nonpolar substances may also disrupt normal protein structure in cases where hydrophobic interactions are essential to maintain the structure f. Molecular Chaperones
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