Proteins, Carbohydrates, and Lipids

• The following notes cover proteins, carbohydrates, and lipids, focusing on their structure, function, and properties

Objectives

• Identify macromolecules characterizing living things
• Learn functional groups that give macromolecules their chemical properties
• Learn amino acids comprising proteins and how protein structure is determined
• Understand the relationship between protein structure and function
• Understand the relationship between carbohydrate monomers and polymers
• Describe the components of lipids and learn their biological roles

Molecules of Living Things

• Four kinds of molecules are characteristic of living things: proteins, carbohydrates, lipids, and nucleic acids
• Proteins are formed from different combinations of 20 amino acids
• Carbohydrates are formed by linking together monosaccharides
• Nucleic acids are formed from four kinds of nucleotides
• Polymers are constructed by covalent bonding of smaller molecules called monomers
• Large structures are also formed from a limited set of smaller molecules, but these are maintained by noncovalent forces

Functional Groups

• Certain small arrangements of atoms, called functional groups, occur frequently in biological molecules
• Functional groups, when attached to larger molecules, give the larger molecule specific chemical properties

Classes of compounds and their properties:

• Hydroxyl group (R-OH): Found in alcohols, it is polar, forms hydrogen bonds with water to help dissolve molecules, and enables linkage to other molecules by condensation
• Aldehyde group (R-CHO): Found in aldehydes, it is polar, very reactive, and important in building molecules and in energy-releasing reactions
• Keto group (RCOR): Found in ketones, it is polar and important in carbohydrates and in energy reactions
• Carboxyl group (R-COOH): Found in carboxylic acids, it is charged, acidic, ionizes in living tissues to form -COO- and H+, enters into condensation reactions by giving up -OH, and some carboxylic acids are important in energy-releasing reactions
• Amino group (R-NH2): Found in amines, it is charged, basic, accepts H+ in living tissues to form -NH3+, and enters into condensation reactions by giving up H+
• Phosphate group (R-OPO3^2-): Found in organic phosphates, it is charged, acidic, enters into condensation reactions by giving up -OH, and when bonded to another phosphate, hydrolysis releases much energy
• Sulfhydryl group (R-SH): Found in thiols, by giving up H, two -SH groups can react to form a disulfide bridge, stabilizing protein structure
• Methyl group (R-CH3): Found in hydrocarbons, it is nonpolar, important in interacting with other nonpolar molecules, and in energy transfer

Macromolecule Formation and Breakdown

• Most macromolecules are formed by condensation reactions, producing water
• Macromolecules are broken down by hydrolysis reactions, which consume water

Proteins

• Proteins are polymers made up of 20 amino acids in different proportions and sequences
• Proteins range in size, from small (e.g., 51 amino acids in insulin) to huge (e.g., 24,000-36,000 amino acids in titin)
• Proteins consist of one or more polypeptide chains
• Polypeptide chains are unbranched (linear) polymers of covalently bonded amino acids
• Each chain folds into a particular 3D shape

Amino Acids

• Amino Acids can exist as optical isomers
• Have two forms D (dextro, right) and L (levo, left)
• Only L-amino acids are found in proteins of most organisms

Isomers

• Isomers are molecules that have the same chemical formula but with the atoms arranged differently
• Isomers come in different forms: structural, cis-trans, and optical

Behavior of Amino Acids

• At the pH levels found in cells (usually pH 7.0–7.4), both the carboxyl and amino groups of amino acids are ionized
• Amino acids show both acidic and basic properties
• The side chains (or R groups) contain functional groups that are important in determining the 3D structure and function of a protein

Amino Acid Groups

• Five amino acids have electrically charged side chains at pH levels typical of living cells
• Charged amino acids attract water (are hydrophilic) and oppositely charged ions

Electrically Charged Amino Acids

• Arginine, histidine, and lysine have a charge of +1
• Aspartic acid and glutamic acid have a charge of -1

Amino Acids with Polar Side Chains

• Five amino acids have polar (δ+ and δ-) side chains
• Polar amino acids attract water (are hydrophilic)
• Form hydrogen bonds with water and other polar substances
• Serine, threonine, asparagine, glutamine, and tyrosine are examples of polar amino acids

Amino Acids with Nonpolar Side Chains

• Seven amino acids have nonpolar hydrocarbon side chains
• Nonpolar amino acids are hydrophobic
• Tend to cluster together in aqueous solution
• Alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, and valine are examples of nonpolar amino acids

Special Amino Acids

• Three amino acids are special cases which influence protein structure: cysteine, glycine, and proline

Cysteine

• Has an -SH group
• Reacts with another cysteine side chain in an oxidation reaction
• Forms a covalent bond, creating a disulfide bridge

Glycine

• Has a side chain consisting of a single H atom
• Small enough to fit into tight corners of the interior of a protein
• Allows protein to be flexible at its location
• Generally hydrophobic

Proline

• The amino group is modified
• Lacks an H atom and covalently bonds to a hydrocarbon side chain
• Has a ring structure
• Has limited hydrogen bonding capability and rotation around the alpha carbon
• Found where a protein bends or loops
• Generally hydrophobic

Polypeptides

• The primary structure of a protein consists of amino acids joined by peptide bonds, forming a polypeptide
• Short polymers of less than 20 amino acids are called oligopeptides, or simply peptides