Amino_Acids_and_proteins (2025)

• An Introduction to Biochemistry
• Protein Structure and Function: An Overview
• Amino Acids
• Acid–Base Properties of Amino Acids
• Handedness
• Molecular Handedness and Amino Acids
• Primary Protein Structure
• Shape-Determining Interactions in Proteins
• Secondary Protein Structure
• Tertiary Protein Structure
• Quaternary Protein Structure

• The principal classes of biomolecules are proteins, carbohydrates, lipids, and nucleic acids. We will briefly cover the first three.
• Some biomolecules are small and have only a few functional groups, others are huge and their biochemistry is governed by the interactions of large numbers of functional groups.

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• Protein: A large biological molecule made of many amino acids linked together through peptide bonds.
• Amino acid: Compound with an amino group bonded to the C atom next to the -COOH group.
• Peptide bond: An amide bond linking 2 amino acids.
• A dipeptide results from the formation of a peptide bond between 2 amino acids. A tripeptide results from linkage of 3 amino acids via 2 peptide bonds. Any number of amino acids can link together to form a linear chainlike polymer—a polypeptide.

• Proteins have four levels of structure,
• Primary structure is the sequence of amino acids in a protein chain
• Secondary structure is the regular and repeating spatial organization of neighboring segments of single protein chains.
• Tertiary structure is the overall shape of a protein molecule produced by regions of secondary structure combined with the overall bending and folding of the protein chain.
• Quaternary structure refers to the overall structure of proteins composed of more than one polypeptide chain.

• Nature uses 20 -amino acids to build the proteins in all living organisms; 19 of them differ only in the identity of the R group, or side chain, attached to the carbon. The remaining amino acid (proline) is a secondary amine whose nitrogen and carbon atoms are joined in a five-membered ring.
• Each amino acid has a three-letter shorthand code: Ala (alanine), Gly (glycine), Pro (proline), etc.
• The 20 protein amino acids are classified as neutral, acidic, or basic, depending on the nature of their side chains.

• The 15 neutral amino acids are further divided into those with nonpolar side chains and those with polar functional groups such as amide or hydroxyl groups in their side chains.
• It is the sequence of amino acids in a protein and the chemical nature of their side chains that enable proteins to perform their varied functions.
• Intermolecular forces are of central importance in determining the shapes and functions of proteins.
• Noncovalent forces act between different molecules or between different parts of the same large molecule, which is often the case in proteins.

• The nonpolar side chains are described as hydrophobic (water-fearing)—they are not attracted to water molecules.
• To avoid aqueous body fluids, they gather into clusters that provide a water-free environment, often a pocket within a large protein molecule.
• The polar, acidic, and basic side chains are hydrophilic (water-loving)—they are attracted to polar water molecules. They interact with water molecules much as water molecules interact with one another.
• Attractions between water molecules and hydrophilic groups on the surface of folded proteins impart water solubility to the proteins.

• Chiral: Having right- or left-handedness with two different non- superimposable mirror image forms.
• One hand does not match the other when superimposed.

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• Achiral: The opposite of chiral; having superimposable mirror images and thus no right- or left- handedness.
• It is easy to visualize the chair on top of its mirror image.

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• A dipeptide results from the formation of a peptide bond between 2 amino acids. A tripeptide results from linkage of 3 amino acids via 2 peptide bonds. Any number of amino acids can link together to form a linear chainlike polymer—a polypeptide.

• Without interactions between atoms in amino acid side chains or along the backbone, protein chains would twist about randomly in body fluids like spaghetti strands in boiling water.
• The essential structure–function relationship for each protein depends on the polypeptide chain being held in its necessary shape by these interactions.

• Some amino acid side chains can form hydrogen bonds. Side chain hydrogen bonds can connect different parts of a protein molecule, sometimes nearby and sometimes far apart along the chain.
• The H in the –NH- groups and the O in the C=O groups along protein backbones hydrogen bond.

• The spatial arrangement of the polypeptide backbones of proteins constitutes secondary protein structure.
• The secondary structure includes two kinds of repeating patterns known as the -helix and the -sheet.
• In both, hydrogen bonding between backbone atoms holds the polypeptide chain in place.

• The overall three-dimensional shape that results from the folding of a protein chain is the protein’s tertiary structure.
• In contrast to secondary structure, which depends mainly on attraction between backbone atoms, tertiary structure depends mainly on interactions of amino acid side chains that are far apart along the same backbone.

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• Native protein: A protein with the shape (secondary, tertiary, and quaternary structure) in which it exists naturally and functions in living organisms.
• Simple protein: A protein composed of only amino acid residues. Ribonuclease is classified as a simple protein because it is composed only of amino acid residues (124 of them).
• Conjugated protein: A protein that incorporates one or more non–amino acid units in its structure. The conjugated protein myoglobin has a heme group embedded within the polypeptide chain.

• The fourth and final level of protein structure, and the most complex, is quaternary protein structure—the way in which two or more polypeptide subunits associate to form a single three-dimensional protein unit.
• The individual polypeptides are held together by the same noncovalent forces responsible for tertiary structure. In some cases, there are also covalent bonds and the protein may incorporate a non–amino acid portion.

Denaturation: The loss of secondary, tertiary, or quaternary protein structure due to disruption of noncovalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.

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• Agents that cause denaturation include heat, mechanical agitation, detergents, organic solvents, extremely acidic or basic pH, and inorganic salts.
• Heat: The weak side-chain attractions in globular proteins are easily disrupted by heating, in many cases only to temperatures above 50°C.
• Mechanical agitation: The most familiar example of denaturation by agitation is the foam produced by beating egg whites. Denaturation of proteins at the surface of the air bubbles stiffens the protein and causes the bubbles to be held in place.
• Detergents: Even very low concentrations of detergents can cause denaturation by disrupting the association of hydrophobic side chains.

• Organic compounds: Organic solvents can interfere with hydrogen bonding or hydrophobic interactions. The disinfectant action of ethanol results from its ability to denature bacterial protein.
• pH change: Excess H⁺ or OH^- ions react with the basic or acidic side chains in amino acid residues and disrupt salt bridges. An example of denaturation by pH change is the protein coagulation that occurs when milk turns sour because it has become acidic.
• Inorganic salts: Sufficiently high concentrations of ions can disturb salt bridges.
• Most denaturation is irreversible. Hard-boiled eggs do not soften when their temperature is lowered.

• Amino acids in body fluids have ionized carboxylic acid groups, ionized amino groups, and a side-chain R group.
• Twenty different amino acids occur in proteins, connected by peptide bonds.
• R groups are acidic, basic, or neutral. Neutral groups are either polar or nonpolar. The dipolar ion in which the amino and carboxylic acid groups are both ionized is known as a zwitterion. Each amino acid has an isoelectric point—the pH at which the numbers of (+) and (-) charges in a sample are equal.

• A molecule is chiral when it has no plane of symmetry and thus has mirror images that are nonsuperimposable. A carbon atom bonded to four different groups is a chiral center. All -amino acids except glycine are chiral.
• Proteins are polymers of amino acids. Their primary structure is the linear sequence in which the amino acids are connected by peptide bonds. Using formulas or amino acid abbreviations, the primary structures are written with the N-terminal end on the left and the C-terminal end on the right. To name a peptide, the names of the amino acids are combined, starting at the N-terminal end, with the endings of all but the C-terminal amino acid changed to -yl.

• The -helix is a coil with H bonding between carbonyl O’s and amide H’s four amino acid residues farther along the same chain. The -sheet is a pleated sheet with adjacent protein chain segments connected by H bonding between peptide groups. Secondary structure mainly determines the properties of fibrous proteins, which are tough and insoluble.
• Tertiary structure is the overall three-dimensional shape of a folded protein chain. Tertiary structure determines the properties of globular proteins, which are water soluble, with hydrophilic groups on the outside and hydrophobic groups on the inside. Globular proteins contain regions of -helix and/or -sheet secondary structures.

• In a quaternary structure, two or more folded protein subunits are united in a single structure by noncovalent interactions. Hemoglobin consists of two pairs of subunits. Collagen is a fibrous protein composed of triple helixes.
• The end result of hydrolysis is production of the individual amino acids from the protein. Denaturation is the loss of overall structure by a protein while retaining its primary structure. Agents that cause denaturation are heat, mechanical agitation, pH change, and exposure to a variety of chemical agents, including detergents.

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