Chapter 18: Amino Acids

protein hydrolysis

-the reverse of protein formation, peptide bonds are hydrolyzed to yield amino acids. • Digestion of proteins in the diet involves hydrolyzing peptide bonds in the stomach and small intestine, where the process is catalyzed by enzymes. Amino acids are absorbed through the wall of the intestine. • A chemist might hydrolyze a protein by heating it with hydrochloric acid. • Endoproteases are enzymes that hydrolyze the peptide bonds in proteins at specific points within their sequences. - Chymotrypsin hydrolyzes a peptide bond on the carboxyl-terminal side of aromatic amino acids. - Trypsin hydrolyzes peptide bonds on the carboxyl side of lysine and arginine.

Zwitterion

A neutral dipolar ion that has one positive charge and one negative charge • Amino acids contain both an acidic group, -COOH, and a basic group, -NH2 . • These two groups can undergo an intramolecular acid-base reaction to form a zwitterion. • This gives amino acids many of the physical properties of salts: crystals, high melting points, and water solubility. • In acidic solution, amino acid zwitterions accept protons on their basic -COO- groups to leave only the positively charged -NH3 + groups. • In basic solution, amino acid zwitterions lose protons from their acidic -NH3 + groups to leave only the negatively charged -COO- groups.

Peptide bond

An amide bond that links two amino acids together • A dipeptide results from the formation of a peptide bond between the -NH2 group of one amino acid and the -COOH group of a second amino acid. • Three amino acids linked by peptide bonds will form a tripeptide. • Any number of amino acids can link together to form a linear, chainlike polymer—a polypeptide. • Very large peptides (oligopeptides) contain hundreds of amino acids and are referred to as proteins. • The exact sequence of amino acids in a peptide or protein chain is important; variation in the sequence indicates a different molecule. • A pair of amino acids can be combined to form two different dipeptides.

Conjugated proteins

proteins with covalently attached molecules • Conjugated proteins are aided in their function by an associated non-amino acid unit. • The oxygen-carrying portion of myoglobin has a heme group embedded within the polypeptide chain.

Biochemistry

the study of molecules and their reactions in living organisms. -The goal of biochemistry is to understand the structures of biomolecules and the relationship between their structures and functions. -The principal classes of biomolecules are proteins, carbohydrates, lipids, and nucleic acids.

Agents That Cause Denaturation

• *Heat*—The weak side-chain attractions in globular proteins are easily disrupted by heating. • *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 disrupt the association of hydrophobic side chains. • *Organic compounds*—Polar solvents interfere with hydrogen bonding by competing for bonding sites. • *pH change*—Excess H+ or OH- ions react with basic or acidic side chains in amino acid residues and disrupt salt bridges. • *Inorganic salts*—High concentrations of ions can disturb salt bridges.

hemoglobin

• Hemoglobin is a conjugated quaternary protein composed of four polypeptide chains (two each of two polypeptides called a-chain and b-chain) held together by hydrophobic interactions and four heme groups. • The a-chains have 141 amino acids, and the b-chains have 146 amino acids. • The heme groups each contain an iron. Hemoglobin is the oxygen carrier in red blood cells. In the lungs, O2 binds to Fe2+ so that each hemoglobin can carry a maximum of four O2 molecules. • In tissues in need of oxygen, O2 is released, and CO2 is picked up and carried back to the lungs. • Hemoglobin is a cellular protein, normally found only inside cells and carried throughout the body inside red blood cells. • Serum albumin is referred to as a mobile protein because it is dissolved in an extracellular (outside the cell) fluid. It carries CO2 to the lungs for disposal.

Molecular forces

• Intermolecular forces are of central importance in determining interactions between amino acids. • The intermolecular forces present between amino acids or between protein chains are hydrogen bonding, Van der Waals forces, ionic bonding, and disulfide bonds.

Peptides

• Peptides and proteins are always written with the amino-terminal amino acid (N-terminal, the one with the free -NH3 + ) on the left and carboxyl-terminal amino acid (C-terminal, the one with the free -COO- ) on the right. • The individual amino acids joined in the chain are referred to as residues. • A peptide is named by citing the amino acid residues in order, starting at the N-terminus and ending with the C-terminus.

Secondary Protein Structure (2°) Continued

• Proteins are classified in several ways, one of which is to identify them as either fibrous proteins or globular proteins. • Each have functions made possible by distinctive structures. • *Fibrous protein*: A tough, insoluble protein whose protein chains form fibers or sheets. -Keratins, coolagens, elastins, myosins, fibrin • *Globular protein*: A water-soluble protein whose chain is folded in a compact shape with hydrophilic groups on the outside -insulin, ribonuclease, immunoglobulins, hemoglobin, albumins -The enzyme ribonuclease can be drawn in a style that shows the combination of a-helix and b-sheet regions, the loops connecting them, and four disulfide bonds. -Ribonuclease is classified as a simple protein because it is composed only of amino acid residues.

Quaternary Protein Structure (4°)

• Quaternary protein structure is the way in which two or more protein chains aggregate to form large, ordered structures. • Polypeptides are primarily held together by noncovalent forces, but covalent bonds and non-amino acid portions may also be incorporated.

Side Chains

• The nonpolar side chains are described as hydrophobic (water-fearing). To avoid aqueous fluids, nonpolar side chains gather into clusters to create a water-free environment. • The polar, acidic, and basic side chains are hydrophilic (water-loving). Attractions between water molecules and hydrophilic groups on the surface of folded proteins impart water solubility to the proteins.

isoelectric point (pI)

describes the pH at which a sample of an amino acid has equal numbers of + and - charges. • At this point, the net charge of all the molecules of that amino acid in a pure sample is zero. • The pI for each amino acid is different, due to the influence of the side chain. • A few amino acids have isoelectric points that are not near neutrality (pH 7). Because the side-chain groups of these compounds are substantially ionized at physiological pH of 7.4, these amino acids are usually referred to by the names of the ions formed when the groups in the side chains are ionized. • Side chain interactions are important in stabilizing protein structure. Thus, it is important to be aware of their charges at physiological pH. • Isoelectric points influence protein solubility and determine which amino acids in an enzyme participate directly in enzymatic reactions.

Tertiary Protein Structure (3°) Continued

*Hydrogen Bonds of R Groups with Each Other or with Backbone Atoms*: -Side chain hydrogen bonds can connect different parts of a protein molecule, whether they are in close proximity or far apart along the polypeptide chain. *Ionic Attractions between R Groups (Salt Bridges)*: -Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates salt bridges. *Hydrophilic Interactions between R Groups and Water*: -Amino acids with charged R groups will interact with water through hydrogen bonding. *Hydrophobic Interactions between R Groups*: -Hydrocarbon side chains are attracted to each other by dispersion forces (primarily Van der Waals forces), which can create a water-free pocket in the protein chain. *Covalent Sulfur-Sulfur Bonds: The Disulfide Bridge* -Cysteine amino acid residues have side chains containing thiol functional groups (-SH) that can react to form sulfur-sulfur bonds (-S-S-). -*Disulfide bond*: An S-S bond formed between two cysteine side chains that can join two separate peptide chains, or cause a loop in a single peptide chain

Amino Acid Classifications

-*Nonpolar, Neutral Side Chains*: Alanine, Glycine, Isoleucine, Leucine, Methionine, Phenylalanine, Proline, Tryptophan, Valine -*Polar, Neutral Side Chains*: Asparagine, Cysteine, Glutamine, Serine, Threonine, Tyrosine -*Acidic Side Chains*: Aspartic acid, Glutamic acid -*Basic Side Chains*:Arginine, Lysine, Histidine • 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. • The sequence of amino acids in a protein and the chemical nature of their side chains enable proteins to perform their functions. • Noncovalent forces act between different molecules or between different parts of the same large molecule. • 19 of the common amino acids are chiral; only glycine is achiral. • a-amino acids can exist as D- or L-enantiomers. - Nature selectively uses only L-amino acids for making proteins.

Classification of Proteins by Function

-*enzymes*: catalyze biochemical reaction (ex. amylase = begins digestion of carbohydrates by hydrolysis -*hormones*: regulate body functions by carrying messages to receptors (ex. insulin = facilitates use of glucose of energy generation -*storage proteins*: make essential substances available when needed (myoglobin = stores oxygen in muscles) -*transport proteins*: carry substances through body fluids (ex. serum albumin = carries fatty acids in blood) -*structural proteins*: provide mechanical shape and support (ex. collagen = provides structure to tendons and cartilage) -*protective proteins*: defend the body against foreign matter (ex. immunoglobulin = aids in destruction of invading bacteria) -*contractile proteins*: do mechanical work (ex. myosin and actin = govern muscle movement)

Proteins and Their Functions

-Approximately 50% of your body's dry weight is protein. - They provide structure (keratin) and support (actin filaments) to tissues and organs throughout our bodies. - As hormones (oxytocin) and enzymes (catalase), they control aspects of metabolism. - In body fluids, water-soluble proteins pick up other molecules for storage (casein) or transport (transferrin, Fe3+). - Proteins of the immune system provide protection (Immunoglobulin G) against invaders, such as bacteria and viruses. *The overall shape of a protein molecule is essential to the role of that protein in our metabolism.*

Protein Structure: An Overview and Primary Protein Structure (1°)

-Primary structure is the sequence of amino acids in a protein chain. • Along the backbone of a protein is a chain of alternating peptide bonds and a-carbon atoms. • The amino acid side chains are substituents along the backbone, where they are bonded to the a-carbon atoms. • The carbon and nitrogen atoms along the backbone lie in a zigzag arrangement, with tetrahedral bonding around the a-carbon atoms. • The primary structure of a protein is the result of amino acids being lined in precisely the correct order. • Primary structure is so crucial to function that the change of only one amino acid can drastically alter a protein's biological properties.

Amino Acids

-Proteins are polymers of amino acids. •Every amino acid contains an amine group (-NH2 ), a carboxyl group (-COOH), and an R group called a side chain, bonded to a central carbon atom. • The central carbon is the alpha carbon, named so because it is the carbon atom directly adjacent to a carboxyl functional group. • Amino acids in proteins are alpha-amino (a-amino) acids because the amine group in each is connected to the alpha carbon. • Each a-amino acid has a different R group. This is what distinguishes them from one another. • R groups may be hydrocarbons, or may contain a functional group.

Secondary Protein Structure (2°)

-The spatial arrangement of the polypeptide backbones of proteins determines secondary protein structure (2°). • The secondary structure includes two kinds of repeating patterns known as the alpha-helix (a-helix) and the beta-sheet (b-sheet). • Hydrogen bonding between backbone atoms holds the polypeptide chain in place and connects the carbonyl oxygen atom of one peptide unit with the amide hydrogen atom of another peptide unit. • *Alpha-helix (a-helix)*: A secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone • The hydrogen bonds are between each carbonyl oxygen atom and an amide hydrogen atom four amino acid residues farther along the backbone. • *Beta-sheet (b-sheet)*: A secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheetlike structure

Tertiary Protein Structure (3°)

-The way in which an entire protein chain is coiled and folded into its specific three-dimensional shape. • Each protein molecule folds in a distinctive manner that is determined by its primary structure and results in its maximum stability. • A protein with the shape in which it functions in living systems is known as a native protein. • A protein composed only of amino acid residues is a simple protein. • Tertiary structure is drawn in a style that shows the combination of a-helix and b-sheet regions, the loops connecting them, and disulfide bonds.

Denaturation

-the loss of secondary, tertiary, and quaternary protein structure that leaves primary structure intact. • Solubility is often decreased by denaturation. Enzymes lose their catalytic activity and other proteins are not able to carry out biological functions when denatured. • Most denaturation is irreversible, but renaturation is accompanied by recovery of biological activity. • All the information needed to determine protein shape is present in the primary structure. • Misfolding of proteins leads to abnormal secondary and tertiary structures that compromise the function of the protein.

Protein Structure Summary

• *Primary structure* is the sequence of amino acids connected by peptide bonds in the polypeptide chain, for example, Asp-Arg-Val-Tyr. • *Secondary structure* is the arrangement in space of the polypeptide chain, which includes the regular patterns of the a-helices and the b-sheet motifs (held together by hydrogen bonds between backbone carbonyl and amino groups in amino acid residues) plus the loops and coils that connect these segments. • *Tertiary structure* is the folding of a protein molecule into a specific three-dimensional shape held together by noncovalent interactions primarily between amino acid side chains that can be quite far apart along the backbone and, in some cases, by disulfide bonds between side-chain thiol groups. • *Quaternary structure* is two or more protein chains assembled in a larger three-dimensional structure held together by noncovalent interactions

Amino Acids Continued

• All of the proteins in living organisms are built from 20 amino acids. • Each amino acid has a three-letter shorthand code. • For 19 of these amino acids, only the identity of the side chain attached to the carbon differs. • The remaining amino acid (proline) is a secondary amine whose nitrogen and carbon atoms are joined in a five-membered ring.

An Introduction to Biochemistry

• Biochemical reactions must continuously break down food molecules, generate and store energy, build up new biomolecules, and eliminate waste. • Despite the huge size and complexity of some biomolecules, their functional groups and chemical reactions are no different from those of simpler organic molecules.

Collagen

• Collagen is the major constituent of connective tissues. • The basic structural unit of collagen (tropocollagen) is three intertwined chains of about 1000 amino acids each. Each chain is loosely coiled in a left-handed (counterclockwise) direction. • Three of these coiled chains wrap around one another (in a clockwise direction) to form a stiff, triple helix in which the chains are held together by hydrogen bonds. • All collagens have a glycine every three residues, and prolines are hydroxylated in a reaction that requires vitamin C