CHEM 102 Lecture Notes on Proteins and Amino Acids

CHEM 102 Learning Objectives

• Categorize amino acids based on functional group and polarity.
• Explain the amphoteric property of amino acids due to its amino and carboxyl groups.
• Illustrate the formation of peptides as a reaction of different amino acids.
• Determine the sequence of amino acids and name of peptides.
• Explain the importance of small peptides.
• Describe the different levels of proteins structure and their interrelationship with one another.
• Relate protein structure to its physiological function.
• Differentiate hydrolysis and denaturation of proteins.

Overview

• The term protein is derived from the Greek word proteios, which means “of first importance.”
• It is the most important bioorganic molecule in the body as it plays a lot of important physiological functions.
• It accounts for about 15% of total cell’s mass and for almost half of its dry weight.

What Makes Proteins Proteins?

• Proteins are naturally occurring unbranched polymers of amino acids connected together by peptide bonds.

Functions of Proteins

• Structure – Proteins are the main structural material for animals, e.g. collagen and keratin.
• Catalysis – almost all the reactions that take place in living organisms are catalyzed by proteins called enzymes.
• Movement – muscles allows mobility of the human body, and muscles are made up of proteins, particularly myosin and actin.
• Transport - a lot of proteins are involved in the transport of molecules through the blood and across cell membrane, e.g. hemoglobin.
• Hormones – most hormones are proteins.
• Protection – proteins, in the form of antibodies, are formed in the body whenever foreign materials enter. Other proteins are also involved in blood clotting.
• Storage – some proteins store materials. For example, casein in milk and ovalbumin in eggs store nutrients for newborn mammals and birds. Ferritin, a protein in the liver, stores iron.
• Regulation – some proteins not only control the expression of genes, thereby regulating the kind of proteins synthesized in a particular cell, but also dictate when such manufacture takes place.

Classification of Proteins

• Fibrous proteins – insoluble in water and are used mainly for structural purposes.
• Globular proteins – more or less soluble in water and are used mainly for non-structural purposes.

Amino Acids

• An amino acid is an organic compound containing a carboxyl group (–COOH) and amino group (–NH2) at the same time.
• There are more than 300 naturally occurring amino acids, but only 20 of them are found in humans, known as the “Standard Amino Acids” (SAA)
• Most of the SAAs are in the form of ɑ-amino acid, except for proline which has a secondary amino group.

General Structural Feature of Amino Acids

• An alpha amino acid is an amino acid whose carboxyl group and amino group are attached to a common carbon, known as the alpha carbon.
• The nature of the side chain distinguishes amino acids from each other.

Enantiomers of SAAs

• The alpha carbons of the SAAs are stereogenic centers except for glycine.
• Because 19 of the SAA has stereogenic centers, they also exist as enantiomers –D or L.
• To represent the D and L enantiomers of the SAAs, we use the Fischer projection like in monosaccharides.

Classifications of SAAs

• The standard amino acids are commonly grouped according to the polarity of their side-chains.
  • Non-Polar Amino acids
  • Polar Neutral Amino acids
  • Polar Acidic Amino acids
  • Polar Basic Amino acids

Essential Amino Acids

• Essential amino acids are SAA that the body cannot adequately synthesize and must be obtained from dietary sources. There are 10 essential amino acids necessary for normal growth of a child.
• Arginine is only essential for infants for normal growth, it becomes nonessential amino acid as they grow into adulthood.
• Infants that are born prematurely cannot make sufficient quantities of some nonessential amino acids and thus becomes conditionally essential until the baby matures.
• In this situation the conditionally EAAs must be obtained through diet.
• The human milk and infant formula milk contain adequate amounts of these conditionally EAAs.

Complete Dietary Protein

• Is a protein that contains all the essential amino acids in adequate amounts as the body needs them. Proteins from animal sources are usually complete dietary protein.
• An incomplete dietary protein is a protein that does not contain in adequate amounts, relative to the body’s needs, of one or more of the essential amino acids. The essential amino acid that is missing or present in an inadequate amount in a incomplete dietary protein is known as a limiting amino acid. Gelatin is an incomplete dietary protein having tryptophan as its limiting amino acid.
• Proteins from plant sources are generally incomplete dietary proteins, with three common limiting AA: lysine, methionine, and tryptophan.
• Soy proteins is the only common plant protein that is considered complete dietary protein. However, mix of plant proteins generally provide complete dietary protein, such as in the case of rice and beans.
• Proteins from rice and beans when eaten together are known as complementary dietary protein.

Amphoteric Properties of SAAs

• The SAAs have both carboxyl group and amino group in one molecule. -COOH is an acidic group while -NH2 is a basic group.
• At pH near neutral, -COOH has the tendency to lose a proton (H+), producing a negatively charged conjugate base known as carboxylate.
• In the same manner, -NH2 have the tendency to accept a proton (H+), producing a positively charged conjugate acid known as quarternary ammonium ion.
• Because of this acid-base property of the carboxyl and amino groups, in aqueous solutions, the -COOH of the SAA is deprotonated while the -NH2 is protonated.
• When an aqueous solution of an amino acid is made more acidic, the zwitterion changes its structure because the carboxylate ion in this case is protonated because of the high concentration of \text{H+}.
• When an aqueous solution of an amino acid is made more basic, the zwitterion also changes its structure because the substituted ammonium ion is deprotonated because of the high concentration of \text{OH-}.
• In summary, the structure of an amino acid varies at varying pH.
• For acidic amino acids, there are actually for structures that can be observed when in solution: The carboxyl group of the a-carbon ionizes first before the carboxyl group of the side chain.
• For basic amino acids, there are also four structures that can be observed when in solution: In lysine and arginine, the quat. Ammonium group of the a-carbon ionizes first before the one found in the side chain.
• Histidine undergoes a different ionization from lysine and arginine. The imidazolium group of the side chain ionizes first before the quat. Ammonium of a-carbon.

Peptides

• A peptide is formed when the carboxyl group of the a-carbon of one amino acid condenses with the amino of the a-carbon of a second amino acid.
• Peptides are classified based on the number of amino acid residues present in a peptide.
• By convention, the N-Terminal amino acid residue is taken as the beginning of the polypeptide chain.

Nomenclature of Peptide

• The C-terminal amino acid residue keep its full name.
• All the other amino acid residues have names that end in –yl. The –yl suffix replaces the –ine or –ic ending of the amino acid name, except for tryptophane (tryptophyl), cysteine (cysteinyl), glutamine (glutaminyl), and asparagine (asparaginyl).
• The amino acid naming sequence begins at the N-Terminal acid residue.
• Isomeric Peptides: These are peptides containing similar amino acid residue but different in order.

Small Peptides of Physiological Importance

• Oxytocin and Vasopressin
  • Oxytocin regulates uterine contraction and lactation. Also called the love hormone since it associated with trust, sexual arousal and relationship building
  • Vasopressin, also called as antidiuteric hormone, regulates the excretion of water in kidneys and affects blood pressure.
• Glutathione
  • This is present in significant concentrations in most cells which serves as an antioxidant, protecting cellular component against oxidizing agents, such as peroxides and superoxides.

Proteins

• The term protein is reserved for polypeptides with a large number of amino acid residues. Usually more than 40 residues. It may contain one or more polypeptide chain.
  • Monomeric proteins
  • Multimeric proteins
• Proteins may also contain non-amino acid groups known as prosthetic groups.
  • Simple proteins
  • Conjugated proteins
• Peptide Bonds: The peptide bond has a partial double bond character, meaning the C-N bond has no free rotation
• Solubility: Proteins are least soluble in water at their isoelectric points and can be precipitated from their solutions. For example, casein (protein found in milk) is extracted by adjusting the pH milk to around pH 4, casein’s isoelectric point. Excess of insufficient acid would affect the pH, therefore it will not precipitate out casein.
• Cross-links in Structure: The linear polypeptide chain in some proteins are cross-linked, usually by disulfide bond bridges.
• Native Confirmation: Native conformation of a protein refers to its three–dimensional (3D) structure with biological function.

Levels of Protein Structure

• Primary Structure of Proteins
  • The primary structure denotes the number, kind and sequence of amino acids in a protein.
  • The amino acid sequence of a protein, its primary structure, determines its three-dimensional structure, which, in turn, determine its functions.
  • The sequence of amino acids in a protein’s primary structure is decided by the genes.
  • Human hemoglobin contains 4 polypeptide chains, 2 a-chains and 2 B-chains with a total of 574 amino acid residues.
  • An amino acid substitution (Glu \rightarrow Val) at the 6th amino acid reside of only one of the B-chains causes sickle cell anemia.
• Secondary Structure of Proteins
  • The secondary structure denotes regular localized arrangement of polypeptide backbone arrangement.
  • This is stabilized by hydrogen bonds between the C=O and N-H groups within and between peptide bonds.
  • A-helix
    • The a-helix is a spiral, repeating structure of a polypeptide chain.
    • The shape of the helix is maintained by hydrogen bonds between the C=O of an amino acid and the N-H of another amino acid located four residues further along the polypeptide chain.
    • Factors that disrupt the a-helix:
      • The presence of the amino acid proline (helix breaker)
      • The presence of adjacent similarly charged group causing electrostatic repulsion.
      • Presence of adjacent bulky groups causing steric repulsion.
  • B-Pleated Sheets
    • In the B-pleated sheet, the peptide backbone of two protein chains in the same or different molecules is held together by hydrogen bonds.
  • Turns and Loops
    • Reversals in the direction of polypeptide chains are accomplished by a common structural element called the reverse turn (aka the β turn or hairpin turn), and Ω loops.
• Tertiary Structure
  • The tertiary structure is the overall three-dimensional structure of proteins, also known as folding.
  • The folding results from the interaction of the side chains of the different amino acid residues and the prosthetic groups.
• Quaternary Structure
  • The quaternary structure is the non-covalent association of protein subunits into a supramolecule in a multimeric protein.
  • Not all protein have quaternary structure.
  • Proteins have different quaternary structure based on the number of subunits present.
• Allosteric Proteins
  • Allosteric proteins are proteins that have quaternary structures, and when subtle changes in structure at one site on a protein molecule may cause drastic changes in properties at a distant site.
• Protein Hydrolysis
  • Hydrolysis of proteins causes disruption of the peptide bonds causing liberation of free amino acids.
  • This can be carried out in the presence of strong acids, strong bases, and enzymes (proteases).
  • Hydrolysis can be complete or partial.

Protein Denaturation

• Denaturation causes disruption (unfolding) of a protein’s three – dimensional structure due to the breakdown of the non-covalent interaction.
• Since the three-dimensional structure of proteins is very much related to their functions, denaturation, therefore, causes loss of biological activity.
• Denaturation can be reversible or irreversible.

Factors that Causes Denaturation

• Heat: Affected Regions - H bonds
• 6 M urea: Affected Regions - H bonds
• Detergents: Affected Regions - Hydrophobic regions
• Acids, bases: Affected Regions - Salt bridges, H bonds
• Salts: Affected Regions - Salt bridges
• Reducing agents: Affected Regions - Disulfide bonds
• Heavy metals: Affected Regions - Disulfide bonds
• Alcohol: Affected Regions - Hydration layers