Amino Acids and Proteins Chemistry

Chemistry of Amino Acids & Proteins

• All cells contain thousands of proteins; amino acids are the building blocks.
• Alpha amino acids are biologically important.

General Structure of Amino Acids

• Consist of a basic amino group (NH3).
• Consist of an acidic carboxylic group (COOH).
• Features an organic R group (side chain).
• Includes a central carbon atom (alpha carbon).
• Amino acids differ in their side chains, which vary in structure, size, and electric charge.
• General structure: Amino group - Alpha carbon - Carboxylic group w/ R-side Chain

The Genetic Code Specifies 20 Alpha Amino Acids

• Out of more than 100 amino acids, only 20 alpha amino acids can undergo protein synthesis.
• The following are the 20 alpha amino acids used in protein synthesis:
  • Glycine (Gly)
  • Alanine (Ala)
  • Valine (Val)
  • Leucine (Leu)
  • Isoleucine (Ile)
  • Glutamate (Gl)
  • Glutamine (Gln)
  • Aspartate (Asp)
  • Asparagine (Asn)
  • Methionine (Met)
  • Cysteine (Cys)
  • Serine (Ser)
  • Threonine (Thr)
  • Tyrosine (Tyr)
  • Phenylalanine (Phe)
  • Tryptophan (Trp)
  • Lysine (Lys)
  • Histidine (His)
  • Proline (Pro)
  • Arginine (Arg)

Classification of Amino Acids Based on Polarity

• Amino acids are classified into four groups based on polarity:
  • Non-polar and neutral amino acids
  • Polar and neutral amino acids
  • Acidic (polar and charged) amino acids
  • Basic (polar and charged) amino acids
• Acidic amino acids:
  • Have a carboxylic (COOH) group in their side chain.
  • Examples: Aspartic acid and glutamic acid.
• Aliphatic amino acids:
  • Contain only carbon and hydrogen.
  • Examples: Alanine, Valine, Leucine, Isoleucine, Proline and Cysteine
• Aromatic amino acids:
  • Any amino acid with a benzene ring like Tyrosine, Phenylalanine, Tryptophan.
• Non-polar and Neutral Amino Acids:
  • Contain an amino group, carboxylic group, and a non-polar (hydrophobic) side chain.
  • Include alkyl side chains (alanine, valine, leucine, isoleucine).
  • Include cyclic structures and aromatic side chains (phenylalanine, tryptophan).
  • Include sulfur-containing side chains (methionine).
• Polar Neutral Amino Acids:
  • Contain a side chain that is polar but neutral at physiological pH.
  • Are more soluble than other amino acids with the exception of glycine
  • Examples: Glycine, Tyrosine, Threonine, Serine, Cysteine.
• Polar Acidic Amino Acids:
  • Contain one amino group and two carboxylic groups.
  • The second carboxylic group is part of the side chain.
  • Examples: Glutamate, Aspartate
  • The side chains are weaker acids than the primary carboxylic group but are able to exist as COO- at neutral pH.
• Polar Basic Amino Acids:
  • Contain one carboxylic group and two amino groups.
  • The second amino group is attached to the side chain.
  • Examples: Lysine, Arginine, Histidine

Classification of Amino Acids Based on Nutritional Requirement

• Essential amino acids:
  • Cannot be synthesized by the body and must be obtained from the diet.
  • Examples: Histidine, lysine, methionine
• Non-essential amino acids:
  • Can be produced by the body and do not need to be obtained from diet
  • Examples: All Alanine, All Glycine, Cysteine, serine, proline
• Conditionally essential amino acids:
  • Become essential under certain conditions.

Amino Acids with Acetic Side Chains

• Aspartic Acid
• Glutamic Acid

Amino Acids with Amide Side Chains

• Asparagine
• Glutamine

Amino Acids with Hydroxyl-Containing Side Chains

• Serine
• Threonine
• Tyrosine

Amino Acids with Sulfur-Containing Side Chains

• Cysteine
• Methionine

Aliphatic Amino Acids

• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine
• Proline

Aromatic Amino Acids

• Phenylalanine
• Tyrosine

Properties of Amino Acids

• Chirality (Stereo-isomerism):
  • The ability of a compound to exist in optically active, asymmetric forms (enantiomers) that are mirror images of each other.
  • All amino acids except glycine are chiral compounds.
  • Chiral compounds can rotate plane-polarized light in either a clockwise (dextrorotatory) or counterclockwise (levorotatory) direction.
• Only L-amino acids are constituents of proteins and are in the L configuration.
• Using the CORN rule:
  • Identify the configuration of the amino acid.
  • Anticlockwise = L-Alanine
  • Clockwise = D-Valine
• Acid-Base Properties:
  • Amino acids are ampholytes, having both acidic and basic properties.
  • In solution at neutral pH, amino acids exist predominantly as dipolar ions (zwitterions).
  • Zwitterions: amino acids containing an equal number of positive and negative charges due to their carboxylic and amino groups.
• At low pH, the amino group accepts protons and becomes protonated.
• At high pH, the amino group is deprotonated.
• Electrophoresis:
  • A method to separate amino acids in an electric field according to their charges.
  • Cations move to the negative electrode.
  • Anions move to the positive electrode.
  • Neutral amino acids do not migrate.
• Peptide Bond Formation:
  • Amino acids can join through a peptide bond.
  • Formed in a head-to-tail fashion excluding a water molecule.
  • This allows them to polymerize into peptides and proteins.
  • Head: Carboxylic
  • Tail: Amino Group
• Disulfide Bond Formation:
  • Cysteine is the only amino acid that forms disulfide bonds.
  • Formed because it has a sulfhydryl group.

Proteins: Formation and Structure

• Proteins are the most abundant biomolecules in cells.
• They are formed from amino acid monomers linked by peptide bonds
• Primary Structure:
  • Simplest form of proteins with a linear sequence of covalently linked amino acids backbone
  • Example sequence of insulin amino acids
• Secondary Structure:
  • Folded structure of polypeptide amino acids linked with adjacent amino acids through helical or pleated sheet-like spring coil
• Tertiary Structure:
  • When the polypeptide chain of a protein molecule binds folding into a three-dimensional shape

Protein Functions

• Act as catalysts (enzymes). Examples: Transferase, dehydrogenase, reductase, lipase
• Regulatory function: Examples: Insulin, somatotropin
• Transport roles: Examples: Hemoglobin, albumin, membrane proteins
• Storage: Examples: Ovalbumin, casein
• Structural roles: Examples: Keratin, collagen
• Protecting role: Examples: Immunoglobulin, blood clotting proteins, antibodies
• Insulin: Regulates sugar level in the blood.
• Myoglobin: Carries oxygen around the red-blood cells.
• Ovalbumin: Located in egg whites and helps developing provide nutrient
• Casein: Found in milk, source of nitrogen for infants
• Keratin: Forms hair and gives hair a shape.
• Immunoglobulin and anti-bodies help in protecting body and neutralize foreign activity in entering the body
• Swat clotting factor protects wasting blood

Chemistry of Carbohydrates

• Carbohydrates are one of the four major classifications of biomolecules.
• Made up of carbon, hydrogen, and oxygen.
• Classified as polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis.
• Conform to the general formula CnH2nOn (though there are exceptions).

Classification of Carbohydrates

• Monosaccharides: one sugar unit.
• Disaccharides: two sugar units.
• Oligosaccharides: ten linked sugar units (3-10 saccharides).
• Polysaccharides: many sugars (more than ten saccharide units).
• Monosaccharides are found in most disaccharides
• Monosaccharides:
  • Possess one sugar unit & Maximum sugar found in monosaccharides.
  • Classification: Based on functional group (aldoses or ketones) and carbon atom number.
  • Trioses (3 carbons), tetroses (4 carbons), pentoses (5 carbons), hexoses (6 carbons), heptoses (7 carbons).
• Disaccharides:
  • Two sugar units linked by a glycosidic bond.
  • Examples: Maltose (glucose + glucose), lactose (glucose + galactose), sucrose (glucose + fructose), trehalose (glucose + glucose)
  • Classification: Based on composition or reduction ability during chemical processes.

Types of Carbon in Monosaccharides

• Functional or carbonyl carbon.
• Asymmetric (or chiral) carbon.
• Symmetric carbon.
• Reference (or penultimate) carbon.

Isomerism in Carbohydrates

• Isomerism: defined as the name of compund that molecular and or structural formula
• Divided into different structure

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