Amino Acids and Proteins: Biochemistry

• Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group).
• The amine group (-NH2) is basic, while the carboxyl group (-COOH) is acidic.
• Reactions with amino acids are highly pH-dependent.
• Approximately 300 amino acids occur in nature, but only 20 are incorporated into proteins.

The 20 Amino Acids and Their Abbreviations

• Alanine (Ala)
• Arginine (Arg)
• Aspartic Acid (Asp)
• Asparagine (Asn)
• Cysteine (Cys)
• Glutamine (Gln)
• Glutamic Acid (Glu)
• Glycine (Gly)
• Histidine (His)
• Isoleucine (Ile)
• Leucine (Leu)
• Lysine (Lys)
• Methionine (Met)
• Phenylalanine (Phe)
• Proline (Pro)
• Serine (Ser)
• Threonine (Thr)
• Tryptophan (Trp)
• Tyrosine (Tyr)
• Valine (Val)

Classifications of Amino Acids Based on R Group Nature

• Hydrophobic amino acids are non-polar and include:
  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Proline
  • Phenylalanine
  • Tryptophan
• Hydrophilic amino acids are polar and include:
  • Tyrosine
  • Serine
  • Threonine
  • Cysteine
  • Glutamine
  • Asparagine
  • Glutamic acid
  • Aspartic acid
  • Lysine
  • Histidine
  • Arginine

Nutritional Classification of Amino Acids

• Essential amino acids cannot be synthesized in the body and must be obtained from food. Their deficiency impacts growth, health, and protein synthesis. Leucine
  • Isoleucine
  • Lysine
  • Threonine
  • Methionine
  • Phenylalanine
  • Valine
  • Tryptophan
  • Histidine
• Semi-essential amino acids cannot be synthesized in sufficient quantities during growth periods such as pregnancy, adolescence, or recovery from trauma like:
  • Arginine
  • Histidine
• Non-essential amino acids are synthesized in the body, either produced directly or obtained from protein breakdowns like:
  • Alanine
  • Asparagine
  • Aspartic acid
  • Cysteine
  • Glutamic acid
  • Glutamine
  • Glycine
  • Proline
  • Serine
  • Tyrosine

Metabolic Classification of Amino Acids

• Glycogenic amino acids form a precursor to the formation of either glucose or glycogen, for example:
  • Alanine
  • Aspartate
  • Glycine
  • Methionine
  • Serine
• Ketogenic amino acids synthesize fat, like:
  • Leucine
  • Lysine
• Glycogenic and Ketogenic amino acids act as precursors for glucose and fat synthesis, like:
  • Phenylalanine
  • Isoleucine
  • Tryptophan
  • Tyrosine

Physical Properties of Amino Acids

• Amino acids are generally colorless and crystalline in form.
• Taste: Amino acids can be sweet (Glycine, Alanine, Valine), tasteless (Leucine), or bitter (Arginine, Isoleucine).
• Monosodium glutamate, a salt of glutamic acid, is a flavoring agent in the food industry.
• Solubility depends on:
  • Polarity
  • Iso-electric point
  • Solvent pH
  • Temperature
• Amino acids are soluble in:
  • Water and ethanol
  • Solvents (i.e., polar solvents)
• Amino acids are insoluble in:
  • Benzene, ether etc
  • Non-polar solvents
• They are also insoluble at the iso-electric point. Tyrosine's solubility is impacted by pH and temperature.
• Tyrosine, for instance, is soluble in hot water.
• Melting point is high, between 200-300°C, due to their ionic property.

Amino Acids as Ampholytes

• Amino acids act as ampholytes because they contain both acidic (-COOH) and basic (-NH2) groups.
• They can donate or accept a proton.
• At acidic pH, an amino acid is positively charged (cation).
• At alkaline pH, an amino acid is negatively charged (anion).
• Each amino acid has a specific pH where it carries both positive and negative charges, existing as a Zwitterion

Absorption Spectrum and Optical Properties

• Amino acids absorb light at 280nm, which can be used to measure their concentration.
• All amino acids, except glycine, possess optical isomers due to an asymmetric carbon atom, existing in D and L forms.

Chemical Properties of Amino Acids: Reactions Involving the Carboxyl (-COOH) Group

• Salt formation occurs with bases, creating (-COONa).
• Ester formation occurs with alcohols, creating (-COOR).
• Decarboxylation produces corresponding amines; for instance, histamine, tyramine, and γ-amino butyric acid (GABA) come from histidine, tyrosine, and glutamate, respectively.
• Reaction with ammonia: The carboxyl group of dicarboxylic amino acids react with NH3 to form amide, for instance:
• Aspartic acid + NH3 -> Asparagine Glutamic acid + NH3 -> Glutamine

Chemical Properties of Amino Acids: Reactions Involving the Amino (-NH2) Group

• Amino groups act as bases, combining with acids to form salts.
• Reaction with ninhydrin: α-amino acids react with ninhydrin to form a purple, blue, or pink complex (Ruhemann's purple)
• Transamination involves transferring an amino group from one amino acid to a keto acid, forming a new amino acid.
• Oxidative deamination involves amino acids undergoing oxidative deamination to liberate free ammonia.
• The conversion of glutamate to α-keto glutarate, catalyzed by glutamate dehydrogenase, is an example of oxidative deamination.

Peptide Bond Formation

• Amino acids link to create polypeptide chains.
• A peptide bond forms when the α-carboxyl group of one amino acid (R1) links with the α-amino group of another (R2), releasing a molecule of water.
• A dipeptide, resulting from this process, consists of two amino acids joined by one peptide bond.

Examples of Peptides

• Dipeptides consist of two amino acids joined by one peptide bond. For example, Aspartame (aspartic acid and phenylalanine) acts as a sweetener.
• Tripeptides have three amino acids linked by two peptide bonds. An example is GSH (glutamic acid, cysteine, and glycine), which aids in amino acid absorption, protects against hemolysis in red blood cells by breaking down H2O2.
• Polypeptides contain 10-50 amino acids.
• Insulin is an example.
• Polypeptides with 50 or more amino acids get classified as a protein.

Naming Peptides

• Replace the "ine" or "ate" ending with "yl," leaving the last (C-terminal) amino acid unchanged.
• Alanine-proline = alanylproline
• Serine-histidine-glycine = serinylhistidylglycine
• Lysine-methionine-tyrosine-alanine = lysylmethionyltyrosylalanine

Functions of Amino Acids

• Some are converted to carbohydrates and are called glucogenic amino acids such as glycine and valine
• Tryptophan is a precursor for neurotransmitters such as serotonin, hormone melatonin, and vitamin B3 (niacin).
• Fructose malabsorption causes improper absorption of tryptophan in the intestine, reducing its levels in the blood.
• Phenylalanine serves as precursor for tyrosine, dopamine, norepinephrine, epinephrine, and melanin.
• A genetic disorder called phenylketonuria is characterized by the body's inability to metabolize phenylalanine due to a deficiency in phenylalanine hydroxylase
• Alanine, is synthesized from pyruvate including branched chain amino acids, playing a crucial role in the glucose-alanine cycle between liver and tissues, and it enables pyruvate and glutamate removal from muscle and liver.
• Alterations in the alanine cycle elevate levels of ALT (alanine transferases) which often link to type II diabetes development.
• Valine is critical for hematopoietic stem cell (HSC) self-renewal.
• A single glutamic acid in β-globin is replaced with valine, a sickle-cell disease. Since valine is hydrophobic, it causes hemoglobin to clump abnormally, whereas glutamic acid is hydrophilic.
• Leucine's metabolic end products include acetoacetate and acetyl-CoA, and it is a vital ketogenic amino acid. It is used in muscle and adipose tissue for sterol production.
• A deficiency in branched-chain α-keto acid dehydrogenase complex causes (maple syrup urine disease) MSUD and leads to toxicity in branched-chain amino acids and their ketoacid products.
• Isoleucine: Supporting wound healing, detoxifying wastes of nitrogen, enhancing immune responses, and inducing hormone secretion are some of its many physiological roles
• Methionine: Homocysteine regeneration or conversion to cysteine depends on methionine levels which acts as cysteine and taurine's substrate, and antioxidant glutathione. Atherosclerosis can result from improper conversion and homocysteine accumulation
• Threonine: Threonine residues undergo phosphorylation (process involving phosphothreonine) via threonine kinase, which can be referred to as cell signal transduction and neural activity role player
• Histidine serves as a precursor to histamine, which is necessary for inflammation. Histidine ammonia-lyase converts histidine to ammonia and urocanic acid.
• Deficiency in this enzyme causes histidinemia, an uncommon metabolic disorder.
• Lysine: Lysine contributes to protein stability through hydrogen bonding and salt bridges and plays a role in:
  • Schiff base formation
  • Epigenetic regulation
  • Modification of histones
• It plays a key role in structural proteins for connective tissues as well; calcium and fatty-acid metabolism, also lack of lysine catabolism results in accumulation of amino acids and leads to hyperlysinaemia (patients experience this)

Proteins

• Proteins are natural biopolymers of amino acids, and are one of the 3 key nutrients in the function and cell structure, as they provide protection, and transport. Also, hormones and enzymes play a part, and native functional protein folding is based on the primary amino acid sequence.

Structure of Proteins

• Primary
• Secondary
• Tertiary
• Quaternary
• Protein structure determines function.
• Denaturation is disruption of higher-order structures.
• This does not affect its primary structure.

Primary Protein Structures

• This refers to the linear chain of amino acids through biosynthesis. A specific number of amino acids make up a certain function. The primary structure is held together by petide bonds. Many diseases come from changed sequences of amino acids

Secondary Protein Structures

• This is formed from hydrogen bonds in the peptide chain. Common structures:
• Alpha-helix
• Beta-pleated sheets
• Random coils.
• Structures called alpha-helices are springs that act as linkages between the hydrogen in the N-H bond to the atom inside the C=O bond. Alpha-helices are tightly coiled protein structures stabilized by hydrogen bonding.
• Beta-pleated sheets: chains linked together by hydrogen bonding between NH and carbonyl oxygen.
• They create zig-zag pleat structures through interaction.
• Polypeptide strands in beta-sheets are configured in parallel/anti-parallel orientation in which sheets have segments with max bonds from hydrogen.

Alpha-Helix

• This is the most recognizable protein with tightly bound coiled protein structure, the side chains act as outwards (center axis) . H atom joins P-N/ peptide C with oxygen atom and that forms stabilization for A/H (weak bond + strong structure). All P-bonds take part in hydrogen bonding while polypeptide chain acts as exception because helix rotation measures 36/ amino acids plus 0.54 nm length. AA spacing measures 0.15 nm (AAs such as proline might break helix) as numerous Aas intervene/ mess with structure.

Tertiary Protein Structure

• The three-dimensional structure results from attractions/repulsions between Aas and polypeptide chains to give shapes which occur via disulfide bonds, interaction with molecules plus salt bridges + hydrophobic interactions. Hydrophilic-side exterior interaction to protein is where its inside chains have been set (molecules become stabile)

Bonds in Tertiary Structures

• The hydrogen bonds
• Disulfide bonds (-S-S-)
• Hydrophobic interactions occur
• Ionic/electrostatic interactions occur

Quaternary Protein structure

• Includes at least a couple of (tertiary-protein subs) which interact, held via similar tertiary-structures-forces used by bioactive prots (present, quaternary form), plus the subunits-interaction produces complex-structure. Example is hemoglobin which contain 4.

Bonds Responsible for Protein Structure

• Covalent bonds like peptide and Disulphide are strong protein structure links
• H-bonds are weaker + H-sharing happens from H-atoms within oxygen/carbonyls of various P-bonds (structure benefits) due to size.
• Molecules merge by Hydrophobic bonds (non-polarized side neutral Aas + Aqueous molecule forces in aqueous zone) occurs when the structures stick
• Electrostatic bonds link electrically charged molecules from AA acids via interaction.
• With dipole presence, neutral molecules bond via non-charged Vander-Waals strengths

Structural/Composition-Based Protein Classification

• Fibrous proteins are elongated/fiber-like with simple and static structures and small biological output that exist as conjugated/simple proteins found in fauna

• Simple-fibrous prots: keratine (elastin/collagen) found among scleroprotein (albuminoids) produce animal structure/insoluble liquids

• Conjugated proteins are insoluble and provide feather/pigment in fauna

• Globular prots have high-complexity (spherical + mobile with wide usage) in biological capacity and include hormones/enzymes, and get defined through composition/solubility. Consist of:

• Simple-globular prots include +charged animals/ protamine-fish (sperm cell) prots which occur in the sperm, link DNA while creating the protein histone via water soluble + ammonium

• Histone: In comparison to what it does relative to protamine, weak base/soluble which do not result in coagulation but produce low mass.

• Abundant plant glob: Albumin (nature type + animal tissues), that consist of water and can be produced out of seeds.

• Other globular structures

  • pseudo globulin/(H2O); euglobulin (insoluble)
  • gluttelin (wheat), and orzenin
  • prolamine: Seed with acidic/detergent (water insoluble) or alcohol 7 or higher

• Examples such as gliadin (wheat), zein (corn), Hordein (barley), Avenin (oats) are rich with glutamine.

• Complex globulars are heteros (moiety linked), non/protein comps (component) such as what’s called a prosthetic and consists of -metallic clusters that (have) -metal groups bonded with proteins (proteins).

• Examples such as mercury, that are coupled with SH AA-side chains.

Classification based on Prosthetic Group

• Metallic clusters are the metals bonded, (ex cuprum within the group + calsequestrin) (nucleic acid).
• Chromoprotein is a colored moiety like hemoglobin (includes cytochromes, clorophyl, hemocyanin, myoglobin, peroxydase and B2) is yellow+orange (FAD linked cells)
• Mucoprotein is groups of sugar that protect cells with hyaluronic acid.
• Groups bonded with phosphorus (phosphoprotein) occur as Caesein cell types by lipo+prot cells (Lipo = lipid carrier) inside Caesein
• (Derivs: cell alteration via chemicals) are made + artificially group with AA derivatives + Primary altered size + (Myosins, proteans, action) .
• Metaprotein: Proteins produce from 0- 60 degrees while known as prot which make up Infra with + Alkali. (Also by heat), prot not soluble.

Derived Proteins -Secondary

• Secondary are hydrolyzed to smaller mass. digestive prote and are albuminous.

Classifying by function

• The catalytic type speed up + support with cell enzymes. structural makes are key to beings elastin generates ligaments keratin provides with hair and nails (Nutritious +milk like) provide benefit to people . Regular cellular type. cell + like type. Antibody kills harmful cells.

Protein Types that

• Transport + Transfer Molecules. Haemoglobin occurs
• Conserve within tissues
• mobile assists motions of skeleton areas.
• Actin
• Myosin
• Toxic are harmful (snake venom)

Denaturation

• Occurs through changes in structure/non-covalent bonds.
• The processes impact biological molecules like P bonds Denature traits = structure loss.

D-Agents

• Temperature is where radiation or UV light is used, which chemicals/alcohol metal salts do. During denaturation + helices/cell P damage will happen

• loss in solubility exposure to enzymes by H chains and denatured cell results.

• Irreversible reactions are denaturation and with renaturation; haemoglobin or salicylic molecules will get restored via semiprecips with viscous properties

• Precipation by Irreciprocation is similar to coagulation

Explore amino acid conversions, peptide bond formation, and the roles of peptides like aspartame and glutathione. Learn about tetrapeptide nomenclature, tryptophan's role as a precursor, and glutamate dehydrogenase in amino acid metabolism. Discover derived proteins produced by hydrolysis.