Molecular Biology PDF

Molecular Biology Sherin DR, SoDS, DUK Module 2 Amino acids: Amino acids as the building blocks of proteins Structure of standard amino acids Classification of amino acids Essential amino acids Zwitterions Physical and chemical prope...

Molecular Biology Sherin DR, SoDS, DUK Module 2 Amino acids: Amino acids as the building blocks of proteins Structure of standard amino acids Classification of amino acids Essential amino acids Zwitterions Physical and chemical properties Proteins: Classification of proteins on the basis of composition and solubility, nutritive value, conformation, and function Structural organization of proteins – primary, secondary, tertiary, and quaternary structures Forces stabilizing protein structure and shape Structure of peptide bond Denaturation of proteins Ramachandran Plot  Proteins Most abundant organic molecules of the living system Forms the fundamental basis structure and function of life The term derived from the Greek word proteios (holding the first place) Proteomics –the study of a galaxy of proteins Functions-Structural (static) and Dynamic Structural –brick and mortar role responsible for structure and strength of the body. eg.: collagen, elastin, keratin… Dynamic- enzymes, hormones, immunoglobulins, blood clotting factors  Collagen is the most abundant protein in the human body, found in muscles skin ▪ The body makes collagen on its own in a tendons complex series of processes that involve blood vessels amino acids, copper, zinc, and vitamin C cartilage bone ▪ With age, the body’s collagen production connective tissue becomes low and collagen diets may help reverse some of the signs of aging ✓ The most abundant amino acids in collagen are glycine, lysine, and proline. ✓ Plant-based foods high in all three amino acids include: soy products, black beans, kidney beans, many other legumes… ✓ seeds: especially pumpkin, sunflower, chia… ✓ nuts: pistachio, peanut, cashew… ✓ found in animal parts, like chicken, meat, fish, and dairy products  Elastin It is one of the most abundant proteins in your body It’s a stretchy protein that resembles a rubber band — it can stretch out (extend) and shrink back (recoil) It’s a major component of tissues in your body that require stretchiness- like your lungs, bladder, large blood vessels, and some ligaments Smaller amounts exist in your skin and ear cartilage ▪ The main amino acids that makeup elastin are proline, glycine, desmosine, and isodesmosine ▪ Many foods can help increase elastin, including leafy greens, citrus fruits, berries, fatty fish and nuts  Keratin It is a protein that helps form hair, nails, and your skin’s outer layer (epidermis) It helps support your skin, heal wounds, and keep your nails and hair healthy ▪ Sources: Vegetables like broccoli, onions, garlic, liver, fish, yogurt, and low-fat milk ▪ There are two forms of keratin Alpha-keratin is in the hair, epidermis, horns, and nails of mammals Type I and type II keratins are alpha-keratins Beta-keratin is in the feathers, claws, beaks, and scales of birds and reptiles There are 54 kinds of keratin in your body 28 of them are type I - of those, 17 are skin cell (epithelial) keratins, and 11 are hair keratins 26 are type II- of those, 20 are skin cell keratins, and six are hair keratins  Hormones are chemical messengers that coordinate different functions in your body Several glands, organs, and tissues make and release hormones, many of which make up your endocrine system Hormones control many different bodily processes, including: ✓ Metabolism ✓ Homeostasis (constant internal balance), such as blood pressure and blood sugar regulation, fluid (water) and electrolyte balance and body temperature ✓ Growth and development ✓ Sexual function ✓ Reproduction ✓ Sleep-wake cycle ✓ Mood about 20 amino acids are necessary to synthesize all the proteins in the human body and most other forms of life.  Nutritionally, amino acids are divided into 3 groups Essential (indispensable) Nonessential (dispensable) semi-essential (partially essential) ▪ Nine amino acids, including histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine, are classified as essential amino acids because they cannot be synthesized by human or other mammalian cells ▪ Therefore, these amino acids must be supplied from an exogenous diet ▪ Non-essential amino acids not primarily derived from the diet are synthesized by the body ▪ Alanine, Asparagine, Aspartic acid, Glutamic acid, Serine  Conditionally-Essential Amino Acids ▪ Six amino acids are termed conditionally essential because healthy bodies can generate them under normal physiologic conditions. They become essential under certain conditions, like starvation or inborn errors of metabolism. ▪ Semi-essential amino acids are growth-promoting amino acids. They are essential in growing children, pregnant women, and lactating women Arginine Cysteine Glutamine Glycine Proline Tyrosine Classification -based on polarity Besides 20 amino acids that participate in protein synthesis, recently, 2 more new amino acids have been described— selenocysteine and pyrrolysine. Physical Properties Amino acids are colorless, crystalline solid. They may be sweet, tasteless or bitter All amino acids have a high melting point greater than 200 °C. Solubility: soluble in water, slightly soluble in alcohol. R-group of amino acids and pH of the solvent play important role in solubility. On heating to high temperatures, they decompose. All amino acids (except glycine) are optically active. ▪ Zwitterionic property The -NH2 group is the stronger base, and so it picks up H+ from the -COOH group to leave a zwitterion. The (neutral) zwitterion is the usual form of amino acids that exist in the solution. The pH at which a molecule exists as a zwitterion or dipolar ion is called isoelectric point. ▪ Amphoteric property (ampholyte) Amino acids are amphoteric in nature that is they act as both acids and bases. ▪ Ninhydrin test The formation of a violet color on reaction with Ninhydrin indicates the presence of α-amino acids. ▪ Xanthoproteic test When the sample is treated with a hot, concentrated nitric acid it reacts with aromatic amino acids such as phenylalanine, tyrosine and tryptophan and forms a yellow colored product known as Xantho protein. ▪ Reaction with Sanger’s reagent Sanger’s reagent (1-fluoro-2, 4-dinitrobenzene) reacts with a free amino group in the peptide chain in a mild alkaline medium under cold conditions. ▪ Reaction with nitrous acid Nitrous acid reacts with the amino group to liberate nitrogen and form the corresponding hydroxyl. Chemical Properties ❑ Reaction due to -COOH group Amino acids commonly form esters (-COOR’) with alcohols, and salts (-COONa) with bases. Amino acids produces amines through the process of decarboxylation. Biologically important amines – histamine, tyramine, γ-amino butyric acid (GABA) from histidine, tyrosine, glutamate. The carboxyl group of dicarboxylic amino acids reacts with amnio acids reacts with ammonia to form amide. Aspartic acid + NH3 ——-> asparagine Glutamic acid + NH3 ——-> glutamine ❑ Reaction due to -NH2 group Amino group behaves as bases and it reacts with acids and produces salts. Reaction with Ninhydrin: The alpha amino acids react with ninhydrin and produces blue, pink or purple color complex (Ruhemann’s purple). Amino acid + Ninhydrin ——> keto acid + NH3 + CO2 + Hydrindantin. Hydrindantin + NH3+ Ninhydrin ——> Ruhemann’s purple. (Proline and hydroxyproline give yellow colour) Color reactions with amino acids: They are generally identified by specific color reactions. Transamination: Transfer of an amino group from an amino acid to a keto acid to form a new amino acid, one of the most important reaction in amino acids metabolism. Oxidative deamination: liberates free ammonia Functions of Amino acids ✓ Standard amino acids are crucial for life and are known to be the building blocks for all living things. ✓ The linear sequence of amino acid residues in a polypeptide chain determines the three-dimensional configuration of a protein and the structure of a protein that determines its function. ✓ Amino acids are imperative for sustaining the health of the human body. They largely promote the:- Production of hormones Structure of muscles The human nervous system’s healthy functioning The health of vital organs Normal cellular structure  The amino acids are used by various tissues to synthesize proteins and to produce nitrogen-containing compounds (e.g., purines, heme, creatine, epinephrine), or they are oxidized to produce energy. The breakdown of both dietary and tissue proteins yields nitrogen- containing substrates and carbon skeletons. The nitrogen-containing substrates are used in the biosynthesis of purines, pyrimidines, neurotransmitters, hormones, porphyrins, and nonessential amino acids. The carbon skeletons are used as a fuel source in the citric acid cycle, for gluconeogenesis, or in fatty acid synthesis. Aminoacids as Drugs N-Acetylcysteine α and β chains-141 and 146 amino acids  Temperature elevation extremes in pH changes in chemical or physical environment ✓ Denaturation involves the breaking of many of the weak linkages, or bonds ✓ Denatured proteins have a looser, more random structure; most are insoluble ✓ Ramachandran Plot is a graph introduced by Dr. G.N. Ramachandran. ✓ It is a space-filling model of peptides used to visualize energetically possible (i.e. sterically permitted) values for dihedral angles Ψ against Φ for a polypeptide chain. ✓ The amino acid glycine occupies the maximum region in the graph because of its optical inactivity. ✓ Whereas the imino acid, proline occupies the least area on the graph. ✓ This graph was initially defined for parallel/antiparallel beta-sheets, left/right-handed alpha-helix, and collagen triple helix. ✓ It is used in the analysis of the structure of a protein, and the conformation of amino acids found in the protein. ✓ It is used to design proteinaceous drugs and artificial enzymes.