BCMC 2305 Biomolecules 1 Lecture Notes PDF

BCMC -2305 Biomolecules 1 Dr. Heba M. Kamal Associate professor of Biochemistry Content Introduction Classification and structure of amino acids Non-standard Amino Acids Functions of Amino Acids Amino acid properties  Proteins Definit...

BCMC -2305 Biomolecules 1 Dr. Heba M. Kamal Associate professor of Biochemistry Content Introduction Classification and structure of amino acids Non-standard Amino Acids Functions of Amino Acids Amino acid properties  Proteins Definition:- *proteins are organic compounds with high molecular weight and they consider also the most structurally complex molecules known. *Each type of protein has a complex 3-dimensional shape or conformation. *All protein polymers are constructed from the same set of 20 monomers , called [L,α- amino acids] , which connected together by peptide linkages and composed mainly from C,H , O and N and sometimes Sulfur. *Nitrogen is a characteristic component of proteins, forming about 16% of their weight. *polymers of proteins are called polypeptides. *A protein may consists of one or more polypeptides folded and coiled into a specific conformation. Biological importance of proteins:- (Protein Functions) of all molecules encountered in living organisms, proteins have the most essential and most diverse function: 1-Tarnsport:- Many proteins as carriers of molecules or ions across membranes or between cells (ie. act as gates or pumps). Examples /of membrane transport proteins include the a- enzyme Na.k. ATP ase. b- glucose transporter Other transport proteins include c-Hemoglobin Which carries O2 to the tissues from the lungs. d- lipoproteins LDL and HDL which transport water insoluble lipids in blood from the liver. e- Transferrin and ceruloplasmin are serum proteins that transport iron and copper respectively. 2- Catalysis:- Catalytic proteins called the enzymes accelerate thousands of biochemical reactions in such processes as digestion, energy capture and biosynthesis. 3-Structure:- Structural proteins often have very specialized properties for example: a-Collagen (The major component of connective tissues) b-fibroin (silk worm protein) have significant mechanical strength. c- Elastin: Rubber like protein found in elastic fibers , is found in blood vessels and skin that must be elastic to function properly. 4- Movement:- Proteins are involved in all cell movements. ex. Actin, tubulin and other proteins comprise the cytoskeleton. Cytoskeleton proteins : …………are active in **cell division , **endocytosis **exocytosis , **Ameboid movement of WBCs (white blood cells) Actin and myosin are contractile proteins in muscle movement. 5- Defense:- Wide variety of proteins are protective. ex. 1- In vertebrates: Keratin (protein found in skin cells ) helps in protecting organism against mechanical and chemical injury and moist. ex. 2- Blood clotting proteins: fibrinogen and thrombin prevent blood loss when blood vessels are damaged ex. 3- The immunoglobulins (or antibodies) ( Abs) Are produced by lymphocytes when foreign organisms such as bacteria invade an organism. In which binding antibodies to invading organism is the 1st step in its destruction. 6- Regulation:- Binding a hormone molecule or a growth factor to its specific receptors on its target cell changes cellular function. ex1: Insulin and glucagon :- Are peptide hormones that regulate blood glucose levels. ex2 :Growth Factors (GFs) Are polypeptides that control animal cell division and differentiation. GFs like→platelet derived growth factor (PDGF) → Epidermal growth factor 7- Storage:- Certain proteins serves as a reservoir of essential nutrients for example: Ovalbumin (in bird eggs) Casein (in mammalian milk) are rich sources of organic nitrogen during development. Ex. Zein (plant proteins) → perform a similar role in germinating seeds. Other Functions:- Certain proteins bind to DNA , the carrier of genetic information to regulate its activity. In addition protein broken into amino acids which are converted to other nitrogenous substances of great physiologic importance Such as creatine , heme , purines , pyrimidines.  Amino acids Protein molecules are very large molecules with a high molecular weight ranging from 5000 to 25,00,000. Proteins can be broken down into smaller units by hydrolysis. these small units the monomers of proteins are called as amino acids Proteins are made up from, 20 such standard amino acids in different sequences and numbers. so, an indefinite number of proteins can be formed and do occur in nature. Proteins are the unbranched polymers of L- α-amino acids. the L- α-amino acids has a general formula as shown. Amino Acids:Classification  ACIDS: CLASSIFICAT ION the 20 amino acids in proteins encoded by DNA are shown; each can be designated by a three-letter abbreviation and one-letter symbol. they are grouped as per the classification schemes based on: A) Polarity and charge on R groups B) Structure of side chains C) Catabolic fate of the amino acid D) Body’s ability to synthesize the amino acid  Based On Polarity And Charge On R Groups AMINO ACIDS Can be classified into 3 groups depending on their reaction in solution: A. Non-polar R group B. Polar but uncharged R groups C. Charged polar R groups. The allocation of the 20 amino acids among the three different subgroups is somewhat arbitrary. the following examples illustrate this point Tryptophan with its heterocyclic aromatic R group may be thought of as uncharged polar amino acid (not uncharged non-polar amino acid). Glycine with its smallest R group might as well be classified as non-polar amino acid. Side chains of tyrosine and cysteine are ionizable, particularly at higher pH values, and so they might be classified as charged polar amino acids.  Cont….Non-polar R Group Phenylalanine with its phenyl moiety and tryptophan with its indole group contain aromatic side chains, and (together with the aliphatic amino acids) contribute to the internal hydrophobic interactions of the proteins. they are also responsible for the ultraviolet absorption of most proteins methionine has a thiol ether side chain. proline differs from other amino acids in that its side chain pyrrolidine ring. chemically speaking proline is not an α-amino (–NH2) acid but rather an α-imino (– NH) acid. Phenylalanine (Phe) α-amino-β-phenyl propionic acid. Tryptophan (Trp) α-amino-β-3-indole propionic acid Methionine (Met) α-amino γ-methylthio-η-butyric acid Proline (Pro) pyrrolidone-2-carboxylic acid  B.Uncharged Polar R Groups Side chains of these amino acids are uncharged, and they have polar groups (–OH, –SH, –NH, C=O) that can hydrogen bond to water. Serine and Threonine, for example, bear hydroxylic groups of different sizes. Tyrosine has a phenolic group (and like phenylalanine and tryptophan are aromatic) Serine (Ser) α-amino-β-hydroxy propionic acid Threonine (Thr) α-amino-β-hydroxybutyric acid Tyrosine (Tyr) or parahydroxy phenylalanine α-amino-β-parahydroxy phenylpropionic acid  Cont..Uncharged Polar R Groups Asparagine and glutamine have amide- bearing side chains of different sizes Asparagine (Asn) γ -amide of α-aminosuccinic acid Glutamine (Gln)-amide of glutamic acid( δ-amide of α-aminoglutaric acid) Cysteine has a thiol group that can form disulphide bond with another cysteine through oxidation of the two thiol groups to form cystine. The carboxyl group is acidic , and can be dissociated into a negatively charged carboxylate ion and hydrogen ion The amino group is basic, it combines with a hydrogen ion to form the positively charged ammonium ion, can be dissociated to form the uncharged amino group and a hydrogen ion. Protonation- deprotonation:- (pk- dissociation constant) The PKR of the imidazole ring of histidine is about 6.5. Thus, it can easily undergo protonation-deprotonation at physiological pH (or near) This allows it to function as an acid or base catalyst (buffer)