Unit 4- Amino Acid and Protein Chemistry PDF

CHY2026: General Biochemistry Unit 4:Amino Acid Chemistry http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid_structure_2.jpg  Hydrogen Amino group Carboxyl group Unique Side Chain R Alpha Carbon Amino Acids ❖ The mol...

CHY2026: General Biochemistry Unit 4:Amino Acid Chemistry http://www.hcc.mnscu.edu/programs/dept/chem/V.27/amino_acid_structure_2.jpg  Hydrogen Amino group Carboxyl group Unique Side Chain R Alpha Carbon Amino Acids ❖ The molecule is comprised of the elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and small quantities of sulphur (S) – CHONs ❖ The α- carbon in all amino acids is asymmetric (except glycine) ❖ Because of this two optically active forms exist ❖ The –NH2 is to the right of the –COOH: D-form ❖ The –NH2 is to the left of the –COOH: L-form ❖ Only L- forms are used to make proteins  Amino Acids ❖ Glycine does not contain any asymmetric carbon ❖ This is the simplest amino acid  Properties of Amino Acid ❖ Amino acids are dipolar ions (zwitterions) in solution ❖ In the dipolar form amino group becomes positively charged (NH3+) and the carboxylic acid becomes negatively charged (COO-) ❖ The dipolar ion exists as a neutral ion and will have zero mobility in electrophoresis http://cyberlab.lh1.ku.ac.th/elearn/faculty/veterin/vet69/Biochemistry%20Web%20Job/amino%20and%20protein/zwitteri on2.jpg  Properties of Amino Acid ❖ Amino Acids are amphoteric ❖ There is no pH at which a.a have no ionic character ❖ The pH value at which the number of cations is equal that of anion is called the isoelectric point (pI) ❖ Every a.a have a different pI: The 3 basic a.a have higher pI and the 2 acidic a.a have lower pI ❖ At pH lower than the pI, the protein will have a net positive charge and as a cation will migrate towards the negative electrode (cathode) during electrophoresis ❖ At pH higher than the pI, the protein will have a net negative charge and the anion will migrate towards the positive electrode (anode) during electrophoresis Properties of Amino Acids ❖ Notice that the isoelectric point depends on the amino acid structure in a predictable way acidic amino acids: aspartic acid (2.8), glutamic acid (3.2) neutral amino acids: (5.0 to 6.3) basic amino acids: lysine (9.7), arginine (10.8), histidine (7.6)  Electrophoresis ❖ Electrophoresis uses differences in isoelectric points to separate mixtures of amino acids. A streak of the amino acid mixture is placed in the centre of a layer of acrylamide gel or a piece of filter paper wet with a buffer solution.Two electrodes are placed in contact with the edges of the gel or paper, and a potential of several thousand volts is applied across the electrodes. Positively charged (cationic) amino acids are attracted to the negative electrode (the cathode), and negatively charged (anionic) amino acids are attracted to the positive electrode (the anode) ❖ An amino acid at its isoelectric point has no net charge, so it does not move.  Amino Acids ❖ There are 20 amino acids that can make up proteins 9 essential amino acids 11 non essential amino acids ❖ Essential amino acids – they are not synthesized in the body and are normally required in the diet ❖ Non essential amino acids – they are synthesized de novo in humans Essential Non essential Histidine (His) Alanine (Ala) Isoleucine (Ile) Arginine (Arg) Leucine (Leu) Asparagine (Asn) Lysine (Lys) Aspartic acid (Asp) Methionine (Met) Cysteine (Cys) Phenylalanine (Phe) Glutamic acid (Glu) Threonine (Thr) Glutamine (Gln) Tryptophan (Trp) Glycine (Gly) Valine (Val) Proline (Pro) Serine (Ser) Tyrosine (Tyr) Amino Acids ❖ Amino acids can be grouped based on the properties of the R group non polar polar uncharged acidic (negatively charged) basic (positively charged) Proteins ❖ Proteins are made up of amino acids linked together by peptide bonds (condensation reaction) ❖ The peptide bonds in proteins are metastable, meaning that in the presence of water they will break spontaneously, releasing 2-4 kcal mol-1 of free energy, but this process is extremely slow ❖ In living organisms, the process is facilitated by enzymes ❖ Living organisms also employ enzymes to form peptide bonds; this process requires free energy Proteins ❖ 2 amino acids react → dipeptide ❖ 3 amino acids → tripeptide…e.g. glutathione (Glu-Cys-Gly) ❖ Less than 10 amino acids – oligopeptide… e.g. angiotensin (Asn-Arg-Val-Try-Val-His-Pro-Phe) ❖ 4 or more amino acids → polypeptide ❖ Polypeptide with a MW > 6000 or ≥ 100 amino acids → protein ❖ Each amino acid in a chain is termed a residue ❖ The two ends of the chain are named amino acid terminal (N- terminal) and carboxylic terminal (C-terminal) respectively ❖ These terminals are the only ionizable groups (except for the side chain) in a protein Hydrolysis ❖ Proteins can be hydrolyzed (using acid or a suitable enzyme) to form individual amino acids http://quizlet.com/31428351/proteins-flash-cards/  Peptides ❖ A peptide is any combination of amino acids Prefixes for short peptides in which the alpha amino group (-NH) of one acid is united with the alpha carboxylic group (-CO2H) of another through an amide bond. ❖ The amide bonds formed in peptides always involve the alpha amino and alpha carboxylic acid groups and never those of side chains. ❖ More amino acids maybe added in the same fashion ❖ Amino acids that have been incorporated into peptides are called amino acid residues  Naming Peptides ❖ Names of peptides are derived from names of amino acid residues ❖ By convention, names of peptides are always written from left to right starting with the N- terminal end ❖ E.g. a peptide that contains N-terminal glycine, followed by a histidine, followed by C -terminal phenylalanine is named gly cyl - his tidyl - phenylalanine. The sequence is extremely important; glycyl-histidyl-phenylalanine is a different molecule from phenylalanyl-histidyl-glycine ❖ Peptide structures can be written using the three letter abbreviations… glycyl-histidyl- phenylalanine can be written as Gly-His-Phe Biological Roles of Peptides ❖ Intermediates for the formation of proteins ❖ Antibacterial properties e.g. penicillin ❖ Growth factors e.g. folic acid ❖ Hormone e.g. insulin; angiotensin ❖ Control oxidation-reduction potential of cell e.g. glutathione ❖ Increased levels in urine may be indicative of psychological/neurological disorders such as depression and schizophrenia (gluten/casein peptides) Glutathione ❖ Natural antioxidant ❖ Glutathione is produced in cells as needed. It is used as an antioxidant to prevent damage to cells from heavy metals, free radicals and peroxides ❖ It is made from γ-glutamic acid – cysteine – glycine, which is also written: γ-Glu – Cys – Gly http://guweb2.gonzaga.edu/faculty/cronk/biochem/images/glutathione.gif  Angiotensin ❖ Angiotensin is a potent vasodilator that is synthesized by cells ❖ Angiotensin I is a decapeptide. It is biologically inactive and acts solely as a precursor for angiotensin II ❖ Angiotensin II is an octapeptide and causes blood vessels to constrict when there is a cut (to stop the bleeding) ❖ Angiotensin I is converted to angiotensin II when needed by the angiotensin converting enzyme – ACE Industrial Importance of Peptides ❖ Inhibitory peptides are used in clinical research to examine the effects of peptides on the inhibition of cancer proteins and other diseases ❖ Peptides are used in imaging where specific peptides in the fluorescing material help with early detection of potentially life-threatening cancers ❖ Peptides are used in skin care to increase the amount of collagen being produced in the skin, stimulate fibroblast growth, and stimulate the production of keratinocytes ❖ The zero-calorie sweetener found in many diet beverages is a synthesized peptide (aspartame) Biological Role of Proteins ❖ They are biological catalysts – enzymes ❖ They act as carrier molecules transporting small molecules and ions e.g. haemoglobin (protein) transports oxygen in the erythrocytes ❖ Responsible for the high tensile strength of the skin and bone ❖ Immunoregulation ❖ Receptor proteins help in the transmission of nerve impulses ❖ Major component of muscle Protein Classification 1. Classification based on source (a) Animal protein – higher quality protein (b) Plant protein – low quality protein (does not mean it’s a poor protein source) 2. Classification based on shape (a) Globular/Corpuscular proteins: spherical or ovoid shape, soluble in water or aqueous media.Tertiary and quaternary structures are usually associated with this class Further classified as: Cytochrome C Blood proteins: serum albumin, glycoproteins, antibodies, haemoglobin, hormones Enzymes Nutrient Proteins (b) Fibrous/Fibrillar proteins: serve in structural or protective roles ❖ They can stretch and later recoil e.g. collagens, elastins, keratins and fibroin Protein Structure Protein structure can be grouped into four levels of organization 1. Primary structure – linear sequence of amino acids. Main linkage – peptide bonds How important is the primary sequence? ❖ Some small change in a.a can make a big difference ❖ Normal Hb has 2 alpha chains and 2 beta chains Normal Hb - Thr-Pro-Glu-Glu-Lys-Ala Sickle cell Hb - Thr-Pro-Val-Glu-Lys-Ala ❖ Red blood cells carrying HbS behave normally when there is an ample supply of oxygen. Reduced oxygen concentration results in the rbc becoming sickle-shaped ❖ Sickled cells may clog capillaries ❖ The body’s defenses destroy the clogging cells and the loss of blood cells causes anaemia Gel Electrophoresis: Sickle Cell Anaemia Hydroxyurea (Droxia) is used to control ❖ symptoms of the disease It prompts the bone marrow to manufacture HbF which does not have the beta chains where mutation occurs Rbc containing HbF do not sickle. Even with❖hydoxyurea, the body still produces HbS but the presence of cells with HbF reduces the concentration of cell with HbS hence relieving the symptoms of the disease 2. Secondary structure – spatial arrangement of a portion of the polypeptide. Main linkage- H bonding (a) α- helix e.g. α-keratin (b) β- pleated sheets e.g. silk fibroin (c) β- bends α-keratin Silk fibroin  Protein Structure 3. Tertiary structure – describe the shape of the entire polypeptide…folding of the helices of globular proteins. All the chemical bonds are found in the structure e.g. myoglobin (cardiac and red skeletal muscle) Chaperones – a protein that helps other proteins to fold into the biologically active conformation and enables partially denatured proteins to regain their biologically active conformation 4. Quaternary structure – spatial arrangement of many polypeptide subunits…all chemical bonds are found in the structure e.g. haemoglobin (tetrameric protein)  Haemoglobin ❖ In the adult human, Hb (tetramer) consists of 4 polypeptide chains (globins) – 2 identical α chains (141 residues) and 2 identical β chains (146 residues) ❖ Each globin chain surrounds an iron-containing heme ❖ It is a conjugated protein – proteins that contains non-amino acid portion Prosthetic group – the non-amino acid portion of a conjugated protein ❖ The globins are the amino acid portion and the prosthetic groups are the haem units Myoglobin ❖Myoglobin is a small oxygen heme protein found in the muscle ❖ Myoglobin consist of 1 polypeptide chain, 153 residues long Comparison between Haemoglobin and Myoglobin Haemoglobin Myoglobin 1 Hb can bind to 4 O2 1 myoglobin binds to 1 O2 The binding of oxygen to Hb exhibit positive Oxygen binding to myoglobin does not cooperativity (when 1 oxygen molecule is exhibit positive cooperativity bound it becomes easier for the other oxygen to bind Hb functions in oxygen transport. It must Myoglobin has the function of oxygen bind strongly to oxygen and be able to release storage in muscles it easily http://www.contexo.info/DNA_Basics/images/proteinstructuresweb.gif  Conformation of Proteins ❖ Protein folding is the physical process by which a polypeptide folds into its characteristic and functional three dimensional structure ❖ Each protein exists as an unfolded polypeptide when translated from a sequence of mRNA to a linear chain of amino acids ❖ This polypeptide lacks any developed three dimensional structure ❖ Amino acids interact with each other to produce a well-defined three dimensional structure, the folded protein is known as the native state ❖ The resulting three dimensional structure is determined by the amino acid sequence ❖ The correct three dimensional structure is essential to function, although some parts of functional proteins may remain unfolded Conformation of Proteins ❖ Failure to fold into native structure produces inactive proteins that are usually toxic ❖ Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrills formed by misfolded proteins ❖ Many allergies are caused by the folding of the proteins, for the immune system does not produce antibodies for certain protein structures  Chemical Bonds in Protein Structure 1. Primary Bond: Peptide bond…backbone of the protein chain 2. Secondary Bonds: Hold the chain in its natural configuration (a) Disulphide Bond – formed by the oxidation of the thiol or sulphurhydryl groups (- SH) of two cysteine residues to form cystine Disulphide linkages can occur in two cysteine molecules that are apart in a polypeptide chain. This will cause the polypeptide chain to be folded back on itself e.g. insulin (c) Hydrogen Bond: This occurs when a group containing a H atom is bonded to the electronegative atoms O or N. H-bond plays a role in stabilizing some conformations of the polypeptide chain e.g. silk fibroin 3. Nonpolar/ Hydrophobic Bond formed among amino acids with hydrophobic side groups 4. Ionic/Electrostatic Bond/Salt Bridge/Salt linkage: Ions possessing similar charge repel each other…ions possessing dissimilar charge attract each other e.g. acidic and basic R groups Ionic bonds are responsible for maintaining the folded structure of globular proteins Denaturation ❖ This refers to a change in the properties of a protein resulting in a loss of biological activity Denaturation can be brought about by physical agents (a) shaking (b) heat treatment (c) cooling or freezing (d) UV rays and chemical agents (a) ionizing radiation (b) organic solvents (c) detergents When proteins are denatured the molecule unfolds causing disorganization of internal structure …(bonds are broken) Some denatured proteins cannot be brought back to their original state....however generally its a reversible process  Methods of Protein Separation ❖ Electrophoresis - used to separate complex mixtures of proteins and to purify the protein for subsequent applications ❖ Western blotting is used to identify a specific protein in a complex mixture of proteins. The technique exploits both the efficiency of SDS-PAGE to separate a mixture of proteins into distinct protein bands, and the ability of immunochemical reagents to interact specifically with a given protein antigen ❖ Column Chromatography can be used to fractionate proteins. The mixture of proteins in solution is passed through a column containing a porous solid matrix The 3 types of matrices used are: (1) Ion-exchange chromatography, (2) gel-filtration chromatography and (3) affinity chromatography  Protein Quantification ❖ Knowing the quantity of a protein after each separation step is useful in checking the progress of purification and evaluating the technique's efficiency ❖ The concentration of a protein can be measured by immunological techniques such as ELISA or Western Blotting ❖ Activity can be measured using fluorescent techniques ❖ Mass spectrometry is another accurate analytical technique for determining protein mass. In this technique, atoms are ionized through a machine and passed through a vacuum into the detector  Industrial Importance of Proteins ❖Denatured protein - used in the formation of gelatin, which is used in many foods, in the pharmaceutical and cosmetic industries ❖Collagen has been widely used in cosmetic surgery, as a healing aid for burn patients for reconstruction of bone and a wide variety of dental, orthopedic and surgical purposes ❖Collagens are also used in the construction of artificial skin substitutes used in the management of severe burns ❖Corn gluten is used in feed concentrates and in small amounts as extenders for commercial resins and glues ❖Corn gluten is sometimes destarched by acid or enzyme hydrolysis to yield a product that is almost entirely protein and is used in paints. ❖…Sometimes it is broken down by complete hydrolysis to yield monosodium glutamate, a seasoning for food