Amino Acids and Proteins PDF

BIOCHEMISTRY LECTURE (PRELIM) According to the polarity of their side chains: Hydrophobic (Nonpolar) Amino Acids Amino Acids and Proteins - i...

BIOCHEMISTRY LECTURE (PRELIM) According to the polarity of their side chains: Hydrophobic (Nonpolar) Amino Acids Amino Acids and Proteins - is an amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain Proteins - Prefer contact with one another over contact with water; ⊙ Derived from a Greek word “proteios” that means “of first hydrophobic importance” - Generally found buried in the interior of proteins, where ⊙ molecule consisting of one or more polypeptide chains they can associate with one another and remain isolated ⊙ are made of amino acids from water - 9 amino acids Amino Acids (α) a. Alanine - Proline ⊙ Building blocks of proteins b. Valine - Glycine ⊙ Contains both an amino (-NH2) group and a carboxyl (- c. Leucine - Methionine COOH) group. d. Isoleucine - Phenylalanine ⊙ Amino group and carboxyl group are attached to the α- e. Tryptophan carbon atom ⊙ Soluble in water but insoluble in organic solvents Hydrophilic Amino Acids (chloroform, acetone, ether) - Attracted to polar water molecules - Are often found on the surfaces of proteins - 3 Classes: Polar, neutral is an amino acid that contains one amino group, one carboxyl group, and a side chain that is polar but neutral at physiological pH, the side chain of a polar neutral amino acid is neither acidic nor basic more soluble in water than the nonpolar amino acids as, in each case, the R group present can hydrogen bond to water Polar, Acidic (Negatively Charged) is an amino acid that contains one amino group and two carboxyl groups, the second carboxyl group being part of the side chain at physiological pH, the side chain of a polar acidic amino acid bears a negative charge They are acidic amino acids because ionization of the carboxylic acid releases a proton Examples: o Glutamate o Aspartate Polar, Basic (Positively Charged) is an amino acid that contains two amino groups and one carboxyl group, the second amino group being part of the side chain At physiological pH, the side chain of a polar basic amino acid bears a positive charge Groups of Amino Acids Are basic because the side chain reacts with water, According to the side chains present: picking up a proton and releasing a hydroxide anion 1. Sulfur Atoms Examples: - Cysteine, Methionine Lysine 2. Acidic groups Arginine - Aspartic acid, Asparagine, Glutamic acid, Glutamine Histidine 3. Basic groups - Arginine, Lysine, Histidine Nutritional Classes of Amino Acids 4. Aromatic Rings Essential Amino Acids - Histidine, Phenylalanine, Tyrosine, Tryptophan - Are those that cannot be synthesized by the body and are 5. Imino Acids required in the diet - Proline Nonessential Amino Acids  - Are those amino acids that can be synthesized by the body and need not be included in the diet Classification of Peptides 1. DIPEPTIDES 2. OLIGOPEPTIDES - Composed of 10-20 amino acids linked together through peptide bond. - Examples: - Tripeptide: 3 amino acids linked by 2 peptide bonds - Tetrapeptide: 4 amino acids linked by 3 peptide bonds A complete dietary protein is a protein that contains all the essential 3. POLYPEPTIDES amino acids in approximately the same relative amounts in which - Composed of 11-100 amino acids linked together by peptide the human body needs them bonds 4. PROTEINS - Composed of more than 100 amino acids linked together by peptide bonds Naming of Proteins Peptides and Proteins Peptide ⊙ Unbranched chain of amino acid ⊙ Peptide bond ○ Amide group that links amino acids ○ Dipeptide – the molecule formed by condensing two amino acids ○ N-terminal amino acid – with a free N+H3 ○ C-terminal amino acid – with a free –COO- group Classes of Proteins Types of Protein Based on the Number of Peptide Chains 1. MONOMERIC PROTEIN ○ is a protein in which only one peptide chain is present 2. MULTIMERIC PROTEIN ○ is a protein in which more than one peptide chain is present ○ peptide chains present in multimeric proteins are called protein subunits Types of Protein Based on its Function 1. CATALYTIC PROTEINS  Enzymes Movement or Are biological catalysts (speed up chemical Myosin & Actin; muscle contractions Contractile reaction) Examples: amylase, pepsin, trypsin, lipase Hemoglobin; transports O2 2. IMMUNE FUNCTIONS (DEFENSE PROTEIN) Transport Lipoproteins; transports lipids Defend organisms against invasion by other species or protect them Nutrient Casein; in milk. Albumin; in eggs Immunoglobulin or antibodies Are specific protein molecules Insulin; regulates blood glucose produced by specialized cells of the Messenger Growth hormone; regulates growth immune system (plasma cells) in response to foreign bodies (antigens) Immunoglobulins; stimulate immunity Defense 3. TRANSPORT PROTEINS Snake venom; plant toxins; Carry materials from one place to another in the body Sucrase; catalyzes sucrose hydrolysis Catalytic Examples: lipoproteins, transferrin, hemoglobin, Pepsin; catalyzes protein hydrolysis myoglobin 4. MESSENGER PROTEINS Types of Protein Based on Structure These proteins transmit signals to coordinate biochemical processes between different cells, 1. Primary tissues, and organs - Is the amino acid sequence of the protein chain Examples: protein hormones (GH, FSH, Insulin) - It results from the covalent bonding between the amino 5. STRUCTURAL PROTEINS acids in the chain (peptide bonds) Provide mechanical support to large animals - Are translations of information contained in genes and provide them with their outer coverings Confer stiffness and rigidity to otherwise fluid- 2. Secondary like biochemical systems - Where the peptide chains are folded regularly Example: collagen and keratin - Is the result of hydrogen bonding between the amide 6. MOVEMENT / CONTRACTILE PROTEINS hydrogens and carbonyl oxygens of the peptide bonds Necessary for all forms of movements Examples: myosin and actin ALPHA HELIX 7. NUTRIENT PROTEINS ⊙ is a protein secondary structure in which a single protein These proteins are particularly important in the chain adopts a shape that resembles a coiled spring early stages of life from embryo to infant (helix), with the coil configuration maintained by hydrogen Serve as sources of amino acids for embryos bonds and infants Examples: albumin (egg) and casein (milk) BETA PLEATED SHEET 8. STORAGE PROTEINS ⊙ is a protein secondary structure in which two fully These proteins bind (and store) small molecules extended protein chain segments in the same or different for future use molecules are held together by hydrogen bonds Example: Ferritin (iron storage protein) and Myoglobin (oxygen storage protein in the 3. Tertiary muscles) - Three-dimensional structure 9. REGULATORY PROTEINS - Polypeptide chain with its regions of secondary structure These proteins are often found embedded in the exterior further folds on itself surface of cell membranes - Interactions responsible for tertiary structure: They act as sites at which messenger - Covalent disulfide bond molecules, including messenger proteins can - Electrostatic attractions bind and thereby initiate the effect that the - Hydrogen bonds messenger carries - Hydrophobic attractions are often the molecules that bind to enzymes (catalytic proteins), thereby turning them “on” 4. Quaternary and “off,” and thus controlling enzymatic action - is the organization among the various peptide chains in a multimeric protein - Hemoglobin FUNCTION EXAMPLES - With four individual globular peptide subunits - 2 identical alpha-subunits Collagen; bones, tendons, cartilage - 2 identical beta-subunits Structural - Heme group - iron portion Keratin; hair, skin, wool, nails, feathers - Can bind four molecules of oxygen  The primary structure of a protein is simply the amino acid sequence. 2. Compound or Conjugated Proteins The secondary structure of a protein describes how - A protein that incorporates one or more non-amino acid segments of the peptide backbone orient into a regular units in its structures pattern. - Amino acid portion is called apoprotein and non-amino The tertiary structure describes how the entire protein acid portion which may be organic or inorganic is called molecule coils into an overall three-dimensional shape. the prosthetic group (define the characteristics of these The quaternary structure describes how different protein proteins) molecules come together to yield large aggregate - Name of the conjugated protein is derived from the structures prosthetic group 3. Derived Proteins - Proteins derived from simple or conjugated proteins by physical or chemical means Types of Protein Based on Molecular Length and Shape 1. Fibrous Proteins o is a protein whose molecules have an elongated shape with one dimension much longer than the others o Are tough, insoluble, and composed of fibers and sheets o When the axial ratio of length:width is more than 10 o Examples: collagen, keratin, elastins, myosins, fibrin 2. Globular Proteins ○ is a water-soluble protein whose molecules have peptide chains that are folded into spherical or globular shapes ○ When axial ratio of length:width is less than 10 ○ Examples: hemoglobin, myoglobin, insulin, immunoglobulins 3.Membrane Proteins ○ a protein that is found associated with a membrane system of a cell ○ Example: ion channels, receptor proteins, and proteins that allow cells to connect to each other Types of Protein Based on Solubility and Physical Properties 1. Simple Proteins - A protein composed of only of amino acid residues - These are the proteins which on complete hydrolysis yield only amino acids - Examples: - globulin - albumin Physical and Chemical Properties of Proteins ⊙ Generally tasteless ⊙ Mostly are colorless, few are colored and crystalline ⊙ Insoluble in fat solvents and present varied degrees of solubility in water, salt solution, dilute acids, and alkalis ⊙ Mostly are with high molecular weight ⊙ Most of them form non-diffusible colloid solutions of the emulsoid type ⊙ Are amphoteric ⊙ Most of them are labile and readily modified in solution when subjected to alterations in pH, UV, heat, and organic solvents ⊙ Very reactive and highly specific Amphoteric ⊙ Can act as an acid or base (depends on the pH of the medium) ⊙ In acid solution it acts like a base ⊙ In alkaline solution it acts like an acid Isoelectric Point o is the pH at which an amino acid solution has no net charge because an equal number of positive and negative charges are present o At the isoelectric point, almost all amino acid molecules in a solution (more than 99%) are present in their zwitterion form Zwitterion or Dipolar Forms o from the German term meaning double ion” o is a molecule that has a positive charge on one atom and a negative charge on another atom, but which has no net charge o Amino acid are completely ionized (zwitterion or dipolar view) but the positive and negative charges neutralizes each other  Denaturation of Proteins ⊙ is the partial or complete disorganization of a protein’s characteristic three-dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions FACTORS: Temperature As the temperature increases, it also increases the rate of molecular movement within the solution and the bonds within the proteins begin to vibrate more violently Lose their characteristic 3-dimensional conformation and become completely disorganized 56-60 degrees Celsius Coagulation will occur as the protein molecules then unfold and become entangled; they have aggregated to become a solid Electrophoresis Principle: is the process of separating charged molecules on the basis of their migration toward charged electrodes associated with an electric field If the acidity or alkalinity of the solution is made less and less, a point will be reached when the amino acid group pH tends to migrate equally on both directions this pH is ⊙ When the pH of a protein solution is above the pI, all the called the isoelectric point protein molecules will have a net negative surface charge ⊙ Below the pI, they will have a net positive charge ⊙ At the pI, the protein molecules no longer have a net surface charge, as a result they no longer strongly repel one another and are at their least soluble Organic Solvents ⊙ Polar organic solvents denature proteins by disrupting hydrogen bonds within the protein, in addition to forming hydrogen bonds the solvent, water Detergents - Have both a hydrophobic region and a polar or hydrophilic region - When interacts with proteins, they disrupt the hydrophobic interactions, causing the protein chain to unfold Heavy Metals Mercury or Lead May form bonds with negatively charged side chain groups  This interferes with the salt bridges formed between amino acid R group, resulting in loss of conformation Mechanical Stress Stirring, whipping, or shaking can disrupt the weak interactions that maintain protein conformation Immunoglobulins ⊙ Antibodies ⊙ Produced by plasma cells ⊙ Highly specific ⊙ Has a memory ⊙ Can recognize “self” from “non-self” ⊙ Contain 4 peptide chains that are connected by disulfide bonds and arranged in a Y-shaped quaternary structure