Amino Acids and Proteins PDF

Amino Acids and Proteins Introduction to General, Organic, and Biochemistry, 11th Edition by Bettelheim, Brown, Campbell, Farrell, Torres Organic Chemistry, 11th Edition by Solomons et.al. Olivert M. Sitoy, M.Sc., R.Ch....

Amino Acids and Proteins Introduction to General, Organic, and Biochemistry, 11th Edition by Bettelheim, Brown, Campbell, Farrell, Torres Organic Chemistry, 11th Edition by Solomons et.al. Olivert M. Sitoy, M.Sc., R.Ch. Chemistry Department College of Arts and Sciences Xavier University – Ateneo de Cagayan  Proteins Proteins: Naturally-occurring, unbranched polymer of Amino Acids. ▪ Provide nitrogen and sulfur for the diet ▪ Most abundant macromolecules in the cell ▪ Carry out most of the work of the cell ▪ Composed of at least 40 amino acid residues:  Proteins Proteins: Naturally-occurring, unbranched polymer of Amino Acids. ▪ Provide nitrogen and sulfur for the diet ▪ Most abundant macromolecules in the cell ▪ Carry out most of the work of the cell ▪ Composed of at least 40 amino acid residues:  Proteins Proteins: Naturally-occurring, unbranched polymer of Amino Acids. ▪ Structure: Collagen and keratin in skin, bone, hair, and nails. ▪ Catalyst: Reactions in living systems are catalyzed by proteins (enzymes) ▪ Movement: Myosin and actin in the muscle. ▪ Transport: Hemoglobin for oxygen transport, and other transport proteins (lipoproteins) ▪ Hormones: Insulin, oxytocin, and human growth hormones. ▪ Protection: Fibrinogen for blood clotting, and Antibodies to fight diseases. ▪ Storage: Casein in milk and ovalbumin in eggs for storage of nutrients, and ferritin in liver for iron storage. ▪ Regulation: Control of gene expression.  Proteins Proteins: Naturally-occurring, unbranched polymer of Amino Acids. Typically, 9000 different proteins is in a cell (10000 in humans) Can either be Fibrous or Globular: Collagen: a fibrous protein Hemoglobin: a globular protein  Amino Acids Amino Acids: compound that contains an amino and a carboxyl group. ▪ α-amino acid: amino acids in which the amino group and the carboxyl group are attached to the α-carbon. R = side chain – vary in size, charge, acidity, functional groups present, hydrogen-bonding activity, and chemical reactivity.  Amino Acids Amino Acids: compound that contains an amino and a carboxyl group. ▪ Although α-amino acid are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt form. Unionized Form Zwitterion – a positive charge on one atom and a negative charge on another atom  Chirality of Amino Acids Excluding glycine, all protein- derived amino acids have at least one stereocenter (the α-carbon) and are chiral. ▪ Most of protein derived amino α-amino acids have Naturally occurring Form L-configuration at the α– carbon. ▪ For example: a comparison of stereochemistry of D- Glyceraldehyde and L- Alanine Naturally occurring Form  Protein-Derived Amino Acids Non-polar Amino Acids: Contains non-polar (hydrophobic) side chains  Protein-Derived Amino Acids Polar Neutral Amino Acids: Contains polar, uncharged side chains  Protein-Derived Amino Acids Polar Acidic/Basic Amino Acids: Contains polar, charged side chains  Protein-Derived Amino Acids Amino Acids: compound that contains an amino and a carboxyl group. ▪ All 20 are α-amino acid ▪ For 19 of the 20 amino acids, the α-amino group is primary; for proline, it is secondary ▪ Except glycine, the α-carbon of each is a stereocenter ▪ Isoleucine and threonine each contains a second stereocenter  Ionization vs. pH The net charge on amino acid depends on the pH of the solution. ▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a zwitterion. ▪ Adding a strong acid (e.g. HCl), pH becomes 2.0 or lower. ▪ The acid donates H+ to the COO- of the amino acid, turning the zwitterion to a positively charged ion.  Ionization vs. pH The net charge on amino acid depends on the pH of the solution. ▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a zwitterion. ▪ Adding a strong base (e.g. NaOH), pH becomes 10.0 or higher. ▪ The NH3+ of the amino acid is transferred to the base, turning the zwitterion to a negatively charged ion.  Ionization vs. pH The net charge on amino acid depends on the pH of the solution. ▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a zwitterion. ▪ The acid donates H+ to the COO- of the amino acid, turning the zwitterion to a positively charged ion. (pH < 7.0) ▪ The NH3+ of the amino acid is transferred to the base, turning the zwitterion to a negatively charged ion. (pH > 7.0)  Isoelectric Point Isoelectric point: pH where majority of molecules has no net charge. Amino Acid Name Isoelectric point Amino Acid Name Isoelectric point Alanine 6.01 Leucine 5.98 Arginine 10.76 Lysine 9.74 Asparagine 5.41 Methionine 5.74 Aspartic Acid 2.77 Phenylalanine 5.48 Cysteine 5.07 Proline 6.48 Glutamic Acid 3.22 Serine 5.68 Glutamine 5.65 Threonine 5.87 Glycine 5.97 Tryptophan 5.88 Histidine 7.59 Tyrosine 5.66 Isoleucine 6.02 Valine 5.97  Cysteine: A Chemically Unique Amino Acid Cysteine: An amino acid with –SH (sulfhydryl) group  Amino Acids with Aromatic Side Chains ▪ Key precursor to neurotransmitters ▪ Tryptophan: Converted to serotonin (5-hydroxytryptamine)  Amino Acids with Aromatic Side Chains ▪ Key precursor to neurotransmitters ▪ Tyrosine and Phenylalanine: Precursor to norepinephrine and epinephrine (i.e. catecholamines)  Uncommon Amino Acids ▪ Post-translational modification: modification of amino acids by certain organism after biosynthesis. ▪ Hydroxylation (oxidation) of proline, lysine, and tyrosine. Stabilization of collagen fibers  Uncommon Amino Acids ▪ Post-translational modification: modification of amino acids by certain organism after biosynthesis. ▪ Iodination of tyrosine. ▪ Animals and humans that exhibit sluggishness and slow metabolism are often given thyroxine to help ramp up their metabolism  Peptides ▪ Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds (1902). ▪ Peptide Bond: Amide bond between the α-carboxyl group of one amino acid and the α-amino group of another amino acid  Peptides ▪ Peptide: A short polymer of amino acids joined by peptide bonds; classified by the number of amino acid residues ▪ Dipeptide: A molecule compose of two (2) amino acids connected by a peptide bond  Peptides ▪ Peptide: A short polymer of amino acids joined by peptide bonds; classified by the number of amino acid residues ▪ Tripeptide: A molecule compose of three (3) amino acids connected by a peptide bond  Peptides ▪ Peptide: A short polymer of amino acids joined by peptide bonds; classified by the number of amino acid residues ▪ Polypeptide: A macromolecule compose of amino acids connected by a peptide bond. ▪ Protein: A biological macromolecule containing at least 30 to 50 amino acids connected by a peptide bond.  Writing Peptides ▪ Convention: Left to right, starting with free –NH3+ group and ending with the free –COO- group. ▪ C-terminal amino acid: amino acid at the end of the chain bearing the –COO- group. ▪ N-terminal amino acid: amino acid at the beginning of the chain bearing the –NH3+ group.  Peptides and Proteins ▪ Proteins behaves as zwitterion and have an isoelectric point. ▪ At isoelectric point (pI), proteins have no net charge. ▪ At any pH above (more basic than) the pI, it has a net negative charge. ▪ At any pH below (more acidic than) the pI, it has a net positive charge. ▪ Example: Hemoglobin has an almost equal number of acidic and basic side chains; its pI is 6.8. ▪ Example: Serum albumin has more acidic side chains; its pI is 4.9. ▪ Proteins are least soluble in water at their isoelectric point and can be precipitated from solution at this pH.  Levels of Protein Structure ▪ Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain (e.g., α-helix, β-pleated sheets and random coils) ▪ Tertiary Structure: Complete three-dimensional arrangement of atoms in a polypeptide chain. ▪ Quaternary Structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain. Levels of Protein Structure Levels of Protein Structure  Primary Structure of Proteins Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Translation of information contained in the genes The number peptides possible from the 20 protein-derived amino acids is enormous. ▪ 400 possible dipeptides, 8000 possible tripeptides and so on. ▪ Rule of Thumb: 20n = number of peptides possible with n number of amino acids ▪ For small proteins of 60 amino acids, the number of proteins possible is 2060 = 1078, which is possible greater than the number of atoms in universe.  Primary Structure of Proteins Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Translation of information contained in the genes  Primary Structure of Proteins Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Translation of information contained in the genes Human insulin consist of two polypeptide chains having a total of 51 amino acids; the two chains are connected by two interchain disulfide bonds.  Primary Structure of Proteins Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Translation of information contained in the genes ▪ Vasopressin and oxytocin are both nonapeptides but quite different biological functions. ▪ Vasopressin is an antidiuretic hormone. ▪ Oxytocin affects contraction of the uterus in childbirth and the muscle of the breast that aid in the secretion of milk.  Primary Structure of Proteins Primary Structure: Sequence of amino acid in a polypeptide chain. ▪ Translation of information contained in the genes  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain. ▪ Commonly α-helix and β-pleated sheet. ▪ α-helix: a section of polypeptide chain coils into spiral, most commonly a right-handed spiral ▪ β-pleated sheet: two polypeptide chains or sections of the same polypeptide chain align parallel to each other (can either be parallel or antiparallel)  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain.  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain.  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain. In α-helix: ▪ 3.6 amino acids per turn of the helix ▪ Six atoms of each peptide bond lie on the same plane ▪ N-H groups of amide bonds point in the same direction, roughly parallel to the axis of the helix. ▪ C=O group of amide bonds point in the opposite direction, also roughly parallel to the axis of the helix. ▪ Hydrogen bonding between C=O and N-H groups exist. ▪ All R- side chains points outward the helix  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain.  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain. In β-pleated sheet: ▪ Six atoms of each peptide bond lie on the same plane. ▪ The C=O and N-H groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them. ▪ All R- side chains on any one chain alternate. First above, then below the plane of the sheets, etc.  Secondary Structure of Proteins Secondary Structure: Conformation of amino acids in localized regions of a polypeptide chain.  Collagen Triple Helix Tropocollagen: Three polypeptide chains wrapped around each other forming a triple helix. ▪ Collagen: A structural protein of connective tissues (bone, cartilage, tendon, blood vessels, skin) ▪ 30 amino acids in each are proline and L-hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs. ▪ Every third position is glycine and repeating sequence are X-Pro- Gly and X-Hyp-Gly ▪ Each polypeptide chain is a helix but not α-helix. ▪ The three strands are held by hydrogen bonding between hydroxyproline and hydroxylysine. ▪ During aging, collagen helices becomes cross-linked by covalent bonds between the side chains of lysine.  Collagen Triple Helix Tropocollagen: Three polypeptide chains wrapped around each other forming a triple helix. Collagen Triple Helix  Tertiary Structure of Proteins Tertiary Structure: overall conformation of an entire polypeptide chain. Tertiary structure are stabilized in five ways: ▪ Covalent Bonds: disulfide bonds between cysteine side chains. ▪ Hydrogen Bonding: interaction between polar groups of the side chains (e.g. –OH group of serine and threonine). ▪ Salt Bridges: attraction of the –NH3+ group of lysine and the COO- group of aspartic acid. ▪ Hydrophobic Interaction: interaction between non-polar chains (e.g. side chains of phenylalanine and isoleucine) ▪ Metal Interaction: interaction of same charged side chains with a metal ion in between  Tertiary Structure of Proteins Tertiary Structure: overall conformation of an entire polypeptide chain.  Tertiary Structure of Proteins Tertiary Structure: overall conformation of an entire polypeptide chain.  Tertiary Structure of Proteins Tertiary Structure: overall conformation of an entire polypeptide chain.  Tertiary Structure of Proteins Tertiary Structure: overall conformation of an entire polypeptide chain.  Quaternary Structure of Proteins Quaternary Structure: arrangement of polypeptide chains into a non- covalently bonded aggregation Quaternary structure are stabilized in four ways: ▪ Hydrogen Bonding: interaction between polar groups of the side chains (e.g. –OH group of serine and threonine). ▪ Salt Bridges: attraction of the –NH3+ group of lysine and the COO- group of aspartic acid. ▪ Hydrophobic Interaction: interaction between non-polar chains (e.g. side chains of phenylalanine and isoleucine)  Quaternary Structure of Proteins Quaternary Structure: arrangement of polypeptide chains into a non- covalently bonded aggregation In Hemoglobin: ▪ Adult Hemoglobin: two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each. ▪ Each chain surrounds an iron-containing heme unit ▪ Fetal Hemoglobin: two alpha chains, and two gamma chains; has greater affinity to oxygen relative to adult hemoglobin  Quaternary Structure of Proteins Quaternary Structure: arrangement of polypeptide chains into a non- covalently bonded aggregation  Hemoglobin ▪ Oxygen binds to heme in hemoglobin; when one O2 bind, the binding of the next O2 is easier. ▪ The first 2,3-bisphospho- glycerate to leave deoxyhemoglobin. ▪ During binding, shape changes which favors more reaction of oxygen  Hemoglobin ▪ H+ from metabolizing cells (low pH) favors oxygen release from Hb. ▪ When the oxygen concentration is low, as in the peripheral tissues, H is bound and O2 is released. ▪ Higher pH in the lungs favors binding of oxygen to Hb. ▪ When the oxygen concentration is high, as in the lungs, hemoglobin binds O2 and releases protons  Oxygen Transport: Mother-Fetus ▪ Fetal Hb is different from adult Hb ▪ It does not bind to BPG and has higher affinity to O2  Oxygen Transport: Mother-Fetus ▪ Sickle cell hemoglobin (Hb S) has a valine substituted for glutamic acid in the beta chain. ▪ Deoxy version clumping and forming the characteristic sickle cells ▪ Early death; sickle cell trait = malaria resistance  Quaternary Structure of Proteins Quaternary Structure: arrangement of polypeptide chains into a non- covalently bonded aggregation 1RSS = Ribosomal Protein S7 from Thermus thermophilus 2AWK = Green Fluorescent Protein (GFP) R96M mature chromophore The 8 β strands in these eight structural motifs associate in the center of the molecule to form a so called β–barrel.  Denaturation Denaturation: destruction of native conformation of protein by chemical or physical means. ▪ Some denaturation are reversible, while some are permanent. Denaturation includes: ▪ Heat: disrupts hydrogen bonding; in globular proteins, it can lead to unfolding of polypeptide chains which might results to coagulation and precipitation. ▪ 6M aqueous urea: disrupts hydrogen bonding ▪ Surface-active agents: disrupts hydrogen bonding (e.g. detergent) ▪ Reducing agents: cleavage of disulfide bonds through reduction (e.g. 2-mercaptoethanol)  Denaturation Denaturation: destruction of native conformation of protein by chemical or physical means. ▪ Some denaturation are reversible, while some are permanent. Denaturation includes: ▪ Heavy metal ions: formation of water-insoluble salts with thiol side chains (e.g., Pb2+, Hg2+, and Cd2+) ▪ Alcohol: sterilization of skin before injection due to complete denaturation of proteins (e.g. 70% ethanol).  Denaturation Denaturation: destruction of native conformation of protein by chemical or physical means. ▪ Some denaturation are reversible, while some are permanent.  Protein Digestion and Diet Digestion: degradation of proteins in the diet. ▪ Stomach: Facilitated by the enzyme, pepsin. ▪ Small Intestine: trypsin, chymotrypsin, elastase, etc. Essential Amino Acids: Cannot be synthesized by humans ▪ Ile, Leu, Lys, Met, Phe, Thr, Tyr, Val, His* Complete protein from animal provides essential AA in proper proportions. Imbalanced protein from vegetables sources must be balanced. (e.g., beans (Lys +Trp) and corn (Met))