Biochem-Lecture PDF

BIOCHEMISTRY PROTEINS AND PEPTIDE BONDS Proteios” meaning “of the first Carboxyl Group Can donate a rank” (-COOH): acid proton Most abundant organic molecule Amino Group...

BIOCHEMISTRY PROTEINS AND PEPTIDE BONDS Proteios” meaning “of the first Carboxyl Group Can donate a rank” (-COOH): acid proton Most abundant organic molecule Amino Group Can accept a in the human body (-NH2): base proton Contain CHON, others also contain Sulfur and Phosphorus Side Chain Group Dictates the Monomer Unit: Amino Acid (R- Group) function of the Bond between Amino Acids: amino acid Peptide Bond (AKA Amide Bond) Peptide- unbranched chain of amino acid Oligopeptide- 10-20 amino acids residue Functions of Proteins Structural Support Enzymes Hormones and Receptors Chirality Immunity A chiral molecule is Fluid and Acid Base Balance non superimposable on its mirror image Amino Acid - building blocks of protein Enantiomers - contains both an amino group and a L- and D- configuration can exist carboxyl group L amino acids are constituents of - α-amino acid - amino group and the proteins in humans carboxyl group are attached to the D amino acids – in bacterial cell α-carbon atom walls and antibiotics - R denotes a side chain group Glycine Polar Neutral Amino Acid Simplest of the standard amino Serine (Ser, S) acids Cysteine (Cys, C) Achiral Threonine (Thr, T) R-group: Hydrogen Asparagine (Asn, N) Glutamine (Gln, Q) Tyrosine (Tyr, Y) Polar Acidic Amino Acid Aspartic acid (Asp, D) Glutamic acid (Glu, E) Non- Polar Amino Acid Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) Proline (Pro, P) Phenylalanine (Phe, F) Polar Basic Amino Acid Methionine (Met, M) Histidine (His, H) Tryptophan (Trp, W) Lysine (Lys, K) Arginine (Arg, R) Classification of Amino Acids base on At the End of Two weeks of training you be their structure ketogenic! Nonpolar Amino Acids I LIVe for this BRANCH of the Military Zero net charge Forms hydrophobic reaction BRANCHed Chain Amino Acids Found in the interior of the protein Leucine Glycine, Alanine, Valine, Leucine, Isoleucine Isoleucine, Phenylalanine, Valine Tryptophan, Methionine, Proline There will be... No HISsy fits Polar Uncharged Amino Acids No ARGuing & Zero net charge No LYing Forms hydrogen bonds in the BASIC Training HALL! Found in the surface of the protein -OH : Serine, Threonine, Tyrosine BASIC Amino Acids -SH: Cysteine HIStidine Amide: Asparagine, Glutamine ARGinine LYsine Charged Amino Acids Positive (acidic) or negative (basic) Acid-Base Properties net charge At physiologic pH (7.4) Forms Ionic interactions Carboxyl group is dissociated or Found in the surface of the protein deprotonated → COO- Acidic: Aspartate, Glutamate Amino group is protonated → NH3+ Basic: Arginine, Lysine, Histidine Essential Amino Acid These are amino acids which cannot be synthesized in the body Semi-essential amino acid: required for growth in children but is not an essential amino acid for adults Barone Essential Amino Acid Mnemonic Zwitterion- has a positive charge on PVT. TIM HALL one atom and a negative charge on Phenylalanine, Valine, Tryptophan another atom; has no net charge Threonine, Isoleucine, Methionine Because amino acids can accept or Histidine, Arginine, Lysine(ketogenic), donate protons, amino acids can Leucine (ketogenic) serve as buffers in aqueous solution. Isoelectric point (pI): pH value at which an amino acid is electrically neutral Peptide Bond A covalent bond between the pKa1– pKa of carboxylic acid carboxyl group of one amino acid pKa2– pKa of ammonium and the amino group of another amino acid. Example: Glycine pKa1- 2.34 pKa2- 9.60 What is the isoelectric point? = 2.34+9.60 =11.94 = 11.94/2=5.97 [Answer] Proteins - Fibrinogen – for clotting of blood Peptides with at least 40 amino acid Regulatory residues - Controls turning “on” and “off” of Functions: enzymes and genes - Lac repressor 1. Structure - Transcription factors 2. Catalysis 3. Movement Monomeric protein- one peptide 4. Transport chain present 5. Hormones Dimeric protein- contain two 6. Protection polypeptide chains 7. Storage Multimeric protein- > 2 peptide 8. Regulation chains present Homomultimer– one kind of chain Classification Based on Functions Heteromultimer– two or more different chains Structural - Provides rigidity and stiffness for Classification Based on Structure structural support - Collagen, Keratin Fibrous Proteins Contractile/Movement Insoluble in water - Necessary for movement Mainly structural - Actin, Myosin Globular Proteins Transport More soluble in water - Carry essential substances throughout the body - Hemoglobin, Lipoproteins Storage - Store nutrients for future use - Casein – stores protein in milk - Ferritin – stores iron in liver and spleen Catalytic/Enzyme - Responsible for catalysis - Maltase – catalyze the hydrolysis of maltose - Trypsin – catalyze the hydrolysis of Fibrous proteins (insoluble) proteins keratins Protective/Defense - found in wool, feathers, hooves, silk, - Recognize and destroy invading and fingernails foreign substances collagens - Immunoglobulins – immune defense  - found in tendons, bone, and other Lipoproteins connective tissue - Prosthetic Group: Lipid elastins - low-density lipoprotein (LDL), - found in blood vessels and high-density lipoprotein (HDL) ligaments - lipid carrier myosins Glycoprotein - found in muscle tissue - Prosthetic Group: Carbohydrate fibrin - gamma globulin mucin interferon - found in blood clots - antibody, lubricant in mucous Globular proteins (soluble) secretions, antiviral protection insulin Phosphoproteins - regulatory hormone for controlling - Prosthetic Group: phosphate glucose metabolism group myoglobin - glycogen phosphorylase - involved in oxygen storage in - enzyme in glycogen phosphorylation muscles Nucleoproteins hemoglobin Prosthetic Group: nucleic acid - involved in oxygen transport in blood - ribosomes, viruses transferrin - site for protein synthesis in cells, - involved in iron transport in blood self-replicating, infectious complex immunoglobulins Metalloproteins - involved in immune system - Prosthetic Group: metal ion responses - iron ferritin, zinc-alcohol dehydrogenase Classification Based on Composition - storage complex for iron, enzyme in Simple proteins– only amino acid alcohol oxidation residues are present Conjugated proteins– has one or Primary Structure more non-amino acid entities in its - Sequence of amino acids in a chain structure - The sequence of amino acid Prosthetic group– non-amino acid residues component of conjugated proteins Derived protein - obtained from simple or conjugated proteins by partial or complete hydrolysis (Ex. denatured proteins, peptides) Types of Conjugated Proteins Hemoproteins - Prosthetic Group: heme unit - hemoglobin, myoglobin - carrier of O2 in blood, oxygen binder in muscles Secondary Structure Protein Stability - Conformation of the polypeptide Chemical Factors backbone Disulfide bonds - The spatial arrangement of the Hydrophobic interactions - polypeptide backbone predominant Hydrogen bonding van der Waals interactions ↑ IMF, more stable due to ↓ ΔG Peptide Bond Rigid planar trans configuration Partial (about 40%) double bond character between α- amino nitrogen of one amino acid to the carbonyl carbon of the next Conformation vs Configuration Keeps the peptide links relatively resistant to conformational change Conformation - spatial relationship of every atom in a molecule - Interconversion between conformers occurs with retention of configuration,generally via rotation about single bonds. Configuration - geometric relationship between a given set of atoms - Interconversion of configurational alternatives requires breaking and reforming covalent bonds Conformation Spatial arrangement of atoms in a molecule (protein) Native proteins – functional and TORSIONAL ANGLES folded conformation Ψ (psi) – allowed rotation for Folding must achieve ↓ ΔG (Gibbs –Cα–C=O free energy change) for proteins to Ф (phi) – allowed rotation for be stable –N–Cα– Stability – tendency to maintain a Limited rotation due to steric and native conformation torsional strains Ramachandran diagram indicates allowed conformations of polypeptides Beta-Pleated Sheet Highly extended polypeptide Alpha Helix backbone Right-handed coiled spring shape Zigzag or pleated pattern (helix) R groups of adjacent AA residues Stabilized by intramolecular H project in opposite direction bonds H bonds occur between neighboring H bonds parallel to the axis of the polypeptide chains helix 3.6 AA residues per turn Pitch: 5.4 Å (0.54nm) rise per turn AA side chain (R group) project outward from the helix Parallel β sheet – H-bonded chains run in the same direction Antiparallel β sheet – H-bonded chains run in the opposite direction Core of helix is tightly packed van der Waals interactions exist in its atoms Best at forming Helices: Alanine α-Helix Breakers: Proline β-Loops Glycine short segments of AA that join two units of the secondary structure, such as two adjacent strands of an antiparallel β sheet.  180° turn involving 4 AA residues Long narrow rod Amino acids often present in β turn: Structural role Glycine - small and flexible Mostly insoluble in water Proline– cis configuration Repetitive AA sequence Examples: collagen, keratin Globular Rounded/spherical Functional role Mostly water soluble Irregular AA sequence Examples: hemoglobin, enzymes, β-Bulge immunoglobulins, Irregularity in antiparallel β-sheets Keratin H-bonding between 2 residues from Occurs in all higher vertebrates one strand with 1 residue from the Found in hair, nails, claws, wool, other quills, feathers, horns, hooves and skin Supersecondary Structure Also called motifs α-Keratins – found in mammals Intermediate in scale between right–handed α–helix secondary and tertiary structures 2 α–helices coil each other to form a A recognizable folding pattern left-handed supercoil involving 2 or more element of Rich in Cys residues – forms secondary structure and the disulfide bonds, link filaments connection/s between them HARD Keratin – hair, horn, nail (less Examples: pliable) β-α-β loop SOFT Keratin – skin, callus α-α unit (helix-turn-helix) β-Keratins – occur in birds and reptiles β-meander provides waterproofing and prevents Greek key motif drying β-sheet pattern in native state Fibrous and Globular Proteins Permanent Wave in Hair Fibrous  Forces Involved in 3° Structure Collagen 1. Covalent Disulfide Bonds Most abundant protein in the body 2. Hydrogen Bonds (30% of body total protein) 3. Salt Bridges (Electrostatic Extended helix (triple helix) attractions) Found in connective tissues 4. Hydrophobic Interactions (tendons, cartilage, bones, cornea, 5. Metal Ion Coordination blood vessels, skin) Provides strength and elasticity 3 left-handed α–chains → right handed supercoil Stabilize by steric repulsions Gly – X – Y (tripeptide repeating unit) X = about 1/3 is Proline Y = often Hydroxyproline Examples of Globular Proteins Quaternary Structure Hemoglobin (Transport) Organization among the various Insulin (Hormone) peptide chains in a multimeric Immunoglobulin (Protection) protein The spatial arrangement of Tertiary Structure polypeptide chains in a protein with 3-D conformation of a polypeptide multiple subunits Interaction of AA side chains are involved The three-dimensional structure of an entire polypeptide, including all its side chains  Consist of more than 1 polypeptide Agitation chain pH changes Same forces as that found in tertiary Concentration of salt structures Miscible organic solvents Subtle change at one site may lead ethyl alcohol, acetone to drastic change in properties Detergents Example: hemoglobin (an allosteric Alkaloidal reagents tetramer) Salts of heavy metals (Mercury, Lead Acetate, Silver Nitrate) Protein Folding Chaperones– help other proteins to fold into the biologically active conformation and enable partially denatured proteins to regain their biologically active conformation Ex. Heat-shock proteins Domain- section of the protein structure sufficient to perform a Causes of Protein Denaturation particular chemical/physical task Protein Hydrolysis Heat End-product are free amino acids - disrupts hydrogen bonds by making Amine and carboxylic acid functional molecules vibrate too violently; groups are regenerated produces coagulation, as in the Can be done enzymatically (e.g. frying of an egg proteases) or chemically (i.e. with Microwave Radiation strong acids or strong bases) - causes violent vibrations of molecules that disrupt hydrogen bonds Ultraviolet Radiation - operates very similarly to the action of heat (e.g., sunburning) Violent Whipping or Shaking - causes molecules in globular shapes to extend to longer lengths, which then entangle (e.g., beating egg white into meringue) Detergent Protein Denaturation - affects R-group interactions organic Loss of three-dimensional structure Solvents (e.g., ethanol, sufficient to cause loss of function 2-propanol, acetone) Causes: - interferes with R-group interactions Heat because these solvents also can UV radiation form hydrogen bonds; quickly  denatures proteins in bacteria, killing them (e.g., the disinfectant action of 70% ethanol) Strong Acids and Bases - disrupts hydrogen bonds and salt bridges; prolonged action leads to actual hydrolysis of peptide bonds Salts of Heavy Metals (e.g., salts of Hg2, Ag+, Pb2+) - metal ions combine with —SH groups and form poisonous salts Reducing Agents - reduces disulfide linkages to produce —SH groups Protein Renaturation Regain of native structure and biological activity Requires return of condition in which the native conformation is stable Not all denatured proteins can undergo renaturation Proteins usually fold spontaneously as they are synthesized in the cell Diseases Caused by Protein Misfolding Alzheimer’s Disease Parkinson’s Disease Huntington’s Disease Prion diseases: Creutzfeldt-Jakob Disease Kuru Bovine Spongiform Encephalopathy (Mad Cow Disease)