Protein Structure and Functions PDF

LECTURE 7 Protein Structure and Functions  Topic Outline Characteristics of a Protein Levels of Protein Structure Protein Classification based on functions, structural shape and composition Protein Hydrolysis and Denaturation Diseases caused by changes in protein structure  PROTE...

LECTURE 7 Protein Structure and Functions  Topic Outline Characteristics of a Protein Levels of Protein Structure Protein Classification based on functions, structural shape and composition Protein Hydrolysis and Denaturation Diseases caused by changes in protein structure  PROTEIN naturally-occurring, unbranched polymer in which the monomer units are amino acids biochemical molecules consisting of polypeptides joined by peptide bonds between the amino and carboxyl groups of amino acid residues Proteins are most abundant molecules in the cells after water – account for about 15% of a cell’s overall mass. Elemental composition - Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and Sulfur (S)  PROTEIN A protein is a polypeptide in which at least 40 amino acid residues are present: Several proteins with >10,000 amino acid residues are known Common proteins contain 400–500 amino acid residues Small proteins contain 40–100 amino acid residues More than one polypeptide chain may be present in a protein: Monomeric : Contains one polypeptide chain Multimeric: Contains 2 or polypeptide chains  Protein Classification Based on Chemical Composition Simple proteins: A protein in which only amino acid residues are present: - More than one protein subunit may be present but all subunits contain only amino acids Conjugated (complex) proteins: A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure: - One or more polypeptide chains may be present - Non-amino acid components - may be organic or inorganic - prosthetic groups - Lipoproteins contain lipid prosthetic groups - Glycoproteins contain carbohydrate groups, - Metalloproteins contain a specific metal as prosthetic group {{PEPTIDE S Carboxyl group + amino group form a strong covalent bond releasing water in the process = a condensation reaction By convention, peptides are written from the left, beginning with the free - NH3+ group and ending with the free –COO– group on the right. {{Nomenclature of Peptides The C-terminal amino acid residue keeps its full amino acid name. All of the other amino acid residues have names that end in -yl. The -yl suffix replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan, for which -yl is added to the name. The amino acid naming sequence begins at the N-terminal amino acid residue. Example: Ala-leu-gly has the IUPAC name of alanylleucylglycine {{Cross links between peptide chains Cysteine: the only standard amino acid with a sulfhydryl group ( — SH group). The sulfhydryl group imparts cysteine a chemical property unique among the standard amino acids. Cysteine in the presence of mild oxidizing agents dimerizes to form a cystine molecule. Cystine - two cysteine residues linked via a covalent disulfide bond. { LEVELS OF PROTEIN STRUCTURE 1°structure: the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end 2°structure: the ordered 3-dimensional arrangements (conformations) in localized regions of a polypeptide chain; refers only to interactions of the peptide backbone e. g., -helix and  -pleated sheet 3˚ structure: 3-D arrangement of all atoms 4˚ structure: arrangement of monomer subunits with respect to each other { PROTEIN STRUCTURE { PRIMARY STRUCTURE the linear sequence of the side chains that are connected to the protein backbone changes in just one amino acid in sequence can alter biological function Each protein has a unique sequence of amino acid residues that cause it to fold into a distinctive shape that allows the protein to function properly. { PRIMARY STRUCTURE Insulin is the smallest protein consisting of 51 amino acid residues in two chains linked by disulfide bonds Same protein from different sources:, e.g., Insulin from pigs, cows, humans, are similar but not identical. { PRIMARY STRUCTURE { Hydrogen SECONDARY STRUCTURE bonding causes protein chains to fold and align to produce orderly patterns Two bonds have free rotation: 1. Bond between  -carbon and amino nitrogen in residue 2. Bond between the  - carbon and carboxyl carbon of residue { SECONDARY STRUCTURE { SECONDARY STRUCTURE -Helix - Coil of the helix is clockwise or right- handed - There are 3.6 amino acids per turn - Repeat distance is 5.4Å (angstroms) - Each peptide bond is trans and planar - C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away - C=O----H-N hydrogen bonds are parallel to helical axis - All R groups point outward from helix { SECONDARY STRUCTURE -Helix Several factors can disrupt an  -helix stability - - proline creates a bend because of (1) the restricted rotation due to its cyclic structure and (2) its  -amino group has no N-H for hydrogen bonding - strong electrostatic repulsion caused by the proximity of several side chains of like charge, e.g., Lys and Arg or Glu and Asp - steric crowding caused by the proximity of bulky side chains, e.g., Val, Ile, Thr { SECONDARY -Pleated Sheet STRUCTURE -Polypeptide chains lie adjacent to one another; may be parallel or antiparallel -R groups alternate, first above and then below plane -Each peptide bond is trans and planar -C=O and N-H groups of each peptide bond are perpendicular to axis of the sheet -C=O---H-N hydrogen bonds are between adjacent sheets and perpendicular to the direction of the sheet { SECONDARY STRUCTURE { SECONDARY STRUCTURE Supersecondary structures: the combination of - and -sections, as for example b unit: two parallel strands of -sheet connected by a stretch of -helix  unit: two antiparallel -helices -meander: an antiparallel sheet formed by a series of tight reverse turns connecting stretches of a polypeptide chain Greek key: a repetitive supersecondary structure formed when an antiparallel sheet doubles back on itself -barrel: created when  -sheets are extensive enough to fold back on themselves { Schematic Diagram of the Supersecondary Structures Porin Staphylococcus Nuclease { TERTIARY STRUCTURE refers to the bending and folding of the protein into a specific three- dimensional shape (3D) Results from the interactions between amino acid side chains (R groups) that are widely separated from each other. In general, 4 types of interactions are observed. Disulfide bonding Electrostatic interactions H-Bonding Hydrophobic interactions { TERTIARY STRUCTURE Four Types of Interactions 1. Disulfide bond: covalent, strong, between two cysteine groups 2. Electrostatic interactions: Salt Bridge between charged side chains of acidic and basic amino acids -OH, -NH2, -COOH, -CONH2 3. H-Bonding between polar, acidic and/or basic R groups. - For H-bonding to occur, the H must be attached to O, N or F 4. Hydrophobic interactions: Between non-polar side chains { TERTIARY STRUCTURE { QUATERNARY STRUCTURE refers to the organization among the various polypeptide chains in a multimeric protein: Highest level of protein organization Present only in proteins that have 2 or more polypeptide chains (subunits) Subunits are generally independent of each other - not covalently bonded Proteins with quaternary structure are often referred to as oligomeric proteins Contain even number of subunits { PROTEIN STRUCTURE SUMMARY  PROTEIN STRUCTUR E SUMMARY { REVIEW  PROTEIN CLASSIFICATION BASED ON FUNCTIONS 1. Catalytic function: nearly all reactions in living organisms are catalyzed by proteins functioning as enzymes. Without these catalysts, biological reactions would proceed much more slowly. 2. Structural function: in animals structural materials other than inorganic components of the skeleton are proteins, such as collagen (mechanical strength of skin and bone) and keratin (hair, skin, fingernails). 3. Storage function: some proteins provide a way to store small molecules or ions, e.g., ovalbumin (used by embryos developing in bird eggs), casein (a milk protein) and gliadin (wheat seeds), and ferritin (a liver protein which complexes with iron ions).  PROTEIN CLASSIFICATION BASED ON FUNCTIONS 4. Protective function: Antibodies are proteins that protect the body from disease by combining with and destroying viruses, bacteria, and other foreign substances. Another protective function is blood clotting, carried out by thrombin and fibrinogen. 5. Regulatory function: Body processes regulated by proteins include growth (growth hormone) and thyroid functions (thyrotropin). 6. Nerve impulse transmission: Some proteins act as receptors for small molecules that transmit impulses across the synapses that separate nerve cells (e.g., rhodopsin in vision).  PROTEIN CLASSIFICATION BASED ON FUNCTIONS 7. Movement function: The proteins actin and myosin are important in muscle activity, regulating the contraction of muscle fibers. 8. Transport function: Some proteins bind small molecules or ions and transport them through the body. A typical human cell contains 9000 different proteins; the human body contains about 100,000 different proteins. PROTEIN CLASSIFICATION BASED ON FUNCTIONS PROTEIN CLASSIFICATION BASED ON FUNCTIONS PROTEIN CLASSIFICATION BASED ON SHAPE Fibrous Proteins Fibrous proteins are made up of long rod-shaped or stringlike molecules that can intertwine with one another and form strong fibers. –insoluble in water –major components of connective tissue, elastic tissue, hair, and skin –e.g., collagen, elastin, and keratin. Globular Proteins - more spherical in shape - dissolve in water or form stable suspensions. - not found in structural tissue but are transport proteins, or proteins that may be moved easily through the body by the circulatory system e.g., hemoglobin and transferrin.  PROTEIN CLASSIFICATION BASED ON SHAPE Fibrous Proteins: Alpha-Keratin - Provide protective coating for organs - Major protein constituent of hair, feather, nails, horns and turtle shells - Mainly made of hydrophobic amino acid residues - Hardness of keratin depends upon -S-S- bonds - More –S-S– bonds make nail and bones hard and hair brittle  PROTEIN CLASSIFICATION BASED ON SHAPE Fibrous Proteins: Alpha- Keratin - The  -keratin of hair lengthen when exposed to moist heat - The hydrated, stretched  - keratin adopt a more ß conformation-like structure.  PROTEIN CLASSIFICATION BASED ON SHAPE Fibrous Proteins: Collagen - Most abundant proteins in humans (30% of total body protein) - Major structural material in tendons, ligaments, blood vessels, and skin - Organic component of bones and teeth - Predominant structure - triple helix - Rich in proline (up to 20%) – important to maintain structure  PROTEIN CLASSIFICATION BASED ON SHAPE Fibrous Proteins: Collagen - a structural protein found in connective tissue such as tendons, cartilage, the organic matrix of bone, and the cornea of the eye. The collagen helix has a unique secondary structure which is left-handed and has three amino acids per turn. - diseases such as osteogenesis imperfecta and Ehlers-Danlos syndrome are caused by mutant alleles of collagen genes. - commonly an amino acid with a relatively large R group such as Cys or Ser replaces Gly residues in mutant collagens, disrupting their structure and function  PROTEIN CLASSIFICATION BASED ON SHAPE Globular Proteins: Myoglobin - An oxygen storage molecule in muscles. - Monomer - single peptide chain with one heme unit - Binds one O2 molecule - Has a higher affinity for oxygen than hemoglobin. - Oxygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles  PROTEIN HYDROLYSIS and DENATURATION Protein Hydrolysis - Amides can be hydrolyzed under acidic or basic conditions. - The digestion of proteins involves hydrolysis reactions catalyzed by digestive enzymes. - Cellular proteins are constantly being broken down as the body resynthesizes molecules and tissues that it needs.  PROTEIN HYDROLYSIS and DENATURATION Protein Denaturation - Proteins are maintained in their native state (their natural 3D conformation) by stable secondary and tertiary structures, and by aggregation of subunits into quaternary structures. - alteration or disruption of the secondary and tertiary or quaternary structure of proteins Protein Denaturing agents  Related Diseases to Protein Sickle Cell Misfolding Anemia - cells clump together and wedge in capillaries, particularly in the spleen, and cause excruciating pain. - Cells blocking capillaries are rapidly destroyed, and the loss of these red blood cells causes anemia.  Related Diseases to Protein Creutzfeldt- Misfolding Jakob disease (CJD) - fatal degenerative brain disorder - Caused by abnormal proteins called prions - Memory problems, behavioral changes, poor coordination - Dementia, involuntary movements, weakness and coma  Related Diseases to Protein Alzheimer’s Misfolding Disease - due to an abnormal amyloid-beta proteins - can cause severe memory impairment and loss of brain function in the later stage - common cause of dementia  Enzyme Mechanisms and Control  ENZYME CATALYSIS Enzymes - proteins that act as a catalyst for biochemical reactions. Most enzymes are globular proteins A few enzymes are now known to be ribonucleic acids (RNA) The rate of a reaction depends on its activation energy, DG°‡ - an enzyme provides an alternative pathway with a lower activation energy  ENZYME STRUCTURE Simple Enzymes: composed only of protein (amino acid chains) Conjugated Enzymes : Has a non- protein part in addition to a protein part. - Apoenzyme: Protein part of a conjugated enzyme. - A holoenzyme is the biochemically active conjugated enzyme - Apoenzyme + cofactor = holoenzyme (conjugated enzyme)  Models of Enzyme Action In an enzyme-catalyzed reaction, E + S ES Substrate, S: a reactant enzyme-substrate Active site: the small complex portion of the enzyme surface where the substrate(s) binds by noncovalent forces, e.g., hydrogen bonding, electrostatic attractions, van der Waals attractions - “crevice like” portion  Binding Models Lock-and-key model: substrate binds to that portion of the enzyme with a complementary shape Induced fit model: binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit Formation of Product Enzyme-Catalyzed Reaction  FACTORS THAT AFFECTS ENZYME Enzyme Activity ACTIVITY - A measure of the rate at which enzyme converts substrate to products in a biochemical reaction 1. Temperature Higher temperature results in higher kinetic energy which causes an increase in number of reactant collisions, therefore there is higher activity. Optimum temperature: Temperature at which the rate of enzyme catalyzed reaction is  FACTORS THAT AFFECTS ENZYME ACTIVITY 2. pH Drastic changes in pH can result in denaturation of proteins Optimum pH: pH at which enzyme has maximum activity Most enzymes have optimal activity in the pH range of 7.0 - 7.5 Exception: Digestive enzymes Pepsin: Optimum pH = 2.0 Trypsin: Optimum pH = 8.0  FACTORS THAT AFFECTS ENZYME ACTIVITY 3. Substrate Concentration Substrate Concentration: At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration. Substrate saturation: the concentration at which it reaches its maximum rate  FACTORS THAT AFFECTS ENZYME ACTIVITY 4. Enzyme Concentration Enzymes are not consumed in the reactions they catalyze At a constant substrate concentration, enzyme activity increases with increase in enzyme concentration The greater the enzyme concentration, the greater the reaction rate. Practice Describe the effect that each of the following changes would have on the rate of a reaction that involves the substrate sucrose and the intestinal enzyme sucrase. A. Decreasing the sucrase concentration B. Increasing the sucrose concentration C. Lowering the temperature to 10ºC D. Raising the pH from 6.0 to 8.0 when the optimum pH is 6.2  Nomenclature of Enzymes 1. Suffix -ase identifies it as an enzyme E.g., urease, sucrase, and lipase are all enzyme designations Exception: The suffix -in is still found in the names of some digestive enzymes, E.g., trypsin, chymotrypsin, and pepsin 2. Type of reaction catalyzed by an enzyme is often used as a prefix E.g., Oxidase - catalyzes an oxidation reaction, E.g., Hydrolase - catalyzes a hydrolysis reaction 3. Identity of substrate is often used in addition to the type of reaction E.g. Glucose oxidase, pyruvate carboxylase, and succinate dehydrogenase Practice Predict the function of the following enzymes. Maltase Lactate dehydrogenase Fructose oxidase Maleate isomerase  Classification of Enzymes Enzymes are grouped into six major classes based on the types of reactions they catalyze Class Reaction Catalyzed 1. Oxidation-reductions Oxidoreductases 2. Transferases Functional group transfer reactions 3. Hydrolases Hydrolysis reactions Reactions involving addition or 4. Lyases removal of groups form double bonds 5. Isomerase Isomerization reactions Reactions involving bond formation 6. Ligases coupled with ATP hydrolysis  Classification of Enzymes Oxidoreductase enzyme - catalyzes an oxidation–reduction reaction. An oxidoreductase requires a coenzyme that is either oxidized or reduced as the substrate in the reaction  Classification of Enzymes Transferase - enzyme that catalyzes the transfer of a functional group from one molecule to another Two major subtypes: 1. Transaminases - catalyze transfer of an amino group to a substrate 2. Kinases - catalyze transfer of a phosphate group from adenosine triphosphate (ATP) to a substrate  Classification of Enzymes Hydrolase - enzyme that catalyzes a hydrolysis reaction The reaction involves addition of a water molecule to a bond to cause bond breakage E.g. carbohydrases, proteases, lipases  Classification of Enzymes Lyases - enzyme that catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation 1. Dehydratase: affects the removal of the components of water from a double bond 2. Hydratase: affects the addition of the components of water to a double bonds  Classification of Enzymes Isomerases - enzyme that catalyzes the isomerization (rearrangement of atoms) of a substrate in a reaction, converting it into a molecule isomeric with itself. Ligases- enzyme that catalyzes the formation of a bond between two Practice To what main enzyme class do the enzymes that catalyze the following chemical reactions belong?  ENZYME INHIBITIONS Enzyme Inhibitor - : a substance that slows down or stops the normal catalytic function of an enzyme by binding to it. Two type of enzyme inhibitors: Competitive Inhibitors: Compete with the substrate for the same active site Will have similar charge & shape Noncompetitive Inhibitors: Do not compete with the substrate for the same active site Binds to the enzyme at a location other than active site ENZYME INHIBITIONS ENZYME INHIBITIONS Allosteric Enzymes Allosteric: Greek allo + steric, other shape Allosteric enzyme: an oligomer whose biological activity is affected by other substances binding to it - these substances change the enzyme’s activity by altering the conformation(s) of its 4°structure Allosteric effector: a substance that modifies the behavior of an allosteric enzyme; may be an - allosteric inhibitor - allosteric activator Example: Aspartate transcarbamoylase (ATCase)  Feedback Mechanisms Formation of product inhibits its continued production Positive feedback loop and negative feedback loop  ATCase Feedback Mechanism Aspartate transcarbamoylas e catalyzes a first step in a biosynthetic pathway that produces pyrimidine nucleotides needed for nucleic acids, energy storage and  Allosteric Enzymes The key to allosteric behavior is the existence of multiple forms for the 4°structure of the enzyme allosteric effector: a substance that modifies the 4° structure of an allosteric enzyme homotropic effects: allosteric interactions that occur when several identical molecules are bound to the protein; e.g., the binding of aspartate to ATCase heterotropic effects: allosteric interactions that occur when different substances are bound to the protein; e.g., inhibition of ATCase by CTP and activation by ATP