Chapter 4: Protein Structure and Function Continuation (MTG5_6_c4_proteins_ PDF)

Chapter 4: Protein Structure and Function continuation 01-29 (M), 01-31 (W) Protein Categories Based on Physical Properties  Fibrous- large, elongated, stiff molecules, do not readily dissolve in water, structural role or in cellular movements (collagen)  Globular- generally water soluble, compact...

Chapter 4: Protein Structure and Function continuation 01-29 (M), 01-31 (W) Protein Categories Based on Physical Properties  Fibrous- large, elongated, stiff molecules, do not readily dissolve in water, structural role or in cellular movements (collagen)  Globular- generally water soluble, compactly folded (myoglobin), perform dynamic roles HOW PROTEINS WORK The activity of proteins depends on their ability to bind specifically to other molecules Ligand- the molecule to which a protein binds Binding site- region of the protein that associates with the ligand EXAMPLE: ENZYMES Enzymes are powerful and highly specific catalysts Enzymes greatly accelerate the speed of chemical reactions. Enzymes accelerate reactions by lowering the activation of a reaction. Let’s Review - - recall previous biology and/or chemistry courses Activation energy is the difference in free energy (total energy) between reactant and transition state. rate of reaction is inversely proportional to the activation energy Slower in the presence of an enzyme locate in the graphs where is the: 1. energy of the reactant 2. transition state energy 3. activation energy ENZYMES CAN ENCOURAGE CATALYSIS IN SEVERAL WAYS. binding E-S: bring substrates together Bring together in closer the proximity reactants binding E-S: electronic rearrangement = favoring a reaction HOW PROTEINS WORK Lysozyme Illustrates How an Enzyme Works Schematic view of the enzyme lysozyme (E), which catalyzes the cutting of a polysaccharide substrate molecule (S). Bacterialises Lysozyme and its Enzymatic Action (1)Lysozyme holds its substrate and puts strain on the glycosidic bonds. Binding a lower energy at activation Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company (2) Lysozyme provide functional groups that act on the substrate (reactant) toward a transition state that favor a reaction. glutamic acidamino and aspartic acid acid and aspartic Example: 2 acidic acids (glutamic acid) with COOH: the carboxyl functional group acts as an acid in acid catalysis To Sum it Up: Lysozyme and Its Enzymatic Action  Lysozyme holds its substrate and puts strain on the glycosidic bonds.  Lysozyme provide functional groups that act on the substrate (reactant) toward a transition state that favor a reaction.  Therefore, conditions are created in the microenvironment of the lysozyme active site that greatly reduce the activation energy necessary for the hydrolysis to take place. HOW PROTEINS WORK Many Drugs Inhibit Enzymes A COMPETITIVE INHIBITOR DIRECTLY BLOCKS SUBSTRATE BINDING TO AN ENZYME. They do not change the maximum Velocity ENZYME INHIBITORS small molecules that can bind to the enzyme and disrupt the reaction competitive or noncompetitive Some drugs act as inhibitors of enzymes. Cyclooxgenases are enzymes involved in prostaglandin synthesis pathway.  Prostaglandins are potent mediators of inflammation. Choy H , and Milas L JNCI J Natl Cancer Inst 2003;95:1440-1452 MOLECULAR MOTORS CONVERT ENERGY INTO MOTION. Specialized proteins that convert energy to motion Cells depend on molecular motors or motor proteins for cellular movements Examples: muscle motor proteins called myosinmuscle contraction kinesin- chromosome movement ATP hydrolysis allows motor proteins to produce directed movements in cells. Proteins like the motor proteins undergo conformational changes. Converts energy released by ATP hydrolysis into a mechanical force that generates a linear or rotary motion. HOW PROTEINS WORK The activity of proteins depends on their ability to bind specifically to other molecules. Enzymes bind to the substrate. Enzymes accelerate reactions by lowering the activation of a reaction. Molecular motors (motor proteins) convert energy into motion; uses ATP hydrolysis which provides energy for conformational changes that allow movement of a protein. HOW PROTEINS WORK Tightly bound small molecules add extra functions to proteins. LEARNING OUTCOMES identify, differentiate and explain mechanisms of protein regulation “why is there a need for protein regulation in cells?” identify amino acids S,T,Y and identify their role in protein regulation PROTEIN REGULATION Why is there a need for regulation? How are proteins controlled or regulated? WHY IS THERE A NEED FOR REGULATION? to conserve energy and resources there are adjustments that help cells produce what is only required no more no less a very good control point will be enzyme activity because the enzymes are the ones that control the chemical reactions in the cells that make or degrade the resources/molecules. PROTEIN REGULATION How are proteins controlled? Allosteric control o feedback inhibition Covalent modification o phosphorylation o regulatory GTP-binding proteins are switched on and off by the gain and loss of a phosphate group interaction of proteins with other groups CATALYTIC ACTIVITIES ARE OFTEN REGULATED BY OTHER MOLECULES: ALLOSTERIC CONTROL. These molecules are called allosteric molecules. The most common mode of control. Here, a molecule other than a substrate binds to the enzyme. o It alters the rate at which the enzyme converts substrate to product. ALLOSTERIC CONTROL binding to a site in the enzyme called allosteric site causes a conformational change Another Example:  Does this example show an allosteric inhibitor or an allosteric activator?  Is this an example of a negative allosteric control? ALLOSTERIC CONTROL FEEDBACK INHIBITION an enzyme acting early in the pathway is inhibited by a late product of the pathway If C is high  Control of an enzyme early in the pathway prevents wasteful buildup of intermediates. If [Z] is high HOW PROTEINS ARE CONTROLLED Allosteric enzymes have two or more binding sites that influence one another. Feedback inhibition triggers a conformational change in an enzyme. ALLOSTERIC CONTROL POSITIVE REGULATION  The binding of a regulatory ligand can change the equilibrium between two protein conformations. HOW PROTEINS ARE CONTROLLED Phosphorylation can control protein activity by causing a conformational change. Protein phosphorylation is a very common mechanism for regulating protein activity. Phosphorylation can either increase or decrease the protein’s activity, depending on the site of phosphorylation and the structure of the protein. Proteins can be regulated via covalent modification common method:  protein phosphorylation and dephosphorylation  accomplished by kinases and phosphatases protein enzymes that add or remove phosphate from Serines (S), Threonines (T) and Tyrosines (Y) HOW PROTEINS ARE CONTROLLED Regulatory GTP-binding proteins are switched on and off by the gain and loss of a phosphate group. Many different GTPbinding proteins function as molecular switches. HOW PROTEINS ARE CONTROLLED Covalent modifications also control the location and interaction of proteins. HOW PROTEINS ARE CONTROLLED Proteins often form large complexes that function as machines. The movement of proteins is often coordinated and made unidirectional by the hydrolysis of a bound nucleotide such as ATP. HOW PROTEINS ARE CONTROLLED These machines are made of individual proteins that collaborate to perform a specific task. Conformational changes of this type are especially useful to the cell if they occur in a large protein assembly in which the activities of several different protein molecules can be coordinated by the movements within the complex, as schematically illustrated here. HOW PROTEINS ARE CONTROLLED Many interacting proteins are brought together by scaffolds. Scaffold proteins can concentrate interacting holding proteins in the cell. or a bunch proteins HOW PROTEINS ARE CONTROLLED Weak interactions between macromolecules can produce large biochemical subcompartments in cells. can also bind with molecules other Intracellular condensates can form biochemical subcompartments in cells. HOW PROTEINS ARE CONTROLLED The catalytic activities of enzymes are often regulated by other molecules. Allosteric enzymes have two or more binding sites that influence one another. Phosphorylation can control protein activity by causing a conformational change. Covalent modifications also control the location and interaction of proteins. HOW PROTEINS ARE CONTROLLED Regulatory GTP-binding proteins are switched on and off by the gain and loss of a phosphate group Proteins often form large complexes that function as machines. ATP hydrolysis allows machines to produce directed movements in cells. Many interacting proteins are brought together by scaffolds. Weak interactions between macromolecules can produce large biochemical subcompartments in cells. THE SHAPE AND STRUCTURE OF PROTEINS Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages polypeptide Disulfide bonds help stabilize a favored protein conformation. insidethee condition Disulfide linkaa Fold into secondary and tertiary Structure will be maintained by noncovalent Forces HOW PROTEINS ARE STUDIED Proteins can be purified from cells or tissues Determining a protein’s structure begins with determining its amino acid sequence Genetic engineering techniques permit the large-scale production, design, and analysis of almost any protein The relatedness of proteins aids the prediction of protein structure and function HOW PROTEINS ARE STUDIED Proteins can be purified from cells or tissues. CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS : Velocity Sedimentation distribution on the basis of size CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS Density gradient distribution : on the basis of density some more Polar negatively charge acids amino Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company alows OV separation /proteins molecules Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company correct answer is C from the pic Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Enzymes how - Subtrates enzume to separate Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company will not Differenceo charge but DC by size most mobile will reach the bottom Faster less mobilea Bigger mostile Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company HOW PROTEINS ARE STUDIED Determining a protein’s structure begins with determining its amino acid sequence = primary structure Typical techniques for determining structures of a protein: X-ray crystallography NMR spectroscopy Cryo-electron microscopy Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company HOW PROTEINS ARE STUDIED Genetic engineering techniques permit the largescale production, design, and analysis of almost any protein. Biotechnology companies produce mass quantities of useful proteins. HOW PROTEINS ARE STUDIED Proteins can be purified from cells or tissues. Determining a protein’s structure begins with determining its amino acid sequence. Genetic engineering techniques permit the largescale production, design, and analysis of almost any protein. The relatedness of proteins aids the prediction of protein structure and function.