DOCSLIB.ORG

MCAT Psychology, Potomac Watch -The Insula of the Brain Is Implicated in Conscious Urges and Emotions

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
MCAT Psychology, Potomac Watch -The Insula of the Brain Is Implicated in Conscious Urges and Emotions MCAT Psychology, Potomac Watch -The insula of the brain is implicated in conscious urges and emotions. Therefore smokers with brain damage involving the insula would be more likely to quit smoking more easily without relapse than smokers without brain damage to the insula -Avolition, Avolition amounts to the overall lack of drive to perform activities and pursue objectives. For example, people with this symptom may not have the will to run errands or perform a task, even when those tasks will bring obvious advantages to their lives (e.g., cooking). It is thus a negative symptom -An allosteric enzyme has a site other than the one for the substrate at which a molecule (not the substrate) that directs the function of the enzyme can bind -oxygen in H2O is δ- and thus will be attracted to a δ+ atom. The carbon double bonded to the nitrogen must be δ+ -First, exactly why is DNA negatively charged? The reason why DNA is negatively charged is the phosphate group that makes up every nucleotide (pentose + nitrogenous base + phosphate). When forming part of the phosphodiester bond, the phosphate group (circled in blue below) retains 1 of 2 negatively charges (the other being lost to form the other ester bond to a new pentose, which is the reason for the name "phospho-di-ester") Brain Functioning Heart Physics Senses, Eyes, Ears, Tongue, Skin Sleep Stages, Radiation Waves Lengths Chemistry Nomenclature (Zcis, Etrans) (R Clockwise, S Counterclockwise) DNA Structure, Amino Acids, DNA Nitrogen Bases (AG, TUC) ATP Cycles, Phosphagen Glycolytic Oxidative Colligative Properties gamma > beta > alpha Homophily, Relationships from Shared Characteristics Avolition amounts to the overall lack of drive to perform activities and pursue objectives. For example, people with this symptom may not have the will to run errands or perform a task, even when those tasks will bring obvious advantages to their lives (e.g., cooking). It is thus a negative symptom Apoptosis is the process of programmed cell death that can occur in multicellular organisms The Stressor, Cognitive and behavioral approaches to the treatment of anxiety disorders usually refer to the stimulus that brings anxiety episodes The zygote, undergoes a split for monozygotic twins, whereas dizygotic twins result from two ova Game Theory, The idea that strictly rational and selfish decisions can be prejudicial for all the parties involved was offered by which cooperation theory? Sex linked, means that the gene in question is present on the X chromosome Adrenaline Which of the following hormones found in the human menstrual cycle are produced in the ovary? 2 And 4 -You must be familiar with the graph of the menstrual cycle in order to know which curve refers to which hormone. There are four hormones involved: luteinizing hormone (LH), follicle- stimulating hormone (FSH), estrogen, and progesterone. If the menstrual cycle is understood well, you should immediately know that both estrogen and progesterone are secreted by the corpus luteum, which comes from the ovary. Alternatively, if the pituitary hormones are known, it is easy to eliminate LH and FSH because they are secreted by the anterior pituitary seminiferous tubules → epididymis → vas deferens Ivas deferens → ejaculatory duct → urethra -Not, gametogenesis → seminal vesicles → seminiferous tubules Why Is DNA Negatively Charged? The answer to this question is based on common electrostatics: opposites attract, like charges repel. This basic idea will come in handy for several questions on the real MCAT, including biochemistry and organic chemistry. Because DNA is negatively charged (due to its phosphate backbone), many of the DNA-binding grooves in proteins tend to be positively charged at physiological pH. Thus residues like arginine, lysine, and histidine are good targets for mutagenesis, as they are more likely to be critical for DNA binding. It should be mentioned that charge is not the only thing that determines the specificity of DNA binding (the shape of the pocket and the overall conformation of the protein are important as well for a variety of reasons, including access), but the presence of positively charged amino acids is common for most DNA- binding pockets Of the 20 common amino acids, at pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) {both acidic side chains}, and three are positively charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) {all 3 basic side chains}. Lysine and arginine are present in answer choice C. You will be seeing electrophoretic gels regularly throughout your MCAT preparation since it is part of the assumed knowledge for the new MCAT. So let’s make sure you understand how to interpret Figure 1, which would lead you to the correct answer. First, exactly why is DNA negatively charged? The reason why DNA is negatively charged is the phosphate group that makes up every nucleotide (pentose + nitrogenous base + phosphate). When forming part of the phosphodiester bond, the phosphate group (circled in blue below) retains 1 of 2 negatively charges (the other being lost to form the other ester bond to a new pentose, which is the reason for the name "phospho-di-ester") -In gel electrophoresis, negatively-charged DNA fragments migrate towards the positively- charged anode (i.e. due to the application of a voltage across the gel; regardless of the voltage, ANions migrate to ANodes). Longer molecules migrate more slowly because they experience more resistance within the gel (typically composed of agarose or a polyacrylamide gel-PAGE). Because the size of the molecule affects its mobility, smaller fragments end up nearer to the anode than longer ones in a given period -The experiment visualizes only the radiolabeled DNA in the gel (which can be seen in 6 lanes). According to the passage (Experiment 1), the DNA fragments used in the 6 wells were all “identical in length”, so why did increasing concentration of XBR lead to the content from 2 wells not migrating in their lanes as far as the controls? There must have been an alteration in charge and/or mass. It is because the protein (XBR) bound to the DNA fragment (= DNA + protein complex) which reduced the negatively charge on DNA in a dose-dependent fashion and added to the mass of the fragment: more XBR, less migration. How could XBR do so? Because of positively-charged amino acids binding to a portion of the negatively charges on DNA. The process is summarized in the following diagram which also includes the presence of ions that are typically released when binding occurs -Affinity does not solely depend on electrostatics but may include, depending on the situation and/or to one degree or another, H-bonding, Van der Waal’s interactions (relatively very, very weak), and the shape of the molecules (e.g. a pocketed/cup-shaped/invaginated site matching a relatively large or protuberant ligand or substrate, leading to the imagery of ‘lock and key’ similar to the image above, but more realistically described as ‘induced fit’). In this particular question, we only have information regarding electrostatics: the attraction of negatively charged to positively charged molecules nitrogen is an integral part of the subunits (nucleotides: BCM 1.5, BIO 1.2.2) that polymerize to form DNA. After part 1 of the experiment, essentially all bacterial DNA will contain the isotope of nitrogen 15N. Thus, the original molecules contain only 15N. By semi-conservative replication in the presence of only 14N (parts 2 and 3 in the experiment), the first new molecules will each contain one strand of 15N (= the parent or template) and one strand of 14N (= the new or daughter strand). In the second replication, the 15N/14N molecule created in the first replication will be separated and used as a template. One strand of 15N will be used as a template for a new 15N/14N molecule, and one strand of 14N will be used as a template for a new molecule that will contain only 14N. This will produce equal amounts of the 15N/14N and the 14N molecules in the second generation. On the Surface: The information provided in the first paragraph applies to all subsequent generations: "The method of DNA replication proposed by James Watson and Francis Crick is known as semi-conservative replication since each new double helix retains one strand of the original DNA double helix". That same formula is applied twice to make 2 generations. So if you have been only growing in N15, you begin with 100% N15. The first generation in N14 produces 100% combinations of N15/N14. Now the 2nd generation, you get 50% N15/N14 and 50% N14/N14. In color, here is N15 in blue and N14 in red (note that the question is asking about the 2nd generation, F2, but just as an academic exercise, we have included the 3rd generation, F3): If conservative replication had occurred, the initial strand, which contained only 15N (see previous question), would not separate to form templates for two new strands (conservative = to resist or oppose change). The replication would produce no DNA molecules containing a mix of the old strand (15N) and the new strand (14N) [see Figure 1]. After one generation there would be the original old strand with 15N and an equal number of new daughter strands with 14N Dispersive replication takes the original molecule and produces two new molecules that are both mixtures of the old and new strands (see Figure 1). Therefore, the centrifuge of a mixture that had replicated in this manner would show only a large band of 15N/14N molecules Which of the following statements could be held LEAST accountable for DNA maintaining its helical structure? -Unwinding the helix would separate the base pairs enough for water molecules to enter between the bases, making the structure unstable -(Not The helix is stabilized by hydrogen bonds between bases, The sugar phosphate backbone is held in place by hydrophilic interactions with the solvent, C–G pairs have three hydrogen bonds between them, but A–T pairs only have two) RNA Polymerase, Which of the following enzymes is most important in RNA synthesis during transcription? -(Not DNA polymerase, RNA replicase, Reverse transcriptase) -You are asked for an enzyme that will help synthesize a chain of RNA.
Load more

Recommended publications
  • Statistical Mechanics of Allosteric Enzymes
    Statistical Mechanics of Allosteric Enzymes Tal Einav,† Linas Mazutis,‡ and Rob Phillips∗,¶ Department of Physics, California Institute of Technology, Pasadena, California 91125, United States, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania, and Department of Applied Physics and Division of Biology, California Institute of Technology, Pasadena, California 91125, United States E-mail: [email protected] Abstract The concept of allostery in which macromolecules switch between two different conforma- tions is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic processes, yet a simple and unified treatment of the effects of allostery in enzymes has been lacking. In this work, we take the first step towards this goal by modeling allosteric enzymes and their interaction with two key molecular players - allosteric regulators and competitive inhibitors. We then apply this model to characterize existing data on enzyme activity, comment on how enzyme parameters (such as substrate binding affinity) can be experimentally tuned, and make novel predictions on how to control phenomena such as substrate inhibition. arXiv:1701.03988v1 [q-bio.SC] 15 Jan 2017 ∗To whom correspondence should be addressed †Department of Physics, California Institute of Technology, Pasadena, California 91125, United States ‡Institute of Biotechnology, Vilnius University, Vilnius, Lithuania ¶Department of Applied Physics and Division of Biology, California Institute
    [Show full text]
  • Lec-08-Handout
    NPTEL VIDEO COURSE – PROTEOMICS PROF. SANJEEVA SRIVASTAVA HANDOUT LECTURE-08 ENZYME: BASIC CONCEPTS, CATALYTIC AND REGULATORY STRATEGIES Slide 1 Today, we will talk about enzyme: basic concepts, catalytic and regulatory strategies. Slide 2 Lecture outline: • Basic concepts of enzyme including enzyme kinetics, energetics and enzyme inhibition. • Different type of catalytic strategies and regulatory strategies. Slide 3 So as you all know, enzymes play very important role in biochemistry All enzymes are proteins therefore it will essential to study about enzymes while studying basic concepts of amino acids and proteins. Although it may not be directly linked to the proteomics but understanding of enzyme and proteins is very fundamental for the advanced understanding of concepts related to proteomics. Slide 4 So what are enzymes? • Enzymes are molecular catalysts. • Almost all enzymes are proteins and as we have discussed in the previous lecture there are twenty amino acids that make up the basic building blocks of all proteins. • Enzymes can accelerate a given reaction up to million folds. Let’s take an example of carbonic anhydrase which catalyzes hydration of carbon di oxide. Now this enzyme can catalyze 106 molecules per second. • Enzymes are highly specific and catalyze single or closely related reaction. DEPARTMENT OF BIOSCIENCES & BIOENGINEERING INDIAN INSTITUTE OF TECHNOLOGY (IIT) BOMBAY, MUMBAI, INDIA Page 1 NPTEL VIDEO COURSE – PROTEOMICS PROF. SANJEEVA SRIVASTAVA Slide 5 In terms of enzyme specificity, let me give you few examples- • Trypsin- it is highly specific, it cleaves peptide on carboxyl side of Lys/Arg. • Another enzyme thrombin, which participates in blood clotting, it is even more specific that trypsin.
    [Show full text]
  • Structure and Evolution of Protein Allosteric Sites
    Structure and evolution of protein allosteric sites by Alejandro Panjkovich Thesis submitted to Universitat Aut`onoma de Barcelona in partial fulfillment of the requirements for the degree of Doctor of Philosophy Director - Prof. Xavier Daura Tesi Doctoral UAB/ANY 2013 Ph.D. Program - Protein Structure and Function Institut de Biotecnologia i Biomedicina caminante, no hay camino, se hace camino al andar Antonio Machado,1912 Acknowledgements First of all I would like to thank my supervisor and mentor Prof. Xavier Daura for his consistent support and trust in my work throughout these years. Xavi, I deeply appreciate the freedom you gave me to develop this project while you were still carefully aware of the small details. Working under your supervision has been a rich and fulfilling experience. Of course, thanks go as well to current and past members of our institute, especially Rita Rocha, Pau Marc Mu˜noz,Oscar Conchillo, Dr. Mart´ınIndarte, Dr. Mario Ferrer, Prof. Isidre Gibert, Dr. Roman Affentranger and Dr. Juan Cedano for their technical and sometimes philo- sophical assistance. Help from the administrative staff was also significant, I would like to thank in particular Eva, Alicia and Miguel who where always ready to help me in sorting out unexpected bureaucratic affairs. I would also like to thank Dr. Mallur Srivatasan Madhusudhan and his group (especially Kuan Pern Tan, Dr. Minh Nguyen and Binh Nguyen), and also Dr. Gloria Fuentes, Cassio Fernandes, Youssef Zaki, Thijs Kooi, Rama Iyer, Christine Low and many others at the Bioinformatics Institute BII - A∗STAR in Singapore for the many interesting discussions and support during my stage over there.
    [Show full text]
  • Metabolism of Glycogen Glycogenesis
    LEC: 10Biochemistry Dr. Anwar J Almzaiel Metabolism of glycogen Glycogen is the major storage form of carbohydrate in animal and corresponds to starch in plant. It occurs mainly in liver (up to 6%) and muscle(up to 1%). However, because of great mass, muscle represents some 3-4 times as much as glycogen store as liver. It is branched polymer of α- glucose. The function of muscle glycogen is to act as a readily available source of hexose units for glycolysis within the muscle itself. Liver glycogen is largely concerned with storage and export of hexose units for maintenance of the blood glucose, particularly between meals. After (12-18 hours) of fasting, the liver becomes almost totally depleted of glycogen, whereas muscle glycogen is only depleted significantly after prolonged various exercise. Why the cell can store glycogen but not glucose? Because when glucose increased, osmatic pressure in the cell increase, causing water movement toward the cell and leading to burst so when glucose accumulates in the cell, it will convert to glycogen which consists of branched series of glucose. Glycogenesis The process of glycogenesis start when glucose-6-phosphat is changed to glucose-1-phosphate by mutase mutas glucose-6-phosphatglucosee 1-phosphate The reaction is reversible and depends on concentration of substrate (glucose- 6-phosphat), if there is a large amount or quantities of glucose-6-phosphat will lead to formation of glucose 1-phosphate and the opposite is right. No loss in the energy in this reaction As glucose 1-phosphate formed, it will react with high energy compound UTP (uradin triphosphate), which react with glucose to give UDP glucose (uradin diphosphate glucose) and pyrophosphate released glucose 1-phosphate is high energetic compound and called (active glucose molecule), this reaction is carried by (UDP glucose pyrophosphorylase) 1 LEC: 10Biochemistry Dr.
    [Show full text]
  • Allosteric Enzymes: Properties and Mechanism | Microbiology
    Allosteric Enzymes: Properties and Mechanism | Microbiology In this article we will discuss about the properties and mechanisms of action of allosteric enzymes. Properties of Allosteric Enzymes: Allosteric or Regulatory enzymes have multiple subunits (Quaternary Structure) and multiple active sites. Allosteric enzymes have active and inactive shapes differing in 3D structure. Allosteric enzymes often have multiple inhibitor or activator binding sites involved in switching between active and inactive shapes. Allosteric enzymes have characteristic “S”-shaped curve for reaction rate vs. substrate concentration. Why? Because the substrate binding is “Cooperative.” And the binding of first substrate at first active site stimulates active shapes, and promotes binding of second substrate. A modulator is a me-tabolite, when bound to the allosteric site of an enzyme, alters its kinetic characteristics. The modulators for allosteric enzyme may be ei-ther stimulatory or inhibitory. A stimulator is often the sub-strate itself. The regulatory enzymes for which substrate and modulator are identical are called homo-tropic. When the modulator has a structure different then the substrate, the enzyme is called heterotropic. Some enzymes have more then one modulators. The allosteric enzymes also have one or more regulatory or aliosteric sites for binding the modulator. Enzymes with several modulators generally have different specific binding sites for each (Fig. 12.15). The sigmoid curve is given by homo-tropic enzymes in which the substrate also serve as a positive (stimulator) modu-lator (12.16). Curve for the non-regulatory enzymes is hy-perbolic, as also predicted by the Michaelis-Menten equa-tion, whereas allosteric en-zymes do not show Michaelis- Menten relationship because their kinetic behaviour is greatly altered by variation in the concentration of modula-tors.
    [Show full text]
  • COOPERATIVITY and ALLOSTERISM Dr. Tijani A. S
    COOPERATIVITY AND ALLOSTERISM Dr. Tijani A. S. Learning Objectives At the end of this topic, the student should be acquainted with: Enzyme Cooperativity Description of Allosterism Models of Allosterism and Kinetics of Allosteric Enzymes Cooperativity Cooperativity is a phenomenon displayed by enzymes or receptors that have multiple binding sites. Cooperativity involves an interconversion of the monomer subunits between a tense form (less active subunits) and a relaxed form (more active subunits). Cooperativity can be positive or negative. Positive cooperativity: ligand binding at one site increases the affinity of the other sites. E. g binding of oxygen to hemoglobin Negative cooperativity the affinity of other sites is decreased by ligand binding to the first site. This concept of transmitted structural changes in the protein, resulting in long- distance communication between sites, has been termed allostery, and enzymes that display these effects are known as allosteric enzymes Cooperativity The first description of cooperative binding to a multi-site protein was developed by A.V. Hill The Sigmoid Plot and the Hill Equation Non-allosteric enzyme V0 = Vmax [S] . Hyperbolic plot Km + [S] . MM Kinetics n n Ý = [L] = [L] n n n Allosteric enzyme Kd + [L] K a + [L] ………..Hill Eqn. Sigmoidal plot . Non MM kinetics n = Hill coefficient (sometimes written as nH ) Value gives a measure of cooperativity n = 1: No cooperativity, graph is hyperbolic n > 1: + ve Cooperativity, sigmoidal curve n < 1: - ve Cooperativity, sigmoidal curve Hill Plot Hill plot" is obtained by plotting log Ý vs log [L] . 1- Ý Hill plot of the Hill equation in red, showing the slope of the curve being the Hill coefficient and the intercept with the x-axis providing the apparent dissociation constant.
    [Show full text]
  • Chapter 6: an Introduction to Proteins
    NAME ________________________________ EXAM III I. __________________/45 November 6, 2000 Biochemistry I II. __________________/35 III. __________________/25 TOTAL /100 I. MULTIPLE CHOICE. (45 points; 3 points each) Choose the BEST answer to the question by circling the appropriate letter. 1. In competitive inhibition, an inhibitor: A. binds at several different sites on an enzyme. B. binds reversibly at the active site. C. binds only to the ES complex. D. binds covalently to the enzyme. E. lowers the characteristic Vmax of the enzyme. 2. In a plot of l/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the: A. Vmax. B. intercept on the l/V axis. C. intercept on the l/[S] axis. D. curvature of the plot. E. pK of the plot. 3. Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its Vmax when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that: A. a residue with a pKa of 6.4 is involved in binding B. a His residue on the enzyme is involved in the reaction. C. a Glu residue on the enzyme is involved in the reaction. D. the enzyme is found in gastric secretions. E. the enzyme has a metallic cofactor. 4. An average protein will not be denatured by: A. sodium dodecyl sulfate. B. pH 10. C. heating to 90 °C. D. urea. E. iodoacetic acid. 5. Which of the following is false about the catalytic mechanism of acetoacetate decarboxylase? A.
    [Show full text]
  • Is Allostery an Intrinsic Property of All Dynamic Proteins?
    PROTEINS: Structure, Function, and Bioinformatics 57:433–443 (2004) REVIEW Is Allostery an Intrinsic Property of All Dynamic Proteins? K. Gunasekaran,1 Buyong Ma,1 and Ruth Nussinov1,2* 1Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, National Cancer Institute-Frederick, Bldg 469, Rm 151, Frederick, Maryland 2Sackler Institute of Molecular Medicine, Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel ABSTRACT Allostery involves coupling of con- positive feedback regulation or negative inhibition.1–4 In formational changes between two widely separated 1965, Monod et al. analyzed 24 allosteric enzyme systems binding sites. The common view holds that alloste- and proposed a “plausible model on the nature of allosteric ric proteins are symmetric oligomers, with each transition” (the “concerted” or “MWC” model).5 The propo- subunit existing in “at least” two conformational sition was inspired by the observation of two conforma- states with a different affinity for ligands. Recent tional states of deoxy- and oxyhemoglobin. The MWC observations such as the allosteric behavior of myo- model suggested that allosteric proteins are symmetric globin, a classical example of a nonallosteric pro- oligomers with identical protomers. Each protomer exists tein, call into question the existing allosteric dogma. in “at least” two conformational states (tense, T; relaxed, Here we argue that all (nonfibrous) proteins are R) with different affinities for ligands.5 The basic assump- potentially allosteric. Allostery is a consequence of tion of the model is that the protein interconverts between re-distributions of protein conformational en- two conformations, R and T, in a concerted manner.
    [Show full text]
  • Enzyme & Coenzyme
    King Saud University Foundation Block Enzyme & Coenzyme Lecture 7 + 8 Color Index: Important ⇒ Red Explanation ⇒ Orange Additional ⇒ Purple Mind Map that محفز They are biological catalysts - speed up the rate of a reaction without being consumed by the reaction. - All enzymes are proteins, but not all proteins are enzymes. Substrate is the substance that enzymes act on, and convert it into products. Classification of Enzymes Enzymes are classified into 6 classes according to the reaction catalyzed Classification Type of Reaction Catalyzed 1 Oxidoreductases Oxidation-Reduction reactions 2 Transferases Transfer of functional groups 3 Hydrolases Hydrolysis reaction 4 Lyases Group elimination to form double bonds 5 Isomerases Isomerization 6 Ligases Bond formation + ATP hydrolysis Enzyme Nomenclature (Naming) Enzyme Nomenclature is based on the rules given by EC 3.4.17.1 (Carboxypeptidase) IUBMB (International Union of Biochemistry and EC = Enzyme Commission Molecular Biology. Class.subclass.subsubclass.Enzyme number Properties of Enzymes Active Site Regulation Specificity - The region of - Enzymes can be - Enzymes bind to enzyme that binds activated or their specific with substrate inhibited so that substrates in the the rate of product active site to - Where Catalysis formation convert them to occur responds to the products need of the cell. - All enzymes have - Enzymes are 1 or more active highly specific sites - They interact with only one or few substrates - Catalyze only one reaction Enzyme-Substrate Binding Lock and Key Binding Induces Fit Binding The enzyme has an active site In this case, after binding to the that fits the exact dimensions of substrate, the enzyme changes its the substrate.
    [Show full text]
  • Lecture 7: 9/7 Kinetics and Regulation
    Lecture 7: 9/7 CHAPTER 7 Kinetics and Regulation Chapter 7 Outline The rate or velocity of an enzymatic reaction Consider a simple reaction: The velocity or rate of the reaction is determined by measuring how much A disappears as a function of time or how much B appears as a function of time. Suppose that we can readily measure the disappearance of A. The velocity of the reaction is given by the formula below, where k is a proportionality constant. When the velocity of a reaction is directly proportional to reactant concentration, the reaction is called a first‐order reaction and the proportionality constant has the units s‐1. Many important biochemical reactions are biomolecular or second‐order reactions. or The rate equations for these reactions are: and The proportionality constant for second‐order reactions has the units M‐1s‐1. A common means of investigating enzyme kinetics to measure velocity as a function of substrate concentration with a fixed amount of enzyme. Consider a simple reaction in which the enzyme E catalyzes the conversion of SP. with k1, k2 being the rate constant for the indicated reaction steps. So as to ignore the reverse reaction of PS, we measure activity when [P] ≈ 0. Under these conditions, the velocity is called the initial velocity or Vo. Reaction velocity versus substrate concentration in an enzyme‐catalyzed reaction An enzyme‐catalyzed reaction approaches a maximal velocity when the enzyme is saturated with substrate. The initial velocity is determined by measuring product formation as a function of time, and then determining the velocity soon after the reaction has started.
    [Show full text]
  • Modulating Protein Activity Using Tethered Ligands with Mutually Exclusive Binding Sites
    ARTICLE Received 28 Nov 2014 | Accepted 16 Jun 2015 | Published 22 Jul 2015 DOI: 10.1038/ncomms8830 OPEN Modulating protein activity using tethered ligands with mutually exclusive binding sites Alberto Schena1,2,3,*, Rudolf Griss1,2,3,* & Kai Johnsson1,2,3 The possibility to design proteins whose activities can be switched on and off by unrelated effector molecules would enable applications in various research areas, ranging from biosensing to synthetic biology. We describe here a general method to modulate the activity of a protein in response to the concentration of a specific effector. The approach is based on synthetic ligands that possess two mutually exclusive binding sites, one for the protein of interest and one for the effector. Tethering such a ligand to the protein of interest results in an intramolecular ligand–protein interaction that can be disrupted through the presence of the effector. Specifically, we introduce a luciferase controlled by another protein, a human carbonic anhydrase whose activity can be controlled by proteins or small molecules in vitro and on living cells, and novel fluorescent and bioluminescent biosensors. 1 E´cole Polytechnique Fe´de´rale de Lausanne, Institute of Chemical Sciences and Engineering, Avenue Forel 2, EPFL SB ISIC LIP BCH-4303, CH-1015 Lausanne, Switzerland. 2 E´cole Polytechnique Fe´de´rale de Lausanne, Institute of Bioengineering, CH-1015 Lausanne, Switzerland. 3 National Centre of Competence in Research in Chemical Biology, CH-1015 Lausanne, Switzerland. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to K.J. (email: kai.johnsson@epfl.ch).
    [Show full text]
  • Bioreaction Kinetics 2
    BioreactionBioreactionBioreactionKineticsKinetics Kinetics 222 20042004 SeungwookSeungwookKim Kim Chem.Chem. && Bio.Bio. Eng.Eng. ReferenceReference z Chemistry and the Living Organism, 6th edition, Molly M. Bloomfield, Lawrence J. Stephens, John Wiley & Sons, Inc. EnzymesEnzymes 1. Most enzymes are protein catalysts in biological systems. 2. For an enzyme to catalyze a reaction, the substrate must attach to the surface of the enzyme in a region called the active site. 3. Enzyme activity can be inhibited in several ways. 4. Metabolic processes are the result of sequences of enzyme-catalyzed reactions called multienzyme systems. 5. Enzyme activity in an organism is regulated at many levels, both inside and outside the cell. WhatWhat IsIs Metabolism?Metabolism? z Metabolism : all the enzyme-catalyzed reactions in the cell. z Two types { Catabolic reactions : Molecules are broken down to produce smaller molecules and energy. { Anabolic reactions (Biosynthetic reaction) : The cell uses energy to produce the molecules it needs for growth and repair. EnzymesEnzymes (Biological(Biological catalysts)catalysts) z The largest and most highly specialized class of proteins. z Water-soluble globular proteins that carry out their functions in body fluids or bound to the membranes of the cell. z Molecular weight from 12,000 to over 1 million. z A simple single polypeptide chain or a more complex molecule composed of several polypeptide chains and other nonprotein parts. z Examples { Ribonuclease : A single polypeptide chain of 124 aa Molecular mass: About 13,700 daltons(1 dalton = 1 amu) { Pyruvate dehydrogenase : Macromolecular complex containing 42 individual molecules Molecular mass: About 10 million daltons Important terms used in the study of enzymes.
    [Show full text]