DOCSLIB.ORG

Ch.04Carbon and the Molecular Diversity of Life

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ch.04Carbon and the Molecular Diversity of Life EXPERIMENT “Atmosphere” CH4 Water vapor Electrode Molecular Structural Ball-and-Stick Space-Filling Name Formula Formula Model Model NH 3 H 2 (a) Methane Condenser Cooled water (b) Ethane containing Cold organic water molecules (c) Ethene (ethylene) H2O “sea” Sample for chemical analysis 1 2 Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C Urea 3 4 Fat droplets (stained red) Ethane Propane 1-Butene 2-Butene (a) Length (c) Double bonds Butane 2-Methylpropane (commonly called isobutane) Cyclohexane Benzene (b) Branching (d) Rings 100 µm (a) Mammalian adipose cells (b) A fat molecule 5 6 Effective Ineffective Drug Condition Pentane 2-methyl butane Enantiomer Enantiomer (a) Structural isomers Ibuprofen Pain; inflammation cis isomer: The two Xs are trans isomer: The two Xs are S-Ibuprofen R-Ibuprofen on the same side. on opposite sides. (b) Geometric isomers Albuterol Asthma R-Albuterol S-Albuterol L isomer D isomer (c) Enantiomers 7 8 Estradiol Testosterone L-dopa D-dopa 9 10 CHEMICAL Hydroxyl Carbonyl Carboxyl CHEMICAL Amino Sulfhydryl Phosphate Methyl GROUP GROUP (may be STRUCTURE STRUCTURE written HS—) (may be written HO—) The amino group The sulfhydryl group In a phosphate group, a A methyl group consists of a In a hydroxyl group (—OH), a The carbonyl group ( CO) When an oxygen atom is (—NH2) consists of a consists of a sulfur atom phosphorus atom is bonded to carbon bonded to three hydrogen atom is bonded to an consists of a carbon atom double-bonded to a carbon nitrogen atom bonded bonded to an atom of four oxygen atoms; one oxygen hydrogen atoms. The methyl oxygen atom, which in turn is joined to an oxygen atom by a atom that is also bonded to to two hydrogen atoms hydrogen; resembles a is bonded to the carbon skeleton; group may be attached to a and to the carbon hydroxyl group in shape. two oxygens carry negative carbon or to a different atom. bonded to the carbon skeleton of double bond. an —OH group, the entire skeleton. charges. The phosphate group the organic molecule. (Do not assembly of atoms is called 2– (—OPO3 , abbreviated P ) is an confuse this functional group a carboxyl group (—COOH). ionized form of a phosphoric acid – 2 with the hydroxide ion, OH .) group (—OPO3H ; note the two hydrogens). NAME OF Alcohols (their specific names Ketones if the carbonyl group is Carboxylic acids, or organic NAME OF Amines Thiols Organic phosphates Methylated compounds COMPOUND usually end in -ol) within a carbon skeleton acids COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE EXAMPLE Glycine Glycerol phosphate Ethanol, the alcohol present in Acetone, the simplest ketone Acetic acid, which gives vinegar Because it also has a Cysteine alcoholic beverages its sour taste In addition to taking part in carboxyl group, glycine many important chemical 5-Methyl cytidine is both an amine and Cysteine is an important reactions in cells, glycerol a carboxylic acid; sulfur-containing amino 5-Methyl cytidine is a compounds with both phosphate provides the acid. backbone for phospholipids, component of DNA that has groups are called been modified by addition of amino acids. the most prevalent molecules in Propanal, an aldehyde cell membranes. the methyl group. FUNCTIONAL Is polar as a result of the A ketone and an aldehyde may Has acidic properties FUNCTIONAL Acts as a base; can Two sulfhydryl groups Contributes negative charge Addition of a methyl group PROPERTIES electrons spending more time be structural isomers with because the covalent bond PROPERTIES pick up an H+ from can react, forming a to the molecule of which it is to DNA, or to molecules near the electronegative different properties, as is the between oxygen and hydrogen the surrounding covalent bond. This a part (2– when at the end of bound to DNA, affects oxygen atom. case for acetone and propanal. is so polar; for example, solution (water, in “cross-linking” helps a molecule; 1– when located expression of genes. living organisms). stabilize protein internally in a chain of Can form hydrogen bonds with These two groups are also structure. phosphates). Arrangement of methyl water molecules, helping found in sugars, giving rise to groups in male and female dissolve organic compounds two major groups of sugars: Cross-linking of Has the potential to react sex hormones affects such as sugars. aldoses (containing an cysteines in hair with water, releasing energy. their shape and function. aldehyde) and ketoses proteins maintains the (containing a ketone). curliness or straightness Acetic acid Acetate ion (nonionized) (ionized) of hair. Straight hair can be “permanently” curled Found in cells in the ionized Ionized, with a by shaping it around form with a charge of 1– and charge of 1+, under curlers, then breaking called a carboxylate ion (here, cellular conditions. and re-forming the specifically, the acetate ion). cross-linking bonds. 11 12 Reacts with H2O P P P Adenosine P i P P Adenosine Energy ATP Inorganic ADP phosphate 13 .
Load more

Recommended publications
  • Direct Β‑Functionalization of Cyclic Ketones with Aryl Ketones Via the Merger of Photoredox and Organocatalysis Filip R
    Communication pubs.acs.org/JACS Direct β‑Functionalization of Cyclic Ketones with Aryl Ketones via the Merger of Photoredox and Organocatalysis Filip R. Petronijevic,́† Manuel Nappi,† and David W. C. MacMillan* Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States *S Supporting Information ABSTRACT: The direct β-coupling of cyclic ketones with aryl ketones has been achieved via the synergistic combination of photoredox catalysis and organocatalysis. Diaryl oxymethyl or aryl−alkyl oxymethyl radicals, transiently generated via single-electron reduction of ketone precursors, readily merge with β-enaminyl radical species, generated by photon-induced enamine oxidation, to produce γ-hydroxyketone adducts. Experimental evidence indicates that two discrete reaction pathways can be operable in this process depending upon the nature of the ketyl radical precursor and the photocatalyst. he direct β-functionalization of saturated ketones and T aldehydes is an important yet elusive goal in organic chemistry.1 While carbonyl groups are readily amenable to ipso- and α-carbon substitution with a range of nucleophiles and electrophiles respectively,2,3 activation at the β-methylene position poses a significant synthetic challenge. With a few notable exceptions,1,4 carbonyl β-functionalization has tradition- ally been restricted to the conjugate addition of soft nucleophiles are accessed via carbene catalysis,9,10 nucleophilic addition of into α,β-unsaturated carbonyl systems. As such, the development acetal-protected Grignard reagents,11 or stoichiometric metal- 5 − of a general catalytic platform for the direct β-functionalization activated homoenolate equivalents.12 16 of saturated ketones or aldehydes would represent a conceptual Drawing from the mechanistic insights gained in the course of and practical advance for the field.
    [Show full text]
  • Chapter 21 the Chemistry of Carboxylic Acid Derivatives
    Instructor Supplemental Solutions to Problems © 2010 Roberts and Company Publishers Chapter 21 The Chemistry of Carboxylic Acid Derivatives Solutions to In-Text Problems 21.1 (b) (d) (e) (h) 21.2 (a) butanenitrile (common: butyronitrile) (c) isopentyl 3-methylbutanoate (common: isoamyl isovalerate) The isoamyl group is the same as an isopentyl or 3-methylbutyl group: (d) N,N-dimethylbenzamide 21.3 The E and Z conformations of N-acetylproline: 21.5 As shown by the data above the problem, a carboxylic acid has a higher boiling point than an ester because it can both donate and accept hydrogen bonds within its liquid state; hydrogen bonding does not occur in the ester. Consequently, pentanoic acid (valeric acid) has a higher boiling point than methyl butanoate. Here are the actual data: INSTRUCTOR SUPPLEMENTAL SOLUTIONS TO PROBLEMS • CHAPTER 21 2 21.7 (a) The carbonyl absorption of the ester occurs at higher frequency, and only the carboxylic acid has the characteristic strong, broad O—H stretching absorption in 2400–3600 cm–1 region. (d) In N-methylpropanamide, the N-methyl group is a doublet at about d 3. N-Ethylacetamide has no doublet resonances. In N-methylpropanamide, the a-protons are a quartet near d 2.5. In N-ethylacetamide, the a- protons are a singlet at d 2. The NMR spectrum of N-methylpropanamide has no singlets. 21.9 (a) The first ester is more basic because its conjugate acid is stabilized not only by resonance interaction with the ester oxygen, but also by resonance interaction with the double bond; that is, the conjugate acid of the first ester has one more important resonance structure than the conjugate acid of the second.
    [Show full text]
  • Metabolic-Hydroxy and Carboxy Functionalization of Alkyl Moieties in Drug Molecules: Prediction of Structure Influence and Pharmacologic Activity
    molecules Review Metabolic-Hydroxy and Carboxy Functionalization of Alkyl Moieties in Drug Molecules: Prediction of Structure Influence and Pharmacologic Activity Babiker M. El-Haj 1,* and Samrein B.M. Ahmed 2 1 Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, University of Science and Technology of Fujairah, Fufairah 00971, UAE 2 College of Medicine, Sharjah Institute for Medical Research, University of Sharjah, Sharjah 00971, UAE; [email protected] * Correspondence: [email protected] Received: 6 February 2020; Accepted: 7 April 2020; Published: 22 April 2020 Abstract: Alkyl moieties—open chain or cyclic, linear, or branched—are common in drug molecules. The hydrophobicity of alkyl moieties in drug molecules is modified by metabolic hydroxy functionalization via free-radical intermediates to give primary, secondary, or tertiary alcohols depending on the class of the substrate carbon. The hydroxymethyl groups resulting from the functionalization of methyl groups are mostly oxidized further to carboxyl groups to give carboxy metabolites. As observed from the surveyed cases in this review, hydroxy functionalization leads to loss, attenuation, or retention of pharmacologic activity with respect to the parent drug. On the other hand, carboxy functionalization leads to a loss of activity with the exception of only a few cases in which activity is retained. The exceptions are those groups in which the carboxy functionalization occurs at a position distant from a well-defined primary pharmacophore. Some hydroxy metabolites, which are equiactive with their parent drugs, have been developed into ester prodrugs while carboxy metabolites, which are equiactive to their parent drugs, have been developed into drugs as per se.
    [Show full text]
  • Methyl Substitution Effects on the Proton Chemical Shifts in Benzene *
    Methyl Substitution Effects on the Proton Chemical Shifts in Benzene * G. S. REDDY E. I. du Pont de Nemours & Company, Inc. Explosives Department, Eastern Laboratory, Gibbstown, New Jersey, U.S.A. (Z. Naturforschg. 21 a, 609—615 [1966] ; received 16 December 1965) Methyl substitution effects on aromatic and methyl proton chemical shifts in several mono-, di-, and trimethyl benzenes are studied. A new method for obtaining the changes in the ring proton chemical shifts from those of methyl proton shifts at the corresponding positions is used. The extra jr-electron densities in toluene are calculated using the already known relation between the jr-elec- tron densities and the proton shifts in aromatic systems. An inverse relationship is obtained between the ionization potentials and the total methyl effects on the chemical shifts in this series of com- pounds as one would expect. Dipole moment of toluene is calculated, and a reasonably good agree- ment is found between the experimentally observed and the calculated dipole moment. Several efforts have been made from time to Considerable work has also been done in estimat- time to study the substitution effects on chemical ing ir-electron densities from chemical shift meas- shifts and coupling constants. One of the earliest urements in unsaturated systems. This study in- attempts in this line are those of CAVANAUGH and volves extension of the substitution effects and also DAILEY 1 who tried to study the effect of multiple estimating jr-electron densities in methyl benzenes. methyl substitution in methane. They encountered Eight mono-, di-, and trimethyl substituted benzenes negative shifts contrary to expectations based on have been studied, and a new technique has been inductive and hyperconjugative effects of the methyl deployed to obtain the methyl substitution effects group which eventually was attributed to the an- on the chemical shifts of ring protons from proton isotropy effect of the added C — C bonds 2-7.
    [Show full text]
  • Aldehydes and Ketones
    12 Aldehydes and Ketones Ethanol from alcoholic beverages is first metabolized to acetaldehyde before being broken down further in the body. The reactivity of the carbonyl group of acetaldehyde allows it to bind to proteins in the body, the products of which lead to tissue damage and organ disease. Inset: A model of acetaldehyde. (Novastock/ Stock Connection/Glow Images) KEY QUESTIONS 12.1 What Are Aldehydes and Ketones? 12.8 What Is Keto–Enol Tautomerism? 12.2 How Are Aldehydes and Ketones Named? 12.9 How Are Aldehydes and Ketones Oxidized? 12.3 What Are the Physical Properties of Aldehydes 12.10 How Are Aldehydes and Ketones Reduced? and Ketones? 12.4 What Is the Most Common Reaction Theme of HOW TO Aldehydes and Ketones? 12.1 How to Predict the Product of a Grignard Reaction 12.5 What Are Grignard Reagents, and How Do They 12.2 How to Determine the Reactants Used to React with Aldehydes and Ketones? Synthesize a Hemiacetal or Acetal 12.6 What Are Hemiacetals and Acetals? 12.7 How Do Aldehydes and Ketones React with CHEMICAL CONNECTIONS Ammonia and Amines? 12A A Green Synthesis of Adipic Acid IN THIS AND several of the following chapters, we study the physical and chemical properties of compounds containing the carbonyl group, C O. Because this group is the functional group of aldehydes, ketones, and carboxylic acids and their derivatives, it is one of the most important functional groups in organic chemistry and in the chemistry of biological systems. The chemical properties of the carbonyl group are straightforward, and an understanding of its characteristic reaction themes leads very quickly to an understanding of a wide variety of organic reactions.
    [Show full text]
  • Aldehydes and Ketone
    ALDEHYDES AND KETONE www.gneet.com ALDEHYDES AND KETONES In aldehydes, the carbonyl group is linked to either two hydrogen atom or one hydrogen atom and one carbon containing group such as alkyl, aryl or aralkyl group Examples * In ketones, the carbonyl group is linked to two carbon containing groups which may be same or different alkyl, aryl group. If two R and R’ groups are same, the ketone is called simple or symmetrical ketone and if R and R’ are different, then ketone is known as mixed or an unsymmetrical ketone. STRUCTURE Carbonyl carbon of both aldehyde and ketones is sp2 – hybridised, One of the three sp2 hybridised orbital get involved in σ- bond formation with half –filled p-orbital of oxygen atom whereas rest of the two are consumed in σ-bond formation with hydrogen and carbon depending on the structure of aldehyde or ketone. Unhybridised p-orbital of carbonyl carbon form π-bond with another half-filled p-orbital of oxygen atom by sideways overlapping. ISOMERISM IN ALDEHYDES AND KETONES (a) Chain isomerism: Aldehydes ( with 4 or more carbon atoms) and ketone ( with 5 or more carbon atoms) show chain isomerism. Example i) C4H8O CH3-CH2-CH2-CHO ( butanal) 1 ALDEHYDES AND KETONE www.gneet.com ii) C5H10O (b) Position isomerism: aliphatic aldehydes do not show position isomerism, because –CHO group is always present at the end of carbon chain. Aromatic aldehyde show position isomerism. Example (c) Metamerism: Higher ketones show metamerism due to presence of different alkyl groups attached to the same functional group C5H10O (d) Functional isomerism : Aldehydes and ketones show functional isomerism in them.
    [Show full text]
  • Chapter 14 – Aldehydes and Ketones
    Chapter 14 – Aldehydes and Ketones 14.1 Structures and Physical Properties of Aldehydes and Ketones Ketones and aldehydes are related in that they each possess a C=O (carbonyl) group. They differ in that the carbonyl carbon in ketones is bound to two carbon atoms (RCOR’), while that in aldehydes is bound to at least one hydrogen (H2CO and RCHO). Thus aldehydes always place the carbonyl group on a terminal (end) carbon, while the carbonyl group in ketones is always internal. Some common examples include (common name in parentheses): O O H HH methanal (formaldehyde) trans-3-phenyl-2-propenal (cinnamaldehyde) preservative oil of cinnamon O O propanone (acetone) 3-methylcyclopentadecanone (muscone) nail polish remover a component of one type of musk oil Simple aldehydes (e.g. formaldehyde) typically have an unpleasant, irritating odor. Aldehydes adjacent to a string of double bonds (e.g. 3-phenyl-2-propenal) frequently have pleasant odors. Other examples include the primary flavoring agents in oil of bitter almond (Ph- CHO) and vanilla (C6H3(OH)(OCH3)(CHO)). As your book says, simple ketones have distinctive odors (similar to acetone) that are typically not unpleasant in low doses. Like aldehydes, placing a collection of double bonds adjacent to a ketone carbonyl generally makes the substance more fragrant. The primary flavoring agent in oil of caraway is just a such a ketone. 2 O oil of carraway Because the C=O group is polar, small aldehydes and ketones enjoy significant water solubility. They are also quite soluble in typical organic solvents. 14.2 Naming Aldehydes and Ketones Aldehydes The IUPAC names for aldehydes are obtained by using rules similar to those we’ve seen for other functional groups (e.g.
    [Show full text]
  • Carbonyl Compounds
    CARBONYL COMPOUNDS PART-4, PPT-4, SEM-3 Dr. Kalyan Kumar Mandal Associate Professor St. Paul’s C. M. College Kolkata CONTENTS: CARBONYL COMPOUNDS PART-4 • Formation of Acetal/Ketal • Formation of Thioacetal Reaction of Carbonyl Compounds with Alcohols • Carbonyl compounds react with alcohols. The product of this reaction is known as a hemiacetal, because it is halfway to an acetal. This reaction is analogous to hydrate formation from aldehydes and ketones. The mechanism follows in the footsteps of hydrate formation: ROH is used instead of HOH (water). This Lecture is prepared by Dr. K. K. Mandal, SPCMC, Kolkata Formation of Cyclic Hemiacetal • Hemiacetal formation is reversible, and they are stabilized by the same special structural features as those of hydrates. However, hemiacetals can also gain stability by being cyclic. • Cyclic hemiacetal is formed when the carbonyl group and the attacking hydroxyl group are part of the same molecule. The reaction is an intramolecular (within the same molecule) addition, as opposed to the intermolecular (between two molecules) ones. This is an example of ring-chain tautomerism. This Lecture is prepared by Dr. K. K. Mandal, SPCMC, Kolkata Formation of Cyclic Hemiacetal • Although the cyclic hemiacetal is more stable, it is still in equilibrium with some of the open-chain hydroxyaldehyde form. Its stability, and how easily it forms, depend on the size of the ring. • Five- and six-membered rings involve less strain (their bonds are free to adopt 109° or 120° angles) in comparison to the three- membered rings, and therefore five or six-membered hemiacetals are very common.
    [Show full text]
  • Functional Groups Kimberly Hatch Harrison
    Functional Groups Kimberly Hatch Harrison Functional groups are those small chemical species you see hanging off the outside of a molecule. Just a handful of these functional groups de- termine most of the chemical reactions that happen between biological molecules. If you memorize the chemical behavior of these functional groups, you’ll be able to predict what kinds of reactions biological molecules can do. You can’t open a lock with a screwdriver–the shape of a screwdriver is quite different from a key, which means it has a dif- ferent function. "Form determines function" is something you’ll hear over and over in biochemistry, and that’s because it’s true. The over- all 3-dimensional shape of a molecule allows it to fit into another molecule, like how a key fits into a lock. But not all keys are the same. You have to look closely at the teeth of a key to see which lock it can open. Similarly, you need to look at the details of the outside of a molecule to understand what kinds of chemical interactions it can do with other molecules. How the carbon skeleton of a biological molecule is folded up de- termines its general 3D shape. So that’s one level of understanding– this molecule looks like a key, this one looks like a lock, etc. But then you must look closer, at the surface details, to understand exactly which key, exactly what kind of lock. When you examine the outside of a biological molecule, you can identify which functional groups are standing out on its surface, like little flags.
    [Show full text]
  • Reactions of Aromatic Compounds Just Like an Alkene, Benzene Has Clouds of  Electrons Above and Below Its Sigma Bond Framework
    Reactions of Aromatic Compounds Just like an alkene, benzene has clouds of electrons above and below its sigma bond framework. Although the electrons are in a stable aromatic system, they are still available for reaction with strong electrophiles. This generates a carbocation which is resonance stabilized (but not aromatic). This cation is called a sigma complex because the electrophile is joined to the benzene ring through a new sigma bond. The sigma complex (also called an arenium ion) is not aromatic since it contains an sp3 carbon (which disrupts the required loop of p orbitals). Ch17 Reactions of Aromatic Compounds (landscape).docx Page1 The loss of aromaticity required to form the sigma complex explains the highly endothermic nature of the first step. (That is why we require strong electrophiles for reaction). The sigma complex wishes to regain its aromaticity, and it may do so by either a reversal of the first step (i.e. regenerate the starting material) or by loss of the proton on the sp3 carbon (leading to a substitution product). When a reaction proceeds this way, it is electrophilic aromatic substitution. There are a wide variety of electrophiles that can be introduced into a benzene ring in this way, and so electrophilic aromatic substitution is a very important method for the synthesis of substituted aromatic compounds. Ch17 Reactions of Aromatic Compounds (landscape).docx Page2 Bromination of Benzene Bromination follows the same general mechanism for the electrophilic aromatic substitution (EAS). Bromine itself is not electrophilic enough to react with benzene. But the addition of a strong Lewis acid (electron pair acceptor), such as FeBr3, catalyses the reaction, and leads to the substitution product.
    [Show full text]
  • Educational Research Applications Abebe M, Et Al
    Educational Research Applications Abebe M, et al. Educ Res Appl 5: 175. Review Article DOI: 10.29011/2575-7032.100175 Teaching Students Synthesizing Molecules Mimicking an Existing Drug against Covid-19 Moges Abebe1*, Lashan Eloise Knowles1, Bisrat Hailemeskel2 1Department of Biological and Physical Sciences, Saint Augustine University, Raleigh, NC, USA 2Department of Clinical & Administrative Pharmacy Sciences, College of Pharmacy, Howard University, NW Washington, DC, USA *Corresponding author: Moges Abebe, Department of Biological and Physical Sciences, Saint Augustine University, Raleigh, NC 27610, NC, USA Citation: Abebe M, Knowles LE, Hailemeskel B (2020) Teaching Students Synthesizing Molecules Mimicking an Existing Drug against Covid-19. Educ Res Appl 5: 175. DOI: 10.29011/2575-7032.100175 Received Date: 26 May 2020; Accepted Date: 01 June, 2020; Published Date: 06 June, 2020 Abstract End of semester organic chemistry course projects are valuable learning assessment tools while giving students a creative opportunity and sparking interest for further research investigations. The purpose of this year’s project was to teach students how to synthesize a molecule that potentially mimics an existing drug that works against the COVID-19. The available drugs chosen for the project are those that are proposed to work either by prohibiting the easy entry of the virus into respiratory tissues or those who deprive the virus’s ability to reproduce once they enter the cell. An investigative search in historical literature and the current conditions of the virus enabled students to create a unique and innovative product that requires a cumulative learned knowledge. History has shown that when a new virus becomes pandemic it takes time for researchers to create a drug, test the results, and gets approved by the Food and Drug Administration (FDA) for public availability.
    [Show full text]
  • Transcription 11.12.07
    Lab 17A • 12/07/11 [lab quiz] Nomenclature of alkenes The first molecule that I want to look at is this one, where we have the two methyl groups on one side, two hydrogens on the other side. Would it be appropriate to use cis or trans, or E or Z, or both, or neither? One carbon of the double bond versus the other, those are the two different sides of the double, then the top versus the bottom are the two faces of the double bond. If we notice, on both the top face and the bottom face, we have a methyl group that is pointed the same way as a hydrogen. There is a steric factor as far as what alkene would prefer to form thermodynamically, so there is an importance that there’s some interaction there. That methyl group with one hydrogen is exactly the same interaction as you’d have the methyl group and the other hydrogen pointed the opposite way – meaning that if you were to switch the two hydrogens, you’d end up with exactly the same molecule again. The only reason that we use the term cis or trans or E or Z is to describe that it is one configuration versus another, but since there’s only one configuration possible, there’s therefore no term that should be used. It would, in fact, be wrong to call this cis, trans, E, or Z. When an alkene has two of the same substituent on the same side, there is only one unique configuration of that alkene, and so it cannot be called cis, trans, E, or Z.
    [Show full text]