[BIOCHEM]LAB_001_REVIEW OF ORGANIC CHEMISTRY.pdf

(001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 OUTLINE B. Biochemistry I. BAS...

(001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 OUTLINE B. Biochemistry I. BASIC CONCEPTS - the chemistry of living microorganisms A. Organic Chemistry - the study of biology at the cellular and molecular level B. Biochemistry II. PRINCIPAL AREAS IN BIOCHEMISTRY II. PRINCIPAL AREAS IN BIOCHEMISTRY A. Structure and Function of Biomolecules A. Structure and Function of Biomolecules a. Four major types of biomolecules B. Metabolism Biomolecules - also called biological molecule, any of C. Molecular Genetics numerous substances that are produced by cells III. MOLECULES AND COMPOUNDS and living organisms A. Carbon -have a wide range of sizes and structures and a) Identification of Carbon Atoms perform a vast array of functions. IV. TYPES OF CHEMICAL BONDS A. Ionic Bond 1. Four major types of biomolecules B. Covalent Bond a. Carbohydrates V. CHEMICAL REACTIONS b. Lipids A. Site of Organic Chemical Reactions c. Nucleic acids B. Reaction Intermediates d. Proteins VI. GENERAL TYPES OF ORGANIC REACTIONS A. Addition Reactions B. Metabolism B. Elimination Reactions 1. Anabolic Process C. Substitution Reactions - Build-up of larger molecules out of smaller molecules. D. Rearrangement Reactions 2. Catabolic Process VII. PROPERTIES OF ORGANIC COMPOUNDS - Break down complex molecules into smaller molecules. A. Influenced factors C. Molecular Genetics B. Structural Effects - how life is replicated, regulation of protein synthesis VIII. BOND POLARITY AND ELECTRONEGATIVITY A. Polar Covalent Bonds B. Electronegativity III. MOLECULES AND COMPOUNDS C. Bond Polarity D. Molecule Polarity Formed when two or more atoms unite in the basis of their IX. INTERMOLECULAR FORCES OF ATTRACTION electron structure. A. Physical Properties A. Carbon B. IMFA -Period 2 and Group IV of the Periodic Table of Elements. 1. Types of IMFA -Tetravalent a. London Dispersion Forces -Has the ability to participate in a wide variety of chemical b. Dipole-Dipole Forces reactions and is able to form different compounds with -Assessing Van Der Waals Forces - Hydrogen Bonding other elements c, Ion-Ion Forces - are either numbered or given Greek letters. C. Solubility and Miscibility Based on Polarity D. Isomerism- Isomers 1. Identification of carbon atoms X. ORIGINS OF LIFE a. Carbon atoms are numbered with the A. Vitalism carbon of the most oxidized group B. Evidence designated as carbon 1 C. Biochemical Evolution b. α- carbon is the one next to the carbon D. Organization of Life atom of the most oxidized group. XI. IMPORTANT BIOMOLECULES (polymers) A. Lipids, Proteins, Carbohydrates & Nucleic Acids B. Biomolecules - Structure C. Linking Monomers D. Breaking-down Polymers I. ILIVING THINGS A. Organic Chemistry - Study of carbon and its compounds - Substances that are primarily composed of carbon have Figure 1. Identification of carbon atoms in an organic been known as organic substances. compound. Carbons may be numbered starting with the most oxidized carbon-containing group, or they may be assigned PREPARED AND EDITED BY: TRANS GROUP 3  (001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 Greek letters, with carbon next to the most oxidized group B. Elimination Reactions designated as the α- carbon. -Reverse of addition formation of double bonds C. Substitution Reactions IV. TYPES OF CHEMICAL BONDS -Replacement of one substituent by another A. Ionic Bond D. Rearrangement Reactions - complete transfer of electrons from one atom to -Rearrangement of the structure of a compound another, resulting in the production of charged atoms, known as ions VII. PROPERTIES OF ORGANIC COMPOUNDS -These ions can be positively charged or negatively charged. Largely influenced by these factors: - Ionic elements are usually found in the last two columns A. Intermolecular forces of attraction and first two columns. B. Forces of attraction or repulsion which act between B. Covalent Bond neighbouring molecules. -Results from the sharing of electrons between two C. These forces are weak compared to intramolecular forces. atoms. D. Intramolecular forces of attraction -Covalent bonds can be polar or nonpolar E. Forces of attraction that exist between bond within a molecule. F. Molecular geometry Structural effects: A. Orbital hybridization B. Steric effects C. Inductive effects – distortion of electron cloud D. Resonance – pi electron delocalization E. CH Hyperconjucation – sigma electron delocalization Figure 2. Ionic and covalent bonds VIII. BOND POLARITY AND ELECTRONEGATIViTY V. CHEMICAL REACTIONS A. Polar Covalent Bonds These involve the disruption and formation of chemical bonds. -Unsymmetrical electron distribution Biochemical reactions also involve functional groups of molecules. - A given bond is either ionic and covalent. However, the shared o Oxidation reactions – electrons are lost electrons in covalent bonds tend to be attracted somewhat more strongly by one atom by the other. o Reduction reactions - electrons are gained A. Site of Organic Chemical Reactions B. Electronegativity 1. Multiple Bonds - It has high concentration of molecules. 2. Polar Group - Polarity is good to determine the properties of the molecule. 3. Lewis Acid and Lewis Base Characteristics - Lewis Acid a. Is a species that accepts electron pair, i.e electrophile - Lewis Base b. Is a species that donates electron pair, i.e nucleophile -Bond polarity is due to differences in electronegativity, the intrinsic ability of an atom to attract electrons in covalent bond. B. Reaction Intermediates 1. Bond Polarity 1. Carbocation - Nonpolar covalent bonds – similar or almost the same Has a positively charged carbon ion electronegativity 2. Cabanions - Has a negatively charges carbon ion -Polar covalent bond-between atoms whose 3. Free Radicals electronegativities differ by less than 2 - Unpaired electrons - Ionic bond- bonds with different electronegativities by VI. GENERAL TYPES OF ORGANIC REACTIONS more than 2 2. Molecule Polarity A. Addition Reactions The polarity of a molecule is dictated by its geometry and - Usually a characteristic of unsaturated compound that the individual bonds existing within molecule. usually result to disruption of multiple bonds PREPARED AND EDITED BY: TRANS GROUP 3  (001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 For example: Ammonia and Carbon dioxide c. Ion-Ion Forces -Every ionic compound is held in a well-ordered crystalline state. -The forces that hold ions together are strong electrostatic lattice forces, an adequate amount of energy is needed to break the orderly structure of the crystal. -In sodium acetate, an ionic organic compound, BP is very high that it tends to decompose before it IX. INTERMOLECULAR FORCES OF ATTRACTION boils A. Physical Properties -Solubility is one the most important properties of organic C. Solubility and Miscibility Based on Polarity compounds “Like dissolves like” -These properties of organic compounds are generally -The overall solvation capacity of a solvent depends upon related to the intermolecular forces of attraction or IMFA. its polarity IMFA are the forces that must be overcome or broken during -Polar solvents like water dissolve polar solutes (hydrophilic) melting, evaporation and sublimation. -Nonpolar solvent dissolves nonpolar solutes (hydrophobic) B. IMFA D. Isomerism- Isomers -Atoms in molecules are associated with other atoms by -Isomers are compounds possessing the same molecular covalent bonds formula but different structural formula -These are relatively strong bonds and are called intramolecular forces. -We differentiate this from IMFA, which are forces between molecules. 1. Types of IMFA a. London dispersion forces (Ldf) -Ldf are present in all substance, the only IMFA present in non-polar substances and noble gases. -Usually increase with molar mass (MM); the larger the MM, the stronger the Ldf b. Dipole-dipole forces -Hydrogen Bond -Polar molecules exhibit dipole-dipole forces aside from Ldf. -The more polar molecule, the stronger the dipole- 1. Structural/constitutional isomerism – variation in the dipole interaction. bonding arrangement of atoms or groups a. Skeletal – same molecular formula but different Ldf and Dipole-dipole forces are collectively known as van derWaals forces (vdW) carbon skeleton (involves Hydrocarbons) b. Positional – similar functional groups but the a. Assessing Van Der Waals Forces functional groups are in different position -If the substances are of widely different MM, c. Functional- same molecular formula but different Ldf are considered important than dipole-dipole functional groups that are present interaction in determining the relative strength of vdW forces 2. Stereoisomerism – no variation in bonding arrangement, -If the MM of are relatively close, the presence only in orientation in space. of dipole-dipole interaction greatly contributes in a. Optical – different rotation of the molecules determining the relative vdW b. Conformational -They change in space due to rotational single bond but they easily just go back b. Hydrogen Bonding to their stable form (they are not really an isomer) -Hydrogen bonding is a strong IMFA and a c. Geometric – different orientation in spaces. To add, special type of dipole-dipole interaction. both Conformational and Geometric Isomerism -It is present among molecules which contain have different orientation in spaces. hydrogen bound to small, highly electronegative atom such as N, O and F. PREPARED AND EDITED BY: TRANS GROUP 3  (001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 N2 < F2 < Cl2 D. Organization of Life 1. Elements 2. Simple organic compounds 3. Macromolecules 4. Supramolecular structures 5. Organelles Two main types of Stereoisomers 6. Cells o Diestereomers – Cis and Trans Isomers for the 7. Tissues study of lipids. 8. Organism ▪ Cis – same groups that are attach on the same side of the double bond. ▪ Trans- different groups that are attach on the opposite side of double bond. XI. IMPORTANCE OF BIOMOLECULES o Enantiomers – mirror images that are non- (POLYMERS) A. Lipids, Proteins, Carbohydrates & Nucleic Acids superimposable with each other ▪ Epimers are stereoisomers that differ in the position of the hydroxyl group at only one asymmetric carbon. (BRS Biochemistry and Molecular Biology and Genetics page 23). 1. Lipids (Triglycerides, Phospholipids and Fatty Acids) a. Monoacylglycerol, Diacylglycerol, Triacylglycerol contain one, two, three fatty acids esterified to X. ORIGINS OF LIFE glycerol, respectively A. Vitalism b. Sphingolipids contain ceramide -is the idea that substances and processes associated with i. Sphingomyelin contains phosphocholine. living organisms did not behave according to the known laws of physics and chemistry. c. Cholesterol contains four rings and an aliphatic side chain B. Evidence 2. Proteins -Biochemical can only be produced by living organisms a. Most amino acids contain a carboxyl group, an -Complex bioconversion of chemical substance require living amino group, and a side- chain (R group), all matter attached to the a-carbon. Exceptions are: i. Glycine, which does not have a side chain. It’s a-carbon contains two C. Biochemical Evolution hydrogens. ii. Proline, in which the nitrogen is part of a ring, is an amino acid.. 3. Carbohydrates a. Monosaccharide bonds to another monosaccharide via O- glycosidic acid forming O- glycosides -Urea was synthesized by heating the inorganic compound b. Monosaccharide can be linked via N-glycosidic ammonium cyanate (1828). This proved that compounds bonds to compounds that are not carbohydrates found exclusively in living organisms could be synthesized 4. Nucleic Acids from inorganic substances a. Heterocyclic, basic compounds composed of purines and pyrimidines PREPARED AND EDITED BY: TRANS GROUP 3  (001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 b. Nucleosides- derivatives of nucleotides that contain sugars linked to nitrogenous bases. Functions of nucleotides are the following: i. Serves as energy stores (i.e., adenosine triphosphate [ATP]). ii. Forms portions of several coenzymes (i.e., nicotinamide adenine dinucleotide [NAD+]) iii. Serves as signaling intermediates (i.e., cAMP, cyclic guanosine monophosphate [cGMP]) iv. Is an allosteric modifier of certain regulated enzymes v. Conveys genetic information (DNA and RNA) B. Biomolecules - Structure C. Linking Monomers D. Breaking-down Polymers -Cells break down macromolecules by a process called hydrolysis (adding a molecule of water) Water added to split a double sugar PREPARED AND EDITED BY: TRANS GROUP 3  (001) OVERVIEW OF GENERAL AND ORGANIC CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY DR. EVANGELISTA | 09/14/2020 II. TRUE OR FALSE. Right TRUE if the statement is correct and FALSE if wrong, then change the word that makes the statement incorrect. _______8. Synthesis of Urea by heating ammonium cyanate proved that living organisms can also be synthesized by inorganic substances. _______9. Trans is a type of epimers that are attached on the opposite side of a double bond. _______10. Polar bonds have symmetrical distribution of electrons. ANSWERS 1. Hydrolysis 2.London Dispersion Forces (LDF) 3.Ionic bonds 4. Cell wall 5. Epimer 6.Amino acid 7. Enantiomers are two mirror images if a stereoisomer while epimers are stereoisomers that differ in the position of the hydroxyl group at only one of their asymmetric carbons 8.True 9.False. Diestereomers 10. False. Unsymmetrical TEST YOURSELF 1. What do you call the process of breaking down polymers into monomers? 2.This is the only IMFA present in noble gases. 3.This involves complete transfer of electrons from one atom to another. 4.What is the supramolecular structure of glucose? 5. What type of stereoisomer is shown in the picture? 6. It is the building block of a protein. 7. Differentiate an enantiomer and an epimer. PREPARED AND EDITED BY: TRANS GROUP 3