Bioorganic Chemistry 2nd Assessment PDF

Tabb 1  Bioorganic chemistry 2nd assessment 1. Acid and bases, classification of them (Arrhenius, Bronsted-Lowry, Lewis definitions). Arrhenius: Acts like a donor of protons. The acid in Arrhenius theory it dissociates to produce hydrogen ions (H+) in water. And a base in Arrheni...

Tabb 1  Bioorganic chemistry 2nd assessment 1. Acid and bases, classification of them (Arrhenius, Bronsted-Lowry, Lewis definitions). Arrhenius: Acts like a donor of protons. The acid in Arrhenius theory it dissociates to produce hydrogen ions (H+) in water. And a base in Arrhenius theory produces hydroxide ions (OH-) in water Bronsted- Lowry: Acts like a donor of protons. The acid is a proton donor and the base accepts protons. Lewis acids: Shares electrons. Accept electrons pair. Lewis bases: Shares elections. Donate electrons pair. 2. Electrolytes and non-electrolytes. Electrolytes: Compounds that dissolve by breaking into ions and conduct electricity in solutions are known as electrolytes. Acids can create electricity, it can lead electicity Examples of electrolytes: HCl, NaCl, H2SO4, KOH, Mg, Cl, P, Na, Ca, K, salt. Nonelectrolytes: Compound that dissolve in water but do not conduct electricity are known as nonelectrolytes Examples of nonelectrolytes: CO2, alcohols, sugars, organic solvents (acetone, toluene, benzene) 3. Dissociation constant. Hydrogen ions and pH. Calculations of pH, pOH. pH 7: is when the concentration H3O+ = OH– pH below 7: the concentration of H3O+ is higher than OH– (more H3O+) pH above 7: the concentration of OH– is higher than H3O+ (more OH–) Calculations of pH: -lg[H3O+] Calculations of pOH: pOH= -lg[OH–] pH+pOH = 14.00 Calculations of [H3O+]: [H3O+]= 10–pH Examples calculations 1. In a solution [H3O+] = 0.01 M. What's the pH? Calculation: -lg[H3O+] = -lg[0.01]= 2 2. In a solution [OH–]= 0.01 M. What's the pH? Calculation: pOH= -lg[OH–]= -lg[0.01]= 2 pH- pOH= 2-14= 12 3. In a solution the pH= 4.68. Calculate [H3O+] Calculation: [H3O+]= 10–pH = 10–4.68 = 10–5 * 2.089296 mol/dm3 [H3O+]= 2.1 *10–5 mol/dm3 4. Calculate the pH in HCl where the concentration of HCl = 2.25* 10–5 M Calculation: pH= -lg[H3O+]= -lg[2.25*10–5]= 4.6478 pH in HCl= 4.678 4. Buffer solutions. Composition of it. Calculations of pH of buffer solutions. A buffer solution is a solution that changes pH only slightly when small amounts of a strong acid or strong base are added. Composition of buffer: A buffer contains a weak acid with its salt (conjugate base, the loss of its hydrogen ion) or a weak base with its salt (conjugate acid, accepts a proton in solution). Calculation of buffer some examples: 1. We dissolve 0.1 mol HAc and 0.1 mol NaAc in water, and dilutes up to 1.0 dm3 Ka, HAc = 1.8 *10–5 M What will the diluted solution pH be? Calculation: HAc H+ + Ac– Ka= [H+] [Ac–] / [HAc] [H+] = Ka * [HAc] / [Ac–] x= 1.8 *10–5 * 0.1 / 0.1= 1.8 *10–5 [H+]= 1.8 *10–5 pH= -lg[H+] =-lg[1.8 *10–5]= 4.744 5. Buffer capacity and buffer range. Calculations. The buffer capacity is the amount of acid or base that can be added to a buffer without destroying its effectiveness Buffer capacity, a number of equivalents of strong acid or base, which changes pH of 1 liter of the buffer solution by one unit. A buffer is most effective when the equal concentrations of the acid its conjugate base are equal pH= pKa The more concentration the components of a buffer are, the greater the buffer capacity. Calculations: [H+]= Ka * cacid / cbase pH= pKa -lg(cacid / cbase ) Example 1. We mix 20.0 ml 0.1 M HAc with 30.0 ml 0.1 M NaAc. Calculate pH HAc + NaAc Ac– + c1V1=c2V2 c2, HAc = c1, HAc * V1, HAc / V2 = 0.1 *20 / 20+30 = 0.0400 M c2, NaAc = c1, NaAc * V1, NaAc / V2 = 0.1 * 30 / 20+ 30 = 0.0600 M pH= pKa -lg(cacid / cbase ) = 1.8 *10–5 -lg(0.0400/0.0600) = 4.920 pH= 4.920 6. Instrumental methods of analysis. Spectroscopy. Law of Bouguer – Lambert – Beer. Potentiometry. Chromatography. Spectroscopy is used to determine the structure of materials and changes in chemicals by methods of spectral analysis. is a branch of physics that studies the absorption or scattering of electromagnetic radiation from atoms, their nuclei, molecules, and condensed matter, as well as the spectra of masses, electrons, ions, energy and other spectra. Law of Bouguer – Lambert – Beer: The sample path length and concentration of the sample are directly proportional to the absorbance of the light. Potentiometry: Is the field of electroanalytical chemistry in which potential is measured under the conditions of no current flow. If a metal plate is dipped into water, or solution of its salt an equilibrium potential difference is established called electrode potential. This potential could then be used to determine the concentration of some component of the analyte solution. Chromatography Is a process for separating components of a mixture 7. Classification/ structure/ nomenclature of organic compounds according to the functional group. Homologues of organic compounds. 1. Hydrocarbons (No functional group) Alkanes: Contain only single bonds. - General formula: CnH2n+2Cn​H2n+2​ - Example: Methane (CH4CH4​), Ethane (C2H6C2​H6​) Alkenes: Contain one or more double bonds. - General formula: CnH2nCn​H2n​ - Example: Ethene (C2H4C2​H4​), Propene (C3H6C3​H6​) Alkynes: Contain one or more triple bonds. - General formula: CnH2n−2Cn​H2n−2​ - Example: Ethyne (C2H2C2​H2​), Propyne (C3H4C3​H4​) Aromatic hydrocarbons: Contain benzene rings. - Example: Benzene (C6H6C6​H6​), Toluene (C6H5CH3C6​H5​CH3​) 2. Compounds with Oxygen Functional Groups a. Alcohols Functional group: −OH−OH (hydroxyl group) General formula: R−OHR−OH Example: Ethanol (CH3CH2OHCH3​CH2​OH) Nomenclature: Replace the -e of the alkane with -ol. b. Phenols Functional group: −OH−OH attached to an aromatic ring Example: Phenol (C6H5OHC6​H5​OH) c. Ethers  Functional group: −O−−O− (oxygen bridge) General formula: R−O−R′R−O−R′ Example: Diethyl ether (CH3CH2OCH2CH3CH3​CH2​OCH2​CH3​) Nomenclature: Name the two alkyl groups followed by "ether." d. Aldehydes Functional group: −CHO−CHO (carbonyl group at the end of the chain) General formula: R−CHOR−CHO Example: Formaldehyde (HCHOHCHO), Acetaldehyde (CH3CHOCH3​CHO) Nomenclature: Replace the -e of the alkane with -al. e. Ketones Functional group: C=OC=O (carbonyl group within the chain) General formula: R−CO−R′R−CO−R′ Example: Acetone (CH3COCH3CH3​COCH3​) Nomenclature: Replace the -e of the alkane with -one. f. Carboxylic Acids Functional group: −COOH−COOH (carboxyl group) General formula: R−COOHR−COOH Example: Acetic acid (CH3COOHCH3​COOH) Nomenclature: Replace the -e of the alkane with -oic acid. g. Esters Functional group: −COOR−COOR General formula: R−COOR′R−COOR′ Example: Ethyl acetate (CH3COOCH2CH3CH3​COOCH2​CH3​) Nomenclature: Name the alkyl group from the alcohol followed by the acid with -ate. 3. Compounds with Nitrogen Functional Groups a. Amines Functional group: −NH2,−NHR,−NR2−NH2​,−NHR,−NR2​ Example: Methylamine (CH3NH2CH3​NH2​), Dimethylamine ((CH3)2NH(CH3​)2​NH) Nomenclature: Add "amine" to the alkyl group. b. Amides  Functional group: −CONH2,−CONHR,−CONR2−CONH2​,−CONHR,−CONR2​ Example: Acetamide (CH3CONH2CH3​CONH2​) Nomenclature: Replace -e with -amide. c. Nitro Compounds Functional group: −NO2−NO2​ Example: Nitrobenzene (C6H5NO2C6​H5​NO2​) 4. Compounds with Halogen Functional Groups Functional group: −X−X (where X=F,Cl,Br,IX=F,Cl,Br,I) General formula: R−XR−X Example: Chloroform (CHCl3CHCl3​), Bromoethane (C2H5BrC2​H5​Br) Nomenclature: Use the prefix fluoro-, chloro-, bromo-, or iodo-. 5. Compounds with Sulfur Functional Groups a. Thiols Functional group: −SH−SH Example: Ethanethiol (CH3CH2SHCH3​CH2​SH) Nomenclature: Add "thiol" to the alkane name. b. Sulfides Functional group: −S−−S− Example: Dimethyl sulfide (CH3SCH3CH3​SCH3​) 6. Compounds with Phosphorus Functional Groups Functional group: −PO43−−PO43−​ Example: Organophosphates like ATP (adenosine triphosphate). Summary Table of Common Functional Groups: Functional Group Suffix/Prefix Example Alcohol (-OH) -ol Ethanol Aldehyde (-CHO) -al Formaldehyde Ketone (C=O) -one Acetone Carboxylic Acid (-COOH) -oic acid Acetic acid Amine (-NH2) -amine Methylamine Ester (-COOR) -ate Ethyl acetate Ether (-O-) Prefix: alkoxy- Diethyl ether Halide (-X) Prefix: halo- Chloroethane Homologues organic compounds: 8. Alcohols. Structure, nomenclature, chemical reactions of alcohols. Polyols. Alcohols are organic compounds containing 1 or more hydroxyl (-OH) groups attached to a carbon ( C) They are classified based on the carbon atom bonded to the hydroxyl group: primary (1), secondary (2) and tertiary (3) alcohols. Chemical reactions: 1. Oxidation: - With tromer reagent: Aldehydes are oxidized to carboxylic acids using Tromer reagent, turning Cu(OH)2 into Cu2O (red precipitate)  - With potassium Dichromate or permanganate: Ethanol is oxidized to acetaldehyde (ethanol), and further to acetic acid in acid medium 2. Formation of Esters: Alcohols react with carboxylic acids (COOH) to form esters. For example ethanol reacts with acetic acid to produce ethyl acetate. Polyols: Is an organic compound containing multiple -OH groups 9. Aldehydes. Ketones. Carboxylic acids and their chemical reactions. Aldehydes and ketones: - Aldehydes: Are oxidized to carboxylic acids (containing COOH) Reactions such as Fehling’s test involve the reduction of Cu2+ to Cu2O, indicated by a color change. - Ketones: Generally resist oxidation but can undergo keto-enol tautomerism. Keto-enol tautomerism- Is a chemical equilibrium bw to isomers which is a ketone (or aldehyde) form and its enol form (a compound with a double bond and a hydroxyl group attached to one of the doubly bonded carbons). This equilibrium occurs due to the migration of a hydrogen atom and the shifting of a double bond. Carboxylic acids: - Chemical properties include their weak acidic nature, forming carboxylate salts in reaction with bases. For example CH3COOH + NaOH →CH3COONa + H2O - Preparation: By oxidation of primary alcohols and aldehydes 10. Nomenclature of polyfunctional and heterofunctional carboxylic acids. Polyfunctional carboxylic acids: These acids have additional functional groups like hydroxy (-OH) or keto (=O). Examples include lactic acid and citric acid. Heterofunctional carboxylic acids: Include oxo acids and amino acids with both carboxyl and amino groups. Oxo acids such as pyruvic acid are intermediates in metabolic cycles. 11. Formation of polyfunctional and heterofunctional carboxylic acids. Monofunctonal: compounds that contain only one functional group. Polyfunctional: compounds that have several identical functional groups in the molecule. Hetrofunctional: compounds with several different functional groups. 12. Dicarboxylic and unsaturated dicarboxylic acids: formation, examples, chemical reactions. Saturated: Oxalic acid (HOOC-COOH), succinic acid (HOOC-CH2)2-COOH. Saturated acids has single bonds bw the carbons and more hydrogens Unsaturated: Maleic acid and fumaric acid (cis-trans isomers of butenedioic acid). Has double or triple bonds bw the carbons and fewer hydrogens Chemical reactions: - Decarboxylation: Malonic acid forms acetic acid and CO2 upon heating - Formation of salts and ester: Mono- and disubstitution reactions occur in dicarboxylic acids 13. Hydroxyl carboxylic acids: formation, examples, chemical reactions. 14. Optical isomerization: chirality, examples. Chirality: A molecule is chiral if it has a carbon atom bonded to 4 different groups. Such molecules can exist as non-superimposable mirror images called enantiomers. For example: lactic acid exists as L- and D- forms which rotate plane- polarized light in opposite directions. 15. Oxo acids: examples, reactions, keto-enolic tautomerisation. Oxoacid is an acid that contains hydrogen atoms (H) that can dissociate in water to form hydrogen ions(H+). Contains oxygen atoms (O), and a central atom which is usually a nonmetal or transition metal to which the oxygen is bonded to. Keto-enolic tautomerisation The proton in the α position relative to the carbonyl group is very active. This proton can jump on carbonyl oxygen. In this way, the ketone can be converted into an enol compound 16. Lipids: types, examples, main functions. 19. Structural lipids: types, structures, examples. Lipids are organic compounds that contain hydrocarbons which are the foundation for the structure and function of living cells. Lipids are non polar so they are soluble in nonpolar environments (thus not being water soluble because water is polar). 17. Fatty acids: saturated, unsaturated, examples, properties. Fatty acids are carbon chains with a methyl group at one end of the molecule (designated Ω) and a carboxyl group at the other end. 18. Triacylglycerols: types, formation, hydrogenation, hydrolysis, saponification. Fats and oil are also called Triaclyglycerols, They are produced by esterification. 20. Amides and amines; examples, basic properties. Amines: - Classified as primary, secondary or tertiary based on the number of alkyl grupos attached to the nitrogen atom - Basic properties: Amines react with acids to form alkyl ammonium salts. For example: CH₃NH₂ + HCl → CH₃NH₃Cl Amides: Contain a carbonyl group (C=O) directly bonded to a nitrogen atom (N). Amides participate in hydrogen bonding, contributing to high boiling points. 21. Amino acids: examples (essential amino a.), properties, chemical properties, peptide bond formation. Structure and properties - Contains an amino group (-NH2) and a carboxyl group (-COOH). At neutral pH, amino acids exist as zwitterions, with both positively and negatively charged groups. - Essential amino acids ( for example, lysin, tryptophan) cannot be synthesized by the body and must be obtained from the diet. Peptide bonds formation: - Amino acids link though a condensation reaction bw the carboxyl group of one and the amino group of another, forming a peptide bond. Basically, two amino acids are joined together to form protein.