ML 126 - Bio-Organic Chemistry

Credit Hours: 3

This course introduces the student to the study of organic chemistry which discusses the following topics: alkanes, alkenes, alkynes, aromatic structures, alcohols, aldehydes, ketones, amines, carboxylicacids, anhydrides, esters, and amides. It covers the study of biochemistry of carbohydrates, lipids, proteins, enzymes, and nucleic acids and discusses the nomenclature, structures of molecules, mechanisms of reaction, and metabolic pathways in the body.

Course Outcomes
Upon completion of this course, the student will be able to:

Topic 1 - Introduction to organic and biochemistry;
- define organic chemistry;
- define biochemistry;
- list and compare sources of organic compounds;
- state the number of bonds formed by carbon, oxygen, nitrogen, hydrogen, and the halogens;
- distinguish between structural formulas, molecular formulas, and Lewis structures;
- define functional group;
- discuss 4 reasons why functional groups are important;
- specify and recognize the functional group of an alcohol and classify primary, secondary, and tertiary alcohols;
- specify and recognize the functional group of an amine and classify primary, secondary, and tertiary amines;
- specify and recognize the functional group of aldehydes and ketones and differentiate these structures; and
- specify and recognize the functional group of a carboxylic acid and ester.
Topic 2 - Alkanes, Alkenes, Alkynes, and Aromatic Compounds
- define hydrocarbons and differentiate the types of hydrocarbons;
- list the names of the alkanes up to ten carbons;
- name hydrocarbons using the IUPAC rules of nomenclature;
- write structural formulas of molecules for which IUPAC names are given;
- define and recognize stereoisomers and constitutional isomers;
- characterize the most important chemical and physical properties of the hydrocarbons;
- define polymer and polymerization;
- differentiate aromatic and aliphatic hydrocarbons;
- compare the substitution reactions of aromatic compounds with the addition reactions of alkenes and alkynes; and
- define Markovnikov’s rule as it applies to addition reaction.
Topic 3 - Alcohols, Phenol, Ethers, Thiols
- identify compounds which are alcohols, phenols, ethers, or thiols;
- differentiate primary, secondary and tertiary alcohols;
- given the IUPAC names for simple alcohols, draw the structural formula;
- given the structural formula for an alcohol, name the compound according to IUPAC rules;
- write out reactions for the dehydration of alcohols;
- write out reactions for the oxidation of alcohols; and
- discuss important physical properties of alcohols, phenols, ethers, and thiols.
Topic 4 - Acids, Bases, and Amines
- define and discuss acids, bases, buffers, and the Henderson-Hasselbalch equation;
- define and identify amine structures;
- differentiate primary, secondary, and tertiary amines;
- differentiate aliphatic and aromatic amines;
- define heterocyclic amine and heterocyclic aromatic amine;
- discuss nomenclature of amines;
- define alkaloid and list examples of alkaloids; and
- discuss physical properties of amines.
Topic 5 - Aldehydes and Ketones
- distinguish aldehydes and ketones and name their functional group;
- given the structural formula for an aldehyde or ketone, name the compound using IUPAC rules;
- given the IUPAC or common name for an aldehyde or ketone, write its structural formula;
- discuss important physical properties of aldehydes and ketones;
- discuss oxidation and reduction reactions involving aldehydes and ketones; and
- differentiate and identify hemiacetals and acetals and describe their formation.
Topic 6 - Carboxylic Acids, Anhydrides, Esters, and Amides
- recognize the characteristic functional group of carboxylic acids;
- discuss nomenclature of carboxylic acids;
- recognize fatty acids as examples of carboxylic acids;
- discuss physical properties of carboxylic acids;
- recognize the functional group of a carboxylic anhydride;
- discuss formation of and hydrolysis of carboxylic anhydrides;
- recognize the functional group of a carboxylic ester;
- discuss nomenclature of carboxylic esters;
- define ester and explain esterification and hydrolysis;
- recognize the functional group of a carboxylic amide;
- define and differentiate lactams and lactones;
- recognize the functional group of a phosphoric anhydride;
- differentiate Diphosphate from Triphosphate structures; and
- recognize phosphoric esters.
Topic 7 - Carbohydrates
- define carbohydrate and discuss their importance in plants and humans;
- define chiral and identify a chiral carbon or stereocenter;
- define, identify, and discuss properties of enantiomers;
- differentiate Fisher projection formulas from Haworth projections;
- calculate the maximum number of stereoisomers possible for a given structure;
- differentiate aldoses from ketoses;
- differentiate monosaccharides, disaccharides, and polysaccharides;
- define penultimate carbon;
- differentiate D from L monosaccharides;
- differentiate Alpha from Beta structures;
- compare physical, chemical, and structural properties of monosaccharides;
- differentiate pyranose and furanose rings;
- discuss important reactions of glucose;
- specify the monosaccharide constituents of maltose, lactose, and sucrose; and
- compare the structural composition and distribution of starch, glycogen, and cellulose. List functions of heparin and hyaluronic acid.
Topic 8 - Lipids
- define lipids and discuss their major functions in human biochemistry;
- describe the structure and physical and chemical properties of triglycerides;
- compare saturated and unsaturated fatty acids;
- contrast the structures of glycerophospholipids, sphingolipids, and glycolipids;
- discuss the composition and functioning of membranes;
- describe the steroid ring system and the structure of cholesterol;
- discuss the function and composition of lipoproteins;
- compare HDL, LDL, VLDL, and chylomicrons;
- ciscuss the relationship between atherosclerosis and blood levels of cholesterol, HDL, and LDL;
- specify cholesterol as the starting material for synthesis of the steroid hormones and bile and discuss the functions of these products; and
- describe the prostaglandins, leukotrienes, and thromboxanes.
Topic 9 - Proteins
- list and explain the major functions of proteins;
- draw the general formula of an amino acid;
- recognize the 20 amino acids commonly found in proteins;
- define zwitterions and isoelectric point;
- recognize the unique property of cysteine to form a disulfide linkage;
- identify peptide linkages, peptides, polypeptides, c-terminal end, and n-terminal end, proteins;
- describe and differentiate the primary, secondary, tertiary, and quaternary structures of proteins; and
- discuss denaturation of proteins.
Topic 10 - Enzymes
- define enzymes and discuss their specificity;
- list the 6 major categories of enzymes and identify the type of reaction that is involved in each category;
- distinguish between the terms cofactor, apoenzyme, coenzyme, proenzyme, and active site;
- compare how a competitive and a non-competitive inhibitor produce their effect;
- detail in words and by graph the effect of enzyme concentration, substrate concentration, pH, and temperature on the rate of an enzyme catalyzed reaction;
- discuss the lock and key model and the induced fit model of the mechanism of enzyme action;
- define feedback control as it applies to enzyme regulation;
- define isoenzymes; and
- list examples of enzymes and isoenzymes important in clinical diagnosis.
Topic 11 - Metabolism
- define metabolism, catabolism, anabolism, and biochemical pathway;
- specify the 2 sequences of the common catabolic pathway and the major purpose of catabolic pathways;
- compare the structures of AMP, ADP, ATP, NAD, FAD, and acetyl CoA;
- discuss the role of acetyl CoA in the Krebs cycle;
- identify the major compounds in the Kreb’s (TCA citric acid) cycle;
- describe the citric acid cycle including reactions and carbon balance;
- explain the role of NAD and FAD in the citric acid cycle and in the electron transport chain;
- identify the enzymes of the electron transport chain;
- describe the function of the proton translocating ATPase and specify the final acceptor of oxidative phosphorylation;
- determine the number of ATP molecules produced in the Kreb’s cycle and oxidative phosphorylation as a result of oxidation of one acetyl group;
- define glycolysis, gluconeogenesis, glycogenesis and glycogenolysis;
- detail the 3 stages of glycolysis;
- distinguish between anaerobic and aerobic glycolysis;
- indicate under what conditions pyruvate is converted to (a) lactate, (b) ethanol, or (c) acetyl CoA;
- specify the total net yield of ATP from metabolism of one glucose molecule and compare to the energy yield from fatty acids;
- describe B-oxidation of fatty acids;
- name the ketone bodies and explain their elevated concentration in blood and urine of diabetics;
- discuss transamination, oxidative deamination, and the urea cycle;
- detail the convergence of the specific pathways of carbohydrate, lipid, and protein catabolism into the common catabolic pathway;
- discuss the catabolism of heme and the development of jaundice;
- describe the biosynthesis of carbohydrates, fatty acids, cholesterol, and amino acids; and
- define what is meant by essential amino acids and fatty acids.
Topic 12 - Nucleic Acids and Protein Synthesis
- explain the importance of hereditary information and its storage and expression in DNA;
- define nucleic acid, nucleotide, gene, chromosome, and genetic code;
- detail the 3 units of a nucleotide;
- name the purines and pyrimidines present in DNA and those in RNA;
- compare the sugar components of RNA and DNA;
- describe the primary structure of DNA and RNA;
- describe the secondary structure of DNA;
- summarize the major differences in structure between DNA and RNA;
- compare the types of RNA;
- describe DNA replication, transcription, translation, and protein synthesis;
- discuss DNA fingerprinting; and
- define PCR, detail the steps of PCR, and discuss applications in the Clinical Lab and Forensics.

Prerequisites: CH 146 or CH 180, ML 112
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