CHEM 1023 Final Exam Study Guide: Organic, Biological, and Metabolic Chemistry

Organic Chemistry

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the characteristic chemical reactions of those molecules.

• Naming: Use both IUPAC and common names for functional groups such as alcohols, ethers, aldehydes, ketones, carboxylic acids, esters, amines, and amides.

• Properties: Consider boiling point trends (e.g., alcohols have higher boiling points than alkanes due to hydrogen bonding), solubility (polar groups increase water solubility), and acidity/basicity (carboxylic acids are acidic, amines are basic).

• Classification: Functional groups can be classified as primary, secondary, or tertiary based on the number of carbon atoms attached to the functional group.

• Reactions: Each functional group undergoes characteristic reactions (e.g., alcohol oxidation, esterification, amide formation).

• Key Terms: Isomers (compounds with the same molecular formula but different structures), cis/trans (geometric isomers), and other end-of-chapter terms.

Example: The oxidation of a primary alcohol to an aldehyde, then to a carboxylic acid.

Biological Chemistry

Carbohydrates

Carbohydrates are polyhydroxy aldehydes or ketones and their derivatives, serving as energy sources and structural components.

• Classification: Monosaccharides (single sugar units), disaccharides (two units), polysaccharides (many units).

• Aldose/Ketose: Aldoses contain an aldehyde group; ketoses contain a ketone group.

• Hexose/Pentose: Hexoses have six carbons (e.g., glucose), pentoses have five (e.g., ribose).

• D or L: Refers to the configuration around the chiral carbon farthest from the carbonyl group.

• Haworth Structure: Cyclic forms of sugars; α or β refers to the position of the anomeric hydroxyl group.

• Reducing/Non-reducing: Reducing sugars have a free anomeric carbon; non-reducing do not.

• Types of Bonds: Glycosidic bonds link monosaccharides in di- and polysaccharides.

• Polysaccharide Differences: Starch, glycogen, and cellulose differ in glycosidic linkages and branching.

Example: Sucrose is a non-reducing disaccharide composed of glucose and fructose.

Lipids

Lipids are hydrophobic biomolecules including fats, oils, phospholipids, and steroids.

• Types and Components: Triglycerides (glycerol + 3 fatty acids), phospholipids (glycerol + 2 fatty acids + phosphate), steroids (four fused rings).

• Reactions: Saponification (hydrolysis of triglycerides), hydrogenation (addition of H2 to unsaturated fats).

• Cell Membranes: Composed mainly of phospholipids arranged in a bilayer; contain proteins and cholesterol.

Example: Phospholipids form the structural basis of cell membranes due to their amphipathic nature.

Proteins

Proteins are polymers of amino acids that perform a wide range of biological functions.

• Functions: Enzymes, structural components, transport, signaling, immune response.

• Amino Acids: Classified by R group as nonpolar, polar, acidic, or basic; have amino, carboxyl, and side chain (R) groups; abbreviations (e.g., Gly for glycine); C-terminal (carboxyl end) and N-terminal (amino end).

• Protein Structure:

  • Primary: Sequence of amino acids (peptide bonds).

  • Secondary: α-helix and β-sheet (hydrogen bonds).

  • Tertiary: 3D folding (hydrophobic interactions, disulfide bonds, ionic bonds, hydrogen bonds).

  • Quaternary: Multiple polypeptide chains (subunit interactions).

• Hydrolysis: Breaking peptide bonds with water to yield amino acids.

• Denaturation: Loss of structure and function due to heat, pH, chemicals, or agitation.

Example: Hemoglobin is a quaternary protein with four subunits.

Additional info: Table 19.6 lists denaturation factors such as heat, acids, bases, heavy metals, and agitation.

Enzymes

Enzymes are biological catalysts that speed up chemical reactions without being consumed.

• Catalyzed vs Uncatalyzed: Enzymes lower activation energy, increasing reaction rate.

• Definition and Purpose: Enzymes are proteins that catalyze specific biochemical reactions.

• Mechanism: Lock-and-key model (enzyme active site fits substrate exactly); induced fit model (active site molds to substrate).

• Classification: Six major classes (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases).

• Factors Affecting Activity: Temperature, pH, substrate concentration (see Section 20.3 graphs).

• Regulation: Allosteric (positive/negative), feedback inhibition, covalent modification.

• Inhibition: Reversible (competitive vs noncompetitive), irreversible (e.g., penicillin inhibits bacterial enzymes).

• Cofactors: Metal ions or coenzymes (e.g., B vitamins).

• Vitamins: Fat-soluble (A, D, E, K) vs water-soluble (B, C); fat-soluble vitamins have specific functions (e.g., vitamin A for vision).

Example: Competitive inhibition occurs when a molecule similar to the substrate binds the active site.

Nucleic Acids

DNA and RNA Structure

Nucleic acids are polymers of nucleotides, which store and transmit genetic information.

• Nucleotides: Each consists of a phosphate group, a five-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.

• Linkages: Nucleotides are joined by phosphodiester bonds.

• DNA vs RNA: DNA contains deoxyribose and bases A, T, G, C; RNA contains ribose and bases A, U, G, C.

• Base Pairing: A-T (or A-U in RNA), G-C.

• Primary Structure: Sequence of nucleotides.

Example: In DNA, adenine pairs with thymine via two hydrogen bonds.

Genetic Processes

• Replication: DNA is copied in the nucleus before cell division.

• Transcription: DNA is used as a template to synthesize RNA in the nucleus.

• Translation: RNA directs protein synthesis at ribosomes in the cytoplasm.

• Types of RNA: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

• Codon vs Anticodon: Codon is a three-base sequence on mRNA; anticodon is the complementary sequence on tRNA.

• Mutations: Changes in DNA sequence; can be silent, missense, nonsense, or frameshift, affecting protein function.

Example: Sickle cell anemia is caused by a single base mutation in the hemoglobin gene.

Metabolic Pathways

Overview of Metabolism

Metabolism is the sum of all chemical reactions in the body, divided into catabolic (breakdown) and anabolic (synthesis) pathways.

• Digestion: Begins in the mouth for carbohydrates, stomach for proteins, and small intestine for lipids.

• Key Pathways:

  • Glycolysis: Glucose breakdown to pyruvate (cytoplasm; anaerobic).

  • Glycogenesis: Formation of glycogen from glucose (liver, muscle).

  • Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources (liver).

  • Glycogenolysis: Breakdown of glycogen to glucose (liver, muscle).

  • Citric Acid Cycle: Oxidation of acetyl-CoA to CO2 (mitochondria; aerobic).

  • Electron Transport Chain: Series of redox reactions producing ATP (mitochondria; aerobic).

  • Urea Cycle: Conversion of ammonia to urea for excretion (liver).

  • Beta Oxidation: Fatty acid breakdown to acetyl-CoA (mitochondria).

• For Each Pathway: Know location, starting materials, products, byproducts (e.g., NADH, FADH2), aerobic/anaerobic nature, and regulation (activation/inhibition).

• Electron Transport and ATP Formation: Electrons from NADH and FADH2 pass through complexes, driving ATP synthesis via oxidative phosphorylation.

• ATP Calculation: Each NADH yields about 2.5 ATP; each FADH2 about 1.5 ATP. Beta oxidation of fatty acids yields large amounts of ATP.

• FAD and NAD+: Coenzymes involved in redox reactions; FAD is reduced to FADH2, NAD+ to NADH.

• ATP Structure: Adenine, ribose, and three phosphate groups; high-energy bonds between phosphates.

• Urea Cycle Purpose: Detoxifies ammonia from amino acid breakdown.

• Key Terms: Catabolic (breakdown), anabolic (synthesis), essential amino acid (cannot be synthesized by body), transamination (transfer of amino group), oxidative deamination (removal of amino group as ammonia).

Example: The complete oxidation of one palmitic acid (16 carbons) yields 106 ATP.

Pathway	Location	Starting Material	End Product	Aerobic/Anaerobic
Glycolysis	Cytoplasm	Glucose	Pyruvate	Anaerobic
Citric Acid Cycle	Mitochondria	Acetyl-CoA	CO2, NADH, FADH2	Aerobic
Electron Transport	Mitochondria	NADH, FADH2	ATP, H2O	Aerobic
Beta Oxidation	Mitochondria	Fatty Acids	Acetyl-CoA	Aerobic
Urea Cycle	Liver	Ammonia	Urea	Aerobic

Additional info: For ATP yield calculations, refer to the number of NADH and FADH2 produced in each pathway.