Chapter 3: The Chemistry of Organic Molecules

Vocabulary flashcards covering key terms from the lecture notes on organic molecules, biomolecules, and their properties.

Organic molecules

Molecules containing carbon and hydrogen; the four biomolecule classes are carbohydrates, lipids, proteins, and nucleic acids.

Biomolecules

Carbohydrates, lipids, proteins, and nucleic acids—the essential organic molecules in living organisms.

Carbon

Element with four electrons in its outer shell; can form up to four covalent bonds and create nonpolar or polar bonds.

Tetravalent

Having four valence electrons; carbon’s ability to form four bonds enables complex structures.

Covalent bond

A bond formed by sharing electrons between atoms.

Line-angle formula

A simplified molecular sketch where carbons are at line ends and attached hydrogens are omitted; other elements are shown.

Functional group

A specific group of atoms that imparts characteristic chemical properties and reactivity to organic molecules.

Hydroxyl group

R–OH; polar; forms hydrogen bonds; common in sugars and some amino acids.

Carbonyl group

C=O; present as aldehyde (R–CHO) or ketone (R–CO–R); polar.

Aldehyde

Carbonyl group at the end of a carbon skeleton, e.g., formaldehyde (R–CHO).

Ketone

Carbonyl group within the carbon skeleton, e.g., acetone (R–CO–R).

Carboxyl group

–COOH; acidic; polar; found in fatty acids and amino acids.

Amino group

–NH2; basic; common in amino acids; participates in peptide bonds.

Sulfhydryl group

–SH; forms disulfide bonds; found in some amino acids like cysteine.

Phosphate group

–O–P(=O)(OH)–O–; polar and acidic; found in nucleotides and phospholipids.

Isomer

Molecules with identical molecular formulas but different arrangements of atoms.

Monomer

A single subunit that can join with others to form polymers (e.g., amino acids, monosaccharides, nucleotides).

Polymer

A large molecule made up of many monomer units (e.g., proteins, polysaccharides, nucleic acids).

Dehydration synthesis

Reaction that joins monomers by removing water, forming a covalent bond.

Hydrolysis

Reaction that adds water to break covalent bonds, splitting polymers into monomers.

Enzyme

Protein catalyst that speeds up chemical reactions without being consumed or permanently altered.

Lactase

Enzyme that hydrolyzes lactose into glucose and galactose; deficiency causes lactose intolerance.

Carbohydrates

Biomolecules composed of C, H, O in a 1:2:1 ratio; energy source and structural material; monosaccharides, disaccharides, polysaccharides.

Monosaccharide

Single sugar molecule; 3–7 carbon atoms; examples include glucose, fructose, galactose; hexoses and pentoses.

Hexose

Six-carbon monosaccharide (e.g., glucose).

Pentose

Five-carbon monosaccharide (e.g., ribose, deoxyribose in nucleic acids).

Disaccharide

Two monosaccharides joined by dehydration synthesis (e.g., lactose, sucrose, maltose).

Polysaccharide

Polymer of monosaccharides; starch (plants), glycogen (animals), cellulose (plants), chitin (fungi/arthropods), peptidoglycan (bacteria).

Starch

Polysaccharide used by plants for energy storage.

Glycogen

Polysaccharide used by animals for energy storage.

Cellulose

Structural polysaccharide in plant cell walls; indigestible by most animals.

Chitin

Structural polysaccharide in fungal cell walls and arthropod exoskeletons.

Peptidoglycan

Structural polysaccharide in bacterial cell walls.

Lipids

Nonpolar, large molecules insoluble in water; functions include long-term energy storage, membranes, insulation, protection, and signaling.

Triglyceride

Glycerol linked to three fatty acids; major long-term energy storage molecule formed by dehydration synthesis.

Fatty acid

Hydrocarbon chain; can be saturated (no double bonds) or unsaturated (one or more double bonds).

Saturated fatty acids

No double bonds between carbons; usually solid at room temperature.

Unsaturated fatty acids

Contain one or more double bonds; usually liquid at room temperature; cis or trans configurations.

Cis configuration

Double bond with hydrogen atoms on the same side, causing a bend in the chain.

Trans configuration

Double bond with hydrogen atoms on opposite sides; straighter chain.

Phospholipid

Glycerol + two fatty acids + a phosphate group; amphipathic; forms lipid bilayers in membranes.

Steroid

Four fused carbon rings; cholesterol, testosterone, estrogen; can act as hormones and membrane components.

Cholesterol

Steroid; membrane component; precursor to other steroids; linked to cardiovascular disease risk.

Waxes

Long-chain fatty acids linked to alcohols; solid at room temperature; waterproof and protective.

Proteins

Polymers of amino acids linked by peptide bonds; folded into specific shapes essential for function.

Amino acid

20 common monomers of proteins; have amino and carboxyl groups with an R-side chain determining properties.

Peptide bond

Covalent bond linking amino acids; formed by dehydration synthesis.

Polypeptide

Long chain of amino acids; a protein once folded into a functional shape.

Primary structure

Linear sequence of amino acids in a protein.

Secondary structure

Alpha helices and beta pleated sheets stabilized by hydrogen bonds.

Tertiary structure

Three-dimensional shape of a single polypeptide; stabilized by hydrophobic, hydrogen, ionic, and covalent interactions.

Quaternary structure

Two or more polypeptides associate to form a functional protein.

Chaperone

Proteins that assist in proper folding of other proteins and may help correct misfolding.

Prion

Misfolded protein linked to transmissible spongiform encephalopathies (TSEs) such as mad cow disease.

Nucleic acids

Polymers of nucleotides (DNA and RNA); store, transmit, and express genetic information.

Nucleotide

Monomer of nucleic acids; composed of a phosphate, a five-carbon sugar, and a nitrogenous base.

Purines

Two-ring nitrogenous bases: adenine and guanine.

Pyrimidines

One-ring bases: cytosine, thymine (DNA), uracil (RNA).

Complementary base pairing

A pairs with T (or U in RNA); G pairs with C; hydrogen bonds stabilize the pairing; A+G equals T+C in total counts.

DNA

Deoxyribonucleic acid; double-stranded; sugar is deoxyribose; bases A, G, C, T; forms a double helix.

RNA

Ribonucleic acid; usually single-stranded; sugar is ribose; bases A, G, C, U.

Double helix

The two-stranded, twisted structure of DNA held together by base pairing.

Adenine–Thymine pairing

A pairs with T via two hydrogen bonds in DNA.

Guanine–Cytosine pairing

G pairs with C via three hydrogen bonds in DNA.

ATP

Adenosine triphosphate; nucleotide with three phosphates; high-energy bonds drive cellular work; hydrolysis yields ADP and Pi.

ADP

Adenosine diphosphate; product of ATP hydrolysis.

Ribose vs. Deoxyribose

Ribose has a hydroxyl group at the 2' carbon (RNA); deoxyribose lacks it (DNA).