Chapter 3: The Chemical Basis of Life II: Organic Molecules

Comprehensive practice flashcards defining essential vocabulary terms, functional groups, and structural concepts from Chapter 3: Organic Molecules.

Organic molecules

Carbon-containing molecules that are abundant in living organisms.

Macromolecules

Large, complex organic molecules composed of thousands or millions of atoms.

Vitalism

The 19th-century concept holding that organic molecules were created by and imparted with a vital life force within a plant or animal's body and could not be synthesized; later disproven.

Hydrocarbons

Molecules composed predominantly of carbon and hydrogen linked by electrically neutral, nonpolar bonds, making them poorly soluble in water.

Functional groups

Groups of atoms with special chemical features that are functionally important and exhibit the same chemical properties in every molecule where they occur.

Amino group ($-\text{NH}_2$)

A functional group composed of a nitrogen atom bonded to two hydrogen atoms; it is polar, weakly basic (capable of accepting $\text{H}^+$), and forms part of peptide bonds in amino acids and proteins.

Carbonyl group ($-\text{CO}-$)

A polar, highly chemically reactive functional group containing a carbon atom double-bonded to an oxygen atom that forms hydrogen bonds; exists as a ketone or an aldehyde.

Carboxyl group ($-\text{COOH}$)

An acidic functional group containing a carbon double-bonded to an oxygen and single-bonded to a hydroxyl group; gives up $\text{H}^+$ in water and forms part of peptide bonds in amino acids and fatty acids.

Hydroxyl group ($-\text{OH}$)

A polar functional group consisting of a hydrogen atom bonded to an oxygen atom that can form hydrogen bonds with water; found in steroids, alcohols, carbohydrates, and certain amino acids.

Methyl group ($-\text{CH}_3$)

A nonpolar functional group consisting of a carbon atom bonded to three hydrogen atoms; commonly attached to DNA, proteins, and carbohydrates.

Phosphate group ($-\text{PO}_4^{2-}$)

A polar, weakly acidic functional group that is negatively charged at typical cellular pH; found in nucleic acids, ATP, and phospholipids.

Sulfate group ($-\text{SO}_4^-$)

A polar functional group that is negatively charged at typical physiological pH; may be attached to carbohydrates, proteins, and lipids.

Sulfhydryl group ($-\text{SH}$)

A polar functional group (also known as a thiol) consisting of a sulfur atom bonded to a hydrogen atom; found in the amino acid cysteine and forms disulfide bridges in many proteins.

Isomers

Two or more molecules that possess identical molecular formulas but have different chemical structures and characteristics.

Structural isomers

Isomers that contain the same atoms but differ in the covalent bonding relationships between those atoms.

Stereoisomers

Isomers that share identical bonding relationships but differ in the spatial positioning and orientation of their atoms.

Cis-trans isomers

Stereoisomers that differ in the spatial positioning of atoms or chemical groups relative to a rigid carbon-carbon double bond.

Enantiomers

Stereoisomers that are non-superimposable mirror images of each other; because of differing spatial orientations, enzymes usually recognize only one enantiomer.

Monomer

A small organic subunit (meaning 'one part') that can be covalently linked to other similar units to build larger macromolecules.

Polymer

A large molecule (meaning 'many parts') composed of many repeated monomer units covalently joined together.

Dehydration reaction

An enzyme-catalyzed condensation reaction that links two molecules together through the net removal of one molecule of water ($\text{H}_2\text{O}$).

Hydrolysis reaction

An enzyme-catalyzed chemical reaction that breaks down polymers into smaller units by adding a molecule of water across each cleaved bond.

Carbohydrates

Organic molecules composed of carbon, hydrogen, and oxygen atoms according to the general formula $\text{C}_n(\text{H}_2\text{O})_n$, in which most carbon atoms are linked to a hydrogen atom and a hydroxyl group.

Monosaccharides

The simplest carbohydrate sugars, typically containing 5 carbons (pentoses) or 6 carbons (hexoses), which exist in linear or ring conformations.

Pentoses

Five-carbon monosaccharides, such as ribose ($\text{C}_5\text{H}_{10}\text{O}_5$) and deoxyribose ($\text{C}_5\text{H}_{10}\text{O}_4$).

Hexoses

Six-carbon monosaccharides, such as glucose ($\text{C}_6\text{H}_{12}\text{O}_6$), that serve as primary cellular energy sources.

Disaccharides

Carbohydrates formed by linking two monosaccharides together via a dehydration reaction; examples include sucrose, maltose, and lactose.

Glycosidic bond

The covalent bond that joins two carbohydrate monomers together through a dehydration reaction.

Polysaccharides

Long carbohydrate polymers formed from many monosaccharide subunits linked together; function in energy storage or structural support.

Starch

A moderately branched energy-storage polysaccharide found in plant cells, consisting of glucose units linked by $\alpha\text{-1,4-glycosidic linkages}$ with branches formed by $\alpha\text{-1,6-glycosidic linkages}$.

Glycogen

A highly branched energy-storage polysaccharide found in animal cells, composed of glucose chains linked by $\alpha\text{-1,4-}$ and $\alpha\text{-1,6-glycosidic linkages}$.

Cellulose

An unbranched structural polysaccharide composed of glucose chains linked by $\beta\text{-1,4-glycosidic linkages}$, serving as a primary structural component of plant cell walls.

Lipids

Nonpolar, water-insoluble hydrophobic organic molecules composed predominantly of carbon and hydrogen with some oxygen; comprise approximately $40\%$ of organic matter in the average human body.

Triglycerides (Fats)

Lipids formed by joining a glycerol molecule to three fatty acids via dehydration reactions; primary molecules for long-term energy storage, cushioning, and thermal insulation.

Ester bond

The covalent bond formed between the hydroxyl group of glycerol and the carboxyl group of a fatty acid during a dehydration reaction.

Saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon chain are linked by single covalent bonds and saturated with hydrogen atoms; typically solid at room temperature (e.g., stearic acid).

Unsaturated fatty acid

A fatty acid containing one or more double bonds that create kinks in the hydrocarbon chain; typically liquid at room temperature (e.g., linoleic acid).

Phospholipids

Amphipathic lipids formed from glycerol linked to two fatty acids and a phosphate group, forming the fundamental bilayer structure of cellular membranes.

Amphipathic molecule

A molecule that contains both a hydrophilic (polar) region and a hydrophobic (nonpolar) region.

Steroids

Lipids characterized by a carbon skeleton composed of four interconnected carbon rings; examples include cholesterol, estrogen, and testosterone.

Waxes

Complex, nonpolar lipids secreted onto the surfaces of many plants and animals that contain hydrocarbons and fatty-acid-like structures, serving as water barriers.

Proteins

Polymers composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements (notably sulfur), built from 20 different amino acid monomers.

Amino acids

The monomer building blocks of proteins, each composed of a central $\alpha$-carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain ($R$ group).

Peptide bond

The covalent bond formed between the carboxyl group of one amino acid and the amino group of another during a dehydration reaction.

Polypeptide

A linear polymer chain consisting of multiple amino acids covalently linked in sequence by peptide bonds.

N-terminus

The amino-terminal end of a polypeptide chain featuring a free amino group.

C-terminus

The carboxyl-terminal end of a polypeptide chain featuring a free carboxyl group.

Primary structure

The precise linear sequence of amino acids in a polypeptide chain, encoded and determined directly by genes.

Secondary structure

The localized repeating conformation of a polypeptide chain, such as an $\alpha$ helix or $\beta$ pleated sheet, stabilized by hydrogen bonds between backbone atoms.

$\alpha$ helix

A spiral, helical secondary protein structure stabilized by hydrogen bonds formed along the polypeptide backbone.

$\beta$ pleated sheet

A pleated, sheet-like secondary protein structure formed by hydrogen bonds between parallel or antiparallel polypeptide backbone segments.

Tertiary structure

The complex, three-dimensional folded shape assumed by a single polypeptide chain as its secondary structures and random coiled regions fold together.

Quaternary structure

The biological structure formed when two or more individual polypeptide chains (subunits) associate to create a functional protein.

Disulfide bridge

A covalent bond formed between the sulfhydryl ($-\text{SH}$) groups of two cysteine amino acid side chains, stabilizing protein tertiary and quaternary structure.

Protein domain

A distinct modular structural and functional unit within a protein that possesses a specific biological function, such as ligand binding or DNA binding.

Anfinsen's experiment

A 1961 study demonstrating that denatured ribonuclease can spontaneously refold into its active, functional three-dimensional conformation in vitro upon the removal of urea and $\beta\text{-mercaptoethanol}$, showing that primary structure dictates folding.

Nucleic acids

Macromolecules responsible for the storage, expression, and transmission of genetic information; divided into two classes: DNA and RNA.

Deoxyribonucleic acid (DNA)

A double-stranded helical nucleic acid containing deoxyribose sugar and thymine that stores genetic information encoded in the sequence of nucleotide monomers.

Ribonucleic acid (RNA)

A single-stranded nucleic acid containing ribose sugar and uracil that decodes DNA into instructions for linking amino acids to synthesize polypeptides.

Nucleotide

The monomer subunit of nucleic acids, consisting of a five-carbon sugar (ribose or deoxyribose), a phosphate group, and a nitrogenous base.

Purines

A category of nitrogenous bases characterized by a fused double-ring structure; includes adenine (A) and guanine (G).

Pyrimidines

A category of nitrogenous bases characterized by a single-ring structure; includes cytosine (C), thymine (T), and uracil (U).