Life and Chemistry: Large Molecules

Vocabulary practice flashcards covering the structure, assembly, and biological functions of major macromolecules including proteins, nucleic acids, and carbohydrates from Lecture 3.

Biological macromolecules

Large, complex molecules assembled from smaller molecular building blocks that perform the essential structural, catalytic, transport, informational, and recognition tasks of cells.

True polymer

A large molecule composed of repeating, covalently linked monomeric building blocks; major biological examples include proteins (amino acids), nucleic acids (nucleotides), and polysaccharides (monosaccharides).

Lipids

A major class of biological macromolecules composed of fatty acids, glycerol, and other components that serve in membrane structure, energy storage, and signaling, but are typically not true polymers of repeating monomers.

Amino acid

The monomeric building block of proteins, consisting of a central $\alpha$-carbon covalently bonded to an amino group ($\text{NH}_3^+$), a carboxyl group ($\text{COO}^-$), a hydrogen atom ($\text{H}$), and a variable side chain ($R$ group).

Zwitterion

The dipolar ionic state in which amino acids commonly exist at approximately physiological pH, bearing a positively charged amino group ($\text{NH}_3^+$) and a negatively charged carboxyl group ($\text{COO}^-$).

Peptide bond

The covalent linkage formed between the carboxyl carbon of one amino acid and the amino nitrogen of another via a condensation reaction that releases $\text{H}_2\text{O}$, exhibiting restricted rotation around the $\text{C–N}$ bond.

Polypeptide backbone

The repeating chain of atoms (\text{N–C}_\\text{alpha}\text{–C}) linked by peptide bonds that extends from the N-terminus to the C-terminus, from which variable $R$ groups project.

Primary structure

The unique, linear sequence of amino acids in a polypeptide chain joined by covalent peptide bonds, conventionally written from the N-terminus to the C-terminus.

Secondary structure

Local, regular folding patterns of the polypeptide backbone stabilized by hydrogen bonds between backbone $\text{C=O}$ and $\text{H–N}$ groups, independent of side-chain ($R$ group) interactions.

$\alpha$-Helix

A coiled, right-handed secondary structural motif stabilized by intrachain hydrogen bonds between the backbone $\text{C=O}$ of residue $i$ and the backbone $\text{N–H}$ of residue $i+4$, with $R$ groups projecting outward.

$\beta$-Sheet

A secondary structure consisting of two or more extended $\beta$-strands aligned side-by-side in parallel or antiparallel arrangements, held together by hydrogen bonds between opposing peptide backbone groups.

Tertiary structure

The overall, definitive three-dimensional conformation of a single polypeptide chain, largely driven by interactions among amino-acid $R$ groups, including hydrophobic clustering, hydrogen bonds, ionic bonds, van der Waals forces, and disulfide linkages.

Quaternary structure

The higher-order structural organization resulting from the specific association of two or more polypeptide subunits, stabilized by noncovalent interactions and disulfide bonds.

Sickle-cell hemoglobin (HbS)

A mutant form of hemoglobin where a single amino-acid substitution at position $\beta 6$ replaces a hydrophilic glutamate (Glu) with a hydrophobic valine (Val), creating an abnormal hydrophobic patch that polymerizes into long fibers when deoxygenated.

Denaturation

The loss of a protein's functional native secondary, tertiary, or quaternary three-dimensional conformation caused by disruptions such as heat, extreme pH, detergents, or redox changes, typically without cleaving peptide bonds.

Molecular chaperones

Proteins, such as chaperonins, that assist newly synthesized or unfolding polypeptides in achieving correct folding while preventing inappropriate aggregation and unproductive interactions.

Prions

Infectious misfolded proteins capable of propagating pathology by inducing normally folded counterparts of the same protein to adopt the abnormal, misfolded conformation.

X-ray crystallography

An experimental technique used to determine three-dimensional atomic structure by directing an X-ray beam at a crystallized molecule, recording the resulting diffraction pattern on film or a detector, and reconstructing an electron density map.

Nucleotide

The monomer of nucleic acids, composed of three components: a nitrogenous base (purine or pyrimidine), a five-carbon pentose sugar, and one or more phosphate groups.

Nucleoside

A molecular unit consisting of a nitrogenous base covalently linked to a pentose sugar, lacking the phosphate group(s) present in a complete nucleotide.

Purines

A class of double-ring nitrogenous bases found in nucleic acids, specifically adenine (A) and guanine (G).

Pyrimidines

A class of single-ring nitrogenous bases found in nucleic acids, including cytosine (C), thymine (T in DNA), and uracil (U in RNA).

Phosphodiester bond

The covalent linkage connecting the $3'\text{–OH}$ group of one nucleotide's pentose sugar to the $5'\text{–phosphate}$ group of the adjacent nucleotide, forming the structural backbone of DNA and RNA.

Antiparallel double helix

The structural arrangement of DNA in which two complementary polynucleotide strands run in opposite directions (one $5' \rightarrow 3'$ and the other $3' \rightarrow 5'$), coiling around a common axis with bases directed toward the interior.

Complementary base pairing

Specific hydrogen bonding between nitrogenous bases in DNA and RNA, pairing adenine with thymine/uracil via 2 hydrogen bonds ($\text{A=T}$ or $\text{A=U}$) and guanine with cytosine via 3 hydrogen bonds ($\text{G}\\text{equiv}\text{C}$).

Base stacking

Hydrophobic and van der Waals interactions between the planar, aromatic rings of adjacent nitrogenous bases aligned parallel within the core of a nucleic acid helix, serving as a major stabilizing force.

Ribozymes

RNA molecules with specific catalytic activity capable of facilitating biochemical reactions, demonstrating that RNA can possess enzymatic as well as informational roles.

RNA-world hypothesis

The hypothesis proposing that early evolutionary stages of life relied primarily on RNA molecules to execute both genetic information storage and biochemical catalytic functions.

Monosaccharide

The simplest carbohydrate monomer, classified according to carbon number (e.g., triose, pentose, hexose) and the position of its carbonyl group (aldose versus ketose).

Anomeric carbon

The carbonyl carbon (carbon 1 in glucose) that becomes a chiral center upon ring closure in aqueous solution, creating two distinct stereochemical configurations: $\alpha$ and $\beta$.

Glycosidic bond

The covalent linkage formed between the anomeric carbon of one monosaccharide and a hydroxyl group of another via a condensation reaction that releases water.

Starch

A plant storage polysaccharide composed of $\alpha$-glucose units, existing as unbranched amylose (linear $\alpha(1\rightarrow 4)$ chains) and branched amylopectin ($\alpha(1\rightarrow 4)$ chains with $\alpha(1\rightarrow 6)$ branch points).

Glycogen

An extensively branched animal storage polysaccharide made of $\alpha$-glucose units joined by $\alpha(1\rightarrow 4)$ glycosidic bonds with frequent $\alpha(1\rightarrow 6)$ branch points.

Cellulose

A linear, unbranched structural polysaccharide of plant cell walls composed of $\beta$-glucose monomers linked by $\beta(1\rightarrow 4)$ glycosidic bonds that form hydrogen-bonded parallel microfibrils.

Chitin

A structural polysaccharide made of repeating modified glucose monomers linked by $\beta$-glycosidic bonds, providing mechanical support in arthropod exoskeletons and fungal cell walls.