BSCI170 Biological Chemistry, Macromolecules, and Nucleic Acids

Vocabulary flashcards generated from BSCI170 lecture notes covering nucleic acids, proteins, chemical bonds, chemistry of water, carbon functional groups, and carbohydrates.

Nucleotide

A monomer of nucleic acids composed of three components: a pentose sugar, a nitrogenous base, and at least one phosphate group.

Nucleoside

A compound composed of a pentose sugar and a nitrogenous base, lacking a phosphate group.

Ribose

A five-carbon pentose sugar found in RNA that possesses a hydroxyl group ($-OH$) attached to its $2'$ carbon.

Deoxyribose

A five-carbon pentose sugar found in DNA that has a hydrogen atom ($-H$) instead of a hydroxyl group attached to its $2'$ carbon.

Purines

Nitrogenous bases containing a double-ring structure, which include Adenine (A) and Guanine (G).

Pyrimidines

Nitrogenous bases containing a single heterocyclic ring structure, which include Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA).

Phosphodiester bond

The covalent bond linking nucleotides in a nucleic acid strand, formed between the $5'\text{-phosphate}$ group of an incoming nucleotide and the $3'\text{-OH}$ group of the pentose sugar of the existing chain.

Antiparallel

The arrangement of the two strands in a DNA double helix, running in opposite directions with one strand oriented $5'$ to $3'$ and the other $3'$ to $5'$.

Chargaff's rule

The biological principle formulated by Erwin Chargaff stating that in double-stranded DNA, the percentage of adenine (A) equals thymine (T), and the percentage of guanine (G) equals cytosine (C).

Amino acid

An organic monomer of proteins consisting of a central \begin{equation}\begin{aligned}\alpha\text{-carbon}\end{aligned}\end{equation} bonded to an amino group ($-NH_2$ or $-NH_3^+$), a carboxyl group ($-COOH$ or $-COO^-$), a hydrogen atom, and a variable side chain (R group).

Peptide bond

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

Primary structure

The linear sequence of amino acids in a polypeptide chain, stabilized by covalent peptide bonds.

Secondary structure

Regular, repeated folding patterns of a polypeptide backbone, such as \begin{equation}\alpha\text{-helices}\end{equation} and \begin{equation}\beta\text{-pleated sheets}\end{equation}, stabilized by hydrogen bonds between backbone atoms.

Tertiary structure

The overall three-dimensional shape of a single polypeptide chain, primarily stabilized by noncovalent interactions and covalent disulfide bridges between side chain (R group) atoms.

Quaternary structure

The structural assembly resulting from the association of two or more polypeptide subunits into a larger functional protein molecule.

Disulfide bridge

A covalent bond ($-S-S-$) formed between the sulfhydryl ($-SH$) side chains of two cysteine residues that stabilizes protein tertiary and quaternary structures.

Electronegativity

The relative tendency of an atom to attract shared electrons within a covalent bond.

Polar covalent bond

A covalent bond in which shared electrons are drawn more strongly to one atom's nucleus than another, resulting in partial positive ($\delta^+$) and partial negative ($\delta^-$) charges.

Nonpolar covalent bond

A covalent bond in which electrons are shared equally between two atoms with similar electronegativities, leaving no partial charges.

Ionic bond

A chemical bond resulting from the electrostatic attraction between oppositely charged ions formed by the complete transfer of electrons.

Cation

A positively charged ion formed when an atom loses one or more electrons.

Anion

A negatively charged ion formed when an atom gains one or more electrons.

Hydrogen bond

A weak electrostatic attraction between a partially positive hydrogen atom covalently bound to an electronegative atom (such as O or N) and another electronegative atom with a partial negative charge.

van der Waals interactions

Transient, distance-dependent electrostatic attractions between nonpolar molecules or atoms caused by temporary asymmetrical distributions of electron clouds.

Hydration shell

A sphere of water molecules surrounding a dissolved ion or charged solute, oriented according to partial electrical charges.

Cohesion

The attraction between molecules of the same substance, such as hydrogen bonding between water molecules that generates surface tension.

Adhesion

The attraction between molecules of different substances, such as water forming hydrogen bonds with polar cell wall surfaces.

Acid

A substance that donates hydrogen ions ($H^+$) in aqueous solutions, thereby increasing the $[H^+]$ and decreasing the pH below $7$.

Base

A substance that accepts hydrogen ions ($H^+$) or donates hydroxide ions ($OH^-$) in aqueous solutions, thereby reducing the $[H^+]$ and increasing the pH above $7$.

Buffer

A substance that minimizes rapid or drastic changes in the $[H^+]$ and $[OH^-]$ concentrations of a solution by accepting or releasing $H^+$ ions.

Isomers

Compounds that possess the exact same molecular formula but differ in their structural arrangement or spatial orientation.

Structural isomers

Isomers that differ in the covalent arrangement of their constituent atoms or double bonds.

Cis-trans isomers

Isomers sharing the same covalent bonds that differ in spatial arrangement around a double bond ($C=C$), where cis has functional groups on the same side and trans has them on opposite sides.

Hydroxyl group

A polar functional group represented as $-OH$, characteristic of alcohols, involved in hydrogen bonding and condensation reactions.

Carboxyl group

A charged, acidic functional group represented as $-COOH$ (or $-COO^-$ in ionized form), consisting of a carbon double-bonded to an oxygen and single-bonded to a hydroxyl group.

Amino group

A charged, basic functional group represented as $-NH_2$ (or $-NH_3^+$ in ionized form) that accepts an $H^+$ ion in biological tissues.

Phosphate group

A charged, acidic functional group represented as $-O-PO_3^{2-}$, formed by a phosphorus atom bonded to four oxygen atoms, central to nucleic acid backbones and energy transfer.

Monosaccharide

A monomeric carbohydrate with a molecular formula typically built as a multiple of $(CH_2O)_n$, containing a single sugar ring or linear carbon chain.

Aldose

A monosaccharide possessing a carbonyl group located at the terminus of its carbon chain as an aldehyde group (e.g., glucose, glyceraldehyde).

Ketose

A monosaccharide possessing a carbonyl group located within its carbon chain as a ketone group (e.g., fructose, dihydroxyacetone).

Glycosidic bond

A covalent bond formed between two monosaccharide sugar molecules through a dehydration reaction.

Cellulose

An unbranched structural polysaccharide composed of glucose monomers linked by chemically stable $\beta-1,4$ glycosidic bonds that forms plant cell walls.

Starch

A plant storage polysaccharide composed of glucose monomers linked by $\alpha-1,4$ glycosidic bonds with $\alpha-1,6$ glycosidic branch points.

Glycogen

A highly branched animal storage polysaccharide composed of glucose monomers linked by $\alpha-1,4$ and $\alpha-1,6$ glycosidic bonds, stored in compact deposits.

Central Dogma

The fundamental concept describing the directional flow of genetic information within biological systems from DNA to RNA to Proteins.