Amino Acids, Proteins, and DNA Flashcards

A complete set of vocabulary flashcards covering amino acids, protein structures, chromatography techniques, enzyme kinetics, DNA composition, and medical biochemistry based on the lecture notes.

Amino acids

The building blocks of proteins, these molecules contain two functional groups: a carboxylic acid group and a primary amine group.

$\alpha$-amino acids

Also known as 2-amino acids, these are compounds where the amine group is located on the carbon atom adjacent to the $-CO_2H$ group.

Bifunctional compounds

Compounds that contain two different functional groups within the same molecule.

Chiral

A molecule with a carbon atom bonded to four different groups; almost all naturally occurring amino acids exist as the $(-)$ enantiomer.

Zwitterions

Ions that have both a permanent positive charge and a permanent negative charge, making the overall compound neutral; they typically behave like ionic salts with high melting points.

Protonated

The state of an amino acid in strongly acidic conditions where the lone pair of the $H_2N-$ group accepts a hydrogen ion to form a positive ion.

Deprotonated

The state of an amino acid in strongly alkaline solutions where the $-OH$ group loses a hydrogen ion to form a negative ion.

Peptides

Compounds formed by the linkage of amino acids; molecules with up to 50 amino acids are polypeptides, while those with more than 50 are proteins.

Peptide linkage

The amide linkage $-CONH-$ formed when the amine group of one amino acid reacts with the carboxylic acid group of another.

Primary structure

The fixed sequence of amino acids in a protein chain, held together by stable covalent bonding.

Secondary structure

The arrangement of a protein chain into an $\alpha$-helix or a $\beta$-pleated sheet, held in place by hydrogen bonding between $C=O$ and $-N-H$ groups.

Tertiary structure

The three-dimensional folding of a protein's secondary structure, held in place by hydrogen bonding, ionic interactions, sulfur-sulfur bonds, and van der Waals forces.

Disulfide bridge

A sulfur-sulfur bond formed between two cysteine molecules under oxidising conditions, creating a bridge between protein molecules.

Hydrolysis

A reaction with water, often catalysed by $6\,mol\,dm^{-3}$ hydrochloric acid or enzymes, used to break peptide linkages and return a protein to its constituent amino acids.

Thin-layer chromatography (TLC)

A technique used to separate and identify amino acids using a stationary phase of silica ($SiO_2$) on a plastic or glass sheet and a liquid mobile phase.

Mobile phase

The solvent or mixture of solvents, also called the eluent, that carries substances up a chromatography plate.

Ninhydrin

A developing agent sprayed onto a chromatography plate that reacts with amino acids to form a purple compound, making them visible.

$R_f$ value

A ratio used to identify substances in chromatography, calculated as the distance moved by the spot divided by the distance moved by the solvent.

Enzymes

Globular protein-based catalysts found in living things that speed up reactions by factors of up to $10^{10}$ and act on specific substrate molecules.

Active site

A cleft or crevice in an enzyme's structure where the substrate molecule fits precisely and the reaction takes place.

Stereospecificity

The characteristic of many enzymes to only catalyse reactions for one specific enantiomer of a pair of stereoisomers.

Enzyme inhibition

A process where a molecule with a similar shape to the substrate binds to and blocks the active site of an enzyme, stopping the reaction.

Nucleotides

The monomers from which DNA is made, each consisting of a phosphate group, a 2-deoxyribose sugar, and an organic base.

DNA Bases

The four organic bases that form part of nucleotides: cytosine (C), thymine (T), adenine (A), and guanine (G).

Double helix

The structure of DNA consisting of two strands winding around each other, held together by hydrogen bonding between complementary base pairs.

Complementary DNA strands

Two DNA molecules bonded together where adenine (A) on one strand matches thymine (T) on the other, and guanine (G) matches cytosine (C).

Codons

Three-base sections of DNA that each represent a particular amino acid in a protein sequence.

Replication

The process during cell division where the hydrogen bonds of the DNA double helix break, and new nucleotides pair with exposed bases to form two identical DNA molecules.

Cisplatin

A square planar anti-cancer drug that bonds to nitrogen atoms on adjacent guanine bases in DNA, distorting its shape and preventing cell replication.

Ligand substitution

The reaction mechanism by which cisplatin's chloride ions are displaced by water and then by nitrogen on guanine to bond with DNA.