General Biochemistry (BCHEM 154) - Amino Acids, Proteins, Enzymes, and Nucleic Acids

Comprehensive vocabulary flashcards covering general biochemistry topics including amino acid chemistry, protein structural hierarchy, enzyme kinetics and classification, and nucleic acid functions.

Proteins

Complex organic nitrogenous substances in the cells of plants and animals that contain $C$, $H$, $N$, $O$, and $S$, with amino acids as their building block units.

$\alpha$-carbon

The central carbon atom in an amino acid, adjacent to the carboxylic group, to which the amino group, carboxylic group, a hydrogen atom, and a side chain $R$ group are bonded.

Zwitterion

The dipolar ion form of an amino acid in the crystalline or solid state, where the $COOH$ group exists as a carboxylate ion ($COO^-$) and the $NH_2$ group exists as an ammonium ion ($NH_3^+$).

Isoelectric point ($pI$)

The specific $pH$ value at which an amino acid has no net charge and does not migrate in an electric field.

Essential Amino Acids

Amino acids that cannot be synthesized in the body of higher animals and must be provided in the diet, such as Histidine, Leucine, and Methionine.

Transamination

The process involving the transfer of an amino group from an amino acid to an acceptor keto acid, catalyzed by transaminase enzymes.

Kwashiorkor

A disease in children caused by a prolonged deficiency of essential amino acids in the diet.

Peptide Bond

A covalent link between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another, characterized by a partial double bond character and a rigid, usually trans configuration.

Sanger’s Reagent

$2,4$-dinitrofluorobenzene, used to determine the amino acid sequence by reacting with the free $N$-terminal end to form a yellow dinitrophenyl (DNP) derivative.

Edman’s Degradation

A method for sequencing amino acids using phenylisothiocyanate, which reacts with the $N$-terminal residue to release a stable phenylthiohydantoin derivative while leaving the rest of the chain intact.

Simple Proteins

Proteins that are composed exclusively of amino acids, such as albumin, globulins, and keratin.

Conjugated Proteins

Proteins that contain non-protein portions called prosthetic groups, which yield amino acids and other organic or inorganic components upon hydrolysis.

Fibrous Proteins

Water-insoluble, tough, and thread-like molecules with structural or protective functions, predominantly featuring $\alpha$-helix or $\beta$-pleated sheet secondary structures.

Globular Proteins

Compact, spherical molecules that are soluble in aqueous systems and perform functional roles such as catalysis (enzymes) and transport (hemoglobin).

Primary Structure

The linear sequence or exact order in which amino acids are covalently linked together in a protein.

Secondary Structure

The coiling or folding of a polypeptide chain into structures like the $\alpha$-helix or $\beta$-pleated sheet, stabilized by hydrogen bonding between peptide groups.

Tertiary Structure

The three-dimensional folding of a polypeptide chain into its biologically active native conformation, stabilized by hydrophobic interactions, ionic bonds, and disulfide linkages.

Quaternary Structure

The arrangement of multiple polypeptide chains (subunits or monomers) to form a single functional protein molecule.

Denaturation

The process of unfolding a native protein's ordered conformation, leading to the loss of biological activity, typically caused by heat, extreme $pH$, or chemical agents.

Enzymes

Biological catalysts that accelerate chemical reactions by lowering the activation energy ($E_a$) without being consumed in the process.

Holo-enzyme

The complete enzyme complex consisting of the protein portion (apoenzyme) and its required non-protein portion (prosthetic group or coenzyme).

Michaelis Constant ($K_m$)

The substrate concentration at which an enzyme-catalyzed reaction occurs at half of its maximum velocity ($V_{max}$), indicating the enzyme's affinity for the substrate.

Oxidoreductases

Enzymes that catalyze oxidation-reduction reactions by adding or removing electrons, oxygen, or hydrogen.

Lyases

Enzymes that remove groups non-hydrolytically, often leaving a double bond, or add groups to double bonds (e.g., decarboxylases).

Ligases

Enzymes that catalyze the linking together of two molecules, coupled with the hydrolysis of a high-energy phosphate compound such as $ATP$.

Allosteric Regulation

The control of enzyme activity through effectors that bind non-covalently at a site other than the active site, often resulting in a sigmoidal velocity curve.

Zymogens

Inactive precursor forms of enzymes, such as trypsinogen, which are activated at a physiologically appropriate time and place.

Nucleotide

The building block of nucleic acids, consisting of a nitrogenous base, a pentose sugar, and a phosphoric acid residue.

Watson and Crick Model

The double-helix structure of $DNA$, where two anti-parallel strands are held together by complementary base pairing ($A-T$ and $G-C$) via hydrogen bonds.

Transcription

The process by which the order of bases is passed from $DNA$ to $RNA$ in the nucleus.

mRNA

Messenger $RNA$; a carrier of genetic information from $DNA$ in the nucleus to the cytosol, specifying the amino acid sequence for protein synthesis.

tRNA

Transfer $RNA$; small, clover-leaf shaped molecules responsible for transporting specific amino acids to the ribosomes during translation.

rRNA

Ribosomal $RNA$; the most abundant form of $RNA$ in the cell, serving as a structural and functional component of ribosomes, the site of protein synthesis.