Biochemistry: Amino Acids, Enzymes, Transport, Signaling, and Eicosanoids

Vocabulary flashcards covering core biochemistry topics including amino acid chemistry, protein structure, enzyme kinetics and inhibition, membrane transport mechanisms, signal transduction, and arachidonic acid pathways.

Amino Acid

An organic molecule containing a central $\alpha$-carbon bonded to a basic amino group ($-NH_2$), an acidic carboxyl group ($-COOH$), a hydrogen atom ($-H$), and a distinctive side chain ($-R$).

Proline

An $\alpha$-imino acid exception among the standard 20 amino acids, characterized by its cyclic side chain bonded to the amine nitrogen.

Zwitterion

A dipolar ion form of an amino acid containing equal numbers of positively charged ($-NH_3^+$) and negatively charged ($-COO^-$) groups, resulting in a net charge of zero at neutral $pH$.

Isoelectric Point ($pI$)

The specific $pH$ value at which the zwitterionic form of an amino acid carries a net charge of zero, calculated as the average of the surrounding $pK_a$ values.

Primary Structure

The linear sequence of amino acid residues linked by peptide bonds within a polypeptide chain, directly encoded in DNA.

Secondary Structure

The local spatial arrangement of the polypeptide backbone, such as an $\alpha$-helix or $\beta$-pleated sheet, stabilized by hydrogen bonds between amide $-NH$ and $C=O$ backbone groups.

Tertiary Structure

The overall three-dimensional, biologically active conformation of a single polypeptide subunit, stabilized by disulfide bonds and weak interactions (hydrogen bonds, hydrophobic interactions, electrostatic interactions, and Van der Waals forces).

Quaternary Structure

The structural assembly of two or more separate polypeptide chains (subunits) held together by non-covalent or covalent interactions to form a functional protein complex.

Holoenzyme

A catalytically active complete enzyme complex consisting of the protein component (apoenzyme) combined with its necessary cofactor.

Apoenzyme

The protein component of an enzyme that requires a cofactor for catalytic activity but lacks it, rendering it inactive.

Michaelis Constant ($K_m$)

The substrate concentration at which an enzymatic reaction rate reaches half of its maximum velocity ($\frac{V_{max}}{2}$), serving as an inverse measure of substrate binding affinity.

LineWeaver-Burk Plot

A double-reciprocal linear graph of $\frac{1}{V}$ against $\frac{1}{[S]}$ used to determine kinetic constants, where the x-intercept equals $-\frac{1}{K_m}$ and the y-intercept equals $\frac{1}{V_{max}}$.

Competitive Inhibitor

A substrate analog that competes for binding at the enzyme active site, increasing the apparent $K_m$ (reducing affinity) without changing $V_{max}$.

Uncompetitive Inhibitor

An inhibitor that binds exclusively to the enzyme-substrate ($ES$) complex, resulting in a proportional decrease in both $K_m$ and $V_{max}$.

Noncompetitive Inhibitor

An inhibitor that binds away from the active site on both free enzyme and the enzyme-substrate complex, reducing $V_{max}$ while leaving $K_m$ unaffected.

Allosteric Enzyme

An enzyme containing multiple binding sites that produces a sigmoidal velocity curve due to cooperative interaction between its subunits rather than standard Michaelis-Menten kinetics.

Zymogen

An inactive protein precursor (proenzyme) that requires selective proteolytic cleavage to undergo structural activation into an active enzyme.

Primary Active Transport

The movement of solutes across a biological membrane against their electrochemical gradient, directly powered by the hydrolysis of $ATP$.

Secondary Active Transport

The movement of a substance uphill against its concentration gradient, powered by an ion gradient (such as $Na^+$) created by primary active transport.

Phosphodiesterase (PDE)

An enzyme family that inactivates cyclic nucleotide second messengers by hydrolyzing $cAMP$ and $cGMP$ into 5'-mononucleotides.

Phospholipase A2 (PLA2)

The primary enzyme responsible for hydrolyzing membrane phospholipids to release free arachidonic acid for eicosanoid biosynthesis.

COX-1

A constitutively expressed cyclooxygenase enzyme that generates prostanoids needed for physiological housekeeping tasks, including gastric mucosal protection.

COX-2

An inducible cyclooxygenase isoform upregulated by growth factors and inflammatory cytokines, serving as the dominant prostanoid source in inflammation and malignancy.