Pharmaceutical Biochemistry - Protein Structure, Signaling, Acids, Bases, and Buffers

Vocabulary flashcards covering introductory biochemistry, protein structure, enzymatic targets, cell signaling distance classifications, receptor types, acid-base chemistry, Henderson-Hasselbalch equation, and buffer systems.

Biochemistry

The branch of science that uses the principles of chemistry to explain biology at a molecular level.

Six Major Drug Targets

The primary biochemical targets focused on by small-molecule drugs: enzymes, cell surface receptors, nuclear hormone receptors, ion channels, transporters, and DNA.

Catalyst

Any substance that speeds up a chemical reaction without being consumed or permanently altered in the process.

Enzyme

A biological catalyst produced by a living organism, typically made of protein, that speeds up chemical reactions.

Amino Acid

The small organic building block that the body uses in 20 main varieties to construct peptides and proteins.

Peptide

A short chain of amino acids linked together by peptide (amide) bonds.

Dipeptide

A peptide molecule composed of exactly 2 amino acid residues.

Tripeptide

A peptide molecule composed of exactly 3 amino acid residues.

Oligopeptide

A peptide chain composed of 4 to 20 amino acid residues.

Polypeptide

A long peptide chain composed of more than 20 amino acid residues.

Types of Protein Structures

The four hierarchical levels of structural organization in proteins: Primary, Secondary, Tertiary, and Quaternary.

Primary Structure

The unique linear sequence of amino acids in a polypeptide chain connected by peptide bonds.

Secondary Structure

Local folding structures within a polypeptide chain, such as alpha helices (coils) and beta pleated sheets (folds), stabilized by hydrogen bonds.

Tertiary Structure

The overall three-dimensional folded shape of a single polypeptide chain that determines its biological function.

Quaternary Structure

The structural complex formed when two or more individual folded polypeptide chains (subunits) assemble together.

Conjugated Protein

A complex protein containing a protein attached to a non-protein organic or inorganic prosthetic group.

Glycoprotein

A conjugated protein formed by the attachment of a carbohydrate group to a protein.

Lipoprotein

A conjugated protein formed by the attachment of a lipid group to a protein.

Nucleoprotein

A conjugated protein formed by the attachment of a nucleic acid group to a protein.

Hydrolysis of Peptides

The enzymatic breakdown of a peptide chain into amino acids via hydrolytic enzymes, which add $H_2O$ by placing hydrogen onto the amide nitrogen and hydroxyl onto the carbonyl carbon.

Signals Classified by Distance

The categorization of cell signaling molecules based on reach: Autocrine (cell to itself), Paracrine (to nearby target cells), and Endocrine (long-distance through bloodstream).

Autocrine Signal

A signaling molecule secreted by a cell that binds to receptors on its own cell surface.

Paracrine Signal

A signaling molecule released by a cell to interact with target cells located nearby.

Endocrine Signal

A long-distance signaling molecule (such as a hormone or cytokine) secreted into the bloodstream to reach distant target cells.

Ligand

A signaling molecule that binds specifically to a receptor to deliver a chemical message.

Hydrophobic Ligand

A water-fearing signaling molecule that crosses the fatty cell membrane with carrier proteins and binds to intracellular receptors.

Hydrophilic Ligand

A water-loving signaling molecule that cannot pass through the lipid cell membrane and must bind to receptors on the cell surface.

G-Protein Coupled Receptor (GPCR)

A cell surface receptor with 7 transmembrane passes that activates an intracellular G-protein composed of alpha ($\beta$), beta ($\beta$), and gamma ($\frac{\text{gemma}}{}$) subunits upon ligand binding.

$G_\text{q}$ Subunit

A G-protein subunit that activates phospholipase C upon receptor activation.

$G_\text{s}$ Subunit

A G-protein subunit that stimulates adenylyl (adenylase) cyclase upon receptor activation.

$G_\text{i}$ Subunit

A G-protein subunit that inhibits adenylyl (adenylase) cyclase upon receptor activation.

Brønsted-Lowry Acid

A chemical species that donates a proton ($H^+$) to a solution.

Brønsted-Lowry Base

A chemical species that accepts a proton ($H^+$) from a solution.

Amphoteric

The property of a substance (such as water) that enables it to act as either an acid or a base depending on the reaction conditions.

Strong Acid

An acid that ionizes or dissociates almost completely in water ($K_a \rightleftharpoons 1$), yielding a high concentration of $H^+$ (e.g., $HCl$).

Weak Acid

An acid that only partially dissociates in water ($K_a \rightleftharpoons 1$), resulting in a low concentration of $H^+$ (e.g., $CH_3CO_2H$, $HF$).

pH Scale

A logarithmic scale from 0 to 14 measuring hydrogen ion concentration, where values below 7 are acidic, 7 is neutral, and values above 7 are alkaline.

$$pH$$

A convenient logarithmic measure of the concentration of hydrogen ions in solution, expressed as $pH = -\text{log}[H^+]$.

$$pOH$$

A measure of the concentration of hydroxide ions in solution, expressed as $pOH = -\text{log}[OH^-]$ or $pOH = 14 - pH$.

Acid Dissociation Constant ($K_a$)

An equilibrium constant describing how strongly an acid releases protons in solution, calculated as $K_a = \frac{[H^+][A^-]}{[HA]}$.

$$p K_a$$

A logarithmic measure of acid strength defined as $p K_a = -\text{log}(K_a)$, where a lower $p K_a$ value indicates a stronger acid.

Henderson-Hasselbalch Equation

The mathematical formula $pH = p K_a + \text{log}\frac{[A^-]}{[HA]}$ used to calculate the pH of buffer solutions based on the ratio of conjugate base to weak acid.

Buffer

A solution consisting of a weak acid and its conjugate base that resists drastic changes in pH when small amounts of acid or base are added.

Buffer Capacity

The amount of acid or base a buffer solution can absorb before undergoing substantial pH changes, determined by the total concentration of conjugate base and weak acid.

Respiratory Acidosis

An acid-base imbalance caused by hypoventilation leading to $CO_2$ accumulation, higher $H_2CO_3$, and lower blood pH, compensated by renal retention of bicarbonate ($HCO_3^-$).

Respiratory Alkalosis

An acid-base imbalance caused by hyperventilation leading to excessive loss of $CO_2$, lower $H_2CO_3$, and elevated blood pH, compensated by renal excretion of bicarbonate ($HCO_3^-$).

Metabolic Acidosis

An acid-base imbalance caused by loss of bicarbonate or accumulation of metabolic acids, lowering blood pH and inducing rapid hyperventilation to expire $CO_2$.

Metabolic Alkalosis

An acid-base imbalance caused by loss of acid (such as $HCl$ via severe vomiting) or alkali ingestion, raising blood pH and inducing hypoventilation to retain $CO_2$.