Biochemistry Review for PHR6501 (PODA1) – Key Concepts (Vocabulary Flashcards)

Vocabulary-style flashcards covering the major biochemistry concepts and terminology from the lecture notes.

Hydrogen bond

A noncovalent attraction between a hydrogen atom bound to an electronegative atom (usually O or N) and another electronegative atom with lone pairs; crucial for water interactions, DNA base pairing, and drug binding.

Hydrogen bonding (in biological systems)

A type of noncovalent interaction that stabilizes structures like DNA duplexes, proteins, and drug–target interfaces.

Hydrophobic effect

Tendency of water to minimize contact with nonpolar groups, driving protein folding, membrane formation, and biomolecular binding; entropically driven.

pKa

The negative logarithm of the acid dissociation constant; a measure of acid strength; lower pKa = stronger acid and greater tendency to donate a proton.

pH scale

A measure of how acidic or basic (alkaline) a solution is, based on the hydrogen ion concentration; pH = -log10[H+].

Henderson–Hasselbalch equation

A rearranged expression to relate pH, pKa, and the ratio of conjugate base [A−] to weak acid [HA]: pH = pKa + log([A−]/[HA]).

Ionizable group

A functional group that can gain or lose a proton (H+), altering charge state and solubility depending on pH.

Amino acids

The 20 standard α-amino acids that are the building blocks of proteins; each has an amino group, a carboxyl group, and a variable side chain (R).

Chirality

Property of a molecule that is non-superimposable on its mirror image; many biomolecules are chiral and exhibit stereospecific interactions.

L-configuration

Left-handed chiral configuration commonly found in amino acids of mammalian proteins; described using the Fischer convention.

Fischer convention

A method to assign absolute configuration (D/L) to chiral molecules by comparison to glyceraldehyde; in biology, proteins use the L configuration.

Glycine

The simplest amino acid with a hydrogen as its side chain; lacks a chiral center at the α-carbon.

Aliphatic R group

Nonaromatic, nonpolar hydrocarbon side chains (e.g., Gly, Ala, Val, Leu, Ile, Pro) contributing to hydrophobic character.

Aromatic R group

Ring-containing side chains (Phe, Tyr, Trp) with varying polarity that can participate in stacking interactions.

Charged R groups (acidic)

Aspartate and Glutamate side chains that are deprotonated and negatively charged at physiological pH.

Charged R groups (basic)

Lysine and Arginine side chains that are protonated and positively charged at physiological pH; Histidine can be partially charged near pH 7.

Polar, uncharged R groups

Serine, Threonine, Asparagine, Glutamine; polar but not charged at physiological pH, often involved in hydrogen bonding.

Sulfur-containing R groups

Cysteine (R-SH) and Methionine (thioether); Cys can form disulfide bonds (RS-SR) and act as a nucleophile when deprotonated.

Disulfide bond

Covalent S–S linkage between cysteine residues that helps stabilize protein structure.

Amide (peptide) bond

Bond formed between the carboxyl group of one amino acid and the amino group of the next, releasing water; backbone linkage of proteins.

Glycogen

Branched polymer of glucose used by animals for rapid glucose storage; primarily α-1,4 and α-1,6 glycosidic bonds.

Glycosidic bond

C–O–C linkage between sugar units in carbohydrates; α or β orientation refers to the anomeric carbon configuration.

Anomeric carbon

The carbon in a sugar that forms the glycosidic bond; determines α/β anomer, pivotal for monosaccharide chemistry.

Glucose

A six-carbon aldohexose; central energy source in cells; exists in multiple forms (Fischer, Haworth, chair) in biochemistry.

D-glucose Haworth projection

A cyclic representation of glucose showing the ring form with substituents oriented in the plane of the sugar.

ATP (adenosine triphosphate)

Tri-phosphate nucleotide that serves as the cell’s primary energy currency; hydrolysis releases usable energy.

Nucleotides

Building blocks of nucleic acids (DNA, RNA); consist of a sugar (ribose or deoxyribose), a nitrogenous base, and one or more phosphate groups.

DNA

Deoxyribonucleic acid; the molecule that stores genetic information in cells.

Ribose

Five-carbon sugar in RNA; the sugar component that forms RNA nucleotides.

D-fructose

A six-carbon ketose isomer of glucose; a monosaccharide found in many metabolic pathways.

Carbohydrates (overview)

Class of biomolecules including monosaccharides, disaccharides, and polysaccharides; characterized by multiple hydroxyl groups and carbonyls.

D- and L- isomers

Stereoisomers depending on the orientation of substituents around a chiral center; biological systems often use one configuration (e.g., L- amino acids).

Lipids

Biomolecules including fats, oils, and membrane components; hydrophobic or amphipathic molecules with roles in energy storage and membranes.

Triacylglycerol

Body’s main fuel reserve; glycerol esterified to three fatty acids; highly energy-dense storage fat.

Cholesterol

Steroid lipid component of membranes; precursor to steroid hormones and bile acids.

Phosphatidylcholine

Major phospholipid in cell membranes; glycerophospholipid with a choline headgroup; contributes to membrane structure.

Palmitate

Saturated fatty acid (palmitic acid, 16:0); common lipid constituent in fats and membranes.

Oleate

Monounsaturated fatty acid (oleic acid, 18:1); contains a cis double bond affecting fluidity.

Acetyl-CoA

Coenzyme A–linked acetyl group donor; central to metabolism and fatty acid synthesis; can transfer acetyl groups via thioester bonds.

Isoelectric point (pI)

pH at which a molecule has no net electric charge; for amino acids, depends on the pKa values of ionizable groups.

pH

A measure of how acidic or basic a solution is, defined as the negative logarithm of the hydrogen ion concentration.

Kw (ion product of water)

Product of [H+][OH−] in water; at 25°C, Kw = 1.0 × 10−14; used to relate pH and pOH.

Brønsted–Lowry acids and bases

Acid: proton donor; Base: proton acceptor; defines acid-base reactions beyond just water.

Ka and pKa

Ka is the acid dissociation constant of an acid; pKa = −log10(Ka); lower pKa means stronger acid.

Strong acid

An acid that fully or nearly completely ionizes in solution (Ka very large).

Weak acid

An acid that only partially ionizes in solution (Ka small).

Amino acid pKa values (general)

Ionizable groups in amino acids have characteristic pKa values (carboxyl ~2, amino ~9–10), governing their charge state at a given pH.

Isoelectric point example: glycine

Glycine has pI ≈ 6.1, calculated from its two ionizable groups (pKa1 ≈ 2.4 and pKa2 ≈ 9.8).

Amino acid zwitterion

At neutral pH, amino acids exist as zwitterions with both a positive amino group and a negative carboxylate group.

Amino acid side-chain polarity classifications

Aliphatic, Aromatic, Polar uncharged, Charged (acidic/basic), Sulfur-containing—used to predict interactions and folding.

Enantiomers

Non-superimposable mirror-image stereoisomers; biomolecules often interact stereospecifically.

Eutomer and racemic drugs

Eutomer is the pharmacologically active enantiomer; many drugs are used as racemates or single enantiomers due to stereochemistry.

Amino acid sequence determines protein structure

The order of amino acids (primary structure) governs folding into 3D structure and function.