Study Guide: Chemistry of Life to Enzyme Kinetics (Chapters 2–6) - Vocabulary Flashcards

Vocabulary flashcards covering key concepts across Chapters 2–3 and 5–6: cell chemistry, macromolecules, membranes, and enzyme kinetics.

Relative size of things in the cell

Scale order from small to large: atoms < molecules < organelles < cells; helps compare structures inside the cell.

Hydrophilic

Water-loving; polar or charged regions that interact well with water.

Hydrophobic

Water-fearing; nonpolar regions that tend to avoid water.

Amphipathic

Molecule that has both hydrophilic and hydrophobic regions (e.g., phospholipids).

Covalent bond

Strong bond formed by sharing electrons between atoms.

Noncovalent interactions

Weaker interactions that help stabilize structures: hydrogen bonds, ionic interactions, van der Waals forces, and hydrophobic effects.

Polar

Molecule with uneven charge distribution and partial charges.

Nonpolar

Molecule with even charge distribution; typically hydrophobic.

Hydrogen bond

A noncovalent attraction between a hydrogen attached to an electronegative atom and another electronegative atom.

Ionic interaction

Noncovalent attraction between full charges (e.g., between oppositely charged ions or charged side chains).

Van der Waals forces

Weak, noncovalent attractions due to transient dipoles between atoms in close proximity.

Hydration shell

Layer of water molecules surrounding dissolved ions or polar molecules (e.g., NaCl in water).

Bond strength (covalent vs noncovalent)

Covalent bonds are generally much stronger than noncovalent interactions (hydrogen bonds, ionic, van der Waals, hydrophobic).

Properties of water

Polar, bent molecule with high dielectric constant, high heat capacity, and ability to dissolve many substances.

Macromolecules

Large biological polymers: carbohydrates, proteins, nucleic acids, and lipids.

Building blocks and bonds of macromolecules

Monomers linked by covalent bonds: proteins (amino acids via peptide bonds), nucleic acids (nucleotides via phosphodiester bonds), polysaccharides (monosaccharides via glycosidic bonds); lipids (fatty acids to glycerol via ester bonds, not true polymers).

Amino acid general structure

Amino group, carboxyl group, central α-carbon, and variable side chain (R group).

Peptide bond

Covalent bond linking the carboxyl group of one amino acid to the amino group of the next; formed by a dehydration reaction.

Polar vs nonpolar amino acids

Based on R-group properties: polar (hydrophilic) vs nonpolar (hydrophobic); some are charged. Polarity affects solubility and interactions.

Charged amino acids

Amino acids with charged side chains: acidic (negative) and basic (positive) at physiological pH.

Protein 3D structure levels

Primary (sequence), Secondary (α-helix/β-sheet), Tertiary (overall 3D shape), Quaternary (assembly of multiple polypeptides).

Secondary structure

Local folding stabilized by backbone hydrogen bonds (α-helices, β-sheets).

Tertiary structure

Overall 3D conformation of a single polypeptide, stabilized by ionic, hydrogen, hydrophobic interactions, and disulfide bonds.

Quaternary structure

Arrangement of multiple polypeptide chains into a functional protein.

Interactions by levels

Secondary: hydrogen bonds; Tertiary/Quaternary: ionic, hydrogen, hydrophobic, van der Waals; sometimes disulfide covalent bonds.

Nucleic acids building blocks

Nucleotides (sugar, phosphate, base) are the monomers of nucleic acids.

Nucleoside vs nucleotide

Nucleoside = sugar + base; nucleotide = nucleoside + phosphate group.

DNA vs RNA differences

DNA uses deoxyribose and thymine; RNA uses ribose and uracil; DNA is typically double-stranded, RNA is usually single-stranded; both have 5' to 3' directionality.

Phosphodiester linkage

Bond between nucleotides forming the sugar-phosphate backbone (3' hydroxyl to 5' phosphate of next nucleotide).

Sugar type in nucleotides

Five-carbon sugars: ribose in RNA and deoxyribose in DNA.

Glycosidic bond

Bond linking sugar units in polysaccharides.

Monosaccharide, disaccharide, polysaccharide

Monosaccharide = single sugar; disaccharide = two sugars; polysaccharide = many sugars in a chain.

Building blocks of polysaccharides

Monosaccharides (e.g., glucose) as repeating units.

Functions of polysaccharides

Energy storage (starch, glycogen) and structural roles (cellulose, chitin); includes monosaccharide/disaccharide forms.

Sugar in nucleotides (carbon number)

Five-carbon sugar: ribose (RNA) or deoxyribose (DNA).

Glycosidic bond in polysaccharides

Linkage between sugar units forming polysaccharides.

Dehydration reaction

Condensation reaction that forms a covalent bond with removal of water; e.g., peptide, glycosidic, and phosphodiester bond formation.

Biomembrane building blocks

Phospholipids (glycerol backbone, fatty acid tails, phosphate head) form membranes.

Phospholipid structure

Amphipathic molecule with hydrophilic head and hydrophobic tails; forms lipid bilayers in aqueous environments.

Properties of phospholipids

Amphipathic; fluid mosaic nature; tails may be saturated or unsaturated; key to membrane dynamics.

Differences and similarities of macromolecules

All are biological polymers with monomeric units; differ in monomer types, bonds, and functions (carbohydrates, proteins, nucleic acids, lipids).

Protein folding and unfolding

Process by which a polypeptide attains or loses its native 3D structure; stability can be disrupted by environment.

Monomeric vs multimeric proteins

Monomeric: single polypeptide chain; multimeric: several polypeptide chains assemble into a functional unit.

Motif

A short, recurring structural/sequence element within a protein with a specific function.

Domain

A distinct functional/structural unit within a protein that can fold independently.

Protein degradation vs denaturation

Denaturation: loss of structure without breaking peptide bonds; Degradation: breakdown of the polypeptide chain by cleaving peptide bonds.

Equilibrium constant (Keq)

Ratio of product to reactant concentrations at equilibrium for a given reaction.

Kinetic vs potential energy

Kinetic energy is energy of motion; potential energy is stored energy due to position.

Ultimate energy source

Initial energy source powering life; in photosynthetic organisms, sunlight; in others, chemical energy from nutrients.

First law of thermodynamics

Energy is conserved; cannot be created or destroyed, only transformed.

Free energy (G) and standard free energy (G°')

G is energy available to do work; G°' is the standard-state free energy under defined conditions; relates to reaction direction.

Spontaneous, exergonic, endergonic

Spontaneous and exergonic reactions have G < 0 (release energy); endergonic reactions have G > 0 (require energy input).

Gibbs free energy and Keq relationship

ΔG°' = -RT ln(Keq); equilibrium favors products if Keq > 1.

Standard ΔG from Keq

Use ΔG°' = -RT ln(Keq) to relate equilibrium constant to standard free energy change.

Direction of reaction from concentrations

Compute ΔG = ΔG°' + RT ln([products]/[reactants]); negative ΔG means forward; positive means reverse.

Enzymes and ΔG

Enzymes lower activation energy and increase rate but do not change ΔG or the reaction equilibrium.

Energetically unfavorable reactions

Cellular strategies: couple unfavorable reactions to favorable ones (often ATP hydrolysis) to drive the process.

ATP synthesis and hydrolysis ΔG

Hydrolysis of ATP to ADP + Pi releases energy (negative ΔG); synthesis requires energy input (positive ΔG under standard conditions).

How enzymes catalyze reactions

They stabilize transition states and provide an alternative pathway to lower activation energy.

Enzyme kinetics overview

Study of how enzymes accelerate reactions, including substrates, active sites, and rate parameters like Km and Vmax.

Km (Michaelis constant)

Substrate concentration at which the reaction rate is half of Vmax; indicates enzyme affinity for substrate.

Vmax

Maximum rate of an enzyme-catalyzed reaction when the active sites are saturated with substrate.

Michaelis-Menten plot (M-M plot)

v versus [S]; hyperbolic curve used to derive Km and Vmax.

Lineweaver-Burk plot (LB plot)

Double-reciprocal plot (1/v vs 1/[S]) used to linearize kinetics data and determine Km and Vmax.

Factors affecting reaction rate

Temperature, pH, enzyme concentration, substrate concentration, presence of inhibitors or activators.

Competitive inhibitors

Bind to the enzyme's active site, competing with substrate; increase Km, do not change Vmax.

Noncompetitive inhibitors

Bind to a site other than the active site (allosteric); decrease Vmax, Km unchanged.