Unit 1 – Biochemistry

Vocabulary flashcards covering major biochemistry concepts from Unit 1 lecture notes.

Atomic Structure

The arrangement of protons, neutrons, and electrons in an atom, determining its chemical properties.

Element

A substance that cannot be broken down into simpler substances by chemical means (e.g., oxygen, carbon).

Trace Element

An element required by organisms only in minute quantities (e.g., iron, iodine, copper).

Atom

The smallest unit of an element that retains the element’s properties.

Ground State

The lowest energy level of electrons in an atom.

Excited State

A higher-energy electronic configuration reached after the atom absorbs energy.

Isotope

Atoms of the same element that differ in neutron number (e.g., Carbon-12 vs. Carbon-14).

Radioisotope

A radioactive isotope that decays at a predictable rate (half-life) and emits radiation.

Half-Life

The time it takes for half of the atoms in a radioactive sample to decay.

Tracer

A radioisotope incorporated into a molecule to follow its metabolic pathway (e.g., Carbon-14).

Bond

An attraction between atoms that results in a more stable electron configuration and releases energy.

Ionic Bond

Chemical bond formed by the complete transfer of electrons, producing oppositely charged ions.

Cation

A positively charged ion produced when an atom loses electrons.

Anion

A negatively charged ion produced when an atom gains electrons.

Covalent Bond

Chemical bond formed when atoms share electron pairs.

Nonpolar Covalent Bond

A covalent bond in which electrons are shared equally between atoms.

Polar Covalent Bond

A covalent bond with unequal electron sharing, producing partial charges.

Molecule

Two or more atoms held together by covalent bonds.

Hydrophilic

Water-loving; describes polar or charged substances that dissolve in water.

Hydrophobic

Water-hating; describes nonpolar substances that are insoluble in water and mix with lipids.

Hydrogen Bond

Weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

Specific Heat

Amount of heat needed to raise 1 g of a substance 1 °C; water’s high value stabilizes temperatures.

Heat of Vaporization

Heat required to convert a liquid to gas; high in water, enabling evaporative cooling.

Universal Solvent

Nickname for water because its polarity dissolves most polar and ionic substances.

Cohesion Tension

Attraction between water molecules that contributes to water column pull in plants.

Transpirational Pull

Upward movement of water from roots to leaves driven by water loss from leaves.

Capillary Action

Movement of water up narrow tubes due to cohesion and adhesion.

Surface Tension

Measure of how difficult it is to stretch or break the surface of a liquid; high in water.

Ice Density Anomaly

Solid water is less dense than liquid water, so ice floats.

Spring Overturn

Seasonal mixing in lakes that redistributes oxygen and nutrients when ice melts.

pH

Negative logarithm of hydrogen ion concentration; measures acidity/alkalinity.

Buffer

Substance that resists pH changes by absorbing or donating H⁺ (e.g., bicarbonate ion).

Isomer

Organic compounds with the same molecular formula but different structures.

Structural Isomer

Isomers that differ in the covalent arrangement of atoms.

Cis-Trans Isomer

Isomers with different spatial arrangements around a double bond.

Enantiomer

Mirror-image isomers (L- and D- forms) that may differ biologically.

Carbohydrate

Organic compound of C, H, O with a 2:1 H:O ratio; primary quick energy source (4 cal/g).

Monosaccharide

Simple sugar monomer (e.g., glucose, fructose).

Disaccharide

Sugar formed by two monosaccharides via dehydration synthesis (e.g., maltose, lactose, sucrose).

Dehydration Synthesis

Reaction that joins monomers by removing a water molecule.

Hydrolysis

Reaction that breaks polymers by adding water; reverse of dehydration synthesis.

Polysaccharide

Carbohydrate polymer of many monosaccharides joined by dehydration reactions.

Cellulose

Structural polysaccharide that forms plant cell walls.

Chitin

Structural polysaccharide in arthropod exoskeletons and fungal cell walls.

Starch

Plant storage polysaccharide (amylose and amylopectin).

Glycogen

Animal storage polysaccharide in liver and muscle, also called animal starch.

Lipid

Hydrophobic molecule including fats, oils, waxes, and steroids; stores 9 cal/g.

Saturated Fat

Lipid with only single C-C bonds; solid at room temperature; mainly animal origin.

Unsaturated Fat

Lipid with one or more C=C double bonds; liquid at room temperature; plant origin; healthier.

Steroid

Lipid consisting of four fused rings; includes cholesterol and some hormones.

Phospholipid

Modified lipid with two fatty acid tails and a phosphate head; forms cell-membrane bilayers.

Hydrophilic Head

Polar phosphate-containing part of a phospholipid that faces aqueous environments.

Hydrophobic Tails

Nonpolar fatty acid chains of a phospholipid that avoid water.

Protein

Complex polymer of amino acids (polypeptide) that performs diverse cellular functions (4 cal/g).

Amino Acid

Monomer with an amino group, carboxyl group, hydrogen, and variable R group attached to a central carbon.

Peptide Bond

Covalent bond joining amino acids between carboxyl and amino groups.

Primary Structure

Linear sequence of amino acids in a protein.

Secondary Structure

Regular folding (α-helix or β-pleated sheet) stabilized by hydrogen bonds.

Alpha Helix

Coiled secondary-structure pattern in proteins.

Beta-Pleated Sheet

Accordion-like secondary-structure pattern in proteins.

Tertiary Structure

Three-dimensional protein shape formed by interactions among R groups.

Quaternary Structure

Overall protein structure formed by multiple polypeptide chains (e.g., hemoglobin).

Denaturation

Loss of protein shape and function due to unfavorable pH, temperature, or salt conditions.

Chaperone Protein

Protein that assists other proteins in proper folding (chaperonin).

Bioinformatics

Use of computational tools to analyze biological data and predict protein structure.

Nucleic Acid

Polymer of nucleotides; DNA or RNA; stores and transmits genetic information.

DNA (Deoxyribonucleic Acid)

Double-stranded nucleic acid with deoxyribose sugar and bases A, T, C, G.

RNA (Ribonucleic Acid)

Single-stranded nucleic acid with ribose sugar and bases A, U, C, G.

Nucleotide

Monomer consisting of a phosphate group, five-carbon sugar, and nitrogenous base.

Functional Group

Chemically reactive group of atoms attached to a carbon skeleton.

Amino Group

-NH₂ functional group; compound type: amine.

Carboxyl Group

-COOH functional group; compound type: carboxylic acid.

Hydroxyl Group

-OH functional group; compound type: alcohol.

Phosphate Group

-PO₄ functional group; involved in energy transfer (e.g., ATP).

Free Energy (ΔG)

Energy available to do cellular work; negative ΔG indicates an exergonic reaction.

Exergonic Reaction

Chemical reaction that releases energy (negative ΔG).

Endergonic Reaction

Chemical reaction that absorbs energy (positive ΔG).

Metabolism

Sum of all chemical reactions in a cell, organized into pathways.

Catabolism

Metabolic pathways that break down molecules and release energy.

Anabolism

Metabolic pathways that build complex molecules and consume energy.

Enzyme

Globular catalytic protein that speeds reactions by lowering activation energy.

Active Site

Region on an enzyme where the substrate binds.

Enzyme-Substrate Complex

Temporary complex formed when an enzyme binds its substrate.

Cofactor

Inorganic helper molecule required for enzyme activity (e.g., metal ions).

Coenzyme

Organic helper molecule (vitamin-derived) required for enzyme activity.

Competitive Inhibition

Inhibition where a molecule resembling the substrate binds the active site, blocking it.

Noncompetitive Inhibition

Inhibition where a molecule binds an allosteric site, altering enzyme shape and activity.

Allosteric Regulator

Molecule that binds outside the active site and changes enzyme conformation and function.

Feedback Inhibition

Metabolic control where an end-product inhibits an earlier enzyme in the pathway.

Cooperativity

Allosteric activation in which substrate binding to one active site enhances binding at others.