Water, Organic Compounds, and Free Energy

Element

A substance that cannot be broken down into other substances by chemical reactions.

Compound

A substance consisting of 2 or more different elements combined in a fixed ratio.

Atom

The smallest unit of matter that retains the properties of an element.

Neutrons

Subatomic particles with no charge found in the atomic nucleus.

Protons

Positively charged subatomic particles found in the atomic nucleus.

Electrons

Negatively charged subatomic particles that orbit the atomic nucleus.

Functional group

A specific group of atoms within a molecule that is responsible for the chemical reactions of that molecule.

Carboxyl group

-COOH; a functional group that is weakly acidic and capable of releasing a hydrogen ion.

Amino group

-NH₂; a functional group that makes molecules basic because it can accept a proton.

Carbonyl group

C=O; a functional group that is polar and reactive.

Phosphate group

-PO₄²⁻; a highly reactive functional group involved in energy transfer.

Methyl group

-CH₃; a nonpolar and hydrophobic functional group.

Hydroxyl group

-OH; a functional group that makes molecules polar and hydrophilic.

Macromolecules

Large molecules composed of thousands of covalently bonded atoms.

Polymers

Long molecules consisting of many similar building blocks called monomers.

Monomer

A small building block molecule that can join together to form polymers.

Carbohydrates

Macromolecules that serve as energy sources and structural components in living organisms.

Lipids

Macromolecules that are hydrophobic and serve as energy storage and structural components.

Proteins

Macromolecules made from amino acids that perform a wide range of functions in organisms.

Nucleic acids

Biomolecules that store and transmit genetic information.

Atomic number

The number of protons in the nucleus of an atom.

Atomic mass

The sum of protons and neutrons in an atom's nucleus.

Isotopes

Atoms of an element that differ in the number of neutrons.

Radioactive isotopes

Isotopes that decay spontaneously.

Potential energy

The energy that matter has due to its location or structure.

Valence electrons

Electrons in the outermost energy level of an atom that determine chemical behavior.

Chemical bonds

Interactions that hold atoms together.

Covalent bonds

Bonds formed by the sharing of a pair of valence electrons between atoms.

Structural formula

A notation that represents atoms and bonding in a molecule.

Nonpolar covalent bond

A type of covalent bond where electrons are shared equally.

Polar covalent bond

A type of covalent bond where one atom is more electronegative than the other, leading to unequal sharing of electrons.

Electronegativity

The measure of an atom's attraction for the electrons in a covalent bond.

Ionic bonds

Bonds formed when one atom strips electrons from another, resulting in charged atoms.

Hydrogen bonding

A weak attraction between a hydrogen atom and an electronegative atom.

Intermolecular forces (IMFs)

Forces that act between molecules, holding them together.

Hydrophobic

Substances that repel water.

Hydrophilic

Substances that have an affinity for water.

Acid

Any substance that increases the H+ concentration of a solution.

Base

Any substance that reduces the H+ concentration of a solution.

Buffer

Substances that resist changes in H+ and OH- concentrations in a solution.

Acid rain

Rain with a pH lower than 5.2 that can damage life in lakes and streams.

Organic chemistry

The study of carbon-containing compounds and their properties.

Hydrocarbons

Organic molecules consisting of only carbon and hydrogen.

Isomers

Compounds with the same molecular formula but different structures.

Structural isomers

Isomers that differ in the covalent arrangements of their atoms.

Cis-trans isomers

Isomers that have the same covalent bonds but differ in spatial arrangements.

Enantiomers

Isomers that are mirror images of each other.

ATP

A nucleotide that serves as the primary energy currency of the cell.

Enzymes

Biological catalysts that increase the reaction rate of biochemical reactions.

Substrate

The reactant on which an enzyme works.

Induced fit model

The model that describes how enzymes can change shape to accommodate substrates.

Activation energy

The energy required to initiate a chemical reaction.

Competitive inhibitors

Substances that compete with substrates for the active site of an enzyme.

Noncompetitive inhibitors

Substances that bind to an enzyme away from the active site, changing the enzyme's shape.

Feedback inhibition

A regulatory mechanism where the end product of a metabolic pathway inhibits an earlier step in the pathway.

Allosteric regulation

The regulation of an enzyme's activity by binding of a molecule at a site other than the active site.

Cooperativity

A phenomenon in enzymes where the binding of one substrate enhances the binding of others.

Gene

The unit of heredity made of DNA that codes for a protein.

DNA (Deoxyribonucleic acid)

A nucleic acid that contains genetic information and instructions for protein synthesis.

RNA (Ribonucleic acid)

A nucleic acid involved in protein synthesis, composed of a single polypeptide chain.

Nucleotide

The monomer of nucleic acids, consisting of a nitrogenous base, a sugar, and one or more phosphate groups.

Purines

Nitrogenous bases with a double-ring structure (adenine and guanine).

Pyrimidines

Nitrogenous bases with a single-ring structure (cytosine, thymine, and uracil).

Polypeptides

Unbranched chains of amino acids that make up proteins.

Peptide bond

The covalent bond formed between amino acids during protein synthesis.

Primary structure

The unique sequence of amino acids in a polypeptide chain.

Secondary structure

The coiling or folding of a polypeptide chain due to hydrogen bonds.

Tertiary structure

The overall three-dimensional shape of a polypeptide determined by interactions among side chains.

Quaternary structure

The structure formed when multiple polypeptide chains join together.

Denaturation

The loss of a protein's native structure due to environmental changes.

Hydrophilic R groups

Amino acid side chains that interact favorably with water.

Hydrophobic R groups

Amino acid side chains that do not interact well with water.

Catalysts

Substances that speed up chemical reactions without being consumed in the process.

Lock and Key model

A model describing how enzymes and substrates fit together perfectly like a key in a lock.

Saturated fats

Fats that have no double bonds between the carbon atoms, resulting in a solid form at room temperature.

Unsaturated fats

Fats that contain one or more double bonds between carbon atoms, usually liquid at room temperature.

Cholesterol

A type of lipid that is an essential component of cell membranes and a precursor for steroid hormones.

Hydrophilic interactions

Interactions between polar molecules that favor water; they promote the solubility of substances in water.

Gene expression

The process by which information from a gene is used to synthesize a functional gene product, often a protein.

Transcription

The process of copying a segment of DNA into RNA.

Translation

The process of synthesizing proteins based on the sequence of messenger RNA.

Antiparallel strands

The orientation of two strands of DNA running in opposite directions, crucial for base pairing.

Replication fork

The area where the DNA double helix is unwound and replicated during DNA synthesis.

Mutations

Permanent changes in the DNA sequence that can affect gene function and characteristics.

Polymerase

An enzyme that synthesizes long chains or polymers of nucleic acids, crucial for DNA and RNA synthesis.

Hydrophilic molecules

Molecules that interact favorably with water due to their polar nature.

Hydrophobic molecules

Molecules that do not interact well with water, often nonpolar.

Active site

The specific region of an enzyme where substrate binding occurs.

Cofactors

Inorganic ions or coenzymes that assist enzymes in catalyzing reactions.

Allosteric site

A site on an enzyme other than the active site that can regulate its activity.

Substrate concentration

The amount of substrate present in a reaction that influences the rate of enzyme activity.

Enzyme activity

The rate at which an enzyme converts substrates into products.

Denatured protein

A protein that has lost its unique structure and functionality due to external stressors.

Specificity

The ability of an enzyme to choose exact substrates from a group of similar chemical molecules.

Enzyme assay

A laboratory procedure to determine the activity of an enzyme.

Competitive inhibition

A process where a molecule similar to the substrate competes for binding at the active site of an enzyme.

Noncompetitive inhibition

A process where an inhibitor binds to an enzyme at a site other than the active site, reducing its activity.

Feedback mechanism

A regulatory system where an end product affects an earlier step in a metabolic pathway.

Signal transduction

The process by which a cell responds to signals from its environment through communication pathways.

Glycogen

A polysaccharide that serves as a form of energy storage in animals.