Video Notes: Atoms, Bonding, Water, Organic Molecules, and Nucleic Acids

A comprehensive set of vocabulary flashcards covering atomic structure, bonding, water chemistry, organic molecules, biomolecules, and nucleic acids based on the lecture notes.

Proton

Positively charged subatomic particle located in the nucleus.

Neutron

Electrically neutral subatomic particle located in the nucleus.

Electron

Negatively charged subatomic particle that orbits the nucleus in electron shells.

Nucleon

Protons and neutrons collectively; the particles that make up the nucleus.

Nucleus

Central positively charged core of an atom containing protons and neutrons; houses most of the atom’s mass.

Shell (electron shell)

A region around the nucleus where electrons are found, each shell has specific energy/distance.

Electron cloud

Area around the nucleus where electrons are found.

Atomic number

Number of protons in the nucleus; defines the identity of the element.

Atomic mass

Sum of the protons and neutrons in the nucleus.

Mass of atom

Protons plus neutrons in the nucleus.

Isotopes

Atoms of the same element with different numbers of neutrons.

Ions

Atoms with a different number of electrons than protons, giving a net charge.

Cation

Positively charged ion (atom that has lost electrons).

Anion

Negatively charged ion (atom that has gained electrons).

Charge

Charge = number of protons minus number of electrons.

Atomic identity

Identity of an element is determined by its number of protons (atomic number).

Subatomic placement and charge

Protons and neutrons in the nucleus; electrons in shells around the nucleus; protons are positive, neutrons neutral, electrons negative.

Electron orbital

Region where an electron is likely to be found.

Shell 1 capacity

Maximum 2 electrons.

Shell 2 capacity

Maximum 8 electrons.

Shell 3 capacity

Maximum 18 electrons.

Electron transitions

Electrons move between shells by absorbing or releasing energy.

Ionic bond

Bond formed by transfer of electrons from one atom to another.

Covalent bond

Bond formed by sharing electrons between atoms.

Hydrogen bond

Bond formed between a slightly positive hydrogen and a slightly negative atom (often O, N, F) in another molecule.

Valence electrons

Electrons in the outermost shell that participate in bonding.

Polar covalent bond

Covalent bond where electrons are shared unequally, creating partial charges.

Nonpolar covalent bond

Covalent bond where electrons are shared equally.

Covalent bond strength (basic idea)

Single bonds are generally weaker than double bonds; triple bonds are strong; ionic bonds are strong as well.

Dipole-Dipole interaction

Attractive interaction between polar molecules due to partial charges.

Water as universal solvent

Water dissolves many substances, making it a versatile solvent.

Cohesion

Attraction between molecules of the same substance.

Adhesion

Attraction between molecules of different substances.

Hydrophilic

Substances that interact well with water; polar or charged.

Hydrophobic

Substances that repel water; nonpolar.

Polar molecule

Molecule with uneven distribution of electrical charge due to polar bonds.

Oxygen electronegativity

Oxygen pulls electron density toward itself in bonds (high electronegativity).

Ice density

Ice is less dense than liquid water due to a lattice that creates more space between molecules.

pH

Measure of hydrogen ion concentration in a solution; indicates acidity or basicity.

Acid

Substance that increases H+ concentration (lowers pH).

Base

Substance that decreases H+ concentration (raises pH).

Neutral pH

A pH around 7 (neither acidic nor basic).

Ocean pH

Marine environments typically have a pH around 8.

Carbon

Central element in life; backbone of organic molecules; can form four covalent bonds.

Tetrahedral geometry

Carbon’s single-bond configuration around a carbon atom forms a tetrahedral shape.

Planar geometry

Carbon’s double bonds create a planar arrangement.

Linear geometry

Triple bonds around carbon create a linear arrangement.

Hydroxyl group (-OH)

Functional group found in alcohols; polar and hydrogen-bonding capable.

Carbonyl group (C=O)

Functional group with a carbon-oxygen double bond; polar and reactive.

Carboxyl group (-COOH)

Functional group acting as an acid; common in organic acids.

Amino group (-NH2)

Functional group basic in nature; found in amino acids.

Sulfhydryl group (-SH)

Functional group that forms disulfide bonds in proteins.

Phosphate group (PO4^3-)

Negatively charged group important in energy transfer (ATP) and nucleic acids.

Methyl group (-CH3)

Nonpolar functional group; common in organic molecules and can affect gene expression when attached to DNA.

Monomer

Small building block that polymerizes to form larger molecules.

Polymer

Large molecule made by linking many monomers.

Glycosidic bond

Bond that links two sugar molecules in carbohydrates.

Monosaccharide

Simple sugar; basic building block of carbohydrates.

Polysaccharide

Polymers of sugars; complex carbohydrates.

Lipids

Hydrophobic molecules; include fats and oils; store energy and form membranes.

Glycerol

backbone molecule for many lipids; bonds with fatty acids.

Fatty acid

Hydrocarbon chain that is carboxylated; part of fats and lipids.

Triacylglycerol

A fat molecule made of glycerol linked to three fatty acids; major energy storage molecule.

Ester bond

Bond between glycerol and fatty acids in fats.

Saturated fatty acid

Fatty acid with no double bonds; typically solid at room temperature.

Unsaturated fatty acid

Fatty acid with one or more double bonds; typically liquid at room temperature.

Steroids

Lipids with four fused carbon rings; include hormones and cholesterol.

Phospholipid

Lipid with a hydrophilic head and hydrophobic tail; forms cellular membranes.

Protein

Macromolecule made of amino acids; functions in structure, enzymes, transport, defense.

Amino acid

Building block of proteins; contains amino group, carboxyl group, hydrogen, and a side chain (R group) around an alpha carbon.

Alpha (α) carbon

Central carbon atom in an amino acid to which the amino, carboxyl, hydrogen, and R group are attached.

R group (side chain)

Variable side chain of an amino acid that determines its properties.

Nonpolar (NP) R groups

Hydrophobic amino acid side chains; avoid water.

Polar R groups

Hydrophilic amino acid side chains; interact with water.

Acidic R groups

Negatively charged side chains at physiological pH.

Basic R groups

Positively charged side chains at physiological pH.

Peptide bond

Covalent bond linking amino acids in a protein via dehydration synthesis.

Hydrogen bonds in proteins

Noncovalent bonds help stabilize protein structure.

Phosphodiester bond

Backbone linkage between nucleotides in DNA/RNA.

Nucleic acids

Large molecules (DNA and RNA) that store and transmit genetic information.

DNA (Deoxyribonucleic acid)

Molecule that holds genetic instructions; uses deoxyribose sugar.

RNA (Ribonucleic acid)

Molecule that helps carry out genetic instructions; uses ribose sugar.

Nucleotide

Building block of DNA/RNA; composed of a sugar, a phosphate group, and a nitrogenous base.

Base (in nucleotides)

Nitrogenous base that encodes genetic information (A, T, C, G in DNA; A, U, C, G in RNA).

Purines

Bases with a two-ring structure (Adenine and Guanine).

Pyrimidines

Bases with a single-ring structure (Cytosine, Thymine, Uracil).

Adenine (A)

Purine base found in DNA and RNA.

Guanine (G)

Purine base found in DNA and RNA.

Cytosine (C)

Pyrimidine base found in DNA and RNA.

Thymine (T)

Pyrimidine base found only in DNA.

Uracil (U)

Pyrimidine base found only in RNA.

Ribose

Sugar in RNA.

Deoxyribose

Sugar in DNA (missing one oxygen compared to ribose).

Double helix

Twisted ladder structure of DNA formed by base pairing.

Complementary base pairing

A pairs with T (or U in RNA), and C pairs with G, stabilizing the DNA/RNA structure.

Phosphodiester backbone

Covalent linkage of nucleotides forming the sugar-phosphate backbone of DNA/RNA.