Intro, Terms, and Water

Vocabulary-style flashcards covering core concepts, terms, and definitions from the lecture notes.

Amino acids

Building blocks of proteins; each has an amino group, a carboxyl group, a hydrogen, and a distinctive side chain (R) attached to the α-carbon.

Proteins

Macromolecules made of amino acids that fold into functional three-dimensional structures.

Membranes

Phospholipid bilayers that form barriers, mediate transport, and host signaling in cells.

Hydrogen bond

Weakened electrostatic attraction between a hydrogen bonded to an electronegative atom and another electronegative atom; strong collectively and essential for water properties.

Hydration

Solvation of ions or molecules by water, stabilized by hydrogen bonding and dielectric effects.

Covalent bond

Bond formed by sharing electron pairs between atoms; can be single, double, etc., providing molecule connectivity.

Resonance

Delocalization of electrons across multiple structures; the actual molecule is a weighted blend (e.g., benzene).

Single bond

A sigma bond with free rotation around the bond axis in simple cases.

Double bond

A bond consisting of one sigma and one pi bond; rotation is restricted and the bond is planar.

109.5° (tetrahedral angle)

Ideal bond angle around a carbon with sp3 hybridization; governs geometry of many organic molecules.

Polarity

Uneven distribution of electron density in a molecule, leading to a dipole moment (water is polar; CO2 is nonpolar due to geometry).

Dipole moment

A vector quantity that measures the separation of positive and negative charges in a molecule.

Dihydrogen (H2)

Molecule composed of two hydrogen atoms; simplest molecule.

Ammonia (NH3)

Polar molecule with a lone pair; participates in hydrogen bonding.

Methane (CH4)

Nonpolar hydrocarbon with a tetrahedral geometry and no hydrogen-bond donors/acceptors.

Hydrogen sulfide (H2S)

Polar molecule with weaker hydrogen bonding than water; example of a hydrogen-bond donor/acceptor.

Phosphoric acid (H3PO4)

Phosphate-containing molecule; forms phosphate esters and high-energy phosphate bonds in biochemistry.

Alcohol

R–OH functional group; hydroxyl-containing compound.

Aldehyde

R–CHO; carbonyl group at the end of a carbon chain.

Ketone

R–CO–R'; carbonyl group within a carbon chain.

Carboxylic acid

R–COOH; acidic functional group common in metabolism and fatty acids.

Ester

R–COOR'; a carbonyl adjacent to an alkoxy group; common linkage in lipids and biochemicals.

Ether

R–O–R'; oxygen atom linking two carbon-containing groups.

Phosphoryl

Phosphate group typically depicted as P=O with additional OH or ester linkages (–PO3H2, etc.).

Phosphoanhydride

P–O–P linkage carrying high-energy phosphate bonds (e.g., in ATP and phosphocreatine).

Thioester

Carbonyl attached to sulfur (R–CO–S–R'); high-energy thioester bond common in metabolism.

Disulfide

R–S–S–R' covalent bond, stabilizing protein structure through cysteine crosslinks.

Glycome

The complete set of carbohydrate-containing molecules in a cell.

Proteome

The total complement of proteins expressed in a cell or organism at a given time.

Genome

Complete sequence of an organism's DNA (or RNA for RNA viruses).

Nucleic acids

DNA and RNA polymers composed of nucleotides; store and transmit genetic information.

Polysaccharides

Polymers of simple sugars; energy storage and structural roles in cells.

Biomolecules (building blocks)

Main classes of biological macromolecules: proteins, nucleic acids, carbohydrates, and lipids.

In vitro

Experiments performed outside a living organism, in a controlled environment (e.g., test tubes).

In vivo

Experiments conducted within a living organism.

In silico

Computer-based simulations and analyses.

Cell culture

Growing cells in controlled artificial conditions outside a living organism.

Hydrophobicity

Tendency of nonpolar groups to avoid water and aggregate away from aqueous environments.

Angstrom (Å)

Unit equal to 10^-10 meters; 1 Å = 0.1 nanometers.

Scale prefixes (powers of 10)

Metric prefixes indicating powers of ten (e.g., kilo 10^3, mega 10^6, nano 10^-9, pico 10^-12, etc.).

Polarity in water and CO2

Water is polar due to its bent geometry and O's electronegativity; CO2 is nonpolar because its bond dipoles cancel out.

Amino acids

Building blocks of proteins; each has an amino group, a carboxyl group, a hydrogen, and a distinctive side chain (R) attached to the α-carbon.

Proteins

Macromolecules made of amino acids that fold into functional three-dimensional structures.

Membranes

Phospholipid bilayers that form barriers, mediate transport, and host signaling in cells.

Hydrogen bond

Weakened electrostatic attraction between a hydrogen bonded to an electronegative atom and another electronegative atom; strong collectively and essential for water properties.

Hydration

Solvation of ions or molecules by water, stabilized by hydrogen bonding and dielectric effects.

Covalent bond

Bond formed by sharing electron pairs between atoms; can be single, double, etc., providing molecule connectivity.

Resonance

Delocalization of electrons across multiple structures; the actual molecule is a weighted blend (e.g., benzene).

Single bond

A sigma bond with free rotation around the bond axis in simple cases.

Double bond

A bond consisting of one sigma and one pi bond; rotation is restricted and the bond is planar.

109.5° (tetrahedral angle)

Ideal bond angle around a carbon with sp3 hybridization; governs geometry of many organic molecules.

Polarity

Uneven distribution of electron density in a molecule, leading to a dipole moment (water is polar; CO2 is nonpolar due to geometry).

Dipole moment

A vector quantity that measures the separation of positive and negative charges in a molecule.

Dihydrogen (H2)

Molecule composed of two hydrogen atoms; simplest molecule.

Ammonia (NH3)

Polar molecule with a lone pair; participates in hydrogen bonding.

Methane (CH4)

Nonpolar hydrocarbon with a tetrahedral geometry and no hydrogen-bond donors/acceptors.

Hydrogen sulfide (H2S)

Polar molecule with weaker hydrogen bonding than water; example of a hydrogen-bond donor/acceptor.

Phosphoric acid (H3PO4)

Phosphate-containing molecule; forms phosphate esters and high-energy phosphate bonds in biochemistry.

Alcohol

R–OH functional group; hydroxyl-containing compound.

Aldehyde

R–CHO; carbonyl group at the end of a carbon chain.

Ketone

R–CO–R'; carbonyl group within a carbon chain.

Carboxylic acid

R–COOH; acidic functional group common in metabolism and fatty acids.

Ester

R–COOR'; a carbonyl adjacent to an alkoxy group; common linkage in lipids and biochemicals.

Ether

R–O–R'; oxygen atom linking two carbon-containing groups.

Phosphoryl

Phosphate group typically depicted as P=O with additional OH or ester linkages (–PO3H2, etc.).

Phosphoanhydride

P–O–P linkage carrying high-energy phosphate bonds (e.g., in ATP and phosphocreatine).

Thioester

Carbonyl attached to sulfur (R–CO–S–R'); high-energy thioester bond common in metabolism.

Disulfide

R–S–S–R' covalent bond, stabilizing protein structure through cysteine crosslinks.

Glycome

The complete set of carbohydrate-containing molecules in a cell.

Proteome

The total complement of proteins expressed in a cell or organism at a given time.

Genome

Complete sequence of an organism's DNA (or RNA for RNA viruses).

Nucleic acids

DNA and RNA polymers composed of nucleotides; store and transmit genetic information.

Polysaccharides

Polymers of simple sugars; energy storage and structural roles in cells.

Biomolecules (building blocks)

Main classes of biological macromolecules: proteins, nucleic acids, carbohydrates, and lipids.

In vitro

Experiments performed outside a living organism, in a controlled environment (e.g., test tubes).

In vivo

Experiments conducted within a living organism.

In silico

Computer-based simulations and analyses.

Cell culture

Growing cells in controlled artificial conditions outside a living organism.

Hydrophobicity

Tendency of nonpolar groups to avoid water and aggregate away from aqueous environments.

Angstrom (Å)

Unit equal to 10^{-10} meters; 1 Å = 0.1 nanometers.

Scale prefixes (powers of 10)

Metric prefixes indicating powers of ten (e.g., kilo 10^3, mega 10^6, nano 10^{-9}, pico 10^{-12}, etc.).

Polarity in water and CO2

Water is polar due to its bent geometry and O's electronegativity; CO2 is nonpolar because its bond dipoles cancel out.

ATP (Adenosine Triphosphate)

The primary energy currency of the cell; a nucleotide with high-energy phosphoanhydride bonds, crucial for cellular processes.

Enzyme

Biological catalysts, typically proteins, that speed up biochemical reactions by lowering activation energy without being consumed.

pH

A scale measuring the acidity or alkalinity of a solution, defined as -\log_{10}[H^+], where [H^+] is the hydrogen ion concentration. A pH of 7 is neutral.

Hydrophobic effect

The phenomenon where nonpolar molecules aggregate in aqueous solutions, driven by water's tendency to maximize its hydrogen bonding and minimize contact with nonpolar substances; crucial for protein folding and membrane formation.