Biochemical Foundations and the Matrix of Life

Flashcards covering the basic chemical components of biological systems, functional groups, molecular representations, classes of biomolecules, and the unique properties of water and weak interactions.

Primary Biological Elements

The six elements that compose more than 97% of human mass: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorous (P), and Sulfur (S).

Ether Functional Group

A polar group present in some lipids and found in sugar derivatives and glycosidic bonds that join sugars together in polysaccharides.

Alkane (Alkyl) Group

A non-polar group found in fatty acids, lipids, and amino acids that often contributes to hydrophobic character.

Aromatic (Arene/Aryl) Group

A group found in aromatic amino acids and many vitamins and hormones; it can absorb UV light and is important for stacking interactions in DNA and protein folding.

Phosphate Group

A group associated with organic phosphates, essential for energy storage ($ATP$), biomolecular structure (nucleic acids), and protein regulation.

Ball-and-stick Model Color Code

A molecular representation where Black represents carbon, Red represents oxygen (negative charge), Blue represents nitrogen (positive charge), and Grey represents hydrogen.

Abbreviated Structural Formula

A molecular representation where carbons are implied at junctions and ends.

Four Major Classes of Biomolecular Building Blocks

Amino Acids, Sugars, Lipids, and Nucleotides.

$\\alpha$-Amino Acid

The most common form of amino acid and the building block for polypeptides (proteins), defined by the presence of an amine and a carboxylic acid group.

Peptide Bond

An amide bond that links amino acids together to form proteins.

Sugars (Carbohydrates)

Molecules containing carbonyl and hydroxyl functional groups typically following the formula $(CH_2O)_n$.

Ketose and Aldose

The two classes of monosaccharides (sugars) categorized by the type of carbonyl group they contain.

Lipids

Molecules that are soluble in hydrophobic solutions and do not polymerize, though they form higher order structures like membranes.

Nucleotide Components

The three components forming the basic unit: one or more Phosphate groups, a sugar (ribose or deoxyribose), and a nitrogenous base.

DNA Nitrogenous Bases

Adenine, cytosine, guanine, and thymine.

RNA Nitrogenous Bases

Adenine, cytosine, guanine, and uracil.

Water Molecular Geometry

A bent shape with an $H\text{-}O\text{-}H$ angle of $104.5^\circ$ resulting from tetrahedral electronic geometry.

Hydrogen Bond

An interaction where hydrogen is attracted to the lone pair electrons of an oxygen or nitrogen from another molecule; it has both covalent and electrostatic properties.

Colinear Orientation

The optimal orientation for hydrogen bonds to maximize interaction strength.

Anomalous Properties of Water

Unique characteristics including ice floating, high boiling and freezing temperatures, high heat of vaporization, high heat capacity, and high surface tension.

Salt Bridges

Weak electrostatic interactions between atoms or groups with full electrical charges; these are different from pure ionic bonds used for salts.

Dielectric Constant ($\epsilon_r$)

A value that influences the strength of ionic interactions in a solvent; water has a high value of $80$ while a vacuum is $1.00$.

Hydration Shells

Structures formed by water molecules surrounding ions or polar molecules, which prevent ionic bonds from reforming.

Hydrogen Bond Donor

A molecule or group that has a Hydrogen atom attached to an electronegative atom (N, O, or F).

Hydrogen Bond Acceptor

An electronegative atom (N, O, or F) that possesses a free lone pair of electrons.

London Dispersion Forces

Van der Waals interactions resulting from transient/temporary dipoles formed by shifting electrons in non-polar molecules.

Lennard-Jones Plot

A plot used to describe and predict interactions between molecules, showing an energy well where attraction and repulsion are balanced at the Van der Waal distance.

Hydrophobic Effect

The phenomenon where water excludes non-polar molecules, driven by the Second Law of Thermodynamics to increase the overall entropy ($\Delta S_{universe} > 0$) of the system.

Amphipathic Molecules

Molecules, such as phospholipids, that contain both hydrophilic (water-loving) and hydrophobic (water-hating) sides.

Water Dissociation Constant ($K_w$)

The equilibrium constant for the ionization of water, valued at $K_w = [H^+][OH^-] = 1.0 \times 10^{-14}\,M$ at $25^\circ C$.

pH Definition

The mathematical representation of hydrogen ion concentration: $pH = -\log[H^+]$.