Biochemistry and the Chemical Basis of Life

Flashcards covering vocabulary from biochemistry foundations, including cellular classification, thermodynamics, water chemistry, nucleic acid structure, and protein organization.

Prokaryotes

Unicellular organisms, specifically bacteria and archaea, that lack a nucleus.

Eukaryotes

Organisms that have a complex cellular organization with membrane-enclosed organelles and specialized functions, such as animals, plants, protists, and fungi.

Residue

A monomer that has been incorporated into a polymer.

Polypeptide

A polymer of amino acids linked together by peptide bonds.

Protein

A functional unit consisting of one or more polypeptides.

Exergonic

A process characterized by a negative change in free energy ($\Delta G < 0$), making it spontaneous or favorable.

Endergonic

A process characterized by a positive change in free energy ($\Delta G > 0$), making it nonspontaneous or unfavorable.

Catabolism

The metabolic process of breaking down larger molecules, which usually involves oxidation steps and allows free energy to be conserved.

Anabolism

The metabolic process of building complex molecules at the expense of energy.

Amphipathic

Molecules that contain both polar and nonpolar regions, such as palmitate or oleate.

Hydrophobic effect

The driving force for the aggregation of nonpolar regions in water to maximize the entropy of the surrounding water molecules.

London dispersion forces

Surface area dependent intermolecular forces caused by instantaneous dipoles; they become more significant in larger molecules and atoms.

$$K_w$$

The ion product constant for water, which is equal to $1.0 \times 10^{-14}$ at $25^{\circ}\text{C}$.

$$pK_a$$

The negative logarithm of the acid dissociation constant ($K_a$); it is the pH at which the concentrations of the weak acid ($[HA]$) and its conjugate base ($[A^-]$) are equal.

Buffer

A solution of a weak acid and its conjugate base that resists changes in pH.

Purines

A class of nitrogenous bases with a double-ring structure, specifically Adenine and Guanine.

Pyrimidines

A class of nitrogenous bases with a single-ring structure, specifically Cytosine, Thymine (in DNA), and Uracil (in RNA).

Nucleoside

A molecule consisting of a nitrogenous base attached to a ribose or deoxyribose sugar.

Nucleotide

A nucleoside with one to three phosphates attached; monomers that are linked by phosphodiester bonds to form nucleic acids.

Hyperchromic effect

The increase in UV absorbance that occurs when DNA is denatured (separated into single strands).

$T_m$ (Melting Temperature)

The temperature at which half of the DNA duplexes in a solution are denatured; it increases with DNA length and higher GC content.

Codon

A sequence of three nucleotides that specifies a particular amino acid or signals a stop in translation.

Isoelectric point ($pI$)

The pH at which a molecule has no net charge.

SDS-PAGE

A technique using sodium dodecyl sulfate to denature proteins and impart a uniform negative charge so they can be separated strictly by size during electrophoresis.

Primary structure

The first level of protein structure consisting of the specific sequence of amino acid residues.

Secondary structure

The localized conformation of the polypeptide backbone, primarily alpha helices and beta sheets.

Tertiary structure

The overall three-dimensional structure of an entire polypeptide, including all of its side chains.

Quaternary structure

The spatial arrangement of multiple polypeptide chains in a protein with more than one subunit.

Protein Domain

A region of a polypeptide that folds independently, usually has its own hydrophobic core, and performs a specific function.

Prion

An infectious protein that causes disease by inducing natively folded proteins ($PrP^C$) to adopt misfolded, aggregation-prone conformations ($PrP^{Sc}$).