Biochem Sept. 8th

Vocabulary flashcards covering energy changes (ΔG), the central dogma, and fundamental concepts about amino acids, peptide bonds, and protein structure.

Gibbs free energy change (ΔG)

Difference between the Gibbs free energies of products and reactants. ΔG < 0 means the process releases energy (spontaneous/exergonic); ΔG > 0 means energy input is required (non-spontaneous/endergonic).

Exergonic reaction

A spontaneous reaction that releases free energy (negative ΔG).

Endergonic reaction

A non-spontaneous reaction that requires energy input (positive ΔG).

Coupled reactions

Two or more reactions linked so that an energy-releasing step drives an energy-requiring step, yielding a negative net ΔG.

Central dogma of molecular biology

DNA stores genetic information; transcription copies DNA to RNA; translation uses RNA to synthesize proteins.

DNA

Molecule that stores genetic information used to guide synthesis of RNA and proteins.

RNA

Nucleic acid that carries information from DNA and serves as a template for protein synthesis during translation.

N-terminus and C-terminus

N-terminus has the free amino group; C-terminus has the free carboxyl group; protein synthesis proceeds from N to C via peptide bonds.

Amino acid

Building block of proteins; consists of an amino group, a carboxyl group, an α carbon, and a variable side chain (R group).

Peptide bond

Covalent bond formed between the carboxyl group of one amino acid and the amino group of the next, with release of water (condensation).

Residue

An amino acid that is part of a protein; the position in a chain is described as a residue (e.g., residue four).

Glycine

Smallest amino acid; side chain is a single hydrogen; non-chiral because its α carbon is not stereogenic.

Proline

Unique amino acid whose side chain forms a covalent bond back to the amino group, creating a secondary constraint in folding.

L-form vs D-form

Proteins use the L-enantiomer of amino acids; D-amino acids exist but are not typically used in protein synthesis.

Hydrophobic amino acids

Amino acids with nonpolar, carbon-rich side chains; tend to be buried in protein cores (e.g., alanine, valine, leucine, isoleucine, phenylalanine, tryptophan).

Polar uncharged amino acids

Amino acids with side chains that can form hydrogen bonds with water (e.g., serine, threonine, tyrosine).

Charged amino acids

Amino acids with side chains that carry a charge: acidic (negative, e.g., aspartate, glutamate) and basic (positive, e.g., lysine, arginine, histidine).

Disulfide bond

Covalent bond between two cysteine residues via their thiol (-SH) groups, forming a stabilizing link in proteins.

Histidine ionization

Histidine can switch between neutral and positively charged near physiological pH, influencing enzyme active sites and buffering.,

Methionine vs cysteine sulfur

Methionine contains sulfur in a thioether linkage; cysteine has a thiol (-SH) group that can form disulfide bonds with another cysteine.

Tryptophan

A large, hydrophobic aromatic amino acid; relatively low frequency in proteins and often located in the interior.

One-letter vs three-letter codes

Amino acids are commonly represented by one-letter codes (e.g., G for glycine) or three-letter codes (e.g., Gly).

Amino acid charge and pH

The charge on amino acid side chains depends on pH and pKa values; this determines the net charge of the amino acid and protein.,

Backbone vs side chain (R group)

Backbone consists of repeating N-Cα-C units with peptide bonds; side chains (R groups) determine specificity and folding.

Amino acid sequence and protein folding

The sequence (order of amino acids) dictates how the protein folds, influenced by hydrophobicity, charge, and side-chain interactions.