Chemical Evolution, Biological Macromolecules, and Protein Structure

Vocabulary practice flashcards covering chemical bonding, thermodynamics, functional groups, and hierarchical protein structure from introductory biochemistry lectures.

Covalent Bond

A strong chemical bond formed when two atoms share one or more pairs of electrons, such as two hydrogen atoms sharing electrons to form an $H_2$ molecule.

Electronegativity

The intrinsic ability of an atom to attract shared electrons toward itself in a chemical bond.

Nonpolar Covalent Bond

A covalent bond formed between atoms with equal electronegativities where electrons are shared equally halfway between the two atoms, resulting in no charge on either atom.

Polar Covalent Bond

A covalent bond in which electrons are shared unequally because one atom has higher electronegativity than the other, resulting in partial positive ($\delta^+$) and partial negative ($\delta^-$) charges.

Ionic Bond

A chemical bond resulting from the complete transfer of electrons from one atom to another, producing ions with full electrical charges that are held together by electrostatic attraction.

First Law of Thermodynamics

A physical law stating that energy is conserved; it cannot be created or destroyed, but can only be transferred or transformed.

Exothermic Reaction

A chemical reaction in which the products have lower potential energy than the reactants, resulting in the net release of energy as heat and/or light.

Bond Potential Energy

Chemical energy stored in bonds; nonpolar bonds with equally shared electrons (such as $C-H$) are longer, weaker, and hold high potential energy, whereas polar bonds with tightly held electrons (such as $O-H$) are shorter, stronger, and hold lower potential energy.

Organic Compounds

Molecules that contain carbon covalently bonded to other atoms (such as hydrogen, oxygen, nitrogen, phosphorus, and sulfur) capable of forming vast arrays of molecular chains and rings.

Amino Group

A functional group ($-NH_2$) characteristic of amines that acts as a base by attracting a proton in solution to become $-NH_3^+$.

Carboxyl Group

A functional group ($-COOH$) characteristic of carboxylic acids that acts as an acid by losing a proton in solution to form $-COO^-$.

Carbonyl Group

A functional group containing a carbon double-bonded to oxygen ($C=O$), found in aldehydes and ketones, which acts as a reactive site linking molecules into larger structures.

Hydroxyl Group

A polar functional group ($-OH$) found in alcohols that increases water solubility via hydrogen bonding and can behave as a weak acid by releasing a proton.

Phosphate Group

A functional group ($-PO_4^{2-}$) found in organic phosphates that carries two negative charges and stores large amounts of chemical energy when bonded together in series.

Sulfhydryl Group

A functional group ($-SH$) found in thiols that can react with another sulfhydryl group in proteins to form a covalent disulfide ($S-S$) bond, stabilizing protein structure.

Stanley Miller Experiment

A 1953 chemical evolution experiment simulating early Earth's atmosphere and lightning that demonstrated the spontaneous synthesis of organic building blocks, including amino acids.

Amino Acid Core Structure

A molecular subunit composed of a central carbon ($\alpha$-carbon) covalently bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain ($R$-group).

R-Group (Side Chain)

The variable group attached to the $\alpha$-carbon of an amino acid that confers distinct chemical characteristics, polarity, electrical charge, and solubility in water.

Peptide Bond

The planar covalent C-N bond formed between the carboxyl carbon of one amino acid and the amino nitrogen of another, displaying double-bond characteristics that prevent rotation.

Condensation Reaction

A polymerization reaction (also known as a dehydration reaction) in which monomers join together to form a polymer with the accompanying loss of a water molecule ($H_2O$).

Hydrolysis

A chemical reaction that cleaves bonds in a polymer by adding a water molecule ($H_2O$), separating a monomer from the chain.

N-Terminus

The amino-terminal end of a polypeptide chain featuring a free amino group ($H_3N^+$), which marks the starting point of the sequence by convention.

C-Terminus

The carboxyl-terminal end of a polypeptide chain featuring a free carboxyl group ($COO^-$), which marks the end of the sequence by convention.

Primary Structure

The unique, linear sequence of amino acids linked together by peptide bonds in a polypeptide chain.

Secondary Structure

Localized regular folding patterns within a polypeptide backbone—principally $\alpha$-helices and $\beta$-pleated sheets—stabilized by hydrogen bonds between amino and carbonyl groups.

Tertiary Structure

The overall three-dimensional shape of an entire polypeptide chain, stabilized by interactions involving side chains ($R$-groups), such as hydrogen bonds, hydrophobic interactions, van der Waals forces, ionic bonds, and covalent disulfide bonds.

Quaternary Structure

The multi-subunit three-dimensional protein structure resulting from the association and noncovalent or covalent interactions between two or more individual polypeptide chains.

Molecular Chaperones

Specialized cellular proteins that facilitate proper protein folding by binding to exposed hydrophobic patches on unfolded polypeptides to prevent inappropriate aggregation.

Heat Shock Protein 90 (Hsp90)

A specific molecular chaperone that attaches to exposed hydrophobic patches of newly synthesized or denatured polypeptides, preventing aggregation and allowing them to fold properly.

Denatured Protein

A protein that has lost its native higher-order folded structure (unfolded), rendering it biologically inactive.