Chemistry, Protein Structure, and Nucleic Acids Review

Comprehensive vocabulary flashcards covering basic chemical bonding, water properties, protein structure levels, structural determination methods, prion biology, and nucleic acid fundamentals from the lecture notes.

Protons

Subatomic particles located in the atomic nucleus that determine the atomic number of an atom.

Neutrons

Subatomic particles located in the atomic nucleus that contribute to the atomic mass of an atom.

Valence Shell Electrons

Electrons located in the outermost shell of an atom that determine its chemical behavior; full outer shells render an atom chemically inert.

Ionic Bond

A chemical bond formed when valence electrons are transferred (lost or gained) between atoms, resulting in oppositely charged ions (e.g., $\text{Na}^+$ and $\text{Cl}^-$) that attract each other.

Covalent Bond

A chemical bond formed when two atoms share one or more pairs of valence electrons equally or unequally.

Hydrogen Bond

An attraction between partial positive charges on a hydrogen atom ($\text{H}$) and partial negative charges on electronegative atoms like oxygen ($\text{O}$) or nitrogen ($\text{N}$).

Polar Covalent Bond

A covalent bond in which electrons are shared unequally due to electronegativity differences, resulting in partial positive and partial negative charges across the molecule.

Non-Polar Covalent Bond

A covalent bond characterized by symmetric electron sharing without charge separation (e.g., $\text{H}_2$ or methane).

Van der Waals Forces

Weak, short-range interactions of complex quantum origin that fall off as the 6th power of distance, enabling phenomena such as geckos climbing walls.

pH Formula

The logarithmic scale measuring acidity/alkalinity defined by $\text{pH} = -\log_{10}[\text{H}^+]$, where neutral is $7$, acidic is below $7$, and basic is above $7$.

Lysosomes and Stomach Acid pH

Segregated cellular compartments maintaining an acidic environment with a pH of approximately $4.4\text{--}4.5$.

Water Maximum Density Temperature

The specific temperature at which liquid water reaches its maximum density, occurring at $4^\circ\text{C}$.

Hydrophilic

Describing substances or molecular regions that have a high affinity for water.

Hydrophobic

Describing non-polar molecules or regions that are excluded or segregated from water.

Amphipathic Molecules

Molecules (e.g., phospholipids) that contain both hydrophilic and hydrophobic regions, self-organizing to form biological membranes.

Primary Structure

The unique linear sequence of amino acids in a polypeptide chain.

Secondary Structure

Local polypeptide backbone structures, such as alpha helices or beta sheets, formed through hydrogen bonding.

Tertiary Structure

The overall 3D shape of a single polypeptide chain, combining secondary structure regions and unstructured segments.

Quaternary Structure

The assembly of multiple tertiary-structured protein subunits into a multi-subunit complex.

Anfinsen's RNase Experiment

Nobel Prize-winning experiment by Christian Anfinsen showing that primary structure alone determines tertiary structure, using ribonuclease (RNase) denatured with urea and a reducing agent.

Chaperone Proteins

Proteins (including heat shock proteins) that use ATP to assist proper protein folding or refold misfolded proteins under cellular stress.

Prosthetic Group

A non-protein molecule tightly bound to a protein essential for its function, such as the iron-containing heme group in hemoglobin.

Sickle Cell Disease

A genetic condition caused by a single amino acid substitution of valine at position 6 of beta-hemoglobin, causing mutant subunits to form filaments that distort red blood cells.

X-ray Crystallography

The gold standard structural biology method that analyzes diffraction patterns from protein crystals to infer atomic coordinates.

Cryo-EM

A structural determination technique that freezes purified molecules for direct electron microscopy analysis.

AlphaFold

An artificial intelligence system developed by Google AI that predicts 3D protein structures from amino acid sequences using pattern recognition from known PDB structures.

Prions

Misfolded proteins gaining beta-sheet structure that corrupt normally folded proteins into misfolded forms, causing toxic aggregates in nerve cells.

Central Dogma

The foundational flow of genetic information defined as $\text{DNA} \rightarrow (\text{transcription}) \rightarrow \text{RNA} \rightarrow (\text{translation}) \rightarrow \text{protein}$.

Nucleotide

The monomer of nucleic acids composed of a 5-carbon sugar (ribose or deoxyribose), a nitrogenous base attached at $\text{C1'}$, and a phosphate group attached at $\text{C5'}$.

Nucleoside

A molecular subunit consisting only of a 5-carbon sugar and a nitrogenous base, lacking any phosphate groups.

Pyrimidines

Single-ring nitrogenous bases comprising Cytosine (C), Uracil (U, RNA only), and Thymine (T, DNA only); recalled by the memory aid 'CUT'.

Purines

Double-ring nitrogenous bases comprising Adenine (A) and Guanine (G); recalled by the memory aid 'pure agony'.

Phosphodiester Bond

A covalent linkage formed via a dehydration reaction that connects the $\text{5'}$ phosphate of one nucleotide to the $\text{3'}$ OH of the next nucleotide.