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Module 1

• A prokaryote is a unicellular organism featuring a single chromosome, lacking a nuclear envelope and membrane-bound organelles.
• A eukaryote can be unicellular or multicellular, characterized by cells containing a membrane-bound nucleus, multiple chromosomes, and internal organelles.
• A protein is a macromolecule consisting of one or more polypeptide chains, each with a specific sequence of amino acids connected by peptide bonds.
• Nucleic acids are biologically occurring polynucleotides where nucleotide residues are linked via phosphodiester bonds, including DNA and RNA.
• A polysaccharide is a linear or branched polymer composed of monosaccharide units joined by glycosidic bonds.
• "In vitro" means "in glass," referring to processes in the test tube.
• "In vivo" refers to processes within a living cell or organism.
• Conformation is the spatial arrangement of substituent groups that can freely change positions in space due to bond rotation without breaking bonds.
• Configuration is the spatial arrangement of organic molecules determined by either double bonds (with no rotation freedom) or chiral centers with substituent groups arranged in a specific sequence.

Geometric Isomers and Chirality

• Geometric isomers involve rotation around a double bond, also known as cis and trans isomers.
• A chiral center is an atom with substituents arranged so the molecule is not superimposable on its mirror image.
• A chiral compound contains an asymmetric center (chiral atom or center) and exists in two non-superimposable mirror-image forms, called enantiomers.
• Stereoisomers have the same composition and atomic connections but differ in their molecular arrangements.

Thermodynamics

• Thermodynamics is the study of heat and its relation to energy and work.
• The First Law of Thermodynamics states that the total energy of the universe remains constant in all processes.
• The Second Law of Thermodynamics states that the entropy of the universe tends to increase in any chemical or physical process.
• Enthalpy (H) is the heat content of a system.
• Entropy (S) quantifies the extent of randomness or disorder in a system.
• Enthalpy Change (ΔH) for a reaction is approximately the difference between the energy used to break bonds and the energy gained from forming new bonds.

Reactions

• Endergonic reactions are non-spontaneous processes (DG > 0) that require an input of free energy to proceed.
• Exergonic reactions are chemical reactions that proceed with the release of free energy (AG is negative).
• An exothermic reaction is one that releases heat (ΔH is negative).
• An endothermic reaction is one that takes up heat (ΔH is positive).

Genetics

• Genotype is the genetic constitution of an organism, distinct from its physical characteristics.
• Phenotype refers to the observable characteristics of an organism.

Module 2

• pH is the negative logarithm of the hydrogen ion concentration in an aqueous solution.
• pKa is the negative logarithm of an equilibrium constant.
• A buffer is a solution of a weak acid and its conjugate base that resists pH changes when acid or base is added.
• The buffering region is one pH unit on either side of the pKa.
• The Henderson-Hasselbalch equation relates pH, pKa, and the ratio of proton acceptor (A-) and proton donor (HA) concentrations in a solution.
• An amphipathic molecule contains both polar and non-polar portions.
• An amphoteric molecule can donate and accept protons, acting as an acid or a base.
• Ionic interactions occur between electrically charged groups, attracting opposite charges and repelling like charges.
• A hydrogen bond is a weak electrostatic attraction between one electronegative atom (oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom.
• Intramolecular processes or characteristics are limited within a single molecule's structure.
• Intermolecular processes or characteristics occur between different molecules' structures, such as attraction or repulsion between entities.

Module 3

• Amino acids are the smallest building blocks of proteins; there are 20 standard ones.
• A disulfide bond is a covalent linkage between the sulfhydryl groups of two cysteine residues.
• Amphoteric molecules can accept and donate protons, serving as both an acid and a base.
• A buffering region extends one pH unit above and below the pKa, where pH remains constant with acid or base addition

Module 4

• Diprotic molecules have two functional groups that can accept/donate protons, corresponding to two buffering regions on a titration curve.
• Triprotic molecules have three functional groups that can accept/donate protons, corresponding to three buffering regions on a titration curve.
• Isoelectric point is the pH at which a molecule has a net charge of zero.
• A peptide bond is a covalent linkage formed between the carboxyl group of one amino acid and the amino group of another, fundamental to peptide/protein structures.
• A residue is a single unit within a polymer, like an amino acid in a polypeptide chain.
• Native conformation is the biologically active conformation of a biomolecule.
• Hydrogen bonds are weak electrostatic interactions between an electronegative atom (oxygen or nitrogen) and a covalently linked hydrogen atom.
• Ionic interactions involve attraction or repulsion between charged groups of opposite or like charges.
• Van der Waals interactions are attractive or repulsive forces between molecules due to induced or transient dipoles.
• Hydrophobic interactions refer to the association of non-polar groups in aqueous systems, driving biomolecular structures.
• Denaturation is the partial or complete unfolding of the native conformation of a protein or nucleic acid.
• Primary structure is the linear sequence of amino acids in a peptide/polypeptide/protein.
• Secondary structure is localized folding within a polypeptide chain, forming defined structures like alpha helices and beta sheets.
• Tertiary structure is the pattern of folding of a single polypeptide in three-dimensional space.
• Quaternary structure involves the folding and association of proteins consisting of multiple polypeptide chains.

Polypeptide Chains

• Phi angle is the torsion angle in a polypeptide chain linking the alpha carbon to the amide nitrogen, with theoretical rotation freedom from -180 to +180 degrees.
• Psi angle is the torsion angle in a polypeptide chain linking the alpha carbon to the carbonyl carbon, allowing rotation from -180 to +180 degrees.
• The Ramachandran plot is a graph representing all phi and psi permutations to reveal common structural motifs in polypeptides.
• Alpha helix is a helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding.
• Beta sheets are an extended arrangement of a polypeptide chain made of beta strands that are parallel or antiparallel.
• Helix dipole is the uneven charge distribution along an alpha helix due to electronegativity differences in amide and carbonyl groups, with a partial positive charge at the amino terminus and negative at the carboxy terminus.
• Pseudo-seven repeat is a pattern in keratin's primary structure where the first and fourth positions of a seven-residue repeat are often hydrophobic.
• Amphipathic molecules contain both polar and non-polar groups.
• Supercoils (coiled-coils) are protein structure motifs with a-helical regions that self-associate into stable, rod-like oligomers, common in fibrous proteins like keratin and collagen.
• Scurvy is a disease from Vitamin C deficiency, destabilizing collagen due to the body's inability to introduce stabilizing post-translational modifications.
• Conformation is the spatial arrangement of substituent groups that can freely assume in three-dimensional space due to bond rotation.
• Configuration is the spatial arrangement of a molecule due to double bonds or chiral centers, with specific substituent group arrangements needing covalent bond breakage for interconversion.

Modules 5

• A ligand is a molecule bound reversibly by a protein.
• A binding site is a crevice or pocket on a protein where a ligand binds.
• Induced fit is a conformational change in a protein in response to ligand binding.
• P50 is the oxygen concentration required to half-saturate myoglobin or hemoglobin.
• Allosteric proteins/enzymes have multiple subunits and ligand-binding sites, where ligand binding at one site affects binding at another.
• An allosteric effector (modulator) binds to allosteric proteins at a site distinct from the functional binding site.
• A homotropic allosteric effector is the same as the protein's normal ligand (enzyme).
• A heterotropic allosteric effector differs from the protein's normal ligand (enzyme).
• Hemocyanin is an oxygen transport protein in invertebrates using two copper atoms coordinated by histidines for reversible oxygen binding.
• The Bohr effect describes hemoglobin's oxygen affinity dependence on pH, with decreased affinity at decreased pH.
• Sickle cell anemia is a disease where defective hemoglobin causes red blood cells to sickle when exposed to low oxygen levels.