Thermodynamics: Protein Folding and Interactions

Flashcards about Thermodynamics, Protein folding and interactions

Gibbs Free Energy

A measure of how much energy is free in a system; determines if a reaction can occur spontaneously.

ΔG (Delta G)

Change in Free Energy; involves bond making/breaking.

Entropy (S)

Measure of disorder.

Exergonic

A reaction that releases energy (ΔG is negative).

Endergonic

A reaction that requires energy (ΔG is positive).

Levinthal's Paradox

The idea that a protein doesn't have enough time to randomly sample all conformations to find the correct fold.

Protein folding thermodynamics

Protein retain partially correct intermediates and gravitate energetically towards the lowest free energy conformations

Ligand

A molecule that forms a complex with a receptor biomolecule to serve a biological purpose

Substrate

A molecule that binds to an enzyme and is converted into a product.

Affinity

A measure of the strength of an interaction between molecules

Association Constant (KA)

Measure of how tightly a ligand binds to its receptor.

Dissociation Constant (KD)

Measure of how quickly a ligand dissociates from its receptor.

Cooperativity

When two or more molecules bind to the same receptor molecule and changes the affinity for the subsequent binding events.

Allostery

When a molecule binds to a receptor molecule and changes its affinity for a separate molecule.

Hemoglobin

Main oxygen-carrying protein in the blood.

Myoglobin

Stores oxygen in muscles for use.

Heme

A cofactor within globin subunits that binds oxygen; contains a tetrapyrrole ring molecule in association with an Fe2+ ion.

Tense (T) State

The deoxygenated form of hemoglobin.

Relaxed (R) State

The oxygenated form of hemoglobin where O2 binding sites are open and more able to bind O2.

Concerted Model

All subunits change conformation at the same time.

Sequential Model

Subunits can change conformation individually.

2,3-Bisphosphoglycerate (2,3-BPG)

An allosteric regulator in erythrocytes that binds to the T form of hemoglobin and stabilizes it.

Enzymes

Biological catalysts with an active site

Enzyme Function

Enzymes bind to substrates and cause them to react faster

Enzyme Class

Enzymes are a class of proteins

Lock and Key

A potential substrate recognition and binding.

induced fit

A potential substrate recognition and binding.

Enzyme catalysis

Lower the activation energy of the reaction by stabilising the transition state or introduce intermediates allowing alternative pathways.

Oxidoreductase

Catalyzes Redox reactions.

Ligase

Catalyzes Formation of covalent bonds.

Transferase

Catalyzes Transfer functional groups (e.g. phosphate, amine).

Hydrolase

Catalyzes Hydrolysis.

Isomerase

Catalyzes Rearrange atoms within a molecule (convert one isomer to another).

Lyase

Catalyzes Remove groups of atoms from molecules.