Structural Biochemistry/General Terms

Structural Biochemistry General Terms

INTERACTOME: The complete set of molecular interactions in cells. Molecular interactions can occur between molecules of different groups (proteins, lipids, carbohydrates, etc.) or within the same group.
PROTEOME: The proteome is the complete set of proteins, which encompasses the functional information present in a cell or organism including the function, type and interactions of the proteins.
GENOME: The genome is the complete set of an organism’s genetic or hereditary information.
METABOLOME: The metabolome is the complete set of metabolites in a cell or organism that give insight into the metabolic processes.
CATABOLISM: Catabolism represents the processes that release of energy by breaking down molecules into smaller units.
ANABOLISM: Anabolism represents the processes that require energy for building molecules from smaller units.
METABOLISM: Metabolism is the complete set of processes that maintain life and are divided into catabolism and anabolism.
ENZYME ACTIVITY: Enzymatic Activity represents the ability of an enzyme to promote a particular chemical reaction or function.
SPECIFIC ACTIVITY: Specific Activity represents the ratio of enzyme activity to the amount of protein in a mixture.
BOND DISSOCIATION ENERGY: The bond dissociation energy is the energy required to break a bond for example the energy it takes to break a hydrogen bond is approximately 23kJ/mol.
FLICKERING CLUSTERS: Flickering clusters are short-lived groups of water molecules that are interlinked by hydrogen bonds in liquid water. These clusters are representative of the fact that Hydrogen Bonds are easily broken and reformed.
MICELLES: Micelles represent the non-polar regions that cluster together to present the smallest hydrophobic area to the aqueous solvent. This will remove some of the ordered-ness of water, which is favored due to the increased entropy of water.
ISOTONIC: Isotonic means that the cells osmolarity is equal to its surroundings
HYPERTONIC: Hypertonic means that the osmolarity of the surroundings is higher than the cell’s osmolarity causing the cell to shrink.
HYPOTONIC: Hypotonic means that the osmolarity of the surroundings is lower than the cell’s osmolarity causing the cell to swell.
ACIDOSIS: Acidosis is a condition where the pH of a person’s blood is below the normal blood pH of approximately 7.4.
ALKALOSIS: Alkalosis is a condition where the pH of a person’s blood is above the normal blood pH of approximately 7.4.
CONDENSATION REACTION: A condensation reaction involves the removal or elimination of water. (For example: ADP + P ⇒ ATP + H2O).
HYDROLYSIS REACTION: A hydrolysis reaction involves the addition of water. (For example: the depolymerization of proteins carbohydrates and nucleic acids requires water).
EUKARYOTES: Eukaryotes have a nuclear envelope that has a double membrane where the nuclear material is enclosed. This term literally means true nucleus.
PROKARYOTES: Prokaryotes lack a nuclear envelope, which is typical of Archaea and Bacteria kingdoms. This term literally means before nucleus.
BACTERIA: Bacteria are single celled microorganisms that tend to inhabit soils and surface water.
ARCHAEA: Archaea is a kingdom of single celled microorganisms that inhabit extreme environments and more closely resemble eukaryotes.
PHOTOTROPHS: Phototrophs derive their energy from sunlight.
AUTOTROPHS: Autotrophs derive their energy from sunlight and their source of carbon is from CO2 (for example: vascular plants).
HETEROTROPHS: Heterotrophs derive their energy from sunlight and their source of carbon are organic compounds (for example: green bacteria).
CHEMOTROPHS: Chemotrophs derive their energy from oxidation of chemical fuels meaning they take reduced fuel and oxidize it by usually adding oxygen.
LITHOTROPHS: Lithotrophs derive their energy from oxidation of inorganic fuels (for example: sulfur bacteria).
ORGANOTROPHS: Organotrophs derive their energy from oxidation of organic fuels (for example: people).
AEROBIC: An aerobic environment has a plentiful supply of oxygen allowing for the derivation of energy from the transfer of electrons from fuel molecules to oxygen.
ANAEROBIC: An anaerobic environment is virtually devoid of oxygen meaning organisms obtain energy by transferring electrons to sulfate or nitrate instead of oxygen (forming H2S and N2 respectively).
OBLIGATE ANAEROBES: Obligate anaerobes die when they are exposed to oxygen.
FACULLATIVE ANAEROBES: Facullative anaerobes are able to live with or without oxygen.
ENDOMEMBRANE SYSTEM: The endomembrane system is characteristic of eukaryotes and segregates specific metabolic processes thereby providing specific surfaces on which certain enzyme-catalyzed reactions can occur.

Enthalpy (delta H) - heat at constant pressure

Endothermic(pos. delta H) - heat is added to the system

Exothermic(neg. delta H) - heat is released from the system

Zeroth Law of Thermodynamics - states that two objects in contact with each other will have the same temperature Ex. A thermometer.

Spontaneous change - process that has a tendency to occur without an external influence

Entropy (S) - the measure of ‘disorder’ [Natural process is for system to become less ‘ordered’, or ‘random.’]; to become disordered

Microstate - all the quantized states of the whole system of molecules (number of microstates [W] can go up to 10^10^23)

Second Law of Thermodynamics - states that the entropy of an isolated system increases during the course of any spontaneous change

Thermal disorder - increase heat into which entropy can increase

Positional disorder - increase area into which disorder can occur

Third Law of Thermodynamics - states that a perfect crystal has zero entropy at a temperature of absolute zero: S(sub sys) = 0 at 0 K.

Extensive property - one that depends on the amount of substance Ex. entropy

Standard entropy of reaction - the entropy change that occurs when all reactants and products are in their standard states

Effects on Rate: Magnitude of k

Solvent Effects: Protic solvent: O-H or N-H’s in it v. Aprotic solvent: doesn't - solvate cations but not anions very well Polar v. Nonpolar solvent; acid/base presence can be cruical

Homogeneity Effects: homogeneous(solution) v. heterogeneous(two or more phase); surface area; particle size

Catalyst Effects: catalysts speed reactions up without being used up in the reaction; lower activation energy

Temperature Effects: (most affecting effect) there is a 2 to 4 fold increase in rate for every 10 degree increase in T

Collision Theory: 1)for a reaction to occur, ve- of reacting species must be within bonding distance, so inc. concentrations of reacting species will inc. rates 2) collisions must have correct orientation 3)collisions must have correct energy

Degenerate process - is when molecules collide but nothing is generated

Transition State/Activated Complex Theory - there is a point in a reaction at which the reactants are in transition to products (and vice versa)

References

Berg, Jeremy M., Tymoczko, John L., and Stryer, Lubert. Biochemistry. 6th ed. New York, N.Y.: W.H. Freeman and Company, 2007.