Biochemistry Outcomes 1-3 Revision Questions

Study Notes

Outcomes 1-3 Revision Questions

Catalase A Activity: Researchers studied Catalase A, an enzyme that breaks down hydrogen peroxide. Analysis at different pH levels and substrate concentrations revealed insights into its optimal activity conditions.
Optimal Conditions: Catalase A exhibits optimal activity at a pH range of 5-6 and at substrate concentrations between 30-40 mM.
pH 3 Effect: At pH 3, the protein's amino acid side chains (charged) are modified, impacting their ability to form ionic and polar interactions.
Binding Bonds (Catalase A): Catalase A binds to hydrogen peroxide via hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces.
Dithiothreitol (DTT): DTT reduces sulfur-sulfur bonds to sulfhydryl groups, preserving cysteine groups in their active, reduced state. It protects protein structure.
Low Temperatures: Lower temperatures reduce protease enzyme activity by slowing protein degradation.
High Temperatures: Increasing temperature beyond an enzyme's optimum leads to increased bond vibrations and kinetic energy, breaking bonds and lowering protein activity.
Induced Fit Model: Enzymes with induced fit adjust their active site shape in response to substrate binding, enhancing substrate binding and enzyme activity. Hexokinase is an example.
Cryoprotectants: Cryoprotectants lower the freezing point of water, preventing ice crystal formation and protecting proteins during freezing. Glycerol is one example.
Protease Inhibitors: Protease inhibitors in the lab prevent proteins from being broken down by proteases, preserving the original structure. Proteases are released from breaking open cells.
Structural Analogues: Molecules similar to a ligand, but not interacting the same way with a protein as the ligand. They are useful to determine protein function based on their interactions in the binding site.
Cofactors: Zinc and magnesium are examples of cofactors that assist proteins.
X-Ray Crystallography: X-ray crystallography uses X-rays to analyze protein crystal structures, enabling researchers to visualize the 3D structures of proteins and how these are helpful in their study.
Amino Acid Locations: Specific amino acids, crucial for enzyme function, can be chemically modified to determine their location in a protein. Modifying the residue's alters activity of proteins and thus confirm the location.
Zymogens: Inactive precursors or enzymes, for example, chymotrypsinogen.
SDS-PAGE: SDS-PAGE is used to determine whether protein processing has formed the mature form of a protein from its precursor form, by observing changes in size.
Protein Kinase A: Protein Kinase A is an enzyme with two regulatory and two catalytic subunits, significant in cell signalling and response.
Phosphorylation Cascade: The catalytic subunits of active Protein Kinase A initiate a phosphorylation cascade, amplifying initial signals and causing varied cellular response.
G-Protein Coupled Receptor (GPCR): Receptor is activated when a ligand binds to it, then GDP is exchanged for GTP, initiating G-Protein signaling, which in turn activates its target(e.g. adenylyl cyclase)
Cyclin-dependent Kinases (CDKs): Cyclin-dependent kinases (CDKs) activate or deactivate proteins, regulating cell-cycle progression through interactions with cyclins.
Protein Regulation Mechanisms: Protein regulation can also occur through allosteric regulation or covalent modifications, altering the protein's shape and binding properties to change their functions. Examples include Haemoglobin (oxygen binding) or phosphofructokinase (ATP binding).