Untitled Quiz

Enzymes as Catalysts

• Most enzymes are proteins that bind to their ligand as the first step in a process, with the output of the reaction being called the product.
• Enzymes can repeat these steps many times and rapidly, making them catalysts.
• An enzyme's ligand is called a substrate, which may be one or more molecules.

Enzymes at Work

• Lysozyme is an important enzyme that protects against bacteria by making holes in the bacterial cell wall, causing it to break.
• Lysozyme adds H2O to the glycosidic bond in the cell wall, holding the polysaccharide in a position that allows the H2O to break the bond.
• This is called the transition state, the state between substrate and product.

Features of Enzyme Catalysis

• Enzyme performance involves binding of the substrate (E + S → ES), followed by stabilization of the transition state (ES → EP), and finally the release of the product (EP → E + P).
• Vmax is the maximum rate of the reaction, and the turnover number determines how fast the substrate can be processed.
• KM is the [S] that allows the reaction to proceed at half its maximum rate.

Prosthetic Groups

• Occasionally, the sequence of the protein is not enough for its function, and a non-protein molecule is required to enhance the performance of the protein.
• Hemoglobin requires heme (an iron-containing compound) to carry oxygen.
• When a prosthetic group is required by an enzyme, it is called a co-enzyme, which is usually a metal or vitamin.

Regulation of Enzymes

• Regulation of enzymatic pathways prevents the depletion of substrate, and happens at the level of the enzyme in a pathway.
• Feedback inhibition occurs when the end product regulates the enzyme early in the pathway.

Feedback Regulation

• Negative feedback occurs when the pathway is inhibited by the accumulation of the final product.
• Positive feedback occurs when a regulatory molecule stimulates the activity of the enzyme, usually between two pathways.

Allostery

• Conformational coupling of two widely separated binding sites is responsible for regulation, with the active site recognizing the substrate and the second site recognizing the regulatory molecule.
• Proteins regulated this way undergo allosteric transition or a conformational change.

Allosteric Regulation

• Method of regulation is also used in other proteins besides enzymes, such as receptors, structural, and motor proteins.

Phosphorylation

• Some proteins are regulated by the addition of a PO4 group, which allows for the attraction of + charged side chains, causing a conformation change.
• Reversible protein phosphorylations regulate many eukaryotic cell functions, turning things on and off.
• Protein kinases add the PO4, and protein phosphatases remove them.

Phosphorylation/Dephosphorylation

• Kinases can put the PO4 on three different amino acid residues: serine, threonine, and tyrosine.
• Phosphatases remove the PO4 and may be specific for one or two reactions or non-specific.

GTP-Binding Proteins (GTPases)

• GTP does not release its PO4 group, but rather the guanine part binds tightly to the protein, making it active.
• Hydrolysis of GTP to GDP (by the protein itself) makes the protein inactive.

Molecular Switches

• Proteins can move in the cell, but with very little uniformity.
• The hydrolysis of ATP can direct the movement as well as make it unidirectional.

Motor Proteins

• Motor proteins move along actin filaments or myosin, using the hydrolysis of ATP to direct the movement.

Protein Machines

• Complexes of 10 or more proteins that work together, such as in DNA replication, RNA or protein synthesis, trans-membrane signaling, etc.