Lysozyme

The enzymatic mechanism of lysozyme is one of the classic models to illustrate general principles of enzyme mechanics.

The activity of certain macromolecules as catalysts within living systems is a central biological process. Macromolecules that act as catalysts are enzymes. Most, but not all, enzymes are proteins. A few ribonucleoprotein enzymes have been discovered in which the catalytic activity is in the RNA portion of the molecule rather than the protein part. Enzymes bind temporarily to one or more reactants and lower the activation energy of the reaction.

Enzyme concepts including mechanics, kinetics and regulation are centrally important for the new MCAT, in which biochemistry has such strong emphasis. To understand enzyme activity at the superior level you need to fully involve your general chemistry and organic chemistry. Beyond simple retention of information, try your best to embed your understanding of this material in all of its conceptual underpinnings from the rest of science.

WikiPremed Resources

Learning Goals

Proficiency 

Be able to apply the induced fit model in describing how substrate binding in the active site of an enzyme occurs.

Have a good sense of the mechanisms of enzyme activity as they relate to active site chemical structure as well as the roles of cofactors and coenzymes.

Understand how feedback regulation of enzyme catalysis occurs and the types of inhibition of enzyme activity.

Understand enzyme kinetics, especially the nomenclature and basic problem solving methods of the Michaelis-Menton model.

Understand how to describe the kinetic properties of allosteric enzymes.

Be able to point to a few specific examples demonstrating regulation of enzymes by covalent modification or proteolytic activation.

Suggested Assignments

Conceptual Vocabulary for Enzymes

RNA
Ribonucleic acid or RNA is a nucleic acid polymer consisting of nucleotide monomers, which plays a number of important roles in the processes of translating genetic information from DNA into proteins.
DNA
DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms.
Messenger RNA
Messenger Ribonucleic Acid (mRNA) is a molecule of RNA encoding a chemical blueprint for a protein product.
Base pair
Two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair.
Nucleobase
Nucleobases are the parts of RNA and DNA that may be involved in pairing. These include cytosine, guanine, adenine, thymine, uracil, xanthine and hypoxanthine.
Nucleotide
A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups.
Adenine
Adenine is a purine with a variety of roles in biochemistry including cellular respiration, as part of ATP, NAD, and FAD, and protein synthesis, as a chemical component of DNA and RNA
Adenosine triphosphate
Adenosine triphosphate is a multifunctional nucleotide that is most important as a molecular currency of intracellular energy transfer.
Chromatin
Chromatin is the complex of DNA and protein that makes up chromosomes
Histone
Histones are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation.
Guanine
Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA. In base-pairing it binds to cytosine through three hydrogen bonds.
Uracil
The pyrimidine uracil base pairs with adenine in RNA and is replaced by thymine in DNA
Thymine
Thymine is one of the four bases in the nucleic acid of DNA along with adenine, guanine, and cytosine. It always base-pairs with adenine.
Cytosine
Cytosine is one of the five main nucleobases found in the nucleic acids DNA and RNA. It is a pyrimidine derivative. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.
Transfer RNA
Transfer RNA (abbreviated tRNA) is a small RNA chain that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.
Ribosomal RNA
Ribosomal RNA (rRNA), a type of RNA synthesized in the nucleolus, is the central component of the ribosome, the protein manufacturing machinery of all living cells.
Purine
Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring.
Pyrimidine
Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring
Adenosine
Adenosine is a nucleoside composed of adenine attached to a ribose moiety via a beta-N9-glycosidic bond.
Nucleoside
Nucleosides are glycosylamines made by attaching a nucleobase to a ribose or deoxyribose ring.
Complementarity
Complementarity is a property of double-stranded nucleic acids such as DNA and RNA as well as DNA:RNA duplexes in which base pairs occur between them characterized by non-covalent connections via hydrogen bonds.
Nucleosome
Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin. Each is made up of DNA and four pairs of proteins called histones.
Uridine
Uridine is a nucleoside formed when uracil is attached to a ribose ring via a beta-N1-glycosidic bond.
Cytidine
Cytidine is a nucleoside that is formed when cytosine is attached to a ribose ring via a beta-N1-glycosidic bond.
Cyclic adenosine monophosphate
Cyclic adenosine monophosphate (cAMP or cyclic AMP) is a molecule that is important in many biological processes.
Stacking
Stacking in supramolecular chemistry refers to a stacked arrangement of aromatic molecules, which interact through aromatic interactions.
Deoxyadenosine
Deoxyadenosine is deoxyribonucleotide and is considered a derivative of the nucleoside adenosine.
Guanosine
Guanosine is a nucleoside comprising guanine attached to a ribose ring via a beta-N9-glycosidic bond.
Advanced terms that may appear in context in MCAT passages
Adenosine monophosphate
Adenosine monophosphate, also known as AMP, is the ester of phosphoric acid with the nucleoside adenosine.
Oligonucleotide
Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases.
DNA melting
DNA melting, also called DNA denaturation, is the process by which double-stranded deoxyribonucleic acid unwinds and separates into single-stranded strands through the breaking of hydrogen bonding between the bases.
DNA supercoil
If a DNA segment under twist strain were to be closed into a circle by joining its two ends and then it is allowed to move freely, the circular DNA would contort into new shape, such as a simple figure-eight. Such a contortion is called a supercoil.
A-DNA
A-DNA is one of the many possible double helical structures of DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more compact helical structure.
Z-DNA
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form).
G-quadruplex
Nucleic acid sequences which are rich in guanine are capable of forming four-stranded structures called G-quadruplexes (Also known as G-tetrads or G4-DNA).