The Structure Of Carboxypeptidase A And Its Zinc

Enzymes combine with reactant molecules (substrate) and bind them closely to one another. The three-dimensional shape of the enzyme molecule must be complementary to the shape of the substrate.

Inhibitors - As mentioned earlier, enzymes have an active site specific to the substrate molecules. However, it is possible for other molecules similar to enzyme's substrate to bind with the enzyme's active site and therefore, inhibit the enzyme's task.

B. Catalysis occurs on a specific site on the enzyme (the active site). The active site is usually less than 5% of the surface area of the protein, and is always in a cleft. The rest of the molecule serves to present the active site in a three dimensional structure that is capable of binding substrate and catalyzing the reaction. Binding to a substrate is very specific, and involves ionic interactions, H bonds and van der Waals forces.

Enzymes have an active site which has a complimentary base to a specific substrate, when these bind an enzyme-substrate complex is

enable the substrate to bind to the enzyme and form the enzyme substrate complex and

Figure 1.b shows the ‘Lock and Key’ model where two individual substrates meet the active site where

They are made up of amino acids (consists of amino group, carboxyl group, hydrogen atom, and R group). Polypeptide bonds form between amino acids to form polypeptide chains. Amino acid sequence is primary protein structure. The secondary structure is the bonding pattern of the amino acids (e.g. helix, sheet, etc.). The tertiary structure consists of the domain, where the sheets or helixes fold on each other and become stable. The quaternary structure consists of several polypeptide chains that form advanced proteins such as human leukocyte

Enzymes are biological catalysts. They work by lowering the activation energy needed to initiate a chemical reaction. Enzymes work within an optimal temperature and optimal pH. Enzymes are highly specific for a single substrate. The Enzyme is usually much larger in size than the substrate it binds to. In some cases, an enzyme requires something called a cofactor to begin the chemical reaction. There were four different experiments that were executed in the enzyme lab. Experiment 7.1, the first experiment, was performed to test the effect of temperature on enzymatic

This site is what matches up with specific substrate molecules around it. When an active site and a matching substrate molecule combine, an enzyme-substrate complex is formed. The reaction that the enzyme helps catalyze produces one or more product molecules from the substrate it was paired to.

Enzymes have a quaternary structure as they are globular proteins and have a 3D shape. The primary structure is made up of amino acids joined by peptide bonds. The secondary structure is made up of an alpha helix/beta helix pleated sheet as a result of hydrogen bonding in the backbone. The tertiary structure is made up of 3D polypeptides due to bonding of the “R” group and the Quaternary structure is made up of 2/more polypeptides joined together (globular proteins). “The 3D shape allows the enzyme to have an active site – this is where the substrate (what is being acted on) binds to the enzyme” (Pearce, 2017). Hydrogen peroxide (in this case the substrate) binds to the activation site on the peroxidase (enzyme). When

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

The overall structure of NoV Pro is that of a cysteine protease with a chymotrypsin-like fold and a catalytic triad consisting of His-30, Glu-54, and Cys-139 (71). The structures of Norovirus proteases share a high degree of structural similarity to picornaviral 3C proteases (75, 76), making picornaviral proteases an excellent model for comparison. The mechanism of catalysis for the Norovirus proteases is similar to the serine proteases that contain a Ser-His-Asp triad in the active site. The mechanism of catalysis of serine proteases is shown in Figure 2. The catalysis reaction occurs in two halves, acylation and deacylation. First, the carbonyl of the peptide substrate is attacked by the Serine and His residues of the catalytic triad (77). The result is the first of two tetrahedral intermediates which collapses to form the acylenzyme intermediate (77). The second half of the reaction is very similar where a water molecule and His residue attack the acylenzyme intermediate to yield the second “transition-state” intermediate which collapses to release the carboxylic acid product (77). Similar to the serine proteases, the Cys-139 residue of Norovirus proteases functions similarly to the Ser residue and the Glu-54 functions as the Asp residue of the serine proteases while the His residue function is

For the second part of the experiment, one had to use the knowledge learn from viewing protein molecules in FirstGlance in Jmol to analyze the protein PDB ID: 4EEY. The analysis of this protein was done using the RSCB protein data bank (PDB) at (http://www.rcsb.org/pdb/home/home.do).2

Campbell and Farrell define proteins as polymers of amino acids that have been covalently joined through peptide bonds to form amino acid chains (61). A short amino acid chain comprising of thirty amino acids forms a peptide, and a longer chain of amino acids forms a polypeptide or a protein. Each of the amino acids making up a protein, has a fundamental design that comprises of a central carbon or alpha carbon that is bonded to a hydrogen element, an amino grouping, a carboxyl grouping, and a unique side chain or the R-group (Campbell and Farrell 61).

L-carnitine was discovered in Russia, and one year later in Germany. The proper name, Carnitine, refers to the Latin origin, (carno, caris). Its structural formula was decoded in 1927, and its physiological significance was understood by the 1960's. (http://www.hlthmall.com/l-carnitine.html) L-carnitine is synthesized in the liver and kidneys, from two essential amino acids, lysine and methionine. This synthesis requires the presence of vitamins niacin, B6, and iron.