1 Circle the substrates and label as S 2 Mark the scissile b

1. Circle the substrate(s) and label as “S”
2. Mark the scissile bond in the first figure.
3. Point out 2 places where the His-57 works as a base (extracting H+) (identify the curvy arrows).
4. Point out two tetrahedral intermediates (point out what exactly is the “tetrahedral”)
5. Circle the product(s) label as “P”
6. Which one is the covalent intermediate?
7. Indicate the transition state intermediate(s).
8. Chymotrypsin recognizes Phe/Tyr/Trp residues, and cleaves the peptide bond at the C-terminal of these residues. Which part of the very first figure is the recognized residue?, RN or Rc?

Help with this? I\'m supposed to mark and label, but Im not exactly sure what im marking, or how I\'d know it for an exam problem.

His 57 Ser 195 CHz O--H HTO Re --N Asp 102. H RN His 57 Ser 195 Re-N Asp 102 Ric N His 57 Ser 195 CH Asp 102 HO His 57 Asp 102 CH Asp 102 His 57 Asp 102 Ser 195 Ser 195 Ser 195 CH2

Solution

The compound you are supposed to mark here is the substrate. A substrate is a substance which is used up by a reaction or a pathway. Generally, it is the substance from which the reaction or the pathway starts from. For example, in a glycolysis reaction, the glucose molecule is the substrate which is used to make pyruvate, which in turn acts as the substrate for further reactions. Therefore for glycolysis, all coumpounds formed between glucose and pyruvate which are immediately used up to move the pathway forward are termed as pathway intermediate, and all the compounds which are released and not used up in the same pathway are called metabolites. Some other compounds are also used up and released during the pathway, and they can be put under the classification of substrate and product respectively. In glycolysis, ATP is consumed in the first step and counts as a substrate for that step, while two ATP are released in further steps. In the overall mass balance, a total of one ATP is produced ( two produced - one used) so it is counted as a product when we look at the pathway as a whole. (Please refer to a layout of the glycolysis pathway while reading this part of the answer.)

For the above pathway, the first molecule and water are the substrate as they are taken up the pathway and are not replenished by it. Therefore , the very first molecule in the pathway is the substrate, as all other intermediates come from this molecule.