Research Question:

1. Explain why the substrate’s molecular conformation needs to match the enzyme’s active site
conformation of enzymes to ensure enzyme-substrate interaction. Use an example to support
your answer.

Enzymes are biological catalyst which are specialized proteins with definite structural
conformation. The substrate binds to a specific portion of the enzyme during the
reaction, called the active site (Hein, 2003). Active sites contains amino acid side chains
wherein the substrate are bound to form an enzyme-substrate complex. When this
enzyme-substrate complex is formed, catalysis occurs. However, each enzyme exhibits
specificity wherein it is their ability to choose exact substrate from a group of similar
chemical molecule ("What is Enzyme Substrate Specificity?",2020.). There are two
theories that explains why the substrate’s molecular conformation needs to match the
enzyme’s active site conformation of enzymes to ensure enzyme-substrate interaction
and this is explained by the “lock-and-key” and the “induced fit” model. Lock-and-key
model asserted that the enzyme and substrate have particular shapes that fit together
perfectly in one instantaneous step. But as the enzyme and substrate come together,
their interaction causes a mild shift in the enzymes’ structure for better fitting. This
dynamic binding maximizes the enzymes’ ability to catalyze its reaction. And this model
refers to the “induced fit” model ("Enzyme Active Site and Substrate Specificity", 2020).
According to an article published by Easy Biology Class (2020), substrate specificity
occurs in different degree. All enzymes may possess one type of this specificity. Specific
substrates having similar bonds and similar structure manifest bond specificity. Others
may manifest group specificity, wherein it is specific to a bond and the group
surrounding it. Some manifest substrate specificity, in which it is specific to only one
substrate. Some manifest stereo-specificity, where the enzyme is specific to a substrate
and a particular optical configuration. And some might also manifest dual specificity,
wherein they are categorized into two types: enzyme that reacts on two substrate by one
reaction type or enzyme that acts on one substrate but two reactions.
The specificity of enzyme can be illustrated in the antigen-antibody reactions. The
antibody recognizes a unique part of the foreign target, called an antigen. Each tip of the
“Y” of an antibody contains a paratope that is specific for one particular epitope
(analogous to a lock and key) on an antigen, allowing these two structures to bind
together with precision. Using this binding mechanism, an antibody can tag an infected
cell for attack by other parts of the immune system or it can directly neutralize the target
("Antibodies", 2020).
Hein, M. (2003). Introduction to general, organic, and biochemisty (pp. 618-620). Hoboken, NJ:
John Wiley.

What is Enzyme Substrate Specificity?. (2020). Retrieved 11 December 2020, from

https://www.easybiologyclass.com/enzyme-substrate-specificity-types-
classification/#:~:text=What%20is%20enzyme%20specificity%3F,complementarity%20between
%20enzyme%20and%20substrate

Enzyme Active Site and Substrate Specificity. (2020). Retrieved 11 December 2020, from
https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_%28Boundless
%29/2%3A_Chemistry/2.7%3A_Enzymes/2.7.2%3A__Enzyme_Active_Site_and_Substrate_Spe
 cificity#:~:text=Enzymes%20bind%20with%20chemical%20reactants%20called
%20substrates.&text=The%20positions%2C%20sequences%2C%20structures%2C,enzyme
%20specific%20to%20its%20substrate

Antibodies. (2020). Retrieved 11 December 2020, from

https://courses.lumenlearning.com/boundless-microbiology/chapter/antibodies/#:~:text=The
%20antibody%20recognizes%20a%20unique,to%20bind%20together%20with%20precision.

2. If hydrolytic enzyme are found inside living organisms and organisms have polymeric
biomolecules which are potential substrates for enzymatic hydrolysis, why are organisms not
hydrolyzed by their own enzyme?

The hydrolytic enzymes are present in the lysosome which is a membrane bound
organelle and found in animal cells. Lysosomes contains many different types of hydrolytic
enzymes including proteases, lipases, nucleases, glycosidases, phospholipases, and sulfatases that
usually exert their maximal enzymatic activity at low pH (Boya & Kroemer, 2008). These
enzymes breakdown macromolecules such as nucleic acids, proteins, and polysaccharides
("Lysosome | Description, Formation, & Function", 2019).
Organisms are not hydrolyzed by their own hydrolytic enzymes because high hydrolytic
enzymes are said to be potentially harmful to the cell. The lysosome then will keep these enzymes
from harming the entire cell which may cause hydrolysis or necrosis of the cell (Boya &
Kroemer, 2008). Another reason as to why they are not hydrolyzed by their own enzyme is
because the enzymatic hydrolysis is a chemical digestion that breaks down the bonds of the food
that is passing through the digestive system of an individual, and thus, it does not hydrolyze the
polymeric biomolecules that is outside the digestive tract of an individual ("Digestion – breaking
the large into the small", 2007).

Lysosome | Description, Formation, & Function. (2019). Retrieved 11 December 2020, from
https://www.britannica.com/science/lysosome

Boya, P., & Kroemer, G. (2008). Lysosomal membrane permeabilization in cell

death. Oncogene, 27(50), 6434-6451. doi: 10.1038/onc.2008.310

Digestion – breaking the large into the small. (2007). Retrieved 11 December 2020, from
https://www.sciencelearn.org.nz/resources/1830-digestion-breaking-the-large-into-the-small