How to do best Enzymatic reaction activity experiment [digestion of protein#1]

Purpose of the Science Project:

  This Science Project: Enzymatic reaction activity is designed to conduct a science project in the home itself. Our science project aims to see the Enzymatic reaction activity [digestion of protein] from the things available in our home. Here we are going to perform digestion of protein (egg white) in the presence of enzymes (exonuclease or endonuclease). These enzyme reaction experiments are suitable for science fair projects for 8th grade.

What is amino acid?

    It is an organic molecule and contains both carboxylic and amino functional groups. In nature, we get 21 amino acids. which can be listed as follows.

Reference: D.R. Lide, Handbook of Chemistry and Physics72nd Edition, CRC Press, Boca Raton, FL, 1991.
Science project -digestion of protein-detergent enzymes

Alanine: It is a natural amino acid with a formula(C3H7NO2). Ala is the short abbreviation for alanine amino acid. the molecular weight of alanine amino acid is 89.10.  pKa value is 2.34.

Arginine: It is a natural amino acid with a formula(C6H14N4O2). Arg is the short abbreviation for Arginine amino acid. the molecular weight of Arginine amino acid is 174.20.  pKa value is 2.17.

Asparagine: It is a natural amino acid with a formula(C4H8N2O3). Asn is the short abbreviation for Asparagine amino acid. the molecular weight of Asparagine amino acid is 132.12.  pKa value is 2.02.

Aspartic acid: It is a natural amino acid with a formula(C4H7NO4). Asp is the short abbreviation for Aspartic acid amino acid. the molecular weight of Aspartic acid amino acid is 133.11.  pKa value is 1.88.

Cysteine: It is a natural amino acid with a formula(C3H7NO2S). Cys is the short abbreviation for Cysteine amino acid. the molecular weight of Cysteine amino acid is 121.16.  pKa value is 1.96.

Glutamic acid: It is a natural amino acid with a formula(C5H9NO4). Glu is the short abbreviation for Glutamic acid amino acid. the molecular weight of Glutamic acid amino acid is 146.15.  pKa value is 2.19.

Glutamine: It is a natural amino acid with a formula(C5H10N2O3). Gln is the short abbreviation for Glutamine amino acid. the molecular weight of Glutamine amino acid is 147.13.  pKa value is 2.17.

Glycine: It is a natural amino acid with a formula(C2H5NO2). Gly is the short abbreviation for Glycine amino acid. the molecular weight of Glycine amino acid is 75.07.  pKa value is 2.34.

Histidine: It is a natural amino acid with a formula(C6H9N3O2). His is the short abbreviation for Histidine amino acid. the molecular weight of Histidine amino acid is 155.16.  pKa value is 1.82.

Hydroxyproline: It is a natural amino acid with a formula(C5H9NO3). Hyp is the short abbreviation for Hydroxyproline amino acid. the molecular weight of Hydroxyproline amino acid is 131.13.  pKa value is 1.82. 

For more detail on amino acid properties, please go through the above given reference.   

Generally, These amino acids are building blocks for the protein macromolecules. They arranged in a sequence manner, it varies from one protein to another. This variation in the sequence of protein gives new unique properties for protein. 

What is peptide?

         The small specific sequence of amino acids is called peptides. when two amino acids undergo a condensation reaction. It releases water molecules and the formation of peptide bonds. The number of amino acids in peptide molecules varies from three to a few hundred.       Some peptides act as a promoter for the enzymatic reaction. It starts the enzymatic reaction in our biological system. Some other peptides act as an inhibitor. It kills the reaction. This promotor and inhibitors play a very important in biochemical reactions in our physiology.     But all the functions are not possible only with the help of peptides. In some functionalities, we need higher molecular weight micromoles. What will happen in an increasing sequence of amino acids?

Forming different conformations: 

       When the sequence of amino acids adds up in the peptide molecule, it slowly becomes proteins. It undergoes different conformational changes. All amino acids are optically active except glycine. Around the carbon atom, other different functional groups bonded in space geometry. This gives a chiral center for the carbon atom.      In different conformation of protein changes its physical and chemical characteristics. First, we will discuss the physical characteristics of the protein molecule. Solubility in water is important. It mainly depends on the types of amino acids in the protein molecule.

     If the molecule is soluble in water, it is called hydrophilic (water loving molecule). If the molecule is less soluble in water, it is called hydrophobic (water hating molecule). Here we are not discussing the protein molecules dynamics in the gas phase.   In water, the protein molecule changes its conformation in Femto level time duration. These dynamics are very fast. We need ultrafast femtosecond spectroscopy to see these dynamics. Water molecule is not static. But water molecules stay static with protein due to the hydrogen bonding.   Protein molecules undergo various stages of folding. This folding gives different energy levels to the protein molecules. Another best method to see these folding is single molecule spectroscopy. Now let’s discuss enzymes, what is the difference between proteins and enzymes?

What is Enzyme?

      “All enzymes are proteins, but all proteins are not enzymes.” 

        This is true. But what makes them so different? the sequence of amino acids makes them different. Some sequence is chemically not active, it won’t activate any reaction biochemically. But in another case, some proteins activate the biochemical reaction in biological systems. These types of proteins are called enzymes.

     Enzymes are required for all biochemical reactions. You can take from the synthesis of protein to synthesis of  DNA, we need enzymes. It needs some activators and promotors to initiate the biochemical reactions.

    Generally, these activators and promoters are small molecules or some metal ions. when it binds with them, the enzyme activates the biochemical reactions. It also depends on the folding state of the enzyme molecule.  In some cases it goes unfolded state, it loses its enzymatic reaction activity.  How it goes unfolded state?

Denature of Protein and Enzymatic reaction:

    Some protein undergoes denaturation. It depends mainly on external things such as the pH of the buffer solution, the temperature of storage, and any other impurities.   Denature of protein with temperature is very common.

    For example, egg albumin becomes white hard matter by temperature. Protein unfolded at high temperatures by losing its hydrogen bonds.  This is an irreversible reaction. But in reality, the enzyme loses its activity even at the moderate temperature. 

   pH is very essential for any biochemical reaction. The ideal pH is 8.4 for any biochemical reaction. Tris buffers are used for enzymatic reactions. But we are not using any pH buffer for our science fair experiment.

  During the biochemical reaction, enzymes act as catalysts for the reaction. The outcome product decreases the pH into the acid region. If it reaches the acidic, the enzyme automatically denatures from its activity state.

    We need to monitor the pH during the biochemical enzymatic reaction. If pH moves to the acid region, we can use any dilute alkali solutions to neutralize the biochemical reaction. But choosing the correct alkali is very essential for a smooth reaction.

   We are going to discuss the science project here and some question and answer sections too. It will help to understand things clearly.

1. What are Enzymatic reaction activity and their application in the science project?

 Living systems are made of macro biomolecules. In this category, DNA, Protein, lipid, peptide, etc., All Enzymes come in the protein category. That is made by amino acids. This amino acid acts as the building block for the protein structure.

All enzymes are proteins, whether all proteins are enzymes? No, Not. Proteins are made from amino acid building blocks. Enzymes activate biochemical transformation in the biological systems in vivo and invitro.

            Using these enzymes in the science project depends on the level of a science project. If you have a science project which is related to biomolecules, you should get permission from the science project authority.

After getting permission from the authority, you should develop a good science project. Special care is required for science fair projects for 8th grade.

          In this paragraph, I am going to tell you a few tips for your science project. The enzyme usage could be described in a more detailed way in your science project idea. The safety material data sheets must include in the science project detail proposal and report.

When you are mentioning the name of an enzyme in the science project report, use more bold or some specific font to just differentiate it from other words.

2. What are Invivo and Invitro biological systems in science projects?

          There are different science projects used to understand nature. If you want to do a science project in biology, you should use a specific science project.

           Biology evolved from microscopy invention. In addition to this, we can also use nanoscopy such as atomic force microscopy(AFM), scanning electron microscope(SEM), and Transmission electron microscope(TEM). etc, in a science project and you can use microscopy and nanoscopy in your science project also. Science project needs step-by-step detail science project instructions.

             Invivo means the biological process that takes place inside our body. If we are inducing some biochemical reaction, it gives the change in the living system or living cell. It is one of the best science projects that can use in the science project.

 

You can design more science projects from these science projects. All these science projects should get permission from the authority. Middle school events such as science fair projects for 8th grade get permission easily.

         Invitro means similar cells we are growing outside in the laboratory environment. you can also use them in the science project. But these science projects definitely need step-by-step science project instruction about the in-vitro process.

 

Besides this, a proper laboratory setup is required for this science project. Before implementing any science project, you should design a detailed science methodology for your science project.

3. How does enzyme help in the biological process and from that to generate a science project?

               In the science project of the enzyme, it obviously plays an important role in all biological processes in our body. There are so many different types of enzymes in our bodies. Among them, some enzymes are good, no toxic to our bodies, and that type of enzyme, we can use for our science project.

          Without a doubt, you can plan for your science project with these enzymes. The first step in your science project is to collect information about these enzymes. Nowadays, we are using these enzymes in our detergents.        

          In the biological process, enzymes can either build a biomaterial from small building blocks or some other enzymes which break the big bio-material (biomacromolecules)into small fragments.              


Possible Science Project :

1.Different enzymatic detergent from the marketplace at room temperature.
2.Different food products can be used for enzymatic reaction activity.
3.Different temperature checks for the enzymatic reaction activity of the detergent.

4. How can we classify the enzymes and use them in a science project?

      DNA binding enzymes are classified into the following categories:

       (a) Endonuclease: The enzymes bind in the middle of the DNA strand

       (b) Exonuclease: The enzymes bind at the end of the DNA strand
       (c) Helicase: The enzymes open the DNA double helix

        We can use the enzymes according to their binding affinity in our science project. you can design a science project without using DNA. Here we used them in our science project without using DNA. Our entire science project is using detergent enzymes. These detergent enzymes are used for the digestion of protein from eggs.

Exonuclease Activity:

  Both eukaryotes and prokaryotes have three types of exonuclease families of enzymes. That can be named as follows.

  • 5′ to 3′ exonuclease
  • 3′ to 5′ exonuclease
  • poly(A)-specific 3′ to 5′ exonuclease

     The main cause of RNA degradation in eukaryotes and prokaryotes is nothing but the exonuclease family of enzymes. Generally, large protein subunits inside the exosome consist of a huge number of 3′ to 5′ exonuclease.

DNA polymerase (I) plays a very important role in DNA nucleotide synthesis. Moreover, This particular enzyme shows 3′ to 5′ and 5′ to 3′ exonuclease activity.  This activity helpful in DNA proofreading and error mismatch editing.


     Besides, these two types of exonuclease activity are not similar. Thus, the 3′ to 5′ exonuclease could remove one mononucleotide from the DNA at a time. But, the 5′ to 3′ exonuclease could remove one or 9-10 nucleotides at a time.

From a reactivity point of view, 5′ to 3′ exonuclease is more active than 3′ to 5′ exonuclease. This type of biological process is called exonuclease activity.


science project - digestion of protein- detergent enzymes


Materials Required for experiments:

  1. Aluminum tin                            —           2 nos
  2. Rubber cork and wool wrap    —-          2 nos
  3. Boiled Egg                               —–         1 no
  4. Normal detergent                     —-          one pack
  5. Detergent Enzymes                ——  one pack
  6. water (purified water)              —         1 liter


Standard Operating Protocol(SOP):

  1. Take one boiled egg and cut it into four equal parts.
  2. Two-part egg white is added to aluminum tin-1 and the remaining two-part egg white added to aluminum tin-2. (label them properly).
  3. Add water around half a portion of both labeled aluminum tins.
  4. One tablespoon of normal detergent adds to Aluminium tin-1.
  5. One tablespoon of detergent enzymes adds to Aluminium tin-2.
  6. Close both the tins with a rubber cork and wrap with wool, keep it in warm condition.

 

Science Project: Enzymatic activity with detergent enzymes  [digestion of protein]
Enzymatic reaction experiments

Science Project: Enzymatic reaction activity with detergent enzymes  [digestion of protein]


Observation from Science Project: 

Every eight hours once you observe the changes in the enzymatic reaction activity in the presence of detergent enzymes and note down everything in the record book with photos (if possible). You are going to follow the same method for about three days.


Outcomes from science Project:

  Enzymes in the aluminum tin-2 will break the egg white protein completely. The enzymes convert solid egg white into liquid form.

If you check the same normal detergent reactivity in another aluminum tin-1, then it will be solid form as an outcome. Because we use normal detergent in Aluminium tin-1. You will observe the digestion of protein in the presence of enzymes.


Further Science project plans:


(a)You can plan for many more experiments on the digestion of protein. This process differs from other protein sources. You can observe the different rates of digestion of protein foods.


 (b) You can differentiate the cooked and non-cooked protein sources with the digestion of protein experimentation.

Main highlights of Enzymatic reaction (enzymes activities):

Hydrolysis enzymes: Enzymes are made by peptide bond as their backbone. Breaking down this functional group are called as hydrolysis of enzymes.

ph on enzyme activity: enzyme activity and ph are both inter dependent to each other. If it goes to acidic environment, it protonates the amino group terminals. If it goes to basic environment, it deprotonates the acid group terminals. This affects enzymatic reaction activity.

Enzyme chemical reaction: catalase enzyme activity is a very important biological function. It increases the rate of biochemical reactions. There are different types of enzyme inhibition.

The optimum temperature for enzyme activity: enzymes and temperature are interrelated to each other. At high temperatures, the enzyme loses its activity. At low temperatures, the enzyme inhibits its activity. The optimum moderate temperature on enzyme activity gives the best results.

oxidation enzyme: Enzyme catalytic activity reduces due to the oxidation of enzyme. Oxygen kills the enzymatic activities.

Variable affecting enzyme function: There are different types of variables that affect the enzymatic reaction. The main variables are temperature, pH, pressure, and external chemical agents.


   This particular science project and its experimental results could be displayed in science fair projects for 8th grade.

         This blog, not only focuses on science projects for all grade students. Along with that, other students whoever interest in science can see more experiments on the home page.

Enzymatic Reaction (FAQ)

What is Enzyme?

Enzymes are proteins. But all proteins are not enzymes. Amino acids are the building blocks for proteins. Enzymes are the bio-molecules, which are responsible for biochemical reaction activity.

What type of reaction is the enzymatic reaction?

Enzymatic reactions are biocatalytic reactions. Catalysts are responsible for the faster reaction rate. It reduces the activation energy of any particular reaction. That is the reason it undergoes in faster and selective phase.

What are the steps in an enzymatic reaction?

Four Steps of Enzyme reaction

  • The enzyme and the substrate are in the same area and region. Some special situations have more than one substrate molecules that the enzyme will change physically or chemically.
  • The enzyme binds to the substrate at a special area and region called the active site for the enzymatic reaction. The enzyme acts as a lock and the substrate acts as a key. This is called the Lock-key model.
  • An enzymatic reaction called a catalysis reaction. It accelerates the biochemical reaction and regio-selectivity of the molecule.
  • The enzyme releases the final outcome product in specific regio and stereoselective manner.

How does the concentration of enzyme affect the enzymatic rate?

Concentration of the enzyme plays very important role in enzymatic reaction. If the concentration of enzyme is high, then more number of enzyme molecules will be there. More number of number of enzyme molecules gives increase in the binding site of substrate molecule. It accelerates the enzymatic reaction.

What are some examples of enzymes?

Examples of enzymes

  • Lipase is a group of enzymes that help digest fats and fatty acids in the gut.
  • Amylase chemically changes starches into sugars by breaking them into small ones.
  • Maltase is in saliva, which breaks the sugar maltose into glucose in our mouth. The digestion process starts in the presence of saliva.
  • Trypsin is found in the small intestine in our stomach, which breaks big proteins down into amino acids. These amino acids will be the building blocks for protein synthesis in the body.

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