Enzymes are made up of proteins; which are made up of polypeptide
chains of amino acids. The single unit of protein is an amino acid, the
structure as follows:

   H          
H            O                                                                                   

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OH

 

H

 

       N     
 C      C

                         

 

 

Amino acids join by condensation reactions, to form peptide
bonds. During this, the OH from the carboxyl group and the H from the amino
group, (from another amino acid) is removed in the form of a water molecule: H2O.
The amino acids can now join, a dipeptide bond is formed when two amino acids join
together, a tripeptide is when three amino acids join, and a polypeptide bond
is many amino acids join together.

Proteins have 4 structural levels:

The primary structure has the sequence of
amino acids in a polypeptide chain. As the sequence can vary, this determines
the specific shape of the protein, therefore determines the function.

 

 

 

(Particlesciences.com, 2009)

The secondary
structure has hydrogen bonds between the amino acids within the polypeptide
chain. This causes the chain to coil into an alpha helix or fold into a beta
pleated sheet. The hydrogen bonds are very loose and week.

 

 

The tertiary structure is often the folding or coiling or the
polypeptide chains further, and there are more bonds due to the interactions of
the R group from the polypeptide chains. Within this structure there are
sulphur bridges which keep the structure in place.                                              (Cutteridge,
2005) The hydrogen bonds are still present,
also ionic bonds may occur due to some amino acids containing ions. “Active sites are grooves on the surface of an enzyme,
composed of amino acids that are brought together in the tertiary structure.” (Cooper and Hausman, 2000)The
structure is 3D, for single polypeptide chains, this is the final structure.

The quaternary structure is the way proteins
(made from multiple polypeptide chains) interact with one another and assemble
themselves. To form a larger, more complex structure. This is the final 3D
structure.

 

 

 

 

 

 

(Particlesciences.com, 2009)

 

Enzymes are biological catalysts speeding up metabolic
reactions in the body. The enzymes can be used continuously, because it is not
used up during the chemical reaction. Enzymes are important to living organisms
because most chemical reactions are controlled by the enzyme; without the
catalyst the reaction would be too slow. The enzyme binds to their specific
substrate at the active site, this has a particular shape to fit only one
certain substrate. The shape of the active site is determined by the sequence
of amino acids within the primary structure. Due to the specificity of the
active site to the substrate, named- the lock and key theory. When the
substrate and enzyme bind, products are made.

(BBC, 2017)

This theory has developed, and an adaptation of this theory
is proposed, the ‘induced fit theory’ “the substrate plays a role in
determining the final shape of the enzyme and that the enzyme is partially
flexible.” (Operalt, 2003) The substrate does have to be the right shape to fit
the active sight, but also to change the shape also for it to fit.

There are factors affecting enzyme activity; one is
temperature. As the temperature increases, so does the kinetic energy between
the enzymes and substrates; thus, increasing the number of collisions. Resulting
in more substrates binding to the active sites and reacting. Once the
temperature becomes too high the enzyme will denature, which changes the shape
of the active site. Consequently, the substrate cannot bind and now reactions
cannot take place. Another factor is PH, every enzyme has an optimum PH which
is where it will work best. However above and below that the H+ and
OH- ions from acids and alkalis can interfere with the hydrogen and
ionic bonds, holding the tertiary structure of the enzyme together. Therefore,
the active site can change shape and becomes denatured.  Another factor is substrate concentration “high concentrations can influence the enzyme
activity… sometimes the particular component acts directly as an
inhibitor of the enzyme reaction (e.g. substrate inhibition).”
(Bisswanger, 2014) When the concentration of substrate increases the faster the
reaction, due to the increased number of substrates there are more collisions.
However there becomes a saturation point where every enzyme has a substrate. If
more are added it would not affect the rate of reaction because there are no
more active sites to bind to.  

Calculation of water and hydrogen
peroxide to make different concentration solutions:

Hydrogen peroxide concentration (%)

Volume of hydrogen peroxide (cm3)

Volume of water (cm3)

100%

10cm3

0cm3

90%

9cm3

1cm3

80%

8cm3

2cm3

70%

7cm3

3cm3

60%

6cm3

4cm3

50%

5cm3

5cm3

40%

4cm3

6cm3

30%

3cm3

7cm3

20%

2cm3

8cm3

10%

1cm3

9cm3

0% (control)

0cm3

10cm3

Experiment:

 

Equipment:

Weighing boat

White tile

Weighing scale

Measuring cylinder

Borer

250ml measuring
cylinder

Knife

2x clamp stands

1000 ml beaker

Pestle and mortar

Bung with pipette tube

10x 100ml beaker

5cm3 pipette

1cm3 pipette

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

This method was chosen as it’s easier to measure the amount
of oxygen produced in the measuring cylinder, increasing accuracy and reliable results.
If method number was used it is difficult to measure the amount of oxygen
produced by measuring the height of the foam, as the foam is uneven, therefore
making it difficult to measure. Oppositely, with the chosen method the amount
of oxygen is clearly measurable because the water in the measuring cylinder is
even, and measurable by looking at the meniscus level; giving an accurate
measurement. The potato was purified to increase the surface area of the
reacting particles. This equation enables you to see if the reaction occurs
during the experiment as you can see the products (oxygen) producing. A control
experiment was to conducted to compare to the experiments with a independent
variable. This allows you to see if the independent variable is responsible for
the results.

                2H2O2                                 2H2O
+ O2

Hydrogen peroxide    catalyse      water + oxygen

 

(BBC,2014)

In relation to this graph, the potato whole would be the red
line and would react slower. The pureed potato would be the blue line and would
react faster because there are more surfaces to work on, causing more
collisions. Resulting in a faster rate of reaction.

I chose to measure the amount of oxygen produced every 20
seconds; comparing the rate of reaction along the time limit.

 

Variables:

The independent variable is the
varying concentrations of hydrogen peroxide. The dependant variable is the
amount of oxygen produced.

Prior to the experiment I
conducted a risk assessment, I followed this throughout to reduce risk. (see
Appendix One)

 

“Enzymes act by reducing the activation
energy required to make a reaction proceed” (Lodish, Berk and Zipersky,
2000) observing the results rate of reaction was fastest in the first 20
seconds, especially in the higher concentrations, therefore showing the minimum
energy required for each reaction was low.

 

 

Observing the results, it is evident that as the
concentration of substrate increases so does the amount of oxygen produced. Additionally,
as the substrate concentration increase the rate of reaction is faster because
more of the enzymes active sites are binding with the hydrogen peroxide. “The
concentration of all substrates directly involved in the enzyme reaction should
be saturating. Binding of these components to the enzyme obeys a hyperbolic
saturation function” (Bisswanger, 2014) The saturation point of the results is
from 70% concentration because the amount of oxygen produced has reached its
highest (40.17cm3). at the point all the enzyme active sites have
bound with a substrate molecule and are full. Furthermore, adding higher
concentrations of the substrate (hydrogen peroxide) will not increase the rate
of reaction and will not affect reaction rate and the results. At this
saturation point it has reached it optimum concentration and will work best;
producing more oxygen. At 90% concentration, the amount of oxygen produced
decreased slightly, and at 100% more significantly. Before the experiment it
recorded the pH of 100% hydrogen peroxide, using a strip of universal
indicator. This measured at pH 4 (a weak acid) “at pH levels below 3.5 catalase
is denatured, some catalases will dissociate into two subunits.” (Brennan,
2017) Potentially, my results replicate this
because at these unfavourable pH conditions the catalyse will slow and may
start to change shape. The enzyme cannot bind with the substrate because the
lock (catalase) has changed shape, therefore the hydrogen peroxide cannot fit
into it like a key. Some may start to denature, however because the hydrogen peroxide
is just above pH 3.5 the enzyme may not. As the concentration of hydrogen
peroxide decreases the pH will increase, “Catalase acts well over an extent of
hydrogen ion concentrations ranging from pH 5 to pH 9, but its activity
diminishes decidedly on either side of these limits, the diminution being much
more abrupt on the acid than on the alkaline side. Thus, at pH 4 one-half of
the activity is still present”. (Morgulis, Beber and Rabkin, 1926) Additionally
this proposition also replicates, and further supports the findings of my
experiment. In the

During the experiment there were limiting factors, one is
the reaction time of adding the hydrogen peroxide, pushing the bung in the
tube, and pressing the timer. Due to human error there will be delays in
timings which have affected the results. Also, the few seconds taken to secure
the bung resulted in oxygen loss. Another consequence of human error I the measurement
of the oxygen production. With some measurements the meniscus line was
degreasing rapidly, which increased the difficulty of observing the correct
number. Accompanied by reading the measurement at exactly the correct time with
the stopwatch. An example of this within my results are during the first
results, at 60 seconds and 20% concentration. This result is an anomaly which
continued to affect the results until 100 seconds. To overcome these, I would
have 3 people to conduct the experiment simultaneously, to increase accuracy by
taking three measurements, then average the results. Additionally, to reduce
reaction time by have different roles.   Another implication is the pressure inside the
boiling tube. One anomaly within the results is at 80% at 60 seconds, during
the first results. The bung popped of; releasing oxygen which effected the
results because this could not be measured. To overcome these, I would use a
conical flask to give more space for the reaction, reducing the pressure.  

 

Bibliography

 

·        
BBC. (2017). BBC Bitesize – GCSE Biology –
Biological molecules – Revision 5. online Available at:
https://www.bbc.co.uk/education/guides/z8wsgk7/revision/5 Accessed 2 Dec.
2017.

 

·        
BBC. (2014). BBC – GCSE Bitesize: Effect of
surface area. online Available at:
http://www.bbc.co.uk/schools/gcsebitesize/science/add_ocr_gateway/chemical_economics/reaction3rev1.shtml
Accessed 6 Dec. 2017.

 

·        
Bisswanger, H. (2014). Enzyme
assays. Perspectives in Science, online 1(1-6), pp.41-55. Available at:
https://ac.els-cdn.com/S2213020914000068/1-s2.0-S2213020914000068-main.pdf?_tid=8f952326-d799-11e7-a1e3-00000aab0f02=1512244208_26598f2c72087a0b4f6bd5f09a4e48d7
Accessed 2 Dec. 2017.

 

·        
Brennan, J. (2017). PH Levels of Catalase.
online Sciencing. Available at: https://sciencing.com/ph-levels-catalase-6826245.html
Accessed 6 Dec. 2017.

 

·        
Cutteridge, A. (2005). Understanding the
Relationship Between Enzyme Structure and Catalysis. online Ebi.ac.uk.
Available at: https://www.ebi.ac.uk/sites/ebi.ac.uk/files/shared/documents/phdtheses/alexgutteridgethesis.pdf
Accessed 10 Dec. 2017.

 

·        
Cooper, G. and Hausman, R. (2000). The
cell: A Molecular Approach.. 2nd ed. Sunderland: Sinauer Associates. NCBI.
Available at: https://www.ncbi.nlm.nih.gov/books/NBK9921/
Accessed 10/12/2017

 

·        
Lodish, H., Berk, A. and Zipersky, S.
(2000). Molecular Cell Biology. 4th ed. New York: W. H. Freeman, pp. section
2.5.

 

·        
Morgulis, S., Beber, M. and Rabkin, I. (1926).
STUDIES ON THE EFFECT OF TEMPERATURE ON THE CATALASE REACTION: III. TEMPERATURE
EFFECT AT DIFFERENT HYDROGEN ION CONCENTRATIONS. IV. A THEORY OF THE CATALASE
REACTION. Journal of Biological Chemistry, online 68(547), p.538.
Available at: http://www.jbc.org/content/68/3/547.full.pdf Accessed 6 Dec.
2017.

 

·        
Operalt, C. (2003). Enzymes – Lock.
online Chemistry.elmhurst.edu. Elmhurt College. Available at:
http://chemistry.elmhurst.edu/vchembook/571lockkey.html Accessed 2 Dec. 2017.

 

·        
Particlesciences.com. (2009). Protein
Structure: Primary, Secondary, Tertiary, Quatemary Structures. online
Available at:
http://www.particlesciences.com/news/technical-briefs/2009/protein-structure.html
Accessed 2 Dec. 2017.