08/02/2025, 17:24 Biology Paper III Essays - Evernote
The importance of complementary shapes of
molecules in organisms. (2021)
Enzyme-Substrate Complex
Enzymes are proteins with a very specific tertiary structure resulting in a very
specific active site. This active site is only complementary to one substrate
therefore forms an enzyme substrate complex with this substrate. This
property of enzymes can be seen through the induced fit model. Initially the
enzyme and substrate are not complementary but as the substrate moves into
the enzyme the enzyme slightly changes the shape of its active site so that it
can become complementary to the substrate. By forming this complex the
enzyme lowers the activation energy of the reaction providing strain on the
bonds of the substrate if it needs to be broken down or by overcoming the
forces of repulsion if two substrate molecule need to react together. This
property of enzymes is very important in organisms as it allows them to act as
biological catalysts in many metabolic reactions.
Examples of the importance of enzymes can be seen in DNA replication where
the enzymes DNA helicase and DNA polymerase work together to form a new
semi-conservative strand of DNA. DNA helicase breaks down the hydrogen
bonds between the nucleotides forming two template strands for free DNA
nucleotides to complementary base pair. DNA polymerase binds to opposite
ends of the DNA on both strands due to the anti-parallel nature of DNA. It then
reforms the phosphodiester bonds forming the phosphate-backbone of the
DNA molecule. In ATP synthesis the enzyme ATP synthase forms ATP from
ADP + Pi in a condensation reaction. In the Calvin cycle RuBP and CO2 react
together to form 2 molecules of GP due to the the enzyme rubisco catalysing
the reaction.
Enzyme Inhibitors
Due to the complementary nature of enzymes and substrates, competitive and
non competitive inhibitors can be used to disrupt or block the active site.
Complementary inhibitors bind to the active site of the enzyme blocking the
active site so less enzyme-substrate complexes form. Non-competitive
inhibitors bind to the allosteric site of the enzyme causing the tertiary structure
to become disrupted and the active site to change shape so it is no longer able
to form enzyme-substrate complexes with the intended substrate.
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, 08/02/2025, 17:24 Biology Paper III Essays - Evernote
This is important in organisms as it can treat certain diseases caused by
enzyme activity.
• For example, many antibiotics which target bacteria target the bacteria's
metabolic processes affecting the bacteria's enzymes so they cannot divide
or replicate. Penicillin for example inhibits an enzyme in bacteria used to
produce the cell wall of the bacteria.
• It can damage the bacterial cell wall or prevent protein synthesis.
• An example of a non competitive inhibitor is cyanide which blocks oxygen
from binding to red blood cells preventing aerobic respiration.
Enzymes in digestion
One of the main examples of complementary shapes in organisms are the
enzymes involved in digestion which enable a quick and efficient process of
hydrolysis to release the absorbable products of the reaction.
• Amylase is the enzyme which breaks down starch. It is secreted in the small
intestine and mouth from the salivary glands. It is complementary to the
starch molecule hydrolysing the glycosidic bonds to produce maltose. In
the small intestine membrane bound disaccharidases such as maltase then
hydrolyse the glycosidic bonds in maltose to produce glucose which can be
more easily absorbed into the blood by co-transportation and facilitated
diffusion.
• Protein digestion occurs via three main types of enzymes: exopeptidase,
endopeptidases and dipeptidase. The exo and endo-peptidases work
together to increase the efficiency of digestion. The endopeptidases
hydrolyse the peptide bonds within the protein molecule breaking it down
into smaller sized protein chunks. This increases the surface area for
exopeptidases to work on. The hydrolyse the peptide bonds at the end of
the polypeptide chain removing single amino acids. Dipeptidases hydrolyse
the peptide bonds in between dipeptides producing two amino acid
products.
Antibody-Antigen Complex
Antibodies are secreted during an immune response by B-cells which divide to
form plasma cells. An antibody is made up of 4 polypeptide chains - 2 short
and 2 long held together by a disulphide bridge with a very specific tertiary
structure. The antibody has two variable groups which are complementary to
an antigen. The antibodies when in contact with the antigen would form an
antigen-antibody complex marking, agglutinating or neutralises the invading/
pathogenic cell. This complementary complex is therefore important in fighting
https://www.evernote.com/client/web#/notebook/6023ecd6-5695-e5af-51bd-423d67e1dfa4/note/81fcdb0f-af77-7612-8eab-94d3b39abd73 2/7
The importance of complementary shapes of
molecules in organisms. (2021)
Enzyme-Substrate Complex
Enzymes are proteins with a very specific tertiary structure resulting in a very
specific active site. This active site is only complementary to one substrate
therefore forms an enzyme substrate complex with this substrate. This
property of enzymes can be seen through the induced fit model. Initially the
enzyme and substrate are not complementary but as the substrate moves into
the enzyme the enzyme slightly changes the shape of its active site so that it
can become complementary to the substrate. By forming this complex the
enzyme lowers the activation energy of the reaction providing strain on the
bonds of the substrate if it needs to be broken down or by overcoming the
forces of repulsion if two substrate molecule need to react together. This
property of enzymes is very important in organisms as it allows them to act as
biological catalysts in many metabolic reactions.
Examples of the importance of enzymes can be seen in DNA replication where
the enzymes DNA helicase and DNA polymerase work together to form a new
semi-conservative strand of DNA. DNA helicase breaks down the hydrogen
bonds between the nucleotides forming two template strands for free DNA
nucleotides to complementary base pair. DNA polymerase binds to opposite
ends of the DNA on both strands due to the anti-parallel nature of DNA. It then
reforms the phosphodiester bonds forming the phosphate-backbone of the
DNA molecule. In ATP synthesis the enzyme ATP synthase forms ATP from
ADP + Pi in a condensation reaction. In the Calvin cycle RuBP and CO2 react
together to form 2 molecules of GP due to the the enzyme rubisco catalysing
the reaction.
Enzyme Inhibitors
Due to the complementary nature of enzymes and substrates, competitive and
non competitive inhibitors can be used to disrupt or block the active site.
Complementary inhibitors bind to the active site of the enzyme blocking the
active site so less enzyme-substrate complexes form. Non-competitive
inhibitors bind to the allosteric site of the enzyme causing the tertiary structure
to become disrupted and the active site to change shape so it is no longer able
to form enzyme-substrate complexes with the intended substrate.
https://www.evernote.com/client/web#/notebook/6023ecd6-5695-e5af-51bd-423d67e1dfa4/note/81fcdb0f-af77-7612-8eab-94d3b39abd73 1/7
, 08/02/2025, 17:24 Biology Paper III Essays - Evernote
This is important in organisms as it can treat certain diseases caused by
enzyme activity.
• For example, many antibiotics which target bacteria target the bacteria's
metabolic processes affecting the bacteria's enzymes so they cannot divide
or replicate. Penicillin for example inhibits an enzyme in bacteria used to
produce the cell wall of the bacteria.
• It can damage the bacterial cell wall or prevent protein synthesis.
• An example of a non competitive inhibitor is cyanide which blocks oxygen
from binding to red blood cells preventing aerobic respiration.
Enzymes in digestion
One of the main examples of complementary shapes in organisms are the
enzymes involved in digestion which enable a quick and efficient process of
hydrolysis to release the absorbable products of the reaction.
• Amylase is the enzyme which breaks down starch. It is secreted in the small
intestine and mouth from the salivary glands. It is complementary to the
starch molecule hydrolysing the glycosidic bonds to produce maltose. In
the small intestine membrane bound disaccharidases such as maltase then
hydrolyse the glycosidic bonds in maltose to produce glucose which can be
more easily absorbed into the blood by co-transportation and facilitated
diffusion.
• Protein digestion occurs via three main types of enzymes: exopeptidase,
endopeptidases and dipeptidase. The exo and endo-peptidases work
together to increase the efficiency of digestion. The endopeptidases
hydrolyse the peptide bonds within the protein molecule breaking it down
into smaller sized protein chunks. This increases the surface area for
exopeptidases to work on. The hydrolyse the peptide bonds at the end of
the polypeptide chain removing single amino acids. Dipeptidases hydrolyse
the peptide bonds in between dipeptides producing two amino acid
products.
Antibody-Antigen Complex
Antibodies are secreted during an immune response by B-cells which divide to
form plasma cells. An antibody is made up of 4 polypeptide chains - 2 short
and 2 long held together by a disulphide bridge with a very specific tertiary
structure. The antibody has two variable groups which are complementary to
an antigen. The antibodies when in contact with the antigen would form an
antigen-antibody complex marking, agglutinating or neutralises the invading/
pathogenic cell. This complementary complex is therefore important in fighting
https://www.evernote.com/client/web#/notebook/6023ecd6-5695-e5af-51bd-423d67e1dfa4/note/81fcdb0f-af77-7612-8eab-94d3b39abd73 2/7
