Download Proteins and Enzymes Assessment Statements 7.5.1 Explain the

Proteins and Enzymes
Assessment Statements
7.5.1 Explain the four levels of protein structure, indicating the significance of each level.
7.5.2 Outline the difference between fibrous and globular proteins, with reference to two examples of
each protein type.
7.5.3 Explain the significance of polar and non-polar amino acids.
7.5.4 State the four functions of proteins giving a named example of each.
7.6.1 State that metabolic pathways consist of chains and cycles or enzyme-catalyzed reactions.
7.6.2 Describe the induced fit model
7.6.3 Explain that enzymes lower the activation energy of the chemical reactions that they catalyze
7.6.4 Explain the difference between competitive and non-competitive inhibition, with reference to one
example of each.
7.6.5 Explain the control of metabolic pathways by end product inhibition, including the role of
allosteric sites.
So, the protein has been made using the translation process. What is it used for?
Some proteins have amino acids that are acidic, basic, have hydrophobic properties and have hydrophilic
properties. There are proteins that perform structural tasks, proteins that store amino acids and some that
have receptor functions so cells can respond to chemical signals. In order to do this, they need to
combine into many forms or structures. The function of a protein is very closely related to its structure.
See worksheet on Amino Acids.
Protein Structure (See worksheet – Proteins)
Proteins have four levels of organization:
1. Primary Organization - this is the unique sequence of amino acids held together by peptide bonds.
The order or sequence was determined by the nucleotide base sequence on the DNA. Every
organism has its own DNA, and therefore, every organism has its own unique proteins. The
significance of the primary structure is the sequence determines the higher levels of the protein.
Changing one amino acid may completely alter the structure and function of a protein. Ex. Sickle
cell disease.
2. Secondary Organization – this is created when the hydrogen bonds form between the oxygen
from the carboxyl group from one amino acid and the hydrogen from the amino group of another.
It does not include side chains, the R groups. The significance of the structure is that, even
though the hydrogen bonds are weak, several of them in a row provide strength. The most
common configurations are the helix and the sheet.
3. Tertiary Organization – this is when the polypeptide chain bends and folds over itself, based upon
the interactions among the R groups and the peptide backbone. The result is a definite three
dimensional conformation. Interactions that cause tertiary conformations are:
a. Covalent bonds between sulfur atoms to create disulfide bonds or bridges because they
are so strong
b. Hydrogen bonds between the side chains
c. Van der Waals interactions among the hydrophobic side chains on the amino acids.
These interactions are strong because many hydrophobic side chains are forced inwards
when the hydrophilic side chains interact with water towards the outside of the molecule.
d. Ionic bonds between positively and negatively charged side chains.
Tertiary Organization is significant, because it determines the specificity of the proteins known as
enzymes.
4. Quaternary Organization – this is unique in that is involves multiple polypeptide chains which
combine to form a single structure. Not all proteins have this organization. One example is
haemoglobin, which is four protein chains held around a haem group, in which an atom of iron
occurs. These proteins are called conjugated proteins. This is significant because the structure is
very specialized in terms of its actions.
Fibrous and globular proteins are examples of tertiary organization. Fibrous proteins are those that
are polypeptide chains in a long narrow shape. Examples are collagen, which plays a role in the
connective tissue of humans and actin. Globular proteins are more three dimensional in their shape.
Examples are haemoglobin and insulin. Use the worksheet to add to these notes, as to the differences
between them.
Polar and Non-polar Amino Acids
Amino acids are grouped according to their side chains.
Amino acids with non-polar side chains are hydrophobic. They are found in the regions of proteins
that are linked to the hydrophobic area of the cell membrane. This means they can remain embedded in
the membrane and attract non-polar substances, like fats/lipids. They will also repel water, which is polar.
Amino acids with polar side chains are hydrophilic. They are found in regions of proteins that are
exposed to water. Membrane proteins include polar amino acids towards the interior and exterior of the
membrane, to create polar channels. Polar substances can move through these channels.
Polar and non-polar amino acids are important in determining the specificity of an enzyme. Each enzyme
has a region called the active site. Only specific substrates can combine with particular active sites.
Combination is possible when fitting occurs. The “fitting” involves the general shapes and polar
properties of the substrate and of the amino acids exposed at the active site.
The Functions of Proteins
Proteins can be membranous and non-membranous.
Membrane Proteins, as a review from last year, are responsible for:
1.
2.
3.
4.
5.
Hormone Bonding Sites
Enzyme Receptor Sites
Electron Carriers
Channels for Passive Transport
Pumps for Active Transport
Non-membrane Proteins are responsible for:
1.
2.
3.
4.
Structural Support – Collagen and Keratin (hair)
Transport – Haemoglobin
Movement – Myosin and actin
Defense – Immunoglobulin or antibodies
Others are chemical messengers, or hormones, like insulin and ADH, while others are biological catalysts,
or enzymes, like pepsin. Others are food stores, like casein in milk and pigments, like opsin in our eyes
and some organisms use them as toxins, like snake venom.
Enzymes
Metabolism is the sum of all the chemical reactions in your body. The reactions to build molecules are
called anabolic, and those that break down molecules, are called catabolic. Anabolic reactions require
energy and Catabolic reactions release energy.
Almost all metabolic reactions in organisms are catalyzed by enzymes. Many of the reactions occur
in metabolic or biochemical pathways that occur in a chain or a cycle. A pathway may be like so:
Enzyme 1
Substrate A
Enzyme 2
Substrate B
Final Product
Most metabolic pathways are carried out in designated compartments of the cell, where the necessary
enzymes are clustered and isolated. The enzymes are determined by the cell’s genetic make-up.
The Induced Fit Model (See worksheet on Enzymes)
Last year, you learned about the “lock and key model” of enzyme function. Enzymes are complex
proteins that have unique areas, such as the active sites, where it binds to a particular substrate. The lock
and key model worked, but now we know more about enzymes.
Now we see that enzymes undergo changes in their conformation, when substrates combine with their
active sites. This is called the Induced Fit Model. The binding site changes to fit and accept the
substrate. The enzyme then can weaken bonds and reducing the activation energy of the reaction. The
process occurs faster. This would explain why some enzymes have such a broad specificity, such as
proteases. Therefore, several different but similar substrates could bind to the same enzyme.
A good example is a hand and a glove, the hand being the substrate and the glove being the enzyme. The
glove looks like a hand, but only when the hand is placed in the glove, does the glove actually take the
shape of the hand. Also, several different hands can fit into the same glove.
The changes that occur in conformation are due to the changes in the R-groups of the amino acids at the
active site of the enzyme as they interact with the substrate or substrates.
Mechanism of Enzyme Action
1.
2.
3.
4.
5.
6.
The surface of the substrate contacts the active site of the enzyme
The enzyme changes shape to accommodate the substrate.
A temporary complex, called the enzyme-substrate complex, or activated complex, forms.
Activation energy is lowered and the substrate is altered by the rearrangement of existing atoms
The transformed substrate – product – is released from the active site.
The unchanged enzyme is then free to combine with other substrate molecules.
Enzyme action can be summarized by:
E+S
ES
E+P
Where E is the enzyme, S is the substrate, ES is the complex, and P is the product.
Enzymes work by lowering the activation energy of a reaction. Activation Energy, Ae, is the energy
necessary to destabilize the existing chemical bonds in a reaction. The reaction occurs faster because
the amount of energy needed for the reaction to occur is less. Think about Ae as a wall. You need so
much energy to get over the wall, to get to the other side (products). If you can lower the wall, the
amount of energy you need is less. This is due to the fact that the active site can weaken the bonds,
rearrange them and form the new product.
****Even though the enzymes lower Ae of a particular reaction, they do not alter the proportion of
reactants to products.
Read and do the Enzyme Worksheet.
Inhibition and Enzymes
The effects of pH, temperature and substrate concentration were discussed last year. Different molecules
have effects on the active sites of enzymes. If a molecule affects the active site in some way, the activity
of the enzyme may be altered. This is called inhibition. There are two types: Competitive and NonCompetitive.
Competitive Inhibition
In competitive inhibition, a molecule, called a competitive inhibitor, competes directly for the active site
of the enzyme. The result is that the substrate then has fewer encounters with the active site and the
chemical reaction rate is decreased. The competitive inhibitor must have a similar structure to the
substrate to be able to function in this way.
Competitive inhibition may be reversible or irreversible. Reversible competitive inhibition may be
overcome by increasing the substrate concentration. When this happens, there are more substrate
molecules to bind to the active sites as they become available, and the reaction my proceed more rapidly.
An example is the use of sulfanilamide (a sulfa drug) to kill the bacteria during an infection. Folic acid is
essential as a coenzyme to bacteria. It is produced in bacterial cells by enzyme action on paraaminobenzoic acid (PABA). The sulfanilamide competes with the PABA and blocks the enzyme.
Because human cells do not use PABA to produce folic acid, they are unaffected by the drug.
Another example is the reaction between carbon dioxide and the acceptor molecule in photosynthesis,
called ribulose bisphosphate carboxylase . When there is oxygen in the chloroplasts, the reaction between
the two is inhibited, and photosynthesis slows.
Non-competitive Inhibition
None competitive inhibition involves an inhibitor that does not compete for the enzyme’s active site. The
inhibitor interacts with another site on the enzyme. Non-competitive inhibition is also called allosteric
inhibition, because the inhibitor binds to a site called the allosteric site. These allosteric enzymes have
two non-overlapping binding sites.
Binding at the allosteric site causes a change in the shape of the enzymes active site, making the nonfunctional.
This type of inhibition may be reversible or irreversible. When the inhibitor concentration is low, an
increase in the concentration of substrate increases the enzyme activity. But, since the inhibitor and
substrate are not competing for the same site, the substrate cannot prevent the binding of the inhibitor,
even when the substrate concentration is high. Some of the enzyme molecules remain inhibited and the
maximized activity of the enzyme is lower than when there is no inhibitor.
Examples are opiods that resemble morphine. They inhibit nitric oxide synthase that have signaling roles
in the human body. Another example is mercury, which binds to the sulfur groups of component amino
acids in enzymes. The shape change causes inhibition of the enzyme.
End Product Inhibition
End product inhibition prevents the cell from wasting chemical resources and energy by making more of a
substance than it needs. Many metabolic reactions occur in an assembly line type of process so that a
specific end product can be achieved. Each step is catalyzed by a specific enzyme. When the end
product is made in a sufficient quantity, the assembly line is shut down. This is usually done by
inhibiting the action of the enzyme in the first step of the pathway. This is an example of an
allosteric enzyme. The higher concentrations of the end product bind with the active site on the
first enzyme, inhibition occurs and the reaction stops. As the existing end product is used up by the
cell, the concentrations lower, resulting in fewer bindings with the allosteric site on the first enzyme,
and the enzyme is reactivated, resulting in the pathway starting up again.
The bacterium E. coli uses a metabolic pathway to produce the amino acid isoleucine from threonine. It
is a 5-step process. If the isoleucine is added to the growth medium of E. coli, it inhibits the first enzyme
in the pathway and isoleucine is not synthesized.
The inhibition of the first enzyme is the pathway prevents the build-up of intermediates in the cell.
This is a form of negative feedback.