Download Proteins and Enzymes (p

Proteins and Enzymes (p. 42-47, p. 84 – 85)

So, the protein has been made using the translation process. What is it used for?
Proteins Research
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Some proteins have amino acids that are
__________________________________________________________________
____________________________________________.
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There are proteins that perform ______________, proteins that store amino acids
and some that have ______________ so cells can respond to chemical signals.
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In order to do this, they need to combine into many forms or structures.
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The function of a protein is very closely related to its structure.
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Protein Structure (See worksheet – Proteins)
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Proteins have four levels of organization:
1. Primary Organization - _________________________________________________
________________________________________________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 – ________________________________________________
______________________________________________________________________
_____________________________________. 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 – _______________________________________________
___________________________________________________. 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.
________________________________________________________________________
________________________________________________________________________
4. Quaternary Organization – _________________________________________________
_____________________________________________. 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 and quanternary
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 ____________________.
o They are found in the regions of proteins that are linked to the
hydrophobic area of the cell membrane.
o ____________________________________________________________
____________________________________________________________
___________________________________________________________ .
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Amino acids with polar side chains are ________________________.
o They are found in regions of proteins that are exposed to water.
o ____________________________________________________________
___________________________________________________________.
o _____________________________________________________.
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Polar and non-polar amino acids are important in determining the specificity of an
enzyme. Each enzyme has a region called the _______________.
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Only specific substrates can combine with particular active sites. Combination is
possible when fitting occurs.
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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
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Proteins can be membranous and non-membranous.
Membrane Proteins, as a review from last year, are responsible for:
1.
2.
3.
4.
5.
______________________________
______________________________
______________________________
______________________________
______________________________
Non-membrane Proteins are responsible for:
1.
2.
3.
4.
__________________________________
__________________________________
__________________________________
__________________________________
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Others are _____________________________, like insulin and ADH,
while others are _______________________________, 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
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Metabolism is the sum of all the chemical reactions in your body.

The reactions to build molecules are called _______________.
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Those that break down molecules, are called ______________.
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_____________ reactions require energy and _______________ reactions release
energy.
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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:
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
Substrate A
Enzyme 1
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)
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You learned about the “______________________” of enzyme function.
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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.
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Now we see that enzymes undergo changes in their conformation, when substrates
combine with their active sites.
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This is called the _____________________.
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The _____________________________________________.
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The enzyme then can _____________ and ____________________ of the
reaction. The process occurs faster.
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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.
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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.
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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. _______________________________________________________________________.
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.
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Enzymes work by
___________________________________________________.
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Activation Energy, Ae, is __________________________________________
________________________________________________________________.
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The reaction occurs _________ because the amount of energy needed for the
reaction to occur is ________.
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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.
Inhibition and Enzymes
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The effects of pH, temperature and substrate concentration were discussed last
year.
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Different molecules have effects on the active sites of enzymes.
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If a molecule affects the active site in some way, the activity of the enzyme may
be altered. This is called _______________.
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There are two types: Competitive and Non-Competitive.
Competitive Inhibition
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In competitive inhibition, a molecule, called a ____________________, competes
directly for the active site of the enzyme.
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The result is that the _____________________________with the active site and
the chemical reaction rate is ____________.
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The competitive inhibitor must have a similar structure to the substrate to be able
to function in this way.
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Competitive inhibition may be reversible or irreversible.
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Reversible competitive inhibition may be overcome by ____________ the
substrate concentration. When this happens, there are more substrate molecules
to bind to the active sites as they become available, and the reaction
___________________________________________________________.
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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 para-aminobenzoic 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.
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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
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Non-competitive inhibition involves an inhibitor _________________________
____________________________________________________________.
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The inhibitor interacts with another site on the enzyme.
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Non-competitive inhibition is also called __________________________,
because the inhibitor binds to a site called the allosteric site.
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These allosteric enzymes have __________________________________.
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Binding at the allosteric site causes ________________________________
____________________________________________________________.
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This type of inhibition may be reversible or irreversible.
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When the inhibitor concentration is low, an increase in the concentration of
substrate increases the enzyme activity.
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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.
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Some of the enzyme molecules remain inhibited and the maximized activity of the
enzyme is lower than when there is no inhibitor.
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Examples are opiods that resemble morphine. They inhibit nitric oxide synthase
that have signaling roles in the human body.
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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.