Unit 1 : Enzymes Flashcards
What are the different groups to an amino acid? Which group determines the differentiating properties of the acid and how they react?
Which amino acids are hydrophobic?
Which are hydrophilic?
Amino acids are made of an amino group — H3N+ — a middle carbon, a carboxyl group — C double bond O and O- — a singular hydrogen, and an R group. This R group is the unique group sticking off the backbone of amino acids, and will determine the properties of the molecule.
Hydrophobic amino acids will have carbon-hydrogen non-polar bonds on the R-group, or S-H of N-H. As long as there is no charge indicated they have reached their bond capacity and hence are stable. So they will not react with or dissolve in water.
Hydrophilic amino acids have carbon-oxygen or oxygen-hydrogen, f-o or N-O (anything that can make hydrogen bonds). So if you see a hydroxyl group, or a nitrogen STICKING OFF (not inside) that could be hydrogen bonded, or you see a charge it must be hydrophilic because it is polar and can react with water.
How are amino acids linked together (what reaction and what bonds?) Which molecules make up the backbone of the ______________ and what free group is on the left and right side? Which groups stick off the side of the backbone?
Amino acids are linked together by a dehydration synthesis reaction — causing polymerization. So the oxygen with the negative charge, and two hydrogens off the amino group of the next acid are removed — because this oxygen is the most unstable. These combine as H2O and are released, and then the carbon bonds with nitrogen so that it no longer has a positive charge and is stable. This molecule is then called a peptide, and the backbone of the peptide is NCC repeating, because the middle carbon is attached to the newly available nitrogen from the nitrogen group and the other carbon is available from the newly available carboxyl group. So the amino and carboxyl groups are what react to make up the backbone. The R-groups stick off of the side, and so do the hydrogens.
The left side is the free amino (NH3) group, called the amino terminus. The right side is the free carboxyl group (called the carboxyl terminus or carboxy end).
A peptide is….
A polypeptide is…
A protein is…
A peptide is a polymer of amino acids (many combined together).
A polypeptide is a polymer of these peptides.
A protein is a polypeptide folded into a 3D shape so that it can actually be functional.
Primary structure is…
Primary structure is the actual polypeptide itself, and is the order of amino acids that make up the peptide. Every peptide will be different based on the R-groups of the amino acids and the order of peptides added.
Secondary Structure is…
How does it stay in this structure (what bonds interact?)
Secondary structure contains helices and sheets, this is how the polypeptides fold/twirl in order to produce a new structure.
Helices are swirls of peptides, and sheets are folded peptides. These structures are formed by the H-bonds along the backbone of the peptides. So the double bonded O coming off of the (original carboxyl group) in the peptide bond will interact with the hydrogen coming off of the nitrogen (originally from the amino group). This is because these are both polar bonds and the difference in electronegativity is large enough to allow these to be strong hydrogen bonds — which will weaken as energy (heat) is added to break them.
Tertiary structure is….
Are proteins functional at this level?
How do the peptides interact to produce this shape?
Tertiary structure is formed when the secondary structure is folded into the 3D shape of a protein. Because this is already in a 3D shape, this can be fully functional — and actually 90% of tertiary structure proteins are fully functional.
These peptides interact in multiple levels through the R-groups — not the backbones. Therefore, this can specify and produce different proteins because the R-groups on peptides are going to vary across the different amino acids present. This is why we can specify certain proteins already at this level.
Quaternary Structure is…
Examples of proteins with quaternary structure…
How do we name proteins based on the amount of tertiary structures that were added together?
Do the tertiary structure proteins interact on their own?
What does the suffix -mer mean?
This is when multiple proteins interact to produce a fully functional new protein. The tertiary proteins will not function on their own until they are combined into this new protein. Hemoglobin is an example of a quaternary structure protein.
We can name these proteins based on the number of groups present, and whether those proteins are the same.
For example, if 3 of the same tertiary structures are combined, this is called a HOMOTRIMER.
Same groups: Homo
Different: Hetero
2 = Dimer
3 = Trimer
4 = Tetramer etc.
(Remember, -mer means BODY. Then the prefix indicates how many bodies!)
Most biological reactions are slow, but why is this? And how do we overcome this problem?
This is because the bonds in the substrate molecules are stable — they are at a low potential energy and hence do not have enough free energy to break apart and form a reaction. Even though the reaction may be exergonic, the reactants can still be quite stable and have trouble turning into an even lower energy state. So, ENZYMES / CATALYSTS are used to speed these reactions up by DESTABILIZING the reactants so that they naturally want to turn into products. Essentially, these catalysts reform the molecule in such a way that the bonds are no longer low energy and stable, so there is more free energy available to do work and hence the reaction can occur.
So even with exergonic reactions, energy must be added to get them started. However the net change in energy (G) will still be negative as the products will have lower potential energy then the reactants. Change in G* is what is used to represent the free energy of the activation energy, and change in G by itself represents the overall net change in free energy.
What are the 2 main things needed for reactions to occur? What do catalysts do in order to lower activation energy and allow these two main things to be more easily and quickly reached?
Is breaking or forming bonds endothermic?
What does activation energy do?
The two main things needed for reactions to occur are 1) favourable geometry — opposite charges and shapes facing each other and 2) sufficient energy — needs to be able to overcome the activation barrier and add energy (for endothermic reactions).
Catalysts help by:
Creating an alternate pathway for reaction, or FORCING the normal reaction pathway rather than basing it off random motion and hoping that molecules will collide. So if a particle collides with an enzyme, it is 100% certain that the reactant will actually react, even if it doesn’t have sufficient energy or proper geometry. this is because the enzyme takes care of all of that. So reactions will occur if reactants randomly collide with sufficient energy and proper geometry, however there is now the random collisions with enzymes which drastically increases the number of reactions that will occur in a given period of time.
The enzymes speed up reaction rate and lower activation energy do this by:
-Changing the chemistry of bonds by chemically reacting or attracting due to charges, in order to break those bonds are make them more likely to break. The catalyst can chemically bond with the substrate to rearrange that bond structure into a more unstable one.
-Distorting/physically straining the substrate molecules in order to break those bonds.
-Increase the collision frequency so because it is no longer based on random motion and chance if two molecules will collide, but instead the enzyme attracts those two molecules and helps to bring them together and orient them in the right direction.
-Brings the two molecules together in such a way that this new transition state is extremely unstable and hence will naturally react in an exergonic fashion.
Breaking bonds is endothermic and forming bonds is exothermic. Bonds are more stable as molecules/atoms can be at a lower energy state since those electrons are shared or stolen by the more electronegative atom, meaning that the electrons are closer to where they want o be and do not have a lot of potential/free energy. So to break this energy has to be added! This is also why the activation energy is used; to break the bonds of the reactants so they can be separated and then regrouped into products.
Activation energy is used to kickstart the reaction by destabilizing the reactants so that they will naturally react. Essentially that energy is used by the enzymes to bond with them and distort them in such a way that they can quickly bond with other substrates and produce the products.
What are the ways to speed up a chemical reaction (factors effecting rate?) (3)
What part of the free energy - reaction graph do enzymes effect?
1) Increase the concentration of the reactants present — or decrease the volume of the container — so that the total number of collisions increases and therefore the number of effective collisions occurring will also increasing, contributing to a more efficient overall reaction.
More collisions = more reactions = faster overall rate.
2) Increase the temperature, meaning that the kinetic energy of the system and each individual molecule is increased. So, molecules are moving around at a faster rate and therefore will collide more often! Based on random motion, this means that the total number of collisions will increase! At the same time, each individual molecule is going to have more energy. Energy is going to be randomly dispersed and so each molecule will have a different amount of kinetic energy. But at a higher temperature, all those energies will increase. So a larger proportion of molecules in the system will have enough energy present to produce a reaction when colliding with another molecule — based on the Maxwell Boltzmann curve shifting right. So this then increases the ratio of effective : ineffective reactions as well! More effective reactions means the overall reaction will be more efficient!
However, temperature and concentration cannot be manipulated to the extreme, which is why catalysts can also speed up a reaction!
They do this by creating a new pathway for the reaction to follow where the free energy decreases — is exergonic and can happen spontaneously. Or, it will change the shape/geometry/environment of the reaction site which allows the reactants to easily come together with high potential energy to produce a spontaneous reaction.
Enzymes only affect the activation energy or change in G* on this graph. In other words, they decrease the amount of activation energy necessary to allow the reaction to proceed, meaning that the reaction can proceed faster as it will take less time to garner that amount of energy compared to a larger amount. Enzymes have no effect not he actual reaction and hence the net change in free energy — they are only used to get the reaction started.
Enzyme structure determines what?
Every enzyme has an ____________ which is where it bonds with a “specific” substrate.
What is the lock and key model VS the induced fit model?
Enzyme structure determines function!
Every enzyme has an active site which is where it bonds with. Specific substrate. Some enzymes are more specific to a given molecule than others.
Lock and Key Model:
Enzyme is a solid structure with specific shapes that the substrates come and fit in to. However, this is very inaccurate. If this was the case, then once attached the structure would be very stable and hence would not want to continue reacting. Enzymes are supposed to DESTABILIZE the molecule, and so this model does not work.
Instead we use the Induced Fit model:
The enzyme substrate complex forces the reactants into this transition state. it does this because the enzyme takes in the substrate and rearranges its structure to bond with and do its work on the substrate. Then once it is done it reverts back to its original shape.
Enzyme kinetics: The rate of an enzyme reaction depends on the concentration of enzymes and substrates. (Explain how these work… graphically)
As the number of enzymes increases, the reaction rate will also increase proportionally, (as long as it is assumed that the substrate concentration is constant at a large enough value). Because there are more enzymes present and hence its more likely for substrates to collide with those enzymes and produce a reaction. And when they do it is guaranteed that the reaction will proceed.
But for substrates, at a very low concentration there will be a very low rate of reaction because it will be very hard for those substrates to collide randomly with an enzyme. However as that substrate concentration increases, the rate will exponentially increase because collisions will occur more and more often with enzymes, producing products faster and faster. As well, collisions will occur between substrates which can sometimes produce sufficient reactions on their own.
However, it will level off at a certain point (this is called Vmax), once all the enzymes are saturated. At this point, the rate of the reaction is based on the rate of the enzymes turning reactants into products. So as one reactants is used up, another one will take its place. However if more enzymes were to be added, the graph would increase until it reaches saturation again.
What is denaturation and what is it caused by? Can it be reversed?
What is inactivation and what is it caused by? Can it be reversed?
Denaturation is the loss of protein structure or the 3D shape of the protein which is caused by:
-Changes to pH, temperature, and inhibitors which may interact with the hydrogen bonds holding tertiary and secondary structures together.
This can be partial or complete denaturation, and depending on the extent of the denaturation, it may or may not be reversible.
Inactivation is the loss of enzyme activity, which is usually due to denaturation — because the enzyme needs structure to determine function. This can be reversible or irreversible, also depending on how much of the shape is lost. So extreme change in temperature likely destroys those proteins and is permanent, whilst a minor change — like a fever — will be temporary.
A heterotrimer is….
What does -mer mean? What does hetero- mean?
A heterotrimer is a 3 bodied tertiary protein, wherein one or more of these bodies that make it up are different. If it was a homotrimer then the three bodies would be the same. -mer just means body, so the prefix before will determine how many secondary proteins are combined together.
How do enzymes work? How does the substrate bind to the enzyme and what reactions occur to do this? How do they reduce activation energy? (Generally and then 3 specific ways)
An enzyme has an active site which is specialized for one molecule or a group of specific molecules. When a substrate binds to that active site the enzyme changes conformation to fit it and this forms an enzyme-substrate complex. This chemical reaction changes the shape of the enzyme allowing it to be activated into its functional mode. This chemical reaction can change the polarity of the molecule and hence hydrogen bonding which changes the shape of the enzyme.
Enzymes then reduce activation energy by creating a different (easier) pathway for the reaction to occur, or by changing the chemical makeup of the substrates so that they can more quickly and easily reach the transition state. Because reactions only occur based on:
1) Favourable geometry and
2) Enough energy to react
The enzymes increase the probability of this occurring. Without enzymes, molecules only react by random collisions, which only a small proportion of these have the above two factors. With enzymes, now it is the same likely hood that two molecules may collide, HOWEVER, the likelihood of two molecules colliding with an enzyme is now also present. And if they do this, then it is very likely that they will have sufficient energy and geometry to react, so this greatly increases the probability of more reactions occurring.
3 Specific ways it decreases activation energy:
1) Brings particles close together, so that the randomness of collisions due to particle motion is not in play.
2) Chemically reacts with the substrates in certain places to change charges and H-bonds in order to help it more easily attract and react with other substrate molecules.
3) It physically distorts or strains molecules, making them want to break because they are extremely unstable and want to react and break down. By doing this, the enzyme puts them at that transition state.
