Enzyme structure and function (article) | Khan Academy
An enzymes structure is made up of proteins and the building blocks for these proteins are amino acids. When many amino acids join together. The specificity of an enzyme is dependant on the structure of the enzyme for a few reasons: Depending on the view the full answer. Enzymes are biological catalysts--they catalyze the chemical reactions that happen inside living things. Consider a chemical reaction where a molecule A bonds with a molecule B to create a molecule A-B (A stuck to B). Most catalysts (including enzymes) work the same basic way.
Enzyme converts lysine to hydroxylysine. Requires the same cofactors as prolyl hydroxylase. Lysine and Hydroxylysine, again, are the precursors of the cross-links. The enzyme that forms that cross-links between Lysine and Hydroxylysine.
It converts the OH groups on the hydrolysines to aldehydes. They then form cross-links, aldol condensations, with other aldehydes.
Enzyme structure and function
Type I Collagen defects. One of the disorders is related to a shortened chain deletion. Then the mutated chain is shorter than the other two, ruining the whole structure.
Collagenase is not repressed during adult life, resulting in digestion of collagen in joints. Collagenase is only supposed to be active during development for reshaping of collagen. Tissue proliferates and invades the joints. Proteolytic Enzymes are required for cancer cells to metastasize, as they must degrade the basement membrane of the origin tissue to get through to the lymph system, and degrade the basal membrane of the target tissue to get into it.
A disorder caused by mutation in the enzyme phenylalanine hydroxylase, which converts phenylalanine to tyrosine. Energy is neither created nor destroyed. It only changes form. A process occurs spontaneously only if the sum of the entropy in the system and its surroundings is greater than zero. That depends on the free energy of activation, DeltaG.
Rate of the reaction is constant. At any time, it is equal to rate of reverse reaction - rate of forward reaction Second-Order Kinetics: How to get standard free energy from the Keq Free Energy of any particular reaction: Relation between Free Energy of Activation and K: Increasing the activation energy causes an exponential decrease in the rate constant. The lowest energy and most stable form. The highest energy and least stable form. Enzymes that transfer functional groups to another component.
Cleavage hydrolysis using water. Cleavage of double-bonds reduction. Converting the reactant from one isomer to a different isomer. A non-enzyme component of a reaction that is required for the reaction to run. Usually a vitamin or mineral. Cofactors are usually easily separated from their enzyme. A cofactor that is also itself an enzyme. Cofactors that are more tightly bound to an enzyme, usually covalently, as in the heme group of hemoglobin.
Unique Features of Enzymes: Either much faster, or in the case of collagenase, slower than the reaction would otherwise be.
Binding Specificity Allows reactions to occur under physiological mild conditions. Catalytic activity may be regulated by other enzymes or the physiological environment. The part of the enzyme where the reaction takes place.
It is relatively small. It is a three-dimensional structure. Substrates bind to the active site by multiple weak interactions and sometimes covalent. Active sites are clefts or crevices. Polar residues are often found in active sites, to create a specific electrostatic environment. Active sites change conformation when bound, to accommodate the substrate. Active sites have specificity: Trypsin is specific for Lys and Arg. Chymotrypsin is very similar to trypsin except it has different active sites.
It binds to hydrophobic aromatic residues in its active site. Elastase, also similar, recognizes small residues like Gly and Ala. Contains two Zinc atoms in its active site: When the concentration of substrate, [S], is very high compared to enzyme, the enzyme will be saturated with substrate, and the rate of rxn will depend only on the amount of enzyme present -- not substrate.
A complex between E and S, ES, is formed. The concentration of S is much larger than E. The degradation of Product back to the ES-Complex is ignored. A steady-state concentration of the ES-Complex is established during measurement.
The steady-state forms practically instantaneously. Steady state means that the concentration of ES remains constant, i. Some of the enzyme remains unbound in the steady state. Once Km is known, it is possible to calculate the fraction of sites filled. A plot of the reciprocal of rate -vs- reciprocal of substrate concentration. An inhibitor that covalently and permanently alters an enzyme, rendering it dysfunctional. Iodoacetamide irreversibly inactivates cysteine residues by alkylating them.
It is an irreversible inhibitor of Prostaglandin-H Synthetase, the enzyme that makes prostaglandins. Aspirin is thus an anti-inflammatory drug. Prostaglandin has cyclooxygenase activity: Irreversibly inhibits the synthesis of peptidoglycans in bacterial cell walls. It inhibits glycopeptide transpeptidase, which cross-links poly-Gly with D-Ala. It imitates the Ala-D-Ala.
It has a four-member lactam ring, highly strained, and it imitates the transition state of Ala-D-Ala in the reaction above.
The inhibitor resembles mimics the substrate and thus competes directly with the substrate for the same active site. Competitive Inhibitions increases km -- a higher substrate concentration is required to achieve the same vmax.2.5 Enzyme-substrate specificity
Hence adding more substrate can alleviate the effects of the inhibition. The inhibitor hooks to a different site on the enzyme, which can temporarily render it dysfunctional. No matter how much substrate you add, you can't dilute the effects. Hence vmax is decreased.
A mutation in alpha1-antitrypsin Serine-Proteinase-Inhibitor family, SERPINs caused it to mimic caused the protein to inhibit thrombin instead of trypsin, which led to hemophiliac symptoms! Mutation of Arg for Met.
The alpha1-Antitrypsin normally inhibits trypsin, neutrophil elastase, and cathepsin-G. In its absence emphysema can also form due to the lost inhibition of neutrophil i. Sterically hinders traps endopeptidases.
This enzyme is found in serum in large quantities. Enzymes that cleave proteins only on the inside. Enzymes that cleave proteins only on the outside terminal part.
Exopeptidase that cleaves at the amino terminus. Exopeptidase that cleaves at the carboxy terminus. Molecule has four subunits, two of which are disulfide linked.
There is a bait region which almost all endopeptidases recognize. The peptidases bite the bait, and the macroglobulin changes conformation so as to physically enclose "trap" the molecule. The enzyme is still catalytically active! Figure of nitrogen and oxygen atoms colliding then bonding. This magnet thought experiment is a good approximation of what happens with real-life molecules like nitric oxide. But the alignment is key--nothing will happen without it.
This is where catalysts come in. They help with alignment. The odds favor nothing happening.
This is what happens with nitric oxide molecules in a jar, when no catalyst is present. Figure of nitric oxide molecules in a jar unable to correctly align.
Explain The Relationship Between Enzymes Structure And Enzyme Specificity? - Blurtit
But now imagine that we add an extremely motivated and conscientious magic gnome to the inside of our jar, with the instructions that he is to grab a red-blue in each one of his hands, align them in the right way, and then smash them together. Adding this helpful gnome assistant will increase the rate at which red-reds and blue-blues are made, because achieving the right alignment is no longer a matter of random chance. Figure of nitric oxide molecules in a jar correctly aligning in the presence of a catalyst.
Catalysts are the real-life versions of our imaginary magic gnomes. A platinum screen sits inside a catalytic converter attracting nitric oxide molecules to it and aligning them in just the right way, so that when they collide, the N and O switch places, and nitrogen gas and oxygen gas are created. Catalysts make reactions fast by aligning reactants so that successful reactions are more likely! Enzymes are biological catalysts Enzymes are the catalysts involved in biological chemical reactions.
Why enzymes are so important The big reason enzymes are important to life is because cellular energy is a precious resource.
This increase in the total number of collisions per second would increase, just as a matter of probability, the number of correctly aligned collisions too. So, in the end, shaking the jar harder much harder, perhaps would result in an increase in the speed of red-red and blue-blue production too, just like adding a gnome and keeping the shaking of the jar the same.
Figure of nitric oxide molecules in a shaking jar correctly and incorrectly aligning. By just shaking the jar harder, you choose to do the work yourself and forego the services of the gnome. You get the same end-result, but it requires more energy expenditure on your part.
If you use the gnome, you get to save this energy for other purposes: Or what if you have lots of energy available, but you have to do a lot of work to obtain it?
Or, maybe you have extra energy, but you want to spend it on doing other important things. In any of these three cases, the added savings you get from using the gnome to do the work might make a world of difference. Pretty cool for a few minutes effort! Consider a rabbit in a field. This rabbit has millions and millions of cells, all of which have billions and billions of chemical reactions going on, every second of every day that the rabbit is alive.
The grass gets converted to simple sugars. The simple sugars get converted to fuel molecules. Burning fuel molecules releases energy, and this energy increases the speed with which molecules travel inside cells. A cell burning energy has the same effect on the molecules inside it as shaking our imaginary jar has on the red and blue magnets inside it.
In both cases, work is being done that results in more collisions happening, which in turn results in more reactions happening. With the help of enzymes, this amount of energy is just enough not too much, and not too little to get molecules moving fast enough to react in the ways that the rabbit needs in order to go on living. The energy released from burning the fuel molecules drives the molecules around at a certain speed, and the enzymes make sure that the molecules are aligned in just the right way so that the right kinds of collisions happen.
The molecules would be moving around with the same speed, but the collisions would be totally random: This is a huge problem for the rabbit, because most of what it does depends on the speed of the chemical reactions in its cells.
If the chemical reactions that drive the mechanical actions of its hopping muscles are slowed down even a little bit, the rabbit will go from eating lunch to being lunch. This gets to the point of why enzymes are so very important for life. Think of them as the optimal solution to an equation with two separate variables.
On the one hand, you have the requirement for everything to happen inside the rabbit's body very rapidly—this is how it evades predators, beats other rabbits to food sources, and reproduces. On the other hand, you have the limitation imposed on the rabbit by the environment and its own body.