2. Enzymes Flashcards
What are the enzymatic markers for disease? (3)
- Hepatitis
- Myocardial infarction (heart attack)
- Rhabdomyolysis (muscle breakdown)
What is the issue with this liver?
You will see that there is a nice healthy colour and the liver has a regular size. In contrast, in a patient (top half above) with severe hepatitis (hep = liver, itis =
inflammation), there is hepatomegaly (an enlarged liver) and necrosis (cell death). We will explore the enzymes that are released when hepatocytes (liver cells) are damaged.
How does myocardial infarction take place?
In patients who ingest too much cholesterol, atherosclerotic plaques build up inside the capillaries and block blood flow. Cardiomyocytes (cardiac muscle cells) require oxygen and nutrients, meaning that blockage of the capillaries results in failure to deliver adequate oxygen and nutrients to the cells. Cardiac tissue necrosis occurs, and the enzymes that were present inside the cardiomyocytes are released into the blood.
How is the slide indicative of rhabdomyolysis?
However, from a pathological perspective,
the top slide shows a representative field of skeletal muscle that has the requisite mass and cell component. Panel B is a tissue section taken from a patient with skeletal muscle cell lysis. As such, the muscle component is reduced, with more open areas visible on the slide.
Intracellular enzyme localisation:
Extracellular enzyme localisation:
Digestive gastrointestinal enzymes
Blood enzyme localisation:
Mostly diagnosis and prognosis
Digestive enzymes are found in the lumen (and are thus
extracellular) of the gastrointestinal tract. These enzymes are required for the digestion (breakdown) of macromolecules so that the resultant _______ are absorbed into the bloodstream.
monomers
Amino acids or peptides are the monomers (mono = one), which are used to make the _______ (poly = many). If we write down the sequence (order) of the amino acids in the polypeptide, we end up with a primary structure as shown for ________________ as
shown above.
polypeptides
Met-Asp-Leu-Tyr
These polypeptides eventually fold into a 3-dimensional shape, which is called a protein’s _____ structure.
tertiary
In enzymology we are interested in an enzyme’s
tertiary structure because the enzyme’s function depends on the _______ the enzyme folds
into.
shape
In contrast, when you are learning about the gastrointestinal tract, you will be learning
about protein digestion, whereby a protein’s 3-dimensional structure is ________
(destroyed) so that absorption of the amino acids can occur into the bloodstream.
denatured
Broadly speaking, there are two different types of amino acids:
hydrophilic and hydrophobic amino acids
Hydro is the name for water, phil means love and phobia is a dislike of. Thus, hydrophilic amino acids _______ in water, whereas hydrophobic amino
acids do not.
dissolve
As such, the hydrophobic amino acids tend to cluster amongst themselves as shown in green above, whereas the hydrophilic amino acids form ______ ______ with
water and thus dissolve in physiological fluids.
hydrogen bonds
In the diagram above, polar means that
the molecule is charged and so can form hydrogen bonds with water. Therefore the enzyme conformation depends on the ______ ________ of the constituent amino acids.
spatial arrangement
How did the globular shape of enzymes come about?
As a result of the hydrophilicity or hydrophobicity of the enzyme’s amino acids, the enzyme conformation is generally globular (roughly round in shape).
For enzymes it will suffice to know that amino acids interact together via __________ forces, or van der Waals interactions when they form the enzyme
tertiary structure. _______ (S-S) bonds are also important for linking some polypeptide chains in some multi-subunit (_______) enzymes.
ionic/electrostatic forces
Disulphide (S-S)
(allosteric)
What are the types of enzyme structures? (4)
primary (A)
secondary (B)
tertiary (C)
quaternary (D)
What are the characteristics of enzymes? (5)
What conformation do enzymes have?
Enzymes have a conformation that enables them to tightly bind to molecules that match the enzyme binding site. This occurs because enzymes have a groove in their structure that recognises their substrate. The name of the groove is called an active site. Active sites are so specific such that one enzyme only recognises one substrate molecule. This is a desirable feature because we wouldn’t want enzymes to bind a wide range of molecules as we would lose the metabolic control we are trying to achieve.
How do pharmaceutical companies take advantage of the active site?
Pharmaceutical companies take advantage of this fact when they design drugs to inhibit an enzyme active
site, such that there aren’t many side effects as only the enzyme of interest is inhibited by a particular drug.
However, the strength of the binding between the active site and substrate may be strong (have a ____ affinity) or weak (have a ___ affinity).
high
low
Enzymes are biological ______ that speed up reactions.
catalysts
What is anabolism?
What is catabolism?
Anabolism + catabolism =
metabolism
Eating food enables the nutrients to be digested (broken down), absorbed and used to generate adenosine triphosphate (ATP) or energy. This energy is then used to maintain _______ or grow body tissues.
homeostasis
What are the classes of enzymes? (6)
The human body is generally maintained at 37 degrees Celsius, and exposed to 1 atm of atmospheric pressure. Thus high temperatures or high pressures cannot be used to _______ chemical reactions.
accelerate
How do enzymes lower activation energy?
We can visualise enzyme catalysis as the “hill” shown in the figure above. In this case, a reactant Y needs an energy input (b→a) so that product X is formed. High heat and high pressures can be used to enable molecule Y to undergo the change into product X. The energy input (b→a) is also called the reaction activation energy, which is required to convert Y to X. In the body, enzymes lower the activation energy by reducing the reaction activation energy requirement to (b→d). As a result of the enzyme lowering the activation energy, many more Y molecules have enough energy to form product X. The reaction rate is thus greatly enhanced.
How does Catalysis occur?
For a chemical reaction to take place, the reactants must have enough energy to overcome the energy _____ that is required to force the reactants into forming products.
barrier
Explain this diagram.
When the molecules are sluggish and slow, they do not have much kinetic energy (panel A). In this case the molecules have insufficient energy to form products. Thus all the molecules remain as reactants. In panel B the molecules have gained sufficient energy from heat or an increase in pressure such that some molecules have enough energy to form reactants. When the heat
or pressure is increased to such an extent that all molecules have enough energy to overcome the energy barrier (panel C), then all he reactants are converted to products
What is the mechanism of the lock and key model?
Classically, it is easier to think of enzyme active site and substrate (ligand) binding as a lock and key, respectively. For a substrate to bind the shape must exactly unlock the active site by snugly fitting into the active site. This is what is shown in (A) above whereby the yellow ligand binds into the green enzyme perfectly. (B) shows the sequence in a more step by step manner, whereby the red substrate binds to the green enzyme, is converted to a yellow product. The product diffuses away and the unmodified enzyme is recycled for catalysing repetitive reactions.
An easy reaction equation as written in (C) is thus:
What is the induced-fit hypothesis?
How does the lowering of activation energy take place?
What is the process of biocatalysis?
Reaction velocity=
Vmax=
Km=
What does the value of km tell you?
The smaller the value of Km, the higher the affinity of an enzyme for catalysing the conversion of a substrate into a product. Conversely, the greater the value of Km, the
lower the affinity the enzyme has for binding to the substrate.
These two enzymes have a different protein structure, but they catalyse the same biological reaction because they bind to the same substrate and form the same product. They are thus called _______.
isoenzymes
Based on looking at the graph, which enzyme has a higher affinity for the substrate?
The smaller the value of Km, the higher the affinity, and so in this case Km1 has a smaller value than Km2, which means that enzyme 1 has a higher affinity for the substrate than enzyme 2.
What are the factors that affect enzyme reaction rates? (4)
What does this slide illustrate?
This slide illustrates the effect that changing the pH and substrate concentration has on an enzymes reaction rate.
How is enzyme activity regulated? (4)
What happens if there are lots of hydrophilic enzymes and if there are lots of hydrophobic enzymes?
The enzyme active site may be hydrophobic, hydrophilic or amphipathic (have both hydrophilic and hydrophobic components). However, if there are plenty of hydrophilic
amino acids on the outside of globular (round-shaped enzymes) , this enzyme is likely to be lipid-soluble and will be found in biological membranes. In contrast, if most of the amino acids on the periphery are hydrophilic, hydrogen bonds can be formed with water
and so this enzyme will be found dissolved in water in the cytoplasm or other watery organelle.
Why is the regulation of enzymes by allosterism is important for fine-tuning of enzyme responses?
What is enzyme feedback inhibition?
The secretion of hormones and their resultant physiological effects still takes at least a few minutes. Sometimes this time interval is not rapid enough. A more rapid manner of regulating enzyme activity is by negative feedback pathways. In this case, once a sufficient amount of product has been synthesised, the increased concentration of that product inhibits upstream reactions and thus slows down the cycle, and prevents further formation of product.
What are the features of enzyme inhibitors? (3)
What is reversible competitive inhibition? (4)
What is non-competitive inhibition? (4)
What are co-enzymes and cofactors? (4)
How is gluconeogenesis catalysed?
During gluconeogenesis (formation of glucose from a non-carbohydrate source) an important reaction that you will learn about is the one that is catalysed by pyruvate carboxylase. As you can tell from the name of this enzyme, pyruvate is the substrate and the addition of a carboxylate molecule is the reaction taking place.
How is oxaloacetate formed?
When a carboxylate molecule is added to pyruvate, the molecule oxaloacetate is formed. A new covalent bond is being formed between the carboxylate and pyruvate, and so energy is required for this process. ATP is the energy source. The carboxylate is derived from bicarbonate ions and the helper molecule for this reaction is the coenzyme biotin, which is obtained from ingesting the vitamin biotin. Thus structurally pyruvate
carboxylase is unchanged at the end of the reaction, but it is the coenzyme biotin that is modified during the chemical reaction when pyruvate is converted to oxaloacetate.
What are isozymes (isoenzymes)? (4)
How do enzymes enable this reaction?
Glucose is a small molecule that can cross plasma membranes. The plasma concentration of glucose is kept at a low concentration of about 5 mmol/L. Once glucose enters a cell, it would be undesirable for the glucose to leak out of the cell and so it is rapidly
phosphorylated by hexokinase to form glucose-6-phosphate. Glucose-6-phosphate now has a negative charge and so cannot leak out of the cell and becomes trapped inside the cell for the cell’s use in energy provision.
Which enzyme has a higher affinity for glucose?
…
Which enzyme has a greater capacity to phosphorylate glucose?
….
What is the clinical significance of enzymes? (3)
What are the enzymatic markers for disease? (7)
How do enzymes affect red blood cell damage?
Why are enzymes needed? (5)
