Flashcards in TBR 7 - Metabolic Components Deck (50):
A molecule with (less/more) energy is more stable.
Less. Looking at the reaction chart on page 109, note B, the product, is more stable because it has less energy.
True or false. At low temperatures, fewer molecules have enough energy to surpass the transition state of a reaction.
True. In biological molecules, raising the temperature is usually not a possibility. For many organisms, the temp must be in a certain range.
Describe what transition state analogs are and what purpose they serve in medicine.
TSA are molecules that look like the transition state of molecules belonging to a particular ezymatic reaction. TSA are excellent inhibitors of the catalytic process.
Describe what enzymes are and their role in physiology.
Enzymes are catalysts which are often employed to lower the transition state's activation energy.
Do enzymes alter the equilibrium of a reaction? What do enzymes alter in reactions?
A catalyst will NOT alter the equilibrium of a reaction. A catalyst will alter the RATE of the reaction.
True or false? An enzyme accelerates the forward reaction as well as the reverse reaction by precisely the same factor.
Describe HOW enzymes speed up reactions.
EZ contain specific regions called active sites to which SPECIFIC substrate molecule will bind. EZ also stabilize the TS and they carry out acid-base catalysis by precisely positioning the catalytic groups of certain AAs ( ser, glu, lys, etc.) found within the active site pocket
Vmax = the maximal rate/velocity of a reaction. This reaction rate can be obtained when ALL the enzyme's active sites are saturated with substrate. Vmax = K3[Etotal]
Give the Michaelis-Menten Equation.
V = (Vmax*[S])/([S] + Km)
If you plot the velocity of a reaction as a function of substrate concentration, we will get a _____ curve.
What is Km?
Km = the substrate concentration at which the reaction rate is half its maximal value (Vmax/2).
E + S ES --> E + P, what happens when k2>>>>>>k3?
The EZ-substrate complex (ES) will have a tendency to dissociate to E and S rather than form E and P.
E + S ES --> E + P, what is the Km when k2>>>>>>k3?
Km = K2/K1. It is ONLY in this situation that Km is a measure of the binding strength of the ES complex.
A ___ Km value indicates ____ binding of the ES complex while a ____ Km value indicates a strong binding of the ES complex.
A high Km value indicates a weak binding of the ES complex while a low Km value indicates a strong binding of the ES complex.
Not all cases reactions that involve binding of substrate to protein result in a hyperbolic curve. Allosteric enzymes have a _____ curve.
Allosteric enzymes have a non-hyperbolic, more sigmoidal curve when plotted as velocity versus substrate concentration.
A lineweaver/double reciprocal plot allows us to estimate Vmax and Km. How do we do this?
If we take the best fit line, the y-axis intercept is 1/Vmax. The x-axis intercept will be at -1/Km.
On a Lineweaver and Burk plot, where are HIGH [S] values located.
If 1/[S] is approaching zero, then it must mean that [S] is approaching infinity.
Describe the turnover number.
When an EZ is completely saturated with substrate, then the # of substrate molecules which are converted to product per unit time is referred to as the turnover number. Kcat = Vmax/[total EZ concentration]
Name the two major types of enzyme inhibition.
Reversible and irreversible.
Describe the two types of reversible inhibition.
A competitive inhibitor will compete with the substrate for the active site on the enzyme. The non-competitive inhibitor will bind to another portion of the enzyme. Allosteric inhibition is a subset of this.
How does a competitive inhibitor affect a reaction?
It decreases the rate of catalysis of the enzyme.
How does a competitive inhibitor affect the Vmax of a reaction?
A "CI" can be overcome at high [S]. Initially we have a lower Vmax, but as we approach an infinite [S], the concentration of the "CI" becomes negligible.
How does a competitive inhibitor affect the Km of a reaction.
It results in an apparent change in Km. The Km of a competitively inhibited enzyme appears to shift to a higher value. The word apparent is used because each EZ has a characteristic Km value for a given substrate.
Describe the lineweaver burk plot for competitive inhibition.
Vmax remains constant. There are apparent Km changes. A competitive inhibitor will increase the slope of the lines found in the plot. Intersection of lines at the y-axis.
Methotrexate is an anti-cancer drug that resembles dihydrofolate, a molecule important for synthesis of tetrahydrofolate ( a cofactor for DNA synthesis). What kind of inhibition is this?
Describe what occurs with non-competitive inhibition.
Non-competitive inhibitors do not compete at the active site of an enzyme, but rather bind to some other site on the enzyme. An "allosteric site".
True or false. Non-competitive inhibitors can only bind to free enzymes.
False. These inhibitors can bind to free enzymes AND the enzyme-substrate complex.
How does non-competitive inhibitor affect the Vmax and Km of a reaction?
Non-competitive inhibition CANNOT be overcome by increase [S]. We will have a lower apparent Vmax. The Km will not change. Km is the relationship between substrate and ACTIVE enzyme. The enzyme doesn't change.
Describe the double reciprocal plot for non-competitive inhibition.
Intersection of lines occur on the -x axis. Km remains constant as the Vmax decreases.
What do the following enzymes do: lysozyme, ribonuclease, carboxypeptidase. Hint: these enzymes are known as hydrolases because water is introduced between a particular bond.
Lysozyme: hydrolyzes glycosidic bonds in the polysaccharide component of bacterial cell walls; Ribonuclease: catalyzes hydrolysis of phosphodiester bonds in RNA polymers; Carboxypeptidase: a digestive EZ secreted by exocrine cells of the pancrease that catalyzes the hydrolysis of the carboxy terminal peptide bond of protein polypeptide chains.
What does chymotrypsin do? What are the products?
Catalyzes the hydrolysis of either ester or peptide bonds. The products would be alcohol + acid or amine + acid.
Describe the active site of chymotrypsin.
Contains a catalytic triad of serine, histidine, and aspartic acid.
Chymotrypsin mechanism: at physiological ph, which AA of the catalytic triad is protonated.
Histidine = unprotonated; Aspartic acid = unprotonated; serine = protonated alcohol.
Chymotrypsin mechanism Part 1: describe step 1 and 2.
1) Histidine is basic and will abstract a H off serine, creating a reactive alkoxide. 2) the alkoxide does a nucleophilic attack on the carbonyl of a substrate. This creates an "unstable tetrahedral transition state", stabilized by the enzyme via a glycine residue. H-bonding occurs between NH of serine and glycine.
Chymotrypsin mechanism Part 1: describe step 3.
At this point the electrons of the alkoxide can reverse or 3) proceed through a reaction that collaspses the tetrahedral intermediate to form an "acylenzyme". This results in expulsion of a R-NH leaving group*. The "acyl-enzyme" provides a lower E pathway to get from substrate to the product.
Chymotrypsin mechanism Part 2: describe step 1.
1) His-57 removes an H atom off water; a nucleophilic attack on the carbonyl carbon of the acyl EZ intermediate by OH-. Again a transient tetrahedral intermediate is formed.
Chymotrypsin mechanism Part 2: describe step 2.
2) the His-57 residue donates a H to the serine-195 residue. The tetrahedral collapses and the ACID component of the substrate that we started with is free to leave.
Chymotrypsin hydrolyzes the peptide bond on the carboxyl side of ___, ___, and ___.
Phe, Tyr, and Trp. These are aromatic residues.
True or false. RNA can act as an enzyme.
TRUE. RNA, in the presence of cofactor guanosine G residue, can act on other substrates. It is both a nuclease and a polymerase.
Many enzymes are initially synthesized as proenzymes or _____.
Chymotrypsin is an active form of the enzyme. What is the inactive form and how does it become activated? What can happen if they all become activated?
The inactive form is called chymotrypsinogen. Once chymotrypsinogen is synthesized in the pancreas it is secreted into the intestinal tract and activated by a proteolytic enzyme called TRYPSIN. With a damaged pancreas, all sinogens will be activated and cause pancreatitis.
What prevents digestive enzymes from digesting the rest of your body?
Naturally occurring substances called a1-antitrypsin is an effective inhibitor of trypsin and an even better inhibitor of elastase, which can digest connective tissue in the lungs. Smoking oxidizes the Met residue on antitrypsin; this residue is essential for binding elastase.
`Explain the difference between divergent and convergent evolution.
Speciation is a result of divergent evolution and occurs when one species diverges into multiple descendant species. Darwin's finches are an example of this. Convergent evolution occurs when species have different ancestral origins but have developed similar features.
Describe what a transition state analog is.
TSAs are synthesized with the hopes that they will occupy the active site of an enzyme. The role of an enzyme is to bind the TS and stabilize it. A TSA is a competitive inhibitor.
Define catabolism and anabolism.
Catabolism is the breakdown of complex molecules into smaller and simpler products accompanied by the release of E (usually ATP). Anabolism means build up or become more complex; biosynthesis of small precursor molecules to larger ones.
What is ATP composed of?
Adenine (base); D-ribose (sugar); and three phosphate groups. Adenine + D-ribose = adenosine.
What kind of linkages are formed in ATP.
N-acetal/N-glycosidic linkage between C1' of the ribose ring and N9 of the adenine ring. Ester linkage between first Pi group and C5' of the ribose ring. Phosphoric anhydride linkages between the phosphates.
Define cofactors and coenzymes.
Cofactors are substances other than AA that help enzymes carry out their functions. If cofactors are REQUIRED by an enzyme, they are called coenzymes. A coenzyme is a non-AA substance required for the activity of an enzyme. In many cases the coenzyme is bound non-covalently, but many cases the coenzyme is covalently attached. There may be more than one enzyme.
What does NAD stand for? What role does it play?
Nicotinamide adenine dinucleotide. It is an important coenzyme. Note that it contains and Adenine + a pyridine ring. Humans synthesize nicotinamide portion of the NAD molecule from tryptophan in the diet, making trp an essential AA.