Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
108 Cards in this Set
- Front
- Back
- 3rd side (hint)
|
Where does the word enzyme come from?
|
in yeast or "en zyma."
Hans and Edward Buchner 1897 Therapeutic use of yeast extracts preserved with sugar, discovered fermentation in a cell free extract: something in yeast or En Zyma |
|
|
|
Discuss what this "Golden Rule" means: Each enzyme has a unique specificity.
|
Each enzyme fits with specific substrate. It is a lock and key fit although some enzymes can be stimulated without an exact lock and key fit.
|
|
|
|
Under what condition is ΔGo' = -1.36logKeq?
|
At equilibrium (ΔG = 0)
|
|
|
|
What is the meaning of ΔGo'?
|
ΔGo' is the standard free energy change. pH 7, 1 atm, 25 deg C, 1 M reactant and product concentrations
|
|
|
|
T/F
Enzymes change the equilibrium constant of a reaction. |
False
Enzymes cannot change the equilibrium constant, but increase the rate at which equilibrium is reached. |
|
|
|
What is the significance of Γ: the observed mass action ratio?
|
in a reaction A -> B
[B]obj / [A]obj = Γ (the observed mass action ratio) at equilibrium Γ = k: equilibrium constant Γ is used to show how far a reaction is from equilibrium, by plotting Γ / k vs G |
|
|
|
What does a Ligase do?
|
Ligation of two substrates at the expense of ATP hydrolysis i.e. Aminoacyl-tRNA synthetase.
Ligation Group VI |
|
|
|
What kind of reaction is catalyzed by a protein kinase? To which class do these enzymes belong?
|
Group transferase (phosphorylation) Class 2
|
|
|
This reaction is catalyzed by an enzyme belonging to the class of ?
|
Oxidoreductase Class 1
LEO the Lion says GER |
|
|
|
The turnover number of an enzyme is defined as:
|
The number of substrate molecules converted into product by an enzyme molecule in a unit time when the enzyme is fully saturated with substrate. Vmax reveals the turnover number of an enzyme.
Vmax = k2[Et] Enzyme binding and dissociation from substrate for a defined time. |
|
|
|
The reaction A <--> B with ΔGo' = +2.7 kcal/mol will be at equilibrium when
a) the concentrations of A and B are equal b) the concentration of A will be much higher than B c) the concentration of B will be much higher than A d) can not be determined from this information |
the concentration of A will be much higher than B
|
|
|
|
To which class does the enzyme belong that catalyzes this reaction:
Triacylglyceride + _________ -> Glycerol +3 Fatty Acids |
Hydrolase Class 3
H2O Transfer of functional groups to water |
|
|
|
A certain enzyme follows Michaelis-Menten kinetics, what is meant by this statement?
|
As enzyme concentration increase so does substrate concentration.
Product formation as a function of substrate concentration produces a sigmoidal curve because the binding of the substrate to one active site favors the conversion of the entire enzyme into the R state, increasing the activity at the other active sites. Thus, the active sites show cooperativity. Imagine an allosteric enzyme as a mixture of two Michaelis-Menton enzymes, one with a high value of Km that corresponds to a T state and another with a low value of Km that corresponds to a R state. As the concentration of substrate is increased, the equilibrium shifts from the T state to the R state, which results in a steep rise in activity with respect to substrate concentration. |
|
|
|
A certain enzyme follows Michaelis-Menten kinetics, what is meant by this statement?
|
As enzyme concentration increase, so does substrate concentration.
Product formation as a function of substrate concentration produces a sigmoidal curve because the binding of the substrate to one active site favors the conversion of the entire enzyme into the R state, increasing the activity at the other active sites. Thus, the active sites show cooperativity. |
Imagine an allosteric enzyme as a mixture of two Michaelis-Menton enzymes, one with a high value of Km that corresponds to a T state and another with a low value of Km that corresponds to a R state. As the concentration of substrate is increased, the equilibrium shifts from the T state to the R state, which results in a steep rise in activity with respect to substrate concentration. |
|
|
The Michaelis constant Km is frequently equated with Ks, the dissociation constant of ES, the enzyme substrate complex. However, there is usually a disparity between those values, why? Under what conditions are Km and Ks equivalent?
|
When K3 is very small
|
|
|
|
What is meant by steady-state approximation?
|
It does not matter how the product or substrate concentration changes. The ES will stay the same.
|
|
|
|
Two enzymes: hexokinase I (HI)and hexokinase III (HIII) catalyze the same reaction and have the same Vmax. The Km of HI is 10^-4 and of HIII 10^-2 M. Both enzymes are assayed at a substrate concentration of 10^-2 M. the ratio of the velocities of HI/HIII is approximately:
|
HI/HIII = 10^-4/10^-2 = 1 / (1/2) = 2
|
|
|
|
What is meant with the statement: it is a serine protease?
|
The active site is a serine
(the serine performs the protease activity) |
|
|
|
What is the Haworth projection for D-alpha-Glucopyranose?
|
.
|
|
|
|
What is the Haworth projection for D-alpha-Glucopyranose?
|
.
|
|
|
|
What is the Haworth projection of D-beta-Galactopyranose? Number the carbons.
|
Anomeric carbon is 1 then clockwise through 6th carbon
|
|
|
|
What are anomers?
|
anomers Isomers of cyclic hemiacetals or hemiketals, with different configurations only at the carbonyl carbon atom; that carbon is known as the anomeric carbon.
|
|
|
|
What are epimers?
|
They have all the same chiral centers except for one.
epimers Pairs of molecules, each with more than one asymmetric center, that differ in configuration at only one such center; glucose and galactose are epimers, differing only in the configuration at C-4. |
|
|
|
What are diastereomers?
|
diastereoisomers A pair of molecules, each with more than one asymmetric center, that have opposite configurations at one such center but are not mirror images of each other; in the aldotetrose series, Derythrose and D-threose are diastereoisomers.
|
|
|
|
What are enantiomers?
|
enantiomers A pair of molecules, each with one or more chiral centers, that are mirror images of each other.
L&D |
|
|
|
What is a ketose?
|
ketose A monosaccharide that has a ketone group as its most oxidized carbon.
|
|
|
|
What is the structure of D-glyceraldehyde?
|
.
|
|
|
|
What are the two basic forms of carbohydrates?
|
Aldose & Ketose
|
|
|
|
What is the general structure of an aldose?
|
.
|
|
|
|
What is the general structure of a Ketose?
|
.
|
|
|
|
What is the difference between a D-Glucose and a L-Glucose?
|
Enantiomer
For sugars with more than one chiral center, the D or L designation refers to the asymmetric carbon farthest from the aldehyde or keto group. Most naturally occurring sugars are D isomers. D & L sugars are mirror images of one another. They have the same name. |
|
|
What makes this salicin molecule a Glycoside?
|
glycosides are molecules in which a sugar is bound to a non-carbohydrate moiety, usually a small organic molecule. a glycoside is any molecule in which a sugar group is bonded through its anomeric carbon to another group via a glycosidic bond. Glycosides can be linked by an O- (an O-glycoside), N- (a glycosylamine), S-(a thioglycoside) or C- (a C-glycosyl) glycosidic bond.
|
|
|
Compare the sugar couple D-Glucose & D-Mannose
a) enantiomers b) aldohexoses c) epimers d) anomers |
An aldohexose is a hexose with an aldehyde group on one end
epimers Pairs of molecules, each with more than one asymmetric center, that differ in configuration at only one such center; glucose and galactose are epimers, differing only in the configuration at C-4. |
|
|
Compare D-erythrose and D-threose.
|
Erythrose and Threose are
Erythrose and Threose are Diastereomers: stereoisomers that are not mirror images, that is they are not enantiomers. So what are some other examples of diastereomers? Remember stereoisomers are compounds where the atoms are connected in the same way, but which have different geometries. Thus cis , trans -isomers are diastereomers, as are configurational (optical) isomers, that is isomers differing only by the configurations around chiral centers but for which the entire molecules are not mirror images. |
|
|
Xylulose is a/an
a) aldose b) ketose c) hexose d) triose e) sugar alcohol |
Ketose
|
|
|
Compare L-erythrose and D-threose.
|
Enantiomers
|
|
|
|
alpha-D-galactose and beta-D-galactose are
a) epimers b) diastereomers c) anomers d) structural isomers e) enantiomers |
anomers
|
|
|
|
Write the Fisher projection of L-Glyceraldehyde
|
.
|
|
|
|
What is wrong with this statement: Sucrose is O-beta-D-glucofuranosyl 1->4 fructopyranose
|
O-alpha-D-glucopyranosyl-1-2-beta-D-fructofuranoside
*********************************** |
|
|
|
Ribose and Ribulose are?
|
Structural Isomers
|
|
|
|
D-glucopyranose and D-galactopyranose are?
|
Epimers
|
|
|
|
D-glycerose and L-glycerose are?
|
Enantiomers
|
|
|
D-galactopyranose and D-mannopyranose are?
|
Diastereomers
|
|
|
|
Ribose is a
a) ketohexose b) aldohexose c) furanose d) pentose e) disaccharide |
Pentose
|
|
|
Although lactose is a dissacharide it exists as 2 different anomers. Sucrose exists as only one. Explain this observation.
|
Lactose has glycosidic bond between 1-4 its anomeric carbon is free to make alpha and beta forms. Sucrose has 1-2 glycosidic bonds and is fixed and unable to change positions.
|
|
|
|
Raffinose is the most abundant trisaccharide in nature, it is though to protect plants against frost damage; the systemic name is: D-Galactopyranosyl - (1alpha->6)-D-Glucopyranosyl-(1alpha->2beta) fructoduranoside. Draw the structure of this sugar in Haworth projection, number the carbons and place the OH groups in the correct orientation.
|
remember to number the carbons
Also know D-galactopyranosyl-(1alpha->2beta) fructofuranoside |
|
|
Is Raffinose a reducing sugar?
|
No. The is no active site. All the possible sites of mutarotation are blocked by glycosidic bond.
|
|
|
Does Raffinose sugar show muta rotation?
|
No. Glycosidic bonds do not allow metarotation.
|
|
|
Although Lactose is a disaccharide it exists as 2 different anomers. Sucrose exists as only one. Explain this observation.
|
Lactose has glycosidic bond between 1-4 and its anomeric carbon is free to make alpha and beta.
Sucrose has 1-2 glycosidic bond and its anomeric carbon is blocked so it cannot change positions. |
|
|
|
Define a proteoglycan
|
Protein that has sugar attached by glycosidic bonds.
complex heteropolysaccharides called glycosaminoglycans bound to core proteins. proteoglycans Proteins containing one or more covalently linked glycosaminoglycan chains; cartilage proteoglycan contains keratan sulfate and chondroitin chains linked to a polypeptide backbone. |
|
|
|
What is a Glycoprotein?
|
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently attached to their polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending extracellularly, the extracellular segments are often glycosylated. Glycoproteins are often important integral membrane proteins, where they play a role in cell-cell interactions.
|
|
|
|
What is a glycosaminoglycan?
|
Polymer of amino sugars
GAGs are complex heteropolysaccharides like hyaluronic acid. The O-glycosidic bond is beta-1->3. Glycosaminoglycans (GAGs) or mucopolysaccharides are long unbranched polysaccharides consisting of a repeating disaccharide unit. |
|
|
|
What is an example of nature's use of a proteoglycan and why this structure is so well adapted to its function.
|
Hyaluronic acid. Proteoglycans function as lubricants and structural components in connective tissue, mediate adhesion of cells to the extracellular matrix, and bind factors that stimulate cell proliferation. 95% of proteoglycan is carbohydrate.
These proteoglycans imbibe water and provides a very resilient surface. |
|
|
|
D-glycerose & L-glycerose are?
|
enantiomers
|
|
|
|
D-glucopyranose & D-mannopyranose
|
epimers
|
|
|
|
What is a peptidoglycan?
|
A peptide that has sugar attached by glycosidic bonds
|
|
|
|
What is the structure of Cholesterol?
|
.
|
|
|
|
What two components make up a simple lipid?
|
Polar head (carboxilic acid group)
2 non-polar tails (aliphatic long chain) [lipid=alcohol+glycerol+fatty acid] |
|
|
|
Grease traps in sinks can be cleaned using NaOH. Many other products on the market that are used for opening drains contain NaOH. What is the basis for this treatment?
|
NaOH hydrolyzes oil to glycerol and Na+ salt of fatty acid which is soluble in water. so insoluble oil driven by water after being hydrolyzed by NaOH.
Acids and bases hydrolyze lipids to form glycerol & salt of fa. Na salt of fa are soluble in H2O making good detergent, but Ca Mn are not good, they precipitate. Lipids + NaOH -> glycerol + Na salt of fa soap |
|
|
|
What is the definition of a lipid?
|
Substance that dissolves in organic solvents. They are not macromolecules, but Complex Molecules. Lots of structural differences, in common: they are very hydrophobic molecules.
|
|
|
|
What would be the ω number for C22: 6Δ4,7,10,13,16,19?
|
ω3
|
|
|
|
Young brain cells need for their development the fatty acid C22: 6Δ4,7,10,13,16,19
Explain all the numbers |
C22 = there are 22 carbons
6Δ = 6 double bonds 4-5,7-8,10-11,13-14,16-17,19-20 have double bonds at these positions |
|
|
|
What would be the ω number for C22: 6Δ4,7,10,13,16?
|
C = C- C- C- C- C- C
16 17 18 19 20 21 22 1 2 3 4 5 6 ω = 6 |
|
|
How do Phospholipids differ from Tryacylglycerols?
|
Phospholipids (barrier & dynamic): glycerol + 2 fatty acids with charged group (phosphate +charged alcohols, one ester bond becomes a phosphoester bond)
Triacylglycerols (energy & energy storage): Glycerol + 3 FA, 3 Ester bonds results in loss of the - charge (Alcohol + Carboxylic acid: Ester) Insulation |
|
|
|
What is the difference between a ganglioside and a cerebroside?
|
Ganglioside - Ceramide + Complex Oligosaccharide
Cerebroside - Ceramide + Monosaccharide note: Ceramide = Sphingosine + FA |
|
|
|
What alcohol is present in gangliosides and cerebrosides?
|
Sphingosine
|
|
|
What characteristics do phospholipids and triacylglycerols have?
|
Glycerophospholipids = barrier & dynamic, Amphipathic
Triacylglycerols = energy & energy storage, Non-Polar |
|
|
|
What is an isoprenoid and what relationship does it have to fats?
|
Named after isoprene. C-5 building block of Fatty Acids and it is soluble in organic solvents.
|
|
|
A new organism was discovered by an expedition of CSU biology students. They analyzed the membrane of the organism and discovered that it contained a large amount of glycerophospholipids with saturated C-22 fatty acids. What does this tell you about the organism?
|
glycerophospholipids with C-22 fatty acids make the membrane more rigid and have a high melting point.
Archaebacterium use ether bonds instead of ester bonds. |
|
|
|
One of your colleagues in the lab separated hydrolysis products of membrane lipids thin-layer chromatography. Because you were teaching lab that used ninhydrin to stain amino acids, he took by accident your ninhydrin to stain his chromatogram and found a brightly stained spot. Explain your observation.
|
If the lipid contains phosphotidylserine after hydrolysis, serine will react with ninhydrin showing up brightly colored.
|
|
|
|
The enzyme glycerol-phosphate dehydrogenase would belong to the class of?
|
Oxidoreductase
|
|
|
|
The enzyme tRNA synthetase binds an AMP moiety from ATP to the 3' end of a tRNA, to which group does this enzyme belong?
|
Ligases
|
|
|
|
What is an enzyme and why are enzymes important?
|
Enzymes Lower the Activation Energy of a Reaction. Forward & reverse rxns are catalyzed. Enzymes are very specific; concept of active site. Enzymes DO NOT change the deltaG of a reaction
|
|
|
|
What is a lyase?
|
Breaks the molecule without hydrolysis. Formation of double bonds
|
|
|
|
What kind of reaction is catalyzed by a protein kinase. To which class do these enzymes belong?
|
Transfer of a Phosphoryl Group.
Class II Transferases |
|
|
|
Discuss two features of enzymes that describe what catalysis is and why it is important.
|
General acid base catalysis: proton acceptor/donor: His, Lys, Asp, Glu, in general terms B: + H+ <-->B:H+
Covalent catalysis: enzyme binds the transition state -> nucleophilic or electrophilic attack Catalysis of enzymes are important to lower the energy of activation for a reaction to move forward. |
|
|
|
What is a serine protease?
|
The enzyme will use a strong nucleophile to attack the normally unreactive carbonyl carbon of serine.
|
|
|
Explain what happened to the catalytic power of the enzyme after mutation
|
Kp= Kcat/Km
WT = (21+/-4)/(1.9+/-0.2) Mutant = (120+/-4)/(2+/-0.3) The catalytic power increased |
|
|
What is a reason that the catalytic power might increase?
|
Alanine is smaller than isoleucine so it could possibly be exposed to more substrate.
|
|
|
How is the velocity of the reaction measured?
|
By the intensity of optical activity (yellow color) given off by the binding of substrate/product reaction.
|
|
|
|
If enzyme activity is measured as a function of reaction temperature and is plotted as point A as optimal temperature. How would you point out the error of his ways?
|
This does not mean that the enzymatic activity Max was reached or has stopped.
|
|
|
|
Lysozyme breaks down bacterial cell walls. The Km is 10^-4 M and the Kcat is 1s^-1. If the substrate concentration is 10^-2 M, is lysozyme operating
a) at 1/2 Vmax b) Vmax c) below 1/2 Vmax d) higher than Vmax e) 3/4 Vmax |
Vmax
|
|
|
|
Lysozyme breaks down bacterial cell walls. The Km is 10^-4 M and the Kcat is 1s^-1. The substrate concentration is 10^-2 M and lysozyme is operating at Vmax. Does lysozyme reach catalytic perfection?
|
Kcat/Km = 1/10^-4 = 10^4
No it does Not. Diffusion limits the value of k1, so Kcat/Km cannot be higher than between 10^8 & 10^9 s^-1 M^-1. Their catalytic velocity is restructed only by the rate at which they encounter substrate in the solution. |
|
|
|
If a lysine would be substituted for an aspartate in the S1 pocket of trypsin, would the enzyme specificity stay the same or would it be different, if different what could the specificity be?
|
It will cut in a different place. Trypsin cuts at K&R. For D-, K&R down.
|
|
|
Carbonic anhydrase has a 25,000 fold higher activity (Kcat = 10^6 s^-1) than OMPD (Kcat = 40 s^-1). However, OMPD provides more than a 10^10 higher rate acceleration than CA. Explain this observation.
|
Uncatalysed vs Catalysed...that is all I know
|
|
|
|
What have carbonic anhydrase and a restriction enzyme in common?
|
Both undergo Metal ion catalysis
|
|
|
|
Two enzymes: hexokinase I (HI) and hexokinase III (HIII) catalyze the same reaction and hace the same Vmax. The Km of HI is 10^-4 and of HIII 10^-2 M. Both enzymes are assayed at a substrate concentration of 10^-2 M. The ratio of the velocities of HI/HIII is approximately?
|
HI/HIII = 10^-4/10^-2 = 1/(1/2) = 2
|
|
|
|
Catalytic triads are found in many proteases and related enzymes. Using chymotrypsin as a model how would you arrange the catalytic triads in the following enzymes; show the activation steps needed for a nucleophilic attack on the cleavable bond.
Beta-lactamase Lys Glu Ser bond to be cleaved is a beta-lactam |
.
|
|
|
|
Catalytic triads are found in many proteases and related enzymes. Using chymotrypsin as a model how would you arrange the catalytic triads in the following enzymes; show the activation steps needed for a nucleophilic attack on the cleavable bond.
Asparginase: Thr Asp Lys cleaves peptide bond at C-end of Asp. |
.
|
|
|
|
What characteristics do you expect to find in allosteric enzymes?
|
1) Conformational change
2) Reversible (concentration dependent) 3) Enzyme has multiple subunits 4) Subunits interact -> Cooperative Effect |
|
|
|
From the list below, which is the group that would be involved in covalent catalysis?
a) asparagine b) alanine c) tryptophan d) serine e) glycine f) histidine |
Serine is a highly reactive residue in chymotrypsin
|
|
|
|
The turnover number of an enzyme is defined as:
|
Number of substrate molecules that are converted to products by an enzyme in a unit time when the enzyme is fully saturated with substrate -> Kcat
|
|
|
|
What are the amino acids that would be involved in general acid base catalysis?
a) asparagine b) serine c) glycine d) histidine e) cysteine f) proline g) lysine h) leucine |
Histidine
Lysine |
|
|
|
Compare the two models for allosteric regulation, concerted vs sequential
|
Concerted: T<-->R is all or none: flip/flop, does not explain the mechanism
Sequential: goes through intermediate states |
|
|
|
What is meant when some say that the enzyme uses the pingpong mechanism?
|
Double displacement reaction
one or more products are released before all substrates bind the enzymes. reactions that shuttle amino groups between amino acids and alpha keto acids are examples |
|
|
|
The enzyme tRNA synthetase binds an AMP moiety from ATP to the 3' end of a tRNA, to which group does this enzyme belong?
|
Ligase
|
|
|
|
The enzyme glycerol-phosphate dehydrogenase would belong to the class of:
|
Oxidoreductase
|
|
|
|
What is meant by an enzyme has an active site?
|
Active site is a mirror of the substrate that interacts with the substrate
|
|
|
|
A Michaelis Menten plot
a) takes the form of a straight line b) reflects the saturation of enzyme with substrate at high values for the substrate concentration c) reflects the fact that the ES complex is broken down more rapidly that it is made d) is a plot of 1/vi versus 1/[S] |
reflects the saturation of enzyme with substrate at high values for the substrate concentration
|
|
|
|
Which of the following statements of a Lineweaver burk plot is NOT correct?
a) it is a straight line b) it is difficult to determine the value of Vmax of a reaction c) a lineweaver burk plot is 1/vi vs 1/[S] d) you can convert a lineweaver burk equation into a michaelis menten equation by taking the reciprocate of both sites of the equation |
b is incorrect
|
|
|
|
Two different enzyme A & B catalyze the same rxn and have the same Vmax. The Km of each enzyme are 1/1000 and 1/100 M, respectively. Both enzymes are assayed at a substrate concentration of 1/100 M. The ratio of the velocities of A/B is?
|
A will be Vmax B 1/2 Vmax
1/(1/2) = 2/1 |
|
|
|
How do you determine the Km of an enzyme and why do you want to determine this value anyway?
|
If we draw a Lineweaver burk plot, line cut x-axis where the value is -1/Km. Or if we plot Vs vs [S], substrate concentration value where Vs = 1/2 Vmax is Km. To specify the enzyme we need Km, we can use Km to qualify different enzymes.
|
|
|
|
What is the chemical name of the side chain involved in general acid base catalysis?
|
Hydroxyl Group -OH
|
|
|
|
What is meant by steady state approximation or hypothesis?
|
The steady state approximation states that no matter how much the substrate or product concentration change the [ES] will remain the same
|
|
|
|
The reaction A<--> B with ΔGο' = -2.7 kcal/mol will be at equilibrium when
a) the conc of A & B are equal b) the conc of A will be much higher than B c) the conc of B will be much higher than A |
c) the conc of B will be much higher than A
|
|
|
|
The reaction A<--> B with ΔGο' = +2.7 kcal/mol will be at equilibrium when
a) the conc of A & B are equal b) the conc of A will be much higher than B c) the conc of B will be much higher than A |
deltaGo' = -RT log [B]/A
b) the conc of A will be much higher than B |
|
|
|
What is a Michaelis Menten plot, what information does it provide to the investigator?
|
V vs [S] when V= 1/2Vmax, Km +/-[S] so we can learn Km value of an enzyme. Moreover if [S] is not much higher than enzyme it gives the kinetic rate of [ES] complex
|
|
|
|
Two different enzymes A and B catalyze the same reaction and have the same Vmax. The Km of the enzymes are 10^-3 and 10^-4 M, respectively. Both enzymes are assayed at a substrate concentration of 10^-3 M. The ratio of the velocities of A/B is approximately?
|
VA = Vmax/2
VB ~ Vmax VA/VB = (1/2)/1 = 1/2 |
|
