Exam #3 Material Flashcards
In transforming the Michaelis-Menten equation into a straight line equation, y = mx+b, the Lineweaver-Burk double reciprocal plot, which is not a true representation?
X-intercept is 1/Km
The Km can be considered to be the same as the disassociation constant Kd for E+S binding if:
k2 «_space;k-1
Fetal hemoglobin (Hb F) has an intrinsically greater affinity for O2 than adult hemoglobin (Hb A) because:
Hb F has a diminished capacity to bind BPG compared to Hb A.
The cause of cell sickling in sickle cell anemia is…
Oligomerization of deoxy-Hb S into long, chain-like fibers.
Name the tropism being described:
A)
Carbon source: CO2 energy source: light
B) Carbon source: CO2
energy source: redox reactions
C) Carbon source: organic compounds energy source: light
D) Carbon source: Organic compounds energy source: redox reactions
A) Photoautotroph
2) Chemoautotroph
3) Photoheterotroph
4) Chemoheterotroph
What is a characteristic difference between FAD and NAD+?
NAD+ transfers two electrons while FAD can transfer one or two.
For the first five steps of glycolysis, the appropriate sequence of the enzymes is:
A. Phosphofructokinase-1 (PFK-1)
B. Hexokinase /glucokinase
C. Fructose biphosphate adolase
D. Phosphoglucoisomerase
E. Triose Phosphate isomerase (TPI)
D B A C E
The step that commits glucose to glycolysis is catalyzed by:
Phosphofructokinase
In the second half of the glycolytic pathway, __ ATP molecules are produced and with the offset of __ ATPs consumed in the first half, the net yield is __ ATPs per glucose
4, 2, 2
Which of the following amino acids would NOT provide a nucleophilic center for covalent catalysis?
Cysteine Serine Alanine Lysine Glutamic Acid
Alanine
In the chymotrypsin reaction mechanism, ___ is involved in covalent catalysis.
Ser 195
In the catalytic triad common to many serine proteases, ___ increases the basicity of ___, thus allowing deprotonation of ___ to serve as a nucleophile.
Asp-His-Ser
Which of the following is false regarding serine proteases?
A) they employ metal ion catalysis
B) They contain a catalytic triad of His, Ser, and Asp residues
C) They cleave simple organic ester bonds near larger residues
D) They employ general acid-base catalysis
A) they employ metal ion catalysis
An enzyme that has the maximum activity at pH 4 may indicate the involve of ___ amino aid in acid-base catalysis.
Glutamic acid
All are characteristics of allosteric enzymes except:
A) They obey Michaelis-Menton kinetics
B) Effectors may show stimulatory or inhibitory activity.
C) They have multiple subunits
D) The regulatory effect by altering conformation and interaction of subunits
E) Binding one subunit impacts the binding of substrate to other subunits
A) They obey Michaelis-Menton kinetics
Proinsulin is converted to insulin by:
Proteolytic excision of a specific peptide.
Heme is a porphyrin prosthetic group that coordinates __ at four positions.
Fe 2+
Which of the following is generally true for catabolism, but not anabolism?
A net production of energy results from degradation of large molecules.
All are coenzymes with an adenine nucleotide portion except:
A) NADH B) FADH2 C) Coenzyme A D) ATP E) FMNH2
E) FMNH2
What does not contribute to a large negative delta G of ATP?
All of the above contribute:
Phosphate hydrolysis
Resonance
Stabilization
Electrostatic repulsion
__ can bypass the regulatory step at 3-FTK to enter glycolysis which may be a contributing factor to obesity.
Fructose
All are allosteric regulators of phosphofructokinase-1 except:
glucose-6-phosphate by inhibition
All are true for 2,3-bisphosphoglycerate (2,3-BPG) except:
A kinase converts 2,3-BPG to 3-phosphoglycerate
Which step in metabolism produces a 3-C aldose and a 3-C ketose from a 6-C sugar?
Fructose bisphosphate aldolase
In alcohol fermentation from glucose, the two oxidation-reduction reactions are catalyzed by:
Glyceraldehyde-3-phosphate dehydrogenase and alcohol dehydrogenase
Pyruvate dehydrogenase is a multi-enzyme complex homologous to:
Alpha-ketoglutarate dehydrogenase
Order the coenzymes according to their involvement in the pyruvate dehydrogenase complex:
A) NAD+ B) CoA-SH C) TPP D) Lipoate (lipoamide) E) [FAD]
C D B E A
Allosteric inhibitors of isocitrate dehydrogenase include __ and __, wheras __ acts as an allosteric activator, __ the Km for isocitrate.
ATP; NADH; ADP; lowering
List the names of 5 enzymes that are regulated in the glycolysis and TCA cycle.
__
All are true statements for the glyoxylate pathway except:
Glyoxysomes contain all of the enzymes for the glyoxylate cycle.
Name two investigators who were awarded the Nobel Prize for their work on the structures of hemoglobin and myoglobin.
Perutz, Kendrew
What is the Michaelis-Menton equation formula?
Vo= Vmax [S] / Km + [S]
Where Km = (k-1 + k2)/k1
Km is often interpreted as…
The affinity of enzyme for substrate.
Km is similar to the dissociation constant (Kd) for the ES complex. If k-1»_space; k2, then Km ~ Kd
Kcat =
Kcat = Vmax / [E] total
Catalytic efficiency =
Catalytic efficiency = Kcat/Km
Where Kcat = Vmax / [E] total and Km = (k-1 + k2)/k1
Rates of enzyme catalyzed reactions generally ___ with temperature, however, at temps above 50-60 deg. celsius, enzymes show a ___ in activity.
Increase; decline.
Enzymes typically double in rate for every 10 deg. celsius rise in temperature.
As [S] increases, kinetic behavior changes from 1st order to ___ order kinetics.
Zero
The Lineweaver-Burk plot equation is the Michaelis-Menton rearranged to make it linear. The equation is…
(1/vo) = (Km/Vmax) (1/[S]) + (1/Vmax)
___-___ plot solves the problem of uneven sampling.
Hanes-Woolf
The three main categories of reversible enzyme reactions are:
Competitive
Uncompetitive
Mixed (Noncompetitive): inhibitor binds to sites on E that influence both S binding and catalysis
Explain the double displacement (ping pong) mechanism.
The first substrate is converted to product before the second substrate adds.
This requires two forms of “free” enzyme
Catalytic power is the ratio of the enzyme…
catalyzed rate / uncatalyzed rate
Enzymes often have cofactors such as ___, ___, ___, and ___.
Metal ions, coenzymes, cosubstrates, and prosthetic groups.
In enzymes, an apoenzyme refers to the ___ form ___ the cofactor.
Inactive form; without
In enzymes, a holoenzyme refers to the ___ form ___ a cofactor.
Active; with
Enzymes catalyze reactions by ____ and ___ the activation energy of the reaction.
Stabilizing the transition state; lowering
How does destabilization of ES affect enzyme catalysis?
Raising the energy of ES raises the catalyzed rate.
This is accomplished by a loss of entropy due to formation of ES and destabilization of ES by strain, distortion, and desolvation.
Catalysis via preferential transition state binding is when…
Some enzymes bind the transition state of the reaction with greater affinity than its substrates or products.
Thus, enzymes may mechanically strain substrates to TS geometry.
A transition state analog is a stable molecule that is chemically ___ to the transition state. They often make good ___, since they can make ideal enzyme inhibitors.
Similar; drugs
Specific acid-base catalysis is when…
H+ or OH- is transferred FROM solution
General acid-base catalysis is when…
H+ or OH- is generated in the transition state
___ is often a general acid or base because its side chain is near pKa of 7.
Histidine
Metal ions participate in catalysis in three major ways:
- Binding to substrates to orient them
- Mediating redox reactions through reversible changes in oxidation state
- Electrostatically stabilizing or shielding negative charge
Enzymes facilitate formation of near-attack conformations
Near-attack conformations (NACs) are ___ to reaction transition states. In NACs, reacting atoms are in Van der Waals contact and at an angle resembling the bond to be formed in the transition state.
Precursors
Low barrier hydrogen bonds (LBHB) stabilize the ___ ___. They can be used to lower the ___ barrier.
Transition state; activation
Quantum Mechanical Tunneling
Tunneling provides a path “around” the usual ___ of activation for steps in chemical reactions. Tunneling probably contributes to most ___ transfer reactions.
energy; hydrogen
The most well characterized serine proteases are ___, ___, and ___.
Chymotrypsin; trypsin; elastase
Serine is part of a “catalytic triad” composed of ___, ___, ___.
Ser, His, Asp
Serine proteases differ in their specialties:
Trypsin: Cleaves after ___ amino acid
Chymotrypsin: Cleaves after ___ amino acid
Elastase: Cleaves after ___ ___ residues.
Basic; aromatic; small neutral
Serine proteases serve as enzymes that ___. Serine serves as the ___ amino acid at the enzyme’s active site.
Cleave peptide bonds; nucleophilic
Serine proteases display ___ kinetics, meaning that there are at least 2 steps.
Burst
DIPF, or Diisopropylphosphofluoridate, irreversibly ___ serine proteases.
Inactivates
There are three key residues for the catalytic triad, and each’s function is:
Asp-102:
His-57:
Ser-195:
Asp-102: functions to orient and polarize His-57
His-57: acts as a general acid base
Ser-195: forms a covalent bond with peptide to be cleaved
The oxyanion hole is part of the enzyme that forms hydrogen bonds with the O- in the tetrahedral intermediate. It facilitates ___ of the transition state.
Binding
Bovine Pancreatic Trypsin Inhibitor (BPTI) prevents trypsin synthesized in pancreas from ___ that organ. It prevents H2O from reaching the active site.
Digesting
The aspartic proteases, pepsin, chymosin, cathepsin D, renin and HIV-1 protease all involve two __ residues at the active site. These two residues work together as general acid-base catalysts.
Asp
Enzymes are regulated in multiple ways, such as:
- Genetic regulation of enzyme synthesis and decay
- Allosteric regulation
- Covalent modification
- Availability of substrates and cofactors
Typical enzymes show hyperbolic increase in velocity with respect to [S], while cooperative enzymes exhibit the ___ curve.
Sigmoid
Positive cooperativity implies ___ binding.
Allosteric
In the Monod, Wyman, and Changeux allosteric model, there are two conformational states of the enzyme: ___ and ___. Also, allosteric proteins are oligomers.
It states that S binds ___, because as it shifts the equilibrium to the R state, it opens up more S binding sites.
Relaxed (R); Taut (T); Cooperatively
R: has affinity for S
T: low to no affinity to S
The sequential model for allostery (KNF) says that:
- Protein is ___.
- Does not require all subunits to be in either the R or T state, differing with the ____ model.
- Ligand-induced changes in one subunit lead to conformation changes in adjacent subunits.
Oligomeric; MWC (Monod, Wyman and Changeux)
Covalent Modification Regulation of Enzymes:
-Enzyme activity can be regulated through reversible ___ by protein kinases.
Phosphorylation
In regulation by phosphorylation, protein kinases phosphorylate ___, ___, and ___ residues in target proteins.
Kinases are often regulated by ____ control.
Ser, Thr, Tyr
Intrasteric
An example of allosteric regulation is ___ ____, also called GPase.
It works by breaking down glycogen highly expressed in muscle, and can be phosphorylated at Ser 14. Phosphorylation shifts equilibrium towards R state.
Glycogen n + Pi gives Glycogen n-1 + G1P
Glycogen phosphorylase
Allosteric regulators that influence the R/T equilibrium are called ___.
Effectors
Allosteric regulators that influence the R/T equilibrium are called ___, which can be positive or negative.
Effectors
In regulation by proteolytic activation/inactivation,
___ are inactive precursors of enzymes, and proteolytic cleavage produces the ___ product.
Zymogens; active
Isozymes are enzymes with slightly different ___.
Subunits
Hemoglobin is responsible for _____ in the blood, while Myoglobin is responsible for _____ in the muscle.
O2 transport; O2 diffusion in the muscle.
Hemoglobin is a ___, and has 2 alpha subunits and 2 beta subunits. Myoglobin is a monomer.
Tetramer
Both Hemoglobin and Myoglobin bind ___, which carriers O2.
Heme
Myoglobin has ___ residues, with 8 helices named A-F. Myoglobin binds between helix ___.
153, E-F
___, ___, and ___ can bind to heme groups with a much higher affinity than O2, and can cause toxicity.
CO, NO, and H2S
Oxygen binding by Myoglobin is ___.
Hyperbolic
When interpreting hyperbolic plots of myoglobin, the steepness of the plot indicates ___ ___.
higher affinity
Hemoglobin undergoes conformational change upon binding ___.
It has two conformations, T state, in which it is ___, and R state, in which it is oxyhemoglobin.
O2
deoxyhemoglobin
Hemoglobin has cooperative binding which is ____, and increases the effectiveness of O2 delivery.
Myoglobin has hyperbolic bindining.
Sigmoid
Hemoglobin binds oxygen in the ___ and releases it in the ___.
Lungs; capillaries
Hemoglobin effectors:
-H+ can promote ___ of oxygen from hemoglobin, called the Bohr effect. This works by a pH influence on T to R transition. (decreased pH leads to increased ___ of O2 from hemoglobin).
Dissociation
Deoxy-hemoglobin has a higher affinity for H+ than ___.
Oxy-Hemoglobin
CO2 also promotes the ___ of O2 from hemoglobin. Most of the CO2 is transported in the blood in the form of bicarbonate, and hydration of CO32 in tissues leads to proton production. These protons are taken up by hemoglobin as oxygen dissociates.
Dissociation
___ is a negative allosteric effector of hemoglobin. When it is present, it will bind in the sigmoid curve.
2,3-Bisphosphoglycerate
Fetal hemoglobin has a ___ affinity for O2 because it has a ___ affinity for BPG (bisphosphoglycerate).
Higher; lower
Fetal hemoglobin has a ___ affinity for O2 because it has a ___ affinity for BPG (bisphosphoglycerate).
Higher; lower
Sickle cell anemia is caused by a single amino acid ___ in hemoglobin (Glu to Val). This causes hemoglobin to form a filament.
Substitution
An organism with:
Carbon source: CO2
Energy source: light
Is a…
Photoautotroph
An organism with:
Carbon source: CO2
Energy source: light
Is a…
Photoautotroph
An organism with:
Carbon source: CO2
Energy source: light
Is a…
Photoautotroph
An organism with:
Carbon source: Organic compounds
Energy source: light
Is a…
Photoheterotroph
An organism with:
Carbon source: Organic compounds
Energy source: light
Is a…
Photoheterotroph
An organism with:
Carbon source: Organic compounds
Energy source: light
Is a…
Photoheterotroph
An organism with:
Carbon source: Organic compounds
Energy source: light
Is a…
Photoheterotroph
An organism with:
Carbon source: CO2
Energy source: redox reactions
Is a…
Chemoautotroph
An organism with:
Carbon source: organic compounds
Energy source: redox reactions
Is a…
Chemoheterotroph
In the cytosol, what metabolic pathways occur?
Glycolysis, pentose phosphate pathway, fatty acid biosynthesis, etc.
In the mitochondria, what metabolic pathways occur?
TCA cycle, oxidative phosphorylation, fatty acid oxidation, amino acid breakdown
In the smooth ER, what metabolic pathways occur?
Lipid and steroid biosynthesis
Enzymes at key steps in metabolic pathways are regulated by…
1.
2.
3.
- Allosteric control- feedback inhibition, products inhibit earlier reactions
- Covalent modification- phosphorylation/dephosphorylation can change enzyme kinetics
- Genetic control- control transcription of metabolic enzymes
Phosphocreatine is a high-energy compound used to generate ___ during intense activity. It acts as an ___ buffer.
ATP
