CHM 332 Final
The figure below shows the denaturation curves for three similar size of DNA samples, differing in their composition of bases. In the graph, which line indicates the most Gc-rich DNA sample among the three and what is its melting point
Line C: and its melting temperature is 108C
Based on the following graph for accumulation of product as a function of time for an enzyme catalyzed reaction, which of the following conclusion can be drawn
the rate for this reaction is about 0.5 u M/min
Which 2 of the intermediates given above contain a "high-energy" bond and are used to produce ATP by substrate-level phosphorylation in glycolysis?
(4) and (7)
Which of the following is correct Km for the INHIBITED reaction with raichuic acid
12 mM
Michaelis-menten constant, Km is defined as
(K1+ K2) / K1
(still using the figure above) What is the approximate net charge of the peptide given above at pH 7.0
+1
Bacteria and other microbes can be used to "clean up an oil spill by breaking down oil into carbon dioxide and water. The DNA from one of the microbes isolated from the Deepwater horizon leak in the gulf of mexico was analyzes and its percent thymine was determined to be 29%. assuming this microbe contain normal double strands predict the percent guanidine in this DNA
21%
The Keq for the reaction catalyzed by one of the glycolytic enzymes is 0.041 ΔG of the above reaction at 37C when the concentration of glyceraldehyde 3-phosphate is 1.0 mN and the concentration of dihydroxyacetone is 0.2 mM
3.8 KJ/mol
Which of the following series of amino acids is MOST likey to be at the surface of a water-soluble globular protein
.... Glu/Asn/ Ser/Thr/Arg....
Identify the structures (from A-H in the table 1) of the compound 1 and compound 2 in the reaction shown.
1. Compound 1 is Structure A 2. Compound 2 is Structure G 3. Choose the correct names for the enzymes: The name of enzyme for step 1 is pyruvate decarboxylase (we do not have this, but only yeast has it) and the name of enzyme for step 2 is alcohol dehydrogenase .
One reason that ATP is considered as a "high energy compound" is due to the large negative standard free energy change for the following reaction: ATP+ H2O--> ADP +Pi. Which two of the following statements are the correct reasons for the reaction to have such a large Negative ΔG value
1. Decrease in electrostatic repulsion by the cleavge of phosphoanhydrine bond 4. More resonance stabilization in Pi than in ATP
Still using the data table above: If the amount of enzyme A used in the enzyme reaction above was 5 nM, what is the Kcat of the enzyme A
1.0 x 10^5 / sec
Aspartate can be converted by transamination reaction into Oxaloacetate (OAA). OAA can then be converted to glucose through gluconeogenic pathway. What is the energy yield or cost (in ATP-equivalent) of converting two molecules of OAA to 1 molecule of glucose.
4 ATP (equivalent) consumed
How many peptide bonds and amino acid residues are in the structure shown
4 peptide bonds, 6 residues
A sample of DNA was sequenced using the dideoxy nucleotifr method and the resulting (synthezised) products were resolved on the gel What is the correct sequence of the DNA
5'-ATGCCTGACT- 3'
Which of the following is correct Vmax from the INHIBITED reaction with raichuic acid
5uM/ sec
Which of the following shows the correct order of the above intermediates in glycolysis (not all of the intermediates are shown)?
8-3-1-5-7-2-4-6
What are the correct names of the substrate and products of the reaction given above (the structures are given above)?
A
Which of the following shows the correct structure of B-D Fructose in haworth projection
A
(still using the figure above) What kind of chemical can be used to release a single Cys from the compound shown above
A reducing Agent (2-mercaptoethanol)
Fructose-2,6-bisphosphate is a compound that prevents futile cycle, because it is an activator of __(A)_, and an inhibitor of _(B)_. What are the correct enzymes for the blanks (A) and (B)?
A: phosphofructokinase B: fructose 1, 6-bisphosphatase
The phosphofructokinase (PFK) reaction is a major control point in glycolysis. It is the slowest reaction in glycolysis and is regulated by several molecules, but not by naturally changing concentrations of reactants and products. The molecules mentioned below allosterically regulate PFK activity. Indicate whether each condition described increases or reduces PFK activity (specifically in mammalian liver).
Activation of PFK2: Increase PFK activity Decreasing blood glucose concentration: Decrease PFK activity Increased PEP concentration: Decrease PFK activity Increased levels of fructose 2,6, bisphosphate: Increase PFK activity Increased levels of ADP: Increase PFK activity
The structure shown below depicts a
Antiparallel beta sheet
The pI of one of the histone proteins is 10.5. Answer the following questions about this histone protein
At physiological pH(7.4) what kind of net charge would this protein have : Net charge would be positive From the information given above, you can assume that the histone proetin contains higher than average amount of Histidine
If you run the mixture of all 4 proteins listed above on the SDS- PAGE, where would you likely to find the band for hemoglobin on the gel
At the same position as myoglobin (so not to be able to distinguish Hb and Mb)
What are the correct compounds that should be in the boxes a and b in the above reaction?
B
Acetylcholine is the neurotransmitter used at the neuromuscular junction. Enzyme acetylcholinesterase is one of the serine hydrolases, and use a similar catalytic traid (Ser/ His/ Glu- instead of Asp)... considering these facts, identify the scissile bond in the structue of acetylcholine given belwo
Bond D
The pentose phosphate pathway leads to production of ____ ? (select a correct pair of answers) 1. NADPH for anabolic metabolism 2. NADH for anabolic metabolism 3. NAD+ for glycolysis 4. Ribose-1-P for glycogen synthesis 5. Ribose -5-P for nucleotide production
Both 1 and 5
The following figure depicts the structure of____
Cellulose
What kind of inhibition does raichuic acid exhibit ( still using the data above)
Competitive
Considering Bohr effect, determine which curve in the graph shows the O2 binding of Hb at pH 7.2 if the curve #3 is at pH 7.4
Curve 4
Which of the followings shows the three steps in a typical PCR cycle in correct order in a cycle
Denaturation- annealing- elongation
Enzyme A has Kcat = 0.7 x 10^4 sec^-1, while enzyme B has kcat= 1.5 x 10^2 sec-1. Which of the following comparisions is correct based on these kcat values?
Enz A carries out many more reactions in a given time than does Enz B
Muscle cells are not able to supply glucose for other tissues because they do not contain which of the following enzymes?
Glucose-6-phosphatase
Choose correct terms for each drop down choices.
Glycogen phosphorylase catalyzes a phosphorolysis reaction that breaks alpha 1,4 linkage in glycogen. In the fasting state, the hormone glucagon stimulates this enzyme, resulting in an increase blood glucose levels.
Using the table which protein would be eluted first if a mixture of all 4 proteins listed above is subjected to the gel filtration chromatography
Hemoglobin
Phosphoglycerate mutase Q3: from the figure given above, you can conclude that the catalytic mechanisms performed by His A and His B are--
His A Shows: Covalent catalysis His B shows Acid- Base catalysis
Dideoxy nucleoside triphosphate are used in sequencing reaction. Which is TRUE about ddNTP?
It will terminate DNA synthesis when incorporated into a growing DNA strand
Looking at the carbohydrate structure given above, you can assume that the monosaccharide above is a _____
Ketohexose
Which of two glycolysis enzymes belong to the class of lyase?
In glycolysis, the concentration of its products is very low, thus actual ΔG is a negative value.
The graph shown below is the titration curve of an amino acid. answer the following questions using the titration curve
In this titration curve, the pKa of this amino acid;s side group is shown as point C on the graph, therefore you can identify the amino acid in the solution as His And the PI of this amino acid is marked as point D on this graph
What kind of changes would help release the second protein from the ion exchange chromatography column in the question above
Increase pH, and increase the salt concentration
The sub-enzymes and cofactors of the enzyme above (still referring to the enzyme above), carry out various reactions. The table below summarizes the reactions carried out by them. Choose the correct compound or function for each component of the enzyme. (5 points/ 0.5 point each per cell). The first row has been filled as an example:
Location of the action, Name of compound, Function Substrate → Pyruvate → Carbon Source Cofactor Bound to E1 → TPP →Decarboxylates Pyruvate Cofactor Bond to Lys in E2 → Lipoic acid → Accepts hydroxyethyll group from E1, as acetyl group Substrate for E2 → CoA-SH → Accepts acetyl group from lipoamide Cofactor Bound to E3 → FAD → Reduced by lipoamide Cofactor that accepts electrons from E3: NAD+ → Accepts electrons from FADH
Which of the following pairs of amino acids might form a salt bridge to each other
Lys, Asp
Considering the information given above, which of the following identifies correct proteins for the binding curves X,Y and Z
Myglobin HbMu Hba (normal)
Phosphoglycerate mutase Q2: using the figure above: Identify the nucleophile and electrophile in the STEP 2
Nucleophile is N of His 1; electrophile is P at C3
The steps above shows the formation of the intermediate 2,3-BPG catalyzed by two histidine residues of the enzyme. Identify the nucleophile and electrophile in this step
Nucleophile is O at C2; electrophile is P on His A
The following is a list of possible products of glycolysis. Assuming ONE molecule of glucose is used in glycolysis, fill the blanks with the correct coefficients (number of molecules generated from glycolysis/glucose). You should use ZERO if the molecule is not produced from glycolysis.
One molecule of glucose entering Glycolysis will produce 2 --> pyruvate 2 --> ATP (net amount) 0 --> NAH+ 2 --> NADH
Consider the hypothetical serine protease, which has three specificity pockets (s1 - s3 below). The S1 pocket is deep and hydrophobic, teh s2 pocket is small and hydrophobic, and the S3 pocket has a glutamate in the bottom
Phe -Gly- Lys
When coupled with the synthesis of ATP from ADP+ Pi, which of the following reaction would be spontaneous
Phosphocreatine --> creatine +Pi
A reaction is carried out by adding 50u M of substrate (S) to a mixture containing equivalent amounts of enzyme A and B. After 1 minute of the reaction, which reaction product will be more abundant
Product Q
A biochemist ran a cation exchange chromatography at pH 7.5 to separate proteins from mixture of the Protein 1 and Protein 2. She obtained two well separated protein fractions. Which protein would be eluted first from this column
Protein 1
Which steps in gluconeogenesis consume or produce ATP (or its equivalent)?
Pyruvate carboxylase, PEP carboxykinase, phosphoglycerate kinase
Q1: If the carbonyl carbon atom of acetyl-CoA is labeled with radioactive carbon (14C) and entered the citric acid cycle, which of the carbon atoms of the given molecule (in the diagram) will have the radioactive label at the end of one turn of the citric acid cycle? Choose from A-E in the figure. (Assuming no mixing of symmetric carbons) Q2: If the # 1 carbon of glucose molecule is labeled with radioactive (14C) , and went through glycolysis, PDH step, and entered the Citric Acid Cycle, which of the carbon atoms of the given molecule (in the diagram) will have the radioactive label at the end of one turn of the citric acid cycle? Choose from A-E in the figure. (Assuming no mixing of symmetric carbons):
Q1: A Q2: B
The following reaction is catalyzed by UDP glucose pyrophosphorylase:
Q1: Choose the structure of the compound X that should fit in the parenthesis in the above reaction (choose one from A-H in the table above): A Q2Which is the substrate for glycogen synthase? Choose its structure from the Table above (from A-H). H Q3: Which is the glucose monomer unit that would be produced by glycogen phosphorylase catalytic reaction? Choose its structure from the Table above (from A-H): A Q4: One of the major products of the pentose phosphate pathway is a 5-carbon carbohydrate (ribose-5-phosphate). The structure of this compound is shown in the Table above as: E
Phosphocreatine +ADP --> Creatine + ATP In the cytosol of neurons, the concentrations of the reactants and products of this reaction are found to be: Phosphocreatine at 5.0 mM, creatine at 1.0 mM, ADP at 0.75 mM, and ATP at 2.5 mM
Q1: What is the Keq for the reaction given above: 161.5 Q2: What is the mass action ratio of the reaction in the cytosol of neurons: 0.67 Q3: What is the ΔG of the above reaction in the cytosol of human neurons: -13.6 KJ/mol
In animal cells, the pyruvate produced in glycolysis is converted to lactate under anaerobic condition
Q1: What is the name of enzyme that catalyzes the reaction above? lactate dehydrogenase Q2: What type of chemical change is made to the pyruvate in this reaction? pyruvate is reduced Q3: What is the important product of this reaction (that would fit in the box B), other than lactate? NAD+
Answer the following question using the cyclic monosaccharide shown here
Q1: Which carbon in the figure is its anomeric Carbon: Carbon b Q2: Is the sugar shown an alpha or beta anomer: Beta anomer Q3: Is the molecule shown above a reducing sugar? yes, it is a reducing sugar
The Lineweaver- Burk plots below shows the effect of an inhibitor on the rate of enzymatic reaction. Using the graph, answer the following questions
Q1: Which line in the plot above shows the reaction with the inhibitor? Line A: shown with the equation y= 0.8 x +1.2 Q2: According to the plot above, what type of inhibition does the inhibitor has on the enzyme reaction? Mixed inhibition with decreased Km
The following figure shows one of steps during the chymotrypsin catalytic reaction
Q1: Which of the following describes the process shown by the arrow C in figure above correctly: The side group of a.ac 2 is working as a base, removing the proton from the hydroxyl group from a.ac 3 Q2: Which indicates the scissile bond in the figure that is cleaved by chymtrypsin: F Q3: Which indicates the position where the catalytic residues are to form a low-barrier H-bond to stabilize the transition state from of the reaction: B Q4: Chymotrypsin uses both acid-bas and covalent catalyses in its action. Which amino acid of the enzyme in the above figure forms a covalent bond with the substrate during the catalytic reaction: a.ac 3 Q5: Which amino acid in the substrate is the one that is recognized by the specificity pocket of chymotrypsin in the figure above: a. ac residue R2
When the reaction A--. B is reached its equilibrium at 25C the concentrations of the reactants are found as follows: Concentration of A=3mM, Concentration of B=15mM Q1: is this reaction favorable under standard conditions Q2: Which of the follwoing is correct when the concentrations of reactants in the reaction are changed to A=10mM and B=10mM respectively, while other conditions remain the same as standard condition?
Q1: yea Q2: The reaction would be spontaneous (=favorable) as written
Identify the correct enzyme classification for the reactions shown below
Reaction (A): Oxidoreductase Reaction (B)Isomerase Reaction (C) Transferase Reaction (D) Transferase
Choose the correct unit for each rate constants( k1, k2, k1) shown in the above equation
Row A
Using the info given for above reaction: Is the reaction spontaneous or not?- (i) under the standard condition and (ii) in the cytosol of neurons
Row A
Using the given information, answer the following
The amino acid sequence for the above peptide is: Ala- Tyr- Asp- Gly and the isolectric point of the peptide is 3.7
Use the following reaction to answer the questions.
The compound Z that should fill the parenthesis is Oxaloacetate (OAA) and its structures is Structure C What is the prosthetic group (or cofactor) that the enzyme uses to carry out the reaction given above Biotin The name of enzyme that catalyzes this reaction Pyruvate carboxylase
Glycogen synthesis requires formation of UDP-glucose. The process of UDP-glucose formation is thermodynamically driven by ______?
The hydrolysis of PPi
The Line weaver- Burke plot below shows the enzyme reactions in the presence and absence of an inhibitor. Which of the following describes the type of inhibition mechanism shown by this plot correctly,
The line A indicates the inhibitor that binds to only ES complex
Studies of oxygen transport in mutant Hb (HbMu) show that the O2- saturation curves of the mutant (HbMu) and normal (HbA) hemoglobin are markedly different when measured under the same conditions What is the possible explanation for the oxygen binding behavior of HbMu
The mutation (Ser -->Asp) allows less BPG binding therefore HbMu has higher affinity for O2 than HbA
Which of the following statements is TRUE regarding the binds that are in DNA
The nucleotide monomers are joined by phosphodiester bond, while the double helix are formed by hydrogen bonds between N-containing Bases
(Still Using the reactions given above) What is the importance of Step 2 above to the yeast cell?
The step provides NAD+ that is needed in GAP DH reaction in glycolysis.
The conversion of glucose to pyruvate occurs in a 10-step, unidirectional pathway, called glycolysis (shown as "1" in the figure), while the part 2 shows the circular amphibolic pathway, called Citric Acid cycle (CAC). The process 3 shows the oxidative phosphorylation (to be discussed this week). Notice it only show the summary of the processes, not the balanced equations. Answer the following questions using this figure.
What enzyme catalyzes the step between the pathway 1 and 2 (pyruvate ⟶acetyl CoA) shown and what is its cellular location? Pyruvate Dehydrogenase in Mitochondria
Fill in the blank using the structure below
What is common for these three compound? They are all redox cofactors WHich of the three is usually found in a non-polar environment, such as membranes: A
Coenzyme A is considered a high energy compound: in Acetyl-CoA, the acetyl group is attached to Coenzyme A by a ____ bond. When the acetyl group is cleaved off from CoA, the bond cleavafe reaction is energetically so favorable
Thioester
The following figure shows, the functional group of one of the ion exchange column material. which of the following describes its proper use in protein purification
This can be used to retain acidic proteins in neutral pH (pH 6.8)
You wish to determine the sequence of a short peptide, containing 11 amino acids and the following data were obtained Which of the following shows the correct amino acid sequence of the given peptide
Thr-Lys-Leu-Glu_Arg-His-Met-Lys-IIe-Tyr-Gln
Using the figure determine the catalytic mechanism that are being carried out by the active site amino acids
What kind of catalysis mechanism does the Lys residue in the aldolase carry out? Covalent catalysis What kind of catalysis mechanism does teh Tyr residue in the aldolase carry out? base catalysis
The following is the titration curve of cysteine. different charge states of cys are shown in the table below
Which is the most predominant forms of cysteine at the point A on the titration curve: form 1 (50%) + form 2 (50%) Identify which form would Cys assume when the solutions pH is at its form 2 and Identify the Pi of this amino acid on the graph: it is marked as Point B on graph
Questions based on the picture
Which of the amino acid above has a thiol group as its side group: j What is the netcharge of the amino acid shown as e at pH 3.0: +1 What is the isoelectric point (pl) of the amino acid shown as b in the diagram: 6.25 Whcih one of the followings shows the correct order of solubility of the amino acids d-h: e-h-d-g-f
The following is the structure of ATP which of the arrows in the figure points towards a high energy phosphoanhydride bond
arrow 5
Recall that the carbons in the initial citrate molecule are oxidized as the reactions proceed in the cycle (to produce reduced cofactors). Which of the followings shows the correct order of the above compounds appear in CAC, starting from citrate. Notice that not all of the Citric Acid Cycle intermediates are shown
g-b-c-a-f-e-d
The determine the kinetics of a new enzyme, the follwing intial reaction rates were obtained at various [s] using the data, calculate the Km for this enzyme
km = 0.5 x 10^-4 mM
Which of the following enzymes in the citric acid cycle is regulated by the cellular level of NADH?
lsocitrate dehydrogenase
Samples of a segment of linear DNA are digested using the restriction enzymes EcoRi, BamHI, and a combination of EcoRI and BamHi. The digest are then run on an agarose gel in order to seperate the resulting fragments by size. you are to create a map of the DNA segment, using the result of the gel electrophoresis. Which of the following map shows the correct location where BamHI cuts in this sample DNA?
map D
What are the unique enzymes in gluconeogenesis that are used to reverse the irreversible steps in glycolysis? (they may not be in the order of reactions in gluconeogenesis).
pyruvate carboxylase, fructose bisphosphatase, glucose-6-phosphatase, PEP carboxykinase
