Biochem FInal
What is the abbreviation that is used to represent adenosine diphosphate? A. ATP B. dADP C. DiAdoP D. ADP
ADP
Based on the standard pKa values for each of the following amino acids side chains, indicate the charge that you would expect on the side chain at pH 7? ASP LYS HIS GLU ARG
ASP - NEGATIVE LYS - POSITIVE HIS - NEUTRAL GLU - NEGATIVE ARG - POSITIVE
The net charge of the amino acid lysine at pH=7 is A. -1 B. 0 C. +1 D. +2
+1
The side chain for Histidine has a pKR of around 6.0. Histidine's alpha carboxyl and alpha amino groups have pKas relatively similar to lysine's. What is the charge of the entire Histidine molecule at pH 4.0? A. +1 B. 0 C. +2 D. -1
+1
If sample solutions are starting around room temperature then heating up solutions of DNA and proteins results in which of the following? A. +ΔH and increased ordered structure B. +ΔH and decreased ordered structure C. -ΔH and increased ordered structure D. -ΔH and decreased ordered structure
+ΔH and decreased ordered structure
When you are looking at a CD signal of an alpha helix which of the following intensities would suggest the largest amount of alpha helix? A. - 40 at 222nmm B. -40 at 216 nm C. -30 at 216 nm D. -30 at 222nm
- 40 at 222nmm
Pep2: Calculate the net charge on this peptide at pH 7. Arg-Glu-Tyr-His-Asn A. 0 B. -1 C. +1 D. -2 E. +2
0
Hemoglobin and myoglobin bind oxygen. How many oxygen molecules can bind to one subunit of myoglobin or hemoglobin? A. 1 B. 2 C. 3 D. 4
1
In the hemoglobin mutant HB Providence (described in the Skill exercise) what is the effect of the Lys-->Asn mutation in the central cavity. HB Providence has ["increased", "decreased", "unchanged"] BPG binding in the central cavity and ["increased", "decreased", "unchanged"] oxygen delivery to tissues.
1. DECREASED 2. DECREASED
How many consecutive nucleotides code for an amino acid? A. 2 B. 3 C. 5 D. it depends on the organism
3
The simplest amino acid Glycine can exist in how many different forms (charged states) in solution? A. 2 B. 3 C. 1 D. 4
3
How many amino acids per turn of an alpha-helix? A. 3.6 B. 7.2 C. 1.2 D. 2.4
3.6
pXYZ is a double stranded DNA with 20% A. What percentage C does it have? A. 20% B. 30% C. 40% D. 60% E. not enough information to determine
30%
A strand of double stranded DNA contains 20% T. It also contains A. 30% A B. 30% G C. 20% C
30% G
How many subunits does hemoglobin have? A. 1 B. 2 C. 3 D. 4
4
The pKa of the cysteine side chain is 8. If the pH of a solution is 8.1, what percentage of a cysteine side is protonated? A. 56% B. 44% C. 10% D. 90% E. Not enough information to determine
44%
In class you viewed the titration curve of lysine. The lysine side chain has a pKR of about 10. Using the Henderson-Hasselbalch equation, solve for the ratio of [A-] / [HA] that corresponds to the ratio of deprotonated side chains / protonated side chains when pH 10.7. Choose the answer that is closest to the ratio you obtain using the side chain pKR of 10 and a pH = 10.7. A. 5 B. 0.2 C. 10 D. 0.1
5
The extinction coefficient of a protein at 280 nm is 0.075 µM M-1 cm-1and the Absorbance of a 1:5 diluted stock solution is A280= .98. What is the concentration of the stock solution of protein? A. 65 µM B. 0.7 µM C. 130 µM D. 0.07 µM E. 13 µM
65 µM
Fluorescence spectroscopy can be used to monitor the environment. If you are doing two experiments and the first experiment (A) has your fluorescent protein in buffer but your second experiment(B) has fluorescent protein, buffer and quencher then which of those solutions will have a higher fluorescence? A. B B. A
A
Titr2: The graph below is most likely the titration curve of which of the following amino acids? A. Lysine B. Asparagine C. Valine D. Aspartic acid
Aspartic acid
You have two peptides Peptide A G-A-A-D-A-V-K-E-G-G-A-E-K-G-A Peptide B G-A-A-F-A-V-W-E-G-G-A-E-I-G-A Which peptide will have a greater positive ΔS upon folding? A. A B. B
B
You have two peptides Peptide A : A-A-A-Y-A-F-A-A-F-A-A-A- Peptide B: A-A-A-Y-A-F-A-A-F-A-A-A-A-A-A-Y-A-F-A-A-F-A-A-A- Which peptide will have a more negative ΔH from internal noncovalent interactions upon folding? A. B B. A
B
What are two types of secondary structures other than alpha helices A. alpha-strands and B-sheets B. B-sheets and turns C. alpha-strands and turns
B-sheets and turns
Benzoic acid exists in two forms: The protonated acid form Ph-COOH (Benzoic acid) and the deprotonated carboxylate acid Ph-COO- (Benzoate) The pKa of benzoic acid is 4.2 What is the predominant form of benzoic acid found at pH = 7 A. Benzoic acid B. Benzoate C. equal amounts of benzoic acid and benzoate
Benzoate
Benzoic acid has a lower pKa than acetic acid. A. Benzoic acid is deprotonated at a lower pH than acetic acid because the proton on benzoic acid is more tightly associated with the oxygen of the carboxylic acid B. Benzoic acid is deprotonated at a higher pH than acetic acid because the proton on benzoic acidis more tightly associated with the oxygen of the carboxylic acid C. Benzoic acid is deprotonated at a lower pH than acetic acid because the proton on benzoic acid is more weakly associated with the oxygen of the carboxylic acid D. Benzoic acid is deprotonated at a higher pH than acetic acid because the proton on benzoic acid is more weakly associated with the oxygen of the carboxylic acid
Benzoic acid is deprotonated at a lower pH than acetic acid because the proton on benzoic acid is more weakly associated with the oxygen of the carboxylic acid
What is the primary secondary structural element found in the image below? A. Base pairing B. Base stacking C. Alpha helix D. Beta sheet E. Both c and d are in equal amounts
Beta sheet
Which of the following statements is TRUE? A. Oxygen binds to heme group of hemoglobin B. One oxygen molecules bind to every subunit of hemoglobin C. BPG binding to the heme causes a change in shape of the hemoglobin subunit D. Both A&B E. Both A&C
Both A&B
UV-visible spectroscopy can be used for which of the following? A. Monitor the environment of tyrosine B. Calculate Protein Concentration C. Calculate Protein concentration and monitor the environment of Tyrosines
Calculate Protein concentration and monitor the environment of Tyrosines
The structure below of hemoglobin A. Contains an equal amount of both alpha helix and beta sheets B. Contains primary, secondary, and tertiary structure, but not quaternary structure C. Contains four subunits that interact with each other D. All of the above are true
Contains four subunits that interact with each other
Which of the following amino acids could serve as a buffer around pH 8? A. Tyrosine B. Glutamic acid C. Asparagine D. Cysteine
Cysteine
Scientists observe a decrease in stability of a protein as they decrease the pH. This is most likely because____________ A. Decreases in noncovalent interactions B. Increases in noncovalent interactions C. The hydrophobic effect
Decreases in noncovalent interactions
Fetal hemoglobin has a slightly different structure that prevents 2,3-BPG from binding in the central cavity. What is the effect of this different on oxygen binding to hemoglobin in the fetal bloodstream? A. No effect since the BPG will still bind to the heme group B. Fetal hemoglobin will release oxygen easier C. Fetal hemoglobin will accept oxygen that is released from the maternal hemoglobin
Fetal hemoglobin will accept oxygen that is released from the maternal hemoglobin
Fill in the blanks: _____________ spectroscopy monitors the emission of light and __________________ spectroscopy measures the absorption of light. A. Fluorescence, Circular dichroism B. Fluorescence, UV-Vis C. UV-Vis, Circular dichroism D. UV-Vis, Fluorescence
Fluorescence, UV-Vis
Which amino acid side chain, when deprotonated has a negative charge? A.His B. Lys C. Glu D. Arg E. More than one of the above
Glu
In UV-Vis and fluorescence you might hypothesize that a molecules environment is changing if.... A. the intensity of the absorption or emission peak has changed B. the maximum of the absorption or emission peak has shifted C. If either the intensity or wavelength of the absorption or emission has changed
If either the intensity or wavelength of the absorption or emission has changed
You are following the following reaction in an aqueous solution: Protein folded → Protein unfolded. The ΔS for the protein will _______, while ΔS for the water will ______ A. Increase and increase, respectively B. Decrease and decrease, respectively C. Increase and decrease, respectively D. Decrease and increase, respectively
Increase and decrease, respectively
The strand shown is DNA. You know this because: A. It contains uracil B. It contains deoxyribose C. It is single stranded D. all of the above
It contains deoxyribose
Which of the following interactions will be the weakest? A. Mg2+ and Cl- in a polar solvent B. K+ and Cl- in a polar solvent C. Mg2+ and Cl- in a nonpolar solvent D. K+ and Cl- in a nonpolar solvent
K+ and Cl- in a polar solvent
You have decided that you want to study the unfolding of a protein that is nearly entirely ß-sheet therefore you expect which of the following as the protein unfolds from ß-structure to random coil. A. More negative intensity at 222nm as the protein folds B. More positive intensity at 222nm as the protein folds C. More negative intensity at 216 nm as the protein folds D. More positive intensity at 216 nm as the protein folds
More negative intensity at 216 nm as the protein folds
The pKa of the cysteine side chain is 8. When the pH of the solution is 8.2 A. More of the side chain is protonated and has a positive charge B. More of the side chain is protonated and has a neutral charge C. More of the side chain is deprotonated and has a negative charge D. More of the side chain is deprotonated and has a neutral charge
More of the side chain is deprotonated and has a negative charge
Which of the statements below is TRUE? A. Myoglobin has a higher oxygen P50 than hemoglobin B. Myoglobin has a hyperbolic oxygen binding curve C. Myoglobin binding of oxygen is affected by pH. D. Two of the above are true E. All of the above are true
Myoglobin has a hyperbolic oxygen binding curve
Which of the following amino acid side chains will interact with each other primarily through Hydrogen bonding interactions? A. D and E B. H and K C. L and I D. N and Q E. E and R
N and Q
Lys interacts with an Asp at pH 7.0. The strength of this interactions is greater when the amino acids are? A. On the inside of the protein B. On the outside of the protein C. It doesn't matter
On the inside of the protein
The environment of Fluorophores can be used to study both proteins and DNA. Protein fluorophores, like tyr and trp, would have decreased fluorescence _________ the protein and Ethidium Bromide will have decreased fluorescence ________ of the DNA. A. Inside, outside B. Outside, inside C. Inside, inside D. Outside, outside
Outside, outside
Below is a peptide sequence Glu-Lys-Leu-Phe of the answers below choose which most correctly describes the type of amino acids in order from Glu to Phe assuming PHL stands for hydrophilic and PHO stands for hydrophobic A. PHL-PHO-PHL-PHO B. PHL-PHL-PHO-PHO C. PHO-PHL-PHL-PHO D. PHO-PHO-PHL-PHL
PHL-PHL-PHO-PHO
The side chain for Histidine has a pKR of around 6.0. Histidine's alpha carboxyl and alpha amino groups have pKas relatively similar to lysine's. What is the charge of ONLY the histidine side chain at pH 4? A. positive B. Negative C.No charge
Positive
You are studying two proteins. Protein A has 50 hydrophobic amino acids and Protein B has 75 hydrophobic amino acids. When observing the overall folding process in water, which of these two folding processes will have more positive contributions to the entropy changes in the protein? A. Protein A B. Protein B
Protein A
Select the FALSE statement A. RNA base pairs contain of one purine base and one pyrimidine base B. RNA contains a sugar-phosphate backbone C. RNA mutations are heritable (carried to the next generation) D. RNA contains the bases A, U, G and C E. None of the statements are FALSE
RNA mutations are heritable (carried to the next generation)
In rapidly metabolizing tissue, pH decreases slightly, affecting oxygen binding to hemoglobin. What is the effect of lower pH in the tissue on hemoglobin? A. Tighter binding of oxygen to hemoglobin B. Smaller P50 C. Release of oxygen from hemoglobin in the tissue D. all of the above are true
Release of oxygen from hemoglobin in the tissue
The bases shown in Model 1 and labeled 1, 2 and 3 are A. TAG B. UGA C. CAT D> TGA
TAG
Entropy2: Based on your in class activities which of the following is most true? A. The entropy of the water drives protein folding B. The entropy of the lipid drives lipid bilayer formation C. The entropy of the protein drives protein folding D. Noncovalent interactions provide the thermodynamic driving force for protein folding
The entropy of the water drives protein folding
Compare the shapes of the myoglobin and hemoglobin oxygen binding curves.
The myoglobin binding curve is rectangular hyperbola and the hemoglobin binding curve is sigmoidal (S-shaped)
Select the statement that is FALSE A. Base pairing occurs between A and T or G and C B. DNA is stabilized by base stacking interactions C. A:T base pairing has less interactions than G:C base pairing D. The sequence of the DNA does not affect the stability (melting temp) E. All of the above are true
The sequence of the DNA does not affect the stability (melting temp)
Below are CD spectra of a protein in sol-gels of increasing concentrations. The green CD spectrum is that obtained on the protein with no sol-gel and the purple spectra are those at higher sol gel concentrations. From these experiments you determine which of the following A. The sol gel does not influence protein structure. B. The sol gel is unfolding the protein C. The sol gel is stabilizing the protein
The sol gel is stabilizing the protein
If you have two Histidine side chains situated next to each other in a protein then you would expect which of the following. A. Their pKR to increase and favor the protonated form B. Their pKR to decrease and favor the protonated form C. Their pKR to increase and favor the deprotonated form D. Their pKR decrease and favor the deprotonated form
Their pKR decrease and favor the deprotonated form
Carbon dioxide and protons are both heterotropic effectors of hemoglobin. The concentration of both of these increase in rapidly metabolizing cells and affect oxygen binding to hemoglobin. A. These effectors primarily act to decrease the amount of oxygen picked up in the lungs. B. These effectors decrease the P50 of oxygen binding to hemoglobin C. These effectors cause hemoglobin to shift from the T (deoxy) state to the R (oxy) state. D. These effectors shift the oxygen binding curve to the right E. All of the above are true
These effectors shift the oxygen binding curve to the right
Which of the following techniques can be used to monitor the environment of tyrosines and tryptophans in proteins? A. UV-vis and CD B. fluorescence and CD C. UV-vis, fluorescence and CD D. UV-vis and fluorescence
UV-vis, fluorescence and CD
Where does oxygen bind to hemoglobin? A. adjacent to the heme group B. in the central cavity of hemoglobin C. to the bisphosphoglycerate D. all of the above are oxygen binding sites
adjacent to the heme group
What interactions help stabilize the structure of double stranded DNA? A. hydrogen bonds between bases B. base stacking C. interactions between the DNA and surrounding water D. all of the above stabilize the structure of DNA
all of the above stabilize the structure of DNA
A polylysine peptide has very different structures at different pH values. At pH 10 values above 10, polylysine forms an alpha helix structure, while a lower pH values it is unstructured. This is most likely because READ CAREFULLY A. At pH below 10 the side chains are deprotonated and do not repel each other as much B. At pH above 10 the side chains are more protonated and become attracted to each other C. at pH above 10 the hydroxides can stabilize the helical structure D. at pH below 10, the lysine side chains are more positive and all the positive charges destabilize the helical structure
at pH below 10, the lysine side chains are more positive and all the positive charges destabilize the helical structure
The amino acid lysine is a... A. basic amino acid B. acidic amino acid C. hydrophobic amino acid D. polar but always uncharged
basic amino acid
In protein MacDonald, there are 4 adjacent arginine's. You would predict that the pK's of the arginine side chains would ___________ as compared to the standard lysine pK (in table). A. decrease B. Increase C. Stay the same as the table
decrease
The lysine that normally forms a lysine-glutamic acid salt (ion-ion) bridge in the folded structure of Pierce is mutated to a glutamic acid. You would predict that this mutation (from lys to glu) would ____________ the stability of Pierce. A. decrease B. Increase
decrease
What effect would Ethidium bromide - DNA interactions have on the melting temperature of the DNA? A. stay the same B. decrease C. increase
decrease
In the protein Watkins there is a glutamic acid-lysine interaction (salt bridge) in the folded structure. However, it is known that copper also interacts with this same glutamic acid. Experiments performed on this protein in the presence of copper showed that the stability of the protein ________________ as compared to the stability of the protein in the absence of copper. A. decreases B. Increases
decreases
The entropy of the protein itself always ___________________ upon folding A. increases B. decreases
decreases
Using the information in question 3, lysine's side chain has a pKR of about 10 then lysine's side chains predominant form at pH=10.7 is? A. deprotonated B. protonated
deprotonated
The authors speculated that Myoglobin refolding required co-solvents because? A. the co-solvents disrupted the ordered water found inside the sol-gel B. the co-solvents specifically bound to myoglobin inducing folding C. the co-solvents provided additional noncovalent interactions that stabilized myoglobin
he co-solvents disrupted the ordered water found inside the sol-gel
This paper shows multiple Absorption spectra in the 350 nm - 700 nm region. These absorption spectra are from __________________ A. tyrosine and tryptophan in myoglobin B. heme
heme
Why does DNA denature into two strands at very high pH? A. high pH causes protonation of the bases which disrupts hydrogen bonding B. high pH causes deprotonation of bases which disrupts the non-covalent interactions C. high pH causes the phosphodiester bonds to be hydrolyzed
high pH causes deprotonation of bases which disrupts the non-covalent interactions
Compound A is more acidic than Compound B. That means that Compound A has a _________ Ka, and a __________ pKa than Compound B. A. higher, lower respectively B. lower, higher respectively C. not enough information
higher, lower respectively
The buffering region on a titration curve will be shown as a ? A. you can not tell from the titration curve B. horizontal region in titration curve C. could be vertical or horizontal region D. vertical region in titration curve
horizontal region in titration curve
The interactions between base pairs on complementary strands are A. hydrogen bonds B. covalent bonds C. vanderWaals interactions D. ion-ion interactions
hydrogen bonds
Under appropriate conditions, hemoglobin dissociates into its four subunits. What would the binding curve of an isolated subunit look like? A. sigmoidal like usual B. hyperbolic like myoglobin C. linear D. there will be no binding
hyperbolic like myoglobin
Ethidium Bromide fluorescence will _______________________ in the presence of DNA A. stay the same B. decrease C. increase
increase
After training at high altitude, athletes have a higher concentration of 2,3BPG. This results in A. better binding of oxygen to hemoglobin B. better binding of oxygen to myoglobin C. increased release of oxygen from hemoglobin D. increased release of oxygen from myoglobin
increased release of oxygen from hemoglobin
When a fluorophore moves from a polar to a nonpolar environment the fluorescence of the fluorophore? A. increases B. decreases
increases
Ethidium bromide is a fluorescent molecule that interacts with DNA. Based on the structure of ethidium bromide, how does it interact with the DNA molecule? A. interacts with the phosphate B. disrupts hydrogen bonding interactions between base pairs from each strand C. interacts with the sugar D. intercalates (inserts between) between adjacent base pairs
intercalates (inserts between) between adjacent base pairs
A ribosomal protein, L5 binds to a 5S-ribosomal RNA molecule. The specific secondary structure is show in FOB page 90. How would you expect the tyrosine residues of L5 to interact the RNA shown. Consider the structure of tyrosone side chain and the structure of the RNA. (The side chain of a tyrosine residue has a phenyl ring with an OH attached) A. helix only B. loop only C. it interacts with the loop better, but could interact weakly with the helix
it interacts with the loop better, but could interact weakly with the helix
Water or water-based solutions are the typical solvents used to study biomolecules because it can solvate many biomolecules. The molecules water can solvate include all of the following except: A. Salts B. carbohydrates C. lipids D. weak acids and bases
lipids
Myoglobin unfolding was studied in solution and in sol-gels. The authors found that myoglobin unfolding in the sol-gels occured at ________________________ pH than that required to unfold the myoglobin in solution. A. the same B. higher C. lower
lower
How was myoglobin unfolding induced in this paper? A. lowering pH B. increasing pH C. increasing temperature
lowering pH
The product of transcription is A. mRNA B. tRNA C. DNA D. Protein
mRNA
Why did the authors study myoglobin unfolding instead of some other protein? A. myoglobin unfolding is very well characterized B. myoglobin is the only protein that is stable in sol-gels C. myoglobin in the most important protein
myoglobin unfolding is very well characterized
If you know for any given protein folding reaction under biological conditions that the overall ΔH for folding is negative and the overall ΔS for folding is positive then the ΔG for folding is... A. negative B. positive C. you cant tell
negative
If you know that for a given folding reaction under biological conditions there is a small positive ΔH and a very large positive ΔS then you know that the ΔG for folding is... A. positive B. negative C. it depends on the sequence
negative
Can water pass pass through the center of a single protein alpha-helix? A. yes B. no C. it depends on the composition of the alpha helix
no
In a protein alpha helix, do the amino acid side chains face the inside or the outside of the helix? A. it depends on the helix B. inside C. outside
outside
In the Beer-Lambert A = E c l law the letter (l) stands for which of the following A. pathlength B. Extinction coefficient C. Concentration
pathlength
What does a nucleotide contain that a nucleoside does not contain A. Phosphate B. Ribose C. deoxyribose D. base
phosphate
Unfolding: The ΔH for the unfolding of a protein is? (consider just the protein itself) A. positive B. negative C. 0
positive
Circular dichroism can be used to study which of the following A. Distances of proteins from other proteins B. Three dimensional structure of proteins C. secondary structure of proteins and environments of aromatic amino acids
secondary structure of proteins and environments of aromatic amino acids
Some experiments were performed on myoglobin in a sol-gel. In these cases the diffusion of Mb was__________than that of myoglobin in solution. A. faster B. slower
slower
Which of the following double stranded DNA sequences would you expect to have the higher melting temperature? Strand 1: AAAAAAAAAAAATTTTTTATTTTTTT or Strand 2: AAAAAAAAAAAATTTTTTTTTTTTTT A. strand 1 B. strand 2
strand 2
If an enzyme used NADH to form products then what would happen over time as the enzyme made products. A. the A340 nm would increase and NAD+ would be formed B. the A340 nm would increase and NADH would be formed C. the A340 nm would decrease and NADH would be formed D. the A340 nm would decrease and NAD+ would be formed
the A340 nm would decrease and NAD+ would be formed
The strongest stacking interactions in Model 1 are: A. between the base labeled 1 and the base labeled 2 B. the base labeled 2 and the base labeled 3 C. the base labeled 1 and the base on the complementary strand D. the base labeled 3 and the base on the complementary strand
the base labeled 2 and the base labeled 3
The paper showed multiple UV-vis absorption spectra that gave information about myoglobin folding and unfolding. The UV-vis absorption spectra followed changes in the _____________________ environment. A. tryptophans B. the heme C. tyrosine and tryptophans D. tyrosines
the heme
When an amino acid solution is at a pH equal to its isoelectric point then you know... A. the amino acid has a +2 charge B. the amino acid is positively charged C. the net charge on amino acid is 0 D. the amino acid is negatively charged
the net charge on amino acid is 0
Based on what you learned by evaluating the experimental data presented in FOB 20, which is more important in determining the melting point of a DNA sequence? A. the order of the bases in the sequence B. the composition (total number of A,T, C, or G) in the sequence
the order of the bases in the sequence
The phosphodiester bond connects A. the sugar to the base B. one sugar to the phosphate oxygen C. two sugars to a phosphate
two sugars to a phosphate