Biochemistry Unit 1
Urea (NH2CONH2) dissolves readily in water and the beaker containing the dissolved compound is cold to the touch. What conclusions can you make about the sign of the enthalpy change and the entropy change for this process? ΔG = ΔH - TΔS 1. (+) ΔH; (-) ΔS 2. (+) ΔH; (+) ΔS 3. (-) ΔH; (-) ΔS 4. (-) ΔH; (+) ΔS
(+) ΔH; (+) ΔS
List five differences between prokaryotes and eukaryotes.
(1) Prokaryotes do not have a well-defined nucleus, but eukaryotes have a nucleus marked off from the rest of the cell by a double membrane. (2) Prokaryotes have only a plasma (cell) membrane; eukaryotes have an extensive internal membrane system. (3) Eukaryotic cells contain membrane-bounded organelles, while prokaryotic cells do not. (4) Eukaryotic cells are normally larger than those of prokaryotes. (5) Prokaryotes are single celled organisms, while eukaryotes can be either single-celled or multicellular.
Calculate the pH of a buffer solution prepared by mixing 75 mL of 1.0 M lactic acid and 25 mL of 1.0 M sodium lactate.
(75 mL)(1 M) = (100 mL)(X) -- X = .75 M (25 mL)(1 M) = (100 mL)(X) -- X = .25 M pH = 3.86 + log ([sodium lactate]/[lactic acid]) pH = 3.86 + log (.25/.75) pH = 3.38
In each of the following two groups of amino acids, which amino acid would be the easiest to distinguish from the other two amino acids in the group, based on a titration? (a) gly, leu, lys (b) glu, asp, ser
(a) Lysine - because of the side-chain amino group (b) Serine - because of the lack of a side chain carboxyl
Rationalize the following observations. (a) Serine is the amino acid residue that can be replaced with the least effect on protein structure and function. (b) Replacement of tryptophan causes the greatest effect on protein structure and function. (c) Replacements such as Lys--Arg and Leu--Ile usually have very little effect on protein structure and function.
(a) Serine has a small side chain that can fit in any relatively polar environment. (b) Tryptophan has the largest side chain of any of the common amino acids, and it tends to require a non-polar environment. (c) Lysine and arginine are both basic amino acids; exchanging one for the other would not affect the side-chain pKa in a significant way. Similar reasoning applies to the substitution of a non-polar isoleucine for a non-polar leucine.
What is the basis for the separation of proteins by the following techniques? (a) gel-filtration chromatography (b) affinity chromatography (c) ion-exchange chromatography (d) reverse phase HPLC
(a) Size (b) Specific ligand-binding ability (c) Net charge (d) Polarity
What is the net charge of this peptide at pH 1: Glu-Thr-Val-Asp-Ile-Ser-Ala
+1
Assuming a temperature of 25°C and an entropy change of +75 J/K/mol, the enthalpy change for a ΔG value of -11.0 kJ/mol is 1. +15.2 kJ/mol 2. +22.5 kJ/mol 3. +11.3 kJ/mol 4. -17.4 kJ/mol 5. none of the above
+11.3 kJ/mol Units in kJ/mol (make sure units are consistent) ΔG = ΔH - TΔS T (K) -- 25 C = 298 K ΔG (J/mol) -- -11,000 J/mol -11,000 = ΔH - (298 K x 75 J/K/mol) ΔH = 11,350 J/mol -- 11.3 kJ/mol
What is the net charge on this amino acid at a pH of 5? G-A-M-E-T-H-R-N-E-S A. +2 B. +1 C. 0 D. -1 E -2
0 G - pH < pKa -- protonated (free amine so look at pK2) -- +1 A M E - deprotonated -- -1 (pK3) T H - protonated -- +1 (pK3) R - protonated -- +1 (pK3) N E - deprotonated -- -1 S - pH > pKa -- deprotonated (free carboxy group so look at pK1) -- -1
Calculate the hydroxide ion concentration, [OH-], for intracellular fluid (liver), pH 6.9. Express answer in units of μμM to 2 decimal places.
0.08 14 - 6.9 = 7.1 -- [OH-] = 10^-7.1
Calculate the hydrogen ion concentration, [H+], for saliva (pH 6.5). Express answer in units of μμM to 2 decimal places.
0.32 [H+] = 10^-6.5
Which of the following are spontaneous processes? Explain your answer for each process. 1. The hydrolysis of ATP to ADP and 2. The oxidation of glucose to CO2 and H2O by an organism 3. The phosphorylation of ADP to ATP 4. The production of glucose and O2 from CO2 and H2O in photosynthesis
1 and 2 are spontaneous - represent an increase in disorder/entropy and -dG
Which of the molecules below is (are) amphipathic and can form micelles?
1. H3C-(CH2)11-N+(CH3)2-CH2COO- 2. A triglyceride Both are amphipathic, but (1) forms a micelle while (2) forms a bilayer
Design an experiment to purify protein X on an anion-exchange column. Protein X has an isoelectric point of 7.0.
1. Set up an anion-exchange column, such as Q-sepharose (quaternary amine). 2. Run the column at pH 8.5, a pH at which the protein X has a net negative charge. 3. Put a homogenate containing protein X on the column and wash with the starting buffer. Protein X will bind to the column. 4. Elute by running a salt gradient.
What is the [H+] for urine (pH ~5.5)?
3.2 x 10^-6 M
Calculate the pH of a solution prepared by mixing 300 mL of 0.25 M sodium hydrogen ascorbate (C6H7O6-Na+) and 150 mL of 0.2 M HCl. The pK1 of ascorbic acid (C6H8O6) is 4.04. 1. 4.04 2. 4.64 3. 4.22 4. 5.21
4.22 pH = pKa + log (A-/HA) 0.3L x 0.25M = 0.075 mol A- 0.15L x 0.2M = 0.03 mol H+ A-: 0.075-0.03 = 0.045 mol A- HA: 0.03 mol H+ = 0.03 mol HA ----The amount of H+ added is equal to the amount of HA generated pH = 4.04 + log(0.045/0.03)
What is the pH of a solution made by mixing equal volumes of 1 M sodium acetate and 1 M acetic acid? (The pK of acetic acid is 4.76.) 1. 1 2. 3.76 3. 4.76 4. 5.76
4.76
How many H-bond acceptor atoms are present in Prozac?
5 Electronegative elements with lone pairs can form H bonds 3 F 1 N 1 O (If it asks how many bonds it can make, F(3x3), O(2) and N(1) -- 12 + a donor from the N-H bond ------- 13 bonds)
What is the [CH3COO-]/[CH3COOH] ratio in an acetate buffer at pH 5.00?
5.00 = 4.76 + log ([CH3COO-]/[CH3COOH]) 0.24 = log ([CH3COO-]/[CH3COOH]) [CH3COO-]/[CH3COOH] = 10^0.24 = 1.7/1
How would you prepare 1 L of a 0.050 M phosphate buffer at pH 7.5 using crystalline K2HPO4 and a solution of 1.0 M HCl?
7.5 = 7.2 + log ([HPO4 2-]/[H2PO4 -]) = 2/1 -- need 1/3 of it to be converted into acid form Weigh out 8.7g of K2HPO4 (0.05 mol, based on a formula weight of 174 g/mol), dissolve it in a small quality of distilled water, add 16.7 mL of 1 M HC; (gives 1/3 of 0.05 mol of hydrogen ion, which converts 1/3 of the 0.05 mol of HPO4 2- to H2PO4 -), and dilute the resulting mixture to 1 L.
Urea is an organic compound widely used as a fertilizer. Its solubility in water allows it to be made into aqueous fertilizer solutions and applied to crops in a spray. What is the maximum theoretical number of water molecules with which one urea molecule can hydrogen bond? (Exact whole number required.)
8 O molecule has 2 lone pairs (4 abilities to pair) - 4 hydrogens can bond Each N molecule has 1 lone pair -- there are 2 N atoms and therefore 4 abilities to pair - 4 hydrogens can bond
What is the ratio of TRIS/TRIS-H+ in a TRIS buffer at pH 8.7?
8.7 = 8.3 + log ([TRIS]/[TRIS-H+]) 0.4 = log ([TRIS]/[TRIS-H+]) [TRIS]/[TRIS-H+] = 10^0.4 = 2.5/1
Which of the following is true? - The peptide bonds in the β-sheet are extended. - The peptide bonds in the α-helix coil back on themselves. - Both α-helices and β-sheets can be found as part of tertiary structure. - All of these
????
What is a b-bulge?
A b-bulge is a common non-repetitive irregularity found in antiparallel b-sheets. A misalignment occurs between strands of the b-sheet, causing one side to bow outward.
What are two ways that a compound can be eluted from an ion-exchange column? What could be the advantages or disadvantages of each?
A compound can be eluted by 1) raising the salt concentration or 2) changing the pH. Salt is cheap, but it might not be as specific for a particular protein. Changing the pH may be more specific for a tight pI range, but extremes of pH may also denature the protein.
In any form of chromatography, how will a compound which interacts more strongly with the stationary phase elute compared to one that interacts less strongly? 1. A compound interacting more strongly will elute earlier than one with weaker interactions. 2. A compound interacting more strongly will elute later than one with weaker interactions. 3. The order of elution has nothing to do with interactions with the stationary phase, but with interactions with the mobile phase.
A compound interacting more strongly will elute later than one with weaker interactions.
An amino acid mixture consisting of phenylalanine, glycine, and glutamic acid is to be separated by HPLC. The stationary phase is aqueous and the mobile phase is a solvent less polar than water. Which of these amino acids will move the fastest? Which one will move the slowest?
A non-polar mobile solvent will move the non-polar amino acids fastest, so phenylalanine will be the first to elute, followed by glycine and then glutamic acid.
What is the difference between a primary antibody and a secondary antibody?
A primary antibody is specific for a target protein that a researcher is looking for. A secondary antibody will react with the primary antibody. The secondary antibody carries the tag that makes the complex visible.
What is a reverse turn? Draw two types of reverse turns.
A reverse turn is a region of a polypeptide where the direction changes by about 180 degrees. There are two kinds—those that contain proline and those that do not (find proline and glycine).
Which of the following shows the correct order from most simple to most complex: 1. atom, molecule, organelle, macromolecule 2. molecule, atom, macromolecule, organelle 3. tissue, cell, organ 4. atom, macromolecule, tissue, organ
A. atom, macromolecule, tissue, organ
Identify the conjugate acids and bases in the following pairs of substances: A. (CH3)3NH+/(CH3)3N B. +H3N-CH2-COOH/+H2N-CH2-COO- C. +H3N-CH2-COO-/H2N-CH2-COO- D. -OOC-CH2-COOH/-OOC-CH2-COO- E. -OOC-CH2-COOH/HOOC-CH2-COOH
Acid (CB) - donor Base (CA) - acceptor A. conjugate acid/conjugate base B. conjugate acid/conjugate base C. conjugate acid/conjugate base D. conjugate acid/conjugate base E. conjugate base/conjugate acid
Draw structures of the following amino acids, indicating the charged form that exists at pH 4: histidine, asparagine, tryptophan, proline, and tyrosine.
All of them have NH3+ and COO- in the amino and carboxyl groups. Histidine also has an NH+ is its imidazole ring.
In which of the following processes does the entropy increase? In each case, explain why it does or does not increase. 1. A bottle of ammonia is opened. The odor of ammonia is soon apparent throughout the room. 2. Sodium chloride dissolves in water. 3. A protein is completely hydrolyzed to the component amino acids.
All the answers have an increase in entropy/disorder. The final state is more random than the initial state.
Identify the functional group(s) in the following molecule: 1. Carboxyl 2. Amide 3. Ester 4. Both A and B 5. Both A and C
Amide
Identify the major biomolecule below. 1. Amino acid 2. Nucleotide 3. Lipid 4. Carbohydrate
Amino acid
Are amino acids other than the 20 usual amino acids found in proteins? If so, how are such amino acids incorporated into proteins? Give an example of such an amino acid and a protein in which it occurs.
Amino acids other than usual are post-translational modifications of normal amino acids. Hydroxylysine and hydroxyproline are in collagen. Thyroxine is in the thyroid.
Match each entry in Column a with one in Column b; Column a shows the names of some important functional groups, and Column b shows their structures.
Amino group -- CH3CH2NH2 Carbonyl ketone -- CH3COCH3 Hydroxyl group -- CH3OH Carboxyl group -- CH3COOH Carbonyl aldehyde -- CH3CH2CHO Thiol group -- CH3SH Ester -- CH3COOCH2CH3 Double bond -- CH3CH=CHCH3 Amide -- CH3CON(CH3)2 Ether -- CH3CH2OCH2CH3
Aspirin is an acid with a pKa of 3.5; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine. Electrically neutral molecules can pass through a membrane more easily than can charged molecules. Would you expect more aspirin to be absorbed in the stomach, where the pH of gastric juice is about 1, or in the small intestine, where the pH is about 6? Explain your answer.
Aspirin is electrically neutral at the pH of the stomach and can pass through the membrane more easily than in the small intestine.
A reaction at 23 C has ΔG = 1 kJ/mol. Why might this reaction become spontaneous at 37 C?
Assuming the value of ΔS is positive, an increase in temperature increases the -ΔG contribution of the entropy component to the overall energy change.
Why might you expect to find some Hb F in adults who are afflicted with sickle-cell anemia?
Because people with sickle-cell disease are chronically anemic, some cells with fetal Hb are produced to help overcome the impaired oxygen delivery system.
Carbonic acid (H2CO3) has the following pKa values: pK1 = 6.4 and pK2 = 10.2. Indicate which species are present at a pH of 6.4. 1. H2CO3 2. HCO3- 3. CO32- 4. Both A and B 5. Both B and C
Both A and B At 6.4, the molecule is exactly half ionized, so the original form is there along with the deprotonated form.
Identify the functional group(s) in the following molecule: 1. Carboxyl 2. Amide 3. Amine 4. Both A and B 5. Both A and C
Both A and C
Sephadex G-75 has an exclusion limit of 80,000 molecular weight for globular proteins. If you tried to use this column material to separate alcohol dehydrogenase (MW 150,000) from b-amylase (MW 200,000), what would happen?
Both proteins would elute in the void volume together and would not be separated.
Can you expect to separate the peptides by electrophoresis?
Both the C-terminal and the N-terminal of the open-chain peptide can be charged at appropriate pH values, which is not the case with the cyclic peptide. This can provide a basis for separation by electrophoresis.
Define buffering capacity. How do the following buffers differ in buffering capacity? How do they differ in pH? Buffer a: 0.01 M Na2HPO4 and 0.01 M NaH2PO4 Buffer b: 0.10 M Na2HPO4 and 0.10 M NaH2PO4 Buffer c: 1 M Na2HPO4 and 1 M NaH2PO4
Buffer capacity - based on the amounts of the acid and base forms present in the buffer solution. - A solution with a high buffering capacity can react with a large amount of added acid or base without drastic changes in pH. - A solution with a low buffering capacity can react with only comparatively small amounts of acid or base before showing changes in pH. - The more concentrated the buffer, the higher the buffer capacity. Buffer a has 1/10 the capacity of b, and b has 1/10 the capacity of c. But all three have the same pH because they have the same relative amounts of acid and base forms.
A solution is 0.050 M, even though the concentration of neither the free base nor the conjugate acid is 0.050 M. Why is 0.050 M the correct concentration to report?
Buffer concentrations are typically reported to be the sum of the two ionic forms.
Rank the melting points of the following compounds. A. H3C-CH2-O-CH3 B. H3C-C(=O)-NH2 C. H2N-C(=O)-NH2 D. H3C-(CH2)3-CH3 E. H3C-CH2-CH=O
C > B > E > A > D
All of the following bonds are important in biomolecules, except: 1. C−Cl 2. C−H 3. C−N 4. O−H 5. O−P
C-Cl
Which of the following molecules will not form hydrogen bonds? 1. CH4 2. NH3 3. H2O 4. HF
CH4
Which of the following molecules has polar bonds but is itself NOT polar? 1. NH3 2. CO2 3. CH4 4. H2O
CO2 Carbon dioxide has polar bonds - an unequal distribution of electrons shared between carbon and oxygen. However, it is a linear molecule and the alignment of the bonds means that it is nonpolar overall.
Why is the development of catalysis important to the development of life?
Catalysis allows living organisms to carry out chemical reactions much more efficiently than without catalysts.
The following cellular component is the defining component of most plant cells: 1. Nucleus 2. Ribosomes 3. Chloroplasts 4. Mitochondria 5. Cell walls
Chloroplasts
Which of the following would be the strongest acid? 1. Citrate, pK 4.76 2. Succinic acid, pK 4.21 3. Succinate, pK 5.64 4. Citric acid, pK 3.13
Citric acid - Lowest pKa is the stronger acid
Why was the development of a coding system important to the development of life?
Coding allows for reproduction of cells.
Gelatin is a food product obtained from the thermal degradation of collagen. Powdered gelatin is soluble in hot water and forms a gel upon cooling to room temperature. Why is collagen nutritionally inferior to other types of protein?
Collagen is made of a repeating sequence of X-Pro/Hyp- Gly; gelatin is therefore is nutritionally inferior because it would then generally lack all 20 amino acids and not be considered a complete protein.
Buffering capacity is directly proportional to which of the following factors? 1. Molecular weight of the buffer 2. Concentration of the conjugate acid of the buffer 3. Concentration of the conjugate base of the buffer 4. Concentration of both components of the buffer
Concentration of both components (A- and HA) of the buffer
The terms configuration and conformation appear in descriptions of molecular structure. How do they differ?
Configuration - the position of groups due to covalent bonding (ex. cis and trans isomers and optical isomers) Conformation - the positioning of groups in space due to rotation around single bonds (ex. the difference between the eclipsed and staggered conformations of ethane)
Is there any amino acid that could serve as a buffer at pH 8? If so, which one?
Cysteine is pKa 8.33 - range from 7.33 to 9.33 Asparagine is pKa 8.80 - range from 7.80 to 9.80 Lysine is pKa 8.95 - range from 7.95 to 9.95 (Asp and Lys are possible but near the end of the range, so Cys is best)
How do D-amino acids differ from L-amino acids? What biological roles are played by peptides that contain D-amino acids?
D- and L-amino acids have different stereochemistry around the central carbon. Peptides that contain D-amino acids are found in bacterial cell walls and in some antibiotics.
In oxygenated hemoglobin, pKa = 6.6 for the histidines at position 146 on the b-chain. In deoxygenated hemoglobin, the pKa of these residues is 8.2. How can this piece of information be correlated with the Bohr effect?
Deoxygenated hemoglobin is a weaker acid (has a higher pKa) than oxygenated hemoglobin. In other words, deoxygenated hemoglobin binds more strongly to H+ than does oxygenated hemoglobin. The binding of H+ (and of CO2) to hemoglobin favors the change in quaternary structure to the deoxygenated form of hemoglobin.
Which form of salicyclic acid (pK ~3.0) predominates at the pH of the gastric lavage, pH 8.5?
Deprotonated (pH > pK)
List the three types of van der Waals forces in decreasing order of strength.
Dipole-dipole > dipole-induced dipole > induced dipole-induced dipole
Common proteins are polymers of different 20 amino acids. How big a protein (how many amino acid residues) would be necessary to have an Avogadro's number of possible sequences?
Eighteen residues would give 20^18, or 2.6 x 10^23 possibilities. Thus, 19 residues would be necessary to have at least Avogadro's number (6.022 x 10^23) of possibilities.
What is the order of elution of proteins on a gel-filtration column? Why is this so?
Elution from larger to smaller Larger proteins are excluded from the interior of the gel bead so they have less available column space to travel. Essentially, they travel a shorter distance and elute first.
How does the oxygen-binding curve of fetal hemoglobin differ from that of adult hemoglobin?
Fetal hemoglobin binds oxygen more strongly than adult hemoglobin
What are the requirements for molecules to form hydrogen bonds? (What atoms must be present and involved in such bonds?)
For a bond to be called a hydrogen bond, it must have a hydrogen covalently bonded to O, N, or F. This hydrogen then forms a hydrogen bond with another O, N, or F.
Identify the charged amino acids in the following peptide sequence at pH 1: Glu-Thr-Val-Asp-Ile-Ser-Ala
Glu Free amine group on Glu is ionizable, and the rest are neutral from protonation. pH 1 < any pKa -- more protonated
What is the direct cause of sickle-cell anemia (think primary structure)?
Glu mutates to Val at position 6 on the b-chain
How many water molecules could hydrogen-bond directly to the molecules of glucose, sorbitol, and ribitol?
Glucose = 17 Sorbitol = 18 Ribitol = 15 Each alcohol group can bond to three water molecules and the ring oxygen binds to two. The sugar alcohols bind more than the corresponding sugars.
Identify the functional groups in the following compounds.
Glucose: 5 hydroxyl and 1 aldehyde Triglyceride: 3 ester linkages Peptide: 1 amino, 2 peptide bonds and 1 carboxyl Vitamin A - 5 double bonds and 1 hydroxyl
Calculate the isoelectric point of each of the following amino acids: glutamic acid, serine, histidine, lysine, tyrosine, and arginine. pI = pKa1+pKa2/2 for diprotic/uncharged pI = pKa1 + pKa3/2 for acids pI = pKa2 + pKa3/2 for bases
Glutamate - 3.25 (acid) Serine - 5.68 (uncharged) Histidine - 7.58 (base) Lysine - 9.75 (base) Tyrosine - 5.65 (uncharged) Arginine - 10.75 (base)
Predict the predominant ionized forms of the following amino acids at pH 7: glutamic acid, leucine, threonine, histidine, and arginine.
Glutamate - NH3+, COO- and R-chain COO- Leucine - NH3+, COO- Threonine - NH3+, COO- Histidine - NH3+, COO- Arginine - NH3+, COO- and R-chain NH2+
An amino acid mixture consisting of lysine, leucine, and glutamic acid is separated by cation exchange at pH 3.5. Given the table of pKa values below, which of these amino acids will be the first to elute from the column?
Glutamic acid (then leucine and lysine)
An amino acid mixture consisting of lysine, leucine, and glutamic acid is to be separated by ion-exchange chromatography, using a cation-exchange resin at pH 3.5, with the eluting buffer at the same pH. Which of these amino acids will be eluted from the column first? Will any other treatment be needed to elute one of these amino acids from the column?
Glutamic acid will be eluted first because the column pH is close to its pI. Leucine and lysine will be positively charged and will stick to the column. To elute leucine, raise the pH to around 6. To elute lysine, raise the pH to around 11.
Which of the following has no L or D configuration? - Glyceraldehyde - Proline - Glycine - All of these have an L or D configuration
Glycine
Two amino acids frequently found in reverse turns are
Glycine and proline
Glycine is a highly conserved amino acid residue in proteins (i.e., it is found in the same position in the primary structure of related proteins). Suggest a reason why this might occur.
Glycine is frequently a conserved residue because its side chain is so small (H) that it can fit into spaces that will not accommodate larger ones.
Why must glycine be found at regular intervals in the collagen triple helix?
Glycine is the only residue small enough to fit at crucial points in the collagen triple helix.
Which of the following is a correct listing of electronegativity values, from low to high? 1. C, H, O, N 2. N, H, O, C 3. H, C, N, O 4. H, C, O, N
H, C, N, O
What is the conjugate base of the weak acid H3BO3? 1. BO33- 2. HBO32- 3. H2BO3-
H2BO3-
You wish to prepare 0.5 L of 0.2 M phosphate buffer at pH 7.7. Which is the relevant equation and pKa? 1. H3PO4 → H2PO4- + H+ pKa 2.2 2. HPO42- → PO43- + H+ pKa 12.4 3. H2PO4- → HPO42- + H+ pKa 6.8 4. None of the above
H2PO4- → HPO42- + H+ pKa 6.8 The best buffering components would be those associated with a pKa closest to the target pH.
What would be the pH of the solution in the previous question if you were to add 3 mL more of 1 M HCl?
HCl = 0.006 mols TRIS + H+ -- TRIS-H+ TRIS-H+ = 0.006 + 0.005 = 0.014 mol TRIS = 0.005 - 0.006 ~ 0 mol pH = 8.3 + log (0/0.014) -- log 0 doesn't exist We have used up the buffer capacity of TRIS is we add more acid.
The oxygen-binding curves for normal hemoglobin (Hb A) and a mutant hemoglobin (Hb Great Lakes) are shown in the figure below. Which of the two hemoglobins is most efficient at delivering oxygen from arterial blood (pO2 = 75 torr) to active muscle (pO2 = 20 torr)? 1. Hb A 2. Hb Great Lakes 3. They have the same affinity
Hb A More readily lets oxygen go in the tissue (low affinity... in the tissue)
You recall reading in the medical literature about a dramatic new drug treatment for sickle cell anemia, and you'd like to try it on this patient. The drug is hydroxyurea, and is thought to function by stimulating the afflicted person's synthesis of fetal hemoglobin. Why would increasing the synthesis of fetal hemoglobin result in alleviating the symptoms of sickle cell anemia?
Hb F has alpha-2 gamma-2 chain, while the sickle cell mutation is present in the beta chain of Hb A. That being said, the mutation cannot occur in Hb F because there is no beta chain present and instead a gamma expression.
The oxygen-binding curves for normal hemoglobin (Hb A) and a mutant hemoglobin (Hb Great Lakes) are shown in the figure below. Which of the two hemoglobins has a higher affinity for oxygen when pO2 = 20 torr? 1. Hb A 2. Hb Great Lakes 3. They have the same affinity
Hb Great Lakes Curve shifted left - binds oxygen at a lower concentration = higher affinity
If the following mixture of proteins was applied to a size-exclusion chromatography column, what would be the order of elution? Proteins with molecular weights: myoglobin (17.7 kDa), hemoglobin (64.5 kDa), lysozyme (14.3 kDa) and triose phosphate isomerase (57.4 kDa)
Hemoglobin Triose phosphate isomerase Myoglobin Lysozyme The larger molecules elute first and quicker
In oxygenated Hb, His 146 on the ββ-chain has pKa = 6.6. In deoxygenated Hb, would the pKa value be higher, lower, or the same? 1. Higher 2. Lower 3. The same
Higher This has the do with the Bohr effect and the following equilibrium: HbH+ + O2 <--> HbO2 + H+ Deoxygenated Hb evidently has a higher affinity for protons - so would be less likely to become deprotonated. This means that the pKa value must increase.
Which amino acid takes on a positive charge when the R-group gains a proton? - Glutamic Acid - Glutamine - Tyrosine - Histidine - Glycine
Histidine His is basic charged, and bases accept protons
Predict the predominant forms of histidine, asparagine, tryptophan, proline, and tyrosine at pH 10.
Histidine: imidazole is deprotonated, a-amino group is predominantly deprotonated. Asparagine: a-amino group is deprotonated. Tryptophan: a-amino group is predominantly deprotonated. Proline: a-amino group is partially deprotonated. Tyrosine: a-amino group is predominantly deprotonated, phenolic hydroxyl is approximately a 50-50 mixture of protonated and deprotonated forms.
The typical order for the major steps of enzyme isolation would be (from first to last): 1. Homogenization, salt fractionation, electrophoresis, column chromatography. 2. Homogenization, column chromatography, salt fractionation, electrophoresis. 3. Homogenization, salt fractionation, column chromatography, electrophoresis. 4. Salt fractionation, homogenization, electrophoresis, column chromatography. 5. Homogenization, electrophoresis, salt fractionation, column chromatography.
Homogenization Salt fractionation Column chromatography Electrophoresis
Which of the non-covalent interactions listed below is associated with the strongest force in aqueous solution? 1. Dipole-induced dipole 2. Hydrophobic interactions 3. Hydrogen bonding 4. Van der Waals forces
Hydrogen bonding
The type of bonding labeled "N" in the figure below is: 1. Hydrogen bonding of the peptide backbone 2. Covalent bonding involving the R-groups 3. Hydrophobic interactions 4. Metal ion coordination 5. Electrostatic attraction
Hydrogen bonding of the peptide backbone A connection between the backbone and not side chains (so they are not covalent bonds between R-groups) Fig 8 in Lecture 4 on Squarecap for reference
Salting out with ammonium sulfate is based upon proteins interacting with other proteins via - hydrogen bonds. - ionic bonds. - hydrophobic interactions. - disulfide bonds.
Hydrophobic interactions
For each of the following, name an amino acid in which the R group contains it: a hydroxyl group, a sulfur atom, a second chiral carbon atom, an amino group, an amide group, an acid group, an aromatic ring, and a branched side chain.
Hydroxyl group - serine Sulfur - cysteine Second chiral carbon - isoleucine Amino group - lysine Amide group - asparagine Acid - glutamate Aromatic ring - phenylalanine Branched side chain - leucine
What is the purpose of treating a sickle-cell patient with hydroxyurea?
Hydroxyurea stimulates the bone marrow to produce fetal hemoglobin. Fetal hemoglobin has no b-chain, so the effect of the interactions of those chains is reduced in the presence of increased Hb F.
A frequently recommended treatment for hiccups is to hold one's breath. The resulting condition, hypoventilation, causes buildup of carbon dioxide in the lungs. Predict the effect on the pH of blood.
Hypoventilation decreases the pH of blood (makes it more acidic). Hyperventilation raises blood pH (making it more basic) because it removes CO2 from the blood.
Under what circumstance is a molecule that has a dipole not a polar molecule?
If the dipole is cancelled out by another of equal and opposite orientation. The classic example is CO2. Each carbon-oxygen bond is a dipole, but the two cancel each other out and the molecule is non-polar.
Would you consider HCO3-/H2CO3 (pK 6.1) a good buffer system according to the basic rule for effective buffers (blood pH is ~7.4)? Why or why not? How does it work?
If the pK of the buffer is 6.1, its effective range is from a pH of 5.1 to a pH of 7.1; the normal pH of blood is outside of the effective buffering range. But since the concentrations and components in a living system are always changing, the buffer is good because of this dynamic equilibrium system.
When would you choose to use a Potter-Elvehjem homogenizer instead of a blender?
If you needed to maintain the structural integrity of the subcellular organelles, a Potter-Elvejhem homogenizer would be better because it is more gentle. The tissue, such as liver, must be soft enough to use with this device.
We usually say that a perfect buffer has its pH equal to its pKa. Give an example of a situation in which it would be advantageous to have a buffer with a pH 0.5 unit higher than its pKa.
In a buffer with the pH above the pKa, the base form predominates. This would be useful as a buffer for a reaction that produces H+ because plenty of the base form will be available to react with the hydrogen ion produced.
Why is the order of separation based on size opposite for gel filtration and gel electrophoresis, even though they often use the same compound to form the matrix?
In a polyacrylamide gel used for gel-filtration chromatography, the larger proteins can travel around the beads, thereby having a shorter path to travel and therefore eluting faster. With electrophoresis, the proteins are forced to go through the matrix, so the larger ones travel more slowly because there is more friction.
Describe the effect of 2,3-bisphosphoglycerate on the binding of oxygen by hemoglobin.
In the absence of 2,3-bisphosphoglycerate, the binding of oxygen by hemoglobin resembles that of myoglobin, characterized by lack of cooperativity. 2,3-Bisphosphoglycerate binds at the center of the hemoglobin molecule, increases cooperativity, stabilizes the deoxy conformation of hemoglobin, and modulates the binding of oxygen so that it can easily be released in the capillaries.
Describe the Bohr effect.
In the presence of H+ and CO2, both of which bind to hemoglobin, the oxygen-binding capacity of hemoglobin decreases.
What is the role of the disulfide bond in oxytocin and vasopressin?
It is responsible for the cyclic structure of both oxytocin and vasopressin.
Which of the following amino acid substitutions would be least likely to have a deleterious effect on protein function?
Leu changes to Ile Like substitution because they are similar amino acids
Assume the oligopeptide with the amino acid sequence: ALPHAHELICKS, forms one continuous α-helix. The carbonyl oxygen of the glutamic acid residue is hydrogen bonded to the amide nitrogen of 1. leucine 2. isoleucine 3. cysteine 4. lysine
Lysine Glu is E and Lys is K -- the carbonyl oxygen in 3/4 structures bond to the amide nitrogen af the 4th amino acid after it
A phosphate buffer is prepared with KH2PO4 at 0.02 M and K2HPO4 at 0.03 M. What is the concentration of phosphate buffer?
M = 0.05 Buffer concentration = acid + conjugate base
A sample of peptide of unknown sequence was treated with trypsin to produce the following smaller peptides: 1) Met-Val-Ser-Thr-Lys 2) Val-Ile-Trp-Thr-Leu-Met-Ile 3) Leu-Phe-Asn-Glu-Ser-Arg Another sample of the same peptide was treated with chymotrypsin and gave the following smaller peptides: 1) Asn-Glu-Ser-Arg-Val-Ile-Trp 2) Thr-Leu-Met-Ile 3) Met-Val-Ser-Thr-Lys-Leu-Phe What is the sequence of the original peptide?
M-V-S-T-K-L-F-N-E-S-R-V-I-W-T-L-M-I
Which one of the following sequences of five amino acids would most likely be located in the interior of a globular soluble protein? 1. Tyr-Phe-Glu-Asn-Leu 2. Val-Ala-Val-Glu-Val 3. Met-Phe-Pro-Ile-Leu 4. Glu-Asn-Ser-Thr-Gln 5. Met-Cys-Pro-His-Tyr
Met-Phe-Pro-Ile-Leu
Deduce the sequence of the original peptide. Trypsin: Met-Val-Ser-Thr-Lys Val-Ile-Trp-Thr-Leu-Met-Ile Leu-Phe-Asn-Glu-Ser-Arg Chymotrypsin: Asn-Glu-Ser-Arg-Val-Ile-Trp Thr-Leu-Met-Ile Met-Val-Ser-Thr-Lys-Leu-Phe
Met-Val-Ser-Thr-Lys-Leu-Phe-Asn-Glu-Ser-Arg-Val-Ile-Trp-Thr-Leu-Met-Ile Find sequences corresponding in each (Chymo: Lys-Leu-Phe so that's the sequence) Tryp does not cleave Ile, so that's the C-terminus
Which organelles are the sites of energy-yielding reactions?
Mitochondria (ATP production)
If you have 100 mL of a 0.10 M TRIS buffer at pH 8.3 and you add 3.0 mL of 1 M HCl, what will be the new pH?
Moles of buffer: 0.10 = x/0.1 -- x = 0.01 mol [HA] = [A-] = 0.005 mol (half of 0.01) HCl = 0.003 mols TRIS-H+ --> TRIS + H+ TRIS-H+ = 0.003 + 0.005 = 0.008 moles TRIS = 0.005 - 0.003 = 0.002 moles pH = 8.3 + log (0.002/0.008) pH = 7.7
List the five kingdoms into which living organisms are divided, and give at least one example of an organism belonging to each kingdom.
Monera - bacteria and cyanobacteria Protista - Euglena and Volvox Fungi - molds and mushrooms Plantae - club mosses and oak trees Animalia - spiders and dogs
What is the highest level of organization in myoglobin? In hemoglobin?
Myoglobin - tertiary Hemoglobin - quaternary
You need to carry out an enzymatic reaction at pH 7.5. A friend suggests a weak acid with a pKa of 3.9 as the basis of a buffer. Will this substance and its conjugate base make a suitable buffer? Why or why not?
No - this buffer has a range of 2.9 to 4.9 (and pH 7.5 does not fall under that), so it does not buffer effectively at pH 7.5
Identify the non-polar amino acids and the acidic amino acids in the following peptide: Glu-Thr-Val-Asp-Ile-Ser-Ala
Non-polar - Val, Ile, Ala Acidic - Glu, Asp
What are the protein secondary structures that differ between a normal prion and an infectious one?
Normal form - more a-helices then the b-sheets Abnormal one - increased b-sheet content
Which organelles are surrounded by a double membrane?
Nuclei, mitochondria, and chloroplasts
Which organelles contain DNA?
Nuclei, mitochondria, and chloroplasts, but the DNA found in mitochondria and in chloroplasts differs from that found in the nucleus
Which of the following biomolecules forms the molecular currency of the cell, adenosine triphosphate (ATP)? 1. Nucleotides 2. Esters 3. Amino acids 4. Lipids
Nucleotides
Which of the following statements regarding biopolymers is false? 1. Different sequences of the monomers can lead to different functions. 2. Only soluble polymers can be created from soluble monomers. 3. A wide, almost uncountable variety of polymers can be created from just a few monomers. 4. Different linkages between the monomers can lead to different functions. 5. Biopolymers can fold up into complex shapes.
Only soluble polymers can be created from soluble monomers.
If a protein with the sequence PQRKYPIG is treated with trypsin, what will the products be? - PQR KYPIG - PQRK YPIG - PQ R KPIG - PQR K YPIG
PQR K YPIG Trypsin cuts the carboxyl group (C-terminus) of Arg (R) and Lysine (K) - so the R is cut on the right/C-term side, and the K is too
In biochemistry, the exergonic process of converting glucose and oxygen to carbon dioxide and water in aerobic metabolism can be considered the reverse of photosynthesis, in which carbon dioxide and water are converted to glucose and oxygen. Do you expect both processes to be exergonic, both endergonic, or one exergonic and one endergonic? Why? Would you expect both processes to take place in the same way? Why?
Photosynthesis is endergonic because it requires light energy from the sun. The complete aerobic oxidation of glucose is exergonic and is a source of energy for many organisms, including humans. One uses energy and the other makes energy, making them endergonic and exergonic, respectively.
The accompanying figure is from an electrophoresis experiment using SDS-PAGE. The left lane has the following standards: bovine serum albumin (MW 66,000), ovalbumin (MW 45,000), glyceraldehyde 3-phosphate dehydrogenase (MW 36,000), carbonic anhydrase (MW 24,000), and trypsinogen (MW 20,000). The right lane is an unknown. Calculate the MW of the unknown.
Plot the distance traveled by the log of the MW Answer: 32,400 Da
Identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids, given a peptide with the following amino acid sequence: Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu
Polar - Ser, Arg, Cys, Tyr Aromatic - Phe, Tyr Sulfur - Cys, Met
Both RNA and DNA have negatively charged phosphate groups as part of their structure. Would you expect ions that bind to nucleic acids to be positively or negatively charged? Why?
Positively charged ions bind to nucleic acids as a result of electrostatic attraction to the negatively charged phosphate groups.
Match the following statements about protein structure with the proper levels of organization.
Primary Structure - The order of amino acid residues in the polypeptide chain Secondary Structure - The interaction between subunits in proteins that consist of more than one polypeptide chain Tertiary Structure - The three-dimensional arrangement of all atoms Quaternary Structure - The interaction between subunits in proteins that consist of more than one polypeptide chain
Which amino acid is technically not an amino acid? Which amino acid contains no chiral carbon atoms?
Proline - not an amino acid Glycine - no chiral carbon (R group in H)
Heme would best be described as a - motif - domain - prosthetic group - helix
Prosthetic group
What are some macromolecules that have hydrogen bonds as a part of their structures?
Proteins and nucleic acids
Which of these eukaryotic kingdoms consists primarily of unicellular organisms? 1. Animals 2. Fungi 3. Plants 4. Protista 5. Both fungi and protista.
Protista
Which form of salicyclic acid (pK ~3.0) predominates at the pH of the stomach, which is usually around 2.0?
Protonated (pK > pH)
Why do most people elute bound proteins from an ion-exchange column by raising the salt concentration instead of changing the pH?
Raising the salt concentration is relatively safe. Most proteins will elute this way, and, if the protein is an enzyme, it will still be active. If necessary, the salt can be removed later via dialysis. Changing the pH enough to remove the charge can cause the proteins to denature. Many proteins are not soluble at the isoelectric points.
Which processes are favored: those that require energy or those that release energy?
Release energy
Which cell component is composed exclusively of RNA and protein? 1. Nucleus 2. Mitochondrion 3. Endoplasmic Reticulum 4. Chloroplast 5. Ribosome
Ribosome
Which of the following cellular components is commonly found in bacteria? 1. Nucleus 2. Ribosomes 3. Chloroplasts 4. Mitochondria 5. More than one of these is characteristic of bacteria.
Ribosomes
How does the addition of sodium dodecylsulfate to proteins affect the basis of separation on electrophoresis?
SDS binds to the protein in a constant ratio of 1.4 g SDS per gram of protein. It coats the protein with negative charges and puts it into a random coil shape. Thus, charge and shape are eliminated.
What is meant by "salting out"? How does it work?
Salting out is a process whereby a highly ionic salt is used to reduce the solubility of a protein until it comes out of solution and can be centrifuged. The salt forms ion-dipole bonds with the water in the solution, which leaves less water available to hydrate the protein. Non-polar side chains begin to interact between protein molecules, and they become insoluble.
Hydrogen bonds are most important in this type of structure in proteins: - primary structure - secondary structure - tertiary structure - quaternary structure - All of these
Secondary structure
Given the structures below (not shown), which the principal form of serine at pH 5?
Serine with an NH3+ and O- (Like this because the pH is between both pKas so the protonation and deprotonation equalizes) If pH is 1, only protonated with NH3+
Would the presence of a chiral center in an amino acid side chain affect the formation of a peptide bond?
Side chains do not enter into the peptide bond themselves, but large groups with chiral centers could sterically hinder bond formation.
List two similarities and two differences between hemoglobin and myoglobin.
Similarities: both contain a heme group; both are oxygen binding; secondary structure is primarily a-helix Differences: hemoglobin is a tetramer, while myoglobin is a monomer; oxygen binding to hemoglobin is cooperative, but noncooperative to myoglobin
What physical parameters of a protein control its migration on electrophoresis?
Size, shape, and charge
What are two major advantages of enzyme catalysts in living organisms when compared with other simple chemical catalysts such as acids or bases?
Speed and specificity, but they also work at constant temperature or produce little heat.
Does the thermodynamic term spontaneous refer to a process that takes place quickly?
Spontaneous means energetically favored (not necessarily fast)
Identify the functional group(s) in the following molecule: 1. Carboxyl 2. Hydroxyl 3. Sulfhydryl 4. Aldehyde 5. Ester
Sulfhydryl
The location of prosthetic groups is shown in this level of structure: 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure
Tertiary structure
Rationalize the fact that hydrogen bonding has not been observed between CH4 molecules.
The C-H bond is not sufficiently polar for greatly unequal distribution of electrons at its two ends. Also, there are no unshared pairs of electrons to serve as hydrogen bond acceptors.
Our patient is a 10-year-old African American child named Michael, who was admitted to the hospital for severe chest pain. In the emergency room, oxygen (100%) was administered to the patient. (Inspired air normally is about 20% oxygen.) Why was this an effective treatment? (Which form of hemoglobin is favored at high pO2 and how does this relate to sickling?)
The R form of hemoglobin is favored at high levels of oxygen/pO2, so it is less likely to sickle (whereas the T form is more likely to sickle).
What are Ramachandran angles?
The angles of the amide planes as they rotate about the a-carbon. The angles are both defined as zero when the two planes would be overlapping such that the carbonyl group of one contacts the N-H of the other.
What is the purpose of the tag on a bait protein?
The bait protein is constructed to have a particular affinity tag. The bait protein interacts with cell proteins of interest and then binds to an affinity column via the tag. In this way, the cell proteins of interest can be found and isolated.
What are the two critical amino acids near the heme group in both myoglobin and hemoglobin?
The crucial residues are histidines in both proteins.
Why does the pH change by one unit if the hydrogen ion concentration changes by a factor of 10?
The definition of pH is -log[H+]. By definition of the log function, a change in concentration of 10 leads to a change in pH of 1. (The log of 10 is 1, the log of 100 is 2, etc.)
Can a peptide act as a buffer? If so, why?
The free carboxyl group and the free amino group of a peptide are both titratable and could serve as a buffer, but it would not necessarily be an effective buffer.
Suggest a way in which the difference between the functions of hemoglobin and myoglobin is reflected in the shapes of their respective oxygen-binding curves.
The function of hemoglobin is oxygen transport; its sigmoidal binding curve reflects the fact that it can bind easily to oxygen at comparatively high pressures and release oxygen at lower pressures. The function of myoglobin is oxygen storage; as a result, it is easily saturated with oxygen at low pressures, as shown by its hyperbolic binding curve.
Why is proline frequently encountered at the places in the myoglobin and hemoglobin molecules where the polypeptide chain turns a corner?
The geometry of the proline residue is such that it does not fit into the a-helix, but it does fit exactly for a reverse turn.
Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? It appears that the solution is absorbing energy.
The heat exchange, getting colder, reflects only the enthalpy or ΔH component of the total energy change (which is positive). The entropy change must be high enough to offset the enthalpy component and add up to an overall -ΔG. i.e. If ΔS and ΔH are both positive, ΔS must be a higher number to produce a -ΔG, since the equation is ΔH-TΔS
When electrophoretic separations are done based on molecular weight, the distance that a molecule moves can be graphed as a straight line when compared to: - the MW of the proteins - the negative of the MW of the proteins - the log of the MW of the proteins - none of these
The log of the MW of the proteins
In reverse-phase HPLC, the stationary phase is non-polar and the mobile phase is a polar solvent at neutral pH. Which of phenylalanine, glycine, and glutamic acid will move fastest on a reverse-phase HPLC column? Which one will move the slowest?
The nonpolar amino acids will stick the most to the stationary phase, so glutamic acid will move the fastest, followed by glycine and then phenylalanine.
X-ray crystallography is used to determine protein structure because 1. it can be done on dilute solutions 2. it requires no calculations 3. the positions of all atoms can be found by this method 4. all of these
The positions of all atoms can be found by this method
What is the nature of "random" structure in proteins?
The random portions of a protein do not contain structural motifs that are repeated within the protein, such as a-helix or b-pleated sheet, but three-dimensional features of these parts of the protein are repeated from one molecule to another. Thus, the term random is somewhat of a misnomer.
Why is fetal Hb essential for the survival of placental animals?
The relative oxygen affinities allow oxygen to be taken by the fetal cells from the maternal Hb.
Which would you think would be a stronger interaction and why: an interaction between a sodium ion and the partial negative charge on the oxygen in ethanol (CH3CH2OH), or the interaction between two ethanol molecules?
The sodium ion is a fully charged anion. Therefore, its interaction with the partial negative charge on the oxygen of ethanol would be stronger than the interaction of the same oxygen with a partially positive charge from the hydrogen of another ethanol molecule.
If you mix equal volumes of 0.1 M HCl and 0.20 M TRIS (free amine form), is the resulting solution a buffer? Why or why not?
The solution is a buffer because it contains equal concentrations of TRIS in the acid and free amine forms. When the two solutions are mixed, the concentrations of the resulting solution (in the absence of reaction) are 0.05 M HCl and 0.1 M TRIS because of dilution. The HCl reacts with half the TRIS present, giving 0.05 M TRIS (protonated form) and 0.05 M TRIS (free amine form).
Why is water necessary for life?
The unique fitness of water for forming hydrogen bonds determines the properties of many important biomolecules. Water can also act as an acid and as a base, giving it great versatility in biochemical reactions.
What is the relationship between pKa and the useful range of a buffer?
The useful pH range of a buffer is one pH unit above and below its pKa.
What differences between proteins are responsible for their differential solubility in ammonium sulfate?
Their amino acid content and arrangements make some proteins more soluble than others. A protein with more highly polar amino acids on the surface is more soluble than one with more hydrophobic ones on the surface.
Consider the peptides Gly—Pro—Ser—Glu—Thr (open chain) and Gly—Pro—Ser—Glu—Thr with a peptide bond linking the threonine and the glycine. Are these peptides chemically the same?
These two peptides differ chemically - the open chain has a free C-terminal and N-terminal, but the cyclic peptide has only peptide bonds.
Which statement best explains why nonpolar substances have low solubility in water? 1. They are much larger than water. 2. They are much denser than water. 3. They have strong mutual attractions. 4. They cannot form hydrogen bonds to water.
They cannot form hydrogen bonds to water.
Suggest a reason why amino acids are usually more soluble at pH extremes than they are at neutral pH. (Note that this does not mean that they are insoluble at neutral pH.)
They have a net charge at pH extremes, and the molecules tend to repel each other. When the molecular charge is zero, the amino acids can aggregate more easily.
If you had a mixture of proteins with different sizes, shapes, and charges and you separated them with electrophoresis, which proteins would move fastest toward the anode (positive electrode)?
Those with the highest charge/mass ratio would move the fastest. There are three variables to consider, and most electrophoreses are done in a way to eliminate two of the variables so that the separation is by size or by charge, but not by both.
Which amino acid has a benzene-like ring? - Glutamic Acid - Histidine - Isoleucine - Serine - Tyrosine
Tyrosine Try has a phenol ring bound to it
A friend who is enthusiastic about health foods and organic gardening asks you whether urea is "organic" or "chemical." How do you reply to this question?
Urea, like all organic compounds, has the same molecular structure, whether it is produced by a living organism or not (so it's organic).
Deduce the sequence of the original peptide. Trypsin: Asn-Thr-Trp-Met-Ile-Lys Gly-Tyr-Met-Gln-Phe Val-Leu-Gly-Met-Ser-Arg Cyanogen Bromide: Gln-Phe Val-Leu-Gly-Met Ile-Leu-Gly-Tyr-Met Ser-Arg-Asn-Thr-Trp-Met
Val-Leu-Gly-Met-Ser-Arg-Asn-Thr-Trp-Met-Ile-Lys-Gly-Tyr-Met-Gln-Phe Trypsin - know it cleaves C-term of Arg and Lys -- the middle sequence is the ending CB - we see that Ser-Arg-Asn are sequenced, so that tells the order of the rest
What is the effect of the altered amino acid sequence in Hb S that causes the cells to form sickle shapes?
Valine is a hydrophobic amino acid. The valine is on the outside of the globular protein where the amino acids have to interact with water. The presence of the hydrophobic amino acid at that position causes hemoglobins to clump together via hydrophobic interactions. This clumping causes the cell deformation.
Define denaturation in terms of the effects of secondary, tertiary, and quaternary structure.
When a protein is denatured, the interactions that determine secondary, tertiary, and any quaternary structures are overcome by the presence of the denaturing agent. Only the primary structure remains intact.
Which of the following techniques is useful in determining the tertiary structure of peptides? - Ion exchange chromatography - X-ray crystallography - Mass spectrometry
X-ray crystallography
Calculate the hydrogen ion concentration, , for each of the following materials: (a) Blood plasma, pH = 7.4 (b) Orange juice, pH = 3.5 (c) Human urine, pH = 6.2 (d) Household ammonia, pH = 11.5 (e) Gastric juice, pH = 1.8
[H+] = 10^-pH (a) 4.0 x 10^-8 M (b) 3.2 x 10^-4 M (c) 6.3 x 10^-7 M (d) 3.2 x 10^-12 M (e) 1.6 x 10^-2 M
Identify the functional group indicated in the molecule below. - amide - amine - carboxylate - ketone
carboxylate
Which of the following is not considered a van der Waals force? 1. dipole - dipole bond 2. dipole - induced dipole bond 3. induced dipole - induced dipole bond 4. ion - dipole bond
ion - dipole bond
The peptide bond - is formed by elimination of water between two amino groups in an amino acid - limits the possible orientations of the peptide backbone in a protein - has acidic and basic characteristics - all of these
limits the possible orientations of the peptide backbone in a protein
In the Five Kingdom classification system, Escherichia coli would be considered 1. animals. 2. protists. 3. monera. 4. none of the above.
monera
According to thermodynamics, favored processes are 1. ones that require energy. 2. oxidations. 3. ones that release energy. 4. reductions.
ones that release energy.
Identify the charged groups in the peptide shown below at pH 1 and at pH 7. What is the net charge of this peptide at these two pH values? Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu
pH 1 - NH3+ on valine and protonated guanidino group on arginine == net charge of 2+ pH 7 - NH3+ valine, protonated guanidino group on arginine, and COO- on valine == net charge of 1+
Sketch a titration curve for the amino acid lysine, and indicate the pKa values for all titratable groups. Also indicate the pH at which the amino acid has no net charge.
pK1 = 2.10 pK2 = 8.95 pK3 = 10.53 pI = 9.75 (look at first graph for reference of lysine curve)
Calculate the hydroxide ion concentration, , for each of the following materials: (a) Blood plasma, pH = 7.4 (b) Orange juice, pH = 3.5 (c) Human urine, pH = 6.2 (d) Household ammonia, pH = 11.5 (e) Gastric juice, pH = 1.8
pOH = 14 - pH [OH-] = 10^-pOH (a) 2.5 x 10^-7 M (b) 3.2 x 10^-11 M (c) 1.0 x 10^-8 M (d) 3.2 x 10^-3 M (e) 6.3 x 10^-13 M
Biological catalysts are 1. proteins exclusively 2. RNA exclusively 3. DNA exclusively 4. some proteins and some RNA
some proteins and some RNA
Buffering capacity refers to - the effectiveness of commercial antacids - the extent to which a buffer solution can counteract the effect of added acid or base - the pH of a buffer solution - the molecular weight of the substance used as a buffer
the extent to which a buffer solution can counteract the effect of added acid or base
