biochemistry test 1
For a weak acid with a pKa of 6.0, calculate the ratio of conjugate base to acid at a pH of 5.0.
5=6+ log(a/ha) 10^-1 =.1
What chemical functional groups commonly form hydrogen bonds in biological molecules?
• Alcohols, aldehydes, ketones, and n-h bonds
Which elements are the most abundant in living cells?
• CHON
What is meant by the "bonding versatility" of carbon?
• Carbon can have a broad array of carbon skeletons with several functional groups.
What chemical functional groups commonly form ionic interactions in biological molecules?
• Carboxylic acids, amines, phosphate esters or anhydrides
What is the pH of a solution that contains 0.20 M sodium acetate and 0.60 M acetic acid (pKa = 4.76)?
4.76+log(.2/.6)=4.3
Three membrane receptor proteins bind tightly to a hormone. Based on the data in the table below, (a) what is the Kd for hormone binding by protein 2? (Include appropriate units.) (b) Which of these proteins binds most tightly to this hormone?
(a) 0.5 nM (shortcut: the Kd is equivalent to the ligand concentration where Y = 0.5). (b)Protein 2 has the highest affinity, as it has the lowest Kd
What is the effect of the following changes on the O2 affinity of hemoglobin? (a) A drop in the pH of blood plasma from 7.4 to 7.2. (b) A decrease in the partial pressure of CO2 in the lungs from 6 kPa (holding one's breath) to 2 kPa (normal breathing). (c) An increase in the BPG level from 5 mM (normal altitudes) to 8 mM (high altitudes). (d) An increase in CO from 1.0 part per million (ppm) in a normal indoor atmosphere to 30 ppm in a home that has a malfunctioning or leaking furnace.
(a) Decreases (b) Increases (c) Decreases (d) Increases
(a) Glutenin, a wheat protein rich in disulfide bonds, is responsible for the cohesive and elastic character of dough made from wheat flour. Similarly, the hard, tough nature of tortoise shell is due to the extensive disulfide bonding in its α-keratin. What is the molecular basis for the correlation between disulfide-bond content and mechanical properties of the protein?
(a) Disulfide bonds are covalent bonds, which are much stronger than the noncovalent interactions that stabilize most proteins. They cross-link protein chains, increasing their stiffness, mechanical strength, and hardness.
a)The Hb variant least likely to cause pathological symptoms. (b) The variant(s) most likely to show pI values different from that of HbA on an isoelectric focusing gel. (c) The variant(s) most likely to show a decrease in BPG binding and an increase in the overall affinity of the hemoglobin for oxygen.
(a) Hb Memphis (b) HbS, Hb Milwaukee, Hb Providence, possibly Hb Cowtown (c) Hb Providence
Three polypeptides, the sequences of which are represented below using the one-letter code for their amino acids, are present in a mixture: 1. ATKNRASCLVPKHGALMFWRHKQLVSDPILQKRQHILVCRNAAG 2. GPYFGDEPLDVHDEPEEG 3. PHLLSAWKGMEGVGKSQSFAALIVILA Of the three, which one would migrate most slowly during chromatography through: (a) an ion-exchange resin, beads coated with positively charged groups? (b) an ion-exchange resin, beads coated with negatively charged groups? (c) a size-exclusion (gel-filtration) column designed to separate small peptides such as these? (d) Which peptide contains the ATP-binding motif shown in the following sequence logo?
(a) Peptide 2 (b) Peptide 1 (c) Peptide 2 (d) Peptide 3
(a) In this sequence, which amino acid residues are invariant (conserved across all species)? (b) At which position(s) are amino acids limited to those with positively charged side chains? For each position, which amino acid is more commonly found? (c) At which positions are substitutions restricted to amino acids with negatively charged side chains? For each position, which amino acid predominates? (d) There is one position that can be any amino acid, although one amino acid appears much more often than any other. What position is this, and which amino acid appears most often?
(a) Y (1), F (7), and R (9) (b) Positions 4 and 9; K (Lys) is more common at 4, R (Arg) is invariant at 9. (c) Positions 5 and 10; E (Glu) is more common at both positions. (d)Position 2; S (Ser)
Most globular proteins are denatured and lose their activity when briefly heated to 65 °C. However, globular proteins that contain multiple disulfide bonds often must be heated longer at higher temperatures to denature them. One such protein is bovine pancreatic trypsin inhibitor (BPTI), which has 58 amino acid residues in a single chain and contains three disulfide bonds. On cooling a solution of denatured BPTI, the activity of the protein is restored. What is the molecular basis for this property?
(b) Cystine residues (disulfide bonds) prevent the complete unfolding of the protein.
10. Physical Meaning of pKa Which of the following aqueous solutions has the lowest pH: 0.1 M HCl; 0.1 M acetic acid (pKa = 4.86); 0.1 M formic acid (pKa = 3.75)?
.1 M HCl
Calculate the concentrations of acetic acid (pKa = 4.76) and sodium acetate necessary to prepare a 0.2 M buffer solution at pH 5.0.
1.74+1=2.74 .2/2.74=.073M .073x1.74=.127M
What is the approximate range of the number of amino acids that have been observed in naturally-occurring proteins?
100 to several thousand amino acid residues
At pH 7.0, in what order would the following three peptides (described by their amino acid composition) be eluted from a column filled with a cationexchange polymer? Peptide A: Ala 10%, Glu 5%, Ser 5%, Leu 10%, Arg 10%, His 5%, Ile 10%, Phe 5%, Tyr 5%, Lys 10%, Gly 10%, Pro 5%, and Trp 10%. Peptide B: Ala 5%, Val 5%, Gly 10%, Asp 5%, Leu 5%, Arg 5%, Ile 5%, Phe 5%, Tyr 5%, Lys 5%, Trp 5%, Ser 5%, Thr 5%, Glu 5%, Asn 5%, Pro 10%, Met 5%, and Cys 5%. Peptide C: Ala 10%, Glu 10%, Gly 5%, Leu 5%, Asp 10%, Arg 5%, Met 5%, Cys 5%, Tyr 5%, Phe 5%, His 5%, Val 5%, Pro 5%, Thr 5%, Ser 5%, Asn 5%, and Gln 5%.
17. C elutes first, B second, A last.
What molar ratio of to in solution would produce a pH of 7.0? Phosphoric acid (H3PO4 ), a triprotic acid, has three pKa values: 2.14, 6.86, and 12.4. Hint: Only one of the pKa values is relevant here.
7=6.86+log(hpo4,2-)/(h2po4-) 10^.14 =1.38
4. Calculation of pH from Hydrogen Ion Concentration What is the pH of a solution that has an H+ concentration of (a) 1.75 × 10 -5 mol/L; (b) 6.50 × 10 -10 mol/L; (c) 1.0 × 10 -4 mol/L; (d) 1.50 × 10 -5 mol/L?
=-log(concentration) a.4.76 b.9.18 c.4 d. 4.82
5. Calculation of Hydrogen Ion Concentration from pH What is the H+ concentration of a solution with pH of (a) 3.82; (b) 6.52; (c) 11.11
=10^pH a. 1.51E-4 M b. 3.01E-7 M c. 7.76E-12 M
How are macromolecules defined?
A molecule having a molecular weight in the range of a few thousand to many millions. -Larger than monomeric units, held together by noncovalent interactions. Composed of monomeric units.
The structure of Aba is shown below. Why was this a suitable substitution for a Cys residue? Under what circumstances would it not be suitable?
Aba is a suitable replacement because Aba and Cys have side chains of approximately the same size and are similarly hydrophobic. However, Aba cannot form disulfide bonds, so it will not be a suitable replacement if these are required
Which of these compounds would be the best buffer at pH 5.0: formic acid (pKa = 3.8), acetic acid (pKa = 4.76), or ethylamine (pKa = 9.0)? Briefly justify your answer.
Acetic acid; its pKa is closest to the desired pH
What is the explanation for the effect of the pH changes on the conformations of poly(Glu) and poly(Lys)? Why does the transition occur over such a narrow range of pH?
At pH > 6, the carboxyl groups of poly(Glu) are deprotonated; repulsion among negatively charged carboxylate groups leads to unfolding. Similarly, at pH 7, the amino groups of poly(Lys) are protonated; repulsion among these positively charged groups also leads to unfolding.
Interestingly, the resulting L-protease was active. What does this finding tell you about the role of disulfide bonds in the native HIV protease molecule?
Because the enzyme is functional when Aba is substituted for Cys, disulfide bonds do not play an important role in the structure of HIV protease.
What is the extracellular buffering system that is used by animals with lungs and how does it allow air-breathing mammals to regulate blood pH?
Bicarbonate buffer system, because the H2CO3 of blood plasma is in equilibrium with a large reserve capacity of CO2 (g) in the air space of the lungs
If you were exposed to poison ivy, which of the treatments below would you apply to the affected area? Justify your choice.
Bicarbonate, a weak base, titrates —OH to —O−, making the compound more polar and more water-soluble.
When a vertebrate dies, its muscles stiffen as they are deprived of ATP, a state called rigor mortis. Using your knowledge of the catalytic cycle of myosin in muscle contraction, explain the molecular basis of the rigor state.
Binding of ATP to myosin triggers dissociation of myosin from the actin thin filament. In the absence of ATP, actin and myosin bind tightly to each other.
When a vertebrate dies, its muscles stiffen as they are deprived of ATP, a state called rigor mortis. Using your knowledge of the catalytic cycle of myosin in muscle contraction, explain the molecular basis of the rigor state.
Binding of ATP to myosin triggers dissociation of myosin from the actin thin filament. In the absence of ATP, actin and myosin bind tightly to each other.
what is the primary intracellular buffering system?
Cytoplasm
Explain how the pH of an amino acid's environment can affect the net charge on the amino acid.
If the pH is higher than the isoelectric point then the amino acid acts as an acid and donates a proton from its carboxyl group. This gives it a negative charge.
A host organism needs time, often days, to mount an immune response against a new antigen, but memory cells permit a rapid response to pathogens previously encountered. A vaccine to protect against a particular viral infection often consists of weakened or killed virus or isolated proteins from a viral protein coat. When injected into a person, the vaccine generally does not cause an infection and illness, but it effectively "teaches" the immune system what the viral particles look like, stimulating the production of memory cells. On subsequent infection, these cells can bind to the virus and trigger a rapid immune response. Some pathogens, including HIV, have developed mechanisms to evade the immune system, making it difficult or impossible to develop effective vaccines against them. What strategy could a pathogen use to evade the immune system? Assume that a host's antibodies and/or T-cell receptors are available to bind to any structure that might appear on the surface of a pathogen and that, once bound, the pathogen is destroyed.
Many pathogens, including HIV, have mechanisms for repeatedly altering the surface proteins to which immune system components initially bind. Thus the host organism regularly faces new antigens and requires time to mount an immune response to each one. As the immune system responds to one variant, new variants are created.
What is the mechanism by which solutes affect the melting and boiling points of water?
Melting point is depressed because solute particles interfere with lattice formation.
A team of biochemists uses genetic engineering to modify the interface region between hemoglobin subunits. The resulting hemoglobin variants exist in solution primarily as αβ dimers (few, if any, α2β2 tetramers form). Are these variants likely to bind oxygen more weakly or more tightly? Explain your answer.
More tightly. An inability to form tetramers would limit the cooperativity of these variants, and the binding curve would become more hyperbolic. Also, the BPG-binding site would be disrupted. Oxygen binding would probably be tighter, because the default state in the absence of bound BPG is the tight-binding R state.
Which of the following peptides is more likely to take up an α-helical structure, and why? (a) LKAENDEAARAMSEA (b) CRAGGFPWDQPGTSN
Peptide (a); it has more amino acid residues that favor an α-helical structure
Protein A has a binding site for ligand X with a Kd of 10 −6 M. Protein B has a binding site for ligand X with a Kd of 10−9 M. Which protein has a higher affinity for ligand X? Explain your reasoning. Convert the Kd to Ka for both proteins.
Protein B has a higher affinity for ligand X; it will be half-saturated at a much lower concentration of X than will protein A. Protein A has Ka = 10^6 M−1; protein B has Ka = 10^9 M−1
What is SDS and why is it used in electrophoresis procedures?
Sodium dodecyl sulfate. Used for estimation of purity
(a) Given our current understanding of the structure of wool, interpret Astbury's observations. (b) When wool sweaters or socks are washed in hot water or heated in a dryer, they shrink. Silk, on the other hand, does not shrink under the same conditions. Explain.
Steaming and stretching the fiber yields an extended polypeptide chain with the β conformation, with a distance between adjacent R groups of about 7.0 Å. As the polypeptide reassumes an αhelical structure, the fiber shortens. (b) Wool shrinks in the presence of moist heat, as polypeptide chains are converted from an extended β conformation to the native α-helix conformation. The structure of silk-β sheets, with their small, closely packed amino acid side chains-is more stable than that of wool
Under appropriate conditions, hemoglobin dissociates into its four subunits. The isolated α subunit binds oxygen, but the O2 -saturation curve is hyperbolic rather than sigmoid. In addition, the binding of oxygen to the isolated α subunit is not affected by the presence of H+, CO2 , or BPG. What do these observations indicate about the source of the cooperativity in hemoglobin?
The cooperative behavior of hemoglobin arises from subunit interactions
What is the physiological significance of the different O2 affinities?
The higher O2 affinity of HbF ensures that oxygen will flow from maternal blood to fetal blood in the placenta. Fetal blood approaches full saturation where the O2 affinity of HbA is low.
When all the BPG is carefully removed from samples of HbA and HbF, the measured O2 -saturation curves (and consequently the O2 affinities) are displaced to the left. However, HbA now has a greater affinity for oxygen than does HbF. When BPG is reintroduced, the O2 -saturation curves return to normal, as shown in the graph. What is the effect of BPG on the O2 affinity of hemoglobin? How can the above information be used to explain the different O2 affinities of fetal and maternal hemoglobin?
The observation that the O2 -saturation curve of HbA undergoes a larger shift on BPG binding than that of HbF suggests that HbA binds BPG more tightly than does HbF. Differential binding of BPG to the two hemoglobins may determine the difference in their O2 affinities.
Which hemoglobin has a higher affinity for oxygen under physiological conditions, HbA or HbF? Explain.
The observation that HbA (maternal) is about 60% saturated when the pO2 is 4 kPa, whereas HbF (fetal) is more than 90% saturated under the same physiological conditions, indicates that HbF has a higher O2 affinity than HbA.
What is lost from amino acids in the formation of a peptide bond?
Water
(a) What does the length of the C—N bond in the peptide linkage indicate about its strength and its bond order (i.e., whether it is single, double, or triple)? (b) What do the observations of Pauling and Corey tell us about the ease of rotation about the C—N peptide bond?
a) Shorter bonds have a higher bond order (are multiple rather than single) and are stronger. The peptide C—N bond is stronger than a single bond and is midway between a single and a double bond in character. (b) Rotation about the peptide bond is difficult at physiological temperatures because of its partial double-bond characte
14. Calculation of the pH of a Mixture of a Weak Acid and Its Conjugate Base Calculate the pH of a dilute solution that contains a molar ratio of potassium acetate to acetic acid (pKa = 4.76) of (a) 2:1; (b) 1:3; (c) 5:1; (d) 1:1; (e) 1:10.
a) pH = 4.76 + log(2/1) = 5.06 b)4.28 c)5.46 d)4.76 e)3.76
11. Identifying the Conjugate Base Which is the conjugate base in each of the pairs below? (a) RCOOH, RCOO- (b) h2po4-, h3po4 (e) rnh2, rnh3+ (d) H2CO3, HCO3-
a)RCOO- b)H2PO4- c)RNH2 d)HCO3-
A buffer contains 0.010 mol of lactic acid (pKa = 3.86) and 0.050 mol of sodium lactate per liter. (a) Calculate the pH of the buffer. (b) Calculate the change in pH when 5 mL of 0.5 M HCl is added to 1 L of the buffer. (c) What pH change would you expect if you added the same quantity of HCl to 1 L of pure water?
a)pH = 3.86 + log 0.050/ 0.010=4.56 b)moles H+ added = 5 x 10^-3 L x 0.5 M=0.0025 moles lactic acid = 0.010 + 0.0025=0.0125 moles lactate = 0.050 - 0.0025 = 0.0474 pH = 3.86 + log 0.0474/ 0.0125 =4.44 change = 4.56 - 4.44 =0.12 c) 4 pH units
Which of the following situations would produce a Hill plot with nH < 1.0? Explain your reasoning in each case. (a) The protein has multiple subunits, each with a single ligand-binding site. Binding of ligand to one site decreases the binding affinity of other sites for the ligand. (b) The protein is a single polypeptide with two ligand-binding sites, each having a different affinity for the ligand. (c) The protein is a single polypeptide with a single ligand-binding site. As purified, the protein preparation is heterogeneous, containing some protein molecules that are partially denatured and thus have a lower binding affinity for the ligand.
all solutions are correct -caused by the presence of two or more types of ligand-binding sites with different affinities for the ligand on the same or different proteins in the same solution. Apparent negative cooperativity is also commonly observed in heterogeneous protein preparations
Which amino acid R groups are capable of forming hydrogen bonds?
aromatic
which is the only amino acid that is capable of forming disulfide bonds?
cysteine
Which would be more basic, the amino group of a Val-Val dipeptide or the amino group of a Val-Val-Val tripeptide, and why?
dipeptide because of the R group
What specific information does the equilibrium constant of a chemical reaction provide?
gives the ratio of the units (pressure or concentration) of the products to the reactants when the reaction is at equilibrium.
Does a strong acid have a greater or lesser tendency to lose its proton when compared to a weak acid?
greater
Does a strong acid have a higher or lower value of Ka relative to a weak acid?
higher
At a pH equal to the pKa of a weak acid, what can be said about the relative concentrations of the acid and its conjugate base?
its at equalib. meaning there are equal parts of each concentration
Does a strong acid have a higher or lower value of pKa relative to a weak acid?
lower
Which amino acid R groups are capable of forming hydrophobic interactions?
nonpolar
Which amino acid R groups are capable of forming ionic interactions?
positive
What does a single band on a protein gel represent?
protein
How does information about the sequence of amino acids that make up a protein contribute to an understanding of a protein's function?
protein families that have some shared structural or functional features can be readily identified on the basis of amino acid sequence similarities. Individual proteins are assigned to families based on the degree of similarity in amino acid sequence.
There are many reasons to predict that a protein synthesized, denatured, and folded in this manner would not be active. Give three such reasons
result in an inactive synthetic enzyme. (1) Although Aba and Cys have a similar size and hydrophobicity, Aba may not be similar enough for the protein to fold properly. (2) HIV protease may require disulfide bonds for proper functioning. (3) Many proteins synthesized by ribosomes fold while being produced; the protein in this study folded only after the chain was complete.
Which bonds in a polypeptide backbone contribute to flexibility of the polypeptide chain? Which bonds do not, and why?
single bonds allow flexibility double and triple bonds do not because they are locked in. too bulky to move
Which would be more acidic, the carboxylic acid group of a Gly-Gly dipeptide or the carboxylic acid group of a Gly-Gly-Gly tripeptide, and why?
tripeptide because of the R groups in the peptides
A binding protein binds to a ligand L with a Kd of 400 nM. How much ligand is present when Y is (a) 0.25, (b) 0.6, (c) 0.95?
y=L/kd+L .25(kd+L)=L 100+.25L=L 100=.75L L=133.33 (a) 0.13 pM (b) 0.6 pM (c) 7.6 μM
Why is it that a single stereoisomeric form of a molecule can be biologically active while another stereoisomeric form of the same molecule might be inactive or have a completely different activity?
• Different stereoisomers are different and they behave differently due to bioavailability, rate of metabolism, potency, and selectivity of receptors.
What chemical functional groups commonly form hydrophobic interactions in biological molecules?
• Lipids and waxes
How do hydrogen bonds contribute to the high melting and boiling points of water?
• Liquid water has great internal cohesion, 104.5 degree angle because of crowding by nonbonding orbitals of the oxygen atom.
What might be an advantage of compartmentalization of cells?
• More surface to volume ratio so that there are higher rates of uptake of materials from their surroundings
What are the major structural attributes of bacteria that distinguish them from eukaryotes?
• Nucleus/nucleoid • Nuclear membrane • Membrane bound organelles • Size (bact cells are smaller)
How are supramolecular complexes defined?
• These are the large groups composed of smaller macromolecules and even smaller molecular subunits. like cell wall, chromatin. Composed of macromolecules
How are trace elements important to living cells?
• trace elements represent a miniscule fraction of the weight of the human body, but all are essential to life, usually because they are essential to the function of specific proteins, including many enzymes.
6. Acidity of Gastric HCl In a hospital laboratory, a 10.0 mL sample of gastric juice, obtained several hours after a meal, was titrated with 0.1 M NaOH to neutrality; 7.2 mL of NaOH was required. The patient's stomach contained no ingested food or drink; thus assume that no buffers were present. What was the pH of the gastric juice?
•If x is the concentration of gastric HCl (mol/L): (10 mL) x = (7.2 mL)(0.1 mol/L) x = 0.072 M pH = -log(7.2 x 10^-2) = 1.1
7. Calculation of the pH of a Strong Acid or Base (a) Write out the acid dissociation reaction for hydrochloric acid. (b) Calculate the pH of a solution of 5.0 × 10 -4 M HCl. (c) Write out the acid dissociation reaction for sodium hydroxide. (d) Calculate the pH of a solution of 7.0 × 10 -5 M NaOH
•a) HCl = H+ + Cl- [H+] = [HCl] = 5.0 x 10-4 M pH = -log[H+] = -log(5.0 x 10-4) = 3.3 b) NaOH = Na+ + OH- C) [OH-] = [NaOH] = 7.0 x 10-5 M pOH = -log[OH-] = -log(7.0 x 10-5) = 4.2 D) pH = 14 - pOH = 14 - 4.2 = 9.8