Biochem Exam 2

At pH=0, the net charge on a polypeptide will be negative.

false

Conservative amino acid changes never affect stability or function of a protein.

false

Most proteins have blocked amino and carboxyl terminals.

false

When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity.

false

For which of the following may GFP fusion technology NOT be a good technique to use?

for target proteins whose structure is altered by a GFP fusion

The heavy chain of the muscle form of myosin:

forms a coiled-coil structure with a globular head domain.

All amino acids have a chiral α-carbon EXCEPT ________.

glycine

The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.

histidine

The conserved residues in the hemoglobins and myoglobins include the ________ proximal and distal to the heme iron.

histidines

The secondary structure of a protein results from _____.

hydrogen bonds

Increase in PCO2 from 20 to 40 mmHg

increase in P50

List two different ways you could change the buffer to elute the bound protein(s) and achieve proper separation of the proteins.

increasing the ionic strength of the buffer add a buffer with pH=8.0

GFP fusion technology would be best used for which of the following experiments?

localizing the compartment where Golgi proteins are found

Schematic models of an IgG antibody molecule and an Fab fragment

loss of the antigen binding

What is the net charge on the following peptide at pH = 0?Peptide sequence: DSVK

net charge = +2

Protein folding is a thermodynamically favorable process under physiological conditions because:

of the large negative enthalpy change associated with many noncovalent interactions.

What type of bond joins the monomers in a protein's primary structure?

peptide

Tertiary structure is NOT directly dependent on _____.

peptide bonds

Rank the following in terms of predicted rates: the nucleation of an αα helix; the nucleation of a parallel ββ sheet; the nucleation of an antiparallel ββ sheet. Justify your predictions.

slower: -The nucleation of a parallel sheet -requires a noncontiguous sequence to form H-bonding. faster: -The nucleation of a helix -requires four ordered contiguous residues to initiate H-bonding. fastest: -The nucleation of an antiparallel sheet -requires three ordered contiguous residues to initiate H-bonding.

Use the table to sort the following ten codons into one of the three bins, according to whether they code for a start codon, an in-sequence amino acid, or a stop codon.

start: AUG stop: UAA, UAG, UGA amino acid: AAA, ACU, UGC, GCA, CAC, AUC

Which of the following bands of the sarcomere does NOT change size during muscle contraction?

the A band

Look at the molecular model of myosin II of striated muscle from chicken. Which part of myosin interacts directly with the actin filament?

the cleft between the lower subdomain and upper subdomain in the heavy chain motor domain

Where in a globular protein is the amino acid alanine likely to be located?

the hydrophobic interior

SDS gel electrophoresis can be used to determine:

the molecular mass of denatured protein subunits.

Examine the molecular model of the actomyosin cycle (Section IV). The powerstroke is caused by a conformational change in the myosin molecule that results from __________.

the release of ADP from the catalytic site in the myosin heavy chain

Review the molecular model of the sarcomere from skeletal muscle. Which component of the actin / tropomyosin / troponin complex in the sarcomere is able to bind to four calcium ions?

the troponin C subunit of the troponin heterotrimer

Calcium regulates muscle contraction by binding to:

troponin C.

In size exclusion chromatography, the smallest proteins are eluted last.

true

Protein biosynthesis uses only L-amino acids.

true

The concentration of Ca2+ in the myoplasm can increase as much as 10,000 fold in response to a motor nerve impulse.

true

What peptides are expected to be produced when α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal) is cleaved by

trypsin: SYSMEHFR,WGKPV cyanogen bromide: SYSM,EHFRWGKPV thermolysin: SYS,MEHFRWGKP,V

If the sequence ATGCATGTCAATTGA were mutated such that a base were inserted after the first G and the third T were deleted, how many amino acids would be changed in the mutant protein?

two

Which step of cross-bridge cycling is considered the power stroke?

when the ADP is released and the myosin cross-bridge moves to the right in the animation

When is the force of contraction of the muscle strongest?

when there is maximal overlap between the thick and thin filaments

Cells expressing the GFP fusion protein will show florescence __________.

where the GFP fusion protein is localized in the cell

Is this molecule likely to exhibit a Bohr effect?

yes

Is this molecule likely to show cooperative oxygen binding?

yes

From your answers to Parts A and B, estimate ΔGfolding for this protein at 25 ∘C

ΔG =47.0kJmol

If the protein folds entirely into αα helix with H bonds as the only source of enthalpy of stabilization, and each mole of H bonds contributes −5−5 kJmol to the enthalpy, estimate ΔHfolding. Note that the ends of helices contain fewer hydrogen bonds per residue than in the middle as shown to the left.

ΔH =-480kJ/mol

Based on the possibility of 2.7×10922.7×1092 conformations, estimate the conformational entropy change on folding a mole of this protein into a native structure with only one conformation.

ΔSΔS =-1.77kJ/K⋅mol

What type of protein secondary structure does the structure shown here (Figure 2) represent?

α-helix

What type of protein secondary structure does the structure shown here (Figure 1) represent?

β-sheet

Using the data in the figure (to one significant figure) and table, estimate the extinction coefficient (in units of cm2/mg for vasopressin, using radiation with λλ= 280 nm

ϵϵ =1 cm2/mg

Estimate the net charge at pH=7. Assume the pKa values given in the table above

-1

Calculate to three decimal places the charge on α-melanotropin at pHpH value of 11.

-1.827

Estimate the net charge at pH=12. Assume the pKa values given in the table above.

-4

Which of the following statements about protein folding and structure are true?

-Chaperones, like the GroEL-ES complex, work by providing a sequestered environment in which proteins can safely explore the conformational space towards productive folding. -Misfolded proteins often aggregate in large structures in the cell. -The native structure of a protein is entirely encoded in its amino acid sequence. -Misfolded proteins are thermodynamically stable versions of a protein.

How long could contraction continue using ATP alone?

0.2s

Calculate the overlap of thick and thin filaments in the relaxed and contracted sarcomere.

0.60,0.75 μm

Assuming the Dalai Lama's hemoglobin has a Hill coefficient = 3.2, and a P50 = 31 mmHg, calculate the change in fractional O2 saturation of his hemoglobin going from his lungs (where PO2 = 85mmHg) to his capillaries (where PO2 = 25 mmHg).

0.63

To characterize the thrombin in the sample, you must remove two proteins that interfere with the thrombin activity assay: cytochrome c and lactoglobin. You find some CM-cellulose and a phosphate buffer (pH=6.4) on the shelf in your lab. You decide to load the protein sample onto a column of CM-cellulose equilibrated in the pH=6.4 buffer. Predict the order of elution for the three proteins shown in the table below

1. Lactoglobin 2. Thrombin (wild type) 3. Cytochrome c

Complete the following vocabulary exercise relating to the level of structure in proteins.

1. Quaternary structure is the result of two or more protein subunits assembling to form a larger, biologically active protein complex. 2. Secondary structure describes the alpha-helices and beta-sheets that are formed by hydrogen bonding between backbone atoms located near each other in the polypeptide chain. 3. Tertiary structure is achieved when a protein folds into a compact, three-dimensional shape stabilized by interactions between side-chain R groups of amino acids 4. Primary structure is the sequence of amino acids in a protein.

Do you expect a Pro → Gly mutation in a surface-loop region of a globular protein to be stabilizing or destabilizing? Assume the mutant folds to a native-like conformation. Explain your answer in terms of the predicted enthalpic and entropic effects of the mutation on the ΔGΔG for protein folding compared to ΔGΔG of folding for the wild-type protein.

1. The ΔSsolvent is likely to be small because side-chain solvation is predicted to be similar in both the folded and unfolded states. ΔSprotein changes the most due to the conformational flexibility of Gly compared to Pro. 2. Gly will stabilize both the folded and the unfolded states; however, it will stabilize the unfolded state more due to the dramatic increase in conformational entropy of the unfolded state as a result of this mutation. 3. The stabilization of the unfolded state for the mutant means that Δ Gfolding(wt) less then Gfolding(mut); thus, the mutation is destabilizing. .

If all creatine phosphate were converted into ATP and utilized as well, how long could contraction continue?

1.25s

An individual "step" by a myosin head in one cycle pulls the thin filament about 15 nm. How many steps must each actin fiber make in one contraction?

10 steps

Using the in table below, calculate the average amino acid residue weight in a protein of typical composition. This is a useful number to know for approximate calculations.

110.76

Calculate the molecular weight of α-melanotropin, using data in the table below.

1623.93 g/mol

Determine whether each term describes the primary, secondary, or tertiary structure of proteins (or forces relating to the primary, secondary, or tertiary structure of proteins).

1: amide bond 2: alpha, beta 3: disulfide bond, salt bridge

Match the following characteristics to α helices, β sheets, or both.

1:A; 2:B; 3:A; 4:C

Please match the correct term on the left with the appropriate structural feature of proteins listed on the right.

1:B; 2:C; 3:D; 4:A

Match the appropriate cells with the correct immune response.

1:C; 2:B; 3:B; 4:B

Match the amino acid (AA) with its correct side chain category:

1:D; 2:C; 3:F; 4:E; 5:B; 6:A

Match the codon with the amino acid it encodes:

1:F; 2:D; 3:B; 4:E; 5:C; 6:A

Calculate to three decimal places the charge on α-melanotropin at pHpH value of 5.

2.104

The following describe the binding of oxygen to human myoglobin at 37 ∘C P50

2.6 mmHg

Based on these assumptions, about how many random-coil conformations will be possible for this protein?

2.7×1095

Calculate to three decimal places the charge on α-melanotropin at pHpH value of 1.

3.998

If you sketch the titration curve for α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal), near what pHpH values would you expect the curve to exhibit inflections? Assume the pKaspKas of the NN- and CC-termini are 7.9 and 3.8, respectively. For side chains, assume the pKapKa values given.

4,7,9,10,12

Under these conditions, what percentage of the oxygen bound in the lungs is delivered to the tissues?

42%

Support your answer with the calculation of the pI of the mutant at pH=5.5. Assume that the only factors impacting the change in the pI are the side chains of the mutant protein.

5.1

Estimate the percent oxygen saturation of blood at 30 mmHg, the approximate partial pressure of O2 in venous blood.

56%

Given what you know about the Bohr shift, what is the difference in O2 saturation of hemoglobin in the lungs versus hemoglobin in exercising tissues, as represented on this graph? Keep in mind that the pH of blood in the lungs is not the same as the pH of blood in exercising tissues.

57%

If the reduced unfolded protein were oxidized prior to the removal of the urea, what fraction of the resulting mixture would you expect to possess native disulfide bonds?

6.67×10−2

Using the data in the figure below, repeat the calculation of the previous part if the pHpH drops to 6.8 in capillaries but goes back to 7.4 as CO2 is unloaded in the lungs

63%

Calculate the pIpI (isoelectric point) of α-melanotropin.

8.813

the fraction saturation of myoglobin at 30 mmHg, the partial pressure of O2O2 in venous blood

92%

Estimate the percent oxygen saturation of blood at 100 mmHg, the approximate partial pressure of O2 in the lungs.

99%

Using the information in table, explain how a point mutation could change a codon for Glu to a codon for Val.

A change of the A in the GAG codon for glutamate to a U would change the codon to GUG, which codes for valine.

Which of the following statements about mutations is false?

A knock-out mutation results in a total absence of the mutated protein.

Which of the following statements is NOT true?

A protein stripped of its cofactor or metal ion is known as a holoprotein.

Applications of mass spectrometry include:

A, B, and C.

Which of the following statements about muscle contraction is TRUE?

ATP hydrolysis causes a conformational change in the myosin head.

Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.

Acidic: glut acid Basic: Arg, Lys Neutral polar: serine, asp, cys, glut, threonine Neutral nonpolar: alanine, proline, meth, phenyl, valine, tyrosine, trypto

Which technique is able to investigate secondary structural features of proteins?

All of the above

Which of the following definitions are correct? 1) An antigen is the substance that elicits an immune response. 2) An epitope is a portion on the surface of an invading particle to which specific antibodies bind. 3) An antibody is a specific immunoglobulin that binds to an antigen.

All of the listed definitions are correct.

Which of the following statements about globular proteins are true?

All of the listed statements are correct.

Which of the following statements about protein quaternary structure are correct?

All of the listed statements are correct.

Which statement correctly describes amphipathic (or amphiphilic) helices and sheets?

Amphipathic helices and sheets have predominantly hydrophilic (or hydrophobic) residues on one face. Submit

If a mutated DNA sequence produces a protein that differs in one central amino acid from the normal protein, which of the following kinds of mutations could have occurred?

An addition mutation and a deletion mutation. Submit

Which of the following is NOT true of immunoglobulin molecules?

Antigenic determinants reside only in the variable region of the light chains.

Do you think apamine is synthesized in the form CNCKAPETALCARRCQQH, or is it more likely a product of proteolytic cleavage of a larger peptide? Explain.

Apamine does not have an N-terminal methionine, so at least some proteolytic cleavage must be involved in its synthesis.

Identify the amino acids in the following tripeptide.

Arg-Val-Tyr

Why might crocodiles have a hemoglobin that is responsive to HCO−3 instead of 2,3-BPG? Recall that crocodiles hold their prey underwater to kill them

As the crocodile stays underwater, its hemoglobin delivers most of the bound O2 as a result of increased binding of HCO3− to the T conformation.

hich of the following statements is true about a protein that is in an aqueous solution that has a pH equal to the pI of the protein?

At pH = pI, there is no net charge on the protein.

At PO2 = 40 mm Hg, which statement about the saturation of either myoglobin (Mb) or hemoglobin (Hb) is true?

At this partial pressure of oxygen, Mb would be almost completely saturated but Hb would not.

Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen?

B and C

Which of the following events could result in a frameshift mutation?

Base deletion

Why do you suppose the Dalai Lama's hemoglobin has a P50 higher than normal (where "normal" = 27 mmHg)?

Because Dalai Lama's concentration of 2,3-BPG is increased.

For the more likely symmetry, what kinds of interactions (isologous, heterologous, or both) would you expect? Why?

Both. There must be heterologous interactions about the 4-fold axis and isologous interactions about the twofold axes.

Suppose a tetramer, like hemoglobin, consists of two each of two types of subunits, αα and ββ. What is the highest symmetry now possible?

C2

A protein is found to be a tetramer of identical subunits. Name two symmetries possible for such a molecule. What kinds of interactions (isologous or heterologous) would stabilize each?

C4 symmetry with heterologous interactions D2 symmetry with isologous interactions

Name two symmetries possible for this molecule.

C8, D4

Why is Ca2+ important to the process of sarcomere shortening?

Ca2+ binds to the troponin complex, which results in exposure of the myosin binding sites on actin. Submit

The Ca2+ transporter in sarcomeres that keeps the [Ca2+]∼10−7M requires ATP to drive transport of Ca2+ ions across the membrane of the sarcoplasmic reticulum. How would a loss of this Ca2+ transport function result in the initiation of rigor mortis?

Ca2+ will leak across the membrane from the side of high Ca2+ concentration (in the transverse tubule) to the side of lower Ca2+ concentration (inside the sarcomere). As [Ca2+] increases, it will bind TnC, thereby stimulating myosin binding to actin.

The most critical substance in stimulating muscle contraction is:

Ca2+.

Explain these results in terms of a model for the protein.

Cleavage of disulfide bondes, after thrombin cleavage, yields two fragments. Protein must have an extended structure, which cleavage at a critical Arg residue can relax, giving faster migration. The little effect of disulfide reduction means that the protein is a single chain.

What do these answers tell you about the role of ATP in providing energy to cells?

Creatine phosphate must be continually produced in active muscle.

At pH=6.4, which protein(s) do you predict will remain bound to the column with minimal flow through CM-cellulose?

Cytochrome c

Identify each amino acid shown below in Fischer projection. Indicate whether the D- or L- enantiomer is shown.

D-Valine D-Threonine D-Asparagine

Which do you think is more likely?

D4, because it involves more subunit-subunit interactions.

There is another melanocyte-stimulating hormone called β-melanotropin. Cleavage of β-melanotropin with trypsin produces the following peptides plus free aspartic acid.WGSPPK, DSGPYK, MEHFR

DSGPYK,MEHFR,WGSPPK

Rigor mortis is maximal at ∼12hrs after death, and by 72hrs is no longer observed. Propose an explanation for the disappearance of rigor mortis after 12hrs.

Decomposition includes cleavage of actin and myosin by intracellular proteases.

If a DNA sequence is altered from TAGCTGA to TAGTGA, what kind of mutation has occurred?

Deletion

Explain your answer.

Deprotonation of histidine 13 destroys the salt bridge, allowing easier opening of the O2 binding site.

What are the N-terminal and C-terminal residues for the following peptide sequence?Peptide sequence: EASY

E is the N-terminal residue; Y is the C-terminal residue.

Which of the following is FALSE when considering the standard genetic code?

Each of the three stop codons can also encode rare modified amino acids.

In the protein adenylate kinase, the CC-terminal region has the sequenceVal-Asp-Asp-Val-Phe-Ser-Gln-Val-Cys-Thr-His-Leu-Asp-Thr-Leu-Lys-The hydrophobic residues in this sequence are presented in boldface type. Suggest a possible reason for the periodicity in their spacing.

Each residue that is hydrophobic lies on one side forming amphipathic αα-helix.

Suggest a method for separating the peptides produced by chymotrypsin treatment.

Electrophoresis Chromatography on a cationic column, at pH=7

Antibodies cannot be used to purify proteins because the antibody-antigen interaction is too strong.

False

Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.

False

F-actin is a polymer of G-actin monomers and exhibits symmetry.

False

Fetal hemoglobin has a higher affinity for oxygen than does maternal hemoglobin because it has a higher affinity for the allosteric regulator 2,3-bisphosphoglycerate.

False

Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state.

False

Proteins cannot self-assemble into a functional conformation after they have been denatured.

False

The greatest conformational change in the neck piece of myosin occurs during ATP hydrolysis.

False

The interactions that stabilize multisubunit complexes are different to those that stabilize tertiary structure.

False

Tropocollagen is a double helix of two left-handed polypeptide chains.

False

True or false? A codon is a group of three bases that can specify more than one amino acid.

False

Which nucleotide will base‑pair with the enol form of 5‑bromouracil?

Guanine

________ between amide protons and carbonyl oxygens is necessary to stabilize a regular folding of protein secondary structure.

Hydrogen bonding

Which of the following is CORRECT when considering the tertiary structure of globular proteins?

Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.

Which of the following statements regarding the folding of proteins is NOT true?

Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions.

Which of the following effects is NOT true?

If stripped Hb is treated with 2,3-BPG, the O2-binding curve for Hb will shift left.

The effect of replacing the proximal histidine in hemoglobin with a glycine residue and adding a noncovalently bonded imidazole. Suggest an explanation.

In native Hb, the binding of oxygen is actually hindered by the fact that pulling on helix F must move it against constraints within the molecule. In the imidazole replacement, there is no need to do the extra work of moving helix F. This difference shows up as a more favorable free energy for binding.

What chromatographic method should make it possible to isolate pure A and B chains?

Ion exchange chromatography. The A chain contains no basic residues in comparison with the B chain, so ion-exchange chromatography should work well.

Polyglycine, a simple polypeptide, can form a helix with ϕ=−80∘ϕ=−80∘ , ψ=+150∘ψ=+150∘. From the Ramachandran plot (see the figure on the left), describe this helix.

It could have polypeptide II helix structure.

Given the helix formed by polyglycine, what can be inferred about its handedness?

It is left-handed.

If ATP was removed from the cell, would the muscle be stiff or flaccid?

It would be stiff because the myosin head would be unable to release the actin binding site.

Find a start signal, and write the amino acid sequence that is coded for.5'...GCCAUGUUUCCGAGUUAUCCCAAAGAUAAAAAAGAG...3'

MFPSYPKDKKE

During translation, nucleotide base triplets (codons) in mRNA are read in sequence in the 5' → 3' direction along the mRNA. Amino acids are specified by the string of codons. What amino acid sequence does the following mRNA nucleotide sequence specify? 5′−AUGGCAAGAAAA−3′

Met-Ala-Arg-Lys

What amino acid sequence does the following DNA template sequence specify? 3′−TACAGAACGGTA−5′

Met-Ser-Cys-His

Are the helices bound to the DNA likely to be amphiphilic? Explain.

No. DNA is charged and therefore polar, so the DNA-binding helix is likely to be composed of polar residues that interact with either the DNA or the solvent.

The estimate obtained in Part A is surely too large. Give one reason why.

Not all of these conformations will be sterically possible.

Which mutation(s) would not change the remainder of the reading frame of a gene sequence that follows the mutation(s)?

One addition and one deletion mutation. Submit

Glycine and proline are both non-polar amino acids, and both are very likely to be found at the surface of proteins. What physical characteristic of each is responsible for this observation?

Only statement 2 is correct.

Which of the following statements about the Bohr effect are true?

Only statements 1 and 2 are correct.

Which of the following characteristics are true about a typical peptide (amide) bond?

Only statements 1 and 3 are correct.

Hemoglobin (Hb) can be viewed as having two quaternary states, a low oxygen affinity state (T), and a high oxygen affinity state (R). Which of the following statements about the binding of O2 by Hb are true?

Only statements 1, 2, and 3 are true.

Which statements regarding shape and charge complementarity are true?

Only statements 1, 2, and 3 are true.

Which statements about the generation of antibody diversity are true?

Only statements 1, 2, and 4 are true.

Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid?

Only statements 2, 3, and 4 are valid.

Which of the following statements about α-keratins is FALSE?

Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions.

Give two reasons to explain why a proline residue in the middle of an α-helix is predicted to be destabilizing to the helical structure.

Pro is not able to adopt the ideal ϕ and ψ angles for an α -helix.Pro does not have the α−NH group that acts as a stabilizing H-bond donor in the middle of the helix.

Which of the following amino acids would most likely be found on the surface of a protein?

Proline Aspartic acid

A ________ plot describes which structures in a polypeptide are sterically possible and which are not based on the angles of rotation about the backbone Namide -Cα and Cα-Ccarbonyl bonds.

Ramachandran

Consult the figure on the left and describe, in terms of the six-step model of muscle contraction, how a lack of ATP in sarcomeres would result in rigor mortis.

Release of the myosin headpiece from the thin filament requires ATP binding. Until ATP binds, the myosin-actin cross-bridge will remain intact, thereby preventing extension of the sarcomeres.

The melanocyte-stimulating peptide hormone α-melanotropin has the following sequence:Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val

SYSMEHFRWGKPV

Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally?

Selenocysteine

What is a potential limitation of GFP?

Short wavelengths of excitation light can damage the cell's DNA.

Human and sperm whale myoglobin have very similar primary structures. Which of the following statements are correct?

Statements 1 and 2 are correct.

The side chain of histidine has a typical pKa value in the range of 6.5-7.4. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which of the following statements correctly explain this anomaly?

Statements 1 and 2 are correct.

Which statements about β and γ turns are correct?

Statements 1, 2, and 4 are correct.

In considering protein secondary structure which of the following is INCORRECT?

The 310 helix is right-handed and often contains proline residues.

What is important in cloning the GFP cDNA into the vector?

The GFP cDNA is in the same reading frame as the target protein.

Where do you predict the N- and C-termini are located for Max?

The N-terminus is interacting with the DNA. The α-amino group of the N-terminus is positively charged and will interact favorably with the negative charge on the phosphodiester backbone of the DNA.

For an amino acid such as aspartic acid, what impact do you expect the two neighboring carboxylic acids to have on the pKa values for each?

The acid with the lower pKa value would increase the pKa value for the other acid.

Which of the following statements about antibody structure is NOT true?

The constant domains are located at the ends of the Y-like fork of the antibody, where they form two identical binding sites for antigens.

Which of the following statements about insulin is INCORRECT?

The disulfide bonds form after the final proteolytic cleavage to yield mature insulin.

Which search do you predict will give you alignments with "expect scores" closer to one? Explain your reasoning.

The expect score for the shorter sequence is more likely to be closer to one (i.e., the shorter sequence is more likely to match many entries in the database). Submit

Is the folded form of the protein stable at 25 ∘C

The folded form of the protein is not stable at 25 ∘C

It has been found that in some of the αα-helical regions of hemerythrin, about every third or fourth amino acid residue is a hydrophobic one. Suggest a structural reason for this finding.

The four helices could be arranged so that to stabilize hydrophobic core.

Which of the following statements is FALSE?

The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen.

Which statement about the binding of oxygen to heme is NOT true?

The iron ion bound to the porphyrin group is +3.

Explain your answer.

The linkage between subunits is such that forcing one pair of helices apart favors moving the other pair apart, making O2 binding easier in the second pair.

Predict the likely effect of a mutation that replaced aspartic acid 85 by a lysine residue.

The molecule would exhibit lesser cooperativity. The molecule would exhibit higher O2 affinity. The whole structure would become unstable.

Is the pIpI of the mutant protein predicted to be greater than, less than, or the same as the pIpI of the normal protein?

The pI of the mutant protein predicted to be less than the pI of the normal protein.

Do you expect the pIpI for the sickle-cell β-globin to be higher or lower than the pIpI for wild-type β-globin? Explain

The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge.

The Foundation Figure began by discussing the importance and relevance of protein structure. Fill in the blanks in the paragraph below with a word or phrase from the word bank that best completes the sentence.

The structure of a protein dictates the partners with which it can interact. Therefore, the structure of a protein is directly related to its function. The contours of a protein determine the shape that its interaction partner must have, whereas the surface chemistry of a protein determines the kinds of chemical interactions that the protein will make with its interaction partner (e.g. Coulombic interactions or hydrogen bonding). Therefore, a protein will only bind to molecules that have the appropriate shape and chemistry (i.e. only those that are complementary to the protein).

A short 8-residue sequence of a polypeptide is determined to have φ angles ranging from -65 degrees to -80 degrees and ψ angles ranging from -40 degrees to -50 degrees. What conclusion can be drawn from this data?

This segment has helical content.

What would be the effect of a mutation that placed a proline residue at point A in the structure?

This would break the helix near the binding sites and Fe2Fe2 could not be bound, and the mutant protein would be nonfunctional.

Comparison of globin sequences from many different species suggests that myoglobin and hemoglobin have evolved from a single myoglobin-like protein.

True

Fibroin is a β-sheet protein, with a high proportion of glycine.

True

Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry.

True

Tautomers of nucleotide bases are isomers that differ from each other in the location of one hydrogen atom in the molecule.

True

The amino acid side chain residues in an α helix point outwards away from the center of the helix.

True

The folded conformation of proteins can be stabilized by the binding of a metal ion or cofactor.

True

The immunoglobulin domain is a stable scaffold containing two antiparallel β- sheets upon which to display hypervariable loops.

True

If apamine does not react with iodoacetate, then how many disulfide bonds are present?

Two disulfides.

You are surprised to observe that the patient's thrombin flows through the CM-cellulose column at pH=6.4pH=6.4 faster than expected based on its pIpI. Confident in your technique, you suspect the patient's thrombin is different from wild-type thrombin. Using a different buffer system, you manage to purify some of the patient's thrombin and you submit the purified sample for amino acid sequencing. The sequence analysis shows that the patient's thrombin contains a mutation in the enzyme active site. A lysine residue in the wild type has been mutated to an asparagine in the patient's thrombin. Does this mutation explain the anomalous CM-cellulose binding behavior you observed?

Yes. Loss of a (+)-charged side chain will increase the (−−) charge density on the protein, making it less likely to bind to the CM cellulose.

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gene

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH−OH groups. Which amino acid side chains, or main chain groups, in a polypeptide are most likely to be modified by treatment with:

acetic anhydride: Lysine, N-terminal amine iodoacetate: Cysteine kinase + ATP: Threonine, Serine, Tyrosine

Proteins are polymers of _____.

amino acids

View the molecular model of the myosin-actin interaction. The actin-binding cleft in myosin contacts residues 335-372 in the actin monomer. What can sterically block this association and keep the muscle in a relaxed state?

binding by tropomyosin

Examine the molecular model of the yeast G-actin monomer. The folding of a loop in subdomain 2 of actin into an alpha helix occurs when __________.

bound ATP is hydrolyzed to ADP Submit

A solution of vasopressin is placed in a 0.5-cm-thick cuvette. Its absorbance at 280 nm is found to be 1.3. What is the concentration of vasopressin, in mg/cm3

cc =2.77 mg/cm3

The specific interaction between an antibody and antigen occurs by virtue of both shape and ________ complementarity.

charge

The protein that makes up about a third of the total protein mass in animals is:

collagen.

Dissociation into monomer polypeptide chains

decrease in P50

What qualitative effect would you expect each of the following to have on the P50P50 of hemoglobin? Increase in pHpH from 7.2 to 7.4

decrease in P50