chapter 6 biochem

Match the following characteristics to α helices, β sheets, or both. 1) 5.4Å/turn 2) antiparallel arrangement 3) large dipole moment 4) extensive H-bonding network A) α helices B) β sheets C) both

1A, 2B, 3A, 4C

Consider a small protein containing 101 amino acid residues. The protein will have 200 bonds about which rotation can occur. Assume that three orientations are possible about each of these bonds. Based on these assumptions, about how many random-coil conformations will be possible for this protein? ***** The estimate obtained in Part A is surely too large. Give one reason why. A) Not all of these conformations will be sterically possible. B) During folding protein does not pass into these conformation because of extra negative ΔHU→F values. C) Majority of these conformations has extra positive ΔSU→F.

2.7 x 10^95 A

Describe the native protein, in terms of the kinds of subunits present, the stoichiometry of subunits, and the kinds of bonding (covalent, noncovalent) existing between subunits. The ____________ units are paired by at least one disulfide bond. The native molecule contains of __________ units that suggested by the pattern of ___________ in the ___________ of BME. There are __________, noncovalently linked subunits that suggested by the pattern __________ of in the ___________ of BME. 1. two identical 2. absence 3. MW≈ 30,000 and MW≈ 40,000 4. MW≈ 70,000 5. four 6. presence

3 5, 3, 6 1, 4, 2

In considering protein secondary structure which of the following is INCORRECT? A) The 310 helix is right-handed and often contains proline residues. B) The most common structures are the α helix and the β sheet. C) The β strands can be in either parallel or antiparallel configuration. D) A network of main-chain hydrogen bonds connect β strands in a β sheet. E) An α helix repeats after 18 residues and has 3.6 residues per turn.

A

What is a potential limitation of GFP? A) Short wavelengths of excitation light can damage the cell's DNA. B) GFP is often cytotoxic. C) GFP can fluoresce only in vitro. D) GFP chimeras are usually recognized as improper and degraded.

A

GFP fusion technology would be best used for which of the following experiments? A) localizing mRNAs for flagellar proteins B) finding the gene for Alzheimer's disease C) determining the lipids in the smooth endoplasmic reticulum membrane D) localizing the compartment where Golgi proteins are found

D

Polyglycine, a simple polypeptide, can form a helix with ϕ=−80∘ , ψ=+150∘. From the Ramachandran plot (see the figure on the left), describe this helix. Check all that apply. A) It could have α helix structure. B) It could have antiparallel β strands structure. C) It could have parallel β strands structure. D) It could have polypeptide II helix structure. E) It could have 310 helix structure.

D

Which statements about β and γ turns are correct? 1) Their purpose is to reverse the direction of the polypeptide chain. 2) There are two types, I and II, which differ mainly in the conformation about the i+1 and i+2 residue amide bond. 3) They typically contain large, hydrophobic residues. 4) Their conformation is held in place through H bonds.

Statements 1, 2, and 4 are correct

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

false

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

false

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

false

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

false

The secondary structure of a protein results from _____. hydrogen bonds bonds between sulfur atoms hydrophobic interactions ionic bonds peptide bonds

hydrogen bonds

The formation of favorable ______ ionic or _______ interactions in a _______ protein replace interactions between solvent (water) and the ionic species (or ______ donors and acceptors) in the _______ state. The favorable ΔH obtained by formation of _______ bonds in the ______ protein is offset by the energy required to _______ many interactions, with solvent going from the ________ to the _______ state. Fill in the blank. intermolecular C-bonding folded unfolded break H-bond restore intramolecular H-bonding C-bond

intramolecular, H-bonding, folded, H-bond, unfolded, intramolecular, folded, break, unfolded, folded

Given the helix formed by polyglycine, what can be inferred about its handedness? A) It is left-handed. B) It is right-handed.

left-handed

The peptide hormone vasopressin is used in the regulation of saltwater balance in many vertebrates. Porcine (pig) vasopressin has the sequence Asp-Tyr-Phe-Glu-Asn-Cys-Pro-Lys-Gly 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 λ= 280 nm. ϵ = ***** 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 . c =

ϵ = 1 cm^2/mg c = 2.77 mg/cm^3

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

true

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

true

Consider a small protein containing 101 amino acid residues. The protein will have 200 bonds about which rotation can occur. Assume that three orientations are possible about each of these bonds. Based on the possibility of 2.7×1092 conformations, estimate the conformational entropy change on folding a mole of this protein into a native structure with only one conformation. ΔS = ***** If the protein folds entirely into α helix with H bonds as the only source of enthalpy of stabilization, and each mole of H bonds contributes −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 = ***** From your answers to Parts A and B, estimate ΔGfolding for this protein at 25 ∘C. ΔG = ***** Is the folded form of the protein stable at 25 ∘C? A) The folded form of the protein is stable at 25 ∘C. B) The folded form of the protein is not stable at 25 ∘C.

-1.77 kJ/Kmol -480 kJ/mol 47.0 kJmol B

Which of the following statements about protein folding and structure are true? Check all that apply. 1) Misfolded proteins often aggregate in large structures in the cell. 2) Misfolded proteins are thermodynamically stable versions of a protein. 3) Chaperones "know" how to actively fold proteins into their proper final structure. 4) Each protein has its own "assigned" chaperone to assist in its proper folding. 5) Misfolded proteins are innocuous and readily cleared by the cell. 6) The native structure of a protein is entirely encoded in its amino acid sequence. 7) Chaperones, like the GroEL-ES complex, work by providing a sequestered environment in which proteins can safely explore the conformational space towards productive folding.

1, 2, 6, 7

Fill in the blanks with primary, secondary, tertiary, or quaternary. 1. _________ 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. 2. __________ structure is achieved when a protein folds into a compact, three-dimensional shape stabilized by interactions between side-chain R groups of amino acids 3. __________ structure is the sequence of amino acids in a protein. 4. ___________ structure is the result of two or more protein subunits assembling to form a larger, biologically active protein complex.

1. secondary 2. tertiary 3. primary 4. quaternary

1. The _______ is likely to be small because side-chain solvation is predicted to be ______ in both the folded and unfolded states. _______ changes the most due to the conformational flexibility of Gly compared to Pro. 2. Gly will _____ both the folded and the unfolded states; however, it will _______ the unfolded state more due to the dramatic increase in conformational entropy of the unfolded state as a result of this mutation. 3. The _______ of the unfolded state for the mutant means that _______ less then _______ ; thus, the mutation is _______ . Fill in the blanks from the word bank. ΔHfoldet ΔGfolding(wt) similar destabilization ΔSsolvent stabilizing stabilize destabilize destabilizing different ΔGfolding(mut) ΔSprotein stabilization ΔHunfoldet

1. ΔSsolvent, similiar, ΔSprotein 2. stabilize, stabilize 3. stabilization, ΔGfolding(wt), ΔGfolding(mut), destabilizating

Please match the correct term on the left with the appropriate structural feature of proteins listed on the right. 1) primary structure 2) secondary structure 3) tertiary structure 4) quaternary structure A) the interaction between two separate protein strands B) the sequence of AA C) small sections of organized protein structure, such as helices D) the overall fold of a single protein strand, such as the globulin fold

1B, 2C, 3D, 4A

Protein must have _____________, which cleavage at a critical Arg residue can relax, giving faster migration. Cleavage of disulfide bondes, after thrombin cleavage, ___________. The little effect of disulfide reduction means that _____________. Fill in the blanks. 1) separates two subunits 2) yields two fragments 3) the protein is a single chain 4) the protein consists of two subunits 5) an extended structure 6) a quaternary structure

5 , 2, 3

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 x 10^-2

Cells expressing the GFP fusion protein will show florescence __________. A) where the GFP fusion protein is localized in the cell B) wherever the GFP gene is normally expressed C) where the injected mRNA or cDNA is located D) wherever the target protein is normally located

A

In the protein adenylate kinase, the C-terminal region has the sequence Val-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. A) Each residue that is hydrophobic lies on one side forming amphipathic α-helix. B) Active site of the adenylate kinase is formed by packed together hydrophobic residues. C) Hydrophobic residues give rise to a helical dipole moment and partial (-) charge of the C-terminus. D) Localization of hydrophobic residues on the one side of β-strand mediates the interactions with other one of the polypeptide chain.

A

What would be the effect of a mutation that placed a proline residue at point A in the structure? A) This would break the helix near the binding sites and Fe2 could not be bound, and the mutant protein would be nonfunctional. B) This would break the helix near the Fe2 binding sites, and the mutant protein would change functions. C) This would break the helix and form hairpin structures, that would make the mutant protein nonfunctional.

A

Where do you predict the N- and C-termini are located for Max? A) 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. B) The C-terminus is interacting with the DNA. The α-carboxyl group of the C-terminus has negative charge that help to relax the super coils of DNA. C) The N-terminus and the C-terminus are hidden in the protein core. Both free ends of the protein should be protected from the action of proteases by intramolecular interactions.

A

Which of the following statements is NOT true? A) A protein stripped of its cofactor or metal ion is known as a holoprotein. B) A prosthetic group is usually a small organic molecule required for activity by a protein. C) A cofactor usually refers to a metal ion required for activity by a protein. D) An intact protein, complete with its cofactor or metal ion, is known as a holoprotein.

A

Which statement correctly describes amphipathic (or amphiphilic) helices and sheets? A) Amphipathic helices and sheets have predominantly hydrophilic (or hydrophobic) residues on one face. B) Sheets are typically hydrophilic on one surface, whereas helices usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure. C) Helices are typically hydrophilic on one surface, whereas sheets usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure. D) Amphipathic helices and sheets have hydrophilic and hydrophobic residues evenly distributed throughout their structure.

A

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? Check all that apply. A) D2 symmetry with isologous interactions B) C2 symmetry with heterologous interactions C) C2 symmetry with isologous interactions D) C4 symmetry with isologous interactions E) D2 symmetry with heterologous interactions F) D4 symmetry with heterologous interactions

A and B

Which of the following statements about globular proteins are true? 1) The protein folds to make itself as compact as possible. 2) The packing of the protein is such that hydrophilic residues appear on the surface where they can interact with an aqueous environment. 3) Irregularities of the protein's surface allow for the formation of clefts, which are often where the protein promotes a chemical transformation. 4) Regions of secondary structures folding on one another are examples of the protein's tertiary structure.

All of the listed statements are correct

Which of the following statements about protein quaternary structure are correct? 1) It involves a complex of two or more proteins interacting with each other. 2) The subunits of the structure can be either identical or different. 3) The interactions between subunits can give rise to indefinite growth of polymeric complexes. 4) Most assemblies of protein subunits have one or more defined axis of rotation.

All of the listed statements are correct.

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? A) This segment is mostly β sheet. B) This segment has helical content. C) The sequence has no defined secondary structure. D) No conclusion can be drawn.

B

It has been found that in some of the α-helical regions of hemerythrin, about every third or fourth amino acid residue is a hydrophobic one. Suggest a structural reason for this finding. A) The hydrophobic residues share polar regions of the helix, forming a regular helical structure B) The four helices could be arranged so that to stabilize hydrophobic core. C) This order of residues stabilize turns and affects the angle of rotation of spiral turns.

B

Protein folding is a thermodynamically favorable process under physiological conditions because: A) there is an increase in entropy associated with protein folding. B) of the large negative enthalpy change associated with many noncovalent interactions. C) there is a decrease in entropy of the solvent by burying hydrophobic groups within the molecule. D) no intermediate stage disulphide bonds form during the folding process. E) all of the above.

B

SDS gel electrophoresis can be used to determine: A) the overall charge on a polypeptide. B) the molecular mass of denatured protein subunits. C) whether subunits in a protein complex are identical or not. D) the molecular mass of a native protein complex. E) none of the above.

B

What is important in cloning the GFP cDNA into the vector? A) The GFP cDNA is inserted after the target protein cDNA. B) The GFP cDNA is in the same reading frame as the target protein. C) The GFP cDNA has its own promoter. D) The GFP cDNA is able to show fluorescence.

B

Where in a globular protein is the amino acid alanine likely to be located? A) the hydrophilic interior B) the hydrophobic interior C) the hydrophilic exterior D) the hydrophobic exterior

B

Which of the following statements regarding the folding of proteins is NOT true? A) Salt bridges stabilize the fold. B) Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions. C) Van der Waals interactions have a stabilizing, cumulative effect. D) Internal H bonds stabilize the fold.

B

Are the helices bound to the DNA likely to be amphiphilic? Explain. A) Yes, it is likely amphiphilic. DNA-binding helix has an affinity to specific DNA sites and has difficult change landscape for interactions with certain sequences of nucleic residues. B) Yes. DNA is uncharged charged, and protein sites that interact with DNA can have either positive or negative charge. Therefor the DNA-binding helix is likely nonpolar. C) 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.

C

For which of the following may GFP fusion technology NOT be a good technique to use? A) for transmembrane proteins with cytoplasmic domains B) for soluble proteins found in the cytosol C) for target proteins whose structure is altered by a GFP fusion D) for proteins restricted to the nucleus

C

Which of the following is CORRECT when considering the tertiary structure of globular proteins? A) β sheets cannot be twisted or wrapped into barrel structures. B) The amino acid proline never occurs in a region where the polypeptide chain bends or turns. C) Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside. D) All parts of the proteins can be classified as helix, β sheet or turns. E) None of the above.

C

Which of the following statements about α-keratins is FALSE? A) Individual molecules are α-helical. B) There is a strip of contiguous hydrophobic surface making a shallow spiral around the helix. C) Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions. D) They include a small globular regions covalently linked to the surface. E) They include a major class of protein that comprises hair, fingernails and animal skin.

C

Which of the following statements is NOT true? A) A cofactor usually refers to a metal ion required for activity by a protein. B) A prosthetic group is usually a small organic molecule required for activity by a protein. C) A protein stripped of its cofactor or metal ion is known as a holoprotein. D) An intact protein, complete with its cofactor or metal ion, is known as a holoprotein.

C

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. Chek all tha apply. A) Pro is nonpolar amino acid that destabilizes polar core of the protein. B) Pro is nonpolar amino acid that does not connect turns of the α-helix. C) Pro does not have the α−NH group that acts as a stabilizing H-bond donor in the middle of the helix. D) Pro is not able to adopt the ideal ϕ and ψ angles for an α -helix. E) Insertion of Pro gives an exceptional conformational rigidity to the protein chain chain.

C and D

Suppose a tetramer, like hemoglobin, consists of two each of two types of subunits, α and β. What is the highest symmetry now possible? C4 C1 D2 D4 C2

C2

Under physiological conditions, the protein hemerythrin exists as an octamer of eight chains of the kind shown in the figure below. Name two symmetries possible for this molecule. Check all that apply. D8 C8 D2 C2 C1 D4 ***** Which do you think is more likely? A) C8, because it increases the value of the free energy. B) D4, because it involves more subunit-subunit interactions. C) C8, because it increases the number of possible conformations. D) D4, because it forms more axes of symmetry. ***** For the more likely symmetry, what kinds of interactions (isologous, heterologous, or both) would you expect? Why? A) Both. There must be heterologous interactions about the 4-fold axis and isologous interactions about the twofold axes. B) Isologous interactions give rise to more complex quaternary structures of higher symmetry and lead to indefinite growth. C) Heterologous interactions set the angle and direction of attachment of oligomers that reduces the number of possible configurations and energy states.

C8 an D4 B A

If this model is correct, what are the implications for structural -prediction schemes? A) Any protein has substantial number of conformations. Sorting of optional secondary/tertiary structures are not a reliable method. B) Prions are formed from normal proteins only under the influence of wrongly folded ones. This event cannot be predicted by existing methods. C) Environmental conditions greatly affect the protein folding. Investigation of unchangeable primary structure provides reliable data. D) More than one secondary/tertiary folding can be observed for the same sequence. Sequence alone cannot dictate folding, and sequence-based predictions must sometimes fail.

D

Which of the following statements regarding the folding of proteins is NOT true? A) Van der Waals interactions have a stabilizing, cumulative effect. B) Internal H bonds stabilize the fold. C) Salt bridges stabilize the fold. D) Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions.

D

The protein that makes up about a third of the total protein mass in animals is: A) β-keratin. B) hemoglobin. C) α-keratin. D) myoglobin. E) collagen.

E

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

Hydrogen bonding

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

Which technique is able to investigate secondary structural features of proteins? A) Ultraviolet spectroscopy B) Circular dichroism C) Fluorescence spectroscopy D) Infrared spectroscopy E) All of the above

all of the above

What type of protein secondary structure does the structure shown here (Figure 2) represent? β-sheet β-helix α-helix α-sheet γ-turn

alpha helix

Proteins are polymers of _____. CH2O units amino acids nucleotides hydrocarbons glycerol

amino acids

How might you show that changes in secondary structure occur? Check all that apply. a) with ultraviolet spectroscopy b) with circular dichroism spectropolarimetry c) with SDS gel electrophoresis d) with fourier transform infrared spectroscopy e) with nuclear magnetic resonance spectroscopy

b, d, e

What type of protein secondary structure does the structure shown here (Figure 1) represent? α-helix α-sheet β-helix β-sheet γ-turn

beta sheet

The structure of a protein dictates the partners with which it can interact. Therefore, the structure of a protein is directly related to its _________. The contours of a protein determine the _______ 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 __________). Therefore, a protein will only bind to molecules that have the appropriate shape and chemistry (i.e. only those that are _________ the protein). Fill in the blanks inside-out opposed to distorted by shape hydrogen bonding location function color size complementary to

function shape hydrogen bonding complementary to

The denaturing of proteins occurs when the stabilizing forces are altered. Below is the set of processes in which proteins are denatured. Classify the following processes according to the denaturing agent involved. Classify as mechanical action, chemical action, or heating action 1) beating of eggs 2) action of gastric juices on consumed food 3) preparation of bread from mixed dough by baking 4) preparation of yogurt by adding bacteria cultures 5) straightening frizzy and tangled hair using hair conditioner

mechanical: 1 chemical: 2, 4, 5 heating: 3

Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid? 1) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. 2) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. 3) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. 4) Protein folding is determined by its primary sequence.

only statements 2, 3, and 4 are valid

What type of bond joins the monomers in a protein's primary structure? peptide ionic S - S hydrogen hydrophobic

peptide

Tertiary structure is NOT directly dependent on _____. peptide bonds ionic bonds hydrophobic interactions hydrogen bonds bonds between sulfur atoms

peptide bonds

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). salt bridge amide bond alpha helix beta-pleated sheet disulfide bond

primary: amide bond and disulfide bond secondary: alpha helix and beta-pleated sheet tertiary: salt bridge

Rank the following in terms of predicted rates: the nucleation of an α helix; the nucleation of a parallel β sheet; the nucleation of an antiparallel β sheet. Justify your predictions. Rank as slower, faster, or fastest. A) the nucleation of a parallel sheet B) the nucleation of a helix C) requires four ordered contiguous residues to initiate H-bonding D) the nucleation of an antiparallel sheet E) requires three ordered contiguous residues to initiate H-bonding F) requires a noncontiguous sequence to form H-bonding

slower: A and F faster: B and C fastest: D and E

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

true

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

true