Chapter 4 Protein Structure BMB HW +RQ

How many ATP molecules are hydrolyzed during a full cycle of GroEL-GroES-aided protein folding? 7 14 21 28

14 The GroEL-GroES complex is made up of seven subunits and each subunit has an ATP binding site. The four-step cycle requires hydrolysis of ATP by each subunit to cause conformational changes to allow for protein folding, as well as hydrolysis of ATP by each subunit to cause conformation changes for protein release. Thus 14 ATP molecules are required.

What is the approximate molecular weight of a protein composed of 70 amino acids?

7700 daltons -average weight of amino acid: 110 (70x 110)= 7700

Which of the following is correct concerning a peptide backbone? The peptide bond allows for free rotation due to its single bond character. The torsional angle between the amide nitrogen and the Cα is called ψ (psi). The torsional angle between the Cα and the R group is called φ (phi). A Ramachandran plot shows the allowable φ and ψ angles for a peptide.

A Ramachandran plot shows the allowable φ and ψ angles for a peptide. The peptide bond has double bond character because of the resonance in the C-N and C=O bonds. This resonance makes the peptide bond rigid. The torsional angle between the amide nitrogen and the Cα is called φ and the torsional angle between the Cα and the carbonyl carbon is called ψ. Ramachandran plots show the allowable angles in a peptide that avoids steric hindrance.

What is the quaternary structure of a hexamer made of three different homodimers?

A2B2C2 dimers-- 2 of each subunit

Another hexamer is composed of two homotrimers. Using the same letter/number designation as before, indicate its quaternary structure.

A3B3 trimers-- 3 of each subunit

An antigen binds to an antibody at which of the following locations? Only at the light chain Only at the heavy chain At the constant domain At the variable domain

At the variable domain Antibodies are made up of two light chains and two heavy chains that are held together by disulfide bonds. The constant domain is the same for all antibodies. The variable region differs depending on that antibody target. This region forms the antigen binding site.

Which of the following fibrous proteins contains 4-hydroxyproline as part of its repeating pattern? Keratin Collagen Fibroin heavy chain Fibroin light chain

Collagen Fibrous proteins have repeating patterns of amino acids that allow for secondary structures to come together into very stable tertiary and quaternary structures. In the case of collagen, the non-standard amino acid 4-hydroxyproline helps stabilize the structure via hydrophobic interactions. The illness scurvy results from a lack of vitamin C, which is necessary to produce 4-hydroxyproline.

Disulfide bonds are covalent interactions formed between which amino acid residues?

Cys

Which of the following protein-folding diseases is a loss-of-function disease? Cystic fibrosis Huntington's disease Alzheimer's disease Creutzfeldt-Jakob disease

Cystic fibrosis Cystic fibrosis results from a genetic mutation that leads to a misfolded protein. This protein is degraded, leading to a loss of function. Huntington's disease, like other triplet expansion diseases, results from proteins with long tracts of a repeating amino acid (i.e., glutamine in Huntington's). These regions produce misfolded and aggregated proteins that result in a gain of function. Alzheimer's disease also results from aggregated protein, but there is no amino acid mutation. Creutzfeldt-Jakob disease, like other transmissible spongiform encephalopathies (TSEs), results from a normal protein existing in two different conformations. One of these conformations leads to aggregation and the disease.

Which of the following is NOT accurately classified as a motif? Four-helix bundle Greek key fold Rossmann fold FERM domain fold

FERM domain fold Motifs are smaller, defined structural units within protein folds. Domains are independently folding modules within a polypeptide chain. The four-helix bundle, the Greek key fold, and the Rossmann fold are common motifs. The FERM domain fold is larger and contains three distinct subdomains.

Multiple sea creatures utilize proteins that interact with light. Why would GFP not be a good choice of light-interacting protein for a creature that lives exclusively in a cold, dark sea cave?

GFP would not emit green light since there is no blue light for it to absorb and re-emit. GFP is a fluorescent protein. It does not generate light, but rather absorbs blue light and re-emits it as lower energy green light. Therefore, in a dark cave, GFP would not emit green light since there is no blue light for it to absorb and re-emit.

Based on the hydrophobic collapse model for protein folding, which of the following conditions can denature a protein?

Heating proteins leads to exposure of the hydrophobic core, disrupting folding. Changes in pH break salt bridge interactions that stabilize the sequesteration of hydrophobic residues into the protected core of the protein.

Rhodopsin is made up of amphipathic α helices and is embedded in the lipid membrane. __________ amino acids are likely to be found on the interior-facing helical surface. Non-polar Aromatic Hydrophobic Hydrophilic

Hydrophilic Amphipathic α helices have hydrophilic and hydrophobic properties. The exterior-facing surface of rhodopsin will be interacting with the lipid membrane, which is hydrophobic. Thus hydrophobic amino acids will be found on the exterior-facing surfaces. The interior-facing helical surface will be made up of hydrophilic amino acids.

Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into the appropriate categories.

Hydrophobic: - methionine, isoleucine, valine, phenyalaline Hydrophilic: - aspartate, lysine

Disulfide bonds in proteins are only involved in tertiary structure. only involved in quaternary structure. irreversible. important for proteins found in oxidizing environments.

Important for proteins found in oxidizing environments Disulfide bonds are involved in both tertiary and quaternary structure. These covalent linkages are stronger than the typical weak interactions responsible for protein structure, but they are also reversible. Disulfide bonds are important in oxidizing environments and help keep proteins active.

Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true?

Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails.

Which of the following residues would you likely find in a transmembrane spanning α helices?

Leucine and isoleucine, since they are hydrophobic (matching the interior of the membrane) and have a high propensity to form α helices.

Which of the following is categorized as a charged amino acid? R A Q M

R Charged amino acids have ionizable side chains. Arginine, or R, has a net positive charge at physiological pH.

globular proteins

Ras (a low molecular weight G protein) Serum albumin Hemoglobin Heterotrimeric G protein

For Anfinsen's studies of RNaseA folding, which of the following is not correct? Urea was used to disrupt polar interactions within the protein. β-mercaptoethanol was used to reduce disulfide bonds. Removal of β-mercaptoethanol, followed by removal of urea, resulted in active RNaseA. Removal of β-mercaptoethanol and urea at the same time resulted in active RNaseA.

Removal β-mercaptoethanol, followed by removal of urea, resulted in active RNaseA. Anfinsen's studies showed that the information needed to fold a protein was in the primary amino acid sequence. Urea and β-mercaptoethanol were used to completely unfold the protein and to disrupt disulfide bonds. By removing both the urea and the β-mercaptoethanol at the same time, the protein was able to refold properly and regained activity. If β-mercaptoethanol is removed first, random disulfide bonds form, which keeps the protein inactive. After removing urea, a small amount of b-mercaptoethanol is necessary to break and reform the appropriate disulfide bonds.

Which of the following is most likely to be found on the exterior of a protein? Glu Trp Pro Ser

Ser Hydrophilic amino acids are most likely to be found on protein surfaces because the surface will interact with the aqueous environment. Serine, or Ser, is hydrophilic.

A __________ mutation will not lead to a change in the protein product of a gene. missense nonsense silent frameshift

Silent A missense mutation leads to a single amino acid change in the resulting protein product, which may or may not affect the activity of the protein. A nonsense mutation causes a premature stop codon and a truncated protein product. A frameshift mutation is due to insertion or deletion mutations, which changes the codon register, or the frame. The amino acid sequence is altered by this new reading frame until a stop codon is reached. A silent mutation is a change at the DNA level that does not change the resulting protein product. Due to the degeneracy of the genetic code, multiple codons can lead to the same amino acid.

Which of the following amino acid sequences could form an amphipathic helix?

TVVEAIDRLVDT

GFP is frequently used as a reporter of expression, being added as a fusion tag to other proteins of interest. What would you expect to observe if you overexpressed a GFP fusion protein in E. coli?

The E. coli would have a green appearance when observed in white light When observed in white light, overexpression of GFP would cause the E. coli to appear green. This occurs since white light has a blue component that can be absorbed by GFP and can then be re-emitted as photons of green light.

If a semi-conservative mutation occurred in the GroEL gene that abolished ATP binding, what functional consequence would you predict?

The GroEL complex would form but would not act as a chaperone.

Which of the following is correct about protein folding? Protein folding in vivo takes place under more dilute conditions than those used in vitro. The amino acid sequence of a protein leads to a limited number of possible folding pathways. The decrease in possible conformations for a polypeptide is a larger contribution to the entropy of folding than the increased disorder of surrounding water molecules. Folding does not begin in vivo until the entire polypeptide chain is synthesized.

The amino acid sequence of a protein leads to a limited number of possible folding pathways. The time required to sample every possible φ and ψ angle in a polypeptide backbone is too great to occur on the timescale of life. Therefore, preferred protein folding pathways must be available. In cells, protein folding occurs under more concentrated conditions than are typically used in in vitro studies. The folding of a protein to its lowest energy state is dictated by changes in enthalpy and entropy. The clustering of hydrophobic side chains away from water, called the hydrophobic effect, and the resulting disorder of the surrounding water molecules is a larger entropic contribution and overcomes the unfavorable loss of conformation states.

If the cytoplasm of a cell were to become a much more oxidizing environment, what do you predict would happen to an existing surface-exposed disulfide bond in a typical cytoplasmic protein?

There would be no change since the disulfide bond is already oxidized.

Quaternary structures provide increased functionality to proteins in which of the follow ways?

They provide structural properties not present in individual subunits. They increase efficiency of biochemical processes.

Transmembrane helices are often angled through the membrane. For the same membrane, how many amino acids are necessary if the transmembrane helix is at an angle of 24° from being perpendicular to the plane of the membrane?

Using the geometry of a triangle: cos(24°) = 40 amino acids / xSolving for x: x = 40/cos(24°) = 44 amino acids

What is the molecular geometry of the constituents of the peptide plane?

amide nitrogen and carbonyl carbon are trigonal planar

Four groups amino acids are divided into

aromatic, hydrophilic or polar charged, hydrophobic or aliphatic, charged

charged amino acids:

aspartate, glutamate, lysine, arginine, histidine

What type of chaperone is GroEL-GroES?

chamber type

The GroEL-GroES complex is

chaperone ATPase

Which amino acid is the smallest and least chemically active?

glycine -smallest R group (H), least chemically active and no chiral center

Structural element motifs

helix-turn-helix B-sheet Greek key fold B-sheet, a helix, B sheet

The __________ model is NOT a proposed model for the folding of globular proteins. hydrophilic collapse hydrophobic collapse framework nucleation

hydrophilic collapse Burying hydrophobic amino acids is a major driving force for protein folding. The hydrophobic collapse model proposes that the interior of the protein is first formed by hydrophobic residues in a molten globule structure. This structure facilitates the formation of the secondary and tertiary structure. The framework model proposes that secondary structures form independently, and then form tertiary structures in a second phase. The nucleation model proposes that random interactions give rise to a localized region of correct three-dimensional structure, which then leads to the formation of secondary and tertiary structure.

Disulfide bond....

indicates oxidized form

fibrous proteins

keratin collagen silk proteins

Structural element domains

ligand binding regions of a G protein-coupled receptor (GPCR) regulatory region of protein kinase C (PKC)

In an α helix, hydrogen bonding occurs between the carbonyl oxygen of residue n and the H on the nitrogen of the peptide bond of which residue? n + 1 n + 2 n + 3 n + 4

n+4 The α helix structure has 3.6 residues per turn. This means that the n residue and the residue 4 amino acids away (n + 4) are aligned for backbone interactions via hydrogen bonding. These hydrogen bonds help stabilize the secondary structure.

If RNase were heated to twice its Tm in the absence of β-mercaptoethanol and then cooled to 4 °C, it would be in what state?

native state Excessive heat will denature a protein. Thus, as the temperature is elevated past the Tm, which is the temperature where half of the protein is denatured, more and more protein becomes denatured. However, if the protein can reversibly refold like RNaseA, the protein will return to its native state as the temperature is decreased. Since 4 ºC is well below the Tm for RNaseA, it is mostly folded in its native state.

aromatic amino acids

phenylalanine, tyrosine, tryptophan

Many diseases, including Alzheimer's disease, are associated with

protein aggregation

Getting your hair permed must involve which of the following?

reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds

What level of protein structure describes the spatial location of every atom in a protein?

tertiary Tertiary structure (3°) describes the relative spatial location of every atom in a protein. It is determined by the amino acid sequence (1°). It shows the spatial relation of all secondary structure elements and includes the location of other subunits (4°), if present.

Disulfide bonds stabilize __________ level of protein structure and above. primary secondary tertiary quaternary

tertiary The primary structure of a protein is simply the string of amino acids. In secondary structure, local interactions and backbone configurations play the major role. Tertiary structure involves long-range interactions within a single peptide, which can be mediated by metal ions and disulfide bonds. Quaternary structure uses the same types of interactions as tertiary structure, including disulfide bonds, but involves more than one peptide.

If the hydrophobic part of a membrane is roughly 60 Å thick, how many amino acids are necessary to form the shortest possible transmembrane spanning an α helix?

α helices extend in length at a rate of 5.4 Å per turn. Each turn is composed of 3.6 amino acids. Thus,5.4 Å per turn at 3.6 amino acids per turn equates to 1.5 Å per amino acid in an α helix. Therefore, 60 Å divided by 1.5 Å per amino acid equals 40 amino acids.