BMB SmartWork5 Chapter 4

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

Answer- 3° 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. Tertiary structure (3°) refers to the spatial arrangement of all atoms in a polypeptide.

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?

Answer- 40 an α helix extends in length 1.5 Å per residue. Rise per residue in alpha helix = 1.5 Å ​Thickness of membrane = 60 Å Number of amino acids necessary to form the shortest possible transmembrane spanning α helix = 60/1.5 = 40

Sort the following structural elements into domains or motifs.

Answer- domains (generally larger parts of proteins that can fold independently) are larger than motifs. Domains are generally composed of multiple motifs.

Order the following amino acids based on their propensity (highest to lowest) to form β sheets.

Answer- these amino acids are ordered based on their propensity to form β sheets.

Sort the following protein structures into their respective classes, either as α helix, β sheet, or mixed α/β proteins.

Answer- α helices are indicated as cylindrical curves whereas β sheets are indicated by arrows. Sort the protein structures based on the predominant type of secondary structure, with combined alpha-helical and β sheet proteins considered as mixed.

Determine whether the following diagrams depict parallel or antiparallel β sheets.

Answer- Parallel β sheets have backbones that are oriented in the same direction. The backbones of antiparallel β sheets are oriented in opposite directions. The relative direction of the polypeptide backbones determines whether β sheets are parallel or antiparallel. Using the figure below, determine the direction of each strand in the β sheet. If they are in the same direction, they are parallel.

Label the antibody.

Answer- The two light and heavy chains of an antibody are held together by disulfide bonds, and the variable antigen binding site is partially formed by contributions from both heavy and light chains. The heavy chains form the Fc region.

Examine the table and then order the following amino acids based on their propensity (highest to lowest) to form α helices.

Answer- These amino acids are ordered based on their propensity to form α helices.

When a protein folds, transitioning from denatured to native state, the change in free energy is favorable (ΔG < 0). In general, the entropic change is (A)__ due to the more limited number of conformations. The enthalpic change is (B)__ due to the many weak interactions that are formed. With the exception of disulfide bonds, weak interactions include the formation of (C)__ and numerous (D)__ interactions in the native state.

Answer- (A) Unfavorable, (B) favorable, (C) hydrogen bonds, (D) vander waals interactions (A) Constraining the number of conformational states is entropically unfavorable. (B) The favorable enthalpic term (from formation of hydrogen bonds, salt bridges, and disulfide bonds) overcomes the unfavorable entropic term. (C) Energetically favorable hydrogen bonds are formed when secondary structure elements are formed. (D) The van der Waals interactions provide favorable interactions contributing to protein folding.

What is the amino acid sequence of the pictured tripeptide, in order from N terminus to C terminus? 1st Amino Acid: 2nd Amino Acid: 3rd Amino Acid:

Answer- 1st Amino Acid: Asn 2nd Amino Acid: His 3rd Amino Acid: Arg The first amino acid is at the N terminus and the side chain is that of asparagine. The second amino acid is in the middle and is a histidine. The last amino acid is at the C terminus and the side chain is that of arginine.

From the partial nucleotide sequence given below, what peptides could be encoded?5'-GCCUCCAAACCCCUCCA-3'

Answer- Ala-Ser-Lys-Pro-Leu Pro-Pro-Asn-Pro-Ser Leu-Gln-Thr-Pro-Pro three different reading frames could result in these three amino sequences from the given nucleotide sequence.

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

Answer- 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. Heat and changes in pH can disrupt interactions that contribute to protein folding.

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

Answer- TVVEAIDRLVDT All the hydrophobic residues lie on one side of the helix. A helical wheel diagram (like that in Figure 4.34a) allows determination of relative residue positions.

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

Answer- They provide structural properties not present in individual sub-units. They increase efficiency of biochemical processes. There are several possible advantages of having multiple sub-units in close proximity, including possible structural properties not in the individual components and potential for increased efficiency of biochemical processes.

For the following charged amino acids at pH 7, determine whether the net charge on the amino acid is positive, negative, or neutral.

Answer- aspartate- negative glutamate- negative lysine- positive arginine- positive methionine- neutral Aspartate- the acidic side chain is deprotonated at pH 7 and therefore negatively charged. Glutamate- the acidic side chain is deprotonated at pH 7 and therefore negatively charged. Lysine- the basic side chain is protonated at pH 7 and therefore positively charged. Arginine- the basic side chain is protonated at pH 7 and therefore positively charged. Methionine- there is no exchangeable hydrogen in the side chain, therefore no pKa, so the side chain cannot be charged.

Which secondary structure elements are stabilized by hydrogen bonds?

Answer- α helices antiparallel β sheets parallel β sheets All regular elements of secondary structure are stabilized by hydrogen bonds.

Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into the appropriate categories. Methionine Isoleucine Valine Phenylalanine Aspartate Lysine

Answer- Hydrophobic: Methionine Isoleucine Valine Phenylalanine Hydrophilic: Aspartate Lysine

Indicate where the protein secondary structures are found on the Ramachandran plot by dragging each letter to the correct circle in the plot.

Answer- A (bottom left) B (top left) C (bottom right) D (top right) the torsion angles of regular secondary structure occupy distinct regions of torsion angle space on the Ramachandran plot.

Given the graph above, calculate the absorbance at 280 nm (UV280) of one mole of the following peptide. Trp-Tyr-Asp-Ala-Trp-Gly-Gly-Lys-Pro

Answer- Abs280 = 11000 M-1 cm-1 Summing the contributions from both tryptophans and the tyrosine yields this value.

The GroEL-GroES complex is

Answer- Chaperone ATPase GroEL-GroES is a chaperone that utilizes ATP to help proteins fold.

Sort the following proteins into their respective classes.

Answer- Fibrous: Collagen, Keratin, Silk Fibrous Globular: Serum Albumin, Hemoglobin, Heterotrimeric G Protein, Ras (a low molecular weight G protein) Long, extended proteins are considered fibrous, whereas relatively spherical proteins are considered globular.

The various chemical properties of the amino acid side chains determine the chemical properties and the three-dimensional structures of proteins. What are the four groups that amino acids can be divided into?

Answer- charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic The amino acids are separated into four categories based on their side-chain properties. The charged amino acids are considered separately from the hydrophic, polar uncharged amino acids.

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

Answer- isoleucine leucine These hydrophobic amino acids, which have a high helical propensity, will likely be found in a transmembrane helix. Transmembrane spanning α helices are predominantly hydrophobic in nature. Moreover, not all amino-acids have a propensity for existing in α helical conformations. The most appropriate choices are D. and E. i.e. isoleucine (high hydrophobicity and fair α helical propensity) and leucine (high α helical propensity and fair hydrophobicity).

As temperature increases, proteins are less likely to be in their native, lowest energy conformational state. What is the approximate Tm (melting temperature) for the protein shown?

Answer- 35 degrees celcius

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?

Answer- 44 The tilted helix is ~1.1 times longer. When the α helix is perpendicular to the plane of the membrane, then it has to traverse 60 Å. When the α helix is at an angle of 24° from being perpendicular to the plane of the membrane, then it has to traverse (60/cos 24) = 65.67 Å. Again, as in part 1, number of amino acids necessary to form the shortest possible transmembrane spanning α helix = 65.67/1.5 = 43.78 ~ 44

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

Answer- 7700 Molecular weight of an amino acid is 110 grams/mol 70*110= 7700

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

Answer- A2B2C2 There are three different subunits, so the initial designation is ABC. Since there are two of each subunit, adding the numerical designation leads to the final answer of A2B2C2. A homodimer is composed of two of the same protein subunit (i.e. A2). Having three different homodimers (A, B, and C) results in a hexamer with the correct quaternary structure.

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

Answer- A3B3 There are two different subunits, so the initial designation is AB. Since there are three of each subunit, adding the numerical designation leads to the final answer of A3B3. There are three of each subunit A and B.

From the plot of torsion angles shown, is this protein mostly composed of α helices or β sheets?

Answer- Alpha Helices While some β sheets are present, the protein is predominantly α-helical.

The side chains of some amino acids are charged at physiologic pH. Place the amino acids that possess a charge on their side chain at physiologic pH into the bin. Most answer choices will not be used.

Answer- Aspartate, Glutamate, Histidine, Arginine, Lysine There are two negatively charged amino acids and three positively charged amino acids. Hydrophilic uncharged amino acids have polar side chains.

Which form of cysteine is oxidized?

Answer- B The disulfide bond form of cysteine (cystine) is oxidized

What type of chaperone is GroEL-GroES?

Answer- Chamber type the GroEL-GroES complex forms a large, barrel-like structure where misfolded proteins are aided in reaching their native state.

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

Answer- Cys The sulfur of the cysteine side chain is reactive.

Due to its partial double bond character, the peptide bond restricts rotation, constraining atoms to lie within the same peptide plane. Rotation in the peptide backbone is around the two bonds that flank adjacent __ atoms, between which a peptide plane is formed.

Answer- Cα rotation cannot occur around the peptide bond, only around the backbone Cα.

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?

Answer- GFP would not emit green light since there is no blue light for it to absorb and re-emit. 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? Being in the dark, there is no source of blue light for GFP to absorb. Thus, GFP would not be able to emit green light.

Which amino acid is the smallest and least chemically active?

Answer- Glycine The side chain of glycine is only composed of a single hydrogen, so it is the smallest amino acid.

What is a major consequence of the partial double bond character?

Answer- Greatly reduced rotational freedom compared to the φ (phi)/ψ (psi) torsion angles The partial double bond character greatly restricts the rotational freedom around the peptide bond, much more so than the restrictions of the phi/psi torsion angles.

Ovalbumin is the major protein constituent of egg white. What is the folded state of ovalbumin in a cooked egg?

Answer- Irreversibly denatured Ovalbumin is irreversibly denatured by excess heat. Cooling does not reverse the process. Thus, unlike RNaseA, ovalbumin does not return to its native state once heat denatured. Overexpression of GFP would result in the emission of green light and a green appearance in white light.

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

Answer- Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. The less rigid behavior of hair is in part due to fewer disulfide bonds between keratin proteins.

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?

Answer- Native state Excessive heat denatures proteins. However, since the disulfide bonds are intact, RNaseA will refold. Most proteins cannot do this.

Of all the different bond types found in proteins, which has partial double bond character?

Answer- Peptide bond The peptide bond has partial double bond character that restricts rotation.

The side chains of some amino acids are aromatic. Place the aromatic amino acids into the bin. Most answer choices will not be used.

Answer- Phenylalanine, Tyrosine, Tryptophan

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

Answer- Protein aggregation After proteolytic processing, remnants of the amyloid precursor protein aggregate.

Which one of the following images represents tertiary structure? Indicate which one by dragging it into the bin labeled Tertiary Structure.

Answer- Ribbon diagrma only This is the only picture that shows the spatial arrangement of atoms, or tertiary structure (3°), for a polypeptide. In this case, it is shown as a ribbon diagram.

It has been observed that in a few cases, the peptide plane is actually bent 4°-5° from being a flat plane. What is the most plausible explanation?

Answer- Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane. While energetically unfavorable, this skewed peptide plane must be held in place by some other interaction whose more favorable energetics are offsetting.

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

Answer- The GroEL complex would form but would not act as a chaperone. Without the ability to bind ATP, GroEL would lose its ability as a chaperone.

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

Answer- The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar. With both being planar in the same plane, they form the peptide plane.

If a mutation occurred in which a codon changed to that for proline, what would you expect if the codon were found in a region that formed an α helix?

Answer- The proline would disrupt the α helix. Proline has a very unfavorable propensity to form α helices and would therefore be disruptive.

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?

Answer- There would be no change since the disulfide bond is already oxidized. Disulfide bonds represent the oxidized state of the cysteine side chain. Thus, in an oxidizing environment, nothing would change.

Getting your hair permed must involve which of the following?

Answer- reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds The covalent disulfide bonds holding keratin proteins together must be broken and then re-formed once the desired shape is made.

The titration of a base into a solution of aspartate is shown in the figure. Examine the figure and answer the following questions. Part One- From the introductory figure, what is the approximate pI of aspartate? Part Two- From the introductory figure, at what pH is the charge on aspartate -1?

Part One- Answer is 3 (2.1+3.9)/2 = 3 The pI can be approximated from the pKas of protonations involving the neutral, or uncharged, species. Part Two- Answer is 6.8 The appropriate pKa values are 3.9 and 9.7, which average to 6.8 for the -1 charged state.

Match the three-letter abbreviations with the names of the following amino acids. Match the one-letter abbreviations with the names of the following amino acids.

These abbreviations allow scientists to write out amino acid sequences in a compact, readily understood format. The one-letter codes are particularly useful for computer-based analysis of polypeptide sequences. The one-letter abbreviations generally correspond to the first letter of the amino acid, with a few exceptions to resolve redundancy. The one-letter codes are particularly useful for computer-based analysis of polypeptide sequences.