Protein Structure
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MCAT Biology › Protein Structure
Which of the following statements is NOT true regarding the comparison of the alpha-helix structure to the beta-sheet structure in proteins?
Each is stabilized by inter-chain hydrogen bonds
All possible hydrogen bonds between the peptide carbonyl oxygen (C=O) and the amide hydrogen (N-H) are formed in each
The peptide bond in each is planar and trans
Each may occur in typical globular proteins
Each is an example of secondary structure
Explanation
Alpha-helices and beta-sheets are secondary structure motifs that occur when sequences of amino acids are linked by hydrogen bonds. These secondary structures are an integral part of globular proteins, such as hemoglobin. Alpha-helices resemble a coiled spring, with hydrogen bonding occurring in an intra-chain arrangement between carbonyl oxygens and amide hydrogens that is parallel to the central axis. Beta sheets, on the other hand, may have either inter- or intra-chain hydrogen bonding between carbonyl oxygens and amide hydrogens. Thus, the correct answer (and false statement) is that each is stabilized by interchain hydrogen bonds.
Collagen, the most abundant protein in the body, is an example of what type of protein?
Structural
Globular
Integral
Peripheral
Explanation
Collagen is a structural protein that adds significant strength and resilience to the skin, tendons, and ligaments. Structural proteins, including collagen, also fall under the category of fibrous proteins. Globular proteins, in contrast, usually act as enzymes in the body or transport channels in the membrane.
Peripheral proteins are a type of globular protein found adjacent to the membrane, while integral proteins are transmembrane globular proteins.
Nuclear transport is a very important concept of study in modern cellular biology. Transport of proteins into the nucleus of an organism requires energy in the form of GTP, which is attached to a protein called Ras-related Nuclear protein (RAN).
RAN is a monomeric G protein found in both the cytosol as well as the nucleus and its phosphorylation state plays an important role in the movement of proteins into and out of the nucleus. Specifically, RAN-GTP and RAN-GDP binds to nuclear import and export receptors and carries them into or out of the nucleus. They also play a role in dropping off cargo that import and export receptors hold onto. RAN's functions are controlled by two other proteins: RAN guanine exchange factor (RAN-GEF) and RAN GTPase activating protein (GAP). RAN-GEF binds a GTP onto RAN, while RAN-GAP hydrolyzes GTP into GDP. As a result, there is a RAN-GTP and RAN-GDP concentration gradient that forms between the cytosol and nucleus.
One of the main roles of RAN is to bind to nuclear import and export receptors and carry them into or out of the nucleus. Given that import and export receptors are proteins, what can we say about the cooperativity displayed by RAN when it comes to binding to import and export proteins?
No cooperativity
Positive cooperativity
Negative cooperativity
Both negative and positive cooperativity
There is not enough information to determine what type of cooperativity exists
Explanation
Binding cooperativity occurs when binding of one substrate increases or decreases the affinity for the other substrates. For cooperativity to work, the protein in question must have multiple subunits, therefore being at least a dimer. RAN is a monomer, and therefore cannot show any cooperativity.
The term "denaturation," when used in conjunction with proteins or nucleic acids, refers to a change in structural characteristics primarily due to __________.
the disruption of non-covalent bonds
the disruption of covalent bonds
changes in primary structure
the binding of toxic compounds
Explanation
The denaturation of proteins and nucleic acids occurs due to the disruption of non-covalent bonds, especially hydrogen bonds. In the case of nucleic acids, covalent bonds can be disrupted by specific enzymes, but this is not a form of denaturation. Changes in the primary structure of nucleic acids and proteins simply result in the net production of different proteins due to sequential changes of amino acids and nucleotides, not denaturation. Toxic compounds can interfere with nucleic acid and protein formation, but they do so by interrupting the non-covalent forces of each, such as hydrophobic forces and hydrogen bonding. Thus, the correct answer is the disruption of non-covalent bonds.
Amino acids are joined together to form polypeptides. Each amino acid is attached to another by a peptide bond.
What functional group is created when amino acids are joined together?
Amide
Ester
Ketone
No new functional groups are created
Explanation
Polypeptide formation involves the C-terminus of one amino acid attaching to the N-terminus of another. This polymerization results in a dipeptide with the byproduct of one water molecule. The newfound combination results in a carbonyl being attached to a nitrogen. This functional group is called an amide.
In 2013, scientists linked a cellular response called the unfolded protein response (UPR) to a series of neurodegenerative diseases, including such major health issues as Parkinson’s and Alzheimer’s Disease. According to their work, the unfolded protein response is a reduction in translation as a result of a series of enzymes that modify a translation initiation factor, eIF2, as below:
In the above sequence, the unfolded protein sensor binds to unfolded protein, such as the pathogenic amyloid-beta found in the brains of Alzheimer’s Disease patients. This sensor then phosphorylates PERK, or protein kinase RNA-like endoplasmic reticulum kinase. This leads to downstream effects on eIF2, inhibition of which represses translation. It is thought that symptoms of neurodegenerative disease may be a result of this reduced translation.
Which of the following is the LEAST important force that promotes protein folding?
Metallic bonding
Dipole interactions
Hydrogen bonding
Covalent bonding
Van der Waals interactions
Explanation
Metallic bonding adheres to the "nuclei in a sea of electrons" model that explains the malleability, conductivity, and ductility of metals. Though some proteins (like hemoglobin) rely on a metallic compound, metallic interactions do not dictate the majority of protein folding interactions.
Proteins have a non-metal backbone, and are more dependent on dipole, hydrogen, covalent, and van der Waals forces to dictate their conformation.
In the crusade to create a vaccine for Poliomyelitis, Jonas Salk and Albert Sabin created two separate vaccines that proved to be successful in preventing Polio onset.
The Salk vaccine, which is given by standard injection, contained virus particles inactivated by an organic solvent. This method has the advantage of inactivating each of the three Polio strains with no bias.
Albert Sabin's vaccine, given by oral inoculation via sugar water, contained live virus particles that had been genetically attenuated. With this method, each of the three Polio strains acquired separate mutations that made them unable to infect the human host cells. Strain 2 in particular contained one single nucleotide polymorphism in the internal ribosomal entry site (IRES) that prevented successful viral replication.
The organic solvent used to inactivate the Poliovirus in the Salk vaccine significantly alters the viral capsid. For the purposes of this question, let us assume that the capsid proteins are bound together by multiple di-sulfide bonds. Given this information, which of the solvents listed below would be most effective in disrupting the Poliovirus capsid?
2-mercaptoethanol
Dimethyl sulfoxide (DMSO)
Ethanol
Methanol
Explanation
The answer is 2-mercaptoethanol because it contains strong reducing groups that are capable of reducing the di-sulfide bonds.
Dimethyl sulfoxide (DMSO), methanol, and ethanol do not contain reducing groups capable of breaking di-sulfide bonds, if at all.
Hemoglobin is the principal oxygen-carrying protein in humans. It exists within erythrocytes, and binds up to four diatomic oxygen molecules simultaneously. Hemoglobin functions to maximize oxygen delivery to tissues, while simultaneously maximizing oxygen absorption in the lungs. Hemoglobin thus has a fundamentally contradictory set of goals. It must at once be opitimized to absorb oxygen, and to offload oxygen. Natural selection has overcome this apparent contradiction by making hemoglobin exquisitely sensitive to conditions in its microenvironment.
One way in which hemoglobin accomplishes its goals is through the phenomenon of cooperativity. Cooperativity refers to the ability of hemoglobin to change its oxygen binding behavior as a function of how many other oxygen atoms are bound to the molecule.
Fetal hemoglobin shows a similar pattern of cooperativity, but has unique binding characteristics relative to adult hemoglobin. Fetal hemoglobin reaches higher saturation at lower oxygen partial pressure.
Because of cooperativity, adult and fetal oxygen-hemoglobin dissociation curves appear as follows.
Beyond its ability to carry oxygen, hemoglobin is also effective as a blood buffer. The general reaction for the blood buffer system of hemoglobin is given below.
H+ + HbO2 ←→ H+Hb + O2
Because hemoglobin can act as a buffer in blood, it helps keep the pH constant. Which of the following portions of an amino acid can change with pH change?
Amino end, carboxy end, and side chain
Amino end
Carboxy end
Side chain
Amino end and carboxy end
Explanation
All three portions can change with pH. The amino end can take on an extra proton to become positively charged, the carboxy end can lose a proton and take on a negative charge, and the side chain can do either depending on its structure. An amino acid with both a positively charged amino end and a negatively charged carboxy end is called a zwitterion.
Which of these choices correctly pairs the level of protein structure with an example of that level of structure?
Tertiary structure is formed from disulfide bonds
Primary structure is formed from alpha-helices
Quaternary structure is formed from amino acids held together by peptide bonds
Tertiary structure is formed from beta-pleated sheets
Explanation
There are four distinct levels of protein structure: primary, secondary, tertiary, and quaternary. Primary structure refers to the actual sequence of amino acids, like Ala-Met-Gly-Trp, which are held together by peptide bonds. Secondary structure, which includes alpha-helices and beta-pleated sheets, is the local three-dimensional shape created by hydrogen bonding. Tertiary structure is the overall shape of the protein subunit, caused by more distant interactions. Disulfide bonds (bonds between the sulfur atoms of two cysteine amino acids) are an example of tertiary structure. Finally, quaternary structure involves interactions between the peptide subunits of a larger protein complex.
Proteins can have a maximum of four levels of structure: primary, secondary, tertiary, and quaternary. Although the proteins can spontaneously fold to a functional conformation, there are a variety of denaturing agents that can be used to disrupt the folding strategies of proteins. Mercaptoethanol is an example of a protein denaturing agent; its mechanism for dismantling proteins is to disrupt the disulfide bonds found in the protein. When urea is introduced to a protein, the hydrogen bonds holding the protein together are disrupted. Heat can also be considered a denaturing agent, which has the potential to disrupt all intermolecular interactions in a protein.
Which of the following levels of structure in a protein would not be disrupted by the introduction of mercaptoethanol?
Secondary structure
Tertiary structure
Quaternary structure
All of the given levels will be affected
Explanation
When discussing the secondary structure of a protein, you can assume that the only forces that are relevant are the hydrogen bonds between the carbonyl oxygen of one amino acid, and the hydrogen on the amino group of another. Because hydrogen bonds are the only intermolecular interaction involved in secondary structure, mercaptoethanol would not affect the secondary structure.
Disulfide bonds are generally integral to defining the tertiary structure of a protein; thus, mercaptoethanol would affect the tertiary structure (and subsequent quaternary structure) of a protein.