Chapter 4
Which part of an amino acid gives it its unique properties?
Side chain. The side chain of an amino acid is what gives the amino acid its unique chemical properties; the side chain is sometimes also called the R-group. All 20 naturally occurring amino acids are identical except in the collections of atoms composing these side chains. Each amino acid contains an amino group (consisting of nitrogen and hydrogen atoms) and a carboxyl group (consisting of carbon, oxygen, and hydrogen atoms) that are covalently bonded to an α-carbon. The side chain is also covalently bonded to the α-carbon. Individual amino acids of all types are covalently linked together into a linear polypeptide by the peptide bond, which is formed between the amino and carboxyl groups of neighboring amino acids.
How do most motor proteins ensure their movements are unidirectional?
They couple a conformational change to the hydrolysis of an ATP molecule. To achieve such directionality, one of the steps must be made irreversible. For proteins that are able to move in a single direction for long distances, this irreversibility is achieved by coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein—which is why motor proteins are also ATPases. A great deal of free energy is released when ATP is hydrolyzed, making it very unlikely that the protein will undergo a reverse shape change, as required for moving backward. Such a reversal would require that the ATP hydrolysis be reversed by adding a phosphate molecule to ADP to form ATP. As a consequence, the protein moves steadily forward, not backward.
You want to test pentapeptides (short peptides with only five amino acids) for their ability to bind to and inhibit a particular receptor. To do this, you set out to synthesize all possible pentapeptides and test each individually. Assuming you'll use just the 20 common amino acids, how many different pentapeptides will you have to test for receptor binding?
3200000. Given that there are 20 different amino acids, the number of different possible proteins is staggering: the answer is 205, or 3,200,000. Instead of individually testing all 205 combinations, you might first sift through all the possible pentapeptides via affinity chromatography (attaching the receptor to the matrix beads) to select for ones that bind. Those that bind can be further studied for their ability to block receptor function. See the panel in your text to review this procedure.
Which statement concerning feedback inhibition is false? A. Feedback inhibition is difficult to reverse. B. Feedback inhibition can work almost instantaneously. C. Feedback inhibition regulates the flow through biosynthetic pathways. D. Feedback inhibition is a feedback system for controlling enzyme activity. E. In feedback inhibition, an enzyme acting early in a reaction pathway is inhibited by a later product of that pathway.
A. Feedback inhibition is difficult to reverse. Feedback inhibition is not difficult to reverse. Rather, it is very easy to do so. In feedback inhibition, for example, an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway. Thus, whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway. Where pathways branch or intersect, there are usually multiple points of control by different final products, each of which regulates its own synthesis. Feedback inhibition can work almost instantaneously and is rapidly reversed when product levels fall.
Which of the following statements is true regarding protein structure determination? A. Mass spectrometry can be used to determine the amino acid sequences of a complex mixture of different proteins. B. Determination of a protein's structure by X-ray crystallography does not require prior knowledge of its amino acid sequence. C. A protein's three-dimensional structure can be reliably predicted from its amino acid sequence by computer algorithms that access the vast quantities of structural information archived in public databases. D. Nuclear magnetic resonance can be used to determine the structure of proteins that are too large to crystallize. E. Mass spectrometry is the fastest way to determine the three-dimensional structure of a polypeptide or protein, regardless of its size.
A. Mass spectrometry can be used to determine the amino acid sequences of a complex mixture of different proteins. To achieve the resolution needed to distinguish between peptides from different proteins, such mixtures are often subjected to tandem mass spectrometry. In this case, peptides that pass through the first spectrometer are digested into even smaller fragments and then analyzed by a second mass spectrometer. Mass spectrometry is used to determine the amino acid sequence of a protein, but it provides no information regarding three-dimensional structure. Nuclear magnetic resonance is used to determine the structure of smaller proteins. Currently, there are no computer programs that can reliably predict the three-dimensional structure of a protein from its amino acid sequence alone.
Which parts of amino acids are involved in a peptide bond?
Amino group of one amino acid and carboxyl group of the other. The peptide bond always comprises both a nitrogen atom and a carbon atom, where the nitrogen atom from the amino group and the carbon atom from the carboxyl group undergo a condensation reaction and eliminate a water molecule in the process. The amino acid side chains do not participate in the peptide bond, meaning that all types of amino acids can form peptide bonds with all other types.
What chemical group interaction occurs between a protein and a ligand?
An -OH of the ligand interacting with an -SH of the protein. One of the red lines in the image could represent an -OH of the ligand interacting with an -SH of the protein. These two chemical groups are both polar, and thus would favorably interact when protein binds with ligand. The phrase "like dissolves like" is based on favorable interactions. A -CH2CH3 of the ligand would not interact with a -NH3+ of the protein; a COO- of the ligand would not interact with a -CH2CH3 of the protein; and an -OH of the ligand would not interact with a -CH2CH3 of the protein. In each of these circumstances, there is a polar/charged chemical group and a nonpolar chemical group, which do not form favorable interactions.
Consider the thermodynamic properties of chemical reactions. Even though enzymes do not affect the overall energy of the reactants or the products (i.e., the thermodynamics), they alter the speed of the reaction. Enzymes accomplish this by doing which of the following? A. increasing the activation energy of a reaction B. eliminating the activation energy of a reaction C. reducing the activation energy of a reaction D. supplying the activation energy for a reaction E. not altering the activation energy of a reaction
C. reducing the activation energy of a reaction. Enzymes reduce the activation energy of a reaction. The activation energy is an energy barrier to reactions. For a colliding water molecule to break a bond linking two sugars, the polysaccharide molecule has to be distorted into a particular shape—the transition state—in which the atoms around the bond have an altered geometry and electron distribution. Conditions are thereby created in the microenvironment of the enzyme active site that greatly reduce the activation energy necessary for the hydrolysis to take place. Other enzymes use similar mechanisms to lower the activation energies and speed up the reactions they catalyze. In reactions involving two or more substrates, the active site acts like a template or mold that brings the reactants together in the proper orientation for the reaction to occur.
Which of the following are methods for isolating a protein of interest? A. chromatography and electrophoresis B. electrophoresis and crystallography C. chromatography and mass spectrometry D. electrophoresis and nuclear magnetic resonance E. nuclear magnetic resonance and crystallography
Chromatography and electrophoresis. Both chromatography and electrophoresis are methods for isolating a protein of interest. The most efficient forms of protein chromatography separate polypeptides on the basis of their ability to bind to a particular molecule—a process called affinity chromatography. Proteins can also be separated by electrophoresis. In this technique, a mixture of proteins is loaded onto a polymer gel and subjected to an electric field; the polypeptides then migrate through the gel at different speeds depending on their size and net charge. Mass spectrometry, crystallography, and nuclear magnetic resonance are each important in experimentally determining structural properties of the protein, but they are not used for isolating a protein.
Which of the following best describes the stable protein-ligand interaction that is represented in the image? Be sure to use the image as a guide but apply your knowledge regarding how protein and ligand commonly interact with each other. A note of caution though: the red lines in the figure are merely representing interactions and are not meant to be quantified. A. The formation of a set of many weak, covalent interactions maintains the interaction between protein and ligand. B. The formation of a set of very few weak, covalent interactions maintains the interaction between protein and ligand. C. The formation of a set of very few weak, noncovalent interactions maintains the interaction between protein and ligand. D. The formation of a set of many weak, noncovalent interactions maintains the interaction between protein and ligand.
D. The formation of a set of many weak, noncovalent interactions maintains the interaction between protein and ligand. The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of a set of weak, noncovalent interactions—hydrogen bonds, electrostatic attractions, and van der Waals attractions—as well as favorable hydrophobic forces. Each individual noncovalent interaction is weak, so effective binding requires many such bonds to be formed simultaneously. This is possible only if the surface contours of the ligand molecule fit very closely to the protein, matching it like a hand in a glove. When molecules have poorly matching surfaces, very few noncovalent interactions occur, and the two molecules dissociate as rapidly as they come together. This is what prevents incorrect and unwanted associations from forming between mismatched molecules.
For a given protein, hydrogen bonds can form between which of the following? A. atoms in the polypeptide backbone B. atoms of two peptide bonds C. atoms in two side chains D. a side chain and water E. all of the above F. none of the above
E. all of the above. For a given protein, hydrogen bonds can form between atoms in the polypeptide backbone, between atoms of two peptide bonds, between atoms in two side chains, and also between a side chain and water. The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of a set of weak, noncovalent interactions—hydrogen bonds. An α helix is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder. A hydrogen bond is made between every fourth amino acid, linking the C=O of one peptide bond to the N-H of another. β sheets are maintained by hydrogen bonds as well.
What are the steps in polysaccharide chain cleavage by lysozyme? What happens to the amino acids at the end of this reaction?
Enzyme active sites bind to the substrates to form an enzyme-substrate complex. The substrate becomes strained within the active site. This forces the substrate to adopt a conformation or shape similar to the transition state. Specific amino acids within the active site of the enzyme chemically interact with the substrate. In the case of lysozyme, glutamic acid 35 donates a proton and aspartic acid 52 attacks a specific carbon. The covalent bond between the two sugars is hydrolyzed as the aspartic acid forms a transient covalent bond with the C1 carbon of the first sugar. The negatively charged glutamic acid then draws a hydrogen off a water molecule, restoring glutamic acid to its starting point. The oxygen from water then attacks and breaks the bond between the C1 carbon and aspartic acid, restoring aspartic acid to its starting point. The enzyme then releases the products and is ready to start another catalysis reaction. Amino acids chemically interact with their substrates but are returned to their starting forms by the end of the reaction so that each enzyme can catalyze many reactions in a short amount of time. In the lysozyme reaction, glutamic acid 35 donates a proton to a sugar, becoming negatively charged for a short time. Aspartic acid 52 attacks the other carbon, hydrolyzing the sugar-sugar bond and forming a transient covalent bond with the C1 carbon of the first sugar. The negatively charged glutamic acid then draws a hydrogen off a water molecule restoring glutamic acid to its starting point. The oxygen from water then attacks and breaks the bond between the C1 carbon and aspartic acid, thereby restoring aspartic acid to its starting point. Lysozyme will then begin catalyzing the same reaction between two new sugar molecules.
What processes can determine 3D structure of a protein?
NMR spectroscopy, X-ray crystallography, and cryo-EM are all used to determine the three-dimensional structure of proteins. NMR spectroscopy can be used with small proteins (those less than about 50,000 daltons). X-ray crystallography requires crystals of the protein of interest, which can be difficult to obtain for large or transmembrane proteins. Cryo-EM, the newest technique of the three, allows atomic resolution of biological macromolecules. Proteins are placed in water, cooled so rapidly that the water solidifies into a glassy state, and then subjected to electron microscopy. The 2017 Chemistry Nobel Prize was awarded to researchers for their development of cryo-EM as a method of biological-structure determination.
Investigators are studying a protein that must be phosphorylated to be activated. Which method could be used to separate the phosphorylated form of the protein from the form that lacks an activating phosphate group?
Ion-exchange chromatography. Ion-exchange chromatography could be used to separate the phosphorylated form of the protein from the form that lacks an activating phosphate group. Ion-exchange columns are packed with small beads carrying either positive or negative charges that retard proteins of the opposite charge. The association between a protein and the matrix depends on the pH and ionic strength of the solution passing down the column. These can be varied in a controlled way to achieve an effective separation. The addition of the phosphate group changes the charge of the protein and therefore can be used to separate the phosphorylated form of the protein from the form that lacks an activating phosphate group. Gel-filtration chromatography separates proteins by their differences in size; the addition of a phosphate group should not drastically alter the size of the protein. Differential centrifugation separates cell components based on their size and density. It is not normally used to separate individual proteins, much less those that are differentially modified. Velocity sedimentation separates cell components based on their size, and equilibrium sedimentation separates cell components based on their density.
How does an allosteric inhibitor work?
It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate. To regulate enzyme activity, an allosteric inhibitor binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate. Unlike competitive inhibition, allosteric inhibition cannot be overcome by experimentally elevating the concentration of the substrate. With allosteric inhibition, there is no direct competition between inhibitor and substrate as both molecules are binding to the enzyme at different locations. There is also no direct interaction between the product of an enzyme and allosteric inhibition of that enzyme. Instead, products from reactions later in the pathway are more likely to act as inhibitors.
What kind of enzyme adds a phosphate group to another protein?
Kinase. Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase. GTPases and ATPases are a class of enzymes that catalyze the decomposition of GTP into GDP and a free phosphate ion and ATP into ADP and a free phosphate ion, respectively. The removal is of a small molecule, not a protein.
Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?
Methionine to arginine. Proteins fold into the conformation of lowest energy. Substituting an amino acid with different chemical properties will impact how the protein folds by disrupting the noncovalent interactions responsible for proper folding that would have been exhibited by the nonmutant version of the protein. Arginine and methionine have different chemical properties. Methionine has a nonpolar side chain that would likely be buried in the protein's interior; arginine, on the other hand, is a positively charged amino acid that would likely be facing the protein's exterior. Replacing methionine with arginine would likely disrupt a protein's structure. Alanine and glycine, leucine and isoleucine, asparagine and threonine, and tryptophan and phenylalanine all have similar chemical properties compared to each other, so these substitutions would probably not greatly perturb the structure of a protein.
To identify genes coding for essential proteins, researchers can create temperature-sensitive mutations. These mutations allow proper protein folding and cell proliferation at the permissive temperature of 22ºC, but they cause protein misfolding and reduced cell proliferation at a higher restrictive temperature, such as 37ºC. Which of the following mutations might increase protein flexibility and lead to a temperature-sensitive phenotype? A. mutation of an alanine to a cysteine, leading to the formation of a new disulfide bond B. a premature stop codon that truncates a protein 10 amino acids from the amino terminus C. mutation of a bulky isoleucine that was buried in the protein interior to a glycine (side chain = H) D. mutation of a lysine (that was involved in an ionic bond with a glutamic acid) to a glycine
Mutation of a bulky isoleucine that was buried in the protein interior to a glycine (side chain = H) and mutation of a lysine (that was involved in an ionic bond with a glutamic acid) to a glycine. Temperature-sensitive mutations are ones in which the protein folds normally at a low, permissive temperature but becomes unstable/misfolded at a higher temperature. Thus mutations that decrease protein stability are most likely to be temperature sensitive. Loss of an ionic bond or reduction of van der Waals interactions will increase protein flexibility and the likelihood of misfolding at lower temperatures compared to the wild-type, unmutated protein. Formation of a new disulfide bond makes a protein less likely to change conformation in response to higher temperatures. A mutation in which only the first 10 amino acids are present is likely to have a complete loss of function at all temperatures.
What are the two types of β sheets?
Parallel and antiparallel. The two types of β sheets are parallel and antiparallel. In a β sheet, several segments (strands) of an individual polypeptide chain are held together by hydrogen bonding between peptide bonds in adjacent strands. The amino acid side chains in each strand project alternately above and below the plane of the sheet. The adjacent chains run in opposite directions, forming an antiparallel β sheet. Parallel β sheets have more elongated loops that double back in the structure to maintain the parallel nature of the sheet.
What kind of enzyme removes a phosphate group from a protein?
Phosphatase. The addition or removal of a phosphate group is a common mechanism by which the function of proteins are regulated. Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase. GTPases and ATPases are a class of enzymes that catalyze the decomposition of GTP into GDP and a free phosphate ion and ATP into ADP and a free phosphate ion, respectively. The removal is of a small molecule, not a protein.
What determines the specificity an antibody has for its antigen?
Polypeptide loops in its variable domains. The polypeptide loops in its variable domains determine the specificity an antibody has for its antigen. A detailed examination of antibody structure reveals that the antigen-binding sites are formed from several loops of polypeptide chains that protrude from the ends of a pair of closely juxtaposed protein domains. The amino acid sequences in these loops can vary greatly without altering the basic structure of the antibody. An enormous diversity of antigen-binding sites can therefore be generated by changing only the length and amino acid sequence of these "hypervariable loops," which is how the wide variety of different antibodies is formed. With their unique combination of specificity and diversity, antibodies are not only indispensable for fighting off infections, they are also invaluable in the laboratory, where they can be used to identify, purify, and study other molecules.
What is the best type of model for visualizing the surface of a protein? What are the four models for a protein and their properties?
Space-filling. The space-filling model is the best type of model for visualizing the surface of a protein. This model provides a contour map of a protein's surface, which reveals which amino acids are exposed on the surface and shows how the protein might look compared to a small molecule such as water or to another macromolecule in the cell. The backbone model shows the overall organization of the polypeptide chain and provides a straightforward way to compare the structures of related proteins. The ribbon model shows the polypeptide backbone in a way that emphasizes its most conspicuous folding patterns like α helices and β sheets. Finally, the wire model includes the positions of all the amino acid side chains; this view is especially useful for predicting which amino acids might be involved in the protein's activity.
Imagine that this experiment uses a mutant version that increases the enzyme's affinity, or ability, to bind its substrate. Using the graph as a comparison, what effect would the mutant version of the enzyme likely have on the KM?
The KM would move to the left (decrease). If a mutant version of the enzyme used to generate these data increased its ability to bind substrate, then we would expect the new KM to move to the left of this graph, meaning that it decreases. In general, a small KM indicates that a substrate binds very tightly to the enzyme (due to a large number of noncovalent interactions). A large KM, on the other hand, indicates weak binding. So, a mutation that decreases the enzyme's binding ability to substrate would increase the KM, causing it to move to the right of the graph.
Within the representation of an antibody, identify the variable and constant regions by dragging the labels to the correct targets. Both targets are on the right side of the antibody representation.
The Y tails are the variable region while the stem of the Y is the constant region. An antibody is Y-shaped and has two identical antigen-binding sites, one on each arm of the Y. The protein is composed of four polypeptide chains (two identical heavy chains and two identical, smaller light chains), stabilized and held together by disulfide bonds (red). Each chain is made of several similar domains, here shaded in blue for the variable domains or gray for the constant domains. The antigen-binding site is formed where a heavy-chain variable domain (VH) and a light-chain variable domain (VL) come close together. Antigen binding happens in the variable domain due to the variation in amino acid sequence, and thus structure, in this location. The numerous antibodies that a human can create are all different in terms of the antigen that they recognize.
Enzymes can have both active and regulatory sites. What is the purpose of these sites?
The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate. Aspartate transcarbamoylase catalyzes the first step in the pyrimidine biosynthetic pathway, the conversion of L-aspartate and carbamoyl phosphate to form carbamoyl aspartate. One of the end products in this pathway, CTP, binds at a regulatory site (a location distant from the active site) on the enzyme, resulting in decreased production of carbamoyl aspartate. CTP is able to achieve this regulatory effect because its binding to aspartate transcarbamoylase causes a conformational change that renders the active site inaccessible to substrate, as shown in the figure. Note that as an allosteric regulator, CTP is a noncompetitive inhibitor and does not compete with substrate for binding to the enzyme's active site.
Investigators wish to purify an enzyme—a serine protease—using affinity chromatography. They attach to the matrix of an affinity column an antibody molecule that binds specifically to a short sequence of amino acids located in the enzyme's active site. When they apply a mixture of proteins to the column, the protease adheres to the column and the other proteins pass through. To extract their purified enzyme from the column, the investigators add a large excess of the peptide that the antibody recognizes. What should they expect to occur after this treatment?
The enzyme will remain bound to the column and none of the fractions will contain the enzyme of interest; only flow-through will leave the column. Only flow-through will leave the column. Antibodies bind to their target molecules extremely tightly. A concentrated salt solution or a buffer with a very different pH is usually used to release proteins that are bound to an affinity column. These conditions weaken the binding of the antibody and protein so that the protein can be eluted. Regardless of whether the peptide is able to displace the enzyme, the antibody will not be released from the column. It is covalently attached to the matrix and is part of the stationary phase of the column.
What does the primary structure of a protein refer to?
The linear amino acid sequence of the protein. Because a protein's structure begins with its amino acid sequence, this is considered its primary structure. That is, the primary structure of a protein refers to the linear amino acid sequence of the protein. The chain of linear polymers of amino acids that compose proteins is termed a polypeptide. The locations of the peptide bonds that form the protein's backbone are between each of the amino acids of the protein. The peptide bonds are involved in maintaining primary structure, but the location of the peptide bonds does not specify the primary structure. The primary structure does determine the secondary and tertiary structures.
How does phosphorylation control protein activity?
The phosphate group induces a change in the protein's conformation. Proteins are commonly controlled by phosphorylation and dephosphorylation. When added to the protein, the phosphate group induces a change in the protein's conformation. Regulation of protein activity in this manner involves attaching a phosphate group covalently to one or more of the protein's amino acid side chains. Because each phosphate group carries two negative charges, the enzyme-catalyzed addition of a phosphate group can cause a conformational change by, for example, attracting a cluster of positively charged amino acid side chains from somewhere else in the same protein. This structural shift can, in turn, affect the binding of ligands elsewhere on the protein surface, thereby altering the protein's activity. Removal of the phosphate group by a second enzyme will return the protein to its original conformation and restore its initial activity.
A protein domain is another phrase describing what type of structure of a protein?
The protein domain is an organizational unit that is distinct from the primary, secondary, tertiary, and quaternary levels of organization. Studies of the conformation, function, and evolution of proteins have also revealed the importance of a level of organization distinct from these four levels of protein structure. Usually, a single domain is responsible for a single function of the protein and some proteins can be composed of multiple domains. Figure 4-20, shown below, highlights protein domain structure using the example of catabolite activator protein (CAP), a bacterial transcriptional activator protein with two distinct domains, each with a unique function.
Electrophoresis separates proteins on the basis of what factor(s)?
The protein's net charge and the protein's size. Electrophoresis separates proteins on the basis of the size and the net charge of proteins. In this technique, a mixture of proteins is loaded onto a polymer gel and subjected to an electric field; the polypeptides then migrate through the gel at different speeds depending on their size and net charge. Denatured protein will travel faster than folded protein due to easier migration of linear sequence as opposed to a folded globular protein.
Predict what would happen to the secondary structure of a protein if an alcohol that disrupts hydrogen-bonding were added.
The α helices and β sheets would unfold, disrupting protein structure. Alcohols can disrupt hydrogen bonds in a protein. Since both α helix and β sheet secondary structures are maintained by hydrogen-bonding of backbone atoms, disruption of hydrogen-bonding will cause both secondary structures to unfold. Individual amino acids are held together in primary structures with covalent peptide bonds and will not be disrupted by the alcohol.
Investigators decide to analyze the purity of a preparation of antibody molecules using SDS polyacrylamide-gel electrophoresis (SDS-PAGE). On Lane 1 of the gel, they load a sample of the antibody. On Lane 2, they load an antibody sample that has been treated with a reducing agent called mercaptoethanol, which breaks disulfide linkages. Following electrophoresis, they see distinct bands representing polypeptides with molecular weights of 50 kD and 25 kD in Lane 2 and only one band weighing 150 kD in Lane 1. What can the investigators conclude about their antibody based on the results of this experiment?
Their antibody is composed of subunits (50 kD and 25 kD in molecular weight) that each must include at least one cysteine residue. Their antibody is composed of subunits (50 kD and 25 kD in molecular weight) that each must include at least one cysteine residue. The untreated antibody in Lane 1 of the gel migrates as a single, distinct band with a molecular weight of 150 kD; the native protein is 150 kD, which is composed of (2 × 50 kD) + (2 × 25 kD) = 150 kD. Thus, the preparation is pure. Treatment with mercaptoethanol, Lane 2, reduces the disulfide linkages that hold together the subunits (those of 50 kD and 25 kD) that are part of the mature antibody molecule. Disulfide linkages form only between cysteine residues. If mercaptoethanol cleaved the polypeptide backbone at random sites, it would generate a large assortment of polypeptide fragments of different molecular weights. Mercaptoethanol does not break the polypeptide backbone.
Organisms that thrive in extremely cold climates often produce proteins that act as "antifreeze." Given that all proteins bind to other molecules, how might such antifreeze proteins work?
They bind by way of their β sheets to tiny ice crystals, preventing their growth. Organisms that thrive in extremely cold climates often produce proteins that act as "antifreeze." Given that all proteins bind to other molecules, such antifreeze proteins bind by way of their β sheets to tiny ice crystals, preventing their growth. Prevention of the growth and expansion of ice crystals can prevent the cell from rupturing. Many of these antifreeze proteins contain a series of parallel β sheets, which form a flat surface that matches the structure of ice crystals and thereby prevents additional water molecules from joining the solid.
A common antibody has how many polypeptide chains?
This antibody is composed of four polypeptide chains. There are two heavy chains and two light chains. The four polypeptide chains (two identical heavy chains and two identical, smaller light chains) are stabilized and held together by disulfide bonds. Each chain is made of several similar domains: variable domains and constant domains.
What are the characteristics of an alpha helix? A beta sheet? What do they share?
α helices form a cylindrical structure with side chains pointing away from the cylinder. One full turn occurs every 3.6 amino acids. β sheets form a rigid sheet consisting of antiparallel or parallel strands of the protein. The side chains alternate extending above and below the plane of the sheet.Both α helix and β sheet secondary structures form from hydrogen-bonding between backbone atoms. Because only backbone atoms are involved (and not side chains), many different sequences can form both α helices and β sheets.
