Cell Bio Chapter 4 (Exam 1)
Discuss the difference(s) between positive and negative regulation.
Both positive and negative regulation occurs when a molecule binds to a protein or enzyme, altering its activity. In positive regulation, the molecule stimulates the activity of the enzyme. In negative regulation, it inhibits enzyme activity. Negative feedback often occurs in biosynthetic pathways where a product formed late in the pathway binds to and inhibits an enzyme early in the pathway.
Peptide bonds are the only covalent bonds that can link together two amino acids in proteins.
False Some proteins also contain covalent disulfide bonds (-S-S- bonds) linking two amino acids
Indicate whether the following statements are true or false. If a statement is false, explain why it is false Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.
False. Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzyme activity, depending on the protein in question.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.
False. Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic activity
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A single polypeptide tends to adopt 3-4 different conformations, which all have equivalent freeenergy values (G).
False. There is a single, final fold for every polypeptide. The fold adopted is the "best" conformation, for which the free energy (G) of the molecule is at a minimum.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. Van der Waals interactions and hydrophobic interactions are two ways to describe the same type of weak forces that help proteins fold.
False. Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution.
Describe the primary and secondary structures of proteins?
The primary structure of a protein is its amino acid sequence. Amino acids are held together in a chain by peptide bonds. The polypeptide chain can then fold into different shapes. These patterns constitute the protein's secondary structure. A common folding pattern is the alpha helix, formed when a single polypeptide chain turns around itself to form a structurally rigid cylinder. The structure is held together by hydrogen bonds made between every fourth amino acid. Another common folding pattering is the beta sheet, formed by hydrogen bonding between segments of polypeptide chains that lie side-by-side.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation
True
Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain."
a protien segment that folds independtly
Enzymes catalyze a chemical reaction by lowering the __________________, because they provide conditions favorable for the formation of a __________________ intermediate called the __________________.
activation energy high energy transition state
On being heated, a protein molecule will become __________________ as a result of breakage of __________________ bonds.
denatured noncovalent
The sequence of the atoms in the polypeptide backbone varies between different proteins.
false Because the sequence of atoms in the polypeptide backbone itself is always the same from protein to protein; it is the order of the amino acid side chains that differs.
Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?
hydrogen bonds along the protein backbone
The enzyme hexokinase is so specific that it reacts with only one of the two __________________ of glucose.
isomers
The final folded conformation adopted by a protein is that of __________________ energy.
lowest
A protein's amino acid sequence is known as its __________________ structure.
primary
Once the reaction is completed, the enzyme releases the __________________ of the reaction.
products
On removal of urea, an unfolded protein can become __________________.
renatured
The α helices and β sheets are examples of protein __________________ structure.
secondary
All the information required to determine a protein's conformation is contained in its amino acid __________________.
sequence
The distinguishing characteristics of proteins are determined by the __________ of their amino acids and the different characteristics of the R groups of those amino acids.
sequence
What factors contribute to the uniqueness of protiens
side- chain interactions hydrogen bonds along the protein back bone hydrophobic-core interactions
A newly synthesized protein generally folds up into a __________________ conformation.
stable
Enzymes bind their __________________ at the __________________.
substartes (or inhibitors) avtive site
A protein such as hemoglobin, which is composed of more than one protein __________________, has quartenary structure.
subunit
The three-dimensional conformation of a protein is its __________________ structure.
tertiary
The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins?
they form protien aggregates
Indicate whether the following statements are true or false. If a statement is false, explain why it is false If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis
true
Indicate whether the following statements are true or false. If a statement is false, explain why it is false GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation
true
Nonpolar amino acids tend to be found in the interior of proteins.
true
To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process?
(b) the solvents break all non covalent interactions (b) In the case of choice (b), the polypeptide is completely unfolded, allowing the complete refolding to be observed. Detergents do not break the covalent bonds of the polypeptide backbone [choice (a)]. Mild detergents that do not break all noncovalent interactions within a protein would not lead to misfolding but instead to partial unfolding [choice (c)]. Proteins fold into only one single, correct conformation. Denaturation followed by renaturation of a protein does not generate a new protein fold [choice (d)]
Which of the following statements is true? (a) Disulfide bonds are formed by the cross-linking of methionine residues. (b) Disulfide bonds are formed mainly in proteins that are retained within the cytosol. (c) Disulfide bonds stabilize but do not change a protein's final conformation. (d) Agents such as mercaptoethanol can break disulfide bonds through oxidation.
(c) Disulfide bonds stabilize but do not change a protein's final conformation Choice (a) is incorrect, because S-S bonds are formed between cysteines. Choice (b) is incorrect, because disulfide bonds are formed mainly in extracellular proteins. Choice (d) is incorrect; the bonds are broken by mercaptoethanol, but by reduction not by oxidation.
Fill in the blank spaces in the table below. The first row has been completed for you. Use figure 4-3 in the book to complete this table.****************************************************
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Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would not occur to help accommodate an internal, polar side chain? A hydrogen bond forms between a polar side chain and an aromatic (non-polar) side chain. A hydrogen bond forms between a polar side chain and the protein backbone. Hydrogen bonds form between polar side chains and a buried water molecule. A hydrogen bond forms between two polar side chains.
A hydrogen bond forms between a polar side chain and an aromatic (non-polar) side chain. Because aromatic side chains are nonpolar, hydrophobic residues and will not interact favorably with a polar, hydrophilic side chain.
Which of the following statements about allostery is true? Allosteric regulators are often products of other chemical reactions in the same biochemical pathway. Allosteric regulation is always used for negative regulation of enzyme activity. Enzymes are the only types of proteins that are subject to allosteric regulation. Binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation.
Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.
One way in which an enzyme can lower the activation energy required for a reaction is to bind the substrate(s) and distort its structure so that the substrate more closely resembles the transition state of the reaction. This mechanism will be facilitated if the shape and chemical properties of the enzyme's active site are more complementary to the transition state than to the undistorted substrate; in other words, if the enzyme were to have a higher affinity for the transition state than for the substrate. Knowing this, your friend looked in an organic chemistry textbook to identify a stable chemical that closely resembles the transition state of a reaction that converts X into Y. She generated an antibody against this transitionstate analog and mixed the antibody with chemical X. What do you think might happen?
If your friend was lucky, she made a "catalytic antibody" that catalyzed the conversion of X into Y. Such catalytic antibodies have been isolated and shown to catalyze a variety of reactions, but with lower efficiency than genuine enzymes.
Any substance that will bind to a protein is known as its __________________.
Ligand
Lysozyme is an enzyme that acts like a natural antibiotic by cleaving the polysaccharide chains that form the cell walls of bacteria. How does lysozyme lower the activation energy of this hydrolysis reaction?
Lysozyme bends the polysaccharide chain into a shape that greatly reduces the activation energy necessary for the hydrolysis to take place. This distortion puts a strain on the bond that will be broken. The enzyme then cuts the polysaccharide chain by catalyzing the addition of a water molecule to the distorted bond, and releases the cleaved substrate.
Synthesis of the purine nucleotides AMP and GMP proceeds by a branched pathway starting with ribose 5-phosphate (R5P), as shown schematically in the figure below. Using the principles of feedback inhibition, propose a regulatory strategy for this pathway that ensures an adequate supply of both AMP and GMP and minimizes the buildup of the intermediates (A-I) when supplies of AMP and GMP are adequate. Schematic diagram of the metabolic pathway for synthesis of AMP and GMP from R5P.
One reasonable proposal would be for excess AMP to feedback inhibit the enzyme for converting E to F, and excess GMP to feedback inhibit the step from E to H. Intermediate E, which would then accumulate, would feedback inhibit the step from R5P to A. Some branched pathways are regulated in just this way. Purine nucleotide synthesis is regulated somewhat differently, however (as seen in the figure below). AMP and GMP regulate the steps from E to F and from E to H, as above, but they also regulate the step from R5P to A. Regulation by AMP and GMP at this step might seem problematical since it suggests that a rise in AMP, for example, could shut off the entire pathway even in the absence of GMP. The cell uses a very clever trick to avoid this problem. Individually, excess AMP or GMP can inhibit the enzyme to about 50% of its normal activity; together they can completely inhibit it. Figure: Pattern of inhibition in the metabolic pathway for purine nucleotide synthesis.