week 14
Which of the following statements is NOT true?
None of the allosterically regulated enzymes have more than one polypeptide.
What happens to the enzyme lipase in the stomach when the pH is lower than 4.0?
The enzyme may change shape, causing a loss of catalytic activity.
What happens to the enzyme lipase in the stomach when the pH is significantly higher than 5.0?
The enzyme may change shape, causing a loss of catalytic activity.
Which among these types of bonds is not seen in the tertiary structure of proteins?
phosphodiester bonds
What will be the net charge on valine at pH 3.0?
positive 1
Prions are a type of protein implicated in bovine spongiform encephalopathy (BSE), also known as "mad cow disease," and related pathologies found in sheep (scrappie) and humans (Creutzfeldt-Jakob disease). The disease occurs when sections of an otherwise healthy protein misfold from alpha-helices to beta-pleated sheets, forming tightly packed sections of beta-pleated sheets that are difficult to break down. The disease propagates because the misfolded prions induce other healthy proteins to misfold as well. Which of the following levels of protein structure is the only one NOT affected by an infectious prion?
primary
With reference to the image below, identify the change in glycine at pH less than 6.0.
protonation
The __________ bonds connect the polypeptide chains A and B of bovine serum albumin together.
s-s
Enzymes are best known for their
specificity
A catalyst will: Select the correct answer below: enhance the percent yield of a reaction reduce the percent yield of a reaction speed up a reaction slow down a reaction
speed up a reaction
Which type of RNA has individual units that read a sequence of bases and attach the corresponding amino acids? Select the best choice below.
tRNA
Which group of an amino acid generally has a positive charge when the pH is less than its isoelectric point?
the amine group
Concerning enzymes and their substrates, which of the following might a relatively small change in pH affect?
the shape of a substrate the tertiary structure of an enzyme
In the amino acid aspartate, the highlighted CH2−COO− portion represents __________.
the side chain that is unique to aspartate
Why do collisions have to have more kinetic energy than the activation energy of the reaction in order for the reaction to proceed?
the valence shells of the colliding atoms must achieve mutual penetration
What happens to the enzymes in thermophiles when the temperature is 100∘C?
there will be no change
Complete the structure of the amino acid, phenylalinine. Type your answer as a chemical formula.
nh2
The transcription process takes place in the
nucleus
Identify the nature of the R Group in the amino acid shown in the figure above.
+ charge
What is the charge of an ionized amino group of the amino acid glycine?
+1
What is the charge of an ionized carboxyl group of the amino acid glycine?
-1
At which of the following temperatures might you expect to find active thermophiles?
100∘C
How many amino acids form the peptide chain A of bovine serum insulin?
21
In the DNA double helix, the base guanine pairs with the base cytosine, and the base adenine pairs with the base thymine via hydrogen bonding. How many hydrogen bonds are in the guanine-cytosine (G-C) pair, and how many are in the adenine-thymine (A-T) pair? Type numbers rather than words.
3,2 three hydrogen bonds with guanine, and adenine forms two hydrogen bonds with thymine.
What is the optimum temperature for most of the enzymes in the human body?
37
What is the optimum pH for most physiological enzymes in the human body?
7.4
Approximately what pH is optimal for the enzyme lipase in the pancreas?Write your answer as a whole number.
8
Which is an example of concentration affecting the rate of reaction?
A reaction slows down as it proceeds.
A phosphodiester bond links:
A nitrogenous base and a phosphate group
Which among the following set correctly identifies the bases present in RNA? Identify the symbols.
A, U, G, and C
Identify a correct codon for the given amino acid sequence: lysine-alanine-cysteine. Use the table below.
AAG GCU UGU
Which of the following is true for the active site? There is a unique combination of amino acid residues within the active site. Each residue is characterized by different properties. Residues can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. all of the above
ALL OF THE ABOVE
Which of the following statements is true about DNA? Select the correct answer below: DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles, chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope. All of the statements are true.
ALL OF THE ABOVE
Which of the following react relatively slowly (hours to years) rather than nearly instantaneously? (select all that apply)
An egg spoiling in a freezer Calcium exposed to water Iron train tracks exposed to the air
In DNA, the base thymine pairs with the base adenine via two hydrogen bonds. Which of the following describes the correct groups engaged in those hydrogen bonds?
An oxygen from a carbonyl group hydrogen bonds to a hydrogen on a substituent amine group, and a hydrogen on a ring nitrogen hydrogen bonds to a ring nitrogen.
Why would it be unusual for enzymes in the human body to have significantly different optimum temperatures?
Because the human body has a temperature that is constant at about 37∘C throughout.
Suppose a chemist was trying to model the effects of a genetic mutation on the functionality of an enzyme by comparing the shapes of the healthy and mutated enzyme to the shape of the substrate. Explain how the induced fit model might differ from the lock-and-key model in this study.
C. According to the lock-and-key model, the shapes of the isolated substrate and enzymes could be compared directly, but according to the induced fit model, the chemist would also have to consider the conformations of the enzymes when bound to the substrate to compare the effectiveness of the enzymes.
What do you call a substance that helps a chemical reaction to occur by decreasing the activation energy?
Catalyst
Identify the true statement(s) regarding reversibility of inhibition.
Competitive inhibition can be reversed by adding a sufficient amount of substrate. Noncompetitive inhibition can be reversed by a chemical change that removes the inhibitor. Competitive inhibition can be reversed by a chemical change that removes the inhibitor.
Which of the following statements is true regarding inhibitors influencing the rate of reaction?
Competitive inhibitors affect the initial rate. Noncompetitive inhibitors affect the maximal rate. Noncompetitive inhibitors affect the initial rate.
From the figure above, find the amino acid that has a sulfhydryl (SH) group.
Cysteine (Cys)
What is the name given for the special molecules that catalyze biochemical reactions?
ENZYME
An amino acid has an overall neutral charge when the pH is equal to a specific value called the __________.
isoelectric point
mRNA is a copy of a single strand of
DNA
Which of the following statements is NOT true about DNA?
DNA is a single stranded molecule.
Which of the following is the process in which each strand of DNA is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand?
DNA replication
The entire _____ content of a cell is known as its _____?
DNA; genome
Identify the options below that decrease the rate of a reaction. (select all that apply)
Decreasing the temperature of an endothermic reaction Decreasing the concentration of a second order reactant
Which of the following statements about enzymes are true? Select all that apply:
Enzymes increase reaction rates by lowering the activation energy of a reaction. Enzymes increase reaction rates by interacting with the substrate molecules to facilitate the reaction, for example by contorting them to facilitate bond-breakage or orienting them to favor bond formation.
Of the following, which are characteristics of basic solutions? (Select all that apply)
Greater concentration of hydroxide ions than hydronium ions [H3O+]<[OH−]
Consider the reaction below. H3PO4+H2O↽−−⇀H3O++H2PO−4 Which of the above chemical species acts as a Brønsted-Lowry acid? Enter a molecular formula. Do NOT include a phase designation.
H3PO4
Identify the corresponding sequence of amino acids for the following codon CAU AGC UGG using the following table.
Histidine-Serine-Tryptophan
The allosteric activator modifies the binding affinity of the substrate. Where does an allosteric activator attach?
It binds to the enzyme, away from the active site.
An enzyme is placed in the presence of an unknown substance to determine whether the substance is an inhibitor. As the substrate concentration is increased, the rate of reaction is compared to the normal rate of reaction. Initially, the rate is slower than normal, and as the substrate concentration is increased more and more, the rate of reaction stays substantially below normal. What can be concluded about the unknown substance?
It could contain noncompetitive inhibitor and little or no competitive inhibitor. It could contain both competitive and noncompetitive inhibitors in an evenly divided mixture.
Which of the following best describes the structure of DNA?
It is an antiparallel double helix.
Which of the following proteins might you expect to find making up a fingernail?
keratin
An enzyme is placed in the presence of an unknown substance to determine whether the substance is an inhibitor. As the substrate concentration is increased, the rate of reaction is compared to the normal rate of reaction. Initially, the rate is equal to normal, and as the substrate concentration is increased more and more, the rate of reaction remains the same as the normal rate. What can be concluded about the unknown substance?
It is neither a competitive nor a noncompetitive inhibitor.
How might a mild change in pH from the optimum pH affect the structure of an enzyme?
It might change the R group interactions in the tertiary structure.
What will be the overall charge of an amino acid when the pH is equal to the specific value called its pI?
NEUTRAL
The phosphate group provides the phosphodiester linkage between two DNA nucleotides. What is the structure of the phosphodiester linkage?
Oxygens from the phosphate group are attached to the 3′ carbon of one sugar and the 5′ carbon of the sugar of the next nucleotide.
What type of bonds are found between the DNA sugar hydroxyl groups? What are their corresponding carbon numbers?
Phosphodiester; 3′,5′
Which of the following is an example of reactant concentration affecting the rate of a reaction?
Phosphorus burns much more rapidly in an atmosphere of pure oxygen than in air, which is about 21% oxygen.
Consider the reaction below. H2S+SO2−4⇌HS−+HSO−4 Which of the above chemical species is the Brønsted-Lowry base in the forward reaction?
SO2-4
One of the reasons that silk is sought after as a fabric is because it has great tensile strength; that is, it resists breaking down under tension. It is been shown that this is due to the regular β-pleated sheet structure of the silk proteins. Would you expect the proteins in silk to contain large or small R-groups? Explain your answer.
The R-groups must be small because, while the R-groups point above and below the main plane of the sheet, if they are large, they prevent the amino acid chains from lining up in a proper parallel fashion, and interfere with strong β-pleated sheets.
Which of the following statements are NOT true regarding the ionization of nonacidic and nonbasic amino acids?
The amino group will be ionized when the pH is above the isoelectric point. The carboxyl group will be ionized when the pH is below the isoelectric point.
From the image given below, what does the falling curve describe?
loss of catalytic activity
What happens to an amino acid as the pH is decreased from the isoelectric point?
The ionized carboxyl group is protonated, becoming neutral.
How do acidic and basic R groups affect the isoelectric point of amino acids?
The isoelectric point is lowered by acidic R groups and raised by basic R groups.
What happens to the enzyme amylase in the pancreas when the pH is 6.8?
There will be no change in the enzyme. Enzymes generally have a pH of optimum activity. The pH range from 6.7 to 7.0 is optimal for the pancreatic amylase. So, at 6.8, the enzyme doesn't change its shape and activity. The optimum pH range for pancreatic amylase is 6.7 to 7.0. So the enzyme will not be affected by a pH of 6.8.
Is the following statement true? If not, explain why not: Since the secondary structure of a protein results from hydrogen bonding between components shared by all amino acids (a hydrogen on an amide N on one amino acid interacts with an oxygen on the carbonyl of another amino acid), the secondary structure does not depend on the specific amino acid groups (the R-groups) in the amino acid chain.
The statement is false because even though the R-groups are not responsible for the hydrogen bonding, they can still interact in ways that lead to a preferential secondary structure.
Which of the following best describes the relationship between an enzyme and a substrate?
The substrate is a reactant, and the enzyme is a catalyst that acts on a specific substrate, increasing its rate of consumption.
Review the figure below of a nucleotide. Explain how one nucleotide connects to another in single strand of DNA or RNA.
The sugars are connected to the phosphates on adjacent nucleotides, creating a backbone of alternating -sugar-phosphate-sugar-phosphate-sugar-phosphate-, etc.
Which one of the following nucleotide bases is not found in RNA?
Thymine
Identify the three-letter abbreviation and single-letter code of the amino acid tryptophan, using the table below.
Trp, W
Under what conditions does the amine group on an amino acid become deprotonated?
When the pH is greater than the isoelectric point.
Which type of RNA is the most common form of RNA used to communicate between DNA and the rest of the cell?
mRNA
Identify the statement that is true about protonation and deprotonation of amino and carboxyl groups of amino acids. a. The amino group is basic, which can lead to a positive charge when it is protonated at lower pHs. b. The carboxylic group is acidic and can be protonated at higher pHs to gain a negative charge.
a
Which of the following are components of nucleic acids? Select all that apply:
a nitrogenous base a pentose sugar
Which is an example of temperature affecting the rate of reaction? Select the correct answer below:
a reaction proceeds more quickly in the laboratory when placed over a Bunsen burner
Which is an example of concentration affecting the rate of reaction?
a solution containing two moles of each reactant has a faster instantaneous rate of reaction than a solution of the same volume with only one mole of each reactant
Another term for transition state would be
activated complex
Enzymes reduce __________ to reach the transition state.
activation energy
A competitive inhibitor molecule competes with the substrate for __________ binding and blocks the substrate binding.
active site
Which of the following actions increases the rate of a chemical reaction? (select all that apply)
adding a catalyst lowering the activation energy increasing the concentration of a first order reactant increasing the temperature
Which of the following statements is true? Select the correct answer below: A competitive inhibitor binds at the enzyme's active site. A noncompetitive inhibitor binds at a different location and changes the shape of the enzyme's active site. An allosteric inhibitor binds to an enzyme and modifies the shape of the active site, thereby reducing the binding affinity of substrate. All of the above
all of the above
In noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than the active site, called __________.
an allosteric site
The two strands of the DNA double-helix run in opposite directions, meaning that the 5' carbon end of one strand will face the 3' carbon end of its matching strand. What is the specific name for this type of orientation in DNA?
antiparallel orientation
A portion of a strand of mRNA is AAU GUG UCG. Identify the corresponding sequence of amino acids.
asparagine-valine-serine
A solution that has a greater hydroxide concentration than hydronium concentration will be:
basic
Noncompetitive inhibition affects
both initial and maximal rate
When an inhibitor molecule binds to the active site and blocks the substrate from binding, what type of inhibition occurs?
competitive inhibition
Arrange the following events in the correct order. An enzyme/substrate complex is formed. Products leave the active site of the enzyme. A substrate is converted to products and enzyme/products complex is formed. A substrate enters the active site of the enzyme.
d, a, c, b A substrate enters the active site of an enzyme. An enzyme/substrate complex is formed. The substrate is converted to products, and the products leave the active site.
An increase in temperature of ten degrees Celsius will have what effect on the rate?
depends on the reaction
α-helix and β-pleated sheet structures of protein form because of __________ bonding between the carbonyl and amino groups in the peptide backbone.
hydrogen
The shapes of both α-helices and β-pleated sheets are maintained by a particular kind of force that is often described as an intermolecular force, but which is actually acting between atoms in the same molecule in these structures. What kind of force is it?
hydrogen bonding
The coiling of an α-helix is maintained in position by which of the following bonds?
hydrogen bonds between the oxygen atom in the carbonyl group in one amino acid and the hydrogen atom in the amine group of another amino acid that is four amino acids farther along the chain
The rate of a reaction usually increases as temperature _________________ and concentration ________________.
increases, increases
What is the condition for the enzyme pepsin to get activated in the stomach?
when the pH is about 2 Enzymes in the stomach work best at a low pH because of the acidic environment of the stomach. When food comes into the stomach, HCl is secreted, lowering the pH to 2, which activates the pepsin. If there is no food in the stomach, the pH is about 5, and the pepsin won't be activated.
What will be the net charge when the pH is equal to the isoelectronic point (pH=pI) for an amino acid with a neutral side chain?
zero