1- Combined Lecture 2 material

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Bacterial and eukaryotic transcription of which of the following DNA sequences would be slowest?

5' CCGGCAATAT 3'

Which codon would recognize the following anticodon: 5'-CCU-3'?

5'-AGG-3'

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule has only dispersion forces between like molecules?

CH4

Which molecule has only dispersion forces between like molecules? CHCl₃ CH₄ NH₃ H₂O

CH₄

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule has only dispersion forces with like molecules?

CO2

Which of the following amino acid sequences would NOT be produced by the translation of the repeating mRNA sequence (CUU)n (where n = number of repeating units)?

CORRECT ANSWER: (-Pro-Pro-Pro-)n

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CH3OCH3?

Dispersion and dipole-dipole forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in H2S?

Dispersion and dipole-dipole forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in SF4?

Dispersion and dipole-dipole forces

What types of intermolecular forces are found in CH₂Cl₂?

Dispersion and dipole-dipole forces

What types of intermolecular forces are found in CH₃OCH₃?

Dispersion and dipole-dipole forces

What types of intermolecular forces are found in H₂CO?

Dispersion and dipole-dipole forces

What types of intermolecular forces are found in H₂S?

Dispersion and dipole-dipole forces

What types of intermolecular forces are found in SF₄?

Dispersion and dipole-dipole forces

What type of interaction occurs between two nonpolar substances?

Dispersion forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CH3OH?

Dispersion forces, dipole-dipole forces, and hydrogen bonding

What types of intermolecular forces are found in CH₃OH?

Dispersion forces, dipole-dipole forces, and hydrogen bonding

What types of intermolecular forces are found in HF?

Dispersion forces, dipole-dipole forces, and hydrogen bonding

What types of intermolecular forces are found in H₂O?

Dispersion forces, dipole-dipole forces, and hydrogen bonding

ecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CH3OCH3?

Dispersion forces, dipole-dipole forces, and hydrogen bonding

What is the total charge for arginine at pH = 1?

What is the total charge for arginine at pH=1

Indicate the net charge of cysteine at the chosen pH.

-0.99

Section 2-10

...

Which of the following aqueous solutions has the lowest pH?

0.1M HCl (pKa = -7)

Which of the following aqueous solutions has the highest pH?

0.1M Tris (pKa = 8.3)

At what pH values would the tripeptide Cys-Tyr-His serve as a good buffer?

1-3 and 5-11

the following structure of arginine is depicted at which pH

the following structure of glycine is depicted at which pH

|How many plateaus will the titration curve for aspartic acid have between the pH range of 0-14?

The __________ activity of DNA polymerase I from E. coli acts on __________, to facilitate proofreading for the replication process.

: 3' exonuclease; ssDNA

Section 2-1 3) Which substance do you expect to be most soluble in water? A) Ammonia, NH3. B) Methane, CH4. C) Carbon dioxide, CO2. D) Nitrogen, N2.

Section 2-10 63) Since HCl is a strong acid its value of Ka is ________. A) effectively equal to infinity B) equal to Kw C) zero D) dependent on the concentration of HCl

Section 2-10 68) pKa values of phosphoric acid are 2.2, 7.2 and 12.7. A phosphate buffer of pH = 7.4 can be prepared using A) H2PO4- and HPO42-. B) HPO42- and PO43-. C) H3PO4 and HCl. D) None of the above.

Section 2-5 28) Which of these noncovalent forces in biological systems is usually the strongest? A) Hydrogen bonds. B) London dispersion forces. C) Hydrophobic interactions. D) Van der Waals forces.

According to Chargaff's rule, which of the following is correct in reference to a double-stranded DNA molecule?

A + C = G + T

Section 2-10 65) Blood pH is primarily regulated by A) a protein buffer system. B) the carbon dioxide - carbonic acid - bicarbonate buffer system. C) the phosphate buffering system. D) carbonic acid (H2CO3). E) B and C.

Section 2-10 69) Acetic acid has a pKa of 4.8. How many milliliters of 0.2 M acetic acid and 0.2 M sodium acetate are required to prepare 1 liter of 0.1 M buffer solution having a pH of 4.8? A) 500 ml acetic acid and 500 ml sodium acetate. B) 250 ml acetic acid and 250 ml sodium acetate, then 500 ml water. C) 250 ml acetic acid and 500 ml sodium acetate, then 250 ml water. D) 500 ml acetic acid and 250 ml sodium acetate, then 250 ml water.

Section 2-3 11) A molecule or ion is said to be hydrated when it ________. A) is neutralized by water B) is surrounded by water molecules C) reacts and forms a covalent bond to water D) aggregates with other molecules or ions to form a micelle in water

Section 2-3 17) The osmotic pressure of an aqueous solution depends on A) the chemical nature of the solute. B) the molar concentration of solute. C) the hydrophobic effect of the solute. D) All of the above. E) None of the above.

Section 2-5 36) The three dimensional structure of most proteins is largely determined by A) other proteins which fold them. B) weak noncovalent interactions. C) denaturation. D) hydrogen bonds. E) All of the above.

Section 2-8 51) Basic solutions form when chemicals are dissolved in water and remove A) OH-. B) H+. C) Na+. D) A and B. E) A, B and C.

Section 2-4 23) Which molecule or ion below is amphipathic? A) H2NCH2COOH (glycine) B) H2O C) CH3(CH2)14COO- D) CH3CH2CH2CH2CH3

Section 2-10 70) The pH of human blood is primarily maintained at 7.4 by A) ATP. B) carbon dioxide-carbonic acid buffer systems. C) a bicarbonate buffer system. D) B and C. E) A, B and C.

Section 2-2 5) What is the maximum number of hydrogen bonds that one water molecule can have with neighboring water molecules? A) 1 B) 2 C) 3 D) 4

Section 2-2 6) Which statement is true about hydrogen bonds between water molecules? A) They are about as strong as the covalent bonds in a water molecule. B) They arise because of the linear geometry of water. C) They cause water to have an unusually low freezing point for its molecular weight. D) They involve the unequal sharing of a proton between water molecules. E) In liquid water the same molecules attract to each other over long time periods.

Section 2-3 15) Which is true about the solubility of electrolytes in water? A) They are all insoluble in water. B) They are usually only sparingly soluble in water. C) They often form super-saturated aqueous solutions. D) They readily dissolve and ionize in water.

Section 2-3 20) Oil and water do not form a solution due to ________. A) the hydrophobic effect B) the inability of oil to hydrogen bond with water C) the nonpolarity of oil D) All of the above. E) A and C only.

Section 2-4 25) Some ions such as thiocyanate that are poorly solvated in water and can enhance the solubility of nonpolar compounds in water by disordering the water molecules are called ________. A) azeotropes B) hydrophobic ions C) zeolytes D) chaotropes

Section 2-5 29) Hydrogen bonds can occur when hydrogen is covalently bonded to atoms like nitrogen and oxygen. What property of nitrogen and oxygen is important for this? A) Atomic mass. B) Ionizability. C) Hydrophobicity. D) Electronegativity.

Section 2-5 32) Which is true about hydrogen bonding for biological molecules? A) Hydrogen bonds are strong enough to confer structural stability, for example in DNA. B) Hydrogen bonds are weak enough to be easily broken (weaker than covalent bonds). C) They contribute to the water solubility of many macromolecules. D) All of the above.

Section 2-6 38) Water is a nucleophile, yet it does not usually hydrolyze macromolecules in cells because A) covalent bonds linking macromolecule subunits are stable at cell pH. B) covalent bonds linking macromolecule subunits are stable at cell temperature. C) the concentration of water is much too small in cells. D) A and B.

Section 2-7 49) A solution containing 10-8 M HCl and 10-8 M acetic acid contains H+ which is supplied mostly by A) the strong acid. B) the weak acid. C) both the strong and the weak acids. D) water. E) All of the above.

Section 2-7 42) What is the concentration of hydroxide ion in an aqueous solution with an H+ concentration of 2 × 10-5 M? A) 2 × 109 M B) 2 × 10-19 M C) 2 × 10-19 M D) 5 × 10-10 M E) Cannot calculate from the information given.

Section 2-7 44) Pure water has a concentration of A) 18 g/ml. B) 1 g/ml. C) 1000 g/ml. D) 55 M.

Section 2-7 46) Which statement below is true about the relative lifetime of a hydrogen bond, compared to the rate of water's ionization to hydroxide ions and hydronium ions? A) The strength of hydrogen bonding makes its dissociation much slower than the ionization of water. B) The rate of dissociation of a hydrogen bond is the same order of magnitude as the rate of ionization of water. C) The two rates are linked in such a way that the more the water is ionized, the stronger and longer lasting hydrogen bonding will be. D) The lifetime of a water molecule before it is ionized is about 109 greater than the lifetime of a hydrogen bond.

Section 2-8 54) If human blood is not maintained at close to pH = 7.4, a person can develop A) acidosis. B) alkalosis. C) diabetes. D) Both A and B. E) None of the above.

Section 2-8 55) The Henderson-Hasselbalch equation can be used to calculate A) the pH of a solution of an organic acid. B) the amount of salt and acid to add to form a specific buffer. C) the pKa of a weak acid. D) All of the above. E) A and C only.

Section 2-9 62) The imidazolium ion has a pKa = 7.0. Imidazolium buffers can be prepared for pH values of A) 6.5 to 7.5. B) 6.1 to 7.1. C) 5.5 to 8.5. D) 6.0 to 8.0. E) 6.0 to 7.5.

Section 2-9 60) At the midpoint of a titration curve A) the concentration of a conjugate base is equal to the concentration of a conjugate acid. B) the pH equals the pKa. C) the ability of the solution to buffer is best. D) All of the above. E) A and B only.

cluster

Electrolytes dissolve readily in water because Water molecules can _____ around cations and anions

Amphipathic molecules are not able to interact via Van der Waals forces. True or false?

False

decreases, limited, cage-like

For hydrophobic molecules: Dissolving in water _________ the entropy of the mixture.They have ____ solubility in water.Water forms a ______ structure around them.

Which of the following is a ribonucleoside?

Guanosine

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule will experience hydrogen bonding with like molecules?

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule will have dipole-dipole forces with like molecules?

Which molecule will experience hydrogen bonding with like molecules? HF CH₂Cl₂ H₂S H₂CO

Which molecule will have dipole-dipole forces with like molecules HF SF₆ XeF₂ BF₃

Which of the following DNA replication proteins unwinds the parental dsDNA?

Helicase

electronegativity

Hydrogen bonds can occur when hydrogen is covalently bonded to atoms like nitrogen and oxygen. What property of nitrogen and oxygen is important for this?

Which of the following enzyme(s) are required for lagging strand synthesis? I. DNA polymerase II. Primase III. 3' exonuclease IV. 5' exonuclease V. DNA ligase VI. Okazaki ligase

I, II, and V

Which of the nucleotides below contain pyrimidine bases? I. dCTP II. AMP III. GTP IV. dTTP V. UMP

I, IV, and V

Polycistronic operons can be found in which of the following? I. Heart muscle cell II. Escherichia coli III. Saccharomyces cerevisiae IV. Clostridium perfringes

II and IV

Which of the following is/are required for the polymerization reaction catalyzed by RNA polymerase? I. RNA primer II. DNA primer III. RNA template IV. DNA template V. NTPs VI. dNTPs VII. Magnesium VIII. Calcium

IV, V, and VII

Which of the following statements is true concerning the sequence pTACGTAACGTA?

If the complementary strand were present, the number of purines would be equal to the number of pyrimidines.

Based on the structure of ethidium bromide that is shown, how would you predict that it interacts with DNA?

Intercalating between consecutive base pairs

What type of interaction will occur between Na⁺ and H₂O?

Ion-dipole forces

ntermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What type of interaction will occur between Na+ and H2O?

Ion-dipole forces

electrostatic

Ionic compounds can be readily dissolved in water because the high dielectric constant of water screens and decreases the ________ force between the oppositely charged ions.

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What type of forces occur between a cation and an anion?

Ionic forces

What type of forces occur between a cation and an anion?

Ionic forces

Which would be better for separation: gel electrophoresis or isoelectric focusing?

Isoelectric focusing

Acetylation of histones occurs on which amino acid residue type?

Considering the wobble hypothesis, which amino acid would be incorporated for the following anticodon: 5'-IAG-3'?

Which of the following is NOT a function of RNA?

Long-term storage of information

Rifampicin, an antibiotic, is added to isolated E. coli RNA polymerase in vitro, but mRNA was still isolated after this addition. What might be concluded?

Many RNA polymerases were in the elongation phase where rifampicin can't bind.

Considering that bacteria and eukaryotes perform translation similarly, why are many antibiotics that target the ribosome relatively harmless to humans?

Many antibiotics cannot cross the eukaryotic cytoplasmic membrane.

Which molecule has dipole-dipole forces between like molecules? I₃⁻ NH₃ CCl₄ CO₂

NH₃

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CH4?

Only dispersion forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CO2?

Only dispersion forces

A deficiency in intracellular rRNA can be attributed to which eukaryotic enzyme?

RNA polymerase I

Telomerase is best described as a __________.

RNA-dependent DNA polymerase

Choose the image with two different possible hydrogen-bonding interactions between molecules of formamide (HCONH2).

The fourth image is correct.

If the DNA polymerase builds both chains from the same fork, how is the second strand built if DNA polymerase only synthesizes DNA one direction (5' to 3')?

The lagging strand is synthesized discontinuously using many short fragments, called Okazaki fragments.

The structure of arginine is shown. How many total functional groups are ionizable in this structure at pH values between 0-14?

Water is both a hydrogen bond donor and acceptor. True or false?

True

What is the maximum number of hydrogen bonds that one water molecule can have with neighboring water molecules?

hydrophobic interactions

Which of the following weak interactions is NOT an electrostatic interaction? Charge-charge interactions Hydrophobic interactions Hydrogen bonds Van der Waals forces

Is this statement about Hydrogen-bonding correct? Hydrogen bonds are the interaction between a hydrogen atom bonded to an electronegative element and the lone pair of electrons on a nearby electronegative atom.

Yes, this is correct. (1, 2, and 4 is the answer in the original question.)

Is this statement about Hydrogen-bonding correct? Hydrogen bonds can be stronger interactions than even charge-charge interactions.

Yes, this is correct. (1, 2, and 4 is the answer in the original question.)

Is this statement about Hydrogen-bonding correct? The atom to which the hydrogen atom is covalently bonded is the hydrogen-bond donor.

Yes, this is correct. (1, 2, and 4 is the answer in the original question.)

Based on the structure depicted, which form of DNA is represented? Form of DNA

Z DNA

Hydrogen bonding occurs between _________________.

a hydrogen attached to a fluorine, oxygen, and nitrogen and a fluorine, oxygen, or nitrogen with a lone pair of electrons on a neighboring molecule

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Hydrogen bonding occurs between _________________.

a hydrogen attached to a fluorine, oxygen, and nitrogen and a fluorine, oxygen, or nitrogen with a lone pair of electrons on a neighboring molecule

For molecules with multiple ionizable groups, such as glycine, which of the following statements is true? a. At pH near the pI, nearly all the molecules carry no net charge. b. When the pH is near the pI, the solution is near its maximum buffering ability. c. At a pH near the pI, nearly all the molecules carry a net positive charge. d. At a pH near the pI, nearly all the molecules carry a net negative charge.

a. At pH near the pI, nearly all the molecules carry no net charge.

Which of the following statements is false? a. Biological systems are highly ordered so entropy changes are not relevant. b. Biological systems expend energy to overcome entropy. c. The entropy of an isolated system will tend to increase to a maximum value. d. Entropy is a measure of disorder. The entropy of a biological system can decrease.

a. Biological systems are highly ordered so entropy changes are not relevant.

If Ca2+, Na+, and F− each have ionic radii ∼1.16Å. Which ionic bond is stronger: Ca−F or Na−F? a. Ca-F b. Na-F

a. Ca-F

The phosphodiester bonds in DNA __________.

are linked between the 3' hydroxyl of one ribose to the 5' hydroxyl of the next ribose

A spontaneous chemical reaction always has a _______ change. a. positive Gibb's free energy b. negative Gibb's free energy c. postitive enthalpy d. negative enthalpy

A technique for determining protein structure that requires crystals of the protein is______ a. NMR spectroscopy b. X-ray crystallography c. electron crystallography d. mass spectrometry e. chromatography

A titration curve for a weak acid is shown at the right. Which point shows the most buffering? (Test 1 #9) a.A b.B c.C d.D e.E

Calculate the standard free energy change for the reaction FADH2+1/2 O2-->FAD+H2O given that the standard reduction potential for the reduction of oxygen to water is +0.82V and for the reduction of FAD to FADH2 is -0.22V a. -152kJ b. -200kJ c. -220kJ d. -164kJ

Which of the following does NOT apply to the reaction catalyzed by the pyruvate dehydrogenase complex? a. The process is highly exergonic and essentially irreversible in vivo b. each intermediate in the five step reaction is able to diffuse to the next active site in a sequential manner c. it takes place in the mitochondrion d. it is an oxidative decarboxylation

Which of the following is CORRECT when considering the tertiary structure of globular proteins? a. beta sheets are usually twisted or wrapped into barrel structures b. hydrophobic residues are normally on the inside and hydrophilic residues are on the outside c. the amino acid proline never occurs in a region where the polypeptide chain bends or turns d. all parts of the proteins can be classified as helix, beta sheet or turns

Which of the following shows the buffer that is found in the cytosol of cells? a. H3PO4-->H2PO4^2- + H+ B. H2PO4- -->HPO4^2- + H+ C. HPO4^2- -->PO4^3- + H+ D. H2CO3 --> HCO3- + H+ E. HCO3- --> CO3^2- + H+

Briefly explain your choice. a. The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is greater than the target pH of 7.0. b. The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is close to the target pH of 7.0. c. The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is lower than the target pH of 7.0.

b. The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is close to the target pH of 7.0.

At the melting temperature of water, which of the following statements is true? a. The reaction is spontaneous because ΔH is greater than -TΔS. b. The value of TΔS must equal the value of ΔH. c. The value of TΔS must be greater than the ΔH component. d. There is not enough information to answer this question.

b. The value of TΔS must equal the value of ΔH.

As biochemistry has matured as a science, new branches of the field have developed to maintain the ever-growing database of information. Assign the purpose on the right with the field on the left. metabolomics a. assess the expression and function of genes. b. determine the intraceullular concentrations of small molecules. c. mathematic analysis of DNA sequence data. d. identify the function of proteins.

b. determine the intracellular concentrations of small molecules.

Shine-dalgarno sequences __________.

base pair with rRNA in untranslated regions of bacterial mRNA

All amino acids have a chiral a-carbon EXCEPT a. proline b. alanine c. glycine d. tryptophan

Glucose in adipocytes are converted in to triacylglycerol by converting glucose to _______ and further association with fatty acids a. phosphoenol pyruvate b. pyruvate c. glycerol-3-phosphate d. fructose-6-phosphate

Glycolysis is regulated primarily by ________ a. the availability of glucose-6-phosphate b. three strongly endergonic, non-equilibrium reactions c. three strongly exergonic, non-equilibrium reactions d. allosteric effectors of pyruvate kinase

How does the reaction catalyzed by malate dehydrogenase proceed despite a change in G prime of 29.7 kJ/mol? a. an elevated [H+] allows the reaction to proceed b. high levels of NAD+ allow the reaction to proceed c. concentrations of oxaloacetate are kept very low by rapid use in subsequent step d. the enzyme is unique in its ability only to catalyze the reaction in one direction

In an anabolic reaction, the most likely cofactor would be a. NADH b. NAD+ c. NADPH d. NADP+

Proteolytic cleavage is an example of ________ post-translational modification a. reversible b. non-covalent c. irreversible d. electrostatic

Reactions that replenish the pool of citric acid cycle intermediates are called a. anabolic reactions b. catabolic reactions c. anaplerotic reactions d. reductive reactions

The anabolic and catabolic processes of cellular metabolism can be coupled by _________ a. a 2nd anabolic process b. carbohydrate hydrolysis c. ATP hydrolysis d. lipid hydrolysis

The carbon skeleton left after the transamination process are used for oxidation in the ________ cycle a. transamination b. Cori c. Citric acid d. alanine-pyruvate

The families of lipoproteins are classified, based on their _________ a. volume b. mass c. density d. diameter

The formation of an enzyme-substrate complex tends to be thermodynamically favorable due to _______ interactions between substrate and enzyme. a. covalent b. carbon-based c. non-covalent d. nominal

The metabolic pathway for the production of compound X requires multiple enzyme catalyzed reactions. The product of the pathway, compound X, binds to one of the enzymes early in the pathway and acts as an inhibitor of the enzyme. This is best described as________. a. substrate level control b. product level control c. feedback control d. allosteric regulation

Which is NOT a similarity between active transport proteins and enzymes? a. both undergo conformational changes upon binding a substrate b. both are susceptible to inhibition c. both cause chemical modification to the substrate d. both can reach a saturation limit

Which of the following is not classed as a lipid? a. Palmitic acid b. Phosphatidyl serine c. Glycerol d. Cholesterol e. Triacylglycerol

c. Glycerol Glycerol forms the backbone of glycerolipids via ester bonds. It is not in itself a lipid.

Much of water's ability to dissolve a wide variety of molecules and yet, one of its most important characteristics is its effect on nonpolar, uncharged molecules. Which of the following statements is not true about this effect? a. water molecules from clathrates or cages that surround nonpolar molecules or particles. b. The hydrophobic effect plays an important role in the folding of proteins and the assembly of lipid bilayers. c. Hydrophobic molecules are driven together largely because of forces of attraction between them. d. All of the listed statements are true.

c. Hydrophobic molecules are driven together largely because of forces of attraction between them.

Which of the following statements is FALSE? a. Proteins can be both hormones and hormone receptors. b. Proteins can transmit signals between cells. c. Proteins are the only biological polymer that can catalyze biochemical reactions. d. Proteins can be structural components of cells. e. Proteins can transport molecules within cells and between cells.

c. Proteins are the only biological polymer that can catalyze biochemical reactions. This is false.

Which of the following is FALSE when considering Van der Waals interactions? a. Van der Waals radii can determine molecular surfaces. b. Molecules that interact by van der Waals forces do not interpenetrate. c. They are not important in determining the stability of three-dimensional structures of proteins. d. The total interaction energy is the sum of the attractive and repulsive forces. Submit

c. They are not important in determining the stability of three-dimensional structures of proteins.

Is the value of average charge you calculated in part C reasonable, given the pI you calculated in part A? Explain your answer. a. No. When pH < pI the molecule is predicted to carry a negative charge. b. No. When the molecule has two amino groups it is predicted to carry a positive charge. c. Yes. When pH < pI the molecule is predicted to carry a positive charge. d. Yes. When the molecule has two amino groups it is predicted to carry a negative charge.

c. Yes. When pH < pI the molecule is predicted to carry a positive charge.

Small ions in biological fluids: a. have large effects on pH. b. encourage strong electrostatic interactions between oppositely charged macroions at high ionic strengths. c. encourage strong electrostatic interactions between oppositely charged macroions at low ionic strengths. d. tend to cluster around macroions of the same charge. e. have no effect on the interactions between oppositely charged macroions.

c. encourage strong electrostatic interactions between oppositely charged macroions at low ionic strengths.

Biochemistry is focused on four biological molecules: proteins, carbohydrates, nucleic acids, and lipids. Of these, which are NOT polymers? a. nucleic acids b. proteins c. lipids d. carbohydrates

c. lipids Polymers are a chemical compound or mixture of compounds formed by polymerization and consisting essentially of repeating structural units. Lipids are formed when a glycerol molecule combines with fatty acids, therefore they are not polymers because they contain one molecule and are not macromolecules.

Which of the following subunits in the E. coli RNA polymerase is responsible for specificity?

What is the total charge for aspartic acid at pH = 1?

What is the total charge for aspartic acid at pH = = 1?

What is the total charge for arginine at pH = = 1?

What is the overall charge of cysteine at pH = 8.5

-1

What is the overall charge of cysteine at pH = 8.5?

-1

which of the following aqueous solutions has the highest pH

.1M Tris (pKa = 8.3)

Indicate the net charge of arginine at the chosen pH.

0.24

Calculate the average charge on arginine when pH = 9.20. (hint; find the average charge for each ionizable group and sum these together.)

0.38

Which statements regarding the Henderson-Hasselbalch equation are true? 1) If the pH of the solution is known as is the pKa for the acid, the ratio of conjugate base to acid can be determined. 2) At pH = pK a for an acid, there is an equal amount of conjugate base to acid in solution. 3) At pH >> pK a for an acid, the acid will be mostly ionized. 4) At pH << pK a for an acid, the acid will be mostly ionized.

1, 2, and 3 are true

Which of the following statements details the role of lipids? 1. some serve as a fuel source 2. some provide structure to membranes 3. some transport small molecules and ions across membranes. 4. some are precursors to steroids.

1, 2, and 4 are correct. Lipids can serve as a fuel source, they can provide structure to membranes, and they can be precursors to steroids.

At what pH values would the tripeptide cys-tyr-his serve as a good buffer

1-3 and 5-11

At what pH values would histidine serve as a good buffer?

1-3, 5-7, and 8-10

The following structure of glycine is depicted at which pH

What is the OH ion concentration in an aqueous solution with a pH of 12? Assume the temperature is near 20 °C.

1x10-02 M

What is the OH- ion concentration in an aqueous solution with a pH of 12? Assume the temperature is near 20 °C.

1x10-02 M

What is the H* ion concentration in an aqueous solution with a pOH of 3? Assume the temperature is near 20 °C.

1x10-11 M

What is the H+ ion concentration in an aqueous solution with a pOH of 3? Assume the temperature is near 20 °C.

1x10-11 M

How many plateaus will the titration curve for glycine have between the pH range of 0-14?

How many plateaus will the titration curve for arginine have between the pH range of 0-14

How many plateaus will the titration curve for arginine have between the pH range of 0-14?

How many plateaus will the titration curve for aspartic acid have between the pH range of 0-14?

How many plateaus will the titration curve for cysteine have between the pH range of 0-14?

The structure of arginine is shown. How many total functional groups are ionizable in this structure at pH values between 0-14?

The structure of aspartic acid (aka asparate) is shown. How many total functional groups are ionizable in this structure at pH values between 0-14?

The structure of aspartic acid (aka asparate) is shown. How many total functional groups are ionizable in this structure at pH values between 0-14? Aspartate structure

the structure of arginine is shown below. how many total functional groups are ionizable at ph values between 0-14

The side chain of tyrosine has a pKa of about 10. What percent of tyrosine side chains would be deprotonated at pH 8.5?

the side chain of tyrosine has a pKa of about 10. what percent of tyrosine side chains would be deprotonated at pH 8.5

Amino acids are attached to the __________ of a tRNA.

3' terminus

Which of the following represents the correct sequence of events in bacterial translational initiation?

30S binds Shine-dalgarno N-formylMet-tRNA binds AUG 50S binds 2nd aminoacyl-tRNA binds in the A site

The side chain of cysteine has a pKa of about 8.3. What percent of cysteine side chains would be deprotonated at pH 8.3?

50%

Carbon dioxide is dissolved in blood (pH 7.4) to form a mixture of carbonic acid and bicarbonate. Neglecting free CO2, what fraction will be present as carbonic acid? Would you expect a significant amount of carbonate?

7.4*10^-2 No, you would not expect a significant amount of carbonate.

The following structure of cysteine is depicted at which pH Cysteine structure

the following structure of cysteine is depicted at which pH (equil arrows)

The following structure of tyrosine is depicted at which pH?

9.5

The side chain of histidine has a pKa of about 6. What percent of histidine side chains would be deprotonated at pH 7.5?

97%

The side chain of histidine has a pKa of about 6. What percent of histidine side chains would be deprotonated at pH= 7.5?

97%

Which of the following amino acid sequences would NOT be produced by the translation of the repeating mRNA sequence (GCU)n (where n = number of repeating units)?

: (-S-S-S-)n

Section 2-2 8) Compounds that ionize when dissolved in water are called ________. A) electrolytes B) polar compounds C) hydrophobic compounds D) amphipathic compounds

Section 2-3 16) What is the difference between a particle being hydrated versus being solvated? A) A hydrated particle is surrounded by a shell of water. A solvated molecule is surrounded by a shell of solvent molecules, not necessarily water. B) The terms hydrated and solvated mean exactly the same thing. C) A hydrated particle has reacted with hydrogen. A solvated particle is dissolved in a solvent. D) The word hydrated is used only when the solute is an electrolyte.

Section 2-3 12) Which would you expect to be most soluble in water? A) I B) II C) III D) IV

Section 2-4 22) Molecules that are both hydrophobic and hydrophilic are ________. A) amphipathic B) amphoteric C) bipolar D) not possible

Section 2-5 31) Attractions of oppositely charged functional groups of proteins are sometimes called ________. A) salt bridges or ion pairing B) disulfide bridges C) London bridges D) hydrophilic bridges

Section 2-5 33) London dispersion forces are attractive forces that arise due to A) infinitesimal dipoles generated by the constant random motion of electrons. B) permanent dipoles of molecules containing covalent bonds between atoms of very different electronegativities. C) the hydrophobic effect. D) ion pairing between oppositely charged functional groups.

Section 2-5 35) Water molecules clustered about nonpolar molecules contribute to hydrophobic interactions because A) their number is minimized to increase the total entropy of water. B) nonpolar molecules are more highly organized than polar molecules. C) water molecules in the cell are more organized in the regions away from the nonpolar molecule. D) All of the above. E) B and C.

Section 2-7 41) Which parameter has the greatest correlation to reaction rate? A) Activation energy. B) Gibb's free energy. C) Enthalpy. D) Entropy. E) None of the above.

Section 2-7 48) How does the ion-product of water, Kw, relate to the equilibrium constant, Keq, for the dissociation reaction of water? A) Kw is found by multiplying Keq by the concentration of water. B) Kw just another symbol for Keq , so they are equal. C) Kw is found by dividing Keq by the ideal gas constant. D) Kw is found by multiplying Keq by the concentrations of hydronium ion and hydroxide ion.

Section 2-7 45) Which statement best characterizes the distribution of charge in the hydronium ion, H3O+? A) The positive charge is distributed over all of the atoms in the ion. B) The positive charge is localized only on the oxygen atom. C) The positive charge is distributed between the three hydrogen atoms only. D) The positive charge is localized on only one of the hydrogen atoms.

Section 2-8 50) In pure water, the concentration of H+ plus equals A) 1 × 10-7 M. B) 1 × 10-14 M. C) 1 M. D) .07 M.

Section 2-9 56) Two weak acids, A and B, have pKa values of 4 and 6, respectively. Which statement is true? A) Acid A dissociates to a greater extent in water than acid B. B) For solutions of equal concentration, acid B will have a lower pH. C) B is the conjugate base of A. D) Acid A is more likely to be a polyprotic acid than acid B. E) The equivalence point of acid A is higher than that of acid B.

Section 2-9 58) What is the approximate pH of a 0.10 M solution of a weak acid that has a Ka of 5 × 10-5 M? A) 2.7 B) 5.3 C) 4.8 D) 11.3 E) Cannot determine from the information given.

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which compound will experience ionic forces?

AlCl3

Which compound will experience ionic forces? BF₃ SiH₄ AlCl₃ CO₂

AlCl₃

The ribosome catalyzes the formation of which functional group?

Amide

Considering that the formation of the peptide bond is readily reversible and thermodynamically favors peptide bond hydrolysis (as seen in the diagram below), how do cells overcome this for favorable translational events?

Amino acids are activated before peptide bond formation.

both polar and nonpolar

Amphipathic molecules are ________; not able to interact via van der Waals forces.

Clearly label the hydrogen-bond donor and acceptor atoms as donors or acceptors.

As labelled.

salt bridges/electrostatic interactions

Attractions of oppositely charged functional groups of proteins are sometimes called ________.

Section 2-1 4) Which is NOT a proper way to form a hydrogen bond? (The symbol "R" represents a general organic group. The hydrogen bonding is represented by dashed lines.) A) I B) II C) III D) IV

Section 2-4 21) Micelles, formed by detergents in water, have A) hydrophilic interiors and hydrophobic exteriors. B) hydrophobic interiors and hydrophilic exteriors. C) hydrophilic interiors and exteriors. D) hydrophobic interiors and exteriors. E) None of the above.

Section 2-4 24) Which statement explains the cleaning action of soap on greasy dishes? A) The soap changes the water-solubility of the grease so that it is easily dissolved by the water. B) The grease is trapped inside the hydrophobic interior of micelles made of soap molecules. C) The soap chemically breaks down the grease into smaller, more water-soluble molecules. D) The soap hydrates the grease with its polar head groups and holds it in suspension.

Section 2-5 30) Which statement is true about the ability of carbon to participate in hydrogen bonds in living organisms? A) There are too many carbon atoms competing for the hydrogens in biomolecules to allow for the stable formation of hydrogen bonds. B) Carbon's electronegativity is too low to participate in hydrogen bonding. C) Most carbons in biomolecules are hydrogen bonded to water. D) Carbon is too large to participate in hydrogen bonding.

Section 2-6 39) Enzymes which condense subunits of macromolecules during their synthesis usually A) transfer an acyl or carbonyl group to an electrophile. B) exclude water from the active site. C) contain inhibitors of hydrolases. D) are catalyzing thermodynamically favored reactions. E) All of the above.

Section 2-7 43) In pure water hydronium ions are formed by ________ attack of oxygen on a proton in an adjacent water molecule. A) ionic B) nucleophilic C) electrophilic D) covalent

Section 2-7 47) The self-ionization of water is ________. A) a unimolecular dissociation of a single water molecule to H+ and OH- B) a biomolecular reaction between two water molecules to yield H3O+ and OH- C) a result of hydrophobic interactions D) a termolecular reaction involving the simultaneous collision of H2O, H+ and OH-

Section 2-9 57) Calculate the value of pKa for an acid when Ka = 2.6 × 10-4. A) -3.59 B) +3.59 C) -8.25 D) +8.25 E) +3800

Section 2-9 61) A titration curve for a weak acid is shown. Which point shows the most buffering? A) A B) B C) C D) D E) E

From the previous part, estimate the H−O bond energy.

Bond energy = 463 kJ/mol

1) Which statement does NOT explain the polarity of water? A) Oxygen is more electronegative than hydrogen. B) Water molecules have a bent geometry (V-shaped). C) The oxygen in water has sp2 hybrid orbitals. D) In water the hydrogen carries a partial positive charge (δ+).

Section 2-10 66) The pKa of lactic acid is 3.9. A lactate buffer will be useful from pH values A) 3.5 through 4.4. B) 3.0 through 4.5. C) 2.9 through 4.9. D) 3.8 through 4.0.

Section 2-2 7) The abundance of water in the cells and tissues helps to minimize temperature fluctuations. This is due to what property of water? A) Density. B) Viscosity. C) Specific heat. D) Boiling point.

Section 2-3 13) Solutes diffuse more slowly in cytoplasm than in water because of A) the higher viscosity of water. B) the higher heat of vaporization of water. C) the presence of many crowded molecules in the cytoplasm. D) the absence of charged molecules inside cells.

Section 2-3 14) The ________ pressure is the pressure required to prevent the flow of solvent through a solvent-permeable membrane that separates two solutions of different solute concentration. A) hydrostatic B) electromotive C) osmotic D) partial

Section 2-3 19) The osmotic pressure of a 0.010 M sucrose (C12H22O11) solution at 25°C is 0.24 atm. How does the osmotic pressure of a 0.010 M glucose (C6H12O6) solution at 25°C compare to this? Note that neither solute is volatile or ionizable. A) The glucose solution has a lower osmotic pressure because its molar mass is lower than sucrose. B) The glucose solution has a higher osmotic pressure because its molar mass is lower than sucrose. C) The osmotic pressures are equal because the solutions have the same molar concentration. D) Nothing can be said about the osmotic pressure of the glucose solution without more information.

Section 2-3 9) Poorly soluble molecules such as lipids and nucleoside bases can be made more soluble in cells by attaching ________ to them. A) water B) oxygen C) carbohydrates D) salt ions

Section 2-4 26) Which of the following is NOT a "weak" interaction? A) Hydrogen bonds B) Van der Waals forces. C) Disulfide bonds. D) Ionic interactions. E) Hydrophobic interactions.

Section 2-5 27) Which of the following weak interactions is NOT an electrostatic interaction? A) Hydrogen bonds. B) Charge-charge interactions. C) Hydrophobic interactions. D) Van der Waals forces.

Section 2-5 34) The aggregation of nonpolar molecules or groups in water is thermodynamically due to the A) increased entropy of the nonpolar molecules when they associate. B) decreased enthalpy of the system. C) increased entropy of the water molecules. D) very strong van der Waals forces among the nonpolar molecules or groups.

Section 2-5 37) The oxygen atom of water is nucleophilic because A) it has a negative oxidation number. B) it carries a partial positive charge. C) it has two unshared pair of electrons. D) it seeks electron-rich molecules. E) All of the above.

Section 2-6 40) The ion-product constant for water, Kw, is A) 1 × 10-7 M2. B) 1 × 10-7 M. C) 1 × 10-14 M2. D) 1 × 10-14 M.

Section 2-8 52) The pH of a 10-4 M solution of HCl is A) 3. B) 3.5. C) 4. D) 4.5. E) greater than 4.5.

Section 2-8 53) Compare solution A with pH = 4 to solution B with pH = 6. A) The concentration of hydronium ion in solution A is twice that in solution B. B) Solution A has greater buffering capacity than solution B. C) The concentration of hydronium ion in solution A is 100 times that in solution B. D) The hydroxide concentrations are equal in the two solutions since pH only measures the concentration of H+.

Section 2-9 64) For a weak acid with a pKa = 6.5, the effective buffering range is usually considered to be A) pH 6 to pH 7. B) pH 6.4 to pH 6.6. C) pH 5.5 to pH 7.5. D) dependent on the molarity of the acid. E) B and C.

Which molecule will have hydrogen-bonding between like molecules? H₂ CH₃OCH₃ CH₄ CH₃OH

CH₃OH

Considering the wobble hypothesis, which codon would NOT recognize the following anticodon: 5'-IAG-3'?

CORRECT ANSWER: 5'-CUG-3'

What is the strongest non-covalent interaction that attracts complementary base pairs in dsDNA?

CORRECT ANSWER: Hydrogen bonding

Which molecule has only dispersion forces with like molecules? CH₂Cl₂ H₂CO CO₂ CH₃OH

CO₂

If the 3' nucleotide of tRNA was replaced with a dNTP, which of the following would result?

Class I tRNA synthetases would not catalyze the formation of aminoacyl-tRNAs.

Section 2-10 67) Intracellular buffers include A) proteins. B) inorganic phosphate. C) cellulose. D) Both A and B. E) A, B and C.

Hoogsteen base pairs can be found in __________.

DNA triple helices

Primase is best described as a __________.

DNA-dependent RNA polymerase

RNA polymerase is best described as a __________.

DNA-dependent RNA polymerase

Which of the following describes a nucleotide found in DNA?

Deoxyribose + phosphate group(s) + adenine

Section 2-1 2) The polarity of small molecules is a result of A) the presence of oxygen. B) the geometry of the bonds in the molecule. C) the polar covalent bonds. D) All of the above. E) B and C.

Section 2-3 10) Electrolytes dissolve readily in water because A) they are held together by electrostatic forces. B) they are hydrophobic. C) water molecules can cluster about cations. D) water molecules can cluster about anions. E) water molecules can cluster about cations and anions.

Section 2-3 18) Cells keep the osmotic pressure from being too great by A) existing in hypertonic solutions. B) making macromolecules from smaller molecules. C) existing in a hypotonic solution. D) existing in an isotonic solution. E) Both B and D.

Section 2-9 59) The ratio of the concentration of a ________ over ________ describes the proportions of forms of a weak acid necessary to satisfy the Henderson-Hasselbalch equation. A) conjugate acid; conjugate base B) conjugate base; conjugate acid C) proton donor; proton acceptor D) proton acceptor; proton donor E) B and D

carbon-hydrogen

Each of the following is a noncovalent interaction EXCEPT ________. - hydrogen - carbon-hydrogen - dipole-dipole - van der Waals

Which of the following is NOT a difference between prokaryotic and eukaryotic DNA replication?

Eukaryotic replication has one origin of replication, whereas prokaryotic replication has several.

Glycine cannot serve as a buffer because it has two ionizable groups. True or false?

False

Oxidation-reduction reactions, which are the basis of many biochemical reactions and pathways, cannot take place in the absence of oxygen. True or false?

False

The change in enthalpy (ΔH) for the complete oxidation of a fatty acid is different depending on whether it occurs via a biochemical pathway or combustion to CO2 and H2O. True or false?

False

The pKa of each amino acid residue in a protein will not be influenced by the adjacent residue. True or false?

False

The principle component of a biological membrane is a triglyceride. True or false?

False

Amino acids and simple organic compounds like carbon dioxide and hydrogen cyanide cannot be produced without the use of enzymes. True or false?

False.

Which of the following diseases, related to DNA replication, results from DNA polymerase slippage errors resulting in tandem repeats?

Huntington's disease

Which of the two possible hydrogen-bonding interactions is more likely to occur? 1 is between a H and a double-bonded O. 2 is between an H and a neutrally charged N.

Hydrogen bond 1 is more likely to occur.

electronegative

Hydrogen bond donors must be covalently attached to atoms that are ________.

What type of interaction occurs between hydrogen of water and the oxygen of another water molecule?

Hydrogen bonding

The four most abundant chemical elements in living systems are...

Hydrogen, Carbon, Nitrogen, and Oxygen

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule has dipole-dipole forces between like molecules?

NH3

What structural part of the DNA is responsible for the signal in a denaturation curve?

Nitrogenous base

Is this statement about Hydrogen-bonding correct? The distance between the covalently bound H atom and its hydrogen-bonding donor is the sum of its van der Waals radii.

No, this is not correct. (1, 2, and 4 is the answer in the original question.)

The peptidyl transfer mechanism catalyzed by the ribosome is considered which type of chemical transformation?

Nucleophilic acyl substitution

The polymerization reaction catalyzed by DNA polymerase undergoes which type of chemical transformation?

Nucleophilic substitution

The polymerization reaction catalyzed by RNA polymerase undergoes which type of chemical transformation?

Nucleophilic substitution

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in BF3?

Only dispersion forces

What types of intermolecular forces are found in BF₃?

Only dispersion forces

Indicate the direction of migration and relative mobility of each amino acid in the electric field.

Order; + Cys, Lys, Arg -

Amide bond formation occurs between aminoacyl-tRNAs bound in the __________.

P and A sites

The chemical element ____________ has a role in both transfer of energy as well as in the structure of nucleic acids.

Phosphorus

What is the strongest non-covalent interaction that attracts consecutive base pairs in dsDNA?

Pi stacking

Which amino acid would be incorporated based on the following anticodon: 5'-CCU-3'?

How can any RNA nucleotide be easily distinguished from a DNA nucleotide?

RNA nucleotides have an -OH on the 2' carbon of the ribose.

Considering that RNA transcription is much slower than DNA replication (50 nucleotides added/second versus 500-1000 nucleotides/second), how is it possible that RNA >> DNA in living cells?

RNA polymerases >> DNA polymerases

Which of the following statements concerning bacterial transcription is true?

RNA transcription and protein translation occur roughly simultaneously in bacteria.

Retroviruses (like HIV) replicate their genome by a __________ called __________.

RNA-dependent DNA polymerase; reverse transcriptase

The peptidyl transferase mechanism, catalyzed by the ribosome, uses which monomer to facilitate catalysis?

Ribonucleic acid

Glucose transporters are initially translated in which cellular location?

Rough endoplasmic reticulum

Complementary base pairing is considered which level of structure?

Secondary

Which of the following DNA replication proteins keeps the parental strands separate after being unwound and separated?

Single-stranded binding protein (SSB)

Which of the following enzymes in DNA replication is strongly correlated with aging?

Telomerase

hydrophobic effect

The ________ describes the tendency for hydrophobic molecules to aggregate because of the exclusion of water with the consequent increase of entropy of the solvent.

Considering the zinc finger motif (shown below), which is a common motif in DNA binding proteins like RNA polymerase III, which part of the structure will bind directly to DNA?

The alpha helix

noncovalent

The combined effect of many weak ________ interactions can be very significant in determining factors such as three-dimensional structure for large biological molecules.

2431

The energy of a noncovalent interaction is dependent on their range. Organize the following types of noncovalent interactions from longest range to shortest range interactions. 1. Van der Waals interaction (dispersion force) 2. Charge-charge interaction 3. Dipole-induced dipole interaction 4. Dipole-dipole interaction

Eukaryotic translation differs in many ways from prokaryotic translation but which of the following is NOT one of them?

The first aminoacyl-tRNA in eukaryotic translation initiation is N-methyl-Met-tRNA.

Choose the structure of lysine in the protonation state that would predominate at the pH you have chosen.

The first one is correct.

pH = 10

The following structure of arginine is depicted at which pH?

pH = 3

The following structure of aspartic acid (aka asparate) is depicted at which pH?

pH = 9

The following structure of cysteine is depicted at which pH?

pH = 12

The following structure of glycine is depicted at which pH?

pH = 9.5

The following structure of tyrosine is depicted at which pH?

Which of the following statements concerning the tautomers of thymine is true?

The keto form is more stable.

Indicate the net charge of lysine at the chosen pH.

The net charge is 0.0

The accompanying graph depicts the interaction energy between two water molecules situated so that their dipole moments are parallel and pointing in the same direction. Choose an approximate curve for the interaction between two water molecules oriented with antiparallel dipole moments.

The second graph is the curve for the interaction between two water molecules oriented with antiparallel dipole moments. It is a positive-direction curved graph approaching the 0 line. It is opposite the original graph.

Choose the structure of arginine in the protonation state that would predominate at the pH you have chosen.

The second one is correct

Choose the structure of cysteine in the protonation state that would predominate at the pH you have chosen.

The third one is correct.

polar

The unequal sharing of electrons within a water molecule makes the water molecule _____

Which of the following DNA replication proteins alleviates the torsional stress caused by unwinding of parental strands?

Topoisomerase

Eukaryotic RNA polymerase II requires which proteins for selective binding?

Transcription factors

Hydrogen bonds share features of both covalent and noncovalent bonds. True or false?

True

Many biochemical reactions that form biopolymers from monomeric units involve the removal of water. True or false?

True

The average charge on an amino acid below its pI will be positive. True or false?

True

Which of the following is NOT a post-transcriptional processing event for mRNA in eukaryotes?

Turnover by the degradosome

From the standpoint of entropy, consider the following processes: water boiling, mixing cola and root beer sodas, and assembling a house of cards. Based on your understanding, which of the following statements is true? a. Water boiling is a favorable process, but mixing cola and root beer sodas and assembling a house of cards are not. b. Water boiling and mixing cola and root beer sodas are favorable processes, but assembling a house of cards is not. c. Water boiling and mixing cola and root beer sodas are not favorable processes, but assembling a house of cards is. d. All of the listed processes are favorable.

Water boiling and mixing cola and root beer sodas are favorable processes, but assembling a house of cards is not.

hydrogen

What name is given to the bond between water molecules?

oxygen and nitrogen

Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond? - hydrogen and carbon - oxygen and nitrogen - nitrogen and hydrogen - hydrogen and oxygen

1,2,3

Which of the following statements about noncovalent interactions are true? 1. Charge-charge interactions (salt bridge, ionic bond) are electrostatic interactions between a pair of ions. 2. The energies of dipolar interactions depend on the relative orientation of the dipole. 3. Van der Waals interactions have the shortest interaction range of noncovalent interactions. 4. Hydrogen bonds are not directional.

They involve the unequal sharing of a proton between water molecules

Which statement is TRUE about hydrogen bonds between water molecules? -They involve the unequal sharing of a proton between water molecules. -They are about as strong as the covalent bonds in a water molecule. -They cause water to have an unusually low freezing point for its molecular weight. -They arise because of the linear geometry of water

Carbon's electronegativity is too low to participate in hydrogen bonding

Which statement is TRUE about the ability of carbon to participate in hydrogen bonds in living organisms? - Most carbons in biomolecules are hydrogen bonded to water. - Carbon's electronegativity is too low to participate in hydrogen bonding. - Carbon is too large to participate in hydrogen bonding. - There are too many carbon atoms competing for the hydrogens in biomolecules to allow for the stable formation of hydrogen bonds.

ammonia

Which substance do you expect to be most soluble in water? n, N2Ammonia, NH3Carbon dioxide, CO2Methane, CH4

Is this statement about lipid bilayers true? The amphipathic molecules that make up the bilayers orient themselves such that their polar head groups point out toward the aqueous solvent and their hydrophobic tails are pointed toward the interior of the bilayer.

Yes. (All of the listed statements are true in the original question.)

Is this statement about lipid bilayers true? Their formation is driven by the hydrophobic effect.

Yes. (All of the listed statements are true in the original question.)

Is this statement about lipid bilayers true? They are made primarily from phospholipids.

Yes. (All of the listed statements are true in the original question.)

Is this statement about lipid bilayers true? They serve the role of physical compartmentalization of components within a cell.

Yes. (All of the listed statements are true in the original question.)

Active transport can move a substance across a membrane against its ________ a. concentration gradient b. pH gradient c. proton gradient d. electron gradient

The _____ describes the tendency for hydrophobic molecules to aggregate because of the exclusion of water with the consequent increase of entropy of the solvent. a. hydrophobic effect b. hydrophilic effect c. hypertonic effect d. hypotonic effect

The production of carbon dioxide during respiration in aerobic tissues lowers the pH in erythrocytes, which in turn _____ the affinity of oxygen binding to hemoglobin a. decreases b. increases c. equilibrates d. none of the above

The structures of D-ribose and D-arabinose are shown. These two molecules are ________. (Test 2, #4) a. epimers b. enantiomers c. tautomers d. anomers

The ultimate product of complete oxidation of carbohydrates is _______ a. carbon dioxide b. acetyl CoA c. pyruvate d. acetate ion

Two curves showing the rate versus substrate concentration are shown at the right for an enzyme-catalyzed reaction. Once curve is for the reaction in the presence of substance X. The other curve is for data in the absence of substance X. Examine the curves and tell which statement below is TRUE for the observation made. a. X is an activator of the enzyme b. The catalysis shows Michaelis-Menten kinetics, with or without X c. X increases the activation energy for the catalytic reaction d. X could be a competitive inhibitor

What is the by-product in oxidation of odd-numbered carbon chain fatty acid? a. propionyl-CoA b. methylmalonyl-CoA c. Acetoacetyl-CoA d. Glutaryl-CoA

What is the difference between de novo and salvage pathway of nucleotides? a. the former relates to synthesis of nucleotide from its precursor molecule and later involves in synthesis of nucleotide from nucleobases b. there is no significant difference c. the de novo pathway occurs only in microbes d. the salvage pathway occurs only in microbes

What is the order for the flow of electrons through the electron transport chain in mitochondria? a. NADH, coenzyme Q, cytochrome c, oxygen b. NADH, cytochrome c, coenzyme Q, oxygen c. Oxygen, cytochrome c, coenzyme Q, NADH d. Cytochrome c, coenzyme Q, NADH, oxygen

What would occur if both phosphofructokinase and fructose bisphosphatase were active simultaneously? a. a futile cycle b. a substrate cycle c. an inhibitor cycle d. the Cori cycle

Which elements are found in simple carbohydrates? a. carbon, hydrogen, and oxygen b. carbon, hydrogen, oxygen, nitrogen c. carbon, hydrogen, oxygen, phosphorous d. carbon, hydrogen, oxygen, sulfer e. none of the above

Which of the following statements is FALSE about most metabolic pathways? a. most pathways are reversible under physiological conditions b. pathways serve to increase the efficiency of energy transfers c. the rates of pathway reactions vary to respond to changing conditions d. the enzymes that catalyze reactions in metabolic pathways generally catalyze only a single step

Which of the following would be the strongest acid? a. formic acid, pK=3.75 b. succinic acid, a diprotic acid with pK=4.21 and 5.64 c. acetic acid, pK=4.76 d. ammonium ion, pK=9.25

Calculate the pH values and draw the titration curve for the titration of 500 mL of 0.010 M acetic acid (pKa 4.76) with 0.010 MKOH. a. Calculate the pH of the solution after 0 mL of the titrant have been added. b. Calculate the pH of the solution after 250 mL of the titrant have been added. c. Calculate the pH of the solution after 490 mL of the titrant have been added. d. Calculate the pH of the solution after 500 mL of the titrant have been added. e. Calculate the pH of the solution after 510 mL of the titrant have been added. f. Calculate the pH of the solution after 750 mL of the titrant have been added. g. Choose the titration curve for this titration.

a. 3.39 b. 4.76 c. 6.45 d. 8.23 e. 10.00 f. 11.30 g. see attached image. Positive graph with two steps.

The water content in the human body is approximately: a. 70% b. 90% c. 50% d. 60% e. 80%

a. 70%

Which of the following statements is not true about adaptability? a. It is the capacity of populations of organisms to respond to environmental changes. b. It is the capacity of individual representatives of an organism to respond to environmental changes. c. It is a characteristic of living organisms. d. It is the capacity to change in response to environmental changes.

a. It is the capacity of populations of organisms to respond to environmental changes.

Which of the following statements about biomolecules is true? a. Nucleic acids (DNA/RNA) are responsible for information storage, transmission, and expression. b. Proteins are broken down as a primary fuel source. c. Lipids are responsible for the transport of substances into the cell. d. Carbohydrates are responsible for the catalysis of chemical reactions.

a. Nucleic acids (DNA/RNA) are responsible for information storage, transmission, and expression.

Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond? a. Oxygen and Nitrogen b. Nitrogen and Hydrogen c. Hydrogen and Carbon d. Nitrogen and Carbon e. Hydrogen and Oxygen

a. Oxygen and Nitrogen

Which of the following statements about acids and bases is INCORRECT? a. Water acts as a weak acid b. Bases need not contain -OH directly; instead, they can increase the concentration of -OH by deprotonating water. c. A bronsted base is a proton acceptor d. a strong acid has a weak conjugate base

a. Water acts as a weak acid

Based on the thermodynamic functions of enthalpy and entropy, can an unfavorable reaction that has a positive ΔG at RT be made favorable by increasing the reaction temperature? a. Yes, regardless of the sign of ΔH, if ΔS is positive, a reaction can be rendered favorable by increasing the temperature. b. yes, but only if ΔH is positive and ΔS is negative c. No, an unfavorable reaction cannot be rendered favorable. d. only if both ΔH and ΔS are negative

a. Yes, regardless of the sign of ΔH, if ΔS is positive, a reaction can be rendered favorable by increasing the temperature.

Each of the following is a noncovalent interaction EXCEPT: a. a carbon-hydrogen bond b. the interaction between an amino and a carboxylate group c. a hydrogen bond d. an interaction between NH3+ and a water molecule. e. a van der Waals interaction

a. a carbon-hydrogen bond This is not a noncovalent interaction.

As biochemistry has matured as a science, new branches of the field have developed to maintain the ever-growing database of information. Assign the purpose on the right with the field on the left. genomics a. assess the expression and function of genes. b. determine the intraceullular concentrations of small molecules. c. mathematic analysis of DNA sequence data. d. identify the function of proteins.

a. assess the expression and function of genes.

What pH gradient would you choose for this experiment? a. between 2.0 and 7.0. b. between 7.0 to 10.0 c. between 2.0 to 5.0 d. between 8.0 to 12.0

a. between 2.0 to 7.0

The activity of an enzyme requires a glutamic acid to display its −COOH functional group in the protonated state. Suppose the pKa of the −COOH group is 4.07. Will the enzyme be more active at pH 3.5 or 4.5? Explain. a. pH 3.5 because protonation is favored when pH < pKa b. pH 4.5 because protonation is favored when pH > pKa

a. pH 3.5 because protonation is favored when pH < pKa

If Ca2+ is often bound on the surface of a protein by carboxylic acid functional groups. If the pKa of a particular −COOH group is 4.2, would you predict Ca2+ to be most tightly bound at pH 8, pH 4.2, or pH 3? a. pH 8 b. pH 4.2 c. pH 3

a. pH 8

Many proteins interact with DNA at physiological pH because: a. the negatively charged DNA is electrostatically attracted to positively charged regions on proteins b. proteins and DNA interact using mainly hydrophobic interactions c. the positively charged DNA is electrostatically attracted to negatively charged regions on proteins d. both proteins and DNA are at their isoelectric points at psychological pH and tend to aggregate. e. proteins are naturally attracted to DNA regardless of the pH

a. the negatively charged DNA is electrostatically attracted to positively charged regions on proteins

Match the class of biomolecule listed with the specific example. Lipids a. triacylglycerols b. starch c. ribozymes, RNA molecules capable of catalyzing reactions d. receptors

a. triacylglycerols These are lipids.

Phosphates cannot be near the axis of the double helix because __________.

at physiological conditions they are negatively charged and would repel each other

In the figure, which bond would be unable to rotate? (Test 1, #13) a. a b. b c. c d. d

Molecular chaperones assist proteins in the formation of ____? a. aggregates b. tertiary structures c. peptide bonds d. primary structure e. none of these choices

Myristoyl-CoA, a 14-carbon fatty acid, will oxidize to yield how many moles of Acetyl CoA? a. 14 b. 7 c. 28 d. 35

Overall, how many protons are pumped by the membrane-associated electron transport system across the membrane for every molecule of NADH that is oxidized? a. 12 b. 10 c. 8 d. 4

Protein kinases add a phosphoryl group to the -OH group of a _______,__________, or _________ residue of the target protein a. Ser, Tyr, Ala b. Ser, Tyr, Thr c. Ser, Trp, Gly d. Thr, Trp, Gly

The glucose-6-phosphate isomerase reaction is a near-equilibrium reaction. Therefore, at any time in a cell there is _________ a. little or no glucose-6-phosphate remaining b. about equal amounts of glucose-6-phosphate and fructose-6-phosphate c. an accumulation of fructose-6-phosphate d. all of the above

Where in the cell does the synthesis of 16-carbon fatty acid palmitate occur? a. nucleus b. cytosol c. mitochondria d. endoplasmic reticulum

Which bond in ATP is primarily responsible for its being a high energy molecule? (Test 3, #8) a. A b. B c. C d. D

Which equilibrium applies to mixed inhibition? (Test 2, #9) a. I b. II c. III d. IV

Which model holds TRUE to explain the synthesis of ATP by energy released form electron transport chain? a. Mosaic model b. chemiosmotic coupling c. passive diffusion d. facilitated diffusion

Which statement is NOT true about catabolic pathways? a. they have a net release of energy b. they have a net consumption of ATP c. they liberate smaller molecules from larger ones d. they include the citric acid cycle

Which statement is TRUE about the ability of carbon to participate in hydrogen bonds in living organisms? a. there are too many carbon atoms competing for the hydrogens in biomolecules to allow for the stable formation of hydrogen bonds b. Carbon's electronegativity is too low to participate in hydrogen bonding c. Most carbons in biomolecules are hydrogen bonded to water d. Carbon is too large to participate in hydrogen bonding

Which statement is TRUE about the side chains of residues in an alpha-helix? a. They extend above or below the pleats b. They extend radially outward from the helix axis c. They point toward the center of the helix d. They hydrogen bond extensively with each other

Why can germinating plant seeds convert acetyl-CoA from fatty acids into carbohydrates, while animals are incapable of converting fatty acids into glucose? a. animals have glycogen and don't need to make glucose from fatty acids b. plants, not animals, use the glyoxylate cycle to convert acetyl CoA to oxaloacetate c. plant seeds use photosynthesis to make sugar d. animals use the citric acid cycle exclusively for energy production, plants only use glycolysis for energy

Which of the following is not a function of an organelle? a. mitochondria specialize in oxidative metabolism b. lysozymes are used for storage and replication c. ribosomes are involved in protein synthesis d. chloroplasts are the sites for photosynthesis

b. lysozymes are used for storage and replication

Suppose a chloride ion and a sodium ion are separated by a center-center distance of 5Å. Is the interaction energy (the energy required to pull them infinitely far apart) predicted to be larger if the medium between them is water, or if it is n-pentane? a. water b. n-pentane

b. n-pentane

What is the optimum pH to separate a mixture of lysine, arginine, and cysteine using electrophoresis? (See the table at the left.) a. pH 7.0 b. pH 9.5 c. pH 10.8 d. pH 5.1

b. pH 9.5

Which statement about the various classes of organisms is false? a. eukaryotic cells are compartmentalized b. prokaryotes have a well-defined nucleus that houses DNA c. fungi are eukaryotic organisms d. eukaryotes can be unicellular or multicellular organisms.

b. prokaryotes have a well-defined nucleus that houses DNA

Match the class of biomolecule listed with the specific example. Carbohydrates a. triacylglycerols b. starch c. ribozymes, RNA molecules capable of catalyzing reactions d. receptors

b. starch Starches are carbohydrates.

Homeostasis is ________________. a. a function of proteins b. the ability to maintain cellular conditions over time. c. the ability to maintain nutrient concentrations equal on both sides of the cell membrane. d. the same as equilibrium.

b. the ability to maintain cellular conditions over time.

Which of the following is NOT a characteristic of a living system? a. the ability to couple energy-releasing reactions with energy-requiring processes, thereby allowing the creation of complex molecules. b. the ability to resist change over generations of progeny. c. the ability to replicate and regenerate. d. the ability to respond to changes in the environment.

b. the ability to resist change over generations of progeny.

Why is the entropy change so favorable for this reaction? The decomposition products are _____________, and therefore have significantly __________ _________________ freedom compared to the initial solid. Thus, entropy _______________.

both gases, more, translational and rotational increases

Compare solution A with pH 4 to solution B with pH 6 a. the concentration of hydronium ion in solution A is twice that in solution B b. solution A has greater buffering capacity that solution B c. The concentration of hydronium ion in solution A is 100 times that in solution B d. The hydroxide concentrations are equal in the two solutions since pH only measures the concentration of H+

If an ATP synthase has 12 c subunits, how many protons must move through the enzyme to produce one ATP? A) 2.5 B) 3 C) 4 D) 10 E) 12

If you were conducting research on a particular protein and wanted to identify where in the cell the protein occurs, which of the following techniques would be most useful a. ELISA b. Western blot c. immunocytochemistry d. SDS PAGE electrophoresis

The pentose phosphate pathway provides_________ for reductive biosynthesis and _________ for nucleic acid biosynthesis a. NADPH, deoxyribose-5-phosphate b. NADH, deoxyribose-5-phosphate c. NADPH, ribose-5-phosphate d. NADH, ribose-5-phosphate

The shape of the myoglobin binding curve that shows that it is NOT regulated allosterically is.... a. gaussian b. sigmoidal c. hyperbolic d. linear

The sickle cell mutation causes oxyhemoglobin molecules to ________ due to hydrophobic interactions because a glutamate residue is replaced with a valine. a. dissociate b. ionize c. aggregate d. dissolve

The storage polysaccharides are _________ in plants and __________ in animals. a. glucose, galactose b. amylose, amylopectin c. starch, glycogen d. cellulose, cellobiose

What is the terminal electron acceptor in the electron transport chain and ATP synthesis in mitochondria? a. carbon dioxide b. hydrogen peroxide c. oxygen d. ozone

Which molecule of ion below is amphipathic? a. H2NCH2COOH (glycine) b. H2O c. CH3(CH2)14COO- d. CH3CH2CH2CH2CH3

Which of these molecules can act as an O2 reserve for the tissue energy needs? a. hemoglobin b. globin c. myoglobin d. nephroglobin

Which of these organs can act as a glucostat to monitor blood sugar levels? a. heart b. lungs c. liver d. gall bladder

Which structure is NOT a carbohydrate? (Test 2, #18) a. A b. B c. C d. D

Which of the following statements about noncovalent bonding interactions is not true? a. Van der Waals interactions, also known as dispersion forces, are the weakest of the attractive noncovalent bonding interactions. b. All noncovalent bond interactions are inherently electrostatic in nature. c. Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms. d. A charge may induce formation of a dipole in a nearby polarizable molecule.

c. Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms. This is not true.

As biochemistry has matured as a science, new branches of the field have developed to maintain the ever-growing database of information. Assign the purpose with the field. bioinformatics a. assess the expression and function of genes. b. determine the intraceullular concentrations of small molecules. c. mathematic analysis of DNA sequence data. d. identify the function of proteins.

c. mathematic analysis of DNA sequence data.

Match the class of biomolecule listed with the specific example. Nucleic acids a. triacylglycerols b. starch c. ribozymes, RNA molecules capable of catalyzing reactions d. receptors

c. ribozymes, RNA molecules capable of catalyzing reactions.

The combustion of palmitic acid in a bomb calorimeter yields energy in the form of heat released upon oxidation. From a thermodynamic perspective and with respect to the calorimeter experiment, what would you expect the combustion of the same amount of palmitic acid in our body to yield? a. more energy b. less energy c. the same amount of energy d. the calorimeter experiment is irrelevant to the combustion of palmitic acid in the human body.

c. the same amount of energy.

Part complete What must be the sign of ΔS for the change: native → denatured? a. ΔS must be positive because the increase in conformations with different energy in the denatured state decreases the entropy of the denatured state relative to the folded state. b. ΔS must be negative because the increase in isoenergetic conformations in the denatured state decreases the entropy of the denatured state relative to the folded state. c. ΔS must be positive because the increase in isoenergetic conformations in the denatured state increases the entropy of the denatured state relative to the folded state. d. ΔS must be negative because the increase in conformations with different energy in the denatured state increases the entropy of the denatured state relative to the folded state.

c. ΔS must be positive because the increase in isoenergetic conformations in the denatured state increases the entropy of the denatured state relative to the folded state.

A reaction at equilibrium can be driven in one direction or the other by changing the ________ of reactants or products.

concentration

Alpha-ketoglutarate dehydrogenase would be translated in the __________ cellular region and post-translationally moved to the __________.

cytosol; mitochondrial matrix

After prolonged starvation the source of energy to the brain is mainly derived from ________ a. muscle protein b. fatty acid c. cholesterol d. ketone bodies

If the following mixture of proteins was applied to a size-exclusion chromatography column, what would be the order of elution? (myoglobin 17.7, hemoglobin 64.5, lysozyme 14.3, triose phosphate isomerase 57.4) a. lysozyme, myoglobin, triose phosphate isomerase, hemoglobin b. triose phosphate isomerase, hemoglobin, lysozyme, myoglobin c. hemoglobin, myoglobin, lysozyme, triose phosphate isomerase d. hemoglobin, triose phosphate isomerase, myoglobin, lysozyme e. cannot be determined

In mammals, urea is almost exclusively produced in ________? a. heart b. muscle c. kidney d. liver

Polysaccharide structure can be varied by differences in ____________. a. chain length (number of sugars in each polysaccharide) b. the kind(s) of sugars in each polysaccharides c. the presence of branching d. all of the above

The conserved residues in the hemoglobins and myoglobins include the ______ proximal and distal to the heme iron. a. lysine b. arginine c. histidine d. alanine

The functional organization of proteins where specific complexes of two or more polypeptides are formed is called _____ structure a. primary b. secondary c. tertiary d. quaternary

The image at right shows a portion of what type of secondary structure? (Test 1, #16) a. parallel alpha-helix b. parallel beta-sheet c. antiparallel alpha-helix d. antiparallel beta-sheet

The imidazolium ion had a pKa=7.0. Imidazolium buffers can be prepared for pH values of _____? a. 6.5-7.5 b. 6.1-7.1 c. 5.5-8.5 d. 6.0-8.0

The primary gluconeogenic organ in animals is ________ a. skeletal muscle b. brain c. heart muscle d. liver

The side chain of _____ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis. a. Asp b. Glu c. Arg d. His

The specific interaction between an antibody and antigen occurs by virtue of both shape and ______ complementarity a. induced fit b. binding affinity c. structure d. charge

Which form of lipoprotein is formed in the digestive tract? a. VHDL b. HDL c. IDL d. chylomicrons

Which of the following must be true if the steady state assumption is to be used for the derivation of the Michaelis-Menten equation? a. (k2-k^-1)/k1= 1 b. k1[E][S]=k2[ES] c. k1[E][S]=k2[ES]-k^-1[ES] d. d[ES]/dt=0

Which of the following properties of water make(s) life possible? a. Water has strong hydrogen bonding interactions between molecules, which allow it to exist at ambient temperature as a liquid. b. Water is less dense as a solid than as a liquid. c. Water's high dielectric constant allows it to dissolve polar and charged molecules alike. d. All of the listed properties of water make life possible.

d. All of the listed properties of water make life possible.

Explain your answer for the previous part. a. Ca2+ will be bound more tightly by a −COOH group. At pH 3 the −COO− form will predominate. At pH 4.2 the −COOH and −COO− forms will be in equal concentration. At pH 8 the −COOH will predominate. b. Ca2+ will be bound more tightly by a −COOH group that is fully deprotonated. At pH 3 the −COOH and −COO− forms will be in equal concentration. At pH 4.2 the −COOH form will predominate. At pH 8 the −COO− will predominate. c. Ca2+ will be bound more tightly by a −COOH group. At pH 3 the −COO− and −COOH forms will be in equal concentration. At pH 4.2 the −COO− form will predominate. At pH 8 the −COOH will predominate. d. Ca2+ will be bound more tightly by a −COOH group that is fully deprotonated. At pH 3 the −COOH form will predominate. At pH 4.2 the −COOH and −COO− forms will be in equal concentration. At pH 8 the −COO− will predominate.

d. Ca2+ will be bound more tightly by a −COOH group that is fully deprotonated. At pH 3 the −COOH form will predominate. At pH 4.2 the −COOH and −COO− forms will be in equal concentration. At pH 8 the −COO− will predominate.

Which of the following statements about macroions, large polyelectrolyte molecules, is NOT true? a. Concentrations of salts that mimic the ionic strength of cells tend to keep macromolecules in solution. b. At high pH, macromolecules often carry net negative charges and therefore repel each other. c. These large molecules can often interact tightly with other molecules of opposite net charge. d. Maximum solubility is achieved when the solution containing such a molecule is near the pI for that molecule.

d. Maximum solubility is achieved when the solution containing such a molecule is near the pI for that molecule.

A solution of 2M NaCl in water is separated from pure water by a semipermeable membrane. Which of the following is true? a. Water will move from the 2M NaCl solution to the pure water compartment. b. Nothing will happen because the system is at ΔG = 0. c. The crossing of NaCl is an endergonic process. d. NaCl will migrate (diffuse) across the membrane until there is an equal concentration on both sides.

d. NaCl will migrate (diffuse) across the membrane until there is an equal concentration on both sides.

Which of the following statements is false? a. In an open system energy can be converted from one form into another. b. Energy can be transferred between a system and the surroundings. c. In biochemical processes, energy can neither be created or destroyed. d. Organisms are open systems as they can create energy from their environments. e. Organisms are open systems as they can exchange both energy and materials with their environments.

d. Organisms are open systems as they can create energy from their environments. This is false.

You can neglect contributions from form I. Why? a. Species I can be neglected because they are not involved in the calculations of the pI value. b. Species I can be neglected because they are not responsible for the ionization of water. c. Species I can be neglected because they are not charged. d. Species I can be neglected because they are present at an insignificant concentration.

d. Species I can be neglected because they are present at an insignificant concentration.

Explain the differences in the pH values between the solutions in the previous parts a. Weak acids have a lower pH in comparison with a strong acid of the same concentration because they produce more hydrogen ions in solution. For acetic acid more H+ dissociates as the concentration of HA increases. b. Strong acids have a lower pH in comparison with a weak acid of the same concentration because they produce more hydrogen ions in solution. For acetic acid more H+ dissociates as the concentration of HA decreases. c. Weak acids have a lower pH in comparison with a strong acid of the same concentration because they produce more hydrogen ions in solution. For acetic acid more H+ dissociates as the concentration of HA decreases. d. Strong acids have a lower pH in comparison with a weak acid of the same concentration because they produce more hydrogen ions in solution. For acetic acid more H+ dissociates as the concentration of HA increases

d. Strong acids have a lower pH in comparison with a weak acid of the same concentration because they produce more hydrogen ions in solution. For acetic acid more H+ dissociates as the concentration of HA increases

A student is carrying out a biological preparation that requires 1 M NaCl to maintain an ionic strength of 1.0. The student chooses to use 1.0 M ammonium sulfate instead. Why is this a serious error? a. The ionic strength of 1.0 M ammonium sulfate is three times lower than the ionic strength of NaCl. b. The ionic strength of 1.0 M ammonium sulfate is two times lower than the ionic strength of NaCl. c. The ionic strength of 1.0 M ammonium sulfate is two times greater than the ionic strength of NaCl. d. The ionic strength of 1.0 M ammonium sulfate is three times greater than the ionic strength of NaCl.

d. The ionic strength of 1.0 M ammonium sulfate is three times greater than the ionic strength of NaCl. three, greater

What fraction of the enzymes will be active at pH=4.07? Explain. a. When pH=pKa the ionizable group is 100% protonated; thus, 0% of the enzymes will be in an active state. b. When pH=pKa the ionizable group is 100% protonated; thus, 100% of the enzymes will be in an active state. c. When pH=pKa the ionizable group is 0% protonated; thus, 100% of the enzymes will be in an active state. d. When pH=pKa the ionizable group is 50% protonated; thus, 50% of the enzymes will be in an active state. At what pH will the enzyme show 78% of maximal activity?

d. When pH=pKa the ionizable group is 50% protonated; thus, 50% of the enzymes will be in an active state. pH = 3.52

Noncovalent bonds are critically important to the function of biomolecules. Which of the following is/are (a) valid reason(s) for this importance? a. noncovalent interactions are made up of hydrogen bonding, electrostatic interactions, and dispersion forces. b. the effect of these weak interactions is cumulative. c. their bond energies are ~10-100 times weaker than ordinary covalent bonds. d. all of the listed statements are valid reasons for this importance.

d. all of the listed statements are valid reasons for this importance.

As biochemistry has matured as a science, new branches of the field have developed to maintain the ever-growing database of information. Assign the purpose on the right with the field on the left. proteomics a. assess the expression and function of genes. b. determine the intraceullular concentrations of small molecules. c. mathematic analysis of DNA sequence data. d. identify the function of proteins.

d. identify the function of proteins

The equilibrium constant of a reaction: a. can change if the concentration of reactants and products are changed. b. is not related to the change in free energy of the reaction. c. cannot be used to determine whether a reaction will proceed in the direction as written under non-standard conditions. d. is related to the change in free energy of the reaction. e. is the same as the mass action ratio when the reaction is displaced from equilibrium.

d. is related to the change in free energy of the reaction.

Match the class of biomolecule listed with the specific example. Proteins a. triacylglycerols b. starch c. ribozymes, RNA molecules capable of catalyzing reactions d. receptors

d. receptors Receptors are proteins.

Nearly all proteins contain: a. cobalt b. phosphorus c. selenium d. sulfur e. none of the above.

d. sulfur

Which of the following is true regarding transition state analogs? a. they are competitive inhibitors b. they bind to an active site with much higher affinity than most inhibitors c. they are much more stable than the transition state d. their affinity for an enzyme is often much greater than the substrate e. all of the above

You need to make a buffer whose pH is 7.0, and you can choose from the weak acids shown in table below Which conjugate pair is suited best to make this buffer? a. Formic acid HCOOH and formate ion HCOO− b. Acetic acid CH3COOH and acetate ion CH3COO− c. Lactic acid CH3CH(OH)COOH and lactate ion CH3CH(OH)COO− d. Phosphoric acid H3PO4 and dihydrogen phosphate ion H2PO4− e. Dihydrogen phosphate ion H2PO4− and monohydrogen phosphate ion HPO42− f. Monohydrogen phosphate ion HPO42− and phosphate ion PO43− g. Carbonic acid H2CO3 and bicarbonate ion HCO3− h. Bicarbonate ion HCO3− and carbonate ion CO32− i. Phenol C6H5OH and phenolate ion C6H5O− j. Ammonium ion +NH4 and ammonia NH3

e. Dihydrogen phosphate ion H2PO4− and monohydrogen phosphate ion HPO42−

Which of the following is true of the hydrophobic molecules? a. they have limited solubility in water b. water forms a cage-like structure around them. c. they self-associate by releasing some of the surrounding water molecules. d. dissolving in water decreases the entropy of the mixture. e. all of the above.

e. all of the above.

A biochemical reaction will proceed in the direction as written if: a. ΔH > 0. b. ΔG = zero. c. ΔH < 0. d. ΔG > 0. e. ΔG < 0.

e. ΔG < 0.

In eukaryotes, the 5'-AAUAA-3' sequence in RNA is a signal for __________ to __________.

endonuclease; remove nucleotides from the 3' end

A reaction at its lowest energy state for the system and with equal rates in the forward and reverse directions is said to be at ________.

equilibrium

The polymerization reaction catalyzed by DNA polymerase III is readily reversible but it is pulled forward by __________.

hydrolysis of pyrophosphate into two Pi molecules

An amphipathic molecule provides the foundation for biological membranes because they have both __________ and ____________ functional groups.

hydrophilic and hydrophobic

In the post-transcriptional processing of eukaryotic pre-mRNA, __________ are excised by the __________.

introns; spliceosome

Streptomyces cerevisiae is treated with a low concentration of alpha-amanitin. The synthesis of which of the following will be inhibited?

mRNA

Treating Clostridium perfringes (the causative bacterium of gas gangrene) with rifampicin will inhibit the synthesis of __________.

mRNA, tRNA, and rRNA

Considering that RNA polymerases bind to dsDNA or DNA-RNA hybrids during polymerization, one would predict this enzyme to be __________.

mostly alpha-helical

Temporary dipoles occur in _____ molecules while permanent dipoles occur in _____ molecules.

nonpolar; polar

The following structure of arginine is depicted at which pH?

pH 10

The following structure of glycine is depicted at which pH?

pH 12

The following structure of aspartic acid (aka asparate) is depicted at which pH?

pH 3

What is the pI of aspartic acid (aka aspartate) assuming the alpha-amino pKa = 10, and the carboxyl functional groups both have a pKa = 4?

pH = 4

What is the pl of aspartic acid (aka aspartate) assuming the alpha-amino pKa = 10, and the carboxyl functional groups both have a pKa = 4?

pH = 4

What is the pH of each of the following solutions? 0.35 M hydrochloric acid 0.35 M acetic acid 0.035 M acetic acid

pH hydrochloric acid = 0.46 pH 0.35 M acetic acid = 2.61 pH 0.035 M acetic acid = 3.11

What is the pI of arginine assuming the alpha-amino and guanidinium functional groups have a pKa = 10, and the carboxyl pKa = 4?

pH= 10

The amino acid arginine ionizes according to the following scheme. Calculate the isoelectric point of arginine.

pI = 10.7

What do you expect the sign of ΔS to be for this process? Explain your answer. This process _____________ the entropy of the solvent water, which becomes ___________ ordered in the clathrate structures. This is the _________ effect.

reduces, more. hydrophobic

The ribosome is best described as a(n) __________.

ribozyme

The single-charge difference would result in a _______ difference in mobility in a normal _________ experiment (which separates chains based on size), but would make a detectable difference in pI. Word blank options; gel electrophoresis isoelectric focusing large small

small, gel electrophoresis

How will the contribution of ΔS for native → denatured affect the favorability of the process? What apparent requirement does this impose on ΔH if proteins are to be stable structures? Since _____________, a __________ value forΔS results in a _______________ contribution to ΔG (T is always ____________ in the Kelvin scale). Thus, for proteins to be stably folded (which requires ΔG to be ______________ for the process described in the question), it would appear that ΔH must be large and ______________. This is generally true; however, this simple analysis does not consider the _____________ effect, which results in a more ______________ overall ΔS. Thus, the requirement that ΔH is large and ____________ is not absolute because the hydrophobic effect _____________ the magnitude of ΔS.

ΔG=ΔH−TΔS, positive, negative, positive. positive, positive. hydrophobic, negative. positive, reduces.

The process of a protein folding from an inactive unfolded structure to the active folded structure can be represented by the following equation: unfolded protein folded protein The values of ΔH∘ and ΔS∘ for the folding of the protein lysozyme are: ΔH∘=−280kJ/mol ΔS∘=−790J/mol⋅K Calculate the value of ΔG∘ for the folding of lysozyme at 25 ∘C. At what temperature would you expect the unfolding of lysozyme to become favorable?

ΔG∘ = -44.6 kJ/mol T = 354 K

The decomposition of crystalline N2O5 N2O5(s)⟶2NO2(g)+12O(g) is an example of a reaction that is thermodynamically favored even though it absorbs heat. At 25 ∘C we have the following values for the standard state enthalpy and free energy changes of the reaction: ΔH∘=+109.6kJ/mol ΔG∘=−30.5kJ/mol Calculate ΔS∘ at 25 ∘C.

ΔS∘ = 470 J/mol⋅K

The growing amino acid protein chain is transferred to the aminoacyl-tRNA bound in the __________ after amide bond formation.

A site

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule will have hydrogen-bonding between like molecules?

CH3OH

What types of intermolecular forces occur between two polar molecules?

Dipole-dipole forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in CH2Cl2?

Dispersion and dipole-dipole forces

Diphtheria toxin, an extremely deadly toxic protein enzyme, targets which stage in eukaryotic translation?

Elongation

The "transcription bubble" is formed during which stage of transcription?

Elongation

A TATA box can be found in the promoter region of which of the following? I. Heart muscle cell II. Escherichia coli III. Saccharomyces cerevisiae IV. T4 bacteriophage

I and III

Which of the following is/are function(s) of the poly(A) tail processing of eukaryotic mRNA? I. Signalling initiation of translation II. Signalling the termination of transcription III. Stabilizing the mRNA IV. Facilitating mRNA entry into the cytosol

III and IV

Mitochondrial proteins may contain "zip-code" sequences indicating where (in or out of the cell) they need to travel for optimum function after translation in the cytosol. Where on a typical protein is this "zip-code" sequence located?

N-terminus

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. A hydrogen in NH3 will experience hydrogen bonding with _________.

O in H2CO

A hydrogen in NH₃ will experience hydrogen bonding with _________.

O in H₂CO

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in I3−?

Only dispersion forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in SF6?

Only dispersion forces

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. What types of intermolecular forces are found in XeF4?

Only dispersion forces

What types of intermolecular forces are found in CH₄?

Only dispersion forces

What types of intermolecular forces are found in CO₂?

Only dispersion forces

What types of intermolecular forces are found in I₃⁻?

Only dispersion forces

What types of intermolecular forces are found in SF₆?

Only dispersion forces

What types of intermolecular forces are found in XeF₄?

Only dispersion forces

Acetylation of histones __________ DNA binding, and therefore __________ the rate of transcription.

disrupts; increases

Which molecule has dipole-dipole forces but no hydrogen bonding? butane dimethyl ether water methanol

dimethyl ether

Intermolecular forces are the interactions between molecules and are generally weaker than bonds within molecules. Which molecule has dipole-dipole forces but no hydrogen bonding?

dimethyl ether, Lewis structure of CH3OCH3

Analysis of an in vitro protein translation steady-state kinetics experiment where chloramphenicol was added __________ the KM and __________ the Vmax. (Assume the experiment follows uncooperative Michaelis-Menten kinetics.)

increases; does not change

During splicing, __________ of the spliceosome will base pair with a(n) __________ in pre-mRNA.

snRNA; intron-exon boundary

Treatment with the antibiotic __________ will result in deviant proteins in __________.

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