Mastering Biochemistry Chapter 2 Post-Lecture Hydrogen Bonding/ Acid Base

Part C Part complete At what pH will the enzyme show 77 % of maximal activity? Express your answer using two decimal places.

pH = 3.55

Calculate the pH of a 1.0 MNH4Cl solution. (Ka for NH4+ is 5.62×10−10) Express your answer to two decimal places.

pH = 4.63 pH==−log(2.4×10−5)4.63

If the normal physiological concentration of HCO3− is 24 mM, what is the pH of blood if PCO2 drops to 35.0 mmHg ? Express your answer numerically using two decimal places.

pH = 7.46

Calculate the pH of the solution that results following addition of 11 mL of 1.0 MNaOH to 45 mL of 1.0 MNH4Cl.

pH = 8.76

Calculate the pH of the solution that results following addition of 25 mL of 1.0 MNaOH to 45 mL of 1.0 MNH4Cl. Express your answer to two decimal places.

pH = 9.35

Calculate the isoelectric point of arginine. Express your answer using three significant figures

pI = 10.7 pI= (pKa2+pKa3)/2 (8.99+12.52)/2=10.7

Place these hydrocarbons in order of decreasing boiling point. (Highest to lowest)

parraffin C35H72, Hexadecane C16H34, Heptane C7H16, 2,2,3-trimethylbutane C7H16, Methane CH4

Clearly label the hydrogen-bond donor and acceptor atoms.

A hydrogen-bond donor is the atom to which the hydrogen is covalently bonded. In formamide, the hydrogen atoms are covalently bonded to the carbon atom of the aldehyde group and the nitrogen atom of the amine group. However, only N is highly electronegative allowing the attached hydrogen to participate in hydrogen bonding. Thus, nitrogen is the hydrogen-bond donor. The hydrogen-bond acceptor is the atom which has a pair of nonbonded electrons. Since both nitrogen and oxygen atoms have nonbonded electron pairs they are hydrogen-bond acceptors. This can be visualized in the following structure:

Part B - Properties of waterPart complete Classify each statement as an example of adhesion, cohesion, or surface tension. Drag each statement to the appropriate bin.

Adhesion: Water molecules cling to the side of a beaker Water molecules cling to plant cell walls. Cohesion: Water molecules are attracted to each other A drop of water spilled on a table forms a drop on the table, rather than spreading out over the surface Surface Tension: A water strider runs across a pond without breaking the surface. A sewing needle floats when it is place gently on top of water in a bucket

Part B Part complete Now assume you wish to make a buffer at the same pH, using the same substances, but want the total phosphate molarity ([HPO42−]+[H2PO4−]) to equal 0.25 M. What concentration of the KH2PO4 would be required? Express your answer to two significant figures.

0.11 M [H2PO4−]+[HPO42−]=0.25M [H2PO4−]=0.25M−[HPO42−] 7.00==pKa+log([HPO42−][H2PO4−])6.86+log(0.25−[H2PO4−][H2PO4−]) log(0.25−[H2PO4−][H2PO4−])=0.14 100.14==(0.25−[H2PO4−][H2PO4−])1.38 1.38=0.25−xx Solve for x: x=0.11M=[KH2PO4]

Now assume you wish to make a buffer at the same pH, using the same substances, but want the total phosphate molarity ([HPO42−]+[H2PO−4]) to equal 0.25 M. What concentration of the Na2HPO4 would be required? Express your answer to two significant figures.

0.14 M

Suppose you wanted to make a buffer of exactly pH 7.00 using KH2PO4 and Na2HPO4. If the final solution was 0.16 M in KH2PO4, what concentration of Na2HPO4 would you need? (pKa for H3PO4, H2PO4−, and HPO2−4 are 2.14, 6.86, and 12.40, respectively.)

0.22 M H2PO4−+OH−⇌HPO42−+H2O pKa=6.86 pH=7.00 [H2PO4−]=0.16M pH=pKa+log([A−][HA])=7.00 7.00=6.86+log([A−]0.16) 0.14=log([A−]0.16) [A−]=0.22M

Part C Part complete Calculate the average charge on arginine when pH=9.40. (Hint : Find the average charge for each ionizable group and sum these together.) Express your answer using two significant figures.

0.28

Watch the animation and identify the correct conditions for forming a hydrogen bond. Check all that apply. Hydrogen bonding occurs when a hydrogen atom is covalently bonded to an N, O, or F atom. A hydrogen atom acquires a partial positive charge when it is covalently bonded to an F atom. A hydrogen bond is equivalent to a covalent bond. A hydrogen bond is possible with only certain hydrogen-containing compounds. The CH4 molecule exhibits hydrogen bonding.

Hydrogen bonding occurs when a hydrogen atom is covalently bonded to an N, O, or F atom. A hydrogen atom acquires a partial positive charge when it is covalently bonded to an F atom. A hydrogen bond is possible with only certain hydrogen-containing compounds.

Identify the predominant type of intermolecular force in each of the following compounds.

London: CF3 Dipole-Dipole: OF2, CHF3 Hydrogen bonding: HF

The table shown here lists the specific heat of several substances. Substance. Specific heat J/g/∘C water 4.18 ethyl alcohol 2.44 benzene 1.80 sulfuric acid 1.40 Based on the information in the table, which of the following statements are true?

More heat is required to raise the temperature of 1 g of water 1 ∘C than to raise the temperature of 1 g of ethyl alcohol 1 ∘C. Water has a high specific heat due to the hydrogen bonding between water molecules. Benzene is more resistant to temperature change than sulfuric acid. Sulfuric acid is less resistant to temperature change than water.

The hydrides of group 5A are NH3, PH3, AsH3, and SbH3. Arrange them from HIGHEST to LOWEST boiling point.

NH3, SbH3, AsH3, PH3

Part B Part complete Would you expect a significant amount of carbonate (CO32−)?

No Since the pKa for dissociation of HCO3− is 10.25, we expect the [CO32−] to be negligible at pH=7.5.

Part B Part complete You can neglect contributions from form I. Why?

Species I can be neglected because they are present at an insignificant concentration. Species III is the isoelectric species (no net charge); thus, the pKa that describe ionization equilibria that include this species will be used to calculate the pI. Since Species I is not one of these (and Species I is present at an insignificant concentration), we can ignore it for this simple case (i.e., a molecule with only three ionizable groups).

As a technician in a large pharmaceutical research firm, you need to produce 300. mL of 1.00 M potassium phosphate buffer solution of pH = 7.10. The pKa of H2PO4− is 7.21. You have the following supplies: 2.00 L of 1.00 M KH2PO4 stock solution, 1.50 L of 1.00 M K2HPO4 stock solution, and a carboy of pure distilled H2O. How much 1.00 M KH2PO4 will you need to make this solution? Express your answer to three significant digits with the

Volume of KH2PO4 needed = 169 mL

Covalent bonding is important between atoms of biological molecules, but other factors are important for self-assembly. For example, hydrogen bonds between base-pairs in DNA hold the two strands together. Complete the sentences describing the general principles regarding how groups or molecules interact. Match the words in the left column to the appropriate blanks in the sentences on the right.

1. When deciding which side of a biomolecule would orient itself toward the water in cytoplasm, the polar groups would be directed toward the water molecules. 2. When deciding which biomolecules would interact with a hydrocarbon chain, the nonpolar portions of a biomolecule would orient themselves toward the chain. 3. Polar groups in biomolecules are often characterized by functional groups containing elements such as oxygen, or nitrogen. 4. Nonpolar groups in biomolecules are often characterized by functional groups containing the element carbon. 5. When looking at ionizable groups, two ions of the same charge, such as two cations, are repelled by each other while two ions of the opposite charge, such as one cation and one anion, are attracted to each other.

Neglecting free CO2, what fraction will be present as carbonic acid? (pKa for H2CO3 and HCO3− are 6.3 and 10.25, respectively) Express your answer using two significant figures.

5.9×10−2 The relevant equations describe the dissociation of carbonic acid to bicarbonate ion and H+: pKa=6.3. CO2+H2O⇌H2CO3 H2CO3⇌H++HCO3− HCO3−⇌H++CO32− From the Henderson-Hasselbalch equation: 7.5=6.3+log([HCO3−][H2CO3]) [HCO3−][H2CO3]=15.8 molefractionH2CO3/(molH2CO3 + molHCO3−)+molH2CO3 1/(15.8+1)=0.059

Which of these two possible hydrogen-bonding interactions is more likely to occur? (Hint: Consider resonance structures for formamide.)

As you determined in Part B, N is the hydrogen-bond donor while N and O are hydrogen-bond acceptors. Since the more electronegative atom, N, of the amine group withdraws electrons from the hydrogen to which it is bonded, it develops a partial positive charge on the hydrogen atom. As a result, this hydrogen is more strongly attracted to the electron pair of the acceptor. The appropriate hydrogen-bond acceptor atom between N and O is identified from the resonance structure of formamide. This can be visualized in the following resonance structure: There is a resonance structure of formamide that is the following: HCNH2 with a double bond between the carbon atom and the nitrogen atom and an oxygen atom attached to the carbon atom by a single bond. The N atom has a positive charge and no lone pairs. The O atom has three lone pairs and a negative charge. This resonance structure for formamide shows that the lone pair on the nitrogen is partially tied up in a double bond while the oxygen atom carries a negative charge. Hence, the hydrogen carrying a partial positive charge from one formamide molecule is more strongly attracted to the electron pair of the oxygen atom from another formamide molecule. Thus, the most likely hydrogen bonding interaction occurs between an H atom of the amine group and the oxygen acceptor.

Rank the following compounds in order of decreasing vapor pressure. (Highest to Lowest)

CH4... CH3ChCH3Ch2CH3... CH3CH2CH2CH2CH3... CH3CH2CH2CH2OH

Rank the following substances in order from most soluble in water to least soluble in water: methane, CH4; propanol, C3H7OH; copper sulfate, CuSO4; and butane, C4H10. Rank from most to least soluble in water. To rank items as equivalent, overlap them.

Copper Sulfate, Propanol, butane, methane

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

Hydrogen-bonding interactions occur between a hydrogen atom that is covalently bonded to another highly electronegative atom and a pair of nonbonded electrons on a separate atom; most often an O or an N atom. The structure of formamide has an aldehyde group and an amine group with pairs of nonbonded electrons on both the N and O atoms. The hydrogens in the amine group are covalently bonded to the N atom. Thus, there are two possible hydrogen-bonding interactions between two molecules of formamide. These are as follows: Between an H atom of the amine group of one molecule and the O atom of the other molecule. Between an H atom of the amine group of one molecule and the N atom of the other molecule. These two possible hydrogen bonding interactions between two molecules of formamide are shown by dotted lines in the following structure:

What happens to these physical properties as the strength of intermolecular forces increases?

Increase: Boiling Point, Surface Tension, Viscosity, Melting Point. Decrease: vapor pressure

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. Part A Part complete Will the enzyme be more active at pH 3.5 or 4.5?

The enzyme will be more active at pH=3.5 because the −COOH group will be more protonated at that pH (protonation is favored when pH<pKa).

Part A - Hydrogen bondingPart complete Label the following diagram of water molecules, indicating the location of bonds and the partial charges on the atoms. Drag the labels to their appropriate locations on the diagram of the water molecules below. Labels can be used once, more than once, or not at all.

The image on the left shows the unequal sharing of electrons in a water molecule. Notice that the electrons are pulled toward the oxygen atom, which is more electronegative than a hydrogen atom, resulting in a partial negative charge (δ−) on the oxygen atom and a partial positive charge (δ+) on each hydrogen atom. The image on the right shows hydrogen bonding between two water molecules: the partially negative oxygen atom of one water molecule is attracted to the partially positive hydrogen atom of another water molecule. Hydrogen bonds are much weaker than covalent bonds. In liquid water, hydrogen bonds last only a fraction of a second, breaking and re-forming with great frequency. In a given instant, one water molecule can be hydrogen bonded to up to four other water molecules.

Substances with weak intermolecular forces tend to be in the gas state at room temperature. Moderate intermolecular forces are required to liquefy or solidify a substance at room temperature. Classify the types of intermolecular forces as moderate or weak.

Weak: London Dispersion, Dipole-Dipole Moderate: hydrogen bonding, ion-dipole

What fraction of the enzymes will be active at pH=4.07?

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

Part D Part complete Is the value of average charge you calculated in part C reasonable, given the pI you calculated in part A? Explain your answer.

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