VET 115

Tutorial # 1

Organization of living systems, biomolecules and functional groups, thermodynamics & water
chemistry.

1. The Biosynthetic Capacity of Cells

The nutritional requirements of Escherichia coli cells are far simpler than those of humans,
yet the macromolecules found in bacteria are about as complex as those of animals.
Because bacteria can make all their essential biomolecules while subsisting on a simpler
diet, do you think bacteria may have more biosynthetic capacity and hence more metabolic
complexity than animals? Organize your thoughts on this question, pro and con, into a
rational argument.

Answer: Although it is true that Escherichia coli are capable of producing all of their essential
biomolecules (e.g. there is no minimum daily requirement for vitamins in the world of wild-
type E. coli), they are rather simple, single-cell organisms capable of a limited set of responses.
They are self sufficient, yet they are incapable of interactions leading to levels of organization
such as multicellular tissues. Multicellular organisms have the metabolic complexity to
produce a number of specialized cell types and to coordinate interactions among them.

2. Cell Structure
Without consulting figures in this chapter, sketch the characteristic prokaryotic and
eukaryotic cell types and label their pertinent organelle and membrane systems.

Answer: Prokaryotic cells lack the compartmentation characteristic of eukaryotic cells and are
devoid of membrane bound organelles such as mitochondria, chloroplasts, endoplasmic
reticulum, Golgi apparatus, nuclei, peroxisomes and vacuoles. Both cell types are delimited
by membranes and contain ribosomes.

3. The Principle of Molecular Recognition Through Structural Complementarity

Biomolecules interact with one another through molecular surfaces that are structurally
complementary. How can various proteins interact with molecules as different as simple
ions, hydrophobic lipids, polar but uncharged carbohydrates, and even nucleic acids?

Answer: The amino acid side chains of proteins can participate in a number of interactions
through hydrogen bonding, ionic bonding, hydrophobic interactions, and van der Waals
interactions. For example, the polar amino acids, acidic amino acids and their amides, and the
basic amino acids all have groups that can participate in hydrogen bonding. Those amino acid
side chains that have net charge can form ionic bonds. The hydrophobic amino acids can
interact with nonpolar, hydrophobic surfaces of molecules. Thus, amino acids are capable of
participating in a variety of interactions. A protein can be folded in three dimensions to
organize amino acids into surfaces with a range of properties.

4. The Properties of Informational Macromolecules

What structural features allow biological polymers to be informational macromolecules? Is
it possible for polysaccharides to be informational macromolecules?

Answer: Biopolymers, like proteins and nucleic acids, are informational molecules because
they are vectorial molecules, composed of a variety of building blocks. For example, proteins
are linear chains of some 20 amino acids joined head-to-tail to produce a polymer with
distinct ends. The information content is the sequence of amino acids along the polymer.
Nucleic acids (DNA and RNA) are also informational molecules for the same reason. Here, the
biopolymer is made up of 4 kinds of nucleotides. Monosaccharides can be linked to form
polymers. When a polymer is formed from only one kind of monosaccharide, as for example
in glycogen, starch, and cellulose, even though the molecule is vectorial (i.e., it has distinct
ends) there is little information content. There are, however, a variety of monosaccharides
and monosaccharide derivatives that are used to form polysaccharides. Furthermore,
monosaccharides can be joined in a variety of ways to form branch structures. Branched
polysaccharides composed of a number of different monosaccharides are rich in information.

5. The Importance of Weak Forces in Biomolecular Recognition

Why is it important that weak forces, not strong forces, mediate biomolecular recognition?

Answer: Life is a dynamic process characterized by continually changing interactions.

Complementary interactions based on covalent bonding would of necessity produce static
structures that would be difficult to change and slow to respond to outside stimuli.

6. The Strength of Weak Forces Determines the Environmental Sensitivity of Living Cells
Why does the central role of weak forces in biomolecular interactions restrict living systems
to a narrow range of environmental conditions?

Answer: The weak forces such as hydrogen bonds, ionic bonds, hydrophobic interactions, and
van der Waals interactions can be easily overcome by low amounts of energy. Slightly
elevated temperatures are sufficient to break hydrogen bonds. Changes in ionic strength, pH,
concentration of particular ions, etc., all potentially have profound effects on macromolecular
structures dependent on the weak forces.

7. Cells As Steady-State Systems

Describe what is meant by the phrase "cells are steady-state systems".

Answer: Life is characterized as a system through which both energy and matter flow. The
consequence of energy flow in this case is order, the order of monomeric units in
biopolymers, which in turn produce macromolecular structures that function together as a
living cell.

8. Biological molecules often interact via weak forces (H bonds, van der Waals interactions,
etc.). What would be the effect of an increase in kinetic energy on such interactions?

Answer: Weak forces are easily disrupted by increases in the kinetic energies of the
interacting components. Thus, slight increases in temperature can disrupt weak forces.
Biological molecules, like proteins whose three-dimensional structures are often determined
by weak force interactions, may undergo conformational changes even with modest changes
in temperature leading to inactivation or loss of function.

9. Proteins and nucleic acids are informational macromolecules. What are the two minimal
criteria for a linear informational polymer?

Answer: Informational macromolecules must be directional (vectorial) and they must be

composed of unique building blocks. Both nucleic acids and proteins are directional polymers.
The directionality of a single nucleic acid is 5’ to 3’ whereas that of a protein is N-terminus to
C-terminus. The repeat units in nucleic acid polymers are four different nucleoside
monophosphates. The repeat units in proteins are 20 amino acids. The information content
of a nucleic acid, especially dsDNA, is its linear sequence. The same is true for proteins;
however, proteins typically fold into unique three-dimensional structures, which show
biological

10. Give a common example of each of the weak forces at work.

Ice is an example of a structure held together by hydrogen bonds. Sodium and chloride ions
are joined by ionic bonds in table salt crystals. A stick of butter is a solid at room temperature
because of van der Waals forces. The energetically unfavorable interactions between water
and oil molecules cause the oil to coalesce.

11. The first law of thermodynamics states that there are only two ways to change the
internal energy of any system. What are they?

Energy flow in the form of heat or work.

12. Enthalpy, H, is defined as H = E + PV and ∆E = q + w. Under what conditions is ∆H = q?

In general, ∆H = ∆E + P∆V + V∆P = q + w + P∆V + V∆P. When the pressure of the system remains
constant (i.e., ∆P = 0) and work is limited to only mechanical work
(i.e., w = -P∆V ) then ∆H = q.

13. The condensation of two functional groups can result in the formation of another
common functional group, which can be referred to as a compound functional group.
Examine the functional groups in the table below. Which compound functional groups are
the combination of two other functional groups found in the table? Show how these
compound functional groups form.
Answer:
14. Distinguish between enthalpy and energy. Under what conditions are they equivalent?

Enthalpy is defined as H = U + PV. Hence ΔH = ΔU + Δ(PV). The enthalpy of a system is

equal to its energy change when Δ(PV) = 0, which occurs at the constant pressure and volume
conditions typical of living things.

15. What does it mean when q and w are positive?

If q is positive, then heat has been transferred to the system, increasing its internal energy. If
w is positive, then work has been done by the system, decreasing its internal energy.

16. When crystalline urea is dissolved in water, the temperature of the solution drops
precipitously. Does the enthalpy of the system increase or decrease? Explain.

In this example, urea and the water are the system, and the vessel and beyond are the
surroundings. As urea dissolves, the enthalpy increases (an endothermic process). Heat is
absorbed into the interactions between the urea and water, making the solution cooler.

17. List and define the four major thermodynamic state functions.

Energy is measured as the heat absorbed by a system minus the work done by the system on
its surroundings. Enthalpy, or heat content, is the amount of heat generated or absorbed by a
system when a process occurs at constant pressure, as in biological systems, and no work is
done other than the work of expansion or contraction (ΔV) of the system. Entropy is a measure
of the heat absorbed or generated by a system at constant temperature and reflects the number
of equivalent ways of arranging a system with no change in its internal energy. Gibbs free
energy is the energy available to do work; it is a combination of enthalpy and entropy (ΔH –
TΔS) and an indicator of the spontaneity of a process at constant pressure and temperature.

18. Which of the following pairs of states has higher entropy?

(a) Two separate beakers of NaCl and KCH3COO in solution and a beaker containing a
solution of both salts.

(b) A set of dice in which all the dice show 6 dots on the top side and a set of dice in
which the 6’s show up on one of the side faces.

(c) A small symmetric molecule that can form a polymer through reaction at either end,
and a small asymmetric molecule that can polymerize from only one end.

Answer:

(a) The beaker containing the solution with both salts has higher entropy. The molecules in this
solution can be arranged in many more ways with respect to each other than each salt solution
alone.

(b) The set of dice with the 6’s showing on the side faces has more entropy since there are
many more ways to obtain this configuration.
(c) The symmetric molecule has greater entropy, since it can polymerize by joining reactions
involving either end. Note that the information content of the asymmetric molecule is higher,
however. All biological polymers are formed from asymmetric subunits.

19. Rationalize the temperature dependence of Gibbs free energy changes when both the
enthalpy and entropy terms are positive values or when they are both negative values.

When enthalpy and entropy are both positive, ΔG decreases with increasing temperature, and
the temperature at which the reaction occurs spontaneously must be high enough that the TΔS
term is larger than the ΔH term in the equation ΔG = ΔH – TΔS. For instance, dissolving
crystalline urea in water is endothermic; however the process is spontaneous when it is carried
out at room temperature. When enthalpy and entropy are both negative, ΔG decreases with
decreasing temperature, and for the reaction to be spontaneous, the temperature must be low
enough that the TΔS term is not more negative than the ΔH term.

20. Evaluate the following statement: Enzymes accelerate the rate of a reaction by
increasing the spontaneity of the reaction.

This statement is incorrect. An enzyme does not alter the spontaneity of a reaction; rather, it
increases the rate at which a reaction reaches equilibrium.

21. Which gas in each of the following pairs would you expect to be more soluble in water?
Why?

(a) oxygen and carbon dioxide

(b) nitrogen and ammonia
(c) methane and hydrogen sulfide

(a) Carbon dioxide (O=C=O), which is more polarizable than oxygen (O=O).
(b) Ammonia (NH3), which is more polar than nitrogen (N N).
(c) Hydrogen sulfide (HS), which is more polar than methane (CH4).

22. Mixing olive oil with vinegar creates a salad dressing that is an emulsion, a mixture
of vinegar with many tiny oil droplets. However, in a few minutes, the olive oil separates
entirely from the vinegar. Describe the changes in entropy that occur during the initial
mixing and the subsequent separation of the olive oil and vinegar.

When the olive oil and vinegar (which is an aqueous solution) are mixed, the entropy of the
solution decreases (the action of mixing is an input of energy that drives this process).
Mechanical mixing results in an ordering of water around the thousands of oil droplets. Once
the mixing has stopped, the system moves toward equilibrium, which maximizes entropy. As
the oil droplets fuse, the surface-to-volume ratio of all of the oil decreases, thereby decreasing
the amount of ordered water. Consequently, the entropy of the solution increases.

23. The pK’s of trichloroacetic acid and acetic acid are 0.7 and 4.76, respectively. Which
is the stronger acid? What is the dissociation constant of each?

pK is the negative logarithm of the dissociation constant, K, so the smaller the value of pK, the
larger the value of K. The larger the value of K, the greater the dissociation of the acid in water.

Therefore, trichloroacetic acid is the stronger acid since it has a lower pK than acetic acid.

For trichloroacetic acid, pK = –log K

Therefore, K = 10–0.7 = 0.2

Similarly for acetic acid,

log K = – 4.76

K = 10–4.76 = 1.74 X 10–5

24. What is the OH–] in a 0.05M HCl solution? What is the pH?

25. What is a buffer? How does it work? What compounds act as buffers in cells?

A buffer is a solution of a weak acid and its conjugate base. A buffer works by “absorbing”
base or acid equivalents within about one pH unit of its pK. For example, when a small amount
of OH– is added, it reacts with HA to form water and A–, with little change in pH. Similarly,
a small amount of H+ reacts with A– to form HA. In biological systems, protons produced
during catabolic reactions must be buffered by the cell. Phosphate and carbonate ions, as well
as proteins, nucleic acids, and fatty acids, serve as buffers in cells.

26. Biomolecules interact with one another through molecular surfaces that are
structurally complementary. How can various proteins interact with molecules as
different as simple ions, hydrophobic lipids, polar but uncharged carbohydrates, and
even nucleic acids?

The amino acid side chains of proteins provide a range of shapes, polarity, and chemical
features that allow a protein to be tailored to t almost any possible molecular surface in a
complementary way.

27. What structural features allow biological polymers to be informational

macromolecules? Is it possible for polysaccharides to be informational macro- molecules?

Biopolymers may be informational molecules because they are constructed of different

monomeric units (“letters”) joined head to tail in a particular order (“words, sentences”).
Polysaccharides are often linear polymers composed of only one (or two repeat- ing)
monosaccharide unit(s) and thus display little information content. Polysaccharides with a
variety of monosaccharide units may convey information through speci c recognition by other
biomolecules. Also, most monosaccharide units are typically capable of forming branched
polysaccharide structures that are potentially very rich in information content (as in cell surface
molecules that act as the unique labels displayed by different cell types in multicellular
organisms).

28. Why is it important that weak forces, not strong forces, mediate biomolecular
recognition?

Molecular recognition is based on structural complementarity. If complementary interactions

involved covalent bonds (strong forces), stable structures would be formed that would be less
responsive to the continually changing dynamic interactions that characterize living processes.

30. Why does the central role of weak forces in biomolecular interactions restrict living
systems to a narrow range of environmental conditions?

Slight changes in temperature, pH, ionic concentrations, and so forth may be sufficient to
disrupt weak forces (H bonds, ionic bonds, van der Waals interactions, hydrophobic
interactions).

31. Describe what is meant by the phrase “cells are steady-state systems.”

Living systems are maintained by a continuous flow of matter and energy through them.
Despite the ongoing transformations of matter and energy by these highly organized, dynamic
systems, no overt changes seem to occur in them: They are in a steady state.

32. Biological molecules often interact via weak forces (H bonds, van der Waals
interactions, etc.). What would be the effect of an increase in kinetic energy on such
interactions?

Increasing kinetic energy increases the motions of molecules and raises their average energy,
which means that the difference between the energy to disrupt a weak force between two
molecules and the energy of the weak force is smaller. Thus, increases in kinetic energy may
break the weak forces between molecules.

33. Proteins and nucleic acids are informational macromolecules. What are the two
minimal criteria for a linear informational polymer?

Informational polymers must have “sense” or direction, and they must be composed of more
than one kind of monomer unit.

34. Define the central dogma of biology.

The central dogma describes the fundamental information flow in biological systems. DNA is
replicated to form new DNA, which is transcribed into RNA. The RNA is translated into
protein.

35. Define replication, transcription, and translation in regard to the central dogma.

Replication is the generation of two daughter double helices from a single parent double helix.
The process is catalyzed by DNA polymerase. Transcription is the process of copying DNA
information into RNA and is catalyzed by RNA polymerase. Translation converts the sequence
information of RNA into proteins and takes place on ribosomes.

36. Water is said to be polar but uncharged. How is it possible?

Water is polar in that the hydrogen atoms bear a partial positive charge, whereas the oxygen
atom has a partial negative charge owing to the electronegative nature of the oxygen atom.
However, the total charge on the molecule is zero; that is, the positive charges are equal to the
negative charges.

37. Why are weak bonds important in biochemistry?

Many weak bonds allow for highly specific yet transient interactions.

38. What are the common types of weak bonds important in biochemistry. How does
water affect these bonds?

Ionic bonds, hydrogen bonds, and van der Waals interactions. Water disrupts ionic bonds and
hydrogen bonds. Because van der Waals interactions are most common between hydrophobic
groups, water can be said to strengthen these bonds by facilitating their formation through the
hydrophobic effect.

39. What would be the effect of an organic solvent on electrostatic interactions?

Electrostatic interactions would be stronger in an organic solvent relative to a polar solvent

because there would be no competition from the solvent for the components of the electrostatic
interaction.

40. What is an electronegative atom, and why are such atoms important in biochemistry?

An electronegative atom is one that has a high affinity for electrons. Consequently, when
bonded to a hydrogen atom, the electronegative atom assumes a partial negative charge and the
hydrogen atom assumes a partial positive charge. Such polarity allows the formation of
hydrogen bonds.

41. Define the hydrophobic effect.

The hydrophobic effect is the tendency of nonpolar molecules to interact with one another in
the presence of water. The interaction is powered by the increase in entropy of water molecules
when the nonpolar molecules are removed from the watery environment.
42. How does the Second Law of Thermodynamics allow for the formation of biochemical
order?

The Second Law of Thermodynamics states that the entropy of a system and its surroundings
always increases in a spontaneous process. When hydrophobic molecules are sequestered away
from water, the entropy of the water increases. Such sequestration, called the hydrophobic
effect, also leads to the formation of biochemical structures.

43. Using the Henderson–Hasselbalch equation, show that, for a weak acid, the pKa is the
pH at which the concentration of the acid equals the concentration of the conjugate base.

The Henderson–Hasselbalch equation is pH = pKa + log[A-]/ [HA].

If [A-] = [HA], then the equation becomes pH = pKa + log 1.

But the log 1 = 0. Thus, pH = pKa under the conditions stated.