Chem 221 Biochem Practice Questions (Ch.

1 &2)

1. What are the 4 most common elements in living organisms?

- Hydrogen, oxygen, nitrogen, carbon
- The FOUR most abundant elements in living organisms, in terms of percentage of
total NUMBER OF ATOMS, are 1) HYDROGEN 2) OXYGEN 3) CARBON 4) NITROGEN
[ppt 1.1, p 17]

macromolecule simple building blocks = Proteins , Nucleic acids , Carbohydrates ,Lipids

ppt says sugar, amino acids, nucleotides and fatty acids

More complex macromolecules = protein, polysacharide, RNA or DNA, and lipid

2. What is the difference between a diastereoisomer and enantiomer?

- DIASTEREOMERS are stereoisomers that are NOT mirror images of one another and
are non_superimposable on one another. Diastereomerism occurs when two or
more stereoisomers of a compound have different configurations at one or more of
the equivalent stereocenters and are not mirror images of each other.
- Enantionmers are Nonsuperimposable mirror images. [ppt 1.1, p. 39]

3. Why do cells produce only one form of a chiral compound rather than a racemic
mixture?
- Cells produce one form of a chiral compound if there are 4 different molecules
attached to the central carbon????
-

4. What’s the difference between dynamic steady state and equilibrium?

- Dynamic steady state is a level where living organisms are at a balance with their
environment/surroundings, while eqb is a state where living organisms cannot
survive. It is equivalent to cell death.
5. What happens (in terms of electron flow) to the reactant that is oxidized?
6. How are cells able to synthesize polymers if such reactions are thermodynamically
unfavorable?
- Energy coupling I believe
-
7. Does the oxidation of glucose represent an increase or an increase in entropy. Does it
have a positive or negative delta G?
8. Why is the option of increasing temperature to overecome activation barriers not
possible in living cells?
9. Name the four most abundant elements in living organisms.
- Hydrogen, Carbon, nitrogen, and oxygen. IN TERMS OF % of total 3 of atoms [ppt
1.1, p. 17]
10. Explain why butanol has a relatively high boiling point of 117 degrees C, whereas butane
has a boiling point of only 0.5 degrees C.
- The higher boiling point of butane most likely represents the strength in bonds
between neighboring butanol molecules. Bc it’s so strong, a higher amount of heat
energy is required to break the force. [ppt 2.1, pg. 20]

11. Name four unique properties of water.

- High molecular cohesion (capillary action, meniscus and high surface tension)

o
- High specific heat capacity
- High boiling and melting point
o Water has an unusually high melting point, due to the hydrogen bonding
between water molecules.
o In its solid form (ice), each water molecule is subject to FOUR hydrogen
bonds
o Just like with its melting point, water molecules also have a higher boiling
point than other substances.
o Likewise, the reason for this is the hydrogen bonding between neighboring
water molecules. Because hydrogen bonding is a relatively strong
intermolecular force, high heat energy is required to break up the force.
- Unusual liquid and solid phase densities (expansion upon freezing)
o Water is one of the few substances that has the excep3on of having less
dense solid than its liquid.
o Ice is less dense than liquid water
o Each water molecule in ice forms four hydrogen bonds to its neighbors,
creating a regular crystal lattice.
o The hydrogen bonds keep each molecule at a DISTANCE that makes ICE LESS
DENSE THAN LIQUID WATER.
o The expansion upon freezing comes from the fact that water crystallizes into
an open hexagonal form. This hexagonal lattice contains more space than the
liquid state.
 o
- [ppt 2.1, pg. 18]

12. Circle plot….

13. If you titrate 40 mL of HCl 0.1M with NaOH 1M, how many ml of NaOH would you need
to add to reach the equivalence point?
- 4 mL
14. Shade the buffering region in the following plot. Indicate with an arrow the pKa point
and the equivalence point.
- Is the buffering region the area where the ph is not decreasing?? We’ll see I guess

15. Explain why amphypatic molecules can be used as detergents

16. Draw the enantiomer of the following molecule:

17. Draw the cis and trans geometric isomers of COOHCHCHCOOH


18. What six characteristics distinguish living organisms from inanimate objects?
19. All cells are surrounded by a plasma membrane composed of lipid and protein
molecules. What is the function of the plasma membrane?

20. (a) List the types of noncovalent interactions that are important in providing stability to
the three-dimensional structures of macromolecules. (b) Why is it important that these
interactions be noncovalent, rather than covalent, bonds?
- A) linear, branched, and cyclic ???
- B) Noncovalent molecules are important bc this is ideal for carbon atoms which can
form 4 bonds. The bonds can be linear chains, branched chains and cyclic structures.
With the covalent bonds they have more freedom to form a variety of different
molecules. Covalent bonds are more ideal bc they are stronger than ionic bonds and
take more energy to break. In Covalent bonds, atomss share electrons. ????[ppt 1.1,
p. 22]
 - The covalent bonds and functional groups of a biomolecule are, of course, central
to its function, but so also is the arrangement of the molecule’s constituent atoms
in three_dimensional space (stereochemistry). These interaction should be
noncovalent so that …. [ppt 1.2, pg. 38]
- A) noncovalent interactions include hydrogen bonds, ionic interactions between
charged groups, van der waals interactions and hydrophobic interactions.
- B) bc noncovalent interactions are weak, they can form, break and re-form more
rapidly and with less energy input than can covalent bonds. This is important to
maintain the flexibility needed in macromolecules.

21. What is the difference, if any, between cytosol and cytoplasm?

- The CYTOPLASM is composed of an aqueous solution, the CYTOSOL, and a variety of
- suspended particles with specific functions
- The CYTOSOL is a HIGHLY CONCENTRATED SOLUTION containing • enzymes
- • RNA (that encode them) • amino acids and nucleotides from which RNA and
enzymes are assembled • small molecules (metabolites) intermediates in synthetIc
and degradative pathways • coenzymes (to help enzyme- catalyzed reactions) •
ribosomes, small particles (composed of protein and RNA molecules) that are the
sites of protein synthesis. [ppt 1.1, pg. 8-10]
- the cytoplasm is in the INTERNAL volume enclosed by the plasma membrane; the
cytosol is the AQUEOUS portion of the cytoplasm.
-
22. Draw the structures of the following functional groups in their un-ionized forms: (a)
hydroxyl, (b) carboxyl, (c) amino, (d) phosphoryl.
23. What is the underlying, organizing biochemical principle that results in the chemical
similarity of virtually all living things? Given this biochemical similarity, how is the
structural and functional diversity of living things possible?
24. Name two functions of (a) proteins, (b) nucleic acids, (c) polysaccharides, (d) lipids.
25. Why is an asymmetric carbon atom called a chiral center?
26. Differentiate between configuration and conformation.
27. Explain why living organisms are able to produce particular chiral forms of different
biomolceules while laboratory chemical synthesis usually produces a racemic mixture.

28. Describe the relationship between a living organism and its surroundings in terms of
both matter and energy.
- The molecules and ions contained within a living organism differ in KIND and in
CONCENTRATION from those in the organism’s surroundings.
- Although the specific composition of a certain organism changes little through time,
the population of molecules within the organism changes all the time.
- Chemical reactions are constantly happening to replace molecules and cells that are
degraded.
- The constancy of types and concentration of molecules and cells in an organism is
not the results of a static state but instead the result of a DYNAMIC STEADY STATE.
 - In this dynamic steady state, MATTER and ENERGY is EXCHANGED between the
organism and the surrounding, and the separation (unequal composition) between
the two is maintained. MAINTAINING this dynamic steady state requires the
constant investment of energy.
- When the cell can no longer make use of the necessary energy, energy, it DIES and
begins to decay toward EQUILIBRIUM with its surroundings.
- SYSTEM • The system is that portion of the universe with which we are concerned. It
might be a mixture of chemicals in a test tube, or a single cell, or an entire organism.
- SURROUNDINGS • The surroundings include everything else in the universe.
- [ppt. 1.2, pg. 3-8]
- living organisms are open systems and exchange both matter and energy with
their surroundings; that is, the concentrations of molecules inside the cells of the
organism are not the same as their concentrations in the surroundings. To
maintain this situation, the organism must acquire energy from its surroundings,
either in the form of chemical energy or directly from sunlight.

29. The free-energy change for the formation of a protein from the individual amino acids is
positive and is thus an endergonic reaction. How, then, do cells accomplish this process?
- The endergonic (thermodynamically UNfavorable) reaction is coupled to an
exergonic (thermodynamically favorable) reaction through a shared intermediate,
so that the overall free-energy change of the coupled reactions is negative (the
overall reaction is exergonic).

30. a) On the reaction coordinate diagram shown below, label the transition state and the
overall free-energy change (ΔG) for the uncatalyzed reaction A → B. (b) Is this an
exergonic or endergonic reaction? (c) Draw a second curve showing the energetics of
the reaction if it were enzyme-catalyzed.
- Endergonic I think

31. What is meant by feedback inhibition and why is it important in a living organism?
- FEEDBACK INHIBITION is an example of regulation of metabolism.
- The increased concentration of the reaction product inhibits the catalytic activity of
the first enzyme in the pathway, slowing the production of that substance. [ppt 1.2,
pg. 87]
- Such feedback inhibition keeps the production and utilization of each metabolic
intermediate in balance. [6e pDF, p. 28]
 - Feedback inhibition is the regulation of a biochemical pathway in which a reaction
product inhibits an earlier (usually the first) step in the pathway. It is an important
type of regulation because it ensures that energy is not wasted by an organism
producing molecules it does not need.

32. Name and briefly define five types of noncovalent interactions that occur between
biological molecules.
- The monomeric subunits in proteins, nucleic acids, and polysaccharides are joined by
covalent bonds.
- In supramolecular complexes, however, macromolecules are held together by
noncovalent interactions—much weaker, individually, than covalent bonds. Among
these noncovalent interactions are 1) hydrogen bonds (between polar groups), 2)
ionic interactions (between charged groups), 3) hydrophobic interactions (among
nonpolar groups in aqueous solution), and 4) van der Waals interactions—all of
which have energies substantially smaller than those of covalent bonds
- [6e book, p.11] orrrr
- Noncovalent intermolecular interactions include: 1) Electrostatic interactions 2) van
der Waals forces
 3) Hydrophobic interactions 4) Hydrogen bonds. Noncovalent
interactons play important roles because they are collectively strong.
- 1) Electrostatic interactions
o Electrostatic interactions are formed between charged particles. (cation and
anion)
o For example, Mg2+ ions associate with the negatively charged phosphates of
nucleotides.
o Within proteins, SALT BRIDGES can form between nearby charged residues,
for example, between a positively charged amino group and a negatively
charged carboxylate ion.
- 2) van der Waals forces
o van der Waals forces (London forces) are weak forces between temporary
dipoles.
o When nonpolar molecule are very close together, their surrounding electron
clouds influence each other.
o Random variations in the positons of the electrons may create a transient
electric dipole, which induces a transient, opposite electric dipole in the
nearby molecule. The average bond energy for van der Waals forces is on the
order of 10 kJ/mol.
- 3) Hydrophobic interactions
o Hydrophobic interactions result when non-polar molecules are in H2O (polar
solvent). The non-polar molecules group together to exclude water. By doing
so they minimize the surface area in contact with the polar solvent
o The strength of hydrophobic interactions is not due to any intrinsic attraction
between nonpolar.
 o Rather, it results from the system’s achieving greatest thermodynamic
stability by minimizing the number of ordered water molecules required to
surround hydrophobic portions of the solute molecules.
o Many biomolecules are amphipathic; proteins and the sterols and
phospholipids of membranes all have polar and nonpolar surface regions.
o Structures composed of these molecules are stabilized by hydrophobic
interactions among the nonpolar regions.
- 4) Hydrogen bonds
o Hydrogen bonds form between oxygen or nitrogen of a molecule (or part of a
molecule) and a hydrogen atom covalently bonded to another
electronegative atom in another molecule (or in different part of the same
molecule).
o Alcohols, aldehydes, ketones, and compounds containing N-H bonds all form
hydrogen bonds with water molecules.
o Hydrogen bonds play a crucial role in the structure and function of
macromolecules such as proteins, carbohydrates, and nucleic acids.

-
- [ppt. 2.1, p. 50-60]
- 1) hydrogen bonds: weak electrostatic attractions between one electronegative
atom (such as oxygen or nitrogen) and a hydrogen covalently linked to a second
electronegative atom;
- 2) electrostatic interactions: relatively weak charge-charge interactions
(attractions of opposite charges, repulsions of like charges) between two ionized
groups;
- 3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups
together, reducing the total ahead of the two groups that is exposed to
surrounding molecules of the polar solvent (water)
- 4) van der waals interactions: weak interactions between the electric dipoles that
two close-spaced atoms induce in each other
- 5) tightly bound water molecules can form as an essential part of the binding site
in a protein for its ligand

33. Explain the fact that ethanol (CH3CH2OH) is more soluble in water than is ethane
(CH3CH3).
 - Ethanol is more soluble than ethane due to its functional group OH.
- “”Ketones, alcohols, aldehydes, and compounds that have N- H bonds, form
hydrogen bonds with water molecule. These biomolecules tend to be very soluble in
water. “”
- [ppt. 2.1, pg. 64]
- ethanol can form hydrogen bonds with water molecules but ethane cannot. When
ethanol dissolves, the decrease in the systems entropy that results from formation
of ordered arrays of water around the CH3CH2-group is partly compensated by the
favorable interactions (hydrogen bonds) of the hydroxyl group of ethanol with
water molecules. Ethane cannot form such hydrogen bonds.

34. Phosphoric acid (H3PO4) has three dissociable [seperatable] protons, with the pKa’s
shown below. Which form of phosphoric acid predominates in a solution at pH 4?
Explain your answer.
Acid pKa
H3PO4 2.14
H2PO4– 6.86
HPO42– 12.4
- The solution that would predominate in a solution of pH of 4 would be HPO42, bc it
has the highest pH and therefore the lowest dissociation.???
- [ppt 2.2, p. 30]
- at pH 4, the first dissociable proton (pka=2.14) has been titrated completely, and
the second (pka=6.86) just started to be titrated. The dominant form at ph 4 is
therefore H2PO4, the form with one dissociated proton.

35. Define pKa for a weak acid in the following two ways: (1) in relation to its acid
dissociation constant, Ka, and (2) by reference to a titration curve for the weak acid.
- The pkA for a weak acid must be on the higher side but lower than 7. The
dissociation constant will be higher, meaning it will have a higher dissociation?????
- In reference to a titration curve, the weak acid will start off lower on the pH scale
but as the strong base is being added, will climb up the ph scale. The equivalent
point will not always be at …..
- [ppt. 2.2, pg. 48]
- 1) pka = -log Ka.
- 2) pka is the value of pH at the inflection point in a plot of pH vs. extent of titration
of the weak acid. At the pka, the concentration of ionized acid = the concentration
of un-ionized acid.

36. Draw the titration curve for a weak acid, HA, whose pKa is 3.2. Label the axes properly.
Indicate with an arrow where on the curve the ratio of salt (A–) to acid (HA) is 3:1. What
is the pH at this point?
- The plot of pH vs. added base should have the general shape of those show in the
text book, with the midpoint of the titration (inflection point) at ph = 3.2. the ratio of
 A- to HA is 3 when 0.75 equivalents of base have been added. From the henderson
hassel bach eqn, the PH at this point can be calculated as to be 3.68.

37. What is the pH of a solution containing 0.2 M acetic acid (pKa = 4.7) and 0.1 M sodium
acetate?
- pH = 4.4

-
[ppt. 2.2, p. 74]
- ph = 4.4

• spontaneous processes - occur without energy input

– spontaneous does NOT mean fast
– these processes can happen quickly or slowly
– but they do not require energy to proceed
– so spontaneous really means energetically favorable
• for a process to occur spontaneously (without energy) input - it must increase
the entropy of the universe
• living systems ultimately increase the entropy of their surroundings
• it is true that cells create ordered structures from less ordered materials
• BUT - organisms also replace ordered forms of matter and energy with less
ordered forms
• so while an organism may form by increasing its order (decreasing
entropy)– the ultimate effect on the universe is a decrease in order
(increasing entropy)
• the evolution of more complex organisms does not violate the second law of
thermodynamics
– as long as the overall entropy of the universe increases
The free-energy change of a reaction tells us whether or not the reaction occurs
spontaneously
• A living system’s free energy (G) = energy that can do work when temperature
and pressure of a system are uniform – e.g. within a cell
• The change in free energy (∆G) during a process is related to the change in
enthalpy, or change in total energy (∆H), change in entropy (∆S), and
temperature in Kelvin (T)
∆G = ∆H – T∆S
• another way of looking at free energy change ∆G= difference in the free energy
of a system’s final state minus the free energy of the system’s initial state
∆G = G final state – G initial state
• when a process occurs spontaneously – ∆G is negative
– ∆G is negative when the process involves a loss of free energy
– the system in its final state is more stable and less likely to change than
the system in its initial state
• so free energy is a measure of instability
• in terms of biochemistry:
– the higher the G of a compound – the more unstable it is
– more stable compounds have a lower G
– e.g. glycolysis – glucose is more unstable and likely to breakdown than its
products – higher G than the products it produces

• as a reaction proceeds toward equilibrium – the free energy of

the reactants and products decreases
• G is at its lowest possible value in that system
• equilibrium is like a “free-energy valley”
– a process is spontaneous and can perform work only when it
is moving toward equilibrium – going “downhill”
– to “climb” out of this valley will have a positive ∆G and will
not be spontaneous
– so systems never move spontaneously away from
equilibrium
Exergonic reactions
• e.g. cellular respiration
• overall – the ∆G = -686 kcal/mol
(a) Exergonic reaction: energy released, spontaneous
– for each mole of glucose, 686 kcal (2,870
kJ) of energy are made available for work
Reactants
– the products store 686kcal less energy
per mole than the reactants Amount of
energy
– 686kcal less energy stored in their released
(DG < 0)
chemical bonds
Free energy

Energy
• exergonic, spontaneous reaction Products

Progress of the reaction

Initial state Final state

-less stable -more stable
-higher G -lower G
∆G = G final state – G initial state

enegy coupling
 ATP powers cellular work by coupling
exergonic reactions to endergonic reactions
• a cell does three main kinds of work
– Chemical – the “pushing” of endergonic reactions
• e.g. building of a polymer from monomers
– Transport – the pumping of substances against a
concentration gradient
– Mechanical – the beating of cilia, contraction of
muscle cells, movement of chromosomes in mitosis
• to do this work - cells use energy coupling
– using an exergonic process to drive an endergonic one
• most energy coupling in cells is mediated by ATP
– the exergonic process makes ATP
– the endergonic process uses it

energy coupling in cells mediated by ATP

The Activation Energy Barrier
• the chemical reactions in metabolism
involve both bond breaking and bond A B
forming
– changing one molecule to another C D
involves transforming the starting Transition state
molecule into a highly unstable state
before the reaction can proceed
– the bonds absorb energy from the
surroundings to achieve this unstable A B EA
Free energy

state
– in an exergonic reaction - when the C D
newer bonds form – the product is Reactants
more stable (lower G) and the excess
energy released as heat A B
DG < O

C D

Products

Progress of the reaction

 The Activation Energy Barrier
• the initial energy needed to do
create these unstable bonds (i.e. to A B
start a chemical reaction) = free
energy of activation or activation C D
energy (EA) Transition state
• activation energy is often supplied in
the form of thermal energy that the
reactant molecules absorb from their A B
surroundings and use to transform EA

Free energy
into the unstable transition state C D

Reactants
A B
DG < O

C D

Products

Progress of the reaction

How Enzymes Lower the EA Barrier

Course of
reaction
• enzymes catalyze reactions by lowering without EA
without
enzyme
the EA barrier enzyme EA with
enzyme
– allow the reactants to easily absorb is lower

enough energy to reach their unstable

Reactants
transition state
Free energy

– so they can reach this state even at Course of DG is unaffected

reaction by enzyme
moderate temperatures and faster too! with enzyme

• enzymes do not affect the change in free

energy (∆G)
Products
– instead, they hasten reactions that would
occur eventually Progress of the reaction

enzymes lower the ea barrier

Anabolism (Synthesis) – make things
Catabolism (decomposition) – breaks things down

• Anabolic pathways consume energy to build complex molecules from simpler ones
– “uphill” component of metabolism
• also referred to a biosynthesis or biosynthetic pathways
• e.g. synthesis of protein from amino acids
• e.g. gluconeogenesis – the synthesis of glucose de novo
• energy of catabolism can be stored and used to power biosynthesis
• Catabolic pathways release energy by breaking down complex molecules into simpler
compounds
– “downhill” component of metabolism
• e.g. cellular respiration = the breakdown of glucose in the presence of oxygen
• the energy stored in the organic molecules are now available to perform the work of the
cell