Introduction to Biochemistry

1. Define each of the following terms:

A. Biochemistry B. Biochemical Substance

2. Enumerate the different biochemical substances present in the body and account for their relative composition
(by mass percent) in the human body.

3. Living things were thought to possess a certain force unique to themselves. Elaborate on the study that
disproved this theory.

4. A large part of the biochemical substances present in living organisms are made up of carbon and hydrogen (and
are otherwise known as biomolecules). With that being said, the chemistry of biomolecules can be described by
methods of organic chemistry, which look into the functional groups of the compounds.

A. What are functional groups?

B. Tabulate the different classes of organic compounds. Include their functional group, name of the
functional group and a real example containing the least number of carbon atoms possible. An
example is provided for your reference.

Class of Compound Functional Group Name of Functional Group Example

Alcohols R-OH hydroxyl CH3OH, methanol

5. The different biomolecules that we observe today have been postulated to originate from very simple
compounds.

A. Give the details behind the Miller-Urey experiment, which is a simplified explanation of the
aforementioned phenomenon.
B. Arrange the following according to increasing level of structural organization in the human body.
(Hint: It is helpful to define each term to help you organize)
I. Atoms V. Molecules
II. Cell VI. Organ
III. Body System VII. Organelles
IV. Macromolecules VIII. Tissue

6. Differentiate between a prokaryotic and eukaryotic cell in terms of the organelles present between the two
classes. You may also illustrate your answer.

7. Scientists classify living organisms today via the five-kingdom scheme. Enumerate these and outline the basis for
the classification, as well as the different members of the said kingdom.

8. Cells need energy in order for them to function properly. To understand biochemical energetics, define the
following terms:

A. Thermodynamics D. Free Energy

B. Oxidation-Reduction Reactions E. Enthalpy
C. Spontaneous Reaction F. Entropy

9. To predict spontaneity of a reaction, the most useful thermodynamic criterion to base upon is free energy.

A. Provide for the equation that relates free energy with enthalpy and entropy.
B. Discuss the implications of the values obtained for free energy from the given equation.
Water: The Solvent for Biochemical Reactions

10. Water, as discussed previously, is the principal component of all living cells. To account for the properties of water:

A. Draw its Lewis structure and classify its shape.

B. Determine the partial positive and negative centers in the H2O molecule, if present.

11. The versatility of water as a solvent is highly dependent on the intermolecular forces of attraction it possesses.

A. What are intermolecular forces of attraction? Enumerate the 3 basic types and give a concrete example
for each.
B. Based on your answers in A, account for the following properties of water.
I. Dissolution of polar compounds in water.
II. Formation of layers when oil and water is mixed.

12. Hydrogen bonds are very important in biomolecules and are responsible for the many unique characteristics of water.

A. Identify if the following functional groups can participate in hydrogen bonding as donors, acceptors or
both. If neither, write NA.
I. alcohols IV. ethers
II. amines V. ketones
III. carboxylic acids

B. Discuss the implications of hydrogen bonding and its effects to waters:

I. boiling point II. density

13. Understanding the different acid-base properties of biomolecules is key to their respective behaviors in living
organisms.

A. Differentiate acids and bases using the:

I. Arrhenius Theory II. Bronsted-Lowry Theory

B. Give mathematical equations to solve for the following quantities.

I. Acid dissociation constant, kA, of a weak acid, HA
II. pH, from the hydrogen ion concentration
III. pH, using the Henderson Hasselbalch equation

C. Calculate for the following:

I. pH when hydrogen ion concentration is 4.30 x 103 M
II. Hydrogen ion concentration when pOH = 12

14. Buffers are very important in biological systems as they allow for the optimum pH conditions for chemical reactions to
take place.

A. Operationally define buffers according to:

I. Composition II. Function

B. Determine whether the following pairs could function as a buffer system in an aqueous environment:
I. HNO3 and KNO3 III. NaC2H3O2 and KHCO3
II. HF and NaF

C. Mention important buffer systems found in living organisms and describe briefly their buffer mechanism.