Lecture #0: Course Preliminaries

and Review
Asst. Prof. Jet G. Guerrero, R.Ch, M.Sc.
University of Santo Tomas-Legazpi
What is Life Made of?
 Physical and Chemical sciences alone may not completely explain the
nature of life, but they at least provide the essential framework for
such an explanation.

 All students of life must have a fundamental understanding of organic

chemistry and biochemistry.
 Hey, I’ve got a bipolar disorder and have a
δ +
double personality. I’m very positive and
negative at the same time!
Hydrogen bonding is when the
partial + charge on Hydrogen is
attracted to the partial – charge
of another compound.

δ- δ+

Water molecules have polar covalent bonds.

Water is attracted to other through relatively weak Hydrogen
bonds.
 Increasingly Acidic 
Stomach Acid,
[H+] >[OH-]
lemon juice
Vinegar, cola

Tomato juice

Black coffee;
Rainwater
Urine

Neutral Pure water; +

[H ] = -
[OH ]
Human blood

Seawater
 Increasingly Basic

Milk of magnesia

Household ammonia

Household bleach +
[H ] -
<[OH ]
Organic Compounds: An Overview

Besides water, what elements and compounds are

essential to life?
Organic compounds
1. Mostly contain Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulfur*
Carbon H
H H H H H
O
H C C C C C C
O O O H O
H H H H
 Carbon = The element of life!
4
a. Carbon’s Valence has ____ electrons
b. Can bond with ____4elements
c. Can form chains, rings, branches, & isomers

C C C C C C
HO H HO OH
C C C C
H OH H H
Organic Chemistry
 What makes Carbon Special? Why is Carbon so different from all the
other elements on the periodic table?

 The answer derives from the ability of Carbon atoms to bond

together to form long chains and rings.
Organic Chemistry

Carbon can covalently bond with up to four other

atoms.
Carbon can form immensely diverse compounds, from
simple to complex.

Methane with 1 Carbon atom DNA with tens of Billions of Carbon

atoms
 Organic concept I
Covalent bond

 A strong attractive interaction between

neighboring atoms in which a pair of electrons is
roughly equally shared between the two atoms.
Covalent bonds may be single bonds, in which
one pair of electrons is shared; double bonds,
which involve two pairs of electrons; or triple
bonds, which involve three pairs (see above).
Single bonds do not restrict the rotation of other
substituents around the bond; double and triple
bonds do.
Organic concept II
• Ionic bond

a strong attractive interaction

between atoms in which one atom or
group is positively charged, and
another is negatively charged.
 Organic concept III

Hydrogen bond

A weak attractive interaction between neighboring atoms

in which a hydrogen atom carrying a slight, partial positive
charge shares that positive charge with a neighboring
electronegative atom.
 Organic concept IV

• Van der Waals interaction

A weak attractive interaction

between nonpolar atoms,
arising from transient induced
dipoles in the two atoms.
 Organic Concept V

• Chirality

The property of a molecule under

which it cannot be superimposed upon
its mirror image.
Organic Concept VI
acetone propen-2-ol
• Tautomerization
The interconversion of two covalently
different forms of a molecule via a
unimolecular reaction that proceeds
with a low activation energy.
The two forms of the molecule are
known as tautomers: because of the
low activation barrier between the
two forms, we will typically find both
species present.
 Organic Concept VII

• Nucleophilic substitution: a reaction in which

an electron-rich (nucleophilic) molecule
attacks an electron-poor (electrophilic)
molecule and replaces group or atom within
the attacked species.
• The displaced group is known as a leaving group.
• This is one of several types of substitution
reactions, and it occurs constantly in biological
systems.
Biochemistry

 How much biochemistry do you

need to know for this course?
 1. You need to know the structure
and functions of organic
molecules important to major
biological processes.
2. You will be expected to
learn the basic
biochemical processes of
major cell functions, such
as photosynthesis,
respiration, and protein
synthesis.
Organic Compounds: Carbohydrates

Can you believe that each of your cells

contains about 2 meters of me?
Organic compounds (continued…)
2. Four categories of organic compounds:
Hurry up, Lipids! You
Hi there!
Heyshould
Sugar, haveMy am is
name
I suremore
a. Carbohydrates Pollyyou’re
Peptide.
happy
energythat
stored up athan
b. Lipids
Carbohydrate like me.
this!
c. Proteins Awww, how sweet!
Does this bond structure
d. Nucleic Acids make me look fat?
3. Each type of these macromolecules are formed and separated in similar ways
a. Formation (Polymerization): Dehydration Synthesis
b. Separation: Hydrolysis
Bonding: Polymerization

Polymerization
• Polymerization (definition):
• Forming of large organic macromolecules by the joining of smaller repeating
units called monomers
Bonding: Polymerization: Dehydration Synthesis

Dehydration Synthesis
• Dehydration Synthesis is the removal of a water molecule to form a
new bond.

HO 1 2 3 H HO H

Short Polymer Monomer

H2O
Dehydration removes a water molecule
forming a new bond

HO 1 2 3 4 H
Bonding: Polymerization: Hydrolysis

Hydrolysis
• Polymers are broken by adding water.
H2O
• Literally, “Water Splitting”

HO 1 2 3 4 H

Hydrolysis adds a water molecule to break a

bond

HO 1 2 3 H HO H

Short Polymer Monomer

Monomers
Monomer
Macromolecule

Nucleotides
Nucleic acids

Amino acids
Proteins

Monosaccharide
Carbohydrates

Not always polymers; Hydrocarbon

Lipids chains
Course structure
CHAPTER QUIZZES (30%)

A maximum of 4 chapter quizzes may be given per term

Relative weights of each chapter quiz will depend on the coverage
and difficulty of the exam
A student who wants to be exempted in taking the final exam
should have a passing mark for ALL chapter quizzes
Course Structure
TERM EXAM (50%)
A major term exam is given after 6 weeks of academic learning. Refer
to your syllabus for the schedule.
Course Structure
ATTENDANCE (20%)

JOURNAL CRITIQUES, HOMEWORKS, AND PROBLEM SETS (20%)