Biochemistry and the

Organization of Cells
 Learning outcomes
Students should be able to;

Define biochemistry and biomolecules

Recognize various form of biomolecules
Identify functional groups for specific biomolecules
Understand thermodynamics
Identify the differences between laws of
thermodynamics
 What is biochemistry?

• The study of chemical and chemical processes

in any living organism
 Basic themes
• How does biochemistry describe life processes?
 Living things are diverse
 Two things in common
• All cells use the same types of
biomolecules
• Use energy
 What is biomolecule?

 Biomolecules are molecules that are made by

living organisms such as;
 Proteins
 DNA
 Carbohydrates
 Lipids
 How did living things originate
• Since all living cells uses the same biomolecules
and energy, speculating on the origins of life is a
worthwhile question
– How did the components of our bodies do the
things that they do?
– What are the basic molecules of life?
• H2O (water), CH4 (methane), CO2, NH3 (ammonia),
 Introduction to the Chemistry of Life
THE ORIGIN OF LIFE

Universe is 15-20 billion years old –BIG BANG

Initially H2 was made then condensed to He
Over the billions of years under the right conditions complex molecules formed.
Complicated chemical reactions started occurring - intermolecular interactions and
carbon based chemistry developed.

From this milieu sprang the property of

LIFE
 The Physical Laws of Life
•Philosophers thought life contained a “vital force” or vitalism but this has been rejected
by modern science.
The belief dating to around 1600 that matter was divided into two classes based on
behavior with respect to heat: organic and inorganic. Inorganic material could be melted
but could always be recovered by removing the heat source. Organic compounds
changed form upon heating and could not be recovered by removing the heat source.
The proposed explanation for the difference between organic and inorganic compounds
was the Vitalism Theory, which stated that inorganic materials did not contain the "vital
force" of life and lasted until the mid-nineteenth century.

•Haldane – simple organic compounds from H2O, N2 and CO2

•Urey – chemical synthesis of urea

•Living organisms operate within the same physical laws that apply to physics and
chemistry:

•Conservation of Mass, Energy

•Laws of Thermodynamics
•Laws of Chemical Kinetics
•Principles of Chemical Reactions
 What distinguishes living organisms?

1) Structurally complicated and highly organized

a. intricate internal structures
b. many kinds of complicated molecules
proteins, DNA, RNA, starches, and lipids etc

2) Living organisms:

a. extract
b. transform ENERGY
c. store
d. use
Living things can extract energy from the
environment
Chemical: Chemoautotrophs or lithoautotrophs

H2S  2H+ +S +2e-

2NH3 + 4O2  2HNO3 + 2H2O
4FeCO3 + O2 + 6H2O  4Fe(OH)3 + 4CO2
or
Sunlight: Photoautotrophs
nCO2 + nH2O + hu (CH2O) + nO2

Energy is needed to build and maintain structures

a) mechanical energy - muscles
b) chemical energy - electric eel
c) osmotic energy - plant turger
d) light energy -bioluminescence
 3) Most characteristic attribute of living things is
self-replication and self assembly
it is the quintessence of the living state
1 single bacteria  109 in 24 hr
With near-perfect fidelity during replication!

A crystal at equilibrium grows but life at equilibrium is death!

Life is a set of relationships characterizing the nature, function and interaction of

biomolecules.
 Chemical Foundations of Biochemistry

 Cellular apparatus of living organisms is

made up of carbon compounds – thus
biomolecules are part of organic chemistry
 Organic chemistry – the study of
compounds of carbon and hydrogen and
their derivatives.
 Functional groups of molecules
 What are functional groups?
• Specific groups of atoms or bonds
within molecules that are responsible for the
characteristic chemical reactions of those
molecules.

• The reactions of molecules are based on the

reactions of their respective functional groups.

• The number and arrangement of functional groups give

each molecule its unique properties
• The seven functional groups that are most
important in the chemistry of life:
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Sulfhydryl group
– Phosphate group
– Methyl group
Fig. 4-10a
CHEMICAL
GROUP
Hydroxyl
STRUCTURE
(may be written HO—)
In a hydroxyl group (—OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH–.)
NAME OF Alcohols (their specific names
COMPOUND usually end in -ol)
EXAMPLE
Ethanol, the alcohol present in
alcoholic beverages
FUNCTIONAL Is polar as a result of the
PROPERTIES electrons spending more time
near the electronegative
oxygen atom.
Can form hydrogen bonds with
water molecules, helping
dissolve organic compounds
such as sugars.
Carbonyl
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
Ketones if the carbonyl group is
within a carbon skeleton
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
Acetone, the simplest ketone
Propanal, an aldehyde
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Carboxyl
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an —OH group, the entire
assembly of atoms is called
a carboxyl group (—COOH).
Carboxylic acids, or organic
acids
Acetic acid, which gives vinegar
its sour taste
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Acetic acid Acetate ion
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).
Fig. 4-10d

Amino

STRUCTURE NAME OF
Amines
COMPOUND

EXAMPLE FUNCTIONAL
Acts as a base; can PROPERTIES
pick up an H+ from
the surrounding
solution (water, in
living organisms).
Glycine

Because it also has a

carboxyl group, glycine
is both an amine and
a carboxylic acid; (nonionized) (ionized)
compounds with both
groups are called Ionized, with a
amino acids. charge of 1+, under
cellular conditions.
Fig. 4-10e

Sulfhydryl

STRUCTURE NAME OF
Thiols COMPOUND

(may be
written HS—)

EXAMPLE FUNCTIONAL
Two sulfhydryl groups
PROPERTIES
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.

Cysteine Cross-linking of
cysteines in hair
proteins maintains the
Cysteine is an important curliness or straightness
sulfur-containing amino of hair. Straight hair can
acid. be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
Fig. 4-10f

Phosphate

STRUCTURE NAME OF
Organic phosphates COMPOUND

EXAMPLE
Glycerol phosphate
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
FUNCTIONAL
Contributes negative charge PROPERTIES
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Has the potential to react
with water, releasing energy.
Fig. 4-10g

Methyl

STRUCTURE NAME OF
Methylated compounds COMPOUND

EXAMPLE FUNCTIONAL
Addition of a methyl group
PROPERTIES
to DNA, or to molecules
bound to DNA, affects
expression of genes.

Arrangement of methyl
groups in male and female
sex hormones affects
5-Methyl cytidine their shape and function.

5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
 Why are biomolecules special ?
• Living cells include very large molecules, such
as proteins, nucleic acids, and polysaccharides
these biomolecules are polymers (Greek: poly
+ meros, many + parts)
they are derived from monomers (Greek:
mono + meros, single + part)
amino acids proteins
nucleotides nucleic acids
monosaccharides polysaccharides
 Why are biomolecules special ?
• Enzymes: a class of proteins that are biocatalysts
the catalytic effectiveness of a given enzyme
depends on its amino acid sequence

• Genetic code: the relationship between the

nucleotide sequence in nucleic acids and the
amino acid sequence in proteins
theories of the origin of life consider how such
a coding system might have arisen
Organization of cell
 The energetics of life
• Living organisms are highly complicated at the
molecular level. A large amount of energy is
invested in maintaining the ordered and
complicated state of cells and tissues.
• In humans and animals, energy needed for
work and biosynthesis of cellular structures is
derived from organic molecules in the diet.
• Often these come from plant sources, who
derived their energy for synthesis of
biomolecules from sunlight.
• In animals, energy is derived from the
breakdown of fuel molecules by processes
referred to as catabolism.
• In turn, the energy released from catabolism is
used to drive biosynthetic processes
collectively referred to as anabolism.
 How cell use energy?
• Light from the sun is the ultimate source of
energy for all life on earth.
photosynthetic organisms use light energy to
drive the energy-requiring synthesis of
carbohydrates.
non-photosynthetic organisms consume these
carbohydrates and use them as energy
sources.
 Free-Energy Change, G
• A living system’s free energy is energy that can
do work when temperature and pressure are
uniform, as in a living cell
• calculation of free energy changes (∆G) which
can be used to determine the direction of
metabolic reactions and their equilibrium
constants.
• ∆G values are determined by the enthalpy
(∆H, heat transfer) and entropy (∆S, change in
randomness) changes associated with a
reaction through the equation
∆G = ∆H - T∆S.
• Negative values of ∆G signify favorable
reactions, whereas positive values of ∆G are
associated with unfavorable reactions.
• The energetics of a chemical reaction

if the change in free energy (ΔG) is negative

(free energy decreases), the reaction is
spontaneous as written – exergonic (energy
is released) =(favored)

if the change in free energy (ΔG) is positive

(free energy increases), the reaction will not
occur as written unless energy is supplied
from an external source – endergonic
(require additional energy)= (disfavored)
 – At equilibrium, (ΔG) = 0.

• Spontaneous reaction is any reaction that takes

place with no outside intervention – does not
mean fast, can take a long time to complete.