CHEMISTRY OF THE CELL

Five Principles Presence of Functional Groups

1. The importance of carbon
2. The importance of water
3. The importance of selectively permeable
membrane
4. The importance of synthesis by polymerization
of small molecules
5. The importance of assembly
1. Importance of Carbon
Carbon-containing compounds
 Domain of organic chemistry
 Most important atom in biological molecules
 Diversity & stability of carbon-
containing compounds are due to
nature of interactions of c atoms with
one another
Fundamental property = valence electrons (4)
 Carbon atoms form covalent bond with one
another or with atoms of oxygen (O), hydrogen
(H), Nitrogen (N) and Sulfur (S) Functional groups in Biomolecules
A. Simple organic molecule with single bond
a) methane - (CH4)
b) ethanol - (CH3-CH2OH)
B. Simple molecules with double bond
a) ethylene - (CH2=CH2)
b) carbon dioxide - (CO2)
C. Triple Bonds
a) molecular nitrogen - (N2)
b) Hydrogen cyanide - (HCN) 2. Importance of Water
Importance of Carbon a) Universal backbone of biologically important
HYDROCARBONS molecule
 Only H atoms are used to complete the b) Universal solvent in biological system
valence requirements of linear and circular c) 75-85% of cell by weight
molecules d) Polar (asymmetric charge distribution)
Ex. Ethane (Ch3-CH3), Propane (CH3-CH2-CH3), e) H2O are cohesive (HYDROGEN BOND)
Ethylene (CH2=CH2), Acetylene (CH=CH) Benzene f) H2O has high temperature stabilizing capacity
Importance of Hydrocarbons  High specific heat (amount of heat a
 Essentially insoluble in water (universal solvent substance must absorb per gram to increase its
in biological systems) temperature 10C.
 Important role in the structure of biological  specific heatwater = 1.0 calorie/gram
membranes. The interior of every biological  High heat of vaporization (amount of
membrane is a nonaqueous environment energy required to convert one gram of
consisting of the long hydrocarbon “tails” of liquid into vapor)
phospholipid molecules that project into the  cells during metabolism release energy by
interior of the membrane from either surface. breaking H-bonds
 This feature of membranes has important  excellent coolant
implications for their role as permeability g) H2O is an excellent solvent (a fluid in which
barriers, another substance called the solute can be
dissolved.
 Hydrophilic (water loving) – sugar, organic
acids, amino acids
 Hydrophobic (water fearing) – lipids, proteins
“LIKE DISSOLVES LIKE”
3. Importance of selectively permeable Hierarchical Nature of Cellular structures and
membrane their assembly
Physical barrier that controls the exchange of substance
between the internal & external environment
 Bi-lipid layer
(amphipathic)
 Hydrophilic HEAD
 Hydrophobic TAIL

4. Importance of Synthesis by polymerization

5. Importance of self-assembly
- Asserts the information required to specify the folding
of macromolecules and their interactions to form more
complicated structures with specific biological functions
Polymerization is inherent in the polymers themselves.
1. Macromolecules are responsible for most of the
form and function in living systems Properties of Assembly
2. Cells contain 3 different kinds of macromolecules Many proteins self-assemble. Molecular chaperones
3. Macromolecules are synthesized by stepwise assist the assembly of some proteins Non-covalent
polymerization of monomers bonds and interactions are important in the folding of
macromolecules. Self-assembly also occurs in other
cellular structures. Self-assembly has limits
Hierarchical assembly provides advantages for the cell.
Molecular Chaperones
Are proteins that facilitate the correct assembly of
proteins and protein-containing structures but are not
components of the assembled structures.
Ex: Hsp60 and Hsp70.
Cellular structures such as ribosomes, chromosomes, “Hsp” stands for heat-shock protein, they respond to
membranes, flagella, and cell walls are made up of high TO
ordered arrays of linear polymers or Macromolecules
Basic principles in polymerization
1. macromolecules are synthesized by polymerization
of similar small molecules called monomers
2. addition of each monomeric unit occurs with the
removal of water molecule (condensation reaction)
3. the monomeric units that are to be joined together
must be present as activated monomers before
condensation can occur
4. activation involves coupling of the monomer to
some sort of carrier molecule to form activated
monomer
5. energy to couple the monomer to the carrier
molecule is provided by ATP
6. Macromolecules have an inherent directionality
BIOENERGETICS
- Flow of energy in the cell
4 ESSENTIAL NEEDS OF EVERY CELL
1. Molecular building blocks
2. Chemical catalysts – enzymes
3. Information
4. Energy
ENERGY
- Ability or capacity to do work
- Ability to cause specific changes
Kinds of changes made by cells
1. Synthetic work
- changes in chemical bonds that results to:
a) Biosynthesis
b) Growth of new cells
c) Maintenance of existing cells
2. Mechanical Work
Changes in the location or orientation of a cell or sub-
cellular structure. Examples are:
a) Movement of chromosomes during mitosis
b) Flagellated sperm/bacterium
c) Ciliated epithelium in bronchial tubes
d) Cytoplasmic streaming
e) Movement of ribosome along mrna
f) Muscle contraction
3. Concentration Work
Movement of molecules across a membrane against
concentration gradient
- Na+K+ ions across plasma membranes
- Light driven-accumulation of protons within
the chloroplasts of a plant cell
4. Electrical Work
Movement of ions across a membrane against an
electrochemical gradient
- Changes in cell potential
- Eel (electrophorus contains electroplaxes)
- Mitochondria (Respiration) or chloroplast
membranes (photosynthesis)
- Impulses are conducted in the muscle and nerve
cells
5. Heat
An increase in temperature that is useful to warm
blooded animals (Homeotherms)
- Heat released maintains efficiency of
metabolism
6. Bioluminescence
- Bioluminiscent organisms
- Production of light
- Pale blue color
- Fireflies, luminous toadstools, dinoflagellate,
deep sea fish
Sources of energy
- Solar radiation (sunlight)
- Organic Food Molecules
Chemical Energy is released in 2 methods
- Fermentation
- Cellular respiration
Energy availability at Earth’s Surface
1. Solar Radiation (260,000 cal/cm2/y)
2. Lightning (4 cal/cm2/y)
3. Radioactivity (0.8 cal/cm2/y)
4. Volcanoes (0.13 cal/cm2/y)
5. Photosynthesis (100 cal/cm2/y)
Types of organisms based on accumulation of
energy
1. Phototrophs
- use light energy to make all molecules required
for life from inorganic precursors (CO2 and
H2O)
- plants and photosynthetic protists (usually
photoautotrophs); photosynthetic bacteria
photoheterotrophs)
2. Chemotrophs
- use chemical energy to make molecules
required for life
- all animals, fungi, some bacteria/protists
Flow of energy in biosphere
Flow of Energy in Biosphere
1. Energy usually stored as chemical bonds
2. Flow of matter accompanies energy flow
3. Energy enters without matter (light)
4. Energy leaves without matter (radiation)
Bioenergetics
- Flow of energy in living system
- An applied thermodynamics
- Thermodynamics = The principles that govern
energy flow
TYPES OF SYSTEM
1. OPEN. Both energy and matter can pass
through
2. CLOSED. Only energy can pass through
3. ISOLATED. Both energy and matter cannot
pass through
LAWS OF THERMODYNAMICS
Law of conservation of energy
- Energy cannot be created nor destroyed, only
converted from one form to another
Second law of thermodynamics
Expresses the concept that events in the universe have
directions
They tend to proceed to downhill movement – from
higher energy to lower energy state
Law of Entropy
- Predicts the spontaneous reactions that may
occur in the cell.
- Law of disorderliness
Thermodynamic spontaneity is a measure of
whether a reaction or process can go, but it says
nothing about whether it will go.
ENZYMES: The Catalyst of Life
Catalysis:
Importance of Enzymes
- Increases the rate of a reaction by lowering the
activation energy requirement
- Forms transient complexes with substrate
molecules
Enzymes
- Function as organic catalysts. (A catalyst is a
chemical involved in, but not changed by, a
chemical reaction).
- Protein (tertiary type)
Non Protein (Co-factor)
a) Organic groups that are permanently bound
to the enzyme (prosthetic groups)
b) Cations - positively charged metal ions
(activators), which temporarily bind to the
active site of the enzyme, giving an intense
positive charge to the enzyme's protein.
c) Organic molecules, usually vitamins or made
from vitamins (coenzymes), which are not
permanently bound to the enzyme molecule,
but combine with the enzyme-substrate
complex temporarily.
Parts of an enzyme reaction
Substrate activation
Enzyme-catalyzed reaction involves substrate activation
1. Enzymes distort one or more of its bonds,
thereby weakening the bonds – susceptible to
catalytic attack
2. Enzymes accept or donate protons, thereby
increasing the chemical reactivity of the
substrate
3. Enzymes accept or donate electrons – forming
temporary covalent bonds between enzymes
and substrate
Enzyme-substrate complex
Enzyme specificity
Factors affecting Enzyme Activity
1. Temperature
2. pH
3. Substrate Concentration
1. 2.
3.
Inhibition of enzyme activity
Importance
- Control mechanism in cells
- Action of drugs and poisons
- Studies on reaction mechanisms (Enzymologists)
Types of Inhibitions
Irreversible
- Inhibitor binds to the enzyme covalently causing
irrevocable loss of catalytic activity (toxic to
cells)
- Enzymes become permanently inactive
Reversible
- Inhibitor binds to the enzyme in a non-covalent,
dissociable manner, such that the free and
bound forms of the inhibitor exist in equilibrium
- Competitive and Non-competitive
Types of Reversible Inhibition Oxidases
- Catalyze the removal of hydrogen from a
substrate using oxygen as a hydrogen acceptor.
- They form water or hydrogen peroxide as a
reaction product.
Flavoproteins:
a) Flavin mononucleotide (FMN)
b) Flavin adenine dinucleotide (FAD)
*Vitamin B complex
Dehydrogenases
- Transfer hydrogen from one substrate to
another
ENZYME REGULATION - Components in a respiratory chain of electron
Allosteric / Non-competitive - is the regulation of a transport from substrate to oxygen
protein by binding an effector molecule at a site other Examples: Nicotinamide adenine dinucleotide (NAD+),
than the enzyme's active site. The site to which the cytochromes
effector binds is termed the allosteric site. Hydrogen Peroxidases
Two Types:
1. Peroxidases
2. Catalases
*Use Hydrogen peroxide as substrate
Biomedical Importance: Detoxification (H2O2 is
substrate  radicals)
Oxygenases
- Enzymes that catalyze the incorporation of
oxygen into the substrate molecule
- Biomedical Importance: Cytochrome P450;
- Hydroxylation of Drugs
End of the session

Feedback Inhibition - is the phenomenon where the

output of a process is used as an input to control the
behavior of the process itself, oftentimes limiting the
production of more product.

Enzymes involved in oxidation and reduction are

OXIDOREDUCTASES:
Four Groups:
1. Oxidases
2. Dehydrogenases
3. Hydroperoxides
4. Oxygenases
* Electron acceptors