Intro to Biochemistry

By: Roselita O Natividad

Natural Science Department
Ateneo de Zamboanga University

➢ Define as chemistry of the living organism

➢ Living organisms are composed of lifeless molecules, when these molecules are isolated and examined
individually but when in a living organism, they even support life
➢ These lifeless molecules in the living organism conform to all the physical and chemical laws that describe
the behavior of matter
➢ In addition, these molecules possess extraordinary attributes not shown by any random collection of
molecules

Living Matter has Several Characteristics

➢ Structurally complicated yet highly organized
➢ Living organisms extract, transform, and use energy from their environment, usually in the form of either
chemical nutrients or radiant energy from the sun
➢ Have the capacity for precise self-replication and self-assembly

That is ….
➢ The molecules in living organisms conformed to all the laws of chemistry but at the same time they
interact with each other in accordance with another set of principles referred to as the “Molecular Logic
of Life”
➢ The molecular logic of life relates nature, function, and interaction of biomolecules
➢ The basic goal of biochemistry, therefore, is to determine how these molecules interact with each other
to maintain and perpetuate life and ultimately concerned with the wonder of life itself

Water
➢ Most abundant in living organisms, making up approximately 70% of the weight of most organisms
➢ Medium in which the transport of nutrients, enzyme-catalyzed reactions of metabolism, and the transfer
of chemical energy occur

Structure of Water
➢ Composed of two hydrogens and one oxygen
➢ Each hydrogen atom is linked to the oxygen by a single covalent bond
➢ Oxygen is more electronegative than hydrogen, thus, oxygen bears a slightly negative charge and
hydrogen a slightly positive charge resulting to a polar bond
➢ Bond angle in water molecule is 104.50
Properties of Water

Thermal Properties of Water

➢ Acts as an effective modulator of climatic temperature
➢ Can absorb and store solar heat and release it slowly
➢ Water’s high heat capacity coupled with the high water content found in most organisms, helps maintain
an organism’s internal temperature
➢ Evaporation of water is used as a cooling mechanism, since it permits large losses of heat
➢ An adult human, for example, may eliminate as much as 1200g of water daily in expired air, sweat and
urine
➢ The associated heat loss may amount to approximately 20% of the total heat generated by metabolic
processes

Heat of vaporization – energy required to vaporize one mole of a liquid at a pressure of one atmosphere

Heat capacity – energy must be added or removed to change the temperature by one degree Celsius

Solvent Properties of Water

➢ Water’s dipolar structure and its capacity to form H-bonding enable water to dissolve many ionic and
polar substances
➢ Non-polar molecules are not soluble in water because they lack polar functional groups and thus, cannot
form H-bonds

*** the reason why water is being called the universal solvent because of the large variety of ionic and polar
substances it can dissolve and this is due to the large dielectric constant that water possesses (dielectric constant
of a solvent is a measure of its capacity to reduce the attractive force between ions) ***

… the physical and chemical properties of water make it remarkably suitable for its numerous functions in living
organisms…

… non-covalent interactions play a vital role in determining these properties…

Non-covalent Bonding
H-Bonds
➢ because of the large difference in electronegativity of H and O, the hydrogens of one water molecule are
attracted to the unshared pairs of electrons of another water molecule forming H-bond
➢ The H-bond describes an electrostatic interaction rather than a covalent bond
➢ Act as bridge between water molecule
➢ Although weaker than ionic and covalent bonds, hydrogen bonds are stronger than most non-covalent
bonds
➢ Provide the cohesive forces that make water liquid at room temperature and favor extreme ordering of
molecules in ice
➢ Has a significant effect on the structure and function of biomolecules
Electrostatic interaction
➢ Occurs between oppositely charged atoms or group of atoms
➢ Significant role in determining the shape and function of biomolecules such as between –COO- and –NH3+
in determining the three-dimensional structure of proteins
➢ An important aspect of this interaction in aqueous solution is the hydration of ions
➢ Water molecules are polar, thus, they are attracted to charged ions
➢ As ions become hydrated, the attractive force between them is reduced and the charged species dissolves
in the water
➢ Electrostatic interactions between charged groups or polar groups on biomolecules are most significant in
water depleted regions since water competes with great success with electrostatic interactions between
other groups

Hydrophobic interaction
➢ When non-polar molecules enter an aqueous environment, H-bonded water molecules attempt to form a
cage-like structure around them
➢ Primarily responsible for the structure of membranes and the stability of proteins

Other non-covalent interactions are:

➢ Dipole-dipole interactions
➢ Dipole-induced dipole interactions
➢ Induced dipole-induced dipole interactions

Bonding property of carbon

➢ Can form tetrahedral structure that results to two spatial arrangements, one being the mirror image of
the other
➢ In the C=C, cis-trans isomerism exists

The Cell

➢ Cells are the structural and functional units of all living organisms
➢ A meaningful study of the chemical reactions that underlie the processes of life would only be possible if
viewed in different biochemical systems in relation to machineries
 1. Nucleus – main center of biochemical system, that is, main center of biosynthesis of nucleic acids:
DNA, RNA
– called control center

2. Nucleoli – packed with ribosomes, rich in RNA and proteins and appears to be active centers of
protein and RNA synthesis
3. Endoplasmic Reticulum, ER
➢ All cells contain ER
➢ Constitutes more than half of the total membrane
➢ Provides the cells with the mechanism for separating newly synthesized molecules that belong to the
cytosol from those that do not
➢ Plays a central part in the biosynthesis of molecules used to construct other cellular organelles

Rough ER – packed with ribosomes

– protein synthesis/RNA synthesis

Smooth ER – lipid synthesis

4. Ribosomes
➢ Factory site for the manufacture of all cell proteins
➢ Transferring of information from DNA to protein synthesis

5. Mitochondria
➢ Power house of the cell
➢ Site of the oxidation reactions and electron transport chain

6. Lysosomes
➢ Principal sites of intracellular digestion
➢ Can malfunction and cells will rupture, thus, also called suicide sac
➢ For defense

7. Golgi apparatus
➢ Packaging plant of the cell/modification of proteins as well as carbohydrates
➢ Principal director of mammalian traffic in the cell

8. Cell membrane
➢ Controls entry into and out of the cell
➢ regulatory

*** activity on
1. A One-Page Journal writing on “Life Ceases Without Molecules”
Questions
1. Identify the functional groups present in each of the following biomolecules:
a. Fatty acids
b. Sugars
c. Nucleotides
d. Proteins

2. The outer boundary of most eukaryotic cells is a cell membrane, while the outer boundary of a
prokaryotic cell is a cell wall. How do these structures differ in function?

3. Both peroxisomes and mitochondria consume molecular oxygen. How do their functions differ?

4. What intermolecular force of attraction occurs between the following molecules and ions?
a. Water and ammonia
b. Lactate and ammonium ion
c. Benzene and octane
d. Chloroform and diethylether

5. Tyrosine, with the structure given below, is an amino acid. Encircle the part/parts in the molecule that can
form H-bonds with water.