BSES 27 BIOCHEMISTRY

Biochemistry is the branch of science dedicated to the study of

chemical processes within a cell.

 The study of molecules and chemical reactions of life

 Uses principles of Chemistry to explain Biology at the
molecular level
 The application of Chemistry to the study of biological
processes at the cellular and molecular levels

Goals of Biochemistry

This field of chemistry seeks to describe the following:

1. Structure of the components of living matter and the

relationship of biological function to chemical structure
2. Organization and interaction of these compounds
3. Function of living matter in molecular terms
4. The totality of chemical reactions that occur in living
matter

The Cell

 The cell is the basic structural and functional unit of all

known living organisms.
 It is the smallest unit of life that is classified as a living
thing and is often called the building block of life.
 Organisms can be classified as unicellular (consisting of a
single cell; including most bacteria) or multicellular
(including plants and animals). Human contain about 10
trillion (1013) cells.
 The cell was discovered by Robert Hooke in 1665
 The cell theory, first developed in 1839 by Matthias
Jakob Schleiden and Theodor Schwann, states that:
o All organisms are composed of one or more cells;
o That vital functions of an organism occur within
cells;
o That all cells contain hereditary information
necessary for regulating cell functions and for
transmitting information to the next generation of
cells.
The Cell

Metabolism overview
The Cell

The building and breaking down of life-sustaining chemicals

within an organism is known as Metabolism.

Three Main Purposes of Metabolism

1. The conversion of food to energy to run cellular processes.

 2. The conversion of food/fuel to building blocks for the
production of primary metabolites, such as proteins,
lipids, nucleic acids, and other secondary metabolites.
3. The elimination of waste products. These enzyme-
catalyzed reactions allow organisms to grow and
reproduce, maintain their structures, and respond to their
environments.

Metabolic Reactions may be categorized as:

 Catabolic -the breaking down of compounds (for

example, the breaking down of proteins into amino acids
during digestion)
 Anabolic – the building up (synthesis) of compounds
(such as proteins, carbohydrates, lipids, nucleic acids).

Catabolism Releases energy

Anabolism Consumes energy
Cellular Design and Blueprint of Life

 The design for a cell mostly resides in the blueprint for the
cell, the genetic code, which is comprised of
deoxyribonucleic acid (DNA) housed in the cell nucleus
and a small amount in the mitochondria.
 DNA blueprint must be read out or transcribed into
ribonucleic acid (RNA) and then translated to proteins by
ribosome structures, which themselves were encoded by
the DNA and contain a combination of RNA and protein
subunits.
 The genetic code has the master plan that determines the
sequence of all cellular proteins, which then perform
almost all other activities in the cell, including enzymatic
functions, motility, architectural structure, transport, etc.
In contrast to DNA, RNA and protein polymers, the
formation of the other two major macromolecules
(carbohydrates and lipids) are not driven by such template
but rather by the enzymes that catalyzes the synthesis.
Biomolecules

 Essential elements that the body needs

 Contain carbon
 27/90 natural elements are found to be essential
components in various living organisms
 4/47 essential elements: found to be most abundant
comprises 99% of the cell mass (C,H,O,N)

CARBON
HYDROGEN
Composition of NITROGEN
Biomolecules OXYGEN
PHOSPHORUS
SULFURE

 The CHNOPS elements come together to form

biomolecules, the molecules found in all of the living
organisms on earth.
  Carbon, hydrogen, nitrogen, oxygen, phosphorus, and
sulfur are the six most important chemical elements
whose covalent combinations make up most biological
molecules on Earth. All of these elements are non metal.
 Carbon provides the structural framework for
biomolecules.
 Hydrogen, nitrogen, and oxygen are common in living
organisms because they bond easily with the carbon and
are abundant in nature.

Properties of C,H,N,O

 Readily form covalent bond by electron pair sharing

 Versatile for chemical bonding
 The lightest elements capable of forming very strong
covalent bonds

Level of Structural Organization in Living Matter

1. Atom 6. Tissue
2. Molecule 7. Organ
3. Macromolecule 8. Organ System
4. Organelle 9. Organism
5. Cell

Water

 Represent the continuous phase of

living organism
  Bland or inert liquid that makes up 70 to 90% of most
forms of life
 Space filler in living organism
 A nonlinear molecule whose bond angle is 104.50

Biochemical Properties of Water

 Polarity
 Hydrogen Bonding
 Cohesiveness

Polarity

 Polarity is when an entity contains two distinct and

opposite poles that can either attract or repel each other.

Why is Water a Polar Molecule?

 Water is polar because it has bent geometry that places

the positively-charged hydrogen atoms on one side of the
molecule and the negatively-charged oxygen atom on the
other side of the molecules.
 The net effect is a partial dipole, where the hydrogens
have a partial positive charge and the oxygen atom has a
partial negative charge.
 The reason water is bent is because the oxygen atom still
has two lone pairs of electrons after it bonds with
hydrogen. These electrons repel each other, bending the
O-H bond away from the linear angle.

Hydrogen Bonding

 Is the electrostatic force of

attraction between a hydrogen
atom (which is covalently
bonded to a small and highly
electronegative atom) and the
lone pair of electrons of
another small and highly
electronegative atom.

Cohesiveness
  Cohesion is the attraction of molecules for other
molecules of the same kind.
 Adhesion is the attraction between water and other
molecules.

Capillary Action

The cohesive and adhesive

properties of water allow for
another interesting phenomenon
– capillary action. If you place a
thin straw in a glass of water, the
water will be attracted to it. At
the same time, however, the
water wants to stick together with other water molecules. If the
adhesive attraction between the water and straw is stronger than
the water’s cohesive attraction with itself, the water will move up
the straw unassisted. This is how plants bring water from the soil
up into their leaves.

Solution Concentration
In chemistry, the
concentration of a solution
is the quantity of a solute
that is contained in a
particular quantity of
solvent or solution.
Molarity

 The most common unit of concentration

 The molarity (M) is defined as the number of moles of
solute present in exactly 1 L of solution. It is, equivalently,
the number of millimoles of solute present in exactly 1 mL
of solution:

n
M=
v
Where:

M is the molality of the solution that is to be calculated

 n is the number of moles of the solute

v is the volume of solution given in terms of liters

Sample problems:

1. A solution is prepared by bubbling 1.56 grams of

hydrochloric acid in water. Here, the volume of the solution
is 26.8 mL. Calculate the molarity of the solution.

Answer: molarity of the solution is 1.59 M

Solution:

(a) Find the molar mass of HCL: 1.01 g/mol (H) + 35.45 g/mol
(Cl) = 36.46 g/mol

(b) Use the molar mass to convert grams of HCL to moles:

1.56 grams of HCL x (1 mol HCL / 36.46 g HCL) = 0.0428
moles HCL

(c) Convert the volume to liters: 26.9 mL x (1 L / 1000 mL) =

0.0268L

(d) Calculate the molarity (M= n/v); M = 0.0428 moles HCL /

0.0268 L = 1.60 M
2. A solution prepared using 15 g of sodium sulphate. The
volume of the solution is 125 ml. Calculate the molarity of
the given solution of sodium sulphate.

Answer: Molarity of the solution given is 0.85 M.

Solution:

(a) Find the molar mass of sodium sulfate (Na2SO4)

 Na = 22.99 g/mol x 2 = 45.98 g/mol

 S = 32.07 g/mol x 1 = 32.07 g/mol
 O = 16.99 g/mol x 4 = 64.00 g/mol
 Total molar mass = 45.98 + 32.07 + 64.00 =
142.05 g/mol

(b) Calculate the moles of sodium sulfate:

 Moles = mass / molar mass

 Moles = 15 g / 142.05 g/mol
 Moles = 0.106 moles

(c) Convert the volume to liters:

 Liters = milliliters / 1000

 Liters = 125 mL / 1000
 Liters = 0.125 L

(d) Calculate the molarity:

 Molarity = moles / liters

 Molarity = 0.106 moles / 0.125 L
 Molarity = 0.848 M

3. Another solution commonly used for intravenous injections

is normal saline, a 0.16 M solution of sodium chloride in
water. Calculate the mass of sodium chloride needed to
prepare 250 mL of normal saline solution.

Answer:

Solution: The mass of sodium chloride needed is 2.34 g

(a) Convert the volume to liters:

 250 mL x (1L / 1000 Ml) = 0.250 L

 (a) Calculate the moles of NaCl needed:

 Molarity = moles / Liter

 Moles = Molarity x Liter
 Moles = 0.16 M x 0.250 L
 Moles = 0.04 moles

(c) Calculate the molar mass of NaCl

 Na = 22.99 g/mol
 Cl = 35.45 g/mol
 Total = 22. 99 + 35.45 = 58.44 g/mol

(d) Calculate the mass of NaCl needed:

 Mass = Moles x molar mass

 Mass = 0.04 moles x 58.44 g/mol
 Mass = 2.34 g

pH

 Qualitative measure of the strength of an acid or a base

solution
 Based on the concentration of the hydronium (or
hydrogen) ion in aqueous solution

Classification Relative Ion pH at 25 °C

Concentrations
ACIDIC [H+] > [OH-] pH < 7

NEUTRAL [H+] = [OH-] pH = 7

BASIC [H+] < [OH-] pH > 7

 The relationship between [H+] and pH values for several
common materials.

Example:

Label each solution as acidic, basic, or neutral based only on the

stated pH

1. Milk of magnesia, pH = Basic

10.5 Neutral
2. Pure water, pH = 7 Acidic
3. Wine, pH = 3.0

Measuring pH

Using pH meter Using pH paper

 Acid – blue litmus turns red
Base – red litmus turns blue

For dissociation of water,

K=¿ ¿
Where the brackets represent molar concentrations (strictly
speaking, molar activities) and K is the dissociation constant.

Since 1 mole (mol) of water weighs 18g, 1 liter (L) (1000g) of

water contains 1000 divided by 18 = 55.56 mol. Pure water thus
is 55.56 molar.
 pH = -log [H+]

pH = -log [H3O+]

We can also calculate the concentration of OH- ions by using the

pH equation and substituting [OH-] for the [H+]

pOH =−log ¿

Derive the relationship between pH and pOH

Examples

1. Find the pH of a 0.0025 M HCl solution. (The HCl is a

strong acid and is 100% ionized in water. The hydronium
ion concentration is 0.0025 M)

pH = -log [H3O+]
pH = -log (0.0025) = -(-2.60) = 2.60

2. What is the pOH of a solution that has a hydroxide ion

concentration of 4.82 x 10-5 M?

pOH = -log [OH-]

pOH = - log [4.82 x 10-5] = -(-4.32) = 4.32

3. What is the hydronium ion concentration in a solution that

has a pH of 8.34?

pH = -log [H3O+]
8.34 = -log [H3O+]
[H3O+] = 10-8.34 = 4.57 x 10-9 M

4. A Solution has a pOH of 11.76. What is the pH of this

solution?
 pH + pOH = 14
pH = 14 – pOH
pH = 14 -11.76 = 2.24

What is the pH of these solutions?

1. pOH = 5.55 8.45
2. [H3O+] = 10-11 M 11
3. [OH-] = 10-8 M 6

Buffer

 A system which tends to resist drastic change in pH on

addition of moderate strong acid or base.
 Consist of a mixture of a weak acid and its conjugate base.
 Phosphate buffer, bicarbonate buffer and protein buffer
are the three most important buffers in the body.