Chapter 1

Biochemical
Characteristic of
Living Matter
Objectives
 Identify and describe the functions of the cell
 Describe the structure and functions of the different parts
of the cell
 Enumerate the differences between a plant and a animal
cell, and prokaryotic and eukaryotic cell
 Describe cell specialization and list the levels of
organization in organisms from the simplest to the most
complex
 Discuss on the overview of the four biomolecules
What is Biochemistry

 Biochemistry, study of the chemical

substances and processes that occur in
plants, animals, and microorganisms.

 Biochemistry is the application of

chemistry to the study of biological
processes at the cellular and molecular
level.
Cell Structure and Function
THE CELL

 Cells are the basic structural & functional units of an

organism.
 They are highly organized and constant source of energy is
required to maintain the ordered state.
 Certain important rxns E.g. Cellular respiration (
Glycolysis, Kreb Cycle and Electron Transport Chain)
 Two major group of cell
 1. Eukaryote include most other cells & have a nucleus and
membrane-bound organelles (plants, fungi, & animals).
 These cells have a membrane bound nucleus; and hereditary
material is found inside the nucleus.
 Ribosome’s are of large size and are present in endoplasmic
reticulum free in cytoplasm.
 Cellulose is present in cell wall of plant cells. The cell wall of
most of fungi is composed of chitin.
 These cells are complex and of larger size (Average diameter
10-100nm). Contain 3 basic cell structures:
• Nucleus
• Cell Membrane
• Cytoplasm with organelles
 Two major group of cell
 2. Prokaryote include bacteria & lack a nucleus or
membrane-bound structures called organelles.
 The organisms made of prokaryotic cells are called
prokaryotes e.g. bacteria and cyanobacteria.
 These cells lack a membrane bound nucleus.
 The hereditary material (DNA) is found in
cytoplasm.
 Ribosome’s are of small size in and freely scattered
Nucleoid region contains the DNA
cytoplasm. •Cell membrane & cell wall
• Contain ribosomes (no membrane)
 Cellulose is absent in cell wall, rather it is made up to make proteins in
of peptido-glycan or murrain. their cytoplasm

 These cells are simple and of smaller size (average

diameter 0.5 – 10 nm)
Structure & Functions of a cell

A cell has three major components:

1. Cell membrane (plasma membrane)
2. Cytoplasm with its organelles
3. Nucleus
 Cell Membrane/Plasma membrane

- is a biological membrane that

separates the interior of all cells from
the outside environment (the
extracellular space) which protects
the cell from its environment.
-A lipid/protein/carbohydrate complex,
providing a barrier and containing
transport and signaling systems.
Cell Membrane/Plasma membrane

 Function:
 Protective Function
The cell membrane protects the cytoplasm and the
organelles of the cytoplasm.
 Maintenance of shape and size of the cell
 Serves as a semipermeable membrane
-The cell membrane permits only some substances to
pass in either direction, and it forms a barrier for other
substances.
 Cytoplasm and its Organelles

 Cytoplasm – is the internal volume bounded by

the plasma membrane.
Cytosol – clear fluid portion of the cytoplasm
which particles are suspended.
-important organelles that are suspended in the
cytoplasm are:
1. Endoplasmic reticulum 5. Mitochondria
2. Golgi apparatus 6.Vacoule
3. Lysosomes 7. Cytoskeleton
4. Peroxisome 8. Nucleus
1. Endoplasmic reticulum
Rough endoplasmic reticulum (RER)
A network of interconnected
membranes forming channels
within the cell. Covered with
ribosomes (causing the "rough"
appearance) which are in the
process of synthesizing proteins
for secretion or localization in
membranes.

Ribosomes
Protein and RNA complex
responsible for protein synthesis
Smooth Endoplasmic Reticulum (SER)

Smooth endoplasmic reticulum

(SER)
A network of interconnected
membranes forming channels
within the cell. A site for
synthesis and metabolism of
lipids. Also contains enzymes
for detoxifying chemicals
including drugs and pesticides.
Golgi Apparatus
Golgi apparatus
A series of stacked membranes.
Vesicles (small membrane
surrounded bags) carry materials
from the RER to the Golgi
apparatus. Vesicles move between
the stacks while the proteins are
"processed" to a mature form.
Vesicles then carry newly formed
membrane and secreted proteins
to their final destinations including
secretion or membrane
localization.
Lysosome

Lysosymes
A membrane bound organelle
that is responsible for
degrading proteins and
membranes in the cell, and
also helps degrade materials
ingested by the cell.
Peroxisome
Peroxisomes or
Microbodies
Produce and degrade
hydrogen peroxide, a
toxic compound that
can be produced during
metabolism.
Mitochondria
-Surrounded by a double
membrane with a series of
folds
called cristae. Functions in
energy production through
metabolism. Contains its own
DNA, and is believed to have
originated as a captured
bacterium.
“powerplant of the cell”
Vacoules
-Membrane surrounded "bags"
that contain water and storage
materials in plants.

-store large quantities of Secondary

metabolites.

-secondary metabolites include:

ergot alkaloids, antibiotics,
naphthalenes, nucleosides,
phenazines, quinolines, terpenoids,
peptides and growth factors.
Cytoskeleton

Arrays of protein filaments

in the cytosol. Gives the
cell its shape and provides
basis for movement.

E.g. microtubules, actin

filament and intermidiate
filaments
Nucleus
-Double membrane
surrounding the chromosomes
and the nucleolus. Pores allow
specific communication with
the cytoplasm.

The nucleolus is a site for

synthesis of RNA making up
the ribosome
Biomolecules

 Biomolecules are the most

essential organic molecules, which are involved in
the maintenance and metabolic processes of living
organisms.
 Four (4) major types of biomolecules
1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic acids
1. Carbohydrates / Saccharides

 are chemically defined as

polyhydroxy aldehydes or ketones or
compounds which produce them on
hydrolysis. In layman’s terms, we
acknowledge carbohydrates as sugars
or substances that taste sweet.
 They contain the elements carbon,
hydrogen and oxygen.
 CH2O n is the empirical formula of
many simple carbohydrates.
 Function of Carbohydrates
 Source of enery for living beings, e.g. Glucose
 Storage form of energy, e.g. Glycogen in animal tissue and
starch in plants.
 Serve as structural component, e.g. Glycosaminoglycans in
humans, cellulose in plants and chitin in insects.
 Constituent of nucleic acids RNA and DNA, e.g. Ribose and
Deoxyribose sugar.
 Involved in detoxification, e.g. Glucutonic acid.
Classification of Carbohydrates
 Classified into three groups:
a. Monosaccharides
b. Oligosaccharides
c. Polysaccharides

1. Monosaccharides “simple sugars”

- They consist of a single polyhydroxy aldehyde or
ketone and thus cannot be hydrolized into a simpler
form.
 A. Monosaccharides
-they can be subdivided into two groups:
1. Depending on the number of carbon atoms they possess, e.g.
- Trioses - contains 3 carbon (C3H6O3)
- Tetroses – contains 4 carbon (C4H8O4)
- Pentoses – contains 5 carbon (C5H10O5)
- Hexoses – contains 6 carbon (C6H12O6)
- Heptoses – contains 7 carbon (C7H14O7)
2. Depending upon the functional aldehyde (CHO) or ketone (C=O)
group present:
- Aldoses
- Ketoses
B. Oligosaccharides
 Oligo means “few”
 Consist of a short chain of monosaccharide units ( 2-
10 units), joined together by a characteristic bond
called “glycosidic bond”.
 Types of oligosaccharide
1. Disaccharide
2. Trisaccharide
3. Tetrasaccharide
4. Pentasaccharide
1. Disaccharide

 Compose of two monosaccharide

Example of disaccharide
1. Maltose = Glucose + Glucose
2. Lactose = Glucose + Galactose
3. Sucrose = Glucose + Fructose
2. Trisaccharide
 -Consist of 3 monosaccharide
 Example
1. Raffinose = Glucose + Galactose + Fructose

3. Tetrasaccharide
- Consist of 4 monosaccharide
Example
1. stachyose = 2 molecules of Galactose + Glucose +
Fructose
4. Pentasaccharride

- Consist five (5) monosaccharide

Example
1. Verbascose = 3 Molecules of Galactose +
Glucose + Fructose
C. Polysaccharides
 Poly means “many”
 Polysaccharides are polymers consisting of hundreds or
thousands of monosaccharide units.
 They are also called as glycans or complex carbohydrates.
 They may be linear (cellulose) or branched (glycogen) in
structure.
-two (2) types of Polysaccharide
1. Homopolysaccharides (homoglycans)
2. Heteropolysaccharides (heteroglycans)
1. Homopolysaccharide

 Made up of several units of one and the same type of

monosaccharide units
 They serve as storage form of monosaccharide
 Example
- Starch
- Dextrins
- Glycogen
- Inulin
- Cellulose
2. Heteropolysaccharide (Heteroglycans)
 They contain two or more different types of monosaccharide
units or their derivatives.
 They are present in human beings is glycosaminoglycans (GAGs)
also known as mucopolysaccharide
 Example of GAGs
- Heparin
- Chondritin Sulfate
- Hyaluronic acid
- Dermatan sulfate
- Keratan sulfate
- Blood group polysaccharides
 2. Lipids
 Lipids are organic substances that are insoluble in water but soluble
in nonpolar solvents and solvents of low polarity, such as diethyl
ether.
 Functions of Lipids
Lipids serve as:
 Storage form of energy: The fats and oils are used almost
universally as stored forms of enegy in living organisms.
 Structural components of membranes, e.g. phospholipids,
glycolipids, and sterols. Cholesterol, a sterol, is a precursor of many
steroid hormones, vitamin D is also an important component of
plasma membrane.
 Chemical messengers: The primary messengers, such as steroid
hormones, deliver signals from one part of the body to another part.
Secondary messengers, such as prostaglandins and thromboxanes,
mediate the hormonal reponse.
 Important dietary constituents because of the fat soluble vitamins
and essential fatty acids which are present in the fat of natural
foods. Lipids also help in absorption of fat soluble vitamins (A,D,E,
and K). They act as a solvent for the transport of fat soluble
vitamins.
Classification of lipids

 Three (3) classification of lipids

1. Simple lipids
2. Complex or compound lipids
3. Derived lipids
Simple lipids
- They are fatty acids with various alcohols
- 2 types of simple lipids
1. Neutral fats/triglycerides – e.g. Veg.oils, corn oil,
coconut oil
2. Waxes – Lanolin, Bees-wax and spermacetic oil (from
whales)
2. Complex lipids

 Are esters of fatty acids, with alcohol containing

additional (prosthetic) groups.
Types of complex lipid according to type of prosthetic group
present
1. Phospholipids
2. Glycolipids
3. Lipoproteins
3. Derived Lipids
 -these are the products obtained after the hydrolysis of
simple and compound lipids.
 Example
 Fatty acids
 Steroids
 Cholesterol
 Lipid soluble vitamins and hormones
 Ketone bodies
3. Proteins
 Most abundant macromolecules in living
cells.

 Amino acids are the building blocks of

protein.

 Are linear chains of amino acids that are

linked together by covalent, peptide
bonds.

 There are 20 amino acids involved in the

formation of proteins.

 Functions as transport proteins,

structural proteins, enzymes, antibodies,
cell receptors.
 Amino acids are classified as:
1. Neutral amino acids –
-Glycine, Alanine, Valine, Leucine,
Isoleucine, Serine,Threonine,
Cysteine, Methionine, Proline,
Phenylalanine, Tyrosine, Tryptophan,
Aspargine, Glutamine

2. Acidic amino acids – Aspartic acid,

Glutamic acid

3. Basic amino acids – Lysine,

Arginine, Histidine
 4. Nucleic Acids
 Nucleic acids are polymers made of monomers called
nucleotide; linked by phosphodiester bond, therefore they
are called polynucleotides.
 Composing elements: C, H , O, P, N
 Two types of nucleic acids
1. Deoxyribonucleic acid or DNA
2. Ribonucleic acid or RNA
 Nucleotide
Each nucleotide consists of three components:
1. Nitrogenous group – Purine and Pyrimidine
2. Pentose sugar - DNA (deoxyribose) and RNA (ribose).
3. Phosphate group
 DNA contains the purine bases:
adenine (A) and guanine (G) and
pyrimidine bases: cytosine (C) and
thymine (T).
 RNA contains uracil (U) instead of
thymine.
 DNA is organized into two strands by
the pairing of bases A to T and G to
C, on complementary strands. In
contrast to DNA, RNA is single
stranded structure.
 The three major types of RNA are
mRNA, tRNA and rRNA, all are
involved in some aspects of protein
synthesis.
 Thank you
Properties and
Biological
Importance of
Water
Objectives
 Discuss the chemical and biological properties of water and of
the importance of weak, noncovalent interactions in
biochemistry
 Explain how water functions as a solvent
 Describe how the ionization of water affects the structures
and actions of biomolecules in the cells
 Calculate the pH, pOH in the solution
 Describe how buffers function to maintain a constant
physiological pH
WATER
 Is a substance composed of the chemical elements
Hydrogen (H) and Oxygen (O).
 It is tasteless and odorless liquid at room
temperature.
 It is one of the most plentiful & essential compound.
 Occur in three (3) states :
1. Gas
2. Liquid
3. Solid
http://www.ufmcpueblo.com/wp-content/uploads/2019/02/drinking-bottled-
water.jpg
Importance of water

 Water gets rid of waste through urination,

perspiration and bowel movements.
 Keeps our temperature normal.
 Lubricates & cushions joints
 Protects sensitive tissues.
Water consumption
 8 glasses of water a day.
 We can survive 3 weeks without food but without drinking water will last only for 3 days.

 Dehydration – consuming too little of water; occurs when you use or lose more fluid than you
take in, and your body doesn't have enough water and other fluids to carry out its normal
functions.
 Water Intoxication- consuming too much of water; is a rare phenomenon that occurs due to an
excessive intake of water, and when the amount of water intake exceeds that of water excretion
in the kidney. It may lead to Hyponatremia.
 Hyponatremia is an electrolyte imbalance indicated by a lower sodium level in the blood.
Properties of Water

 Water is polar
 Water is an excellent solvent.
 Water has high heat capacity.
 Water has high heat of vaporization.
 Water has cohesive and adhesive properties.
 Water is less dense as a solid than as a liquid.
 Water is polar.
 Water molecules are polar, with
partial positive charges on the
hydrogens, a partial negative
charge on the oxygen, and a bent
overall structure. This is because
oxygen is more electronegative,
meaning that it is better than
hydrogen at attracting electrons.
Water is an excellent solvent.
 Water has the unique ability to
dissolve many polar and ionic
substances. This is important to all
living things because, as water
travels through the water cycle, it
takes many valuable nutrients
along with it.
 Example
- a solution of salt in water
Water has high heat capacity
 It takes a lot of energy to raise the
temperature of a certain amount of water by a
degree, so water helps with regulating
temperature in the environment. For example,
this property allows the temperature of water
in a pond to stay relatively constant from day
to night, regardless of the changing
atmospheric temperature.
 Water has high heat of vaporization

 Humans (and other animals that sweat) use

water’s high heat of vaporization to cool off.
Water is converted from its liquid form to
steam when the heat of vaporization is
reached. Since sweat is made mostly of water,
the evaporating water absorbs excess body
heat, which is released into the atmosphere.
This is known as evaporative cooling.
 Water has cohesive and adhesive
properties.
 Water molecules have strong cohesive forces due to their
ability to form hydrogen bonds with one another.
 Cohesive forces are responsible for surface tension, the
tendency of a liquid’s surface to resist rupture when placed
under tension or stress.
 Adhesive properties that allow it to stick to substances other
than itself.
 These cohesive and adhesive properties are essential for fluid
transport in many forms of life. For example, they allow
nutrients to be transported to the top of a tree against the
force of gravity.
Water has cohesive and adhesive
properties.
 Water is less dense as a solid than as a
liquid.
 Water is less dense as a solid than as a
liquid. As water freezes, the molecules
form a crystalline structure that spaces
the molecules further apart than in liquid
water. This means that ice is less dense
than liquid water, which is why it floats.
 This property is important, as it keeps
ponds, lakes, and oceans from freezing
solid and allows life to continue to thrive
under the icy surface.
 Common mistakes and misconceptions
 Water dissolves everything because it is the “universal
solvent." Water has the ability to dissolve many substances
but the term “universal solvent" is misleading. Water is
able to dissolve other polar molecules and ions, such as
sugars and salts. However, nonpolar molecules like oils lack
partial positive or partial negative charges, so they are not
attracted to water molecules. This is why nonpolar
substances like oil remain separate when added to water.
 Acid-Base Balance
 Water is used to reduce or increase pH levels.
What is pH?
- “power of Hydrogen” ; is an important quantity that reflects the chemical
conditions of a solution. The pH can control the availability of nutrients,
biological functions, microbial activity, and the behavior of chemicals. pH needs
to be maintain in humans in order to maintain homeostasis
 pH 7.0 = neutral
 pH below 7.0 = acidic
 pH above 7.0 = basic
 Buffers: chemicals that regulate pH change
What is an acid?
- An acid is a substance that
donates protons (in the
Brønsted-Lowry definition)
or accepts a pair of valence
electrons to form a bond (in
the Lewis definition).

What is base?
A base is a substance that
can accept protons or
donate a pair of valence
electrons to form a bond.
Calculation of pH
To calculate the pH of an aqueous solution you need to
know the concentration of the hydronium ion in moles
per liter (molarity). The pH is then calculated using
the expression:
FORMULA : pH = - log [H3O+]

Example: 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. Thus:
pH = - log (0.0025) = - ( - 2.60) = 2.60
Calculating the Hydronium Ion
Concentration from pH
The hydronium ion concentration can be found from the pH by the reverse
of the mathematical operation employed to find the pH.
[H3O+] = 10-pH or [H3O+] = antilog (- pH)

Example: What is the hydronium ion concentration in a solution that has a

pH of 8.34?

8.34 = - log [H3O+]

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

On a calculator, calculate 10-8.34, or "inverse" log ( - 8.34).

Calculating pOH
To calculate the pOH of a solution you need to know the
concentration of the hydroxide ion in moles per liter
(molarity). The pOH is then calculated using the
expression:

pOH = - log [OH-]

Example: What is the pOH of a solution that has a

hydroxide ion concentration of 4.82 x 10-5 M?
pOH = - log [4.82 x 10-5] = - ( - 4.32) = 4.32
Calculating the Hydroxide Ion
Concentration from pOH
The hydroxide ion concentration can be found from the pOH by the reverse
mathematical operation employed to find the pOH.
[OH-] = 10-pOH or [OH-] = antilog ( - pOH)

Example: What is the hydroxide ion concentration in a solution that has a pOH
of 5.70?
5.70 = - log [OH-]
-5.70 = log[OH-]
[OH-] = 10-5.70 = 2.00 x 10-6 M
On a calculator calculate 10-5.70, or "inverse" log (- 5.70).
Relationship Between pH and pOH

The pH and pOH of a water solution at 25oC are related by the following
equation.
pH + pOH = 14

If either the pH or the pOH of a solution is known, the other can be

quickly calculated.
Example: A solution has a pOH of 11.76. What is the pH of this
solution?
pH = 14 - pOH = 14 - 11.76 = 2.24
 Buffer
 A buffer is a solution that changes pH only slightly when small
amounts of a strong acid or a strong base are added
 They are used as a means of keeping pH at a nearly constant
value in a wide variety of chemical applications.
 Buffers work by neutralizing any added acid (H+ ions) or base
(OH- ions) to maintain the moderate pH, making them a weaker
acid or base.
 Buffers are broadly divided into two types
 acidic buffers
 alkaline buffer
 acidic buffers - Acidic buffers are solutions that have a pH below 7
and contain a weak acid and one of its salts.

 For example, a mixture of acetic acid and sodium acetate acts as

a buffer solution with a pH of about 4.75

 alkaline buffer - An alkaline buffer solution has a pH greater than

7;are commonly made from a weak base and one of its salts.
 For Example, a mixture of ammonia solution and ammonium
chloride solution. If these were mixed in equal molar proportions,
the solution would have a pH of 9.25.
 Assignment
read chapter 2 STRUCTURE AND FUNCTION
OF BIOMOLECULE: Proteins
 Activity2
Calculate the pH and pOH of the following. (2 points
each).
1. Blood has a (H+) = 5x10-8. Calculate its pH.
2. What is the pH of 0.0485 M HCl solution?
3. What is the pOH of 0.0213 M HCl Solution?
4. What is the pH of 5.50x1o-3 M KOH solution?
5. What is the pH of a 5.3 x 10-5 M NaOH solution?
(Problem 4 & 5 Hint: this is a basic solution –
concentration is of OH - )