PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
UNIT 1
INTRODUCTION TO BASIC BIOCHEMISTRY
Introduction to Unit
The main purpose of this course is to give an understanding of the basic
principles and concepts of biochemistry in relation to agriculture thus the
name of the course – Agricultural Biochemistry. The main thrust of each
topic will be on biochemistry but will draw examples mainly from the field
of agriculture. Since biochemistry is the study of the biological processes
of life at the molecular level, this initial unit will expose students to some
key components or elements involve in biochemistry. It starts with the
description of cellular and organizational structure of eukaryotic and
prokaryotic cells, animal and plant cell, followed by water properties (the
main media for biochemical processes), types of chemical reactions,
acidity, alkalinity and buffers in aqueous solutions.
Learning Outcomes
At the end of this unit the students will be able to:
1. Have a general overview of the course
2. Describe the topics that will be discuss in this course
3. Differentiate animal and plant cell structures
4. Explain water properties and its relationship to chemical reactions
involving acids, bases and buffers
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
Main Points
1. Unit 1 is a basic introduction to biochemistry starting with the cellular
organization from eukaryote to prokaryote and differences between animal
cells, an understanding of water properties, different chemical bonding and
the basic explanation on acidity, alkalinity and buffers in aqueous
solutions. The students will learn the differences between eukaryote and
prokaryotes, animal and plant cell structure and appreciate the importance
of water as the main media for all biochemical reactions. In addition the pH
of an aqueous solution and how it affects biochemical reactions will also
be studied.
2. In Unit 2, you will learn about the structure and function of amino acids and
how amino acids are arranged to form polypeptides and then made into
proteins; different structures of the proteins will be described (primary,
secondary, tertiary and quarternary structures) and some examples of
proteins functions are explained using collagen, hemoglobin and
immunoglobin as examples.
3. Unit 3 will give you a description of the role of carbohydrates starting with
simple sugars which form monosaccharides. From monosaccharides,
several
sugars
are
put
together
to
form
polysaccharides thus forming the group of
oligosaccharides
and
polymers known as
carbohydrates.
4. Unit 4 will describe the structure and function of lipids which is formed from
fatty acids. The complex polymers of fatty acids which form triglycerides,
phospholipids, sphingolipids, wax, terpenes and steroids will also be
described. The function and structure of membranes will also be discussed
in this Unit 4. It will include description of lipid and protein bilayer, how
compounds and molecules are transported across membranes using
active and passive transport mechanisms.
5. In Unit 5, you will be taught about the structure and function of nucleic
acids, DNA and RNA which are the basic building blocks for genomic
functions of a cell. Genomic function and organization and a description of
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PJJ UPM / UPMET
information flow from genome to cellular functions will be explained. You
will also learn about the how genetic code is organized, how DNA
replicates and a trait is inherited and how mutations arise in an organism
which leads to different genotypes and phenotypes.
6. Topic of Unit 6 will focus on the function of enzymes which are biological
catalysts. You will learn about enzyme characteristics of an enzyme,
classification and nomenclature, kinetics, regulation of enzyme activities
and how an enzyme assay is conducted.
7. Bioenergetics will be the focus of Unit 7 in which description of energy
generation processes in the cells are discussed. This includes glycolysis
and fermentation, citric acid or tricarboxylic (TCA) cycle, gluconeogenesis
and the electron transport system. Mitochondria function and structure will
also be discussed.
8. Energy and photosynthate generation by plants will be introduced in Unit
8. You will discuss photosynthesis, phosphorylation, Kelvin cycle and how
photosynthesis is regulated under light dependent and light independent
phases.
9. In the final Unit 9, discussion will help you to discover what are hormones,
their effects on living cells and organisms, types of hormones, differences
between exocrine and endocrine glands and the regulation of hormone
reactions and mechanism.
TOPIC 1 : CELL ORGANIZATION
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
Main Points
1.1
The fundamental unit of all living organisms is the cell. Cells are the
component that make up the living organisms which can be unicellular
(single cell) or multicellular.
1.2
Cells are very tiny (size ranging from 0.1 um to 200 um) and if
observed under the microscope, the cellular structure can be classified
into two basic types i.e. eukaryote and prokaryote cells.
1.3
Prokaryote have a size range of diameter from 0.1 um to 50 um (but
the length can reach 0.5 mm) whereas eukaryote has a bigger size
range of 2 to 200 um. Bacteria and Archea represents prokaryotic cell
type where as fungi, algae and protozoa showed the eukaryotic cell
type. Multicellular organisms (plants and animals) are also made-up of
eukaryotic cells.
1.4
Structurally prokaryotes are simpler than eukaryotes. The most obvious
difference between these cell types is the absence of nucleus and
other cell organelles such as mitochondria and chloroplasts (plant and
algal cells) in the prokaryotes..
1.5
The prokaryotic cell can be presented by three main regions:
(a) presence of flagella or/and pili on the outside;
(b) cell is enclosed by a cell envelope and plasma membrane and
(c) a cytoplasmic area containing the chromosomic DNA. The DNA in
prokaryotes is usually arranged in a circular manner - nucleoid.
Some bacteria have extrachromosomal DNA known as plasmids.
1.6
In eukaryotic cells, the outside can be ciliated or flagellated. The cilia
functions as cellular sensor that coordinate signaling pathways.
Eukaryotes can move using the cilia or flagella.
1.7
The plasma membrane is similar to prokaryotes. Cell wall may be
present.
1.8
DNA which made-up the linear chromosomes surrounding histones are
typical of eukaryotes. They are enclosed within the nucleus and
membrane-bound within the cytoplasmic region. Mitochondria, Golgi
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apparatus, lysosomes, ribosomes, vesicles, endoplasmic reticulum are
some of the structures that may be present in the cytoplasm of
eukaryotes.
1.9
A typical representation of prokaryote and eukaryote cell (plant and
animal cell) is given below.
Prokaryote Cell
1.1
Although plant and animal cells are both eukaryotic cells, there are
several differences between the two. A plant cell typically have
chloroplasts, large vacuoles and cell wall which is usually absent in
animal cell. However, animal cell may contain microvilli, lysosomes and
lipid droplets which are not present in plant cells.
Eukaryote cells
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PJJ UPM / UPMET
Plant Cell
1.10
Animal Cell
The common organelles in both animal and plant cells include
nucleolus and nucleus, chromosomal material, smooth and rough
endoplastic reticulum, golgi complex, mitochondria, peroxisome,
vesicles and microtubules.
1.11
Cytoplasm is the interior part of eukaryotic cell surrounded by plasma
membrane excluding the nucleus. It includeorganelles such as
mitochondria and cytosol.
1.12
Cell/Plasma membrane is a semi-permeable barrier separating the
external and internal environment of the cell. Mainly consists of
proteins and complex polar lipids. The lipids exist as phospholipids in
the form of a fluid bilayer interspersed with membrane proteins and
glycoproteins. The membranes are heavily involved in transporting
nutrients and inorganic ions via several mechanisms.
1.13
Nucleus contains chromosomes which are the package of genetic
material containing heritable genetic information encoded by DNA
(deoxyribonucleic acid). The DNA material is binded by histones made
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of lysine- and arginine rich proteins giving structural stability and part of
it are subpackaged into a very dense structure known as the nucleolus.
1.14
There are two types of endoplasmic reticulum (ER):
1) Rough ER coated or embedded with ribosome are sites for protein
synthesis and membrane.
2)
Vesicles carrying newly synthesized protein are located in the
smooth ER (without ribosome).
Vesicles transport protein from ER to Golgi apparatus. The aqueous
portion of ER is known as lumen.
1.15
Golgi complex is a system consisting of membrane bound vesicles
which serve as the cell sorting and processing site.
-Located close to the nucleus and ER
-Receive vesicles from ER
-Process macromolecules
ready for delivery to
other cellular
compartments.
1.16
Mitochondria are organelles surrounded by two membranes - the inner
membrane is known as the matrix which contains many enzymes for
energy metabolism. The mitochondria is the main factory and ultimate
site for generating ATP (adenosine triphosphate) - the energy currency
of all cells from biofuel molecules.
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PRT3402- Agricultural Biochemistry
1.17
PJJ UPM / UPMET
Chloroplasts are the organelles in plants and algae that carry out
photosynthesis. It converts light energy into chemical energy in the
form of ATP. Its structure has some resemblance to a mitochondrion.
Within the chloroplasts are stacks of sac-like membrane structures
known as thylakoids.
1.18
Cytosol is the aqueous part of the cytoplasm excluding the organelles.
It contains many enzymes and is the main site for metabolism. It
contains cytoskeleton which maintains the shape of the cell. It also
contain storage granules such as glycogen (animal cell) and starch
(plant cell).
1.19
Lysosomes and vacuoles are specific vesicles in cells. Lysosomes are
found only in animal cells and contain enzymes that catalyse the
breakdown of proteins and nucleic acids. Vacuoles are membrane
bound vesicles containing fluid, normally found in mature plant cells.
Vacuoles can have waste materials such as excess nitrogenous
compounds.
1.20
Plant cell wall surrounds the plasma membrane. It is made of cellulose
and polysaccharides with repeating glucose units. It provides protection
against osmotic and mechanical rupture but yet porous to very small
molecules. The cell wall gave strength to the cells and plant tissues.
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
TOPIC 2 : WATER, BONDING AND ITS INTERACTIONS
Main Points
2.1
Water, H2O is the most abundant component of a cell and an indispensable
compound for life. Some molecules are attracted to water and interact
extensively with it whilst other molecules or part of it may avoid water
molecules and can be partially or completely insoluble.
2.2
Water is just not only a universal solvent but also provides an aqueous
environment for metabolic activity to function. It is an excellent solvent for both
ionic substances (e.g. salts) and non-ionic substances (sugars, simple
alcohols, amines, aldehydes and ketones). It is also a substrate for many
cellular reactions.
2.3
The processes of life require a wide variety of ions and molecules to move
about in proximity, that is, to be soluble in a common medium. Water serves
as the universal intracellular and extracellular medium, due to its remarkable
solvent ability. This ability is due to its dipolar (bipolar) nature and the
tendency to form hydrogen bonds.
2.4
In a water molecule, the oxygen nucleus attracts electrons stronger than the
single proton in the hydrogen nucleus, thus the oxygen is more
electronegative than the hydrogen atom creating an uneven distribution of
charges within each O-H bond. As a result oxygen will bear a partial negative
charge (δ-) and hydrogen bears a partial positive charge (δ+). This unequal
distribution of charge within a bond is known as dipole and the bond is said to
be polar.
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PRT3402- Agricultural Biochemistry
2.5
PJJ UPM / UPMET
A polar bond is a covalent bond in which the electrons are shared unequally
(e.g. H2O) whilst a non-polar bond is when the bondings electrons are equally
shared (CH4). Polarity is governed by the polarity of its covalent bonds and
geometry of structure. A water molecule is V-shaped with and angle of 104.5o
between the two O-H bonds. This arrangement of the polar O-H bonds
creates a permanent dipole.
2.6
Covalent bonds are the forces that hold atoms together as molecules e.g. the
two O-H bonds in water molecule. Non-covalent interactions or non-covalent
bonds are weak interactions between ions, molecules, and parts of molecules.
They help shape individual molecules and groups of molecules and ions, but
are weak enough to be continually broken and re-formed. Some of the most
important covalent bonds in biology such as C-C and C-H have bond energies
in the range of 300-400 kJ/mol.
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PRT3402- Agricultural Biochemistry
2.7
PJJ UPM / UPMET
Hydrogen bonding is the interaction of a hydrogen atom that is covalently
bonded to one electronegative atom with a second electronegative atom. It
can also be described as an interaction of a covalently bonded hydrogen atom
on a donor group (-OH) and a pair of non-bonded electrons on an acceptor
group,
. The atom which is covalently bonded to hydrogen is the
hydrogen bond donor and the atom with the non-bonded electron pair is the
hydrogen bond acceptor.
2.8
Hydrogen bonds provide forces that help stabilize the structures of
macromolecules, such as DNA and proteins, give a molecule like water its
unusual chemical characteristics for its size and the hydrogen bonds of water
also assist in solubilizing polar compounds.
2.9
The electron arrangement of a single water molecule is shown below. Two of
the outer six electrons of the oxygen atom are involved in bonding to the
hydrogens. The other four electrons exist in non-bonded pairs, which are
excellent hydrogen bond acceptors. The OH groups in water are strong
hydrogen bond donors. Each water molecule is simultaneously a hydrogen
bond donor and a hydrogen bond acceptor, and a sample of water is a
dynamic network of H-bonded molecules. Due to this the boiling point of water
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PJJ UPM / UPMET
(100oC) is high despite the relatively small molecular weight because of the
strong tendency to form hydrogen bonds between the water molecules.
2.10
Substances that readily dissolve in water are hydrophilic (water-loving).
Hydrophilic molecules are also ionic and engage in hydrogen bonding. They
are either soluble in water or at least wettable.
2.11
The solubility of NaCl in water (hydration) is shown below. Each sodium ion
(Na+) and chloride ion (Cl-) will be surrounded by water molecules.
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PRT3402- Agricultural Biochemistry
2.13
PJJ UPM / UPMET
Molecules that are readily soluble in water (e.g. sugar or glucose) have
charged parts that are attracted to the charges within the water molecule. The
presence of polar molecules will attract water molecules and the molecules,
initially in crystal form will go into solution. It remains in solution because the
glucose molecules are surrounded by water molecules. The group of water
molecules surrounding another molecule is known as hydration shell.
A glucose molecule in solution being surrounded by water molecules forming a
hydration shell.
2.14
Hydrophobic (water-hating) molecules as opposed to hydrophilic substances
are non-ionic and non-polar, not wettable and do not readily dissolve in water.
They form a cage-like structure, whereby the water molecules ‘trapped’ the
hydrophobic molecule.
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PJJ UPM / UPMET
A hydrophobic molecule ‘trapped’ in a cage-like structure of water molecules.
2.15
Other properties of water that takes advantage of the unique characteristics of
water molecule and hydrogen bonding includes:
a. a universal solvent
b. occurs in three physical states – gas (steam), liquid and solid (ice)
c. capillary action due to high surface tension
d. absorb heat due to high specific heat index
2.15
Amphiphatic molecules or compounds have both hydrophobic and hydrophilic
parts which are usually at opposite ends. Many biological compounds
exhibited this property as indicated below.
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
TOPIC 3 : ACID, BASE, pH and BUFFERS
3.1
The following table gives a definition of acid and base which are very
important considerations in any biochemical reaction in living organisms. The
biochemical behavior of many biological compounds depend on their acidbase properties since they have functional groups that react with (donate or
accept) H+ ion.
ACID
BASE
Definition
Is a proton (H+) donor
Is a proton acceptor,
Properties
Tastes sour (vinegar –
Tastes bitter
acetic acid, fruit juices-
Turns litmus paper blue
citric acid)
Feel soapy
Turns litmus paper red
React with acids to form
Concntrated acid burns
salts
skins
React with acids to form
salts
Strong
Examples:
Examples:
HCl - hydrochloric acid
NaOH - sodium hydroxide
H2SO4 - sulfuric acid
KOH - potassium
HNO3 - nitric acid
hydroxide
HClO4 - perchloric acid
Ca(OH)2 - calcium
hydroxide
Strong acids ionize
completely in water
Strong bases completely
forming H+ and an anion:
disassociate in water into
HCl (aq) → H+(aq) + Cl-
the cations and OH-:
(aq)
NaOH(s) → Na+(aq) +
OH-(aq)
Weak
hydrofluoric acid - HF
Ammonia - NH3,
acetic acid - CH3COOH.
diethylamine (CH3CH2)2NH.
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Partially dissociates in
Ionize partially in water to
water to give H+ and the
OH- and its cations.
anion.
HF (aq)
H+ (aq) + F-
NH3 (aq) + H2O (aq)
(aq)
3.2
NH4+ (aq) + OH- (aq)
Acid and base will react in a neutralization reaction to form salt:
Acid + base → salt + water
(HCl (aq) + NaOH(aq) → NaCl(aq) + H2O(l)
The following equation will give an indication of acidity or basicity of a
solution.
pH = - log10 [H+],
[H+] = 1 x 10-x
pH = x.
3.3
Substances are considered acidic, basic and neutral solutions based on the
pH values. It is acidic if the pH is less than 7, basic if it is more than 7 and
neutral if it is equal to 7. The ph scale is indicated below:
3.4
Water is amphoteric meaning that it can act as an acid or as a base. Water
behaves as acid: NH3 + H2O
base: HCl
+ H2O →
base: H2O + H2O
3.5
H3O+
→
NH4+
+
OH-. Water acting as a
+ Cl-. Water acting as both acid and
H3O+ + OH-
The dissociation constant of water will show that pH of water is equivalent to
7.
Kw = [H3O+] [OH-] = [H+][OH-]
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Kw = 1.0 x 10 -14
[H3O+] = [OH-] = 1.0 x 10 -7
3.6
Buffering refers to the ability of a solution to resist change in pH when acids or
bases are added. A buffer solution contains a weak acid + its conjugate base
or a weak base + its conjugate acid.
H+
CH3COOH
Acid
conjugate base
NH4+
NH3 + H2O
Base
3.7
CH3COO-
+
+ OH-
conjugate acid
The Henderson-Hasselbalch equation describes the chemical composition of
a buffer as a function of pH. The equation is useful for estimating the pH of a
buffer solution.
[HA]=concentration of undisociated weak acid
[A-]=concentration of the conjugate base [HA]
pKa = -log10 Ka
The Ka and pKa values of weak acids are useful when calculating the pH of
buffer solutions. For e.g., what is the pH of a buffer solution containing 1M
acetic acid and 0.5M sodium acetate? [Given that acetic acid: K a = 1.8 x 10-5,
pKa = 4.7]. The answer can be calculated using the Henderson-Hasselbalch
equation. The concentration of acetic acid (1M) corresponds to the [HA] term
and the concentration of acetate (from sodium acetate) (0.5M) corresponds to
the [A-] term. Hence,
pH = 4.7 + log ([0.5]/[1.0]) = 4.4
3.8
In biological fluids phosphate (PO4) and carbonate (C03) acts as buffers.
Other buffers such as TRIS and MES are used to buffer solutions at the
appropriate pH in many biochemical laboratories.
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