Botany notes

Lecture and Lab notes

Kaya mo yan forda Iphone

 Lesson 1 - Microscope (Lab)
Microscope - is an instrument used to see objects that
are too small for the naked eye.
Microscopy - The science of investigating small objects using
such an instrument is called.
Microscopy - This means invisible to the eye unless aided by a
microscope.

Types of Microscopes
Simple: Uses single lens party (ex magnifying glass)
Compound: Uses set of lenses or lens system
Electronic: Uses beams of electrons instead of a mirror. Have a higher
magnification and numerical apperature

Mechanical Parts :Provides Adjustments and support.

Base– Bottommost portion that supports the entire/lower microscope.
Pillar – Part above the base that supports the other parts.
Inclination Joint – Allows for tilting of the microscope for the convenience of the
user.
Arm/Neck – Curved/slanted part which is held while carrying the microscope
Stage – Platform where the object to be examined is placed.
Stage Clips - Secures the specimen to the stage.
Stage Opening
Body Tube – Attached to the arm and bears the lenses.
Draw Tube – Cylindrical structure on top of the body tube that holds the ocular
lenses
Revolving/Rotating Nosepiece – Rotating disc where the objectives are attached.
Dust Shield – Lies atop the nosepiece and keeps dust from settling on the
objectives.
Coarse Adjustment Knob – Geared to the body tube which elevates or lowers
when rotated bringing the object into approximate focus
Fine Adjustment Knob – A smaller knob for delicate focusing bringing the object
into perfect focus.
Condenser Adjustment Knob – Elevates and lowers the condenser to regulate
the intensity of light.
Iris Diaphragm Lever - Lever in front of the condenser which is moved horizontally
to open/close the diaphragm
 Lesson 1 - Microscope (Lab)
Illuminating Parts :Providing the light.
Mirror – Located beneath the stage and has concave and plane surfaces to
gather and direct light in order to illuminate the object.
Electric Lamp – A built-in illuminator beneath the stage that may be used if
sunlight is not preferred or is not available.

Magnifying Parts :To enlarge the specimen.

Ocular / Eyepiece – Another set of lens found on top of the body tube that
functions to further magnify the image produced by the objective lenses. It usually
ranges from 5x to 15x.
Objectives – Metal cylinders attached below the nosepiece and contains
especially ground and polished lenses

Types of Objectives
1. Scanning Objective (4X): This shortest objective is
useful for getting an overview of the slide
2. LPO / Low Power Objective – Gives the lowest
magnification, usually 10x.
3. HPO / High Power Objective – Gives higher
magnification usually 40x or 43x.
4. OIO / Oil Immersion Objective – Gives the highest
magnification, usually 97x or 100x, and is used wet
either with cedar wood oil or synthetic oil.

Magnification
Magnification = Objective lens X Eyepiece lens

Caring For the Microscope

1. Do not let any liquids to come in contact with the microscope.
2. Always store the microscope inside a box after use.
3. Return the objective lens to low power after use.
4. Carry the microscope by the arm.
5. Use a soft clean tissue to wipe the lenses
 Lesson 1 - Microscope (Lab)
Preparing the wet mount

Use of Stains
some parts of a plant cell can be clearly seen when the cell is
mounted in water
other cell structures which are not so obvious can often be shown
up more clearly by the addition of dyes called STAINS

Iodine Methylene
Solution Blue
Used to stain Used to stain
plant cells animal cells
 Lesson 1: INTRODUCTION TO BOTANY
(lECTURE)
What is botany?
Botany is a branch of biology that deals with
the study of plants, including their:
Form
Functions
Parts
Classification
Diseases, etc.

The term "botany" comes from the Ancient Greek word βοτάνη
(botanē) meaning "pasture", "grass", or "fodder“.

INTRODUCTION TO BOTANY
Botany is also referred to as “Plant biology”.
Although there are no records of this prehistoric pursuit of
knowledge, evidence points to the vast expertise of many
ancient tribes on plants.
Mainly on which to eat and which are poisonous, which can
be cured, and where to find them.

History of botany
Theophrastus (370-285 BC)
Father of Botany
Crude classification of plants
whether its flowering
(Phanerogams) or not
(Cryptogams)
Further classified plants into herbs,
subshrubs, shrubs and trees
Lesson 1: INTRODUCTION TO BOTANY (lECTURE)

History of botany
Gaius Plinius Secundus (23-79 AD)
‘Pliny the Elder’
Describe substantially the
biological, medicinal, and
agricultural aspects of plants.
With more or less 37 volumes of
Natural History.
First used “stamen”

Padano's Dioscorides (62-128 AD)

Roman Army physician
Compiled the medicinal aspects of
about 600 plant species in
“Materia Medica”.
Introduced the names Aloe,
Anemone, Phaseolus, and
Arisolochia (still used today).
Medicinal values of plants were
given a premium during the Roman
era.

Middle Ages to 17th century

Plant classification was the focus
The invention of printing and the advancement in
navigation led to the discovery of new plant species
Records of medicinal plants and where to find them
Herbals – books, herbalist - authors
Lesson 1: INTRODUCTION TO BOTANY (lECTURE)

Characteristics of Life
1. Are Composed of Cells
Cells are the basic components of all
living things. Some organisms are
single celled, like bacteria, or multi-
celled, like humans.
6. Grow and develop
Growth and development allow the
organisms to replace old and dying
cells in the body and perform
different functions

2. Require Energy 7. Adapt to their

Living organisms require energy, environment
usually in the form of ATP. They use This mechanism allows certain
this energy to carry out energy- individuals to be better than the
requiring activities such as rest
metabolism and locomotion.
3. Reproduce
Organisms in order to grow and
sustain themselves, need to
reproduce organisms similar to
themselves and propagate.

4. Have different levels of

organization
This hierarchy of life roots from the
cell as the basic unit of life and
extends up to the all-encompassing
biosphere where all living organisms
are part of.

5. Respond to the
Environment
• All living things respond to stimuli
in their environment
Lesson 1: INTRODUCTION TO BOTANY (lECTURE)
A set of characteristic sets the plants from
other organisms

1. Plants are multicellular eukaryotes,

distinguishing them from their
evolutionary relatives such as algae.
2. Plants are capable of photosynthesis
autotrophs
photoautotrophs

3. Plant cell walls have cellulose This

differentiates them from the fungi such as
mushroom whose cell walls are primarily
made of chitin.
4. Plants have two adult forms that
alternate in producing each other
(alternation of generations)
Sporophyte generation has
adults that form the spores
that do not need to fuse with
another to form a new plant
Gametophyte generation has,
and there are the adults that
produce the sperms and the
eggs.

5. Plants have a multicellular embryo

protected within the female parent
Lesson 1: INTRODUCTION TO BOTANY (lECTURE)
Scientific Method
1.Ask a Question: The scientific method starts when you ask a question about
something that you observe: How, What, When, Who, Which, Why, or Where?

And, in order for the scientific method to answer the question it must be about
something that you can measure, preferably with a number.
2. Do Background Research: Rather than starting from scratch in putting
together a plan for answering your question, you want to be a scientist using
library and Internet research to help you find the best way to do things and
insure that you don't repeat mistakes from the past.

3. Construct a Hypothesis: A hypothesis is an educated guess about how things

work: "If _____[I do this] _____, then _____[this]_____ will happen."
You must state your hypothesis in a way that you can easily measure, and of
course, your hypothesis should be constructed in a way to help you answer
your original question.
4. Test Your Hypothesis by Doing an Experiment: Your experiment tests
whether your hypothesis is true or false. It is important for your experiment to
be a fair test. You conduct a fair test by making sure that you change only one
factor at a time while keeping all other conditions the same.

You should also repeat your experiments several times to make sure that the
first results weren't just an accident.

5. Analyze Your Data and Draw a Conclusion: Once your experiment is

complete, you collect your measurements and analyze them to see if your
hypothesis is true or false. Scientists often find that their hypothesis was false,
and in such cases they will construct a new hypothesis starting the entire
process of the scientific method over again. Even if they find that their
hypothesis was true, they may want to test it again in a new way.

6.Communicate Your Results: To complete your project you will communicate

your results to others in a final report and/or a display board. Professional
scientists do almost exactly the same thing by publishing their final report in a
scientific journal or by presenting their results on a poster at a scientific meeting
Lesson 2: CHEMICAL BASIS OF LIFE (LECTURE)
What is an atom?
An atom is the smallest indivisible units of
matter; each type of atom is also called a
chemical element. An atom is made up of
protons, electrons and neutrons. These three
subatomic particles characterize the chemical
properties of an atom
Protons, Neutrons and Electrons
The protons are positively charged, while the electrons are negatively
charged. Both the protons and neutrons are confined to a very small
volume at the center of an atom called the atomic nucleus. On the other
hand, electrons are negatively charged and they can be found revolving
around the nucleus.

The Electron
The portion of the atom outside the
nucleus contains the electrons.
Each electron carries a charge of -1
In normal neutral atom, the number of
electrons around the nucleus is exactly
the same on the number of protons in the
nucleus.

Protons, Neutrons and Electrons

The + charge of protons and the – charge of electrons
cancel each other, making the atom neutral.
Electrons are not in fixed position outside the nucleus.
The distance of an electron from the nucleus is a function
of its energy. The higher the energy, the greater its
probable distance from the nucleus.
The volume within which an electron can be found 90% of
the time is known as the orbital of the electron.
The energy level whose orbital is nearest the nucleus is
referred to as the K shell, which contains only 2 electrons.
The next is L,M,N etc.
Although the 3rd and successive levels can accommodate
more than 8, they are in stable configuration when they
contain only 8.
Lesson 2: CHEMICAL BASIS OF LIFE (LECTURE)
Atomic number
This is one characteristic that distinguish
one chemical element from another. An
atomic number is the specific number of
protons found in that chemical element. For
example hydrogen has one proton, thus its
atomic number is one. Looking at the periodic
table, one can also be able to deduct the
atomic number; elements in the periodic table
are usually numbered according to their
atomic numbers.
What is a molecule?
A molecule is made up of two or more
atoms. A good example is water, a
molecule of water contains two
hydrogen atoms and one oxygen atom,
thus water can be represented as H2O.

Practice Activity
Lesson 2: CHEMICAL BASIS OF LIFE (LECTURE)
Important Chemical Bonds
The atoms of most element
possess the property of binding
to other atoms too form
complex aggregates.
When two or more atoms are
bound together the force of
attraction that holds them
together is called chemical bond
Types of Chemical Bonds: Ionic bons
Ionic Bond - formed by transfer of
electrons
atoms tend to form complete outer
shells by reacting with other atoms

What is an Ion?
An atom is characterized as an ion when it loses or gains one
or more electrons. For example, when a sodium atom (Na),
which has 11 electrons, loses one electron, it becomes a
sodium ion with a net positive charge; it still has 11 protons,
but the loss of one electron leaves it without only 10
electrons remaining.
On the other hand a chlorine atom which has 17 electrons
can gain an electron and become a chloride ion with a net
negative charge. This chloride ion now has 18 electrons and
17 protons. Ions that have a net positive charge are called
cations, while those that have a net negative charge are
called anions.
A sodium ion with its positive charge and a chlorine ion
with its negative charge tend to attract each other, since
opposite charges attract, Held together by the attraction
called Electrostatic Attraction
Lesson 2: CHEMICAL BASIS OF LIFE (LECTURE)
Classes of Ionic Compound
Acid – can be characterized simply as a
substance that increases the
concentration of hydrogen ions (H+) in
water. •
Base – a substance that decreases the
concentration of hydroxyl ions, OH-
– The degree of acidity or basicity
(usually called alkalinity) of a
solution is commonly measured in
terms of value known as pH.
On the pH scale, which ranges from 0 on the basic end to 14 to
alkaline end, a solution is neutral if its pH is exactly 7.
Substances with pH of less than 7 are acidic ( that is it
contains a higher concentration of H+ than the OH- ions)
the lower the pH the more acidic the substance.
Substances with a pH higher than 7 are basic (alkaline), that
is it contains a higher concentration of OH- ions than H+ ions.
the Higher the pH the more basic or alkaline the substance.
Living matter is extraordinarily sensitive to pH, functioning
best when conditions are nearly neutral.
Most of the interior material of living cells has a pH of
about 6.8.
The blood plasma and other fluids that bathe the cells in our
own bodies have a pH of 7.2 - 7.3
Special mechanism aid in stabilizing these fluids, so that
cells will not be subject to appreciable fluctuation in pH.
Among these mechanisms are certain substances known as
buffers, which have the capacity to bond to H+ ions,
thereby removing them from solution whenever their
concentration begin to rise and conversely to release H+
ions into solution whenever their concentration begin to
fall.
Buffers help minimize fluctuations in pH, since many of
the biochemical reactions normally occurring in living
organism either release or use up H+ ions.
Lesson 2: CHEMICAL BASIS OF LIFE (LECTURE)
Covalent bond
the joining of atoms by mutually
sharing one or more electron
not all compounds are formed by actual
transfer of electrons from one atom to
another
A compound may be formed by some
atoms sharing common electrons

Covalent Bond may be:

A. Single Bond – one electron is shared
B. . Double Bond – two electrons are shared.
C. Triple Bond – three electrons are shared.
Practice Tasks

1. CH4 2. C2H6

3. C2H4 4. C2H2
 Lesson 3: CLASSES OF ORGANIC MOLECULES
What are organic molecules?
These are molecules that have their basic
skeleton made of carbons atoms,
hydrogen, oxygen and sometimes
nitrogen atoms. Generally organic
molecules in the body can be classified into
one of four groups: carbohydrates, lipids,
proteins and nucleic acid.

Carbohydrates
Carbohydrates are the most
abundant of the four main organic
molecules. They fill numerous roles in
living things, such as the storage and
transport of energy (starch,
glycogen) and structural
components (cellulose in plants,
chitin in animals). Most
carbohydrates taste sweet, and the
carbohydrates include the
substances known as sugars.
Simple sugars/monosaccharides
the basic building block molecules of the
carbohydrates.
The simplest sugars are known as
monosaccharides, a good example of a
monosaccharide is glucose
all sugar, when in straight-chain form,
contain a C=O group. Hydroxyl (OH) groups
are attached to all the carbons except
those with a double bonded oxygen.
glucose
galactose
fructose
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Simple sugars/monosaccharides
In addition to ordinary monosaccharides composed only of
carbon, oxygen and hydrogen, there are a variety of
derivative monosaccharides containing other elements.
Some have a phosphate group attached to one of the carbons
and others an Amino group ( a nitrogen with two hydrogen, NH2
).
glucosamine
Glucose 6-phosphoric acid
Glucose is the major monosaccharide found in the blood,
when two monosaccharide are linked together they form a
disaccharides

Disaccharides
are composed of two single sugars bonded
together through a reaction that involves a
removal of a molecule of water. This kind of
reaction is called condensation reaction or a
dehydration reaction.

Maltose/Malt sugar
this compound is synthesized by a
condensation reaction between two
molecules of glucose.

Lactose/Milk sugar
composed of glucose and galactose
Synthesized by condensation reactions,
disaccharides can be broken down
constituent simple sugars by reverse
process.
This process or reaction is called Hydrolysis,
involves addition of water molecule
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Sucrose/table sugar
it is synthesized by
condensation reaction
between molecules of
glucose and a molecule of
fructose.
Polyssacharide
is a straight or branched chain of hundreds or
thousands of sugar units of the same or different
kinds.
Starches
are the principal carbohydrate storage products of higher
plants
composed of many hundreds of glucose units bonded
together.
Glycogen
the principal carbohydrate storage product in animal
Sometimes called animal starch. Glycogen is found in animal
cells and it serves as primary short term energy storage in
animal cells. It is made primarily by the liver and the muscles.
Cellulose
highly insoluble unbranched polysaccharides common in
plant

POLYMERIZATION REACTIONS.
Reactions like those that form
polysaccharides – are reactions in which
small molecules bond together to form long
chains.
The products formed are called POLYMERS.
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Lipids
Are composed of carbon,
hydrogen and oxygen, but they
may also contain other elements,
particularly phosphorus and
nitrogen.
Lipids are fat-soluble, naturally
occurring molecules; unlike
carbohydrates lipids are insoluble
in water, but they do dissolve in
nonpolar solvent such as ether.
The main biological functions of lipids include energy
storage, acting as structural components of cell membranes,
and participating as important signaling molecules.

Fatty acid
has a long unbranched carbon with a - COOH at the
end.
Each molecule of fat is composed of two different types
of building-block compounds.
An alcohol called glycerol and fatty acids.
Glycerol (also called glycerin) has a backbone of three
carbon atoms, each carrying a carboxyl group – (-OH
group)

A fat
Molecule
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Saturated fats
including butter and lard tend to
be solids at room temperature.
Saturated means all the carbon
atoms in the fatty acid tails are
joined by single C-C bonds and as
many hydrogen atoms as
possible are linked to them.

Unsaturated fats
tend to be liquid at room
temperature. One or more double
bonds occur between the carbon
atoms in the fatty acid tails.
Oils are liquid at room temperature
because the double bond create
kinks that disrupt packing between
tails.

Phospholipids
Contain phosphorus in the form of phosphate
it has glycerol backbone
attached to the backbone are two fatty acid tails, a phosphate
group and a small hydrophilic group
Main component of the cell membrane
Controls the movement of materials in and out of the cell.

Waxes
composed of fatty acids and certain alcohol
some wax secretion form coatings that help
protect, lubricate and maintain the pliability
of skin and hair.
Lipids with no fatty acids
among the lipids that have no fatty acid
tails are the steroids
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Cholesterol
is a steroid which is a key component of animal cell
membranes
Used to synthesize vitamin D which functions in the
development of bones and teeth.
Excess cholesterol also plays a role in
ATHEROSCLEROSIS a disorder in which the lipids
becomes deposited in the walls of arteries. The
deposits build up, arteries narrow and blood flow may
be obstructed.
Many hormones, including sex hormones are steroid.
Hormones help regulate the body’s growth,
development and reproduction, as well as its everyday
functioning.
Unfortunately, use of those steroids can lead to
pronounced behavioral disorders, liver damage and
other abnormalities.

Proteins
Proteins are large organic compounds made up of amino acids
(amino acids are organic molecules that are made of carbon,
nitrogen and hydrogen atoms). These amino acids are arranged
in a linear chain and joined together by peptide bonds between
the carboxyl and amino groups of adjacent amino acid residues.
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Peptide bonds
are formed between the amino and carboxyl group. These bonds
can be broken by hydrolysis to yield individual amino acids. The
figure on the previous slide illustrates the hydrolysis of a protein.

PROTEIN STRUCTURE
Primary Protein Structure
The primary structure of a protein
refers to the number and sequence
of amino acids in the protein. The
primary structure of a protein is
very important in the identification
of a protein.

Secondary Protein Structure

The secondary protein structure
is the specific geometric shape
caused by intramolecular and
intermolecular hydrogen
bonding of amide groups. The
most common secondary
structures of proteins are the
alpha helices and beta sheet.

Tertiary Protein Structure

The third type of structure found
in proteins is called tertiary
protein structure. The tertiary
structure is the final specific
geometric shape that a protein
assumes. This final shape is
determined by a variety of
bonding interactions between
the "side chains" on the amino
acids.
 Lesson 3: CLASSES OF ORGANIC MOLECULES
Side chains
These bonding interactions may be stronger than the hydrogen bonds
between amide groups holding the helical structure. As a result, bonding
interactions between "side chains" may cause a number of folds, bends, and
loops in the protein chain. Different fragments of the same chain may become
bonded together.

Quaternary Protein Structure

The quaternary protein structure
involves the clustering of several
individual peptide or protein chains
into a final specific shape. A variety of
bonding interactions including
hydrogen bonding, salt bridges, and
disulfide bonds hold the various chains
into a particular geometry.

Nucleic Acids
These organic molecules are responsible for the storage, expression, and
transmission of genetic information. It is the expression of genetic information
that determines whether a cell is a muscle cell or a nerve cell. There are
basically two classes of nucleic acids, deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).
Nucleic Acid are the only organic compound capable of replicating
themselves
Involved in the storage and transmission of energy and cellular information.
The structural block of nucleic acid is the nucleotide which is comprised of a
phosphate group (PO4), a five carbon sugar (ribose or deoxyribose) and a
nitrogen base, either a purine ( adenine or guanine) or pyrimidine (cytosine,
thymine or uracil)

Difference
Between DNA
and RNA