Biology Notes Pages 2

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LECTURE ONE: INTRODUCTION TO BIOLOGY
What is Biology?
It is the study of life
How do we know if something is living or non-living?

For something to be living there are 7 basic criteria:
 Can reproduce
 Has order
 Can produce/transfer energy
 Can grow and develop
 Can maintain homeostasis (regulate temp)
 Can evolve and adapt
 Can respond to environment
Hierarchy of Biological Order

Molecules  Organelles  Cells  Tissues  Organs  Organ Systems  Organisms
 Populations  Communities  Ecosystems  Biosphere
Populations
Same kind of organisms living together
Communities
Different kinds of organisms living together and interacting
Ecosystems
Communities of organisms present in a particular area
Biosphere
All of earth’s ecosystems
Emergent Properties
Emergent properties are properties that manifest themselves as the result of various
system components working together, not as a property of any individual
component. They are properties of a group of items, whether insects, atoms or
buildings, that you would not find in any of the individual items.
Example: the brain. No individual neuron is responsible for the processing of

information or the experiencing of emotions, this is only possible through
the linking of millions of neurons together .
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Form Fits Function

Parts of an organism have specific structures that allow them to perform tasks
efficiently. For example, a bird has aerodynamic wings so that they can fly, leaves are flat
to have no shadow and to maximize its exposure to light.
Biological Classification
So in biology there are a lot of different names, organisms, domains, etc. Therefore, in
order to organize this and give organisms a proper name/category, biologists created
something called Taxonomy = the science behind naming/classifying living organisms.
So first we must pick which Domain an organism belongs to:

 bacteria
 Archaea
 Eukarya (plants, animals, protists)
Then we go further and pick its kingdom (only eukarya have kingdoms)
 Kingdom Animalia
 Kingdom Plantae
 Kingdom Fungi
 Kingdom Protists
Then it is phylum, class, order, family, genus, species.
Doing this taxonomy gives us a lot more information on the organisms as well as others
that are similar to it (part of same category).
Binomial System (how to name it)

The name always consists of the Genus and the Species. Note that the Genus is always
first and capital and species is second and lower case.
LECTURE THREE AND FOUR: MACROMOLECULES
What is a macromolecule?
A macromolecule is a large molecule containing a large amount of atoms. They are
considered to be polymers. Monomers are the individual compound (single unit),
therefore polymers are chains of monomers.
It is important to know and understand that it is the molecule’s shape and structure that
determines its function. If one thing is altered, it can have a drastic change on the
function. Shape can also determine the stability of a macromolecule (more spacing =
more stability).
Polymers and Monomers

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Monomer = single unit

Polymer= chain of monomer
Monomer Polymer = DEHYDRATION (or condensation). The monomer must release
H2O molecules in order to bond and form a chain.
Polymer Monomer = HYDROLYSIS. The polymer must add water in order to break its
bond and go back to one single unit (monomer)
EX: 3 water molecules needed to be added or lost
Types of Macromolecules
There are 4 main types of macromolecules
 Carbohydrates
 Protein
 Lipids
 Nucleic Acid
1. CARBOHYDRATES
 Carbohydrates (sugars=simple unit) store potential energy and maintain
structure.
 Monomer= Monosaccharide
 Polymer= Polysaccharide (there is no always a polymer)
 Three types of carbohydrates: monosaccharides (monomer), disaccharides,
polysaccharides (polymers).
Monosaccharides
o They are the smallest unit of carbohydrates (cannot be hydrolysized). They are
simple sugars.
o 3 types of monosaccharides: Glucose, Fructose, Galactose
o Glucose, Fructose, Galactose are known as monosaccharide isomers; meaning
they have the same number of atoms and same elements, however their
structures and properties are different.
o Some monosaccharides are already carbohydrates therefore, there are no
polymers
o In aqueous solutions monosaccharides go into a ring form

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Disaccharides
o Disaccharides form when two monosaccharides undergo dehydration.
o They are two monosaccharides joined by a glycosidic linkage
o 3 types of disaccharides: Sucrose, Lactose, Maltose
Polysaccharides
o they are long chains of monosaccharides linked by glycosidic bonds
o there are considered the polymers of carbohydrates
o There are three types: Cellulose, Starch, Glycogen
 Starch = stores energy in plants (short term)
 Glycogen= stores energy in animals
 Cellulose = makes up most of the plant cell’s wall. It gives support in
plants, as well as it is fiber. Humans and most animals don’t have the
proper enzymes needed to break down cellulose (cows are an exception),
however microorganisms (bacteria, fungi) are capable of breaking down.
Therefore, it is the bacteria in our body that helps us humans to break it
down.
2. LIPIDS
 Lipids are hydrophobic; insoluble in water (ex: oil). This is because of the non
polar covalent bonds (like dissolves like; water is polar)
 Three types of Lipids: Fats, Steroids, Phospholipids
 No monomer, no polymer
Fats
o Fat Function
 Fats store a large amount of energy (which is why we crave it)
 Fats keep us warm (insulation from the cold)
 Fats protect our internal organs (acts as a layer)
o Fat Structure
 The structure consists of 1 molecule of glycerol and 1-3 molecules of fatty
acids (hydrocarbon chain)
 Diversity in fats come from different fatty acids not glycerol
 When there is a double bond, the shape bends

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o Fat Diversity
 Can contain three different types of fatty acids: Monoacylglycerol,
Diacylglycerol, Triacylglycerol
o Saturated Fats vs. Unsaturated Fats

 Saturated fats are fats that are processed. Their fatty acids have no
double bonds causing different fats to compact together which can cause
clogging of arteries
 Unsaturated fats are better for you as they have double bonds which
bends the shape of the fatty acids preventing it to come too close to
another fat.
Prohaselipids
o Function: makes up most cell membranes
o Structure:
 similar to fat structure however this time they have 2 fatty acid, 1 glycerol
molecule and 1 phosphate group
 This makes the structure Amphipathic – both hydrophilic and hydrophobic.
 The phosphate group= hydrophilic, the fatty acid = hydrophobic
Steroids
o Steroids are hormones and cholesterol

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3. PROTEINS
 Proteins are incredibly diverse; there are many different types of protein such as
defensive proteins, storage protein, hormonal protein, etc.
 Monomer= amino acids
 Polymer= polypeptide (linked by peptide bonds)
 A protein is one or more polypeptide
Protein Structure
o There are 4 types of protein structure: primary, secondary, tertiary, quaternary
o Primary: it describes the unique order in which the amino acids are linked
together to form a protein (one polypeptide)
o Secondary: refers to the coiling and folding of a polypeptide
o Tertiary: refers to the 3D shape of the polypeptide chain
o Quaternary: refers to the structure of a protein (fully completed) formed by the
interactions between multiple polypeptides
o All amino acids have a amino group, a carboxyl group, a hydrogen group and an
R group
o The R group is what changes and determines which animo acid it is
Protein Diversity
o there is a lot more diversity when it comes to protein comparing to other
polymers. The reason for this is due to many different reasons
 greater variety of monomers
 protein can be very large, can be made from more than one
polypeptide
 Many different 3D shapes
Sickle-Cell Anemia (A genetic disease)

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o One slight change is the polypeptide sequence can have a drastic change on the
shape of the protein and therefore its function (Form fits function)
o Sickle-Cell Anemia is an example of a change in amino acid. It is an inherited
blood disease caused by the substitution of an amino acid.
o Normal hemoglobins carry oxygen, however this disease causes for the shape to
deform not allowing it to carry oxygen.
Denaturation
o It is possible that physical and chemical conditions can affect the 3D shape of the
polypeptide therefore changing its function. For example, concentration, pH,
temperature, etc.
o These external effects can cause for the protein to lose its form which is what we
call Denaturation
o When a protein is denatured it is biologically inactive (cant perform function
anymore)
o Example an egg: when exposed to certain temperature it denaturates however
after that it cant renaturate causing it to forever be biologically inactive.
. Nucleic Acid
 Monomer= nucleotides
 Polymer= polynucleotide or nucleic acid
 There are two types of Nucleic Acid: deoxyribonucleic Acid (DNA) and
ribonucleic acid (RNA)

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Roles of Nucleic Acid

o DNA codes for genes. It has all the information on how to build a protein (the
architect). It is the genes that carry the info to determine the primary sequences
of the protein. Each gene will code for a different protein.
o In order to create a protein that expresses your genes. The RNA must get
involved and enter nucleus to get DNA copy (information) (RNA is known as the
contractor getting the building blocks). With this the final product, the protein
can be made due to DNA and RNA.
Structure of Nucleic Acid

o A nucleotide has a phosphate group, nitrogenous base (acts a R-group – keeps
changing), and a 5-carbon sugar that can either be deoxyribose sugar or ribose
sugar depending if we are dealing with DNA or RNA.
o Polynucleotides (DNA/RNA) are bonded nucleotides. These bonds are joined by
covalent bonds.
o There are 4 types of nitrogenous bases: Adenine, Thymine (or Uracil), Guanine,
Cytosine
o The complementary base pairing: AT and G C. These nitrogenous connect
via a hydrogen bond, which is considered a very weak bond that can be very
easily broken.
o DNA is in a form of two polynucleotides spiraling around an imaginary axis
creating a double helix. The two must be in opposite direction (3’ 5’ or 5’ 3’)
Differences between DNA and RNA

o DNA= deoxyribose sugar, A T, G C, double stranded
o RNA = ribose sugar, AU, GC, single stranded
Transcription and Translation (to create a Protein)
o In order for a protein to be created, two steps must take place: TRANSLATION
and TRANSCRIPTION
o For a protein to be made, there must be a CODON. A codon is a sequence of
three letters giving the protein a specific function.
1. Transcription

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 It is important to know that DNA hold all the instructions on how to make
a protein, however the problem is is that DNA can’t leave the nucleus.
Therefore, Transcription must take place.
 This is the step where DNA  mRNA (transferring genetic info)
 First thing that happens is that the DNA (double helix) will separate easily
as it is hydrogen bonding. The mRNA
(messenger RNA) will enter nucleus and will
pair up with the DNA (copy).
 The mRNA reads from 5’ to 3’ and therefore
copies 3’ to 5’
 Once the mRNA molecule is complete,
transcription process is over.
 RECAP: separation of DNA, Synthesis of RNA,
release completed mRNA
2. Translation
 Once transcription is complete. Translation begins.
 The mRNA is now in the cytoplasm. However it is not ready to make a
protein yet, since its information is in nucleic acid language when it
needs to be in amino acid language. Therefore, translation will happen.
 In order for it to be understood, the sequence must be in CODONS (3
letter).
 With this, the tRNA comes. This is the translator between nucleic acid
and amino acid. On the tRNA it has an anticodon (complementary to
codons) and an amino acid attached. Therefore it will pair up with the
right codon to decode it.
 tRNA can only transport one animo acid at a time.
 tRNA translates at the start codon (AUG) and will stop at (UAA, UAG,
UGA)
 EX: mRNA= UUU UUU UUU UUU UUU
tRNA= AAA AAA AAA AAA AAA
amino acids = Phe
 Now that we have our animo acids, we are not done as a chain of amino
acids forms a protein. This is where the ribosome comes into play.
 The ribosome is like a factory. They are made in the nucleolus, made
from RNA and proteins, displays quaternary structure

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 The ribosome attaches to start and end of mRNA. As the tRNA attaches
to mRNA, the ribosome will move along with it. As it does, it aligns two
amino acids together, which are then joined by an enzyme. This repeats
until it reaches stop codon. This chain of amino acids is now a protein
and will be released in cytoplasm.
LECTURE FIVE: CELL STRUCTURE
What are cells?

Cells are the smallest unit of life. They are the basic building blocks of all living things. In
short, they provide structure for the body, they take in nutrients from food, convert
those nutrients into energy and carry out a specialized function.
Types of cells
There are two types of cells:
EUKARYOTIC CELLS (plant cells and animal cells)  have a nucleus where they house
DNA, they can be single celled or multi-cellular.
PROKARYOTIC CELLS (bacteria, archea)  do not have a nucleus, do not have organelles,
its DNA is found in the middle of the cell, they are all single celled.
Even though there are different types of cells, every cell has 4 things in common:
 They have a plasma membrane

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 They have a cytoplasm

 They contain genetic information (DNA)
 They have ribosomes (for protein synthesis)
Cell Size
Cells are very small. Most cells are microscopic, however there are some that cannot be
seen using this instrument. It is important to understand that cell size in all living things
are very small. Even though, an elephant is large, it does not mean its cells are large as
well, it means that there simply more of them comparing to a human body.
The reason behind the cell’s size, it due to something called homeostasis. In order to
live, there must always be balance in our body, whether it is balance of temperature,
balance of amount of oxygen, etc. This is known as homeostasis and our body’s remain
in this state due to cells.
Cells’ require oxygen, they need their waste products

to be released from the cell, as well as they need to
exchange food, nutrients and gases. All these things
to enter and leave the cell must take place on the
surface area. Therefore, instead of having one big cell
do exchanges, there are millions of small small cells
doing these exchanges. More surfaces = more
exchanges = more effective and easier to
maintain homeostasis.
Prokaryotic Cell
(Domain= bacteria and archaea)
(no nucleus, no organelles)
1. Plasma Membrane = allow for exchanges and

protect the internal environment of the cell.
2. Cytoplasm = interior of cell

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3. Nucleoid = region of a single loop of DNA (no nucleus, however there is a nucleoid
region that holds the DNA)
4. Ribosome = site of protein synthesis
5. Cell wall = gives cell structure and rigidity, as well as protects it (note only some
prokaryotic cells have cell walls)
6. Flagella = a whip-like structure that allows the cell to move
7. Capsule= a outer layer that protects cells from attacks or dehydration
8. Pili = hair like projections that help cells attach to other surfaces
Cell wall more in depth

 The cell wall in bacteria is very strong, maintain shape and resist bursting.
 For ARCHAEA, cell wall is composed of polysaccharides and proteins
 For BACTERIA, cell wall is composed of peptidoglycan (not cellulose)
 Structure of cell wall is used to classify the bacteria into two categories
o Gram Positive = bacteria that is stained purple due to its thick
peptidoglycan walls
o Gram Negative = bacteria that is not stained purple but rather pink
due to its thin peptidoglycan walls
 Note that not all prokaryotic cells have capsules and cell walls
Eukaryotic Cells: ANIMAL

(Domain= Animal, Plants, Protists)
(yes nucleus, yes organelles)

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1. Plasma Membrane
 Allow for exchanges (promoting homeostasis) and protect the internal
environment of the cell
 It is made up of prophaselipid bi-layer (phospholipid molecules and protein
molecules)
 There are different channels of protein in the membrane for transportation
 A phospholipid is an Amphipathic molecule, meaning its head is hydrophilic and
its tail is hydrophobic. Therefore, when placed in water, they self assemble into a
bi-layer (a double layer) in order to shield the hydrophobic portions, this creates
a membrane.
 The cell’s membrane is selectively permeable, It allows some substances to enter
more easily than others.
2.
Nucleus
 Contains DNA and genes
 It is wrapped in a double membrane known as nuclear envelope (phospholipid
bi-layer)
 Nucleolus= center of nucleus, it makes ribosomes for protein synthesis
 DNA around nucleolus in form of chromatin (unstructured DNA), however when
it comes to cell division it turns into chromosomes (tightly packed DNA)
3. Endoplasmic Reticulum
 Attached to nucleus
 Highly folded, membranous structure, has weave shaped called cisternae
 3 main functions: synthesis of proteins and lipids, transport of protein and lipids,
and detox
 2 kinds: rough ER and smooth ER

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 The rough ER holds ribosomes which makes this in charge of producing proteins
(that will be transported outside cell or needed for
other organelles within cell). It also synthesizes the
membrane as some proteins ends up getting inserted
into the ER causes it to enlarge and will eventually
break off.
 The smooth ER is rich in enzymes; this synthesizes
lipids as well as detoxify poisons and drugs (ex: alc)
4. Golgi Apparatus
 Manufacturing, warehousing, and shipping center for cell products
 Structure is similar to endoplasmic reticulum
 It is responsible for transporting, modifying and
packaging proteins and lipids that came from ER
into vesicles for delivery to a certain destination
 They can also modify carbohydrate portions of
glycoproteins
 The golgi is divided into two parts: cis-golgi
(receiving side of GA) and trans-golgi (shipping
side of GA)
5. Vesicles
 Hollow spherical organelles surrounded by a membrane identical to plasma
membrane
 They are produced by ER and golgi
 They are responsible for storing/transporting chemicals inside/outisde the
cell
Relationship Between Nucleus, ER and Golgi

 The nucleus holds your DNA which codes for certain proteins that are chained
together form amino-acids by the ribosomes on the rough endoplasmic
reticulum (chemical messages sent from nucleus to ER). Most if not all of these
proteins are enveloped in a special vesicles that move between the rough
endoplasmic reticulum and the Golgi apparatus. The Golgi apparatus modifies
them more and puts the proteins in another vesicle to send the protein to there
destination, both in the cell or outside of it.
6. Lysosomes

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 Are tiny sacs with fluid containing enzymes formed by the golgi
 They are responsible for breaking down macromolecules
 These enzymes are only active in the lysosome membrane as its ph is 5,
therefore if there is a rupture the enzymes wont break down the cell itself since
the ph of the cell is 7.2
 They are the main sites of digestion, will break down the food that has entered
the cell in order to get the proper nutrients the cell needs
 They break down cells that have died and recycle chemicals
The Endomembrane system (PM, ER, GA, Vesicles, Lysosomes, Vacuole)
7. Peroxisomes
 Contain a variety of enzymes that get rid of toxic substances in the cell
 Find them in your liver
 The enzymes will take the toxic element in the presence of oxygen and create
hydrogen peroxide. An enzyme will then break it down into water and oxygen
making it not toxic anymore.
 EX: RH2 +O2  R + H2O2 2H2O2  2H2O + O2
 They are responsible for make/break fatty acids, detoxifies harmful substances in
liver, reduces aging, and it can self replicate
9. Mitochondria
 It converts food into energy
 It is the power house of the cell as it produces ATP

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 In order to make ATP (energy), it needs glucose (from food) and oxygen
 It has 2 membranes that are composed of a phospholipid bi-layer
 It holds its own set of DNA
Membranous Organelles
 Mitochondria, peroxisomes, lysosomes, vesicles, plasma membrane, gogli
apparatus, endoplasmic reticulum, the nucleus (all have or are membranes)
Non-Membranous Organelles
 Nucleolus, Ribosomes, Cytoskeleton (microtubules, microfilaments, intermediate
filaments)
10. Ribosomes
 Site of protein synthesis
 Can be found free floating in cytoplasm (make proteins that the cell
will use) or on the rough endoplasmic reticulum (make proteins that
need to be stored and released when ready to use)
11. Cytoskeleton
 A network of protein rods called cytoskeleton giving the cell support and shape.
 It can extend and contract allowing cell shape to change
 Three types of cytoskeleton: microtubules, microfilaments, intermediate
filaments
Microtubules:
 they are the thickest, they are hollow
 they move chromosomes during cell division and act as railroad tracks to move
vesicles to where they need to go
 They make up flagella and cilia
Flagella and Cilia

 They are structures used for movement and are made up by
microtubules
 Flagella = long whip like, long and few, sperm have it
 Cilia = short and numerous, trachea has cilia to capture particles,
fallopian tubes has it to push the egg
Centrosomes
 Centrosomes move chromosomes during division
 They are made up of microtubules
 Centrosomes are made up of two centrioles

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 Spindle fibers extend from centrosomes and attach onto chromosomes
Microfilaments:
 Strings of actin
 Thinner than microtubules
 Maintain cell shape and allow it to move
Extracellular Matrix
 Regulate the cell’s behavior
 Attached to the protein of the plasma membrane there are
microfilaments that it connected the interior to exterior allowing for signals to
be received
 They have cell signalers and cell receptors
 So if you are hungry, full, etc. messages are sent and received.
Eukaryotic Cells: PLANT
When it comes to plant cells, they are very similar to

animal cells and contain most of the same organelles
as they are both eukaryotic cells. However, there still
remains some evident differences between the two:
 Animal cells does not contains cell wall or chloroplasts on the other hand plant
cells does contains it.
 Plant cells are in perfect rectangular shape while animal cells are round and are
mostly in irregular shape.
 Plant cells have a large central vacuole whereas animal cells do not
1. Central Vacuole
 It is a sac with a membrane that takes up most of the cell. It is filled with water
which puts pressure on membrane giving it form.

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 Vacuole store various compounds, such as proteins, inorganic ions, defensive

compounds that protect the plant from herbivores)
 They are responsible for storing and breaking down waste, which is why plant
cells don’t have lysosomes.
2. Chloroplasts
 Solar energy (chloro) and food  energy (mito)
 This allows for the plant to perform photosynthesis, it traps light to make ATP
 It contains a green pigment called chlorophyll which traps light energy for
photosynthesis
 Plant cells have both mitochondria and chloroplasts
 Mitochondria and chloroplasts contain DNA that codes for a small amount of
protein within these organelles
 They are also not considered part of the endomembrane system as even though
they have membranes they are not made from the ER but from ribosomes within
it
Eukaryotic Cells: PROTISTS (vacuole)

 Protists are single cell eukaryotic cells.
 It has cilia around it and can be found in water (pond or lake)
 Since it in found in water, if the concentration is greater
outside than inside the protist, water will flow in through
membrane disturbing homeostasis. That is why protists have contractile
vacuoles that push the water out.
Endosymbiontic Theory
 Endosymbiotic theory proposes that these organelles were
once prokaryotic cells, living inside larger host cells. The
prokaryotes may initially have been parasites or even an
intended meal for the larger cell, somehow escaping
digestion. Therefore, it is believed that a cell engulfed a
non-photosynthetic prokaryote which became a
mitochondria and then it engulfed a photosynthetic
prokaryote which became a chloroplast.
How do cells have different functions if they have same genetic composition?
 The reason is due to differential gene expression
 It means that every cell has the same genetic information and instructions,
however it does not mean that all genes are activated or turned on. Therefore,
each cells are producing different proteins.
 Example, white blood cells will not have same functions as nerve cells
Viruses

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 A virus is an infectious agent (toxin or poison) that attacks cells and takes over
them. They are unable to grow or reproduce outside a host cell, therefore they
are not alive.
 Viruses are very small, they have either DNA or RNA and proteins (not both),
they can’t self-replicate
 Viruses are host-specific because they have specific receptors where they bind
 Once a virus binds to a receptor, they will either enter cell or inject its nucleic
acid into cell
 In either case, the nucleic acid will replicate itself using the machinery of the host
cell
 The Cycle: viral genes are able to take over the host’s metabolic pathways, and
command them to make new copies of the viruses. Once the new copy virus is
made, the original virus will kill the host cell and the newly viruses are released.
LECTURE SIX AND SEVEN: CELL DIVISION
Why do cells divide?

Cells divide for repair, genetic continuity, reproduction, and growth and development.
There are two types of cell division that occurs:
MITOSIS= the reproduction of somatic cells (identical cells)
MEIOSIS = the reproduction of reproductive cells (sex cells)
Mitosis
The whole point of mitosis is to divide a cell into two identical daughter cells to the
parent cell. The mother cell holds the genome (all the genetic material). They have 46

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chromosomes (23 pairs from dad and mom). This cell will undergo mitosis and create
two new cells with 46 chromosomes as well.
Karyotype
When it comes to observing chromosomes, we use a karyotype. This
is a way to organize a person’s DNA. Since a human has 23
chromosomes from the mother and 23 from the father containing
same information coding but different versions of it, the karyotype
will place those two chromosomes next to each other, this is called
homologous chromosomes. The 23rd pair always determines the sex
of the offspring (XX= girl, XY= male). All the other pairs are called
autosomes.
The process of Mitosis

There are two steps to mitosis: Interphase and Mitotic phase
. Interphase
 This is the phase that the cell spends 90-95% of its time
 DNA is in form of chromatin
 G1: this is the first part of interphase; it is the period of active
growth, the cell is getting all the nutrients it needs to reach a
mature size for reproduction
 S: this is second part of interphase; it is when the DNA duplicates
itself. Now the parent cell has 46 double chromosomes (not 92)
 G2: final stage of interphase; the cell is growing again, it is getting ready for
mitosis, the centrosomes duplicate and start producing spindle fibers.
Doubled Chromosomes
They consist of now two sister chromatids bonded together by a centromere.
However even though they are technically two identical chromosomes attached
together, we still consider them as 1 doubled chromosome.
. Mitotic Phase (mitosis, cytokinesis)

 Prophase: take place after interphase; the nucleolus disappears (production of
ribosomes) and the DNA thickens and condenses, spindle fibers begin to form
around centrosome.
 Prometaphase: the nuclear envelope disappears; the centrosomes position
themselves at poles and connect to centromeres.
 Metaphase: the nucleus is completely gone, the chromosomes position
themselves at the metaphase (equatorial) plate

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 Anaphase: the doubled chromosomes are pulled apart to opposite poles

where they are now individual chromosomes (4 turns into 8)(former
chromatid is now chromosome), the cell elongates
 Telophase: nucleoli reappear, the nuclear envelopes develop again, the
spindle fibers break up.
 Cytokinesis: the plasma membrane pinches cytoplasm and creates a cleavage
furrow and splits them into two daughter cells.
Cytokinesis in Plant cells

Since plant cells have a cell wall, it is evident that cytokinesis cannot happen in same
way as in an animal cell. All the steps of mitosis occur the same way. However, for
cytokinesis and end of telophase, small vesicles start to from in between two nuclei and
build a new cell wall.
Problems with Mitosis

Cell division is very controlled. The cells are constantly making sure that everything is
going smoothly. This is called a Checkpoint. The cells will make sure everything is OK
before going to next stage. In the checkpoint, they check size, DNA damage, DNA
replication, chromosomes attached to spindle, etc. HOWEVER, if there is something
wrong or damaged, the cycle of mitosis does not continue until that issue is fixed. If this
error cannot be fixed the cell will undergo Apoptosis = the cell
dies as they do not want to
reproducing damaged cells.
An example of a damaged cell would

be Cancer cells. This is known as
uncontrolled mitosis. It is a disruption of DNA that interferes
with a cell’s ability to control/regulate division. This can create
tumors.
Meiosis
The whole point of meiosis is to reproduce sex cells. It is when two parents produce an
offspring, two sets of genetic material combining together. The main difference between
mitosis and meiosis is that meiosis is producing 4 daughters cell with 23 chromosomes in
each (not identical to parent or one and other).

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Meiosis creates gametes (egg and sperm = reproductive cells). They each have 23
chromosomes that are genetically different in order for when they come together to
create an offspring they equal 46 chromosomes.
Diploid vs. Haploid

Diploid (2N) are cells with two sets of chromosomes equaling 46 in total.
Whereas, haploid (N) are cells that have only one set of chromosomes
equaling only 23 in total. Somatic cells are diploid and sex cells are haploid.
Homologous Chromosomes (Tetrad) (2N)

When you have a diploid cell (look at karyotype above), they have
homologous pairs, which are two chromosomes one coming from
and other from father that code for same gene but not identical.
Same genes, different alleles (different versions).
SO… since somatic cells have 46 chromosome and gametes need

23 chromosomes. Meiosis will occur to convert diploid cells into
haploid sex cells.
The process of Meiosis (meiosis 1 and meiosis 2)

This process involves 2 divisions in order to get 4 haploid daughter cells that are
genetically unique.
1. Meiosis 1
 Interphase: duplicates chromosomes
 Prophase: the homologous pairs stay together because of SYNAPSIS, the
rest is same as mitosis
Synapsis
It is when two chromosomes will give each other some of their genetic information. The
homologous pairs friendly and they start to cross over information to create new genetic
combinations, which is why each sex cell is different. (not crossing over sister
chromatids)
 Metaphase: they homologous pairs still stay together and line up at

metaphase plate.
 Anaphase: SEGREGATION = separate the homologous pairs leaving them
with doubled chromosomes on each side.
 Telophase, Cytokinesis= same as mitosis
Meiosis 1 Conclusion:

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After this we end up with two haploid (double chromosomes) daughter cells with unique
genetic information. Now we want haploid but with single chromosomes, therefore it
will undergo Meiosis 2.
2. Meiosis 2
 No interphase = no duplication of DNA, want double  single
 Exact same steps as mitosis
 Result equal 4 haploid (single chromosomes) sex cells that are genetically
unique
Haploid back to Diploid

In order to get back to diploid, it needs to undergo fertilization. Sperm and egg meet
resulting in 46 chromosomes.
Male vs. Female Gametes

It is important to note that the cell division of eggs and sperms has some differences.
First important difference to acknowledge is that the size difference (egg much bigger).

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EGG= OOGENSIS  out of four, there is only one OVUM, one viable egg
SPERM= SPERMATOGENSIS 4 sperms
Genetic Variation
Mutations are the original source of genetic diversity. The three main ways of getting
genetic diversity is: random fertilization, the crossing over, and the assortment of
homologues.
Independent Assortment of Chromosomes

Homologous pairs orient randomly when in metaphase. The homologous pairs act
independently from the others. Therefore this gives a lot more genetic combinations
possible and increases genetic diversity.
Random Fertilization
Any sperm can fertilize an egg. It is all random – more genetic diversity
Nondisjunction
It is unequal distribution of cell chromosomes during division. It is abnormalities in
chromosome number or structure. It is possible that there can be an extra chromosome
(Trisomy), or lack one (Monosomy). When we want Disonomy (normal).
LECTURE EIGHT: GENETICS

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What is genetics?
Genetics is a branch of biology that deals with biological characteristics inherited from
parents. It therefore, involves sexual reproduction and meiosis.
What are Genes?

 Genes are in our DNA, they are a sequence of nucleotides. They
contain information needed to create a protein, they determine our
characteristics (hair color, eye color, etc.)
 Genes have specific locations on a chromosome, which we call
Gene Locus (specific location on a specific chromosome). When we
observe homologous chromosomes we can see that the gene is the
same in the same location, however different variation of that gene.
What are alleles?

 Alleles are a gene pair. Two homologous chromosomes that have same gene loci
are known as a pair of alleles. Alleles govern the same character but not the
same information.
Dominant and Recessive Alleles

 Knowing that two homologous pairs (one from dad one from mom) have pair of
alleles. You may wonder how is that you have brown eyes when one allele was
brown and other was blue. Well it is because there are Dominant (cap letter) and
Recessive (lower case letter) Alleles.
 Dominant: an allele that masks the presence of another allele (uppercase)
 Recessive: an allele whose presence can be masked by a dominant allele
(lowercase)
 There are 3 different possible combinations possible:
o Homozygous Dominant (PP)
o Homozygous Recessive (pp)
o Heterozygous 8(Pp)
Genotype vs. Phenotype

 Genotype is the combinations of alleles (heterozygous, homozygous)
 Phenotype is the appearance of the characteristic (brown eye, blue eyes)

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 It is the Genotype that will tell us the phenotype, however it does not necessarily
work the other way around.
Genes interact with Environment

 It is impossible to separate nature and nurture. Therefore, the
Phenotype = Genotype + Environment
 The environment molds the phenotype within limits (there is a spectrum).
 For example, living in Florida your skin will adapt and will be more dark
comparing to your natural skin color, however it doesn’t mean that living there
will turn you black.
 Genes therefore set limits.
 Environment that can affect phenotype would be sleep, weather, health, diet
Gregor Mendel
 Gregor was known as the “father of genetics”
 He developed a formal explanation of how characteristics are passed on from
one generation to the next. How did he do this?
 He worked with pea plants and chose flower color as his dependent variable
(easy to observe and quantify)
Mendel’s Model
He created his own model: Mendel’s Model which explained 4 concepts
o There are alternative forms of genes (now known as alleles)
o Each characteristic has two genes coming from each parent
o The two genes can be either dominant or recessive
o Gametes only have one allele due to the law of segregation and then when
sperm and egg unite the second allele is restored
Experiment One
o Pea flowers come in two colors (white –pp or purple –PP )
o He took true breeding plants = plants that are homozygous
o He then artificially crossed a purple flower with a white flower. He removed
stamens (male sex organs) from purple flower and then took pollen from white
flower and lastly fertilized the purple plant.
o RESULT: all offspring’s were purple (Pp) = purple was dominant trait
Experiment Two
o Then he crossed two offsprings (Pp and Pp)
o The result gave a 3:1 ratio. 3 purple, 1 white.
o After many crosses he concluded that the purple somehow always
ended up masking the white resulting dominance.

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o Mendel realized that this was all went back to the LAW OF SEGREGATION. It is a
process in meiosis that separates alleles (splitting homologous pairs and sister
chromatids). This therefore creates the possibility of being white or purple.
Punnett Square
 This a method used in order to predict the ratios of the phenotype
using the genotype.
Test Cross
 When we don’t know the genotype of one parent (for example we don’t know if
its homozygous Dominant or heterozygous), we do a test cross
 This means that we do a punnet square and knowing the genotypes of the
offspring, we are able to determine the unknown genotype
Solving Genetic Problems

 Read problem and record questions to be answered
 Decide on notation for gene and alleles and record decision (chose letters to
represent)
 Decide which combinations result in which genotype (ex: PP homo dom)
 Decide on the genotype of the parents (is it homozygous, heterozygous, must
figure It out using information)
 Do Punnett Squre and record results
 Answer question from beginning

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LECTURE NINE: GENETICS TWO
Dihybrid Cross
 In genetics 1, we were looking at monohybrid crosses, however in this case we
are introducing dihybrid crosses.
 Dihybrid Cross= focuses on two traits, it is two different pairs of alleles on
nonhomologous chromosomes.
 Each pair of alleles are inherited independently due to the law of segregation
(splitting up homologous pairs into sister chromatids)
 It is due independent assortment, each person will give 4 combinations
o Ex: a person who is Rr and Yy will have four possible gamete
combinations of RY, Ry, rY, and ry
Incomplete Dominance
 Before we saw that there is a dominant allele that masks the recessive allele
 However, there are some cases where this dominance does not exist=
Incomplete dominance
 Because of this there will be an intimidate only for heterozygous form between
the 2 forms of homozygous forms.
 Incomplete = blend

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 Codominance = both traits are expressed

o EX: red flower and white flower, will give an incomplete, meaning it
will give a blend of white and red, which equals pink.
o EX: a black chicken and a white chicken, will give a codominance
=both colors white and black are expressed.
Multiple Allelism
 Usually there are only two alleles, however in some cases there can be more
than 2.
 An example of this is blood type, it involves 3 allele options: A (IA), B(IB), O (i).
However, a human can only possess two of them as one comes from mother and
other comes from father
 A and B are codominant to each other and both dominant to O
Pleiotropy (one gene on many different phenotypes)

 Pleiotropy is when one gene will have an affect on multiple aspects of the
phenotype, it affects other gene expressions, one trait influencing another
o EX: cystic fibrosis: a defective protein found in the plasma membrane of
lungs, intestines, pancreas, liver, sweat glands
Polygenic Trait (many genes coding for on phenotype)

 Multiple traits coding for one phenotype. A trait that is influenced by many
different genes
o EX: skin color, there is no just black or just white, it’s a spectrum and will
depend on many genes.
Additive Effects

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 Multiple genes will add up together to form the ultimate phenotype, they all
contribute and come together to make the way you are today.
Sex Chromosomes
 Autosomes are the chromosomes coding for majority of the things in our body,
whereas the sex chromosomes code for the gender
 Sex chromosomes can either be X or Y
 A girl = XX
 A boy = XY
 Sex chromosomes also carry genes for other characteristics known as SEX LINKED
CHARACTERISTICS
o EX: red green colorblindness, hemophilia
o Red-green colorblindness is X-linked and recessive
o For a female to have it both X alleles need to be
recessive (33% to get it)
o For a male to have it only the X allele needs to be
recessive (50% to get it)
Nondisjunction
 The process of meiosis is not perfect, it can make
mistakes
 Nondisjunction is when there is an unequal distribution of chromosomes during
cell division that can happen in autosomal chromosome or sex chromosomes
 Problems from the division of autosomal chromosomes
o Trisomy = 3 instead of 2  down syndrome
 Problems from the division of sex chromosomes
o Turner’s Syndrome = single X chromosome (XO), it lacks a Y so it will develop
as a female
o Klinefelter syndrome = single Y chromosome with two or more X
chromosomes (XXY, XXXXY) because they have Y chromosome they develop
as a male.

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LECTURE 10: ORIGIN OF LIFE AND EVOLUTION
4 main stages required for the process of life

1. The abiotic synthesis of small organic molecules (monomers)
o Stanley Miller experiment discovered the organic molecules formed pn
earth. First, they took water and discovered that smaller molecules
were present in water. With this, their experiment showed the
formation of various simple compounds.
2. The joining of monomers into polymers (monomers polymers)
3. The packaging of these molecules into protobionts, droplets with membranes
that maintain a distinct internal chemistry
4. The origin of self-replicating molecules that would make inheritance possible
o RNA is what allows for replication.
o RNA was known to be created by the ribosomes and to be very flexible.
With this later in time, DNA evolved from RNA. The RNA world was
created before the DNA world.
Cell Life
 Prokaryotes (bacteria) were the first cells to be discovered/created. They
dominated evolutionary history.
o These prokaryotes became autotrophs = producing all required
compounds for life
o A variety of autotrophs emerged, some of which could use energy
(such as light) to form their own food = photoautotrophs
o Types of autotrophs:
 autotrophs = obtain carbon from carbon dioxide
 heterotrophs = obtain carbon from organic molecules
 phototrophs = obtain energy from light
 chemotrophs = obtain energy from chemicals
 Then came Eukaryotic cells, with was created by symbioses and genetic
exchanges between prokaryotes
o Eukaryotic cells were created from the endosymbiont theory: when
mitochondria and chloroplasts derived from prokaryotes that began
living within larger cells and became mutually beneficial.
o Evidence supporting this theory:
 mitochondria and chloroplast about the same size as bacteria
 both have double membranes, circular DNA, and ribosomes (own
protein machinery)

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 As years and years past more lineages ended up becoming extinct, the three
remaining are:
o Bacteria
o Archaea
o Eukarya
History of the Theory of Evolution
 SO before Darwin, many people believed that all species had been created
separately and were unchanging.
 One scientist named Lamarck thought that evolution would happen to the parts
of an individual being used. The parts of the body being used will get stronger
while the parts of the body not used will deteriorate (USE vs. DISUSE).
o EX: a giraffe  believed that if they stretched their necks throughout
their life, their offspring will have a long neck. THIS IS ALL WRONG!
o Lamarck’s thoughts were all wrong, however one thing he did right was
that he was the first to be examining fossils
 Then Darwin and Wallace, came up with the theory of evolution (NATURAL
SELECTION) at the same time
o Darwin observed that birds beck’s changed depending on the seeds eaten
on the Island. He observed 3 similar birds and then created his theory on
evolution
o In in theory there were principles of evolution
1. Variation = due to different alleles, there must be variation within
individuals in a species (needs to be a change/modification)
2. Heredity = the variation is because of differences in their genes
3. Natural Selection = there is a variation in number of offspring
produced associated with the variation trait
4. Survival to the fittest = individuals most suited to the environment
have more chance of survival.
Evolution of Biology
 What is Evolution?
o Definition: An inheritable change from one generation to the next in
characteristics of individuals in a population. A change in the frequencies
of alleles in a population. This change is caused by natural selection.
 Evolutions happen only to Populations NOT individuals. The whole point is that
we are passing on the capacity to change.
 Evolution happens when the alleles change in a population.
o EX: a tiger can have white or orange fur. Originally the proportion of
orange fur alleles were much greater than the white. However, over time
due to adaptation to the environment, the white fur pigment alleles will
increase in proportions.
 What is Natural Selection?

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o Is when organisms with certain characteristics (more suited to their

environment) tend to produce more offspring than other organism in the
same population
o Must follow Darwin’s criteria: variation, inheritance, different offsprings
o It happens at genetic level, with alleles
o It is important to know that evolution and natural selection are not the
same thing. If natural selection happens it does not mean evolution will
100 percent occur.
LECTURE ELEVEN: VALIDATION OF DARWIN”S THEORY
 To validate Darwin’s theory, over the course of years new information arised and
new methods to prove that he was right
 These validations are
o Natural Selection in action
o Homology
o Convergent Evolution
o Biogeography
o Fossils
Natural Selection in Action

 People started to notice that populations would evolve due to the pressures from
changes in the environment.
 An example where people saw this was in moths:
o Before industrialization revolution, the bitch of the trees were white, this
caused for black moths to be eaten by birds more comparing to the white
moths as they were more noticeable. This put a decrease in the black
moth allele frequency and an increased in the white moth allele
frequency.
o However, after the industrialization revolution, the birch became black
putting the white moths more at risk and therefore the opposite
happened; the black moth population started to grow while the white
moths started to die.
o This example allowed people to believe that Darwin’s theory was true
Homology (similarities common ancestor)

 Homology is the study of analyzing similarities between different organisms
resulting from a common ancestor
o Even though structures of organisms have different functions, they have
some similarities that was derived from a common ancestor
 This is an evidence for evolution as we see the similarities yet differences all
coming from one ancestor. There are two types of evidence = the similarities and
the differences:

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o Homologous structures = demonstrate common ancestor (different

organisms coming from one common ancestor = change occurred)
o Vestigial structures = demonstrate descent with modification (structures
that become useless but remain still = shows the change of functions)
 Some homologous structures are Vestigial Structures
o Vestigial structures are useless organs and structures (they are left overs
from ancestors that are not being used nor are harmful)
o It is the vestigial organs that indicate that the organism evolved from the
ancestor in which the organ was functional.
o These vestigial organs continue to persist as they are not harmful
therefore, there is no selective pressure to get rid of them. They become
proof of evolution
o An Example: the skeleton of snakes retain a vestigial structure of an
ancestor. They are not being used and just remain there.
 Embryonic homologies: it is discovered that the embryonic development is very
similar amongst certain organisms. We see this for example in the development
of all vertebrates. Even though we see similarities, these structures end up
developing into different things with different functions.
 Molecular Homology: this reveals that common genetic sequences link all life
forms
o All living organisms share the same genetic code (A, T, G, C)
o Similarities can be found by comparing DNA sequences
Convergent Evolution & Homoplasy (similarities no common ancestor)

 Convergent Evolution = independent evolution where certain organisms will have
similar characteristics due the independent adaptation to similar conditions.
 Homoplasy = occurs when two organisms hold similarities but are not derived
from same ancestor, they just adapt in similar ways but are not related
 This now shows how the environment plays a role
Biogeography
 Biogeography= the study of geographical distribution patterns of living organisms
around the world.
 Species tend to be more closely related to other species from the same area
 WHY? Well due to Pangea = the continent once joined together
o As time evolved the continental plate moved and started to separate. This
caused separation of species and populations. Therefore, from this we
had two of the same species living in two different areas with different
environmental conditions. This caused for their evolution and adaptation
to be different
Fossils
 Fossils are evidence for evolution by natural selection

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 Fossils are mineralized remains of an organisms, looking at line of descent.

 Evolution did not predict that there will be fossilization. It is a geographical
process that occurred proving that evolution does exist as we get to see the
ancestors, the species that got extinct and see the trail to modern versions.
LECTURE TWELVE: EVOLUTION IN POPULATIONS
Populations
 Populations are a group of species living in a particular place at the same time.
 In a population, there can be variation in traits (size, color). These variations
could have been caused by the environment or some due to heredity
(EVOLUTION- inherited from one generation to the next).
 Evolution occurs in a population not in individuals.
Darwin & Mendel

 Darwin discovered natural selection to explain evolution, however he did not
know how these traits would get passed on from one generation to the next.
 Mendel focused on the principles of inheritance.
 Darwin and Mendel combined their theories and created “modern synthesis”
 With this, we started to understand population genetics:
o The science that studies the process of microevolution (how populations
change genetically overtime).
Microevolution
 Microevolution definition:
o Is the change in genetic makeup of a population from generation to
generation (change in allelic frequencies in a population).
o Evolutionary change below the species level. The species does NOT
change, only changes in population
o Example: an area with an abandoned mine, as dramatically been altered
due to the toxic heavy metals. Only grass seeds with heavy metal
tolerances will succeed and end up growing to reproduce. This allele for
tolerance will then pass on to their offspring increasing this variation of
the species. Microevolution as did not change the species but alerted the
allele frequencies.
Gene Pool
 Individuals of a population generally have the same number and kinds of genes,
however these genes come in different allelic forms which leads to variation.
 A gene pool:
o All the alleles for all the loci present in the population (ex: all the alleles
for eye colors, hair types, skin types within a population)
o Diploid organisms have 2 alleles (from mom and dad)

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o Each individual only has a small fraction of the alleles present in a

population’s gene pool.
 When we look at a gene pool and want to see how
many types of genotypes and alleles present in that
gene pool, we can solve it using genotype and allele
frequencies. (ex: solving eye color in a population)
o Note: genotype and allele frequencies must add
up to 1.
o Note: if the population is 1000, then there are
2000 alleles (doubles)
Genetic Equilibrium
 Genetic Equilibrium Definition:
o According to the Hardy-Weinberg Principle: allele and genotype
frequencies do not change from generation to generation (It is the
opposite of evolution) in a population at genetic equilibrium.
 The reason why it is important to look at a population and assume that it at
genetic equilibrium, so we can use it as a control, to see the base line in order to
compare and see the changes.
 Genetic equilibrium happens when in a large population male-female mating are
equally likely and occur randomly. Therefore, allele frequencies in a population
will not change.
 It is still possible to calculate the expected genotype and allele frequencies by
using the phenotype frequencies.
o The equation used:
p + q = 1 (p= dominant allele, q= recessive alleles)
 Genetic equilibrium occurs only if certain conditions are met

o Random mating
o No mutation
o Extremely large population size
o No migration (no gene flow -transfer of alleles from another pop)
o No natural selection
Factors causing Microevolution

 In order for microevolution to occur, certain factors must take place:
o Mutations
o Sexual recombination
o Natural selection

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o Genetic drift
o Gene flow
Mutations
 Mutations create variation
 The only way we can have a new variation of a trait is through mutation
 Mutation Definition
o is a change in the nucleotide sequences of an organism’s DNA (cause new
genes and alleles to arise)
 Mutation can be in somatic cells, however only in mutations in gametes (sex
cells) can be passed on to the offspring.
 Mutation rates tend to be low in animals and in plants (fast in microorganisms)
Sexual Recombination
 Sexual recombination creates variation
 Random independent assortment allows for this variation
 One individual can make multiple offspring with different alleles
 However, this variation does not mean a population will evolve.
 Mutations and Sexual Recombination help great amounts with variations; however
they do not help with modifying the allele frequencies in order for microevolution to
occur (mutations can change allele frequency but small amount, sexual
recombination does not entirely).
Natural Selection
 Natural selection works by differential reproductive succeeds
 In order for natural selection, we need an inheritable variation that makes them
more suited to their environment and more suited for survival
 This results in the potential decline in some alleles and the increase of other
 Natural selection is the only one considered to be adaptive evolution since it
adapts to the environment.
Genetic Drift (works on chance)

 Genetic drift is a mechanism that works entirely on chance. A random change in
allele frequencies in a small population (opposite of natural selection).
 Statistically, the smaller the sample the greater the chance of deviation from a
predicted result.
 One allele may be eliminated from a population purely by chance regardless if
beneficial or harmful
o EX: 10 flowers are exposed to a mowing zone and die depending on
where they are located (chance event). Only 5 out of the 10 were lucky
enough to survive depending on their location. At first the population
had 5 red flowers, however after the
mowing incident, the second population

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only had 2 red flowers. Therefore, as a result in genetic drift we see a

decrease in variation for the red.
 Genetic drift may occur as a result of two situations:

o The bottleneck effect
=occurs when the number of individuals of a large population are
drastically reduced by a disaster (ex: forest fires, hurricanes)
=the ones who survived are totally due to chance
=the genetic drift will continue to change the gene pool until the
population is large enough to eliminate the chance of fluctuations
o The founder effect
= occurs when a few individuals become isolated from a larger
population
=small fraction of a population establishes a new colony; they bring with
them only a small fraction of the genetic variability in the original
population
=allele frequency is different than the parent population
Gene Flow
 Gene flow results from the movement of fertile individuals – migration of
breeding individuals between populations cause a movement of alleles
 May cause a population to lose alleles and the other to gain some
 Mixing of individuals between pops tend to reduce differences between
population over time, which can counter genetic drift and natural selection
 Gene flow happens via migration into or out of a population

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Three ways of frequency distribution due to natural selection

1. Directional Selection
 This is when individuals with one extreme from
the range of variation in the population have
higher fitness (more suited)
 For example: turkeys with large breasts are more
favoured, therefore they will increase
reproduction of turkeys with large breast as they
are more valuable. This causes for an increase in
allele frequencies as large breasts will be more
favoured and more present.
 Therefore, it is going to one extreme
2. Stabilizing Selection
 This is when individuals with intermediate
phenotypes are most fit
 For example, in human birth size. Babies with low
and high birth weights were more vulnerable to
complications, as well as death. Therefore, over
years there were an increase in alleles for the
intermediate birth weight (7-8 pounds) as they were
most fit for survival.
3. Disruptive Selection
 This is when individuals with intermediate phenotypes have the lowest
fitness.
 Both of the extremes had the advantage
 Example: size of male Coho salmon. The larger fish only acquire good
breeding territories, so they usually have high success reproduction.
Whereas, the intermediate fish run out of these good territories. For
the tiny males, they are able to sneak in and fertilize their eggs in good
territories and pass on their genetic material before getting caught.
Therefore, there are more small and large fish.
Sexual Selection
 Is a very specific type of natural selection. It is a type that looks at mating success
 In can result in sexual dimorphism (change in look between males and females),
marked differences between the sexes in secondary sexual characteristics.
 Some traits make individual more attractive to the opposite sex.
 This results in greater reproductive success
 Increase in frequency because they satisfy the conditions of natural selection
LECTURE THIRTEEN: SPECIATION

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Speciation and Macroevolution

 There is a lot of debate and mysteries when it comes to speciation
 Before we were looking at microevolution= change in alleles frequencies in a
population
 However, now when we are talking about speciation, we are talking about
macroevolution
o What is speciation?
= the process by which one species split into 2 or more species (new)
o What is macroevolution?
= evolutionary change above the species level (includes the origin of a
new group of organisms)
Species
 Species are known to be the basic units of biodiversity (life on earth) just how
atoms are the basic unit of chemistry
 What is a species?
o Hard to identify if two things belong to same species as even though it
represent as large group, amongst that group there many variation and
differences causing for our appearances to not be the same.
o So we have to define what a species is:
 According to the biological species concept: Species are natural
populations of organisms that can interbreed with each other and
produce viable, fertile offspring (can reproduce offspring that can also
reproduce). If two organisms cannot interbreed it means that they came
from different species and is what we call reproductive isolation.
Reproductive Isolation
 Reproductive isolation is the existence of biological factors that impede member
of two different species from producing viable, fertile hybrid.
 This causes no exchange of genetic material, no gene flow, it preserve genetic
integrity
 With this, we must question what causes reproduction isolation?
Barriers to Reproduction
 There are many barriers that cause reproduction isolation, however we
categorize them in two aspects:
o Prezygotic barriers (target before fertilization)
o Postzygotic barriers (target after fertilization)
Prezygotic barriers (target before fertilization)

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 make it impossible for individuals to get to the point of mating or if individuals

are able to mate, the male’s reproductive cell is unable to fertilize the female’s
reproductive cells.
 they interfere first with the attempt to mating (getting the opportunity to do so).
This happens due to 3 circumstances
o Habitat isolation = two species live in complete different areas and don’t
have access to one and other (aquatic vs. terrestrial)
o Temporal isolation = certain species breed at different times of the year
o Behavioral isolation = certain females will only mate with a male that will
perform a specific courtship ritual
 They can also interfere after mating occurred (the male reproductive cell
reaching the female’s reproductive cell). This happens due to two circumstances
o Mechanical isolation = some mechanics will prevent mating to be a
success. For example, for snails their shells spiral in different directions
causing for genital openings to not be aligned and not will not fertilize.
o Gametic isolation = sperm will not fertilize egg of another species, sperm
won’t be able to survive, cannot penetrate egg.
 These all prevent the formation of a zygote
Postzygotic barriers (target after fertilization)

 mating’s produce hybrid individuals that do not survive long after fertilization or
if hybrid offspring survive, they are infertile or have reduced fertility.
 result in hybrid offspring = the product of two different species
 The prevention of a hybrid zygote from developing into a viable, fertile adult can
cause 3 possible outcomes:
o Reduce hybrid viability= the result of a hybrid that is very frail and does
not develop into a reproductive adult
o Reduce hybrid fertility = an individuals that grows and is developed and
can live a full life, but is sterile
o Hybrid breakdown= each additional generation, you have more weaker
and sterile individuals
Flaws of the biological species concept

 A useful way to define species, however, there are multiple potential flaws in
this definition:
o First problem is that it is a useless definition for asexual species
o Second problem is that we can have difficulties classifying fossil species.
The different sizes and shapes of fossil bones can’t revel if there was
reproductive isolation between two species. We are unable to know if
one species turned into another.
o Third problem is difficulties in classifying hybridized species. If the
offspring experiences postzygotic barriers then this definition follows.

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However, if the hybrid offspring survives and becomes fertile, then this
definition does not follow. Some examples of this can be in butterflies
or happen due to climate change.
 This leads us to a new concept to define species known as Morphological
species concept
Morphological Species concept (focusing on physical appearance)

 This concept takes an alternative approach to defining species by focusing on
aspects of organisms other than reproduction isolation, such as body size and
shape (focusing on physical features)
 This can be used effectively to classify asexual species.
 Potential problem of this concept: appearances does not always mean that they
are part of same species
Other definitions of Species

 The ecological Species concept = what role does it play in its environment.
 The phylogenetic species concept= evolutionary relatedness, looking at the
closeness of shared ancestor, similarities in molecular sequences.
How do new species arise?

 This is known as speciation = when one species split into two new ones
 The process occurs in two different phases and requires more than evolution
change in a population
o Phase 1 is achieving Reproductive isolation = first we need to get two
groups reproductively isolated, so they end up going on in different
directions where they longer share genes and will evolve independently.
o Phase 2 achieving Genetic divergence = as they evolve separately, they
accumulate physical and behavioral differences overtime that make them
more and more deferent. These differences can be caused by natural
selection, adaptation to their individual environment or mutations.
o Outcome of this: If these differences come to a point where the two
groups cannot interbreed anymore, we say speciation has occurred.
First phase: Reproductive isolation

 Reproductive isolation can occur with or without geographic separation.
 Speciation for this first phase can occur in two way
 Allopatric speciation (geographically separated)
 geographic separation of the populations restricts gene flow (ex: the
separation of the Pangea)
 this will later on lead to genetic divergence due to different
environment
 It is with different selective pressures in differing environments,
mutations and genetic drift that will cause changes enough for that they
no longer interbreed and produce fertile offspring

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 Sympatric speciation (overlap geographically but caused by changes in

chromosomes or habitat)
 it is when two groups still overlap geographically and have access to
one and other but the reproductive isolation will be caused by other
factors such as chromosomal changes and nonrandom mating that will
reduce gene flow. (no geographic isolation)
 this occurs in 2 main ways: a change in ploidy (plants) and a change in
ecology (animals)
 A change in ploidy = polyploidy is the presence of extra sets of
chromosomes in cells due to accidents in cell division (not separating
equally). In some plants, these gametes will be viable which will cause
evolution of plants species.
 a change in ecology = can be some kind of change in the group in their
habitat or sexual selection that will cause for speciation even though their
geographical regions overlap.
Rate of Evolutionary Change

 Evolutionary change can happen a different rates
 Looking at the time course of speciation, there are two different models
o Gradualism= this happens over a course of a long period of time, due to
this fossil records are incomplete as we rarely see all stages of changes
o Punctuated Equilibrium = this is when in a history of a species long periods
of stasis (no evolutionary) change are interrupted by short periods of rapid
speciation I that are perhaps triggered by changes in the environment).
Macroevolution
 all of this brings us back to macroevolution
 This is when we are observing situations where phenotypic differences are so
great that the new species possessing them are assigned to a different taxonomic
category
 Macroevolution requires a complex definition:
o Gradual refinement of existing structure (cumulative change over millions
of speciation episodes)
o Major changes in the body can result from changes in the regulation in
genes that control development of the species and alternation in genes
that control the spatial organization of body parts
 Evolutionary novelties: it is important to recognize that natural selection can only
improve a structure in the context of its current utility, not in anticipation of the
future.
o An example of this are feathers. Before feathers existed, there were light
bones. These light bones did not evolve for the anticipation for flight, they
evolved to improve its current utility on the ground.

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o Also, for feathers, they were originally used for camouflage. Then, once
flight became an advantage, natural selection would have gradually
changed the structures to be adapted for flight.
Adaptive Zones
 Adaptive zones = are ecological niches that are not filled by ancestral organism
(speciation fills new ecological niches)
 They look at where should we anticipate speciation evolution to occur
 Extinction is an important aspect of evolution as it facilitates evolution by
opening adaptive zones (zones that are emptied as a result of an extinction event
and permit adaptive evolution permit other organism to come into that niche
and adapt to it)
o Example: extinction of dinosaurs  massive empty zones which
allowed for mammals to live and adapt into those zones. From there,
species of mammals evolved and diversification increased = this is
called adaptive radiation
Adaptive Radiation
 Adaptive radiation is periods of evolutionary change in which groups of organism
form many new species whose adaptations allow them to fill different ecological
roles or niches.
 It is a period of a burst of speciation
 We see diversification into many different species that fill up the empty zones
 Look at mammal example above
LECTURE FOURTEEN: PROKARYOTES
Domains
 Life on Earth is classified in 3 domains:
o Eukarya (eukaryotic cells)
o Archaea (prokaryotic cells)
o Bacteria (prokaryotic cells)

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Characteristics of Prokaryotic Cells

 most are unicellular
 small (0.5-1 um)
 lack nucleus
 simple genome (one circular chromosome)
 most have cell wall
 ribosome structure different than that of eukaryotes
 Reproduce asexually
What are Bacteria?

 They are simple structures without organelles
 They are commonly classified by shape (3 main shapes):
o COCCI (spherical bacteria)
o BACILLI (rod-shaped bacteria)
o SPIRILLI (spiral-shaped bacteria)
Bacterial Reproduction (very fast)

 Bacteria reproduction and growth happens very fast
 The reason for this is because they carry genetic info in two different ways:
o Chromosome: a single (usually), circular DNA molecule, carries genes for
basic life processes
o Plasmids: Circular DNA molecules that carry genes
for specific functions. Not for basic life, but provide
benefits, such as metabolic plasmids and resistance
plasmids
Binary Fission (asexual)

 Binary Fission is the asexual cell division in bacteria
 They produce 2 daughter cells identical to parent cell (asexual reproduction)
 In order for binary fission to happen, you see a specific environment with certain
conditions (certain temp, pH, etc.)
 If you have ideal conditions some species can double every 20 minutes or for
example a single cell would give rise to a colony outweighing the earth in 3 days
Conjugation (sexual)
 There is another way for bacteria to pass on genetic info, known as conjugation
 It is considered to be sexual reproduction as it involves two individuals
 DNA is transferred by two bacterial cells from same species that were joined
allowing to exchange plasmid information
Evolutionary Significance of Plasmids

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 Why carry plasmids in addition to the main genome? Why are they
significant? It is because Plasmids have add extra pool of genes to a
population that are useful in special circumstances allowing the cell to be
stronger and more resistant to external pressures.
 An example of its importance:
o When a bacterial population is exposed to an antibiotic, the bacterial
cells with the plasmids resistant towards that specific antibiotic will
survive. Since bacteria multiplies very quickly and due to conjugation,
these surviving bacteria cells with the plasmids will quickly reproduce
and exchange genetic info through conjugation so that all the new
reproduced cells will have the antibiotic resistant plasmid. Therefore,
it is a complete cycle that happens often, and it is changing bacterial
species to have them more fit to the environment.
 ENDOSPORES: let’s say there was no plasmids, there are some bacteria that
can survive in hostile conditions by producing endospores, which are
dormant forms (like they go into hibernation). Once the conditions
improve, they can rehydrate and revive. To kill endospores must heat at
high temperatures.
Metabolic Diversity
 Metabolically, bacteria are extremely varied. Many ways where they can
get their energy from. They vary according to:
o Sources of Energy
=Chemotrophs (energy from chemicals)
=Phototrophs (energy from the sun)
o Sources of Carbon
=Autotrophs (atmosphere)
=Heterotrophs (organic compounds such as sugars, fats, etc.)
 Prokaryotic cells can vary also with respect to oxygen:
o Obligate aerobes = require oxygen for cellular respiration (NEED IT)
o Facultative anaerobes = will use oxygen if present but can also grow
by fermentation in an anaerobic environment (the middle ground: it
will use it if it is there, but they can survive in situations where there is
no oxygen present = provide diversity)
o Obligate anaerobes = are poisoned by oxygen
Ecological significance of Bacteria

 When we think of bacteria we think of the harmful things, however they have
an extremely Important significance on our plant
o Most bacteria are saprophytes (decomposers)
o Some are pathogenic (cause diseases)
o Some are also important mutualistic symbionts
o Example of nitrogen fixation

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Saprophytes
 the major role of the bacteria is the decompositions of organic material and
the recycling of nutrients back into the ecosystem. Dead organic matter gets
decomposed by bacteria
Pathogenic
 Bacteria are common animal pathogens and cause diseases, due to medical
advance we are able to fight them
Mutualistic Symbionts:
 Symbiosis = an ecological relationship between organisms of two different
species that live together in direct contact
 Mutualism = a symbiotic relationship in which both partners benefit
o Symbionts in animals: herbivores eat plants (contain cellulose in cell
walls ) but do not produce enzymes to breakdown the cellulose.
Therefore, they house bacteria in their digestive system and the
bacteria have the enzymes to breakdown cellulose.
o Symbionts in Humans: Guts symbionts produce essential vitamins
(ecoli), guts symbionts help prevent pathogens from invading,
symbionts of the skin and the mucus that prevent infection. Note
problems of excessive antibiotic and disinfectant can get rid of our
symbionts that why we must be careful and not take too much.
Nitrogen Fixation
 Perfect example of the importance of bacteria in our ecosystem:
o Gaseous (atmospheric) nitrogen constitutes 78% of earth’s atmospheres
but most life forms are unable to use it in that form. Nitrogen is crucial for
life. In order for nitrogen to be used for growth it must be fixed
(combined) into a molecular form that is usable for life forms, such as in
the form of ammonium or nitrate ions. Bacteria allows that to happen by
fixing nitrogen. They will create these nodules full of nitrogen-fixing
bacteria and will form on the roots of plants allowing for them to grow.
o Bacteria get a supply of energy and the plant gets fixed nitrogen =
mutualistic relationship.
Type of Bacteria: Cyanobacteria

 Cyanobacteria: Anabaena
 Called blue green algae as they were first mistaken to be plan
 They are prokaryotes that are plant-like as they have photosynthetic cells
photoautotrophs (which is not commonly seen in bacteria). Plant-like oxygen
generating photosynthesis.
 Also have specialized cells called heterocyst for nitrogen fixation
 We know they bacteria as they lack a membrane bound nucleus and chloroplasts

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Economic Benefit of Bacteria

 Bacteria provide economic benefits
o Bacteria in the production of antibiotics
o Play a big role in research and technology: Bioremediation, if there is a
contamination, bacteria can be used to breakdown harmful toxins and
decontaminate the area
o Used in sewage treatment and breakdown solid wastes in landfills
Domain Archaea:
 Prokaryotes, most are small (0.5-5 microns)
 Variety in shape: rods, cocci, spirilla and filaments
 Live in extreme environments and therefore called extremophiles
o Methanogens live in areas with no oxygens and release methane as a
waste product
o Extreme Halophiles live in areas where salinity levels are very high,
example the dead sea.
o Extreme Thermophiles live in high temperature, ex: deep sea vents and
highs springs
 No archaea is not known to cause disease in humans
LECTURE FIFTEEN: PROTISTS
Kingdoms of Domain Eukarya

 The Eukarya domain consists of four kingdoms
o Plants, animals, Fungi, and Protists
o Even though, protists are considered to be part of the Eukarya kingdom,
people question it because they are not monophyletic, which means they
do not descend from a common evolutionary ancestor unlike the other
kingdoms.

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 Most of organisms in Eukarya are visible with the naked eye and are multicellular
(plants, animals and fungi kingdoms)
 However, when we look at protists, we see a lot of diversity, they are single cell
and they can only be seen through a microscope
 The first eukaryotes were protists
Characteristics of Protists
 Protists have evolved diverse cell structures, ecological roles, and life histories
 Protists vary in size, structure, mode of locomotions, and reproduction
 Most are motile
 Reproduction ranges from asexual (meiosis) to sexual modes
 Most are aquatic (terrestrial protist are found in mots moist environments)
 Protists may be autotrophic or heterotrophic
 Some are unicellular or multicellular
Types of Protists
 Can classify protists in 3 categories that depend on they eat food
o Animal-Like: ingestive (ingest food) (heterotrophic)
o Fungus-Like: absorptive (absorb food) (heterotopic)
o Plant-Like: photosynthetic (energy from sun) (autotrophic)
Animal-Like
 Mostly single-celled
 Usually motile protists that feed by phagocytosis (cellular uptake of molecules by
the formation of a vesicle formed by the plasma membrane)
 Can be classified into groups according to their mode of locomotion:
o Flagella, cilia, pseudopodia, non-motile parasites
EXAMPLES of Animal-Like
 Amoebas
o They are unicellular
o Have lobe-shaped, pseudopodia (a temporary extension of the amoebas
used for locomotion and feeding)
o Are commonly found in soil as well as freshwater and marine
environments
o Most are heterotrophic (they do this by injesting their prey)
 Ciliates
o Large varied group of protists
o Named for their use of cilia to move and feed
o They have large macronuclei and small micronuclei, which are used for
reproduction and genetic exchange

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o They have a contractile regulation to expel water when necessary to have

a good balance within the cell and the external environment.
 Euglenozoans
o Very diverse
o Include heterotrophs, photosynthetic autotrophs, mixotrophs (they can
do either) and pathogenic parasites
o Ex: Euglena  it is mixotrophic
=they are autotrophs when sunlight is available
=they are heterotrophic in absence of light
o Ex: Trypanosoma  euglenozoan parasite
=causes African sleeping sickness
=transmitted by bite of an infected fly and can enter central nervous
system and if untreated can cause death
o Ex: Giardia  euglenozoan parasite
= intestinal parasite in mammals
=causes “backpackers diarrhea”, common infection among campers
=Giardia is eliminated as cysts in the feces of vertebrates animals
= it is contracted by animals (ex: beavers often implicated as reservoir
host) with cysts contaminating the water and if someone ingests that
contaminated water, then the cysts will start to colonize in the small
intestines
Fungus-Like
 Water molds and slime molds
 They were once considered fungi based on studies
 They are non-photosynthetic, fungus-like organisms (most are decomposers)
 They are found in soil, water and as parasites (on fish and on plants)
 Water Molds
o Ex: the water molds destroyed all the potatoes, event known as the Irish
potato famine
 Slime molds
o Make up the decomposers
o Extends pseudopodia through decomposing material engulfing food by
phagocytosis
o They form a mass of slime during their life cycle
o When conditions become harsh, they develop a different structure until
conditions improve again.
Plant-Like
 EX: Dinoflagellates
o They make up both marine and freshwater phytoplankton (planktonic:
consists of small floating swimming organisms)
o Most are unicellular photosynthetic, flagellated

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o Have a flagellum
o Red tide: when a dinoflagellate population increase out of control and
cause an imbalance in the ecosystem. When this happen, the water
becomes discolored red or brown due to the large presence of
dinoflagellates. In these red tides, the dinoflagellates produce a chemical
which acts as a neurotoxin in other animals, meaning the water will
become toxic prohibiting survival for other animals in that region.
 EX: Zooxanthellae
o They are mutualist symbionts
o Unicellular yellow-brown algae which live symbiotically with corals
o They provide corals with food in the form of photosynthetic products. In
return, the coral provides protection, CO2 and access to the light
o Corals are completely dependent on symbiotic algae
o Zooxanthellae make carbon needed for the coral to build the calcium
carbonate skeleton
 Algae
o They are photosynthetic organisms
o approx. 30% of atmospheric oxygen is produced by algae
o there are unicellular and multicellular forms
o freshwater or marine forms
o Green algae have cellulose in cell walls
o They require light, therefore always found near surface of water
 Desmids
o They are single-celled green algae which can only be found in fresh wate r
 Diatoms
o Mostly unicellular
o Contain silica in cell walls (gives glass-like appearance)
o Unicellular organisms that have yellow-grown chloroplasts that enables
them to photosynthesize
o Are highly diverse in structure
 Green Algae closest relatives to land plants
o They are closet relatives to land plants
=a heterotrophic protist acquired a cyanobacterial endosymbiont and the
photosynthetic descendants of this protists evolved into red algae and
green algae
=they are named for their grass-green chloroplast
=are closely related to plants
Economic Importance of Algae

 Some species are important commercially because they produce agar, which is a
gel-like substance in cell walls and is used to grow bacteria which allows for
experiments to be conducted

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 They also produce Alginates are used as stabilizer in frozen dessert, emulsifiers in
salad dressings, and thickeners in chocolate milk and cream cheeses
 Diatomaceous earth
o this product comes from a large fossil deposits of planktonic algae called
diatoms
o this material is actually the silica cell walls of these protists; it is used as
an abrasive or filtering agent
o ex of products containing diatomaceous earth are: Sensodyne
toothpaste, silver polish, insecticide
Ecological Importance of Protists

 play a key role in the aquatic and terrestrial food chain
 Phytoplankton are the basis of food chains in freshwater and marine
environments
 Phytoplankton = photosynthetic plankton (algae is a major component)
 Zooplankton = non-photosynthetic plankton (includes non-photosynthetic
protists along with other organisms)
LECTURE 16: FUNGI
What are Fungi?

 Eukaryotic cells (part of domain Eukarya)
 Cell walls made out of chitin
 Heterotrophic organisms = they acquire their nutrients by absorption
 They absorb nutrients by secreting exoenzymes = they secret enzymes out into
the environment, breakdown large molecules into smaller more soluble forms
then get absorbed

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Fungal Facts
 They range unicellular organisms (yeasts) to large, complex structures
(mushrooms)
 Most fungi are multicellular
 There are about 1.5 million species just haven’t all been identified yet
 Largest individual organisms = Honey fungus (10 000 kg)
Fungal Body
 Bodies of fungi are made up of tiny filaments called hyphae, which increase the
surface area for absorption.
 Mycelium: filamentous body (mat of hyphae) -usually hidden below the ground
 When we see a lot of mushrooms we can assume that they are connected to one
individual, all connected by mycelium
 Some hyphae are adapted to trap prey not just absorption of nutrients. They are
modified as hoops that construct a nematode and will trap prey
Fruiting Bodies & Spores (reproductive)

 The fruiting bodies is the reproductive structure of a fungus
 A part of the fungus above ground that we know as the mushroom
 After ideal conditions, the fruiting bodies will appear and will produce spores
 Fungi disperse by producing spores (carried by wind, water)
 A variety of fungal fruiting bodies (many different types of mushrooms)
Economic Importance of Fungi and Humans

 Some are used for food:

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o Supermarket mushrooms, morels, truffles

o Ripen some cheese: brie, camembert
o Flavor others: stilton, Gorgonzola
 Some are edible and are very dangerous: ex = Amanita -deadly
Disease and Spoilage in Plants

 There are some species that can cause disease in plants reduce yield or kill plants
 We see this in fruits (berries) or vegetables (potatoes, root crops, corn, grain)
 Eventually if we leave them out we see mould
 Fungal hypha will penetrate the cell wall and will kill the plant
 Mould
o A group of fungi
o Include of fast-growing molds causing for food to rot
Fungal Disease in Humans

 Examples of this (can lead to respiratory issues)
o Athlete’s foot
o Jock itch
o yeast infections
o nail infections
 Fungi in Building – can lead to respiratory issues
o toxigenic fungi produce mycotoxins
o spores and mycelial fragments carry the toxins
o when we inhale those spores, it brings those toxins into the respiratory
system
 Another type that invades lung tissues is Aspergillus
o It is a fungus ball that colonizes in a healed lung scare or abscess from a
previous disease
Types of Fungus: Yeasts

 Fungi that are unicellular
 They reproduce by cell division or by budding (so you have a parent cell with
budding yeast that will come off the parent)
 When we think of yeast we think of bread, bear, wine, etc.
Antibiotics
 Many fungi are natural enemies of bacteria
 Produce chemicals that kill them = Antibiotics (ex: Penicillin is produced from the
fungi penicillium – inhibits the growth of bacterial cells)
Mutualistic Symbionts

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 They are very important to other organism around them and live in a mutualism
with them
An example of this is Lichens = association between fungus and a green algae (not one
organism)
o The lichen can only survive with both of them
o The algae provides fungus with food (organic carbon)
o Fungus provides alga with a suitable physical environment for growth
o They are important pioneers – can break down
rock into soil
o Food source for caribou and reindeer
o When we look at their lichen structures, they
work together, they function as one organism
Mutualism between fungi and plants:

Another example is Mycorrhizae: association between a fungus and a plant
 Mycorrhizae colonize the roots of over 90% of all vascular plants
 Fungus acquires carbon from pant
 Fungus provides plant with nutrients, water, pathogen
resistance, increased resistance to toxic elements in the soil
 Mycorrhizal fungi extend the volume of soil explored by the root
system (increases the surface area allowing them to increase
absorption of nutrients
Special case: Group of achlorophyllous plants

 A family of plants that are entirely achlorophyllous, meaning they are unable to
photosynthesise and produce carbohydrates
 Therefore, in order to survive they have to become parasitic and have to obtain
tehri carbon from other plants like trees
 The way that they do this is by using fungi to steal carbon from photosynthetic
plants
o They will use mycorrhizas to obtain minerals and nutrients , but also to
tap the carbon supplies of nearby plants via tehri roots
o Carbohydrates pass from conifer to the achlorophyllous plants via their
common mycorrhizal partner

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Mutualism between fungi and animals

 They are called Leaf cutter ants = they cut leaves
 They cut these leave and count on a specific type of fungi to break down these
leaves so that they can eat it.
 The ants depend on fungi to convert the plant material in a from that they can
digest
 In return, the fungi depend on the ants to bring them the nutrients from the
leaves, the ants give food to the fungi by transporting the leaves to them
Ecological Significance of Fungi

 They are very important decomposers (decompose plants and animal material
allowing to be digested by other organisms)
 Primary role in ecosystems
 They recycle nutrients in ecosystems
 Many species involved in:
o Break down of wood and leaves
o Some nutrients absorbed and used
o Rest return to soil recycled by plants
o Slow process – years to break down
LECTURE 17: PLANTS
What is a plant?
 Non- motile
 Terrestrial
 Multicellular
 Eukaryotic
 Cellulose in cell wall
 Most contain chlorophyll and produce their own organic compounds
(autotrophic)

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Ecological Importance of a plant

 plant produce oxygen through photosynthesis
 reduce greenhouse gases
 cycle nutrients through ecosystem
 Plants moderate climate (produce shade)
 Plants provide cover and habitat for wildlife
 They build soil (accumulation of dead plant material)
 They hold water and holds soil (a forest prevents soil erosion -keeps in place)
o If no trees are present, then when it rains, it hits the ground with more
force and washes the soil away causing soil erosion
Plant ancestors: Green algae

 Both green algae and plants have:
o same photosynthetic pigments (chlorophyll a and b)
o Both store carbohydrates as starch
o Cellulose- main cell wall component
 The difference:
o Algae adapted for life in water
o Plants adapted for life on land
 Green algae is the closet living relative to land plants
Plant adaptation to land

 A main concern when adapting to land is water loss
o So land plants have a waxy cuticle that covers the epidermis (aerial
portions of plant), prevents desiccation (waterproofing)
o A top layer that prevent water loss
 Another adaption to land, is the stomata
o Tiny pores on the leaf’s surface
o They control the gas exchange (facilitate gas exchange)
o They are made up of guard cells that open and closes the pore
Ancestral Plants
 There are 4 main linages of plants
The Bryophytes (non-vascular plants- mosses, hornworts and liverworts)

 They have no tissues
 Lack vascular system
 Small size (due to reliance eon diffusion to obtain nutrients)
o Do not have true organs (leaves or roots), must rely on diffusion to obtain
nutrients
 Generally, live in moist environments

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 Require water for fertilization (produce a motile sperm that must “swim” to eggs)
 For plants to be successful on land they need a better way of acquiring and
moving water and nutrients
o One way is having tissues
o In order to better adapt to land, plan to had to develop tissues
o Group closely associated cells that work together to perform a specialized
or particular function
o In plants, tissues used in the movement of water and nutrients = Vascular
tissue
o Vascular Tissue are thick walled cells serve as pipes for transporting
water and nutrients throughout the plants
 Vascular Tissue
o Used to transport water and minerals from roots to leaves
o Also transports sugars (fixed carbon) from leaves to storage sites (leaves
or roots)
o There are 2 kinds of vascular tissue:
 Xylem = carries water and nutrients
 Phloem = carries organic molecules (sugar, amino acid, and other
organic products)
o Vascular system: a collection of tissues specialized to transport of water
and nutrients throughout plant
Seedless Vascular Plants (vascular plants- lycophytes, monilophytes)

 Common in moist environments
 Ex: ferns
 They have a sperm that is flagellated therefore still requires water to reach egg,
but unlike the bryophytes they have well developed vascular tissue and plant
organs (leaves, root, stem)
o This supports large upright above ground parts (bigger plants growing
above ground)
o Allows to grow to much larger sizes and grow further above ground
comparing to bryophytes
o With vascular tissue, there is less dependency on water but still needs it
for sperm
 Plants have 3 basic organs
o Root = anchors the plants, nutrients and water uptake, have root hairs to
increaser reface area and used for storage
o Stem = above the ground, provides support for leaves, transport material
from roots to leaves, where we see the growth of plants
o Leaves =site for photosynthesis, large surface area to collect solar energy,
they are flat and thin, they have an epidermal layer (waxy cover) to
reduce evaporation and contain stomata for gas exchange

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 Economic benefit
o Fiddleheads (food)
o Folk medicine (expelling intestinal worms, licorice fern: sore throat and
coughs)
o Fronds thatching houses, basket weaving
 Seedless vascular plants are known to be most primitive vascular plants
o More advanced than mosses: vascular tissue
o Wider range
o Greater size
o Great variety
o However, they are still not as advanced, limited to moist environment due
to flagellated sperm, they lack seeds, so they have to rely on spores
Seed plants - vascular plants (gymnosperms and angiosperms)

 What is a seed
o Specialized structure that contains an embryo in a protective covering
called a seed coat
o It has stored food inside for embryo
o Important means of dispersing offspring
 seeds are an ideal adaptation to land
o it contains developed multicellular embryo (spore single celled)
=root stem and leaves already formed
o contains food supply
=after germination seed nourishes plant until embryo become self-
sufficient
o protected by a seed coat
o does not need to depend on water -no moist environment
 Gymnosperms
o Needle shaped leaves
o Non-deciduous (leaves do not fall off all at once)
o Retain some green leaves year-round =evergreens
o Perennials: live year after year (vs. annuals)
o Evolutionary advancement = it does not rely on water for fertilization
o Cones are the reproductive of gymnosperms
 female cones (megaspores) = produce the egg
 male cones (microspores) = produce pollen grains
o Air borne pollination
= pollen (male gamete) gets to female cone (that contains the egg) via air
=pollen grains have air sacs (provide added buoyancy) allowing them to
be dispersed by winds and get to female cone by great distances

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o The process of fertilization
o Features distinguishing gymnosperms from bryophytes and ferns

= they have vascular plants with seeds
=they produce wind-borne pollen grains
=production of seeds and pollination are features for conifers that allow
for further adaptation to life on land.
o The problem with Gymnosperms is that they carry “naked seeds”
=A naked seed is a conifer seed with their embryos are produced on bare
woody structures (on the cone), they are said to be naked
=producing naked seeds make them vulnerable due to environment
influences, attacked by birds, insects and other animals
 Angiosperms
o They have seeds enclosed in chambers that mature into fruits (not naked
seeds)
o Make up about 90% of all land plants
o They are the most diverse and most successful as they are the most
evolved
o They produce flowers to promote fertilization via animals
o Many of the foods we eat are seeds and fruits of angiosperms
o Floral Structure:
 the base of the flower= receptacle and sepal
 petals attract pollinators
 Petals and sepals are sterile (don’t hold gametes)

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 stamen produce pollen grains, consist of filament and anther, anther is

where pollen is produced
 The carpel produces the megaspores (female gamete), it includes a
stigma, a style, and an ovary (where one or more ovules are contained)
o Once the ovule is fertilized, the ovule becomes seeds and ovary wall
thickens develops into fruit (which protects seeds)
o Flowers are used to attract insects and other animals for pollination.
Leaves are colourful and offers rewards (nectar, wax, pollen)
o There are many different types of pollinators (bees, bats, birds, moths).
Attracted to flowers and will carry pollen

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 Plant Evolution Summary
Plant Adaptation to Hot/Dry Climate

 To limit water loss
o Thick cuticle, fewer stomata, opening stomata only a nighttime to gather
and store CO2
 To store water
o Enlarged stems for water storage. Thicker leaves for water storage
 To take up water:
o Deep root systems

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LECTURE 18: ANIMALIA
Characteristics of Kingdom Animalia

 All are multicellular
 All made up of eukaryotic cells with no cell wall
 They are all heterotrophic (ingest food)
 MOST animals
o Have extensive cell specialization (cells to perform specific functions)
o Animals are motile (at least during one part of their lives)
o They respond quickly to the changes in the environment
o Most animals reproduce asexually (some asexually)
Major Animal Groups

 Very diverse kingdom
 Main groups
Animals are Heterotrophic: Intracellular Digestion

 Animals ingest food, however there are different type of digestion
 Purpose of digestion is to break down edible organic nutrients
 One form of animal digestion is intracellular digestion (simplest
form)

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o It involves the creation of food vacuoles via phagocytosis and breakdown

via release of hydrolytic enzymes from lysosomes
o The sponges perform this (early stages)
Animals are Heterotrophic: Extracellular Digestion

 Another form of digestion is extracellular digestion
 It is the breakdown of food outside cells
 It takes place in a compartment that is continuous with the outside of the
animal’s body
 Like the digestive system of the human body (mouth stomach large and
small intestines)
 Absorption of food via capillaries in small intestines
Exchange with environment

 Animals need to exchange material with their environment
 Cells need a continuous supply of nutrients and wastes must be eliminated
o Imposes limitations to their body plan because we need to have a way to
get material in and release material out
 2 solutions to this problem: (for intracellular digestion)
1. Have a body size and shape such that most cells are in direct contact with the
environment (each cell can exchange material directly with environment).
 small  diffusion (prefer small size)

 Unicellular organisms are in constant contact with the environment (diffusion)
 Simple multicellular organisms have a body size and shape such that most cells
are in direct contact with the environment (diffusion) (flat or simple body plan)
 This allows for circulation through diffusion. They rely on this simple body plan
that absorbs nutrients through diffusion as some simple animals lack an interal
transport system
 Nutrients are passed via diffusion
 Gases and chemical wastes diffuse directly between individual cells and the
environment
2. Circulatory system (A system within the body where this exchange can occur)
 If we have a larger more complex organism, we need another solution:
circulatory system, a system within the body that transports nutrients
 This gives almost every cells access to substances present un the external
environment without having direct contact with it
 Serves to integrate most other body systems (respiratory, digestive, etc.)
 Open circulatory system:
o Bathes the tissues directly (direct exchange between hemolymph & cells)
o Circulatory liquid is hemolymph

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o Animals include arthropods (insects, arachnids,

and most mollusks)
o Heart pumps vessels with open ends. Blood and
interstitial fluid indistinguishable collectively
referred to as hemolymph
o Hemolymph spills out of the open ends of blood
vessels  fill up large spaces called sinuses
o Hemolymph bathes the cells directly
 Closed Circulatory System

o Blood flows through a continuous circuit of blood
vessels
o More efficient at transporting circulatory fluids to
tissues and cells
o Blood flows through a continuous circuit of blood
vessels
o Blood liquid confined to vessels, distinct from
interstitial fluid
o Interstitial fluid = tissue fluid between cells
o Smallest vessels= capillaries
o Capillaries are Thin enough to permit exchange of nutrients, gases,
between blood vessels and interstitial that bathe cells
Shift from water to land

 In order to shift to land there are many systems that need to adapt. For example,
the circulatory system and cardiovascular system
 Movement to land, terrestrial animals must have:
o A moist membrane that allows for adequate gas exchange
o A means of support and locomotion suitable for land
o Means of reproduction and embryotic development in which large
amounts of water are not required
o
Vertebrate phylogeny is reflected in adaptation of the cardiovascular system

 Metabolic rate is an important factor in the evolution of cardiovascular systems
 Close systems allows the higher metabolic rate needed to support an active
terrestrial lifestyle
 When there is an increase in metabolic rates, there is more of complex
circulatory system  powerful hearts

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 There are four different types of hearts
 Fish
 use gills for respiration. Gills are structures specialized for gas exchange
in aquatic environments
 2 heart chambers (1 ventricle and 1 atrium)
 Part of a single circuit blood flow: blood passes through heart
once
 Blood gets oxygenated at gills (capillaries)
 Oxygen rich blood leaving the gills flows to the systemic circulation
(to body capillaries)
 Heart relies on deoxygenated blood (by the time it reaches the
heart there is no more oxygen left to the heart has to rely on
blood with no oxygen, this is only possible because they have a
relatively low metabolic demand)
 blood mixing does not happen
 Consequences: it is less efficient and have low intensity activity
 Amphibians, Reptiles, Birds & Mammals
 One pump the blood gets oxygenated (lungs and or skin)
 Second pump delivers oxygenated blood tissue ells (bring oxygens
to tissues, picks up CO2)
 A double circulations – more efficient hearts
 Amphibians
 Have an intermediate state (an aquatic and terrestrial existence)
 They have 3 heart chambers (2 atria and 1 ventricle with ridge)
=the ridge is not perfect so there is blood
 They have a double circulation = Pulmocutaneous (lung and skin)
and systemic (brings the oxygenated blood to the body)

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 Consequence = they can live on land, however there is mixing of

blood
 Reptile
 They are largely terrestrial, however land and aquatic
 They have a double circulation: pulmonary and systemic
 They have a 3-chamber heart
 They have evolved a wall called a septum. So they have 2 atria and
1 ventricle with septum
 However still this septum is not complete and creates blood
mixing
 Consequences: they can stay underwater but there is still blood
mixing
 Birds and Mammals
 Land
 They have double circulation = pulmonary and systemic
 4 chambered heart = 2 atria and 2 ventricles and a complete
separation between the two, this means that you can take each
system and control is separately which allows for a long more
efficient and lot more output of energy
 Consequence: high output however this means that we need high
energy to sustain this output
 In all mammals and birds (and crocodilian): the ventricle is
completely divided into separate right and left chambers. Four
chambered hearts separate oxygen rich blood from oxygen poor
blood (2 atria and 2 ventricles)
 The left side of the heart pumps and receives only oxygen rich
blood
 While the right side receives and pumps only oxygen-poor blood
 Overview of pulmonary and systemic system of a human
 Contraction of the right ventricle pumps blood into the lungs
through the pulmonary arteries. The blood flows though the
capillaries beds into the left and right lungs where it loads oxygen
and de-loads CO2. Oxygen rich blood returns from lungs through
the pulmonary veins to the left atrium of the heart. The oxygen
rich blood then flows into the left ventricle where it will enter the
systemic circuit and get pump to the rest of the body. This blood
will leave the left ventricle through aorta and will get sent to the
other tissues and get branched into capillaries beds of the arms
and legs, Oxygen poor blood will then come back through veins to
the inferior and superior vena cava and these empty to the right
left atrium and the system starts all over again.

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Structure Of the heart evolved with adaptations to different environments

 Fish least efficient heart and moving up to the other reptile, mammal, etc. the
heart evolved and is more efficient to suit their environment living
Asexual Reproduction in Animals

 There are some animals that reproduce asexually using various methods
 One Method = Regeneration
 this is when a piece of the parent gets detached and it can grow and
develop into a completely new individual
 EX: a sea star
 One method = budding
 when new genetically identical individuals grow out from the parent
organism
 Another method = parthenogenesis
development of an unfertilized egg into adult individual

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 We see this in whiptail lizard

 it is known as an all-female species or population. Only a female, only
an egg and it can develop into an individual without needing a male to
fertilize it
Evolution of Sexual Reproduction in Animals (reproduction in water)

 Animal sexual reproduction was originally adapted for aquatic habitats
 Reproducing in water often involves lack of physical contact between male and
female
 Instead, sperm and eggs released in large numbers into water
 Hopefully some will meet and create zygotes (external fertilization)
Amphibians: reproduction is external

 External fertilization, female releases eggs in water, males releases sperm amid
the eggs
 Eggs must remain in water or else they will dehydrate
Reptiles: reproduction is internal

 Internal fertilization – modification where the sperm can be deposited directly
within the female – remain in her (therefore no longer need to have the zygote
to be in a aquatic environment to keep them from dying out)
 No longer necessary to return to water to reproduce
 Become completely independent of water with the formation of the amniotic
egg (shelled egg)
Amniotic egg
 Is an adaption to internal feralization
 They have an amnion that protects the embryo (in a fluid filed sac) from injury
and dehydration
 Have allantois: collects wastes
 Have a yolk sac: nutrients
 Have a chorion: gas exchange
 Drawbacks of amniotic egg
= insufficient protection from
predators
=cannot survive drastic
environment changes
Mammals

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 They have mammary glands (secrete milk), hair, specialized teeth, enlarged skull
 They have an internal development of young (fertilization is internal)
 This allows for the young to be controlled and not get attacked by predators
 3 groups of Mammals
o Monotremes
o Marsupials
o Placental mammals (eutherians)
Monotremes
 Are a small group of egg-laying mammals consisting of echidnas and the platypus
 Lay eggs (characteristics retained from their reptilian ancestors) and mother
incubate the eggs
 Echidna: after the egg hatches the young echidna, sucks milk from the pores in
the mother’s pouch (they have no nipples)
Marsupials
 Include animals like opossums, kangaroos, and koalas
 The marsupials have internal development of the young however the young are
born prematurely and must be reared in pouches
 In the pouch they attach to a nipple and stay there until they are able to forage
for themselves
Placental Mammals
 The young of placental mammals complete their embryotic development within
a uterus
 Within the uterus, embryo is joined to the mother by the placenta (embryotic
and maternal blood vessels)
 Diffusion and active transport of materials between maternal and embryotic
circulation provides nutrients, exchanges respiratory gases and disposal of
metabolic wastes for the embryo
LECTURE 19: ECOLOGY
Ecology
 The scientific study of the interactions between organisms and the environment
 We are dealing with interactions on different levels
A Hierarchy of Biological Organization

 When we look at the hierarchy and we get to the population level, then we start
to get to ecological organization. We can start looking at interactions
Biomes
 environment spilt into Biomes

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 It is defined by climates and other factors that influence the environment

 It is where individual species can live
 Climate and other factors influence where individual species can live
 Biomes are major life zones characterized by vegetation type (terrestrial) or by
physical environment (aquatic)
 There are different types of major aquatic biomes
o We can’t separate by vegetation by the same way
o We look at aquatic biomes based off certain criteria, such as how deep is
the water, river, lake, etc.)
Ecological Organization
Population
 The lowest level of ecological organization is population
o A population is the same kind of organisms living in one place
 There are factors that may limit geographic distribution of species
o If we see a species is missing from a particular area, we ask why?
o We start thinking and continue to ask questions
Communities
 Includes different kinds of organisms living together and interacting
 When they are interacting, they influence one and other
 The nature of these interactions depends on its species composition (i.e. the
number of different species present, their relative abundance and their feeding
relationships)
 A community
o Association of populations of different species that live and interact in the
same place at the same time

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o Community interspecific interactions
Competition (-/-)
 Interactions between individuals of different species (interspecific competition)
 Negative effect on fitness
 Occurs when necessary resoues are limited and must be shared, i.e, when there
is an overlap in niche
 Mutually detrimental to both od the participants
 Both having to expand energy to compete over food source and has a negative
effect on both. This occurs when necessary resources are limited and must be
shared
Ecological Niche
 The sum of a species use of the biotic and abiotic resources in its environment
 The role of a species in an ecosystem (is a primary, a decomposer(
 It includes spatial or temporal (is there happening during day or night)
 It includes where it lives, what it eats, when it is active, the abiotic conditions it
tolerates (temperature, salinity, etc.)
Fundamental vs realized niche

 Fundamental: Niche that could theoretically be occupied in the absence of
competition and predation (potential)
o When an organism is completely free from limitation (doesn’t have to
deal with competition), it said it be occupied its fundamental niche.
o But there is almost always competition
 Realized: actual occupied niche
o Within the fundamental niche
 However, ecologically similar species can coexist in a community
o If there are one or more significant difference in their niches

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o EX: intertidal zone = challenging environment

 there is high tide and low tide, every time the tide changes the
environment changes
 in this zone there are two different species of barnacles (the
Chthamalus = small and Balanus = large)
 in the natural community, we see that the Chthamalus occupies the
high tide whereas the Balanus were occupied by the low tide
 in the experiment, the Chthamulus were removed and the Balanus did
not go to the high tide, they stayed in their zone. However, when the
Balanus was removed the Cthanmalus moved to the low tide
Competitive Exclusion Principle

 Strong competition can lead to competitive exclusion
o The local elimination of the one of the two competing species
 The competitive exclusion principle
o States that two species competing for the same limiting resources (same
niche) cannot coexist in the same place
o Niche concept and competitive exclusion principle
=two species cannot coexist in a community if their niches are identical
 Gause’s competitive exclusion principle: experiment on two different
paramecium species
= competitive exclusion occurred because both paramecium species have the
same (or very similar) niches
 Does not occur all that often in nature because environmental conditions
fluctuate, genetic changes occur, behavioural changes occur
Resource Partitioning
 Is the differentiation of niches that enables similar species to coexist in a
community
 Different species that utilize resources different parts of niches and reduce
competition of food and allow for overlapping
 Competition for food reduced
Character Displacement
 The process where differences emerge from competition
 Resource partition can cause character displacement
 Darwin’s finches exemplify character displacement
 Competing species evolve slightly different niches to avoid competition
 There is a tendency for characteristics to be more divergent in sympatric
populations of two species than in allopatric populations of the same two species
 2 species will possess greater differences (less niche overlap) when their
populations live together than when they live apart (more niche overlap)

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Predation and Herbivory (+/-)

 Predation = one animal eats another
 Herbivory= animal eats plant or algae
 They both have a positive negative interaction; this means one benefits while the
other does not
 Predation
o An interaction where one species, the predator, kills and eats the other,
the prey
o Feeding adaptations of predators include: claws, fangs, teeth, and poison
o Prey animals also display a great variety of defensive adaptations
o Natural selection shapes the body forms and behaviours of both
predators and prey
Predator Strategies
 Some predators are camouflage to not be noticed by their prey; others may
attract their prey like the anglerfish
Prey Strategies
 Cryptic coloration, or camouflage – makes prey difficult to spot
 Or aposematic coloration warns predators to stay away from prey. Saying “I am
toxic, I will hurt you”
Animals possess a variety of defensive adaptations to avoid predators

 To avoid predation animals may flee, hide, live in groups, or have mechanical
defensives (like a porcupine or skunk) to avoid being preyed upon
Batesian Mimicry (palatable mimicking an unpalatable)

 One interesting defensive type to avoid predation
 This is when one species will gain protection by mimicking the predator
 In some cases, one prey species may gain significant protection by mimicking the
appearance of another
 In Batesian mimicry, a palatable or harmless species mimics an unpalatable or
harmful model
Mullerian Mimicry (both unpalatable)

 This is another type of mimicry
 It is when two or more unpalatable species resemble each other
 Predators will quickly adapt avoiding this particular appearance
 Both species are harmful but by mimicking each other they increase exposure of
predators to this harmful appearance
Herbivory (+/-)
 Herbivory, the process in which an herbivore eats parts of a plant. Therefore, an
advantage for the herbivore and a disadvantage for the plant

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 This has led to the evolution of plant mechanical (spines, tough leaves) and
chemical defenses and consequent adaptations by herbivores
Parasitism (+/-)
 In parasitism, one organism, the parasite derives its nourishments from another
organisms, its host, which is harmed in the process
 EX: Mites living in the trachea of honeybees. They block the airways of the bees,
eventually killing them
 Positive for parasite, negative for host
Mutualism (+/+)
 Both parties benefits
 Relationship that can lead to coevolution
 Two species that rely on one and other
 Ex: Lichen (more examples in other section)
Commensalism (+/0)
 It is a relationship between two species where one species benefits without
really impacting the other (no positive or negative affect on the other species)
 Host – commensal
Interspecific Interactions and Adaptation

 All of these types of interspecific interaction can lead to coevolution
 Coevolution refers to reciprocal evolutionary adaptations of two interaction
species
 It is when one evolution is dependent on another species evolution
 It is a cycle: Adaptation of first species  selective pressure  adaptation of
second species  selective pressure  Adaptation of first species
 EX: with a hummingbird and the flower
 so in some flowers the nectar is deep inside and hard to get, therefore this
puts a selective pressure on humming birds to have a longer beck as in order to
get the nectar it favours birds with longer becks. On the other hand, the flowers
with long bodies will be more protected from predators such as
the birds since it is harder to get. Therefore, this selective
pressure will result in favouring flowers with long bodies. =
coevolution
Food chains
 A community consists of a number of species at multiple
different levels of what we call a food chain
 These trophic levels consist of primary producers, herbivores,
carnivores)
 Energy passes from one trophic level to the next. (from
producers to consumers)

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 If a single plant is consumed by a single grazer, which is eaten by a single

carnivore, then energy is passing through the food chain
 Simple food chains are rare in nature
Food Webs
 In most communities, the animals do not feed in such a way
specialized manner, but may eat many types of plants (creates
more of a food web than a chain) (doesn’t just eat one plant,
will eat many different types)
 At the next level, carnivores also tend to eat a number of
different prey
 This results in an interconnected food web
 Food chains are not isolated units but are linked together in
food webs
Ecological Succession
 Looking at the sequences of changes after a disturbance
 Ecological succession is the transition in species composition In a distributed area
over ecological time. The development of a community after a disturbance
 Let’s say a forest fire took place, how does the area change and rebuild itself?
Primary succession
 This begins in a lifeless area where soil has not yet formed, such a volcanic Island
or moraine left behind as a glacier retreat.
 Initially, only autotrophic prokaryotes may be present
 Next, mosses and lichens colonize and cause the development of the soil
 Once soil is present, grasses, shrubs, and trees sprout from seeds blown or
carried in from nearby areas
Secondary Succession
 Secondary succession occurs where an existing community has been removed by
a disturbance such as a clear-cut or fire, while the soil is left intact
 Herbaceous species grow first, from wind-blown or animal borne seeds
 Woody shrubs replace the herbaceous species and they in turn are replaced by
forest trees
 Stable final stage = climax community (ex: mature hardware forest)

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 Disturbance can distort climax community (fire), it will eventually reconstitute

itself
LECTURE 20: ECOSYSTEMS
Ecosystems
 The ecosystems are the level that includes the community of organisms present
in a particular area and their interactions with their physical surroundings.
Ecosystem Dynamics
 There are two ecosystem dynamics: energy flow and chemical cycling

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Two fundamental processes of the ecosystem

 Regardless of an ecosystem’s size, its dynamics involve two main processes
1) Energy Flow
 energy flows through the system (non-cyclic)
 energy transfer is never 100% efficient
 energy loss as hear dissipated at each step
2) Nutrient Cycling
 nutrients cycle from the abiotic to the biotic
 Energy flows through ecosystems while matter cycles within them
Energy flow through ecosystems

 How does energy an ecosystem
 Energy comes from the sun
 The sun supplies energy that almost all organisms use to carry on their life
processes
 Enters as sunlight  chemical energy (matter) + heat
 Energy trapped by producers  photosynthesis
 Via photosynthesis energy  chemical energy (stored in bonds of organic
molecules ex glucose)
 Energy flow: the passage of energy in a one-way direction thru an ecosystem
 Energy content of organic food passes up food chain; eventually all energy is lost
as heat, therefore requiring continual input

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Trophic efficiency:
• trophic efficiency is the percentage of production transferred from one trophic level
to the next
• range from 5-20% depending on the type of ecosystem
• loss of energy with each transfer in a food chain (energy lost as heat)
Nutrient Cycles in the ecosystem:

• Life depends on recycling chemical elements
• unlike energy, chemical elements are continuously recycled within ecosystems
• 4 main factors in cycles of energy:
• each chemicals biological importance
• forms in which each chemical is available or used by organisms
• major reservoirs for each chemical
• key processes driving movement of each chemical through its cycle
1. Nitrogen Cycle - Bacteria are essential

• Nitrogen contains two nitrogen atoms connected by a triple bond - the reason why
nitrogen is so stable and inert to chemical reactions
• requires a lot of energy to break
• Earths atmosphere is 78% nitrogen
• Essential: proteins, nucleic acids
The terrestrial Nitrogen cycle:

• Main reservoir for nitrogen is in the atmosphere, converted to ammonium or nitrate
for uptake by plants, via nitrogen fixation by bacteria
• nitrogen undergoes a number of microbial transformations

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• organic nitrogen is decomposed to NH4+ by ammonification and the NH4+ is

decomposed to NO3- by nitrification
• Denitrification converts NO3- back to N2
2. Carbon cycle:
• carbon based organic molecules are essential to all organisms
• carbon reservoirs include fossil fuels, soils and sediments, solutes in oceans, plant
and animal biomass, and the atmosphere
• CO2 is taken up and released through photosynthesis and respiration; additionally,
volcanoes and the burning of fossil fuels contribute CO2 to the atmosphere
3. Water cycle
• water moves continually through a cycle of evaporation or transpiration
• Renews the water supply
• Involves an exchange of water between the land, ocean, atmosphere and organisms
• Water enters the atmosphere by evaporation or transpiration
• Water leaves the atmosphere as precipitation
Water Distribution:
• Salt water oceans hold ~97% of surface water
• Glaciers and polar ice caps ~2%
• Land surface water; rivers lakes and ponds ~1%
Cycle:
• Stage 1:
• Evaporation (land to atmosphere)
• Transpiration similar to evaporation, and its the loss of water vapour from
parts of plants
• Stage 2:
• As the water vapour rises in the atmosphere, it cools and condenses, forming
clouds
• The clouds will then produce rain or snow (known as precipitation) which
returns to the Earth’s surface as water
• Stage 3:
• Rain which falls back to Earth lands eventually returns to the ocean
• Percolation through soil - Ground water
4. The Phosphorus Cycle:

• The largest reservoirs are sedimentary rocks of marine origin, the oceans, and
organisms
• weathering and erosion of rocks gradually releases phosphorus as phosphate ions
which are soluble in water
• land plants need phosphate as a fertilizer or nutrient
• when plant materials and waste products decay through bacterial action, the
phosphate is released and returned to the environment for reuse

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• much of the phosphate eventually is washed into the water from erosion and
leaching
• water plants and algae utilize the phosphate as a nutrient
Cycles from land to sediments in ocean back to land

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LECTURE ONE: INTRODUCTION TO BIOLOGY

How do we know if something is living or non-living?

Hierarchy of Biological Order

Example: the brain. No individual neuron is responsible for the processing of

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Form Fits Function

So first we must pick which Domain an organism belongs to:

Binomial System (how to name it)

LECTURE THREE AND FOUR: MACROMOLECULES

Polymers and Monomers

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Monomer = single unit

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o Saturated Fats vs. Unsaturated Fats

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Sickle-Cell Anemia (A genetic disease)

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Roles of Nucleic Acid

Structure of Nucleic Acid

Differences between DNA and RNA

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LECTURE FIVE: CELL STRUCTURE

What are cells?

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 They have a cytoplasm

Cells’ require oxygen, they need their waste products

1. Plasma Membrane = allow for exchanges and

2. Cytoplasm = interior of cell

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4. Ribosome = site of protein synthesis

6. Flagella = a whip-like structure that allows the cell to move

7. Capsule= a outer layer that protects cells from attacks or dehydration

Cell wall more in depth

Eukaryotic Cells: ANIMAL

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Relationship Between Nucleus, ER and Golgi

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The Endomembrane system (PM, ER, GA, Vesicles, Lysosomes, Vacuole)

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Flagella and Cilia

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 Spindle fibers extend from centrosomes and attach onto chromosomes

Eukaryotic Cells: PLANT

When it comes to plant cells, they are very similar to

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 Vacuole store various compounds, such as proteins, inorganic ions, defensive

Eukaryotic Cells: PROTISTS (vacuole)

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LECTURE SIX AND SEVEN: CELL DIVISION

Why do cells divide?

There are two types of cell division that occurs:

MITOSIS= the reproduction of somatic cells (identical cells)

MEIOSIS = the reproduction of reproductive cells (sex cells)