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Title: Biology IGCSE Notes
Description: This note is about all the topic that would appear in the IGCSE exam.
Description: This note is about all the topic that would appear in the IGCSE exam.
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General Biology
Wikibooks
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0 Unported license
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If this document is a derived work
from the contents of one of these projects and the content was still licensed by the project under
this license at the time of derivation this document has to be licensed under the same, a similar or a
compatible license, as stated in section 4b of the license
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Contents
1
Getting Started
2
Biology - The Life Science
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5
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The
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The atom
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Electrons
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Chemical reactions
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11
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The
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6
Chemical Building Blocks of Life
Carbon
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Stereoisomers
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Proteins
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3
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Life:
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History and Origin
Properties of life
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The early earth
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The RNA world?
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Major steps in evolution of life
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19
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6
Cells
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Cell structure
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25
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29
III
Contents
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4
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Microscopes
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1
Biological membranes
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Phospholipid
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Fluid mosaic model
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Membrane proteins
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37
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10 Cell-cell interactions
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11 Energy and Metabolism
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1
Structure of the nucleus
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Chromatin
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Endoplasmic reticulum
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The Golgi apparatus
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Ribosomes
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DNA-containing organelles
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12 Respiration: harvesting of energy
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5 Glycolysis overview
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6 Regeneration of NAD+
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7 Alcohol fermentation
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8 Lactate formation
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9 Krebs cycle: overview
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10 ATP production
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11 Evolution of aerobic respiration
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13 Photosynthesis
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51
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IV
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Chromosome number
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Chromosome organization
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Human chromosomes
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Replicated human chromosomes
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Plant mitosis
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Cancer
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14 Sexual reproduction
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7 Meiosis II
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8 Evolution of sex
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9 Consequences of sex
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15 Genetics
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16 Gregor Mendel and biological inheritance
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17 DNA: The Genetic Material
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4 DNA/RNA components
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5 Chemical structure of DNA
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V
Contents
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DNA replication
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DNA replication complex
DNA replication
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Replication units
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What is gene?
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1 “Central Dogma”
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2 The Genetic Code
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3 Transcription
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4 Transcription bubble
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5 Eukaryote mRNA
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6 Translation
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7 Translation in bacteria
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8 Aminoacyl tRNA synthase
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19 Gene regulation
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2 DNA grooves
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3 Regulatory proteins
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4 Lac operon of E
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1 Point Mutations
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2 Substitution
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3 Larger mutations
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4 Chromosomal mutations
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5 Causes of mutations
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6 Effects of mutations
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7 Further reading
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8 Original notes
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9 Point mutation
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10 Acquisition of genetic variability
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21 Recombinant DNA technology
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VI
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Contents
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13
Restriction endonucleases
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Uses of cloned gene
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RFLP(restriction fragment length
Sanger DNA sequencing
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Genome projects
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DNA chip controversies
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Stem cells
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1 Introduction
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2 Viral Replication
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3 Viral Genome
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4 Viruses Practice Questions
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5 Archaea
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6 Prokaryote evolution
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7 Domains of life: characteristics
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1 Plants
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2 Plant phyla
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3 Plant evolution
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4 Plant phylogeny
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5 Plant life cycles
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6 Moss life cycle
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7 Vascular plants
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8 Vascular plant life cycles
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9 Pterophyta (ferns)
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10 Non-seed plants, continued
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11 Seed plants
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12 Sporophyte/gametophyte
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13 Megasporangium (nucellus)
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14 Pollen
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15 Gymnosperms
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16 Pine life cycle
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17 Other Coniferophyta
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18 Other gymnosperms
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19 Angiosperms
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40
Earliest angiosperm
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Angiosperm life cycle
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Nutrition
...
Types of Fungi
...
Introduction
...
Introduction to animal phyla
Phylum Porifera
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Phylum Platyhelminthes
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Phylum Nematoda
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Phylum Arthropoda
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Phylum Echinodermata
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24 Chordates
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4 Subphylum Vertebrata
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125
...
...
127
127
127
128
128
25 Tissues and Systems
135
26 Epithelial tissue
137
27 Connective tissue
139
28 Muscle tissue
143
29 Vertebrate digestive system
147
30 Circulatory system
151
31 Respiratory system
31
...
31
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31
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155
156
157
157
32 Sensory systems
159
32
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159
32
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159
32
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160
VIII
Contents
32
...
5
Homeostasis
...
161
33 Additional material
165
33
...
166
34 Glossary
167
34
...
168
35 Contributors
169
List of Figures
175
36 Licenses
179
36
...
179
36
...
180
36
...
181
1
1 Getting Started
3
2 Biology - The Life Science
The word biology means, "the science of life", from the Greek bios, life, and logos, word
or knowledge
...
That is why Biology is
sometimes known as Life Science
...
Other branches of science include or are comprised in part of biology studies,
including paleontology8 , taxonomy, evolution, phycology, helimentology, protozoology, entomology, biochemistry, biophysics, biomathematics, bio engineering, bio climatology and
anthropology
...
1 Characteristics of life
Not all scientists agree on the definition of just what makes up life
...
However, with most of the characteristics listed below we can
think of one or more examples that would seem to break the rule, with something nonliving
being classified as living or something living classified as nonliving
...
• Living things are composed of matter structured in an orderly way where simple
molecules are ordered together into much larger macromolecules
...
• Living things are able to grow, develop, and reproduce
...
• All known living things use the hereditary molecule, DNA9
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
wikipedia
...
Living things are organized in the microscopic level from atoms up to cells11
...
Beyond this, cells are organized in higher levels to form entire
multicellular organisms
...
Of course, beyond
this, organisms form populations which make up parts of an ecosystem
...
Example:sub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population,
community, eco systems
2
...
It involves the application
of knowledge
...
Reasoning can be broken down into two categories, induction (specific data is used to
develop a generalized observation or conclusion) and deduction (general information leads
to specific conclusion)
...
Science as we now know it arose as a discipline in the 17th century
...
3 Scientific method
The scientific method is not a step by step, linear process
...
Scientists
must be able to have an "imaginative preconception" of what the truth is
...
They use all
of their knowledge and a bit of imagination, all in an attempt to uncover something that
might be true
...
In an attempt
to find explanations to this curiosity, your mind unravels several different hypotheses
...
Another hunch might be that the
room's lightbulb has burnt out
...
To discover the truth,
10
11
12
13
14
6
http://en
...
org/wiki/homeostasis
http://en
...
org/wiki/cell
http://en
...
org/wiki/macromolecule
http://en
...
org/wiki/organelle
http://en
...
org/wiki/General%20Biology%2FTissues
Scientific method
you experiment
...
No light
...
Still nothing
...
You devise more experiments to test your hypotheses, utilizing a flashlight to prove that
you are indeed not blind
...
If all your predictions
succeed, the original hypothesis is valid and is accepted
...
Perhaps the power is off
...
In order to explain the
observed phenomenon, they develop a number of possible explanations, or hypotheses
...
Experiments are then used to eliminate one of more of the possible
hypotheses until one hypothesis remains
...
After many trials (repeatability) and all predictions have been confirmed, the
hypothesis then may become a theory
...
Inference - Deriving new knowledge based upon old knowledge
...
Rejected Hypothesis - An explanation that has been ruled out through experimentation
...
Experiment - A test that is used to rule out a hypothesis or validate something already
known
...
Theory - A widely accepted hypothesis that stands the test of time
...
The scientific method is based primarily on the testing of hypotheses by experimentation
...
A scientist
will also seek to limit variables to one or another very small number, single or minimum
number of variables
...
Although this may seem unintuitive, the process serves to establish more firmly
what is and what is not true
...
All knowledge
has its relative uncertainty
...
Common
theories include evolution by natural selection and the idea that all organisms consist of
cells
...
8
Charles Darwin
2
...
The seeds of this theory were planted in Darwin's mind through observations made on a
five-year voyage through the New World on a ship called the Beagle
...
Upon his return to England, Darwin pondered over his observations and concluded that
evolution must occur through natural selection
...
However, when another scientist, Wallace, reached similar
conclusions, Darwin was convinced to publish his observations in 1859
...
2
...
These fossils have supported and added subtleties
to Darwin's theories
...
Researchers have also uncovered some of the preliminary mysteries of
the mechanism of heredity as carried out through genetics and DNA, areas unknown to
Darwin
...
Today we can see a bit of evolutionary history in the development of embryos, as certain
(although not all) aspects of development recapitulate evolutionary history
...
2
...
The
challenges have been primarily religious based on a perceived conflict with the preconceived
notion of creationism
...
Some of the proponents of these theories have
suggested that chemical and physical laws that exist today were different or nonexistent in
earlier ages
...
This text is based on notes very generously donated by Dr
...
D
...
15
10
http://en
...
org/wiki/molecular%20biology
3 The Nature of Molecules
3
...
• Particles, from smallest to largest
1
...
Atoms
3
...
Macromolecules
• Origin of matter
1
...
7 billion years ago
2
...
Heavier elements formed in suns, super nova
• Earth's matter predates formation of sun, 4
...
2 The atom
• Example: Hydrogen
• The simplest element
• One proton (+)
• One electron in orbit (-)
• Built by adding one proton (and one electron) at a time
• Number of protons determines atomic number and number of electrons
• Neutrons
• Neutral charge
1
2
3
4
5
6
7
8
9
http://en
...
org/wiki/mass
http://en
...
org/wiki/space%23Physics
http://en
...
org/wiki/volume
http://en
...
org/wiki/Electrons
http://en
...
org/wiki/Protons
http://en
...
org/wiki/Neutrons
http://en
...
org/wiki/Big%20Bang
http://en
...
org/wiki/Hydrogen
http://en
...
org/wiki/Helium
11
The Nature of Molecules
• Contribute mass
• May decay
• Oxygen10
• 8 protons (mass)
• 8 electrons
• 8 neutrons (mass)
3
...
024 x 1023 daltons/gram
• Atoms with same atomic number belong to same element
• Isotopes
• Same atomic number but different atomic mass
• Some are radioactive
• Uses of isotopes
• Radioactive: 3H, 14C, 32P, 35S
• Tracers in biochemical reactions
• Detection of molecules in recombinant DNA technology (genetic engineering)
• Half-life: dating of rocks, fossils
• Non-radioactive (N, C, O)
• Diet of organisms (including fossils)
• Biochemical tracers
3
...
wikipedia
...
5 Chemical bonds
•
•
•
•
Form molecules
Enzymes: make, break, rearrange chemical bonds in living systems
Ionic
Covalent
• Sharing of one or more pairs of electrons
• Called single, double, or triple
• No net charge (as in ionic bonds)
• No free electrons
• Give rise to discrete molecules
• Hydrogen
3
...
7 Water
•
•
•
•
•
•
Essential for life
˜75% earth's surface is water
Life evolved in water
Solvent for many types of solutes
High specific heat
High polarity
• Creates a slightly negative Oxygen and a Slightly positive hydrogen
• allows formation of Hydrogen Bonds
3
...
1 Hydrogen bonding
• A type of polar interaction
• Critical for:
• Protein structure
• Enzymatic reactions
• Movement of water in plant stems
• Weak and transient
• Powerful cumulative effect
13
The Nature of Molecules
• Solubility of many compounds
• Cohesion (capillary action)
• Lower density of ice
• Formed between molecules other than water
• Protein structure
• DNA11 , RNA12 structure
Water organizes nonpolar molecules
• Nonpolar molecules: no polarity (+/-) charges
• Hydrophobic: exclude water because they don't form hydrogen bonds with it
• Consequences:
• Membranes
• Protein structure
• Hydrophilic: polar substances associate with water
Ionization of water: H2 O -> H+ + OH• Forms a Hydrogen ion (H+ ), hydroxide ion (OH- )
• Due to spontaneous breakage of covalent bond
• At 25°C, 1 liter of water contains 10-7 moles of H+ ions: 10-7 moles/liter
pH
•
•
•
•
•
A convenient way of indicating H+ concentration
pH13 = -log[H+ ]
For water, pH = -log[10-7] = 7
Since for each H+ in pure water, there is one OH- , pH of 7 indicates neutrality
Logarithmic scale
Buffer
• Reservoir for H+
• Maintains relatively constant pH over buffering range
This text is based on notes very generously donated by Dr
...
D
...
11
12
13
14
http://en
...
org/wiki/DNA
http://en
...
org/wiki/RNA
http://en
...
org/wiki/pH
4 The Chemical Building Blocks of Life
Building blocks of life
•
•
•
•
•
Carbon based: organic molecules
Carbohydrates: CHO
Lipids: CHO, water insoluble
Proteins: CHONS, structure/function in cells
Nucleic acids: CHONP, hereditary (genetic) information
4
...
2 Carbohydrates
• Principally CHO (rare N, S and P)
• 1C:2H:1O ratio
• Energy rich (many C-H bonds)
• Monosaccharides (principal: glucose3 )
• Simple sugars
• Principle formula: C6 H12 O6
• Form rings in water solution
• Disaccharides (sucrose, lactose)
• Polysaccharides (starch, glycogen, cellulose, chitin)
1
2
3
http://en
...
org/wiki/covalent%20bonds
http://en
...
org/wiki/Hydrocarbons
http://en
...
org/wiki/glucose
15
The Chemical Building Blocks of Life
4
...
4 Lipids
• C-H bonds (nonpolar) instead of C-OH bonds as in carbohydrates
• High energy
• Hydrophobic (insoluble in water)
• Categories
• Fats: glycerol and three fatty acids
• Phospholipids: primary component of membranes
• Prostaglandins: chemical messengers (hormones)
• Steroids: membrane component; hormones
• Terpenes: pigments; structure
4
...
1 Fatty acids
• Hydrocarbon chain
• Even number of C, 14->20
• Terminates in carboxyl group
• Saturated: contain maximum number of hydrogens (all single bonds); maximum energy
• Unsaturated: one or more double bonds
• Usually higher melting point
• Many common oils are polyunsaturated
4
...
5
...
5
...
5
...
• Proteins are often modified after synthesis
• Chemical modification
• Addition of heme groups (hemoglobin, cytochrome)
• Denatured proteins can not function properly
• Proteins are degraded by proteosome as part of constant turnover of cell components
4
http://en
...
org/wiki/Amino%20acid%23List%20of%20amino%20acids
17
The Chemical Building Blocks of Life
4
...
6
...
Paul Doerder, Ph
...
, of the
Cleveland State University
...
The bond connecting 2 of the amino acids
together are called peptide bonds
...
5
18
http://en
...
org/wiki/HIV
5 Life: History and Origin
5
...
Organization: Being structurally composed of one or more cells, which are the basic
units of life
...
2
...
3
...
Growth and Development
5
...
6
...
7
...
5
...
• Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by
natural selection ((macro)Evolution is one example of this)
-This is often attacked for the seeming impossibility for life to have been produced by a
chemical reaction triggered by lightning and the ability of any produced DNA to actually be
in a sequence that could produce a working model of life if replicated
...
It also seems unlikely to some that such huge changes are possible in evolution
19
Life: History and Origin
without evidence of an "in-between stage" that is credible
...
For example, bones from other animals
have been taken accidentally in some cases to be part of a humanoid, and complete skeletons
have been sketched out from a limited number of bones
...
) These explanations contend that life was created by God (or perhaps some other
Intelligent Designer)
...
-This is often attacked for many of the same reasons that religion is attacked, and is often
regarded as superstitious and/or unscientific
...
However, since they are all currently known major hypotheses
(and sometimes hypotheses proven wrong are shown for educational purposes), this
wikibook includes what it can without discriminating unfairly against one hypothesis or
the other
...
3 The early earth
It is believed that the Earth was formed about 4
...
• Heavy bombardment by rubble ceased about 3
...
• Reducing atmosphere: much free H
• also H2 O, NH3 , CH4
• little, if any, free O2
• with numerous H electrons, require little energy to form organic compounds with C
• Warm oceans, estimated at 49-88°C
• Lack of O2 and consequent ozone (O3 ) meant considerable UV energy
Chemical reactions on early earth
• UV and other energy sources would promote chemical reactions and formation of organic
molecules
• Testable hypothesis: Miller-Urey experiment
• simulated early atmospheric conditions
• found amino acids, sugars, etc
...
This is a weak hypothesis at this time
...
5
...
As such, fossils of the earliest cells
do not exist
...
• Bubble hypothesis
• A
...
B
...
Haldane, 1930’s
• Primary abiogenesis: life as consequence of geochemical processes
• Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles
• Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacervates
• Other surfaces for evolution of life
• deep sea thermal vents
• ice crystals
• clay surfaces
• tidal pools
5
...
• Self-replicating RNA molecule may have given rise to life
• consistent with numerous roles for RNA in cells as well as roles for ribonucleotides
(ATP)
• relationship to bubble-like structures is uncertain
5
...
5 by
• resemble bacteria: prokaryotes
• biochemical residues
• stromatolites
• Archaebacteria (more properly Archaea)
• extremophiles: salt, acid, alkali, heat, methanogens
• may not represent most ancient life
• Eubacteria
• cyanobacteria: photosynthesis
• atmospheric O2 ; limestone deposits
21
Life: History and Origin
• chloroplasts of eukaryotes
Cyanobacteria
5
...
Paul Doerder, Ph
...
, of the
Cleveland State University
...
1 What is a cell?
The word cell comes from the Latin word "cella", meaning "small room", and it was first
coined by a microscopist observing the structure of cork
...
Cells are so basic and
critical to the study of life, in fact, that they are often referred to as "the building blocks of
life"
...
According to Cell Theory, first proposed by Schleiden and Schwann in 1839, all life consists
of cells
...
All cells contain:
•
•
•
•
Lipid bilayer boundary (plasma membrane1 )
Cytoplasm2
DNA3 (hereditary information)
Ribosomes4 for protein synthesis
Eukaryotic cells also contain:
• At least one nucleus5
• Mitochondria6 for cell respiration and energy
Cells may also contain:
•
•
•
•
1
2
3
4
5
6
7
8
9
10
Lysosomes7
Peroxisomes8
Vacuoles9
Cell walls10
http://en
...
org/wiki/plasma%20membrane
http://en
...
org/wiki/Cytoplasm
http://en
...
org/wiki/DNA
http://en
...
org/wiki/Ribosome
http://en
...
org/wiki/Cell%20Nucleus
http://en
...
org/wiki/Mitochondrion
http://en
...
org/wiki/Lysosome
http://en
...
org/wiki/Peroxisome
http://en
...
org/wiki/Vacuole
http://en
...
org/wiki/Cell%20Wall
25
Cell structure
7
...
1 Concepts
Plasma Membrane
Phospholipid bilayer, which contains great amount of proteins, the most important functions
are the following:
1
...
2
...
3
...
Model of the fluid mosaic
Describes the structure of the plasma membrane, this model was developed in 1972 by
cellular biologists J
...
Nicholson
...
Proteins
Long chains of amino acids
...
Functions of proteins
Transport oxygen, they are components of hair and nails, and allow the cell interact with
its environment
...
Some
transport proteins called channel proteins form pores or channels in the membrane so
that water soluble molecules pass
...
Reception proteins
They activate cellular responses when specific molecules join
...
Fluid
It is any substance that can move or change of form
...
26
What is a cell?
Gradient
Physical difference between two regions of space, in such a way that the molecules tend to
move in response to the gradients
...
Passive transport
Movement of substances in a membrane that doesn’t need to use energy
...
Facilitated diffusion
Diffusion of molecules across the membranes with the participation of proteins
...
Transport that needs energy
Movement of substances across a membrane generally in opposition to a gradient of
concentration with the requirement of energy
...
Endocytosis
Movement of big particles towards the interior of the cell using energy
...
Pinocytosis
(Literally cell drinking) Form in which the cell introduces liquids
...
It feeds in this case of big particles or entire microorganisms
...
Exocitosis
Movement of materials out of the cell with the use of energy
...
Isotonic
The cytoplasm fluid of the interior of the cells is the same that the outer
...
Hypotonic
The solutions with a concentration of dissolved particles lower than the cytoplasm of a cell
and that therefore do that water enters the cell with osmosis
...
Endoplasmic Reticulum
It is the place of the synthesis of the cellular membrane
...
1
...
Every living organism is formed from one or more cells
2
...
3
...
7
...
3 Common characteristics of all the cells
Molecular components
Proteins, amino acids, lipids, sweeten, DNA, RNA
...
Robert Hooke
He postuled for the first time the term cell
Prokaryotes
Their genetic material is not enclosed in a membrane ex
...
2 History of cell knowledge
The optical microscope was first invented in 17th century
...
Some of the most relevant discovery milestones of the time period include:
• The invention of the microscope11 , which allowed scientists for the first time to see
biological cells
• Robert Hooke12 in 1665 looked at cork under a microscope and described what he called
cork "cells"
• Anton van Leeuwenhoek13 called the single-celled organisms that he saw under the
microscope "animalcules"
• Matthias Jakob Schleiden14 , a botanist, in 1838 determined that all plants consist of
cells
• Theodor Schwann15 , a zoologist, in 1839 determined that all animals consist of cells
• Rudolf Virchow16 proposed the theory that all cells arise from previously existing cells
In 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann
discovered that both plant cells and animal cells had nuclei
...
In 1839, Schwann published 'Microscopic Investigations on the Accordance in the Structure
and Growth of Plants and Animals', which contained the first statement of their joint cell
theory
...
2
...
Rudolf Virchow
famously stated "Omnis cellula e cellula"
...
" The
parts of the theory that did not have to do with the origin of cells, however, held up to
scientific scrutiny and are widely agreed upon by the scientific community today
...
(2) All organisms are made up
of one or more cells
...
(4) Cells carry
genetic material passed to daughter cells during cellular division
...
(6) Energy flow (metabolism and biochemistry) occurs
within cells
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
3 Microscopes
•
•
•
•
•
•
•
Allow greater resolution, can see finer detail
Eye: resolution of ˜ 100 μm
Light microscope18 : resolution of ˜ 200 nm
Limited to cells are larger organelles within cells
Confocal microscopy19 : 2 dimension view
Electron microscope20 : resolution of ˜0
...
4 Cell size
One may wonder why all cells are so small
...
A cell must be able to diffuse gases and nutrients in
and out of the cell
...
Worse, the distance between two points within the cell can
be large enough that regions of the cell would have trouble communicating, and it takes a
relatively long time for substances to travel across the cell
...
They are, once again, less efficient at exchanging
materials within themselves and with their environment, but they are still functional
...
Key concepts: Cell size:
• Is limited by need for regions of cell to communicate
• Diffuse oxygen and other gases
• Transport of mRNA21 and protein22 s
• Surface area to volume ratio limited
• Larger cells typically:
• Have extra copies of genetic information
• Have slower communication between parts of cell
18
19
20
21
22
30
http://en
...
org/wiki/Light%20microscope
http://en
...
org/wiki/microscopy
http://en
...
org/wiki/Electron%20microscope
http://en
...
org/wiki/RNA
http://en
...
org/wiki/protein
8 Structure of Eukaryotic cells
Eukaryotic1 cells feature membrane delimited nucleii containing two or more linear chromosome2 s; numerous membrane-bound cytoplasmic organelles: mitochondria, RER3 , SER4 ,
lysosomes, vacuole5 s, chloroplast6 s; ribosomes and a cytoskeleton7
...
8
...
It is surrounded by a nuclear envelope and has a nucleolus inside
...
1
...
To allow some chemicals to enter the nucleus, the nuclear
envelope has structures called Nuclear pore9 s
...
8
...
2 Nucleolus
The nucleolus appears in a microscope as a small dark area within the nucleus
...
1
2
3
4
5
6
7
8
9
10
http://en
...
org/wiki/Eukaryote
http://en
...
org/wiki/chromosome
http://en
...
org/wiki/RER
http://en
...
org/wiki/SER
http://en
...
org/wiki/vacuole
http://en
...
org/wiki/chloroplast
http://en
...
org/wiki/cytoskeleton
http://en
...
org/wiki/Plasma%20membrane
http://en
...
org/wiki/Nuclear%20pore
http://en
...
org/wiki/DNA%20transcription
31
Structure of Eukaryotic cells
8
...
This is made up of strings of DNA, which typically
measure centimeters in length if stretched out
...
The chromatin14 must be uncoiled for gene expression15 and replication16
...
3 Endoplasmic reticulum
The endoplasmic reticulum17 is a cellular organelle18 made up of a series of extended folded
intracellular membranes
...
There are two main types of endoplasmic reticulum:
• RER: rough endoplasmic reticulum (site of protein synthesis19 ) associated with ribosomes
• SER: smooth endoplasmic reticulum (site of lipid synthesis20 )
8
...
1 Rough Endoplasmic Reticulum
Proteins are directed to the RER by a signal sequence of a growing polypeptide21 s on
the ribosome
...
At the translocon,
the signal sequence and ribosome/polypeptide complex interact with the translocon to open
it
...
The ribosome can continue to
translate the polypeptide into the lumen of the RER
...
1
...
The ribosome can then dissociate, allowing
protein folding within the RER lumen to occur and continuation to the golgi apparatus
for processing of the polypeptide
...
If the protein is destined for storage for later secretion after stimulation or for continuous
secretion then a protease-enzyme which cuts proteins at the peptide bond-can cut the
signal sequence from the growing polypeptide
...
can then
occur
...
wikipedia
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wikipedia
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wikipedia
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wikipedia
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wikipedia
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wikipedia
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wikipedia
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wikipedia
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The proteins are
either modified for extracellular membrane insertion or secretion
...
8
...
2 Smooth Endoplasmic Reticulum
Smooth endoplasmic reticulum produces enzyme22 s for lipid and carbohydrate biosynthesis
and detoxification RER
8
...
3 Sarcoplasmic Reticulum
This is a specialised form of endoplasmic reticulum found in some muscle cell typesparticularly striated, skeletal muscle
...
This reticulum has voltage gated channels which
respond to signals from 'motor neurones' to open and release calcium into the cytoplasm
...
Figure 1 :Image of nucleus23 , endoplasmic reticulum and Golgi apparatus
...
2
...
4
...
6
...
8
...
10
...
Nucleus
...
Rough endoplasmic reticulum (RER)
...
Ribosome on the rough ER
...
Transport vesicle
...
Cis face of the Golgi apparatus
...
Cisternae of the Golgi apparatus
...
22
23
http://en
...
org/wiki/enzyme
http://en
...
org/wiki/cell%20nucleus
33
Structure of Eukaryotic cells
8
...
• Proteins made on the RER are modified and then sorted
• Formation of secretory vesicles
• Formation of lysosomes (intracellular digestion)
Other membrane-bound cytoplasmic organelles include:
• Microbodies25 (generic term)
• Glyoxysome (transforms fat into carbohydrate in plants)
• Peroxisome26 (uses oxidative metabolism to form hydrogen peroxide and is destroyed by
catalase27 )
8
...
Ribosomes themselves are synthesized in the
cell nucleoli28 and are structured as two subunits, the large and the small
...
Prokaryotic and eukaryotic ribosomes are different, the eukaryotic ones being larger and
more complicated
...
6 DNA-containing organelles
Mitochondria
•
•
•
•
Double membrane
Aerobic metabolism, internal membrane
DNA, ribosomes
Give rise to new mitochondria
Chloroplast29
•
•
•
•
Double membrane
Photosynthesis, internal membrane
DNA, ribosomes
Give rise to new chloroplasts
Centriole30 s
24
25
26
27
28
29
30
34
http://en
...
org/wiki/Golgi%20apparatus
http://en
...
org/wiki/Microbody
http://en
...
org/wiki/Peroxisome
http://en
...
org/wiki/catalase
http://en
...
org/wiki/nucleoli
http://en
...
org/wiki/Chloroplast
http://en
...
org/wiki/Centriole
Cytoskeleton
• Microtubule organizing centers
• Animal cells and many protists
• Pair constitutes the centrosome
• Give rise to flagellum during spermatogenesis
• Consist of 9 triplet microtubules
• Mitosis31 , meiosis32
8
...
• Gives the cell shape
• Anchors other organelles
• Vital to intracellular transport of large molecules
The cytoskeleton is composed of 3 main types of filaments:
• Actin33 filaments (7 nm)
• Microtubule34 s: (25 nm) polymer of tubulin; 13/ring
...
8
...
1 Intermediate Filaments
These are rope like filaments, 8-10nm in diameter and tend to give the structural stability to
cells
...
It is keratin which priniciply
makes up hair, nails and horns
...
7
...
They
contain a GTP molecule in order to bind (polymerise)
...
The growth of actin filaments is
concentration dependant-that is, the higher the concentration of free G-actin, the greater
the polymerisation
...
31
32
33
34
35
http://en
...
org/wiki/mitosis
http://en
...
org/wiki/meiosis
http://en
...
org/wiki/Actin
http://en
...
org/wiki/Microtubule
http://en
...
org/wiki/Intermediate%20Filament
35
Structure of Eukaryotic cells
Cilia and flagella are threads of microtubules that extend from the exterior of cells and used
to move single celled organisms as well as move substances away from the surface of the cell
...
1 Biological membranes
Figure 5
Plasma membrane bilayer
37
Membranes
Biological membranes surround cells and serve to keep the insides separated from the outsides
...
Proteins4 serve very important functions in cellular membranes
...
They relay signals in and out of the cell
...
9
...
3 Fluid mosaic model
• Current model of membrane
• Phospholipid bilayer
• Phospholipids
• Move freely in lipid layer, but rarely switch layers
• Different phospholipids in each layer in different organelles
• Glycolipids
• Sterols (cholesterol in animals)
• Transmembrane proteins "float" in fluid lipid bilayer
• also called intrinsic, integral proteins
• Exterior (extrinsic, peripheral) proteins
9
...
wikibooks
...
wikibooks
...
wikibooks
...
wikibooks
...
)
• interact with water, e
...
, hydration shells
• Water moves through aquaporin channels into cell
• Depends upon the concentration of all solutes in solution
• Hyperosmotic solution: higher concentration of solutes
• Hypoosmotic solution: lower concentration of solutes
• Isoosmotic solution: solute concentrations equal
• Water moves from hypoosmotic solution to hyperosmotic solution
Osmotic pressure Bulk transport
• Endocytosis: energy requiring
• Phagocytosis
• Solid material, typically food
• Pinocytosis
• Primarily liquid
** Receptor-mediated endocytosis
• Pits on cell surface coated with clathrin and receptors
• Bind specific proteins
• Exocytosis
• Discharge of materials from vesicle at cell surface
39
Membranes
9
...
g
...
Cotransport channel carries Na+ and another molecule (e
...
glucose)
into cell
• May involve proton (H+ ) pumps (chemiosmosis - ATP production)
This text is based on notes very generously donated by Dr
...
D
...
40
10 Cell-cell interactions
with the environment with each other
10
...
1
...
g
...
g
...
2 Communicating junctions
• Gap junctions
• animals
• small molecules and ions may pass
• Plasmodesmata
• plants
• lined with plasma membrane
• permit passage of water, sugars, etc
...
2
...
Paul Doerder, Ph
...
, of the
Cleveland State University
...
1 Energy
• The capacity to do work
...
jogging)
...
a lion that is about to leap on its prey)
...
g
...
2 Oxidation–Reduction
• Energy flows into biological world from sun
• Light energy is captured by photosynthesis
• Light energy raises electrons to higher energy levels
• Stored as potential energy in covalent C-H bonds of sugars
• Strength of covalent bond is measured by amount of energy required to break it
• 98
...
When
this involves transfer of electrons, it is oxidation–reduction reaction
• Always take place together
• Electron lost by atom or molecule through oxidation is gained by another atom or
molecule through reduction
• Potential energy is transferred from one molecule to another (but never 100%)
43
Energy and Metabolism
• Often called redox reactions
• Photosynthesis
• Cellular Respiration
• Chemiosynthesis
• Autotrophs
• Heterotrophs
11
...
4 Free energy
• Energy required to break and subsequently form other chemical bonds
• Chemical bonds: sharing of electrons, tend to hold atoms of molecule together
• Heat, by increasing atomic motion, makes it easier to break bonds (entropy)
• Energy available to do work in a system
• In cells, G = H - TS
• G = Gibbs’ free energy
• H = H (enthalpy) energy in molecule’s chemical bonds
• TS (T, temperature in °K; S, entropy)
• Chemical reactions break and make bonds, producing changes in energy
• Under constant conditions of temperature, pressure and volume, ∆G = ∆H - T∆S
• ∆G, change in free energy
• If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction,
does not proceed spontaneously; require input of energy (e
...
, heat)
• If negative (–), H is lower, S is higher
...
g
...
5 Enzymes
• Biological catalysts
• Protein
• RNA (ribozyme)
• Stabilizes temporary association between reactants (substrates) to facilitate reaction
• Correct orientation
• Stressing bonds of substrate
44
Enzymes
• Lower activation energy
• Not consumed (destroyed) in reaction
11
...
1 Carbonic anhydrase
• Important enzyme of red blood cells
• CO2 + H2 O → H2 CO3 -> HCO3 + H+
• Carbonic anhydrase catalyzes 1st reaction
• Converts water to hydroxyl
• Orients the hydroxyl and CO2
11
...
2 Enzyme mechanism
• One or more active sites which bind substrates (reactants)
• Highly specific
• Binding may alter enzyme conformation, inducing better fit
11
...
3 Factors affecting enzyme activity
•
•
•
•
•
•
Substrate concentration
Product concentration
Cofactor concentration
Temperature
pH
Inhibitors
• Competitive: bind to active site
• Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation
• Activators
• Bind to allosteric sites, increase enzyme activity
Cofactors
• Required by some enzymes
• Positively charged metal ions
• e
...
, ions of Zn1 , Mo, Mg, Mn
• Draw electrons away from substrate (stress chemical bonds)
• Non-protein organic molecules (coenzymes)
• E
...
, NAD+ , NADP+ , etc
...
wikibooks
...
6 ATP
• Adenosine triphosphate
• Major energy currency of cells, power endergonic reactions
• Stores energy in phosphate bonds
• Highly negative charges, repel each other
• Makes these covalent bonds unstable
• Low activation energy
• When bonds break, energy is transferred
• ATP → ADP + Pi + 7
...
7 Biochemical pathways
• Metabolism: sum of chemical reactions in cell/organism
• Many anabolic and catabolic reactions occur in sequences (biochemical pathways)
• Often highly regulated
Evolution of biochemical pathways
• Protobionts or 1st cells likely used energy rich substrates from environment
• Upon depletion of a substrate, selection would favor catalyst which converts another
molecule into the depleted molecule
• By iteration, pathway evolved backward
This text is based on notes very generously donated by Paul Doerder, Ph
...
, of the Cleveland
State University
...
1 Energy
• Energy is primarily in C-H bonds (C-O too)
• Chemical energy drives metabolism
• Autotrophs: harvest energy through photosynthesis or related process (plants, algae,
some bacteria)
• Heterotrophs: live on energy produced by autotrophs (most bacteria and protists,
fungi, animals)
• Digestion: enzymatic breakdown of polymers into monomers
• Catabolism: enzymatic harvesting of energy
• Respiration: harvesting of high energy electrons from glucose
12
...
3 Respiration of glucose
•
•
•
•
•
C6 H12 O6 + 6 O2 → 6 CO2 + 6 H2 O + energy
∆G = -720 kcal/mole under cellular conditions
Largely from the 6 C-H bonds
Same energy whether burned or catabolized
In cells, some energy produces heat, most is transferred to ATP
12
...
• CO2 is electron acceptor, forming CH4
47
Respiration: harvesting of energy
• Sulfur bacteria
• SO4 reduced to H2 S
• Formation of H2 S set stage for evolution of photosynthesis (H2 S as electron donor
before H2 O)
• About 2
...
5 Glycolysis overview
Glycolysis accounting
• Oxidation
• Two electrons (one proton) are transferred from each G3P to NAD+ forming NADH
2NADH
• Substrate level phosphorylation
• G3P to pyruvate forms 2 ATP molecules
4 ATP (from 2 G3P)
–2 ATP (priming)
2 ATP (net gain)
Summary: The net input of glycolysis is 2 ATP molecules which are used to split one glucose
molecule
...
12
...
7 Alcohol fermentation
12
...
1
48
http://en
...
org/wiki/Lactate
Krebs cycle: overview
12
...
10 ATP production
• Chemiosmosis (Mitchell)
• H+ (from NADH and FADH2 ) is pumped against a gradient into the intermembranal
space of the mitochondrion (creates voltage potential)
• Diffusion back into matrix through ATP synthase channels drives synthesis of ATP (ADP
+ Pi → ATP)
• ATP exits mitochondrion by facilitated transport
12
...
g
...
• Photosynthesis can be divided into two series of chemical reactions: the light (lightdependent) reactions and the dark (light-independent) reactions
...
• Occurs when plants, algae, and autotrophic bacteria absorb light energy and build glucose
...
1 Light Reactions
•
•
•
•
•
Part of the electromagnetic spectrum
Consists of units of energy called photons
Photons at UV end of spectrum have more energy than those at the red end
Occur on the surface of thylakoid disks
Chlorophyll and other plant pigments differentially absorb photons
• Chlorophyll a: light to chemical energy
• Chlorophyll b: accessory chlorophyll
• Chlorophylls absorb primarily blue and red (green reflected back, hence the green
color of plants)
13
...
1 Accessory pigments
• Chlorophyll is a major light gathering pigment
• Absorbs light with considerable efficiency (i
...
, retaining energy)
• Accessory pigments
• Chlorophyll b
• Carotenoinds
• capture light of wavelengths not captured by chlorophylls
51
Photosynthesis
• Confer other colors to plant leaves (autumn colors too)
Photosynthetic steps
• Primary photoevent: light photon captured by photosystem and energy transferred to
electron donated by water
• Electron transport: excited electron is shuttled along imbedded series of electron carriers
to proton pump and electron is transferred to acceptor
• Chemiosmosis: transport of protons back into chloroplast drives synthesis of ATP
13
...
2 The Even More Detailed Light Reactions
What the Light Reactions Do:
The light reactions of photosynthesis occur in chloroplasts in and on the thylakoid disks
...
More specifically, light
turns the chloroplast into an acid battery, and this battery charges up ATP
...
This
means that it contains about a "gazillion" extra electrons
...
The fluid inside the thylakoid disks is positively charged because it contains a lot of hydrogen
(H+) ions
...
The solvent of thylakoid disk
fluid is water
...
Energy is released when H+ ions
(free protons) flow from the inside of a thylakoid disk to the stroma
...
The protons pass through special channels (made of protein) in the thylakoid membrane;
this reaction is 'exothermic
...
Since one reaction wants to go, and the other one doesn't, and since the first reaction releases
energy and the second one absorbs energy, the two reactions are known to be 'coupled'
together so that the first fuels the second
...
Chlorophyll Molecules on a Thylakoid Disk:
Hundreds of chlorophyll molecules cover the surface of a thylakoid disk, making the disk
green
...
52
“Dark” reactions
13
...
2
...
The dark reactions
occur in the stroma of a chloroplast
...
They'll occur in the dark until the chloroplast's supply of ATP runs out
(usually about 30 seconds)
...
This
means that it involves a whole lot of chemical reactions, and it uses a lot of different enzymes
to catalyze the reactions
...
Therefore it takes a lot of energy to break the bonds and separate the carbon
atoms from the oxygen atoms
...
When inorganic carbon (like from CO2) is being added to an organic molecule (such as
sugar), this is called carbon fixation
...
Some portions of this text is based on notes very generously donated by Paul Doerder, Ph
...
,
of the Cleveland State University
...
Doerder
...
3 Prokaryote cell division
• Binary fission
• Doubling of cell contents, including DNA
• Fission to divide contents
• Segregation of replicated genomes by growth of membrane between attachment points
• Partitioning of cytoplasmic components
• Escherichia coli
• Capable of cell division every 20 minutes under optimal conditions (DNA in continuous
state of replication)
• Model organism of bacterial cell division
53
Photosynthesis
13
...
• Genetic evidence showed that the bacterial chromosome is circular long before there was
corroborating physical evidence
...
5 Chromosome number
•
•
•
•
•
1N = number of chromosomes in gamete
1N = haploid chromosome number
2N = number of chromosomes in somatic cells (cells that are not egg or sperm)
2N = diploid
Deviations from N or 2N are usually lethal in animals
Chromosome numbers
13
...
7 Chromosome organization
13
...
9 Chromosomes
• Homologous pairs
• Inherited one from each parent
• Identical in length and position of centromere
• Contain identical or similar genes
• Homologous pair = homologs
• Morphology
• After replication, consist of two sister chromatids attached to a centromere
13
...
11 Mitotic cell cycle
• Cells exiting the cell cycle are said to be in G0
• Cell cycle time varies with stages of life cycle and development, with G1 the most variable
• DNA replication occurs during S phase of the cell cycle following G1
...
55
Photosynthesis
13
...
13 Mitosis
• Nuclear division
• equational division of replicated chromosomes
• chromatids move to opposite poles
• Continuous process
• prophase
• metaphase
• anaphase
• telophase
• Driven by motors and microtubules
• No change in chromosome number
• N → N by mitosis
• 2N → 2N by mitosis
• May be accompanied by cytokinesis
Kinetochore Microtubules attach to kinetochores
...
14 Plant mitosis
• Similar to animal mitosis
• New cell wall formed between cells from membrane partition
Cell cycle control
• Cell cycle events are regulated by protein complexes and checkpoints
• Discovered by microinjection of proteins in to eggs, by mutational analysis and by
techniques of molecular biology
Molecular control of cell cycle: Cdk and cyclin
• Cyclin dependent protein kinase (Cdk)
• Phosphorylate serine/threonine of target regulatory proteins
• Function only when bound to cyclin
• Cyclin: short-lived proteins that bind to cdks
13
...
g
...
16 Cancer
• Unregulated cell proliferation
• Cancer cells have numerous abnormalities
• >46 chromosomes
• Mutations in proto-oncogenes
• Encode proteins stimulating the cell cycle
• May be regulated by phosphorylation
• Often over expressed in cancer cells
• Mutations in tumor-suppressor genes
• Encode proteins inhibiting the cell cycle
• Often bind to products of proto-oncogenes
• May be regulated by phosphorylation
13
...
D
...
57
14 Sexual reproduction
14
...
2 Sexual life cycle
Typical animal life cycle
•
•
•
•
Meiosis occurs in germ line cells in gonads producing haploid gametes
All other cells are somatic cells
Alternation of generations
Sexual intercourse
14
...
4 Prophase I: synapsis
•
•
•
•
•
Complete alignment of replicated homologs
Synapsis occurs throughout the entire length of a pair of homologs
Key to chromosome segregation
Synapsis, crossing over
Subdivided into 5 continuous stages
14
...
6 Microtubules and anaphase I
• During prophase microtubules attach to kinetochores on one side of centromere
• The metaphase checkpoint insures proper attachment
• A phosphorylation event initiates motor activity and anaphase
14
...
8 Evolution of sex
• Asexual reproduction: all offspring genetically identical to parent
60
Consequences of sex
• Sex: recombination destroys advantageous combinations
• So why sex?
• Many hypotheses
• Effect repair of genetic damage?
• Much pachytene repair as well as gene conversion
• Some protists form diploid cells in response to stress
• Recombination breaks up combinations of genes favoring parasites, thus reducing
parasitism?
14
...
D
...
61
15 Genetics
63
16 Gregor Mendel and biological
inheritance
Charles Darwin1 , for all he contributed to the science of biology, never knew about the
mechanism by which living things inherit traits from previous generations, or how new traits
arise
...
DNA allows for stable inheritance of traits: the code in
each strand of DNA is replicated precisely through the pairing of basic units along each
strand
...
However, when even one base pair is added to a new strain of DNA in an order differently
than in the parent chain, it can be the basis of a mutation
...
Even the smallest
difference in a strand of DNA can result in a change in traits that can cost the life of the
organism
...
In humans, the
example of Sickle cell anemia3 is commonly given as its origin is a difference of only one
base pair in a section of DNA that encodes red blood cells
...
Each one has a set nucleotide4 , and together all of the genes (and some
sequence of DNA that apparently do not code for any biologically important functions)
together make up the entire chromosome5
16
...
wikibooks
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
2 Mendel’s experiments
•
•
•
•
•
•
•
•
•
•
•
1856, began experiments with the garden pea, Pisum sativum
1865, presented results to the Bruno natural history society, which he helped found
1866, published his results in proceedings of the society
Naegeli encouraged Mendel to reproduce results in another species, which failed because
the species did not undergo true fertilization
discrete traits in Pisum sativum
• pure-breeding lines
• dominant/recessive alleles
alleles are two alternate versions of a gene
• gametes contain hybridized chromosomes that are formed during meiosis
• homozygous has two of the same allele
• heterozygous has two different alleles
reciprocal F1 crosses (all exhibiting dominant phenotypes); F2; F3
counted offspring, noted ratios
inferred genotypes from phenotypes
tested hypotheses with testcrosses
attempted to repeat with another species
16
...
2
...
4
...
6
...
Seed form (round or wrinkled)
Cotyledon color (green or yellow)
Seed coat color (white or colored)
Pod form (inflated or constricted)
Pod color (green or yellow)
Flower position (axial or terminal)
Plant heights (tall or short)
16
...
5 Modern Y chromosome
Y-chromosome is the most evolved chromosome
...
But if mutation occurs at sex
determining region or zinc factor then it will not code for testis determining factor, and
results in normal female
...
16
...
Trisomy 21 (Down) exception
• Monosomy 2N ** 1
• Lethal except XO
• Usually maternal origin in humans
16
...
16
...
16
...
The individual suffering from this type of
syndrome has 47 chromosomes instead of the normal 46
...
Most cases of mongolism were found to occur in children born by women in their forties
...
Their most prominent feature is the Mongolian folds in their eyes; hence, the
term mongolism
...
Individuals having the syndrome
show the following characteristics:
•
•
•
•
•
testes are small
sperms are never produced
breasts are enlarged
body hair is sparse
individuals are mentally defective
The same abnormal meiotic division may occur in females
...
Such egg, when fertilized by a Y-bearing sperm, will not develop (YO)
...
68
17 DNA: The Genetic Material
17
...
That is, a nucleic acid with two sugars
...
DNA is found in all
kingdoms of life
...
A molecule of DNA is chemically stable (it
does not have a 2-prime alcohol group
...
• antiparallel
• Double helix
• Semiconservative replication
• Sequence of nucleotides encodes functional RNA or polypeptide
17
...
3 Hershey-Chase Experiment
The Hershey and Chase experiment was one of the leading suggestions that DNA was a
genetic material
...
They did two experiments marking either the DNA in the phage with
a radioactive phophorus or the protein of the phage with radioactive sulfur
...
In the bacteria that was infected with the radioactive protein the bacteria
was radioactive, not the DNA
...
17
...
4
...
The "backbone" of the double
helix is composed of phosphates connected to a five carbon sugar called deoxyribose,
...
Purines contain
Adenine(A) and Guanine(G) and have two rings in their structures
...
17
...
6 3D structure of DNA
• James Watson1 and Francis Crick2 ( 19533 )
• Nucleotide
• Keto and amino forms of bases
• Chargaff’s rules
• X-ray crystallographic data ( Rosalind Franklin4 )
17
...
wikipedia
...
_Watson
http://en
...
org/wiki/Francis_Crick
http://en
...
org/wiki/1953
http://en
...
org/wiki/Rosalind_Franklin
DNA replication
DNA model
• Double helix of polynucleotides
• antiparallel
• 3’-5’ phosphodiester bonds
• Base pairs held by hydrogen bonds
• AT
• GC
• There are about 10 base pairs per turn of helix
• model has predictive power
• mode of DNA replication
• encoding of genetic information
17
...
coli bacterium in a culture containing 15N (a heavy isotope of nitrogen)
• bacterium assimilated the 15N into their DNA
• a similar process was then done using 14N, a lighter isotope
• following centrifugation, the densities were observed to be that of combined in the
middle, and 14N on top, thereby confirming the semiconservative model
17
...
10 DNA polymerases
• Prokaryotes, E
...
e
...
11 DNA replication complex
•
•
•
•
Helicase "unzips" the DNA double helix
Primase: synthesize RNA primer
Single-strand binding proteins
DNA gyrase (topoisomerase)
• DNA polymerase III
• DNA polymerase I (remove primer, fill gaps)
17
...
13 DNA replication fork
• primer required by all DNA polymerases
17
...
15 Replicon
A region of DNA that is replicated from a single origin
...
16 What is gene?
• Garrod
• “inborn errors of metabolism”
• Alkaptonuria: enzyme deficiency
72
What is gene?
• Beadle and Tatum
• One gene one enzyme
• Genetic and biochemical analysis in Neurospora
• Today: gene is sequence of nucleotides encoding functional RNA molecule or the amino
acid sequence of a polypeptide
This text is based on notes very generously donated by Paul Doerder, Ph
...
, of the Cleveland
State University
...
1 “Central Dogma”
18
...
3 Transcription
• RNA polymerase
• NTP substrates
• Synthesizes single stranded RNA complementary to template strand of DNA
• New nucleotides to 3’ end
• Begins at promoter site
• no primer necessary
• Ends at terminator site
• Much posttranscriptional modification in eukaryotes
75
Gene expression
18
...
5 Eukaryote mRNA
• Synthesized as pre-mRNA, processed in nucleus
• 5’ end: GTP cap placed in inverted position
• Essential for ribosome recognition
• 3’ end: poly-A tail; non-templated addition of ˜50-250 A nucleotides; stability
• Introns: intervening sequences removed
18
...
7 Translation in bacteria
tRNA
• Transfer RNA
• Two important parts
• Anticodon
• Hydrogen bonds with mRNA codon
• 3’ end
• Accepts amino acid (using energy of ATP)
• Aminoacyl-tRNA synthetase
76
Aminoacyl tRNA synthase
18
...
9 Ribosome structure
18
...
11 Translation
• Initiation complex
• Small ribosomal subunit
• mRNA
• fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)
• Initiation factors
• Elongation
• Ribosome
• mRNA
• tRNAs
• Elongation factors
18
...
13 Elongation, translocation
• incoming tRNA enters the A site
• rRNA catalyzes peptide bond formation
...
• empty tRNA leaves via E site; recycled
• A site ready for next charged tRNA
18
...
3’ AG removal sequence
• Not essential to genes
• May constitute >90% of gene
77
Gene expression
• removed from pre-mRNA to form mRNA
• Exon: often codes for functional domain of protein
• translatable mRNA
This text is based on notes very generously donated by Paul Doerder, Ph
...
, of the Cleveland
State University
...
1 Transcriptional control
• State of chromatin
• Euchromatin: transcriptionally active
• Heterochromatin: transcriptionally inactive
• Chemical modification of histones
• Methylation of bases
• Transcription factors
• Bind to DNA at promoter or other regulatory sites (enhancers)
• Recognize base sequence through major and minor grooves
• Recruit RNA polymerase
19
...
3 Regulatory proteins
• Activity may depend upon allosteric binding of small molecules
• cAMP
• Co-repressors
• Inhibitors
• Binding to promoter region may “bend” DNA, making it accessible to other regulatory
proteins
19
...
coli
•
•
•
•
Single promoter region for cluster of genes
Regulated and transcribed as a single unit
Operons typical in prokaryotes
Repressor: turns OFF gene expression
lac repressor
• Turns off transcription by blocking access by RNA polymerase
• repressor in activated by allosteric binding of lactose
Regulation in eukaryotes
• Both proximal (promoter) and distal (enhancer) to gene
• Typically transcription unit encodes a single polypeptide
• Promoter
• TATA box
• Other elements (regulatory sequences) may be present
• Enhancers
• Work upstream, downstream, close, far from gene
• Bend DNA
19
...
D
...
(This Page was Last Edited December 2005)
80
20 Mutation
A mutation is a permanent change to an organism's genetic material (DNA1 or RNA)
...
An organism's genetic material is made up of polymers (chains) of four different nucleotides3 ,
like a recipe book written in a language of only four letters
...
Mutations come in a number of forms:
20
...
These come in the form
of substitutions, insertions and deletions:
20
...
The altered codon codes for a different amino acid substitution
...
Transitions: It is the replacement of one purine in a polynucleotide chain by another
purine(A by G or C by A) or one pyrimidine by another pyrimidine(T by C or C by T)
2
...
1
2
3
http://en
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org/wiki/DNA
http://en
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org/wiki/General%20Biology%2FEvolution
http://en
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org/wiki/nucleotide
81
Mutation
20
...
1 Insertion
20
...
2 Deletion
20
...
3
...
3
...
3
...
4 Chromosomal mutations
Chromosomal mutations involve changes to entire chromosomes
...
4
...
4
...
4
...
4
...
4
...
4
...
5 Causes of mutations
20
...
Only mutations in germ-line cells can be passed on to children, while mutations
elsewhere can cause cell-death or cancer
...
6
...
They may occur in a non-coding region (outside of a gene or within
an intron), or they may occur within an exon in a manner that does not alter the final
amino acid chain
...
6
...
6
...
This in turn can render the resulting protein
nonfunctional
...
20
...
4 Nonsense Mutation
20
...
7
...
1993
...
Harper Collins ISBN 0006552439
...
7
...
evowiki
...
8 Original notes
• “Rare” change in nucleotide sequence
• Somatic vs germline
• only those in germline are heritable
• Point mutation
• Single nucleotide change
• Change in gene position
4
http://en
...
org/wiki/Mutation
83
Mutation
•
•
•
•
Transposition
Chromosomal rearrangement
Mutagenic agents
Raw material for evolutionary change
20
...
10 Acquisition of genetic variability
• Mutation
• Sex (fusion of genomes)
• Recombination
• Crossing over
• Reciprocal (may result in gene conversion)
• Unequal (gives rise to gene families)
• Independent segregation
• Transposition by transposons
• Conjugation in bacteria
• One way transfer from donor to recipient
20
...
12 Barbara McClintock
• Discovered transposons in perhaps greatest and ultimately most important intellectual
endeavors in genetics
• Maize
• Worked alone
• Transposons: likely responsible for considerable evolution in eukaryotic genomes
• Likely origin of viruses
This text is based on notes very generously donated by Paul Doerder, Ph
...
, of the Cleveland
State University
...
1 Recombinant DNA technology
• Uses
• Detailed study of gene function
• Homeostasis, response to stress
• Development (birth defects)
• Evolution of genes informs on evolution of life
• Human betterment
• Medicine
• Identification, treatment of genetic disorders
• Molecular medicine: from deduced amino acid sequences, design better drugs
• Foods
• Improve crop yield, resistance to disease
• Improve nutritional value
• Forensics
• DNA fingerprinting: guilt or innocence
21
...
g
...
3 Restriction endonucleases
Gene cloning
• Cloning:
• Restriction digestion of DNA
• insertion of restriction fragment into cloning vector
• Bacterial plasmid
• Bacterial virus
• Yeast artificial chromosomes
• Transformation of bacteria with recombinant plasmid, virus
• Screening for clone of interest by using reporter genes or resistance upon exposure to
anti-biotic
21
...
5 Other molecular procedures
• Polymerase chain reaction (Mullis)
• Amplifies target DNA without cloning
• Target amount can be single molecule
• Amplified DNA can be sequenced, cloned, etc
...
6 RFLP(restriction fragment length polymorphism)
analysis
• Basis of DNA fingerprinting using SNP - single nucleotide polymorphisms and repeats of
DNA sequence
• Many uses
• Criminal cases using multiple probes
• Parentage
• Species identification
• Gene evolution
• Species evolution
21
...
8 Automated sequencing
Typical machine
• • 2 hour sequencing run
• 600-1000 bases per sample
• multiple samples
• Up to 500,000 bases per day (12 hr)
• Data processed by computer
• In big labs, sequencing reactions also are automated
21
...
g
...
21
...
• Designed to detect:
• mutated genes (SNPs)
• expressed genes
• Instant DNA profile (“GATTACA”)
21
...
12 Gene patenting
• Techniques to study and manipulate genes are patented (e
...
, cloning and PCR)
• Should genes be patented?
• Are they the intellectual property of the discoverer?
• Don’t they belong to all of us?
• Should indigenous peoples be compensated for useful genes extracted from their local
plants and fungi?
90
Stem cells
21
...
D
...
91
22 Classification of Living Things
22
...
1 Classification of Living Things & Naming
With so many flora and fauna on planet Earth, there must be a method to classify each
organism to distinguish it from others so it can be correctly identified
...
For example, supermarkets and grocery stores organise their
products by classifying them
...
In science, the practice of classifying organisms is called taxonomy (Taxis
means arrangement and nomos means law)
...
He used simple physical
characteristics of organisms to identify and differentiate between different species
...
To distinguish different levels of
similarity, each classifying group, called taxon (pl
...
To remember the order, it is helpful to use a mnemonic device
...
The taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise
things based on new discoveries and information
...
Binomial nomenclature is used to name an organism, where the first word beginning
with a capital is the genus of the organism and the second word beginning with lower-case
letter is the species of the organism
...
The scientific name can be also
abbreviated, where the genus is shortened to only its first letter followed by a period
...
europaeus'
...
They help to eliminate problems, such as mistaken identity and false assumptions, caused
by common names
...
An example of the latter is the comparison between
crayfish and catfish, where one might believe that they both are fish when in fact, they are
quite different
...
22
...
2 Eukaryotes & Prokaryotes
Recall that there are two basic types of cells: eukaryotes and prokaryotes
...
Some characteristics of eukaryotes are:
•
•
•
•
•
•
•
Large (100 - 1000 μm)
DNA in nucleus, bounded by membrane
Genome consists of several chromosomes
...
Bacteria fall under this category
...
Asexual reproduction common, not by mitosis or meiosis
...
0
...
Today's living prokaryotes are extremely diverse and different from eukaryotes
...
g
...
The three domains are as follows:
Archea (Archeabacteria) consists of archeabacteria, bacteria which live in extreme
environments
...
Eubacteria consists of more typical bacteria found in everyday life
...
Eukaryote encompasses most of the world's visible living things
...
94
Stem cells
22
...
4 The Six Kingdoms
Under the three domains are six kingdoms in taxonomy
...
Protista, the third kingdom, was introduced by the German biologist Ernst Haeckel in
1866 to classify micro-organisms which are neither animals nor plants
...
For example, some protists can exhibit
properties of both animals and plants
...
Mushrooms
and moulds belong in this kingdom
...
Eubacteria are bacteria, made up of small cells, which differ in appearance from the
organisms in the above kingdoms
...
They have cell
walls made of peptidoglycan
...
These bacteria are in their own category as detailed studies
have shown that they have unique properties and features (ex
...
Their cell walls lack peptidoglycan
...
0
...
As the world changed
in climate and in geography as time passed, the characteristics of species diverged so much
that new species were formed
...
For an organism to change, genetic mutations must occur
...
For most
eukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces
haploid gametes from the original parent cells
...
Over time, with enough
arrangement of genes and traits, new species are produced
...
One goal of taxonomy is to determine the evolutionary history of organisms
...
The comparison in
anatomy and structure is based on data from development, physical anatomy, biochemistry,
DNA, behaviour, and ecological preferences
...
Their arms' sizes and proportions may be different, but the anatomical
structures are quite similar
...
Biological features from a common evolutionary origin are known as
homologous
...
For
example, although guinea pigs were once considered to be rodents, like mice, biochemistry
led them to be in their taxon of their own
...
0
...
As with the Scientific Method, scientists develop a hypothesis on the
history of an animal and utilise modern science and technology to prove the phylogeny
...
Expanding on phylogeny,
cladistics is based on the assumption that each group of related species has one common
ancestor and would therefore retain some ancestral characteristics
...
Such characteristics are known as derived characteristics
The principles of phylogeny and cladistics can be expressed visually as a cladogram,
a branching diagram which acts as a family (phylogenetic) tree for similar species
...
In
order to determine the most likely cladogram, the derived characteristics of similar species
are matched and analysed
...
0
...
If taxonomists had to select an existing kingdom to reclassify, which of the six would
most likely be chosen? Why?
2
...
What would be the binomial name
of this organism?
b) Give the abbreviation of the binomial name
...
a) Irish moss belongs to the genus Chondrus
...
Give the
binomial name
...
4
...
Which of the following data would most accurately
prove this correct?
a) biochemistry
96
Introduction
b) DNA
c) appearance
d) development
e) A, B, C
5
...
A taxonomist discovers Organism A and Organism B and wishes to classify them
...
b) Both organisms have a tail
...
d) Both organisms are nocturnal
...
DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a
cell's nucleus
...
1
...
a) Chondrus crispus b) C
...
B 5
...
B
22
...
However,
they are not biological organisms so they are not classified in any kingdom of living things
...
Viruses
are merely strands of DNA or RNA surrounded by a protective protein coat called a capsid
...
Outside of a host cell, viruses are
completely inert
...
Viruses are classified based on their shape, replication properties, and the diseases
that they cause
...
Viruses pathogenic to humans are currently classified into 21 groups
...
Such viruses are called bacteriophages
...
2 Viral Replication
As previously stated, viruses are not a biological life form so they cannot reproduce by
themselves
...
In order to enter a cell, a virus must attach to a specific receptor site on the plasma membrane
of the host cell
...
In some viruses, the attachment protein
is not on the surface of the virus but is in the capsid or in the envelope
...
22
...
1 Lytic Cycle
1
...
2
...
Firstly, the virus can inject
its nucleic acid into the host cell
...
When the virus
breaks out of the vacuole, it then releases its nucleic acid into the cell
...
Replication: The virus's nucleic acid instructs the host cell to replicate the virus's
DNA or RNA
...
Assembly: New virus particles are assembled
...
Lysis and Release: The virus directs the production of an enzyme which damages
the host cell wall, causing the host cell to swell and burst
...
22
...
2 Lysogenic Cycle
1
...
Entry: Similar to Lytic Cycle
3
...
When integrated
in a host cell this way, the viral nucleic acid as part of the host cell's chromosome is
known as a prophage
...
Host Cell Reproduction: The host cell reproduces normally
...
5
...
At any time, a cell undergoing the lysogenic cycle can
switch to the lytic cycle
...
A notable
example of a RNA-based virus is HIV, a retrovirus
...
The retrovirus force RNA into cell, by either one of the two methods of entry (See
above)
...
In the retrovirus are reverse transcriptase enzymes, which catalyses the synthesis of a
DNA strand complementary to the viral RNA
...
Reverse transcriptase catalyses a second DNA strand complementary to the first
...
4
...
Similar to the concept of
a prophage, this incorporated DNA is called a provirus
...
5
...
22
...
The
entire genome can exist as a single nucleic acid molecule or several nucleic acid segments
...
Not all viruses can reproduce in a host cell by themselves
...
For example, some viruses have coded instructions for only
making a few different proteins for the viruses' capsid
...
Therefore, the lack of coded instructions
cause some viruses to need the presence of other viruses to help them reproduce themselves
...
Lastly, it is worthy to note that 70% of all viruses are RNA viruses
...
22
...
As the name implies, the Tomato Spotted Wilt Virus targets tomatoes
...
2
...
Many people have had cold sores, which are caused by infection with the herpes
simplex virus
...
Which cycle would the
herpes simplex virus undergo?
4
...
In adulthood, many people suffer from shingles, an altered
form of the varicella zoster virus
...
Would an antibiotic work for a person suffering from a cold of flu? Explain
...
22
...
g
...
5
...
g
...
6 Prokaryote evolution
• Tentative, subject to change
• Derived largely from molecular systematics (rRNA sequences)
• Note: most bacteria can’t be cultured, thus hard to study! (Studied by PCR of water/soil
samples)
1
2
100
http://en
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org/wiki/%2FAnswers
http://en
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org/wiki/General%20Biology%2FClassification%20of%20Living%
20Things%2FEubacteria
Domains of life: characteristics
22
...
D
...
22
...
This is the kingdom of organisms
with strange, atypical characteristics
...
The majority of protists are microscopic
...
9 Classification of Protists
There are three phyla of protists, based on their type of nutrition
...
Protozoa (animal-like protists) are heterotrophs that ingest or absorb their food
...
Algae (plant-like protists) are autotrophs they get nutrition from photosythesis
...
Slime moulds and water moulds (fungus-like protists) are also heterotrophs, like
protozoa
...
10 Protozoa
As heterotrophs, protozoa scavenge materials from their surroundings
...
Protozoa can be parasitic as well; they may live inside larger organisms,
like humans
...
Protozoa are generally difficult to identify due to their varied shape
...
Tiny blood parasites may be only 2
μm long
...
Furthermore, different protozoans have their own complex life cycles
...
Nevertheless, protozoa can move, and so, they are classified based on their methods of
locomotion
...
005 mm to 50 mm
• lack cell walls
they love environment and each other
...
11 Algae
Algae are much simpler than protozoa
...
Algae can
exist as a single cell or as giant seaweeds 60 m in length
...
Since algae belong in the kingdom Protista, algae is a broad term used to
denote all aquatic eukaryotes which photosynthesise; algae can differ in size and shape as
well
...
22
...
1 Chlorophytes
Chlorophytes resemble plants the most
...
Chlorophytes can be unicellular or multicellular
...
22
...
2 Phaeophytes
Phaeophytes are nearly all multicellular marine organisms, which are known to us as seaweeds
...
The cellulose and alignic acid help to retain water and prevent seawood from drying out
when exposed to air at low tide
...
Their bases strongly anchor the algae to the rocky
seabed and prevent them from being washed out to sea
...
22
...
3 Rhodophytes
Rhodophytes are typically found in warmer seawater, and are more delicate and smaller
than brown algae (phaeophytes)
...
They also have mucilaginous material to
resist drying
...
11
...
They are also one
of the biggest components of plankton, a free-floating collection of microorganisms, eggs,
and larvae
...
The reproduction cycle of chryosophytes is particularly interesting
...
Since diatoms have a rigid cell wall with an outer
layer of silica (found in sand and glass), the daughter cells produced by mitosis must fit
inside the original cell wall
...
The reduction in size continues until the diatoms produce sexually, producing a
zygote which eventually grows to the original size as it matures
...
11
...
They have protective coats
composed of stiff cellulose
...
The longer flagellae propels the dinoflagellate, while the second shorter, flatter
flagellae functions as a rudder
...
Since they lack cellulose plates, they make
their home in coral reefs and animals, such as sea anemones, and molluscs
...
This is why there are nutrient-rich coral reefs in malnutritions water
...
Such pyrrophytes can produce toxins which may injure or kill wildlife,
and additionally any consumers of contaminated wildlife
...
11
...
They are mainly autotrophic or heterotrophic, depending if they have a red, light-sensitive
structure called an eyespot
...
12 Slime molds & Water molds
There are two phyla of slime moulds and one phylum of water moulds
...
12
...
Oomycotes differ from other moulds with the presence of spores and their sexual life cycle
...
12
...
This streaming blob containing many nuclei is called a plasmodium
...
12
...
When in unfavourable conditions, each acrasiomycete cell gathers together to form a pseudoplasmodium
...
One acrasiomycete cell joins with others to form a pseudoplasmodium
...
The pseudoplasmodium shrinks and forms a smaller plasmodium
...
The plasmodium migrates to a suitable environment
...
The plasmodium develops a sporangia, where original parental nuclei has divided by
meiosis into haploid spores to be germinated
...
When favourable conditions arise, the spores germinate and are carried away by animals
or the wind
...
Cycle repeats
...
13 Protists Practice Questions
1
...
The protozoan Giardia lamblia can inhabit a human body's intestinal tract and cause
gastroenteritis
...
b) Would the relationship between this protozoan and human being be mutualistic, commensalistic, or parasitic?
104
Protists Practice Questions
3
...
Of the six phyla of algae, which phyllum/phyla would agar be made from?
4
...
Can coral reefs exist in nutrient-poor areas? Explain
...
1 Plants
•
•
•
•
•
•
•
•
•
•
•
Multicellular
Cellulose cell walls
Chlorophylls a and b
Develop from embryophyte
Alternation of generations
Major food source for terrestrial life
Atmospheric O2 and CO2 balance
Coal deposits
Intimate association with mycorrhizal fungi
>250,000 species (˜500,000?)
Taxonomy
• State of flux
• DNA sequencing
• Developmental studies
• Division (old literature) = phylum (new literature)
• ˜12 phyla, 9 of which are vascular plants
23
...
3 Plant evolution
• Evolved from green algae, likely related to charophytes
• Evidence
• DNA sequences
• homologous chloroplasts: chlorophyll b and beta-carotene; thylakoids in grana;
• Cellulose in both groups; also peroxisomes
• Mitosis and cytokinesis similar
• Sperm ultrastructure
107
Multicellular Photosynthetic Autotrophs
23
...
1 Terrestrial adaptations
• Stomata: pores in leaves for exchange of gases; prevent desiccation
• Secondary metabolites:
• cuticle: waxy coating to prevent H2O loss
• lignin: hardens wood
• sporopollenin: resistant polymer; coats pollen
• predator defenses
• Embryonic development
• gametangia in early plants
• spores; seeds
• Mycorrhizae
• Water/food conducting systems
23
...
5 Plant life cycles
• Alternation of generations
• Sporophyte
• diploid
• produces spores in sporangia
• Gametophyte
• develops from spore
• haploid
• produces gametes in gametangia
• Haplodiplontic life cycle
23
...
7 Vascular plants
• Most have roots
• Aerial shoot systems
• Vascular tissue
• xylem: water, mineral transport
• phloem: food transport
• Lignin
• Branched sporophyte is dominant stage
• amplified production of spores
• evolution of complex plant bodies
• Dominated Carboniferous (360 my)
108
Vascular plant life cycles
23
...
9 Pterophyta (ferns)
•
•
•
•
•
•
•
Non-seed plant
Sporophyte conspicuous (vascular tissue)
Rhizome: ground stem, roots
Fronds: leaves
Sori: clusters of sporangia
Motile sperm require external water for fertilization
Originated in Devonian, 350 my
Tree fern Fern life cycle
23
...
g
...
11 Seed plants
• 1st appeared in Devonian, 360 my
• Seed develops from ovule, protects embryo
• withstands drought
• dispersal is enhanced
• no immediate need for water for germination
• Heterosporous
• male gametophyte: arise from microspores
• female gametophyte: arise from megaspores in ovule in ovary
• Two groups
• gymnosperms
• angiosperms
109
Multicellular Photosynthetic Autotrophs
plant
23
...
13 Megasporangium (nucellus)
•
•
•
•
Key to seed development
Nucellus: solid, fleshy, surrounded by integuments derived from sporophyte (seed coat)
Entire structure called ovule
Flower may have many ovules
23
...
15 Gymnosperms
• “naked seed”
• ovule not fully enclosed by sporophyte at time of pollination
• Conifers, cycads, gnetophytes, Ginkgo
• Small, inconspicuous plants to giants like sequoia
• Conifers: to carry cones fv
• male cones, Female conesvv
• evergreen
23
...
17 Other Coniferophyta
• Cycadophyta: cycads
• tropical, subtropical
• flagellated sperm
• Gnetophyta
• e
...
, Ephedra, Mormon Tea
• Ginkgophyta: Ginkgo
110
Other gymnosperms
• only one surviving species
• diocious (separate % and &trees)
23
...
19 Angiosperms
• Flowering plants, Anthophyta
• monocots- single seed leaf (grasses, lilies, etc
...
g
...
19
...
20 Earliest angiosperm
• What is earliest angiosperm?
• Recent analysis of nucleotide and amino acid sequences suggests that Amborella, a tropical
plant found only on the island of New Caledonia, is closest relative to flowering plants
23
...
22 Angiosperm life cycle
This text is based on notes very generously donated by Paul Doerder, Ph
...
, of the Cleveland
State University
...
23 Introduction
Although you may not recognise fungi, they are just as prevalent as plants and animals
...
A few types of fungi are unicellular
...
However, the majority of fungi live are multicellular
...
In a mushroom, the
111
Multicellular Photosynthetic Autotrophs
hyphae are densely packed so it is difficult to see the individual structures when a mushroom
is eaten
...
The main part of the fungi is underground in a whole web of hyphae, called a mycelium
...
Each fungal
cell may have one or more nuclei and remains connected to the mycelium because the septa
are porous, allowing cytoplasm to flow through the hyphae and fungal cell walls, made of a
hard material called chitin
...
23
...
When they find a source of food (e
...
dead wood, orange peel) ,
they decompose it and digest it
...
These smaller molecules diffuse into the fungus, where
they are used to allow growth and repair
...
For example, athlete's foot grows on the
human foot
...
However, they are friendlier species of fungi
...
For example, most trees have fungi living in close contact with their roots
...
The fungi gets its source of food (organic
nutrients) while delivering food to the plant
...
• The fungal cells help to maintain air and water flow in the soil around the roots
...
23
...
Firstly, they make asexually produce through fragmentation
...
The second method is by spores
...
They are additionally light enough to be blown away for hundreds of kilometers
...
Their sexual properties can be analysed to classify the
four phylla of fungi
...
26 Types of Fungi
23
...
1 Zygospore Fungi (Zygomycetes)
This phyllum includes bread moulds and other saprotrophs
...
1
...
2
...
Note that the zygospore is
NOT diploid yet; the haploid nuclei are simply clumped together
...
Immediately, a thick wall develops around the zygospore to protect it from drying and
other hazards
...
4
...
5
...
6
...
7
...
23
...
2 Club Fungi (Basidiomycetes)
This phyllum increases mushrooms and shelf fungi
...
1
...
2
...
The dikaryotic mycelium
grows faster then the haploid parental mycelia
...
Environmental factors cause the dikaryotic mycelium to form compact masses which develop into basidiocarps, short-lived reproductive structures
...
4
...
5
...
They undergo meiosis to develop haploid basidiospores, a
term referring to a basidiomycete's spores
...
Still remaining on the basidiocarp, the haploid basidiospores eject, fall from the basidiocarp,
and are dispersed by the wind when mature
...
In a favourable environment, the basidiospores germinate and grow into short-lived
haploid mycelia
...
Back to Step #1
...
27 Key Terms
synapomorphy
23
...
Ideally, we would NOT define this or any taxon using
symplesiomorphies (shared ancestral or primitive characteristics) or homoplastic characters
(the independent evolution of similarity, or "convergent evolution")
...
32
...
As you consider the characteristics listed
below, ask yourself whether or not each is a synapomorphy
...
29 Characteristics of an Animal
• There is no one universally accepted definition of an animal
...
• Animals:
• Are multicellular, heterotrophic eukaryotes
...
• Share certain reproductive characteristics
...
Animals are multicellular heterotrophic eukaryotes
• Unfortunately, none of these traits is exclusive to animals:
• Plants, fungi, and some algae are multicellular
...
• Everything other than bacteria and archaea are eukaryotic
...
• However, there is a difference here between animals and fungi
...
Fungi are
absorptive heterotrophs; they secrete their digestive enzymes onto their food, and then
absorb the resulting nutrients
...
• Only animals have collagen, a structural protein
• Only animals have the following types of intercellular junctions: (See pages 135 - 139,
Figure 7
...
)
114
Characteristics of an Animal
• Tight junctions (sealing function)
• Desmosomes (anchoring function)
• Gap junctions (communication function)
Animals share certain reproductive characteristics
• Most animals reproduce sexually, with the diploid stage dominating
...
• Mitotic division of the zygote yields a blastula stage, followed by a gastrula stage
...
• Development may be direct to adult form, or there may be a sexually immature stage
(or stages) that are morphologically & ecologically distinct from the adult called a larva
(plural: larvae)
...
Here are a few perspectives from some other texts
...
• Animals are motile, though many are secondarily sessile
...
• Animals are organisms that are multicellular, with more than one type of cell
...
They reproduce sexually (at least sometimes), with a zygote formed
from two different haploid gametes
...
• Animals are not photosynthetic, have no cell wall, and no hyphae or mycelia
...
• There is relatively little dispute over the number of phyla recognized; however, the
phylogenetic relationships among the phyla are hotly debated
...
• Remember that two animals in different phyla generally are considered to be more different
from each other than are animals within one phylum (e
...
, nematodes are more different
from annelids than humans are from sharks)
...
D
...
1
2
http://bgesweb
...
csuohio
...
htm
http://www
...
edu
115
Multicellular Photosynthetic Autotrophs
23
...
Phylum — Number of Species — Common Name
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Placozoa3 — 1
Monoblastozoa4 — 1
Rhombozoa5 — 50
Orthonectida6 — 50
Porifera7 — 9,000 — sponges (figures)
Cnidaria8 — 9,000 — corals (figures)
Ctenophora9 — 100 — comb jellies
Platyhelminthes10 — 20,000 — flatworms (figures)
Nemertea11 — 900 — ribbon worms (figures)
Rotifera12 — 1,800 — rotifers (figures)
Gastrotricha13 — 450 — gastrotrichs
Kinorhyncha — 150 — kinorhynchids
Nematoda — 12,000 — roundworms (figures)
Nematomorpha — 230 — horsehair worms
Priapula — 15
Acanthocephala — 700 — (figures)
Entoprocta — 150
Gnathostomulida — 80
Loricifera — 35
Annelida — 15,000 — segmented worms (figures)
Sipuncula — 250 — peanut worms (figures)
Echiura — 135
Pogonophora — 145 — beard worms
Vestimentifera — 8 — beard worms
Arthropoda — 957,000 — arthropods (figures)
Onychophora — 80
Tardigrada — 400 — water bears
Pentastomida — 95 — tongue worms
Mollusca — 100,000 — molluscs (figures)
Phoronida — 15
Ectoprocta — 4,500 — sessile zooids
Brachiopoda — 335 — lampshells
3
4
5
6
7
8
9
10
11
12
13
116
http://en
...
org/wiki/Placozoa
http://en
...
org/wiki/Monoblastozoa
http://en
...
org/wiki/Rhombozoa
http://en
...
org/wiki/Orthonectida
http://en
...
org/wiki/Porifera
http://en
...
org/wiki/Cnidaria
http://en
...
org/wiki/Ctenophora
http://en
...
org/wiki/Platyhelminthes
http://en
...
org/wiki/Nemertea
http://en
...
org/wiki/Rotifera
http://en
...
org/wiki/Gastrotricha
Phylum Porifera
•
•
•
•
Echinodermata — 7000 — echinoderms (figures)
Chaetognatha — 100 — arrow worms (figures)
Hemichordata — 85 — acorn worms
Chordata — 50,000 — chordates (figures)
23
...
This phylum consists of the sponges
...
All are aquatic and almost all are marine
...
Although sponges are multicellular, they are described as
being essentially at a cellular level of organization
...
Their bodies are porous
...
They have inner and outer cell layers, and a variable
middle layer
...
117
Multicellular Photosynthetic Autotrophs
Choanocytes are flagellated cells lining the inside of the body that generate a current, and
trap and phagocytize food particles
...
This allows for the great regenerative power
sponges have
...
540 mya) and
possibly from the Precambrian
...
They
somehow are protected from predators (spicules? bad taste?)
...
Some sponges harbor
endosymbiotic cyanobacteria or algae (dinoflagellates, a
...
a
...
23
...
Name comes from the Greek knide- meaning "nettle"
...
The body wall
has an outer ectoderm, an inner endoderm, and a variable undifferentiated middle layer
called mesoglea or mesenchyme that may be jelly-like
...
Tentacles usually
extend from the body wall around the mouth/anus
...
The polyp is sessile and
attaches to substrate by the aboral end (i
...
, the end away from the mouth)
...
Some
cnidarians only have the polyp stage, some have only the medusa stage, and others have
both
...
wikipedia
...
wikipedia
...
The tentacles are armed with cnidae (or nematocysts), small intracellular "harpoons" that
function in defense and prey capture
...
The phylum is named after the cnidae
...
They do have a "nerve net
...
This combination is responsible for much of
the primary productivity of coral reefs
...
• Class Anthozoa18 (sea anemones, most corals)
• No medusa (jellyfish) stage, so sexual reproduction occurs in the polyp stage in this
group
...
23
...
Name means "flat worm"
Most members of this phylum are parasitic (flukes and tapeworms), but some are free living
(e
...
, planaria)
...
They are dorsoventrally compressed (i
...
, "flat")
...
Platyhelminths have a simple anterior "brain" and a simple ladder-like nervous
system
...
Flatworms have NO circulatory or gas exchange
systems
...
Platyhelminths are hermaphroditic, and the parasitic species often have VERY complex
reproductive (life) cycles
...
g
...
wikipedia
...
wikipedia
...
wikipedia
...
wikipedia
...
g
...
They do not have a mouth or
digestive system
...
34 Phylum Rotifera
See text page 900
The Rotifers
...
They are triploblastic, bilaterally symmetrical, and unsegmented
...
Most less than 2 mm, some as large as 2 - 3 mm
...
The head has a ciliary organ called the
corona that, when beating, looks like wheels turning, hence the name of the phylum
...
The gut is complete (i
...
,
mouth & anus), and regionally specialized
...
Most live in fresh water, a very few are marine or live in damp terrestrial habitats
...
There are about 2,000 species
...
Males may be absent (as in bdelloid rotifers) or reduced
...
Males develop from unfertilized haploid eggs and
are haploid
...
Sexual reproduction occurs primarily
when living conditions are unfavorable
...
23
...
Name from the Greek for "thread"
...
wikipedia
...
wikipedia
...
wikipedia
...
There are about 12,000 named species but the
true number probably is 10 - 100 times this!
These animals are triploblastic, bilaterally symmetrical, unsegmented pseudocoelomates
...
In cross-section, they are round, and covered by a layered cuticle (remember this cuticle !!)
...
The gut is complete
...
The body has only longitudinal muscle fibers
...
Nematodes can be incredibly common, widespread, and of great medical and economic
importance
...
They can live pretty much
anywhere
...
They have become very important in development studies, especially the species
Caenorhabditis elegans, presumably due to its small size and constancy of cell number
(eutely - 959 cells in C
...
23
...
Name means "ringed", from the Greek annulatus
...
g
...
There are about 12,000 - 15,000 species
...
Development is typically protostomous
...
Typically, each segment has paired epidermal "bristles"
(setae or chaetae)
...
They can be free living, parasitic, mutualistic, or commensalistic
...
There are three main classes of Annelids
• Class Oligochaeta (earthworms)
• Class Polychaeta (marine worms)
• Class Hirudinea (leeches)
122
Phylum Arthropoda
23
...
This phylum consists of spiders, ticks, mites, insects, lobsters, crabs, and shrimp, and is the
largest of all the phyla
...
This phylum also includes the extinct trilobites, which were prevalent in the Paleozoic era
...
These animals are triploblastic, bilaterally symmetrical, segmented, protostome coelomates
...
They
have an open circulatory system
...
It has major implications
in these organisms' locomotion, flexibility, circulatory systems, gas exchange systems, and
growth
...
There are several major groupings of arthropods:
Major subgroups include:
• The chelicerates (eurytperids, horseshoe crabs, scorpions, spiders, ticks) have clawlike
feeding appendages
...
• The Trilobites
...
• The crustaceans (crabs, shrimp, lobsters, barnacles and many others) have two pairs of
antennae and branched (biramous) appendages
...
38 Phylum Mollusca
See text pages 900 - 905
...
This phylum consists of snails, slugs, bivalves, chitons, squids, octopus, and many others
...
• A visceral mass, containing most of the internal organs
...
• Most have a radula, or a rasping organ to scrape food
...
They are coelomates, but
the coelom generally has been greatly reduced; the main body cavity is a hemocoel
...
The gut is complete with marked regional specialization
...
Many molluscan life cycles include a trochophore larva
...
There are several major classes of molluscs:
•
•
•
•
Class
Class
Class
Class
Polyplacophora (chitons)
Gastropoda (snails, slugs, nudibranchs)
Bivalvia (clams, mussels, scallops, oysters)
Cephalopoda (squids, octopuses, chambered nautiluses)
23
...
124
Phylum Chordata
Echinoderms are mostly sessile or very slow moving animals
...
They are considered deuterostomes
...
These canals branch into the tube feet, which function in feeding,
locomotion, and gas exchange
...
40 Phylum Chordata
Name means "the chordates", i
...
, these animals have a notochord at some stage in their
lifecycle
...
There are four major features that characterize the phylum Chordata
...
In most vertebrates, it is replaced developmentally by the vertebral column
...
• A dorsal hollow nerve cord which develops from a plate of ectoderm that rolls into a tube
located dorsal to the notochord
...
A chordate nerve cord splits into the central nervous system: the brain and
spinal cord
...
In many of the invertebrate chordates,
these function as suspension feeding devices; in vertebrates, they have been modified for
gas exchange, jaw support, hearing, and other functions
...
The digestive tract of
most nonchordates extends the length of the body
...
Chordates have a segmented body plan, at least in development
...
Three subphyla make up the phylum Chordata:
• Subphylum Urochordata (tunicates): the adults are enclosed in a tunic made of a carbohydrate much like cellulose
...
Urochordates
are characterized by errant (mobile and active) larvae and sessile adults
...
The only "chordate" characteristics retained in adult life are the pharyngeal slits
...
• Subphylum Cephalochordata: Cephalochordates are known as lancelets because of their
blade-like shape; they are also known as amphioxus
...
• Subphylum Vertebrata (vertebrates)
...
23
...
1 Subphylum Vertebrata
Vertebrata refers to the presence of vertebrae and a vertebral column
...
Vertebrates show extreme cephalization
...
Neural Crest Cells
Later in development, these give rise to many cells of the body, including some cartilage
cells, pigment cells, neurons & glial cells of the peripheral nervous systems, much of the
cranium, and some of the cells of the endocrine system
...
Neural crest cells come from the dorsal edge of the neural plate, thus ectoderm
...
These include vertebrates and invertebrate
chordates
...
1 Characteristics
Notochord: the rod-shaped supporting axis found in the dorsal part of the embryos of all
chordates, including vertebrates
Flexible, non-collapsible rod dorsal to the gut/coelom and below the nervous system,
hydrostatic, fluid wrapped in tough connective tissue
...
This allows much
better locomotion than do cilia for larger animals in water, a crucial victory for later success
...
In humans, present only in embryo
...
Non-synapomorphic characteristics (not limited to chordates):
• bisymmetrical (bilateral symmetry)
• segmented muscles and bones
24
...
Along with the subphylum Cephalochordata,
these two subphyla make up the invertebrate chordates
...
Most adult tunicates are sessile, filter-feeders
which retain their pharyngeal slits
...
Cilia beating within the turnicate cause water to enter
the incurrent siphon
...
Undigested food is removed through
the anus
...
In
urochordates notochord is confined to larval tail
...
These have an open
type of circulatory system
...
127
Chordates
24
...
Along with the subphylum Urochordata, these
two subphyla make up the invertebrate chordates
...
They resemble fish but they are actually scaleless chordates only a few
centimeters long
...
Fossils of lancelets have been found to be over 550 million years old
...
Includes
Branchiostoma (“amphioxus”)
...
4 Subphylum Vertebrata
(Vertebra from Latin vertere, to turn)
...
The backbone supports and protects a dorsal nerve cord
...
All vertebrates share the following characteristics: - segmentation - a true coelom - bilateral
symmetry - cephalization - a backbone - a bony skull - a closed circulatory system - chambered
heart - two pairs of jointed appendages - tissues organized into organs
Vertebrate Organ Systems: - Nervous System - Circulatory System - Digestive System Respiratory System - Reproductive System - Excretory System
• Vertebral column: Not present in higher vertebrate adults
...
Ruptured or herniated disc is
an injury to this
...
Two functions: 1
...
Encloses or partially encloses the brain
...
Some scientists believe that this occurred
in a proto-chordate animal lineage
...
Selection in these proto-chordates maybe began to favor more time in
the larval stage, as feeding was more successful or mortality lower in this stage
...
Is this hypothesis crazy? A similar example of this today is Epemeroptera, the mayfly, which
has almost abandoned its adult stage
...
Tunicate (sea squirt) larva has all four chordate characteristics, although adult sessile
(“attached”)
...
4
...
• Cyclostomes: "circle mouth" - a group of Agnathans which is still alive in the form of
lampreys and hagfish
...
The first group of fish to appear
...
Class Acanthodia
"spiny fish" Appeared about 430 million years ago
...
They had internal skeletons made of cartilage and some bone
...
An
extinct class of fish with massive heads
...
4
...
Includes sharks,
skates and rays, and chimaeras
...
The main characteristics and distinguishing features of this class: - gills - single-loop blood
circulation - vertebral column - presence of placoid scales on their bodies - internal skeleton
of cartilage - paired, fleshy pectoral and pelvic fins - asymmetrical tail fin prevents sinking fatty liver provides neutral buoyancy - visceral clefts present as separate and distinct gills no external ear - oviparous - internal fertilization - ectoderms - cold blooded
24
...
3 Class Osteichthyes
"bony fish" Appeared about 400 million years ago with cartilaginous fish
...
Subclass Sarcopterygii
fleshy-finned fishes
...
Order Dipnoi
lung fishes, two groups isolated when continents separated
129
Chordates
Order Crossopterygii
includes coelacanths and rhipodistians, gave rise to amphibians, had lungs which evolved
into a swim bladder in bony fishes, and labyrinthodont teeth, characterized by complex
folding of enamel
...
24
...
4 Class Amphibia
means “both lives”, aquatic larvae, terrestrial adult Amphibians: - Legs - Lungs - DoubleLoop Circulation - Partially Divided Heart - Cutaneous Respiration (Breathes through
Skin)
Order Salientia
frogs (jumping) (aka Anura)
Order Urodela
salamanders (tailed)
Labyrinthodont amphibians: oldest known amphibians, inherited characteristic teeth from
crossopterygii ancestor, had stocky, aquatic larvae
...
Girdles and vertebral column now more substantial
and connected, support body on legs
...
Amphibians gave rise to cotylosaurs, from which arose dinosaurs, turtles, lizards, and
therapsids
...
(Amnion: protection)
...
Allantois: allows gas exchange and elimination of wastes
...
Sometimes defined as all amniotes that are not birds or mammals
...
Cotylosaurs had Anapsid skull
Dermatocranium: from bony outer skull structure, precursor to human cranium
...
Ancestrally bipedal, secondarily quadripedal
...
Led eventually to
mammals
...
Teeth differentiated into different types, for pre-processing of food needed
by higher metabolism
...
1
2
3
http://en
...
org/wiki/turtle
http://en
...
org/wiki/dinsosaur
http://en
...
org/wiki/snake
131
Chordates
Class Aves
arose late Jurassic, early Cretaceous
...
Feathers:
epidermal derivative, made of keratin (like fingernails)
...
Keeled sternum: breastbone, powerful one needed
to support flight muscles
...
All birds lay eggs (as
contrasted to reptiles, which have developed live birthing over 100 independent times
...
With mammals, only
exothermic animals
...
Good fossils found
in Zolenhoffen, German sandstone mine with fine sand, shows feathers clearly, found shortly
after Darwin’s publication and used to support his hypothesis
...
Archaeornithes: includes archaeopteryx
...
Neognathae: remaining live birds
...
132
Subphylum Vertebrata
Subclass Theria
Metatheria: Marsupials (opossum, kangaroo
...
Gestation period much shorter than
in Eutherian mammals, but after leaving the uterus the tiny offspring crawls into a pouch
where it completes development latched onto a teat
...
Instead of being a “rough draft” for
placental-style live bearing, perhaps the marsupial pouch approach is another solution to
the same problem
...
133
25 Tissues and Systems
135
26 Epithelial tissue
Comes from various sources, ectodermal or endodermal material
...
One side, called freesurface or Apical, is exposed to
• animal interior (forming the lumen) or
• exterior of its body cavity
...
Epithelial tissue is not penetrated by blood vessels
...
)
Cell shape at free surface:
• squamous (broad and flat)
• cuboidal (spherish)
• columnar (tall and thin)
Simple squamous epithelium
usually lines body cavities and vessels,alveoli, glomeruli of kidney; in blood and lymph
vessels called endothelium; in body cavities called mesothelium (serosae): parietal serous
membranes line body wall, visceral serous membranes cover organ
Simple cuboidal epithelium
in ducts like kidney and salivary glands
...
Cells sometimes dead, flat and keratinized,
making them resistant to abrasion
...
Epidermis
137
Epithelial tissue
from epithelium
...
Two specialized epithelia:
• pseudostratified
• transitional
Pseudostratified epithelia
lines the trachea (where it is ciliated)and the male urethra (where it is non ciliated), looks
stratified but not
...
As it stretches it appears to go from 6 to 3 cell
layers deep
...
mostly derived from epithelium
...
Endocrine glands
secrete hormones into the blood without use of ducts
...
Exocrine substances include
sweat, mucous, oil, and saliva
...
138
27 Connective tissue
This is a “grab bag” category of diverse tissue types
...
Types include bone, cartilage, fibrous connective tissue, blood and
adipose (fat) tissue
...
Form: distinctive cells surrounded by a cell matrix made of extra-cellular fiber grounded
in a ground substance (excluding blood)
Types:
1
...
loose or 2
...
special connective tissue (includes blood, bones and cartilage)
...
Ground substance: “unstructured” material that fills space between cells and contains
fibers
...
interstitial fluid (bathes cells)
2
...
cell-adhesion proteins (connect connective tissue cells to the fibers)
...
Collagen (flexible protein resistant to stretching, tensile strength, most abundant
protein in animals, white)
2
...
andreticulin (like collagen)
...
Include fibroblasts, macrophages, mast cells,and adipose cells
...
Ground substance is “syrupy”
...
Dense connective tissue: largely densely packed fibers of collagen or elastin regularly
or irregularly arranged
...
Cartilage vs
...
hyaline cartilage
2
...
elastic cartilage
Hyaline cartilage: most widespread cartilage type, in adults forms articular surfaces of
long bones, rib tips, rings of trachea, and parts of skull
...
In embryo, bones form first as hyaline cartilage, later ossifies
...
Few collagen fibers
...
Found in intervertebral discs, pubic
symphesis
...
Elastic cartilage: springy and elastic
...
Chondrocites (cartilage cells) rely on diffusion for nutrients, as cartilage has no direct
blood supply, and no enervation (nerves)
...
140
Subphylum Vertebrata
Bone: Specialized connective tissue, calcium phosphate arranged in highly ordered unit
called osteon, or Hyvercian system
...
Bone varied, not all vertebrate bone is even cellular
...
Lacuna (spaces in which osteocytes found); canaliculi (little canals) bigger diagonal cells,
layers of bone called lamellae
...
appearance (spongy vs
...
where found (outside or inside)
3
...
In
young mammals, secondary ossification centers then form at bone ends, growth has stopped
by sexual maturity as all primary bone is ossified
...
Three types of intramembrous bone:
1
...
sessamoid bone
3
...
Dermal bone forms skull, shoulder/pectoral girdle, and integument, descended from dermal
armor of ancestor
...
Sessamoid bones: form directly in tendons
...
Deals with
stress
...
Functions in bone repair and in ossification of endochondral bone
...
To combat this, bone is constantly replaced
...
Continually resets mineral structure of bone, and is
preventative maintenance
...
Later, osteoblasts continue fixing over
time and slowly removing imperfection
...
Secondary roles: heat production (shivering a specialized heat production to supplement
metabolism)
...
Some fish formed electric organs, create current strong enough to repel predators
or stun prey
...
(Evolved independently in different groups)
...
)
Striated muscle (or skeletal muscle): under voluntary control
...
Myofibrils founding one cell made of even smaller myofilaments
...
Fibers joined end to end to
form longer composite fibers
...
Two
kinds of myofilaments, thick kind made up of myosin and thin of actin
...
Cardiac muscle: occurs only in heart
...
Each band short, principally mononucleate (occasionally dinucleate) often branched, joined
together with intercollated discs
...
Waves of contraction spread through intercollated discs
...
)
Smooth muscle: no striations visible with light microscope
...
Non-voluntary control
...
Each cell mononucleate, short,
fusiform (spindly) in shape, cells usually uniform in size
...
Repeating units called sarcomeres, consisting of two kinds of myofilaments:
1
...
thin, actin filament
...
Sliding filament theory: thick and thin filaments move past each other in opposite
direction, shortening length
...
Myosin molecule: two polypeptides twisted together with two globular heads at end
...
Actin filament: chain of actin single, tropomyosin strands with repeated globular
troponin, and with actin
...
Myocin heads have sites
that bind to actin
...
Troponin has four sites:
1
...
one for actin
3
...
one for calcium ions
Nerve signal reaches muscle, triggers release of chemical signal called neurotransmitter,
that diffuses across cell membrane (sarcolimic reticulum) and binds to receptors in it
...
When there is enough nerve signal, the message travels
through t-line to sarcoplasmic reticulum to release calcium ions
...
In calcium, myosin binding sites exposed and
heads bind to actin molecules, delivering force to move fibers in relation to each other
...
If there is no further nerve signal,
sarcoplasmic reticulum sequesters Ca+ ions again and no recocking occurs
...
Victim dies of asphyxiation because he can’t
breathe
...
Fast and slow twitch fibers: vertebrate muscle fiber
...
Differences related to differences in enervation, type of myocin, and actin
activation
...
active component 2
...
Stored in muscle elastic tissue
around tendons
...
Up to 90% of stored elastic energy can be recovered
...
rate modulation, derived from frequency of nervous stimulation of muscle, force
increases as frequency of stimulation increases up to point of tetanus
...
selective involvement of motor units, a given neuron enervates a fixed number of
muscle cells, (a motor unit), and force is increased by recruiting more motor units
...
How do muscles grow stronger?
1
...
proliferation in blood vessels and connective tissue around muscle
Muscle strength is relative to cross sectional area, not length
...
Pinnate fibers: oriented obliquely (Y-shaped) to minimize muscle mass, in certain circumstances, like calf muscle
...
Velocity of shortening greater in long muscle than short
...
Both long and short muscles reach same
percentage of contraction in same unit time, but distance covered by the longer muscle is
greater
...
Bicep shares work with brachialis
...
Bicep pulls forearm in, triceps pulls
it back out
...
insertion: origin is the end of the muscle that more fixed in its attachment to
the body
...
Fixators: muscles that act to stabilize a joint or lever system
...
Flexors and extensors: applied mainly to limbs
...
Adductor and abductor: adductor draws a limb toward the ventral surface
...
(Adduct: drawn toward; abduct: carry away)
...
Digestive tract: tube extending from lips of mouth to anus or cloacae in bird, reptile or
monotreme
...
Tract divided into three main regions: 1
...
pharynx 3
...
esophagus 2
...
small intestine 4
...
Includes the salivary glands, liver and pancreas
...
Teeth: capture and hold prey
...
Tooth anatomy: 1
...
root below gum, 3
...
dentin, below enamel,
bone-like and forms bulk of tooth, is harder than bone and contains nerves and blood vessels
...
Pharynx: air passage for adult, gill slits in embryo
...
Features derived from pharyngeal region: first pharyngeal pouch gives rise to parts
of the ear, other pouches give rise to various other structures
...
Esophagus: tube carries food from mouth to stomach
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Secretes mucus for lubrication
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Epiglottis: keeps food out of air tube, an evolutionary “kludge,” or fix
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Absorbs water, alcohol, nutrients, uses gastric juice with enzymes, mucous, HCl,
released by chief and parietal cells (release protein enzymes) in gastric pits
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Sphincter at both ends of stomach, control food passage
...
147
Vertebrate digestive system
Small intestine: three regions, duodenum, jejunum, and ileum
...
Jejunum and ileum do most of intestinal
absorption
...
Structure:
Circular folds covered with villi (singular is villus)
...
Increases surface area by 900x, speeds digestion (break down) and absorption
(taking in nutrients)
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No villi
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Colon: absorbs water left over, also absorbs vitamins released
by bacteria which live there (vitamin K)
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proteins, 2
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carbohydrates 4
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Digestive system breaks foods down
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Polysaccharides to monosaccharides, lipids to fatty acids and monoglycerides to absorb
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Snake venom from oral gland, mixture of toxins and digestive enzymes
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Stomach enzymes: released in inactive form, zymogene, converts to active form in lumen
of gut
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Pepsin
secreted as pepsinogen (-ogen means primitive form)
...
Chyme released to duodenum
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pancreas 2
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Bile made from cholesterol, stored in gall bladder, released in
duodenum, emulsifies fats
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Protein and carbohydrates absorbed in intestine, taken to liver for processing
...
Much variation in digestive systems within mammals:
herbivore, carnivore, insectivore, non-ruminant herbivore
...
Cellulose
resistant to digestion, rely on microorganisms to break down cellulose
...
Bacteria break down
cellulose in rumen, to be taken back to the mouth to chew their cud (ruminate)
...
(Horses not like this)
...
149
30 Circulatory system
Circulatory system functions
1
...
Respiration: gas exchange (O2 and CO2), overcomes limited rate
of
diffusion
b
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Excretory: (remove metabolic wastes)
2
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Transport hormones
b
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Protection
i
...
Immune system (carries white blood cells)
Vasodilation: allows heat loss across epidermis, as seen in elephant ears, takes more blood
to surface of body, sweating may accompany
Countercurrent heat exchange: used by dolphins in fins to conserve heat in cold water
...
Used by dogs in feet, etc
...
plasma and 2
...
Plasma makes up 55% of blood volume
...
Plasma makeup: 90% water, 7-8% soluble proteins (albumin maintains blood osmotic
integrity, others clot, etc
...
In
mammals, red blood cells lose nuclei on maturation, and take on biconcave, dimpled, shape
...
About 1000x more red blood cells than white blood cells
...
151
Circulatory system
Hematocrit: proportion of blood volume that is occupied by cells, about 43% in humans
on average
...
White blood cells (leukocytes): Nucleated, about 10-14 micrometers in diameter, commonly amoeboid, escape circulatory system in capillary beds
...
Platelets (thrombocytes) Membrane bound cell fragments in mammals, no nucleus
...
Accumulate at site of broken blood
vessels, form clots
...
1-2 micrometers in diameter
...
Arteries: carry blood away from heart
...
Veins: return blood to heart
...
Structure of arteries and veins, listed from inside (lumen) out: 1
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elastic connective tissue fibers, 3
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connective tissue
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Capillaries, where exchange of materials occurs, are very thin and narrow, and red blood
cells pass through single file
...
Blood velocity drops in capillaries, picks back up in veins
...
Osmotic pressure draws interstitial fluid from blood in arterioles, but replaces it in venules
...
Low pressure in thoracic cavity caused by breathing
also helps move blood
...
Takes up
interstitial fluid not taken up by venules
...
lymphatic capillaries
2
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lymph nodes
4
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(Some non-mammals have lymphatic hearts of unknown embryonic origin
...
) Lymph rejoins cardiovascular system into a large vein near the
heart via single large thoracic duct
...
Heart: pumps blood, design varies between animals
...
pulmonary circulation to and from lungs and
2
...
Everything in the heart comes in pairs: 2 atria, 2 ventricles (left and right)
...
Pattern of blood flow through heart: blood returning from major veins (vena cava)
enters right atrium, contraction there delivers blood to right ventricle through a tricuspid
valve, one of atrial ventricular valves (AV valve)
...
Blood return to heart in
pulmonary veins, is oxygenated
...
Both atria and ventricles contract in unison, left is more powerful than right (to all system
vs
...
Systole: heart contraction, diastole: heart relaxed
Timing of heart contraction: ventricles rebound to relaxed shape (diastole), and semilunar valves close
...
Pressure rises in the atria and blood begins to move into the
ventricles
...
There is a pause,
then ventricles contract
...
Control for this action doesn’t rely on nervous stimulation, has intrinsic rhythmicity, called
myogenic
...
Other animals have
neurogenic hearts that rely on nervous stimulation for heart action, originating in the
cardiac ganglion
...
This is a phylogenic (based on evolutionary history) remnant of an early vertebrate heart
that had one more chamber than modern hearts
...
Connectile tissue pauses the spread of depolarization at the atrial ventricular
node
...
Contraction starts at bottom of heart at heart apex,then signals spread
through heart
...
(The medulla is part of
the brain, is continuous with the spinal cord, and controls involuntary actions of the
body)
...
Parasympathetic cardio-inhibitory center reaches heart through Vagus
153
Circulatory system
nerve, usesacetylcholine to signal
...
(Autonomic nervous system: two parts working in contra to control from both sides
...
If we cut Vagus nerve, heart rate promptly rises about
25 bpm
...
Other animals, such as insects, have respiratory systems with very simple anatomical features,
and in amphibians even the skin plays a vital role in gas exchange
...
The respiratory system in plants also includes anatomical features such
as holes on the undersides of leaves known as stomata
...
g
...
Respiratory tree: terminates in alveolus, alveoli
...
Alveolus: microscopic air sacs, 300 million of these in human
lungs
...
Gas diffuses micrometer, very tiny distance
...
Basic unit of the nervous system is the neuron1 , a highly specialized cell that uses both
electrical and chemical processes to communicate
...
Likewise, a neuron can "talk" to other neurons or cells that can create an action, like muscle
cells or glands
...
Glia were once thought to only play
a supportive role in helping neurons survive; today we know that they also are important
participants in the communication process
...
There are also oligodendocytes and Schwann
cells that provide a myelin sheath
...
wikipedia
...
1 Neuron structure
Figure 9
Neuron
• Dendrite will receive information from other axons
• Stoma is the neuron body and contains typical cell parts including the mitochondria and
nucleus
...
• Axon hillock is where the cell body and the axon meet
...
• Contains nodes of Ranvier
Types of axons include unipolar, bipolar, pseudopolar
...
On the cellular level, there is a Na+ influx via
channels causing a depolarization of the cell
...
Synapses
Neurotransmitters allow a chemical signal to be sent from one neuron to the other
...
Examples of neurotransmitters
include acetylcholine, epinephrine, and glutamate
...
2 Central nervous system
Central nervous system includes the brain and the spinal cord
...
•
•
•
•
Frontal lobe - decision making
Parietal lobe
Temporal lobe
Occipital lobe - vision
The areas of the brain are also dedicated to different functions
...
Protection also comes from the circulation of cerebral spinal fluid (CSF)
...
CSF is synthesized from the choroid plexus of the lateral ventricles
...
31
...
ANS - Autonomic Nervous System The ANS has two components - parasympathetic and
sympathetic
...
There
is also decreased digestion
...
In this case, the
first neuron is short and the second neuron is long
...
Drugs must be able to pass the blood brain barrier to have an effect on the CNS
...
Stroke occurs when there is a blood clot that goes to the brain and prevent blood flow
...
nature of stimulus, such as mechanical, chemicalor light stimulus, and
2
...
Transduction of sensory input into signal
...
Three sensory processes we cover
1
...
gravity and movement
3
...
1 Taste and smell (chemoreception)
Found in mammal nose and mouth, fly feet, fish bodies, moth antennae
...
Sweet, sour, salty and bitter
...
Other “taste” sensations really
smell
...
Airborne molecules go into solution on moist epithelial
surface of nasal passage
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“Fried
onions” odor not one receptor but a mixture of many odors registered in our mind as one
...
Odor sensation has
relatively unfiltered root to higher brain centers
...
32
...
Three semicircular canals loop in three planes at right angles
to each other, responsible for transduction of movement messages
...
Vestibular apparatus, gives us perception of gravity
and movement
...
Cochlea: bony, coil shaped part of inner ear, where hearing occurs
...
Cochlea has three fluid filled ducts, one of these the organ of Corti
...
Different sound frequencies move different portions
of basilar membrane
...
Humans normally smell more
than 300 odors in a day(Facts and Truth)
...
32
...
Sclera: hardened part behind retina
...
Blind spot where optic nerve attaches, has
no receptors
...
rods - black and white low-light vision, 100 million in each retina in humans
...
cones - color vision, work best under better illumination
...
Fovia: region of most acute vision, has most of the cones, few rods
...
Located in outer parts of rods and cones in pigment discs
...
This
molecular change initiates pathways to result in action potential in downstream neuron
leading to vision center in brain
...
Color blindness:inherited lack of one or more types of these cones
...
32
...
Defined as dynamic constancy of internal environment, maintenance of a relatively stable environment inside
an organism usually involving feedback regulation
...
a varying external environment, or
2
...
Deals with temperature, pH, chemical concentrations,pressure, oxygen levels
...
Various forms: simple thermostat in house turns off heater when above a certain temperature
and on when below a certain temperature Involves stimulus, sensor,integrating center,
effector and response
...
Can be antagonistic to each
other, such as, one cools, the other heats
...
Examples in humans: vasoconstriction, change in metabolic rate,
shivering
...
Positive feedback loop: effector increases deviation from set point
...
Like blood clotting process, uterine contraction during childbirth
...
32
...
Marine invertebrates
a) fully marine invertebrates (not intertidal or estuarine) osmoconformers (set
internal environment same as environment, no net flow of ions) in a stenohaline
(narrow non-changing salt level) environment
b) Coastal, intertidal, estuarine (ion levels fluctuate) invertebrates
...
2
...
Here, environment has lower solute concentrations than do
living organisms so water tends to flow in and solutes out
...
Marine fishes: Here the environment has a higher solute concentration than does
the organism so water tends to flow out and ions in
...
Terrestrial animals: here problem is loss of water to a drier environment, and
regulation of salt levels
...
Terrestrial animal water sources:
1
...
moist foods
3
...
(Desert kangaroo rats get 90% of their
water from metabolism
...
ammonia (aquatic life)
2
...
uric acid (birds)
Ammonia very toxic, soluble, and cheap to produce
...
Urea: low toxicity, good solubility, more costly to lose as it contains other groups on it
...
Uric acid (white part of bird poo) low toxicity, insoluble, secreted with little water loss,
more costly side groups lost than the others
...
About 1/5 of blood from
aorta at any time is passing through kidneys
...
Nephron: structural and functional unit of kidney
...
Proximal convoluted tubule: receives stuff from Bowmans capsule
...
162
Osmotic environments and regulations
Vasa recta: capillaries that surround the Loop of Henle
...
Active transport of solutes from one fluid to another against a concentration gradient,
Na+ actively transported out of filtrate by cells of the thick ascending loop of Henley into
the interstitial fluid
2
...
3
...
Hormonal control of that permeability, antidiuretic hormone(ADH) increases
permeability of collecting due to water, resulting in reduced volume of filtrate and thus
more concentrated urine
...
Increasing solute concentration in the interstitial fluid of the kidney, from the
cortex to the deepest medulla, maintained by a countercurrent multiplier mechanism
163
33 Additional material
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Francis Crick1 chemist and molecular biologist, discovered structure of DNA molecule
Charles Darwin2 the father of the science of evolutionary biology
Richard Dawkins3 zoologist and biology populariser
Stephen Jay Gould4 paleontologist and science populariser
J
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Additional material
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34 Glossary
Autotroph1 : an organism which can make its own energy
Cell2 : Fundamental structural unit of all living things
Ether3 :
Eukaryote4 : an organism5 with a nucleus
Exoenzyme6 : an enzyme used to break down organic molecules7 outside the body
Glycerol8 :
Heterotroph9 : an organism which can not make its own energy
Hydrocarbon10 : an organic compound that contains carbon11 and hydrogen12 only
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This is commonly represented by n
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This is commonly
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List of Figures
• GFDL: Gnu Free Documentation License
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gnu
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• cc-by-sa-3
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• LGPL: GNU Lesser General Public License
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• PD: This image is in the public domain
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Redistribution, derivative
work, commercial use, and all other use is permitted
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The copyright on the design
of the common face of the euro coins belongs to the European Commission
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• LFK: Lizenz Freie Kunst
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• CFR: Copyright free use
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101 Chapter 36 on page 179
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List of Figures
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Unknown, The Hornet is no longer in publication and it is
very likely for a 20-year-old artist in 1871 to have died before
1939
Uploader, CDC
LadyofHats103
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GFDL
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177
36 Licenses
36
...
Preamble
The GNU General Public License is a free, copyleft
license for software and other kinds of works
...
By contrast, the
GNU General Public License is intended to guarantee your freedom to share and change all versions
of a program–to make sure it remains free software
for all its users
...
You can apply it to your
programs, too
...
Our General Public Licenses are designed to make sure that you have
the freedom to distribute copies of free software
(and charge for them if you wish), that you receive
source code or can get it if you want it, that you
can change the software or use pieces of it in new
free programs, and that you know you can do these
things
...
Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect
the freedom of others
...
You must make sure that they, too, receive
or can get the source code
...
Developers that use the GNU GPL protect your
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software, and (2) offer you this License giving you
legal permission to copy, distribute and/or modify
it
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For both users’ and authors’
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be attributed erroneously to authors of previous
versions
...
This is fundamentally incompatible with the aim
of protecting users’ freedom to change the software
...
Therefore,
we have designed this version of the GPL to prohibit the practice for those products
...
Finally, every program is threatened constantly by
software patents
...
To prevent this, the GPL assures that
patents cannot be used to render the program nonfree
...
TERMS AND
CONDITIONS 0
...
“This License” refers to version 3 of the GNU General Public License
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to
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It is safest to attach them to the start of
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> Copyright (C)
This program is free software: you can redistribute
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See the GNU General Public
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see
org/licenses/>
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If the program does terminal interaction, make it
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The hypothetical commands ‘show w’ and ‘show c’
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2 GNU Free Documentation License
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Use in the Title Page (and on the covers, if
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If there is no section Entitled "History" in the Document, create one stating the title,
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Preserve the network location, if any,
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Preserve all
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Such a section may not be included in the
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Do not retitle any existing
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Preserve
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The author(s) and publisher(s) of the Document do
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COMBINING DOCUMENTS
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AGGREGATION WITH
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If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the
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Replacing Invariant
Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections
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Any attempt otherwise to copy, modify, sublicense, or distribute it is void, and will
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FUTURE REVISIONS OF THIS LICENSE
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See http://www
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An MMC is "eligible for relicensing" if it is licensed
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ADDENDUM: How to use this License for your documents
To use this License in a document you have written,
include a copy of the License in the document and
put the following copyright and license notices just
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Copyright (C) YEAR YOUR NAME
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3 or any later version published by the Free Software Foundation; with no
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If you have Invariant Sections, Front-Cover Texts
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with the Invariant Sections being LIST THEIR TITLES, with the Front-Cover Texts being LIST, and
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If your document contains nontrivial examples of
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3 GNU Lesser General Public License
GNU LESSER GENERAL PUBLIC LICENSE
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Copyright © 2007 Free Software Foundation, Inc
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As used herein, “this License” refers to version 3
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You may place library facilities that are a work
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The Free Software Foundation may publish revised
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If the Library as you received it does not
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Title: Biology IGCSE Notes
Description: This note is about all the topic that would appear in the IGCSE exam.
Description: This note is about all the topic that would appear in the IGCSE exam.