Transcript Lecture #2 - Suraj @ LUMS

Assignments and Term Paper
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Grading altered
 10% for assignments – once a week,
presentations twice a week.
 5% for term paper – groups of 4
 25% quizzes
 25% mid-term
 35% final exam
Lecture 2
Variety of Life
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Classification of living organisms
 Methods of classification
 Different kingdoms of living organisms:
Monera, Protista, Fungi, Plantae, and
Animalia.
Classification of Living
Organisms
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At least 1.7 million species of living organisms have been
discovered.
Taxonomy (Gr. taxis, "arrangement, order", nomos, "law") is
the science of classification (Latin, classis, "a class", facere,
"to make").
Two branches, naming an organism, or nomenclature and
placing it in a group, systematics.
The Role of Taxonomy :
1. Taxonomy works out for us a vivid picture of the existing organic
diversity of the earth.
2. Taxonomy provides much of the information permitting a
reconstruction of the phylogeny of life.
3. Taxonomy reveals numerous interesting evolutionary phenomena.
Nomenclature
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Without a set of international rules to follow, the
results of taxonomy would be confusing at best.
International Code of Zoological Nomenclature
(ICZN).
The Linnaean Hierarchy.
Nomenclature based on a binomial system devised
by the Swedish naturalist Carl Linnaeus in 1758.
The scientific name of an organism consists of a
collective generic name, beginning with a capital
letter, and a specific or species name, in lower
case letters. E.g Homo sapiens
Linnaeus Hierarchy
Arranged as a hierarchy, with largest group at the top:
Kingdom
Phylum
Drastic differences
Class
Order
Family-category including 1 genus or a group of genera of
common phylogenetic origin, which is separated from other
families.
Genus-category containing a single species, which is separated
from other taxa by behaviour, morphology, or some other
characteristics.
Species-group of closely related organisms capable of
interbreeding to produce fertile offspring.
How are they classified?
Reductionist Principle
Chemicals
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How similar is the DNA?
What type of cell is it?
Nutrition?
Movement?
Coordination/sensory
system?
Anatomy?
Embryonic development?
Cells
Tissues
Organs
Systems
Organism
Population
Community
Ecosystem
Methods of Classification
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Homology - shared characteristics inherited from a
common ancestor.
The more recently two species have shared a common
ancestor, the more homologies they share.
Study of homologies was limited to anatomical structures
and pattern of embryonic development.
Since the birth of molecular biology, homologies can
now also be studied at the level of proteins and DNA by :
1.
2.
3.
DNA-DNA Hybridization
Chromosome Painting
Comparing DNA Sequences
Molecular Homology
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Protein sequencing provides a tool for establishing homologies
from which genealogies can be constructed and phylogenetic
trees drawn.
Example : Hemoglobins
Human beta chain 0
Gorilla 1
Gibbon 2
Rhesus monkey 8
Dog 15
Horse, cow 25
Mouse 27
Gray kangaroo 38
Chicken 45
Frog 67 Lamprey 125
Sea slug (a mollusk) 127
Soybean (leghemoglobin) 124
Number of amino acid differences between the beta chain of humans and the
hemoglobins of the other species. In general, the number is inversely
proportional to the closeness of kinship.
Domains of Life
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Until comparatively recently, living organisms
were divided into two kingdoms: Animalia and the
Plantae.
Animals fed on organic material – heterotrophic
Plants synthesis own organic material from
inorganic material – auxotrophic.
In the 19th century, evidence began to accumulate
that these were insufficient to express the diversity
of life.
Scheme in widest current use divides all living
organisms into five kingdoms.
Early View
2 Kingdoms
Plants
Whittaker’s View
5 Kingdoms
Animals
Plants
Fungi
Algae
Copeland’s View
4 Kingdoms
Protoctista
Monera
(prokaryotes)
Animals
embryophytes
algae
Protoctista
Monera
Animals
Three Domains of Life
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All cellular organisms fall into two natural groups,
prokaryotes and eukaryotes.
Pro, before; karyon, nucleus DNA is not enclosed
by a nuclear membrane and lies free in the cell.
Eu, true; karyon, nucleus evolved from
prokaryotes.
Recent work, however, has shown that the
Prokaryotae are now divided into two domains,
the Bacteria and the Archaea.
No one of these groups is ancestral to the others
Prokaryotes
Introduction to Bacteria
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Bacteria are often maligned as the causes of human and
animal disease.
The actinomycetes, produce antibiotics such as
streptomycin and nocardicin; others live symbiotically in
plants and animals (including humans). Bacteria put the
tang in yogurt; bacteria help to break down dead organic
matter; bacteria make up the base of the food web in many
environments.
Are of such immense importance because of their extreme
flexibility, capacity for rapid growth and reproduction, and
great age - the oldest fossils known, nearly 3.5 billion
years old, are fossils of bacteria-like organisms.
Classification of Bacteria
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Most bacteria may be placed into
one of three groups in response to
oxygen:
1. Aerobic bacteria thrive in the
presence of oxygen and require
it for their continued growth.
2. Anaerobic bacteria cannot
tolerate gaseous oxygen, such
as those bacteria which live in
deep underwater sediments, or
those which cause bacterial
food poisoning.
3. Facultative anaerobes, which
prefer growing in the presence
of oxygen, but can continue to
grow without it.
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Most bacteria may be placed into one of
two groups depending on what they use
as a source of energy:
Heterotrophs derive energy from
organic compounds that they must take
in from the environment -- this includes
saprobic bacteria found in decaying
material.
Auxotrophs fix carbon dioxide to make
their own food source light energy
(photoautotrophic), e.g the
cyanobacteria, green sulfur bacteria,
purple sulfur bacteria, and purple
nonsulfur bacteria or by oxidation of
nitrogen, sulfur, or other elements
(chemoautotrophic). The sulfur bacteria
use hydrogen sulfide as hydrogen
donor, instead of water like most other
photosynthetic organisms.
Structure of Bacteria
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Prokaryotic - lack the membrane-bound nuclei their DNA forms a tangle
known as a nucleoid.
DNA is not organized into linear pieces, the chromosomes, bacterial DNA
forms loops.
Bacteria contain plasmids, or small loops of DNA, that can be transmitted from
one cell to another, either in the course of sex (yes, bacteria have sex) or by
viruses.
This ability to trade genes with all comers makes bacteria amazingly adaptible;
beneficial genes, like those for antibiotic resistance, may be spread very rapidly
through bacterial populations.
Bacteria do not contain membrane-bound organelles such as mitochondria or
chloroplasts, as eukaryotes do. However, photosynthetic bacteria, such as
cyanobacteria, may be filled with tightly packed folds of their outer membrane.
The effect of these membranes is to increase the potential surface area on
which photosynthesis can take place.
Bacterial Cell Membrane
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The cell membrane is surrounded by a cell wall in all bacteria
except one group, the Mollicutes, which includes pathogens
such as the mycoplasmas.
The composition of the cell wall varies among species and is an
important character for identifying and classifying bacteria.
Danish bacteriologist developed a staining procedure to look for
differences in the cell wall. The Gram Stain.
If a bacteria has a thick cell wall made of peptidoglycan
(carbohydrate polymers cross-linked by proteins); it will retain
a purple colour when stained with a dye known as crystal violet,
and is known as Gram-positive.
If a bacteria has a double cell wall, with a thin inner wall of
peptidoglycan and an outer wall of carbohydrates, proteins, and
lipids it will not stain purple with crystal violet and is known as
Gram-negative.
Introduction to the Archaea
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The Domain Archaea wasn't recognized as a major domain of
life until quite recently.
 In the late 1970s discovery of an entirely new group of
organisms, by Dr.Carl Woese and his colleagues at the
University of Illinois. They were studying relationships among
the prokaryotes using DNA sequences, and found that there
were two distinctly different groups.
 Those "bacteria" that lived at high temperatures or produced
methane clustered together as a group well away from the
usual bacteria and the eukaryotes.
 Because of this vast difference in genetic makeup, Woese
proposed that life be divided into three domains: Eukaryota,
Eubacteria, and Archaebacteria. He later decided that the term
Archaebacteria was misleading, and shortened it to Archaea.
Archaeans
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Inhabitants some of the most extreme environments on
the planet.
 Some live near rift vents in the deep sea at
temperatures well over 100 degrees Centigrade. Others
live in hot springs (such as the ones pictured above), or
in extremely alkaline or acid waters.
 They have been found thriving inside the digestive
tracts of cows, termites, and marine life where they
produce methane.
 They live in the anoxic muds of marshes and at the
bottom of the ocean, and even thrive in petroleum
deposits deep underground.
The Eukaryotae
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The Eukaryota include the organisms that most people are
most familiar with - all animals, plants, fungi, and protists.
Share properties such as a nucleus, cytoskeletons, and
internal membranes.
Eukaryote DNA is divided into linear pieces called
chromosomes (unlike bacterial DNA, which forms loops).
Assignment
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Read pp 52-76
 Give the Linnaeus Classification for
segmented worms and human beings.
 Why have both these living organisms been
placed in the same kingdom of Animalia?