BIOCHEMISTRY

The branch of science concerned with the chemical and physicochemical processes and substances that occur within living
organisms.

Around two dozen of the 92 naturally occurring chemical elements are essential to various kinds of biological life. Most rare
elements on Earth are not needed by life (exceptions being selenium and iodine, while a few common ones (aluminum and
titanium) are not used. Most organisms share element needs, but there are a few differences between plants and animals. For
example, ocean algae use bromine, but land plants and animals seem to need none. All animals require sodium, but some
plants do not. Plants need boron and silicon, but animals may not (or may need ultra-small amounts).
Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus—make up almost 99% of the mass of living
cells, including those in the human body. In addition to the six major elements that compose most of the human body, humans
require smaller amounts of possibly 18 more biochemistry as a specific scientific discipline has its beginning sometime in the
19th century
Six Levels of organization of living things

1. 4.

2. 5.

3. 6.

BIOMOLECULES

The four main classes of molecules in biochemistry (often called biomolecules)

1. carbohydrates,
2. lipids
3. proteins
4. nucleic acids

Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked
together to create large macromolecules known as polymers. When monomers are linked together to synthesize a biological
polymer, they undergo a process called dehydration synthesis. Different macromolecules can assemble in larger complexes,
often needed for biological activity.

Cell theory: The scientific theory that all living organisms are made of cells as the smallest functional unit.

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Prominent Scientist involved in the Systematic Classification of Living Things

Taxonomy- The science of classifying living things.

Scientists classify living things in order to organize and make sense of the incredible diversity of life. Modern scientists base
their classifications mainly on molecular similarities. They group together organisms that have similar proteins and DNA.
Molecular similarities show that organisms are related. In other words, they are descendants of a common ancestor in the past

CARL LINNAEUS (1707-1778) is called the “father of taxonomy.” Linnaean

Classification System

The broadest category in the Linnaean system is the kingdom

Kingdoms are divided, in turn, into phyla. Each phylum is divided into classes, each class into orders, each order into families,
and each family into genera. Each genus is divided into one or more species. The species is the narrowest category in the
Linnaean system. A species is defined as a group of organisms that can breed and produce fertile offspring together.

When Linnaeus was naming and classifying organisms in the 1700s, almost nothing was known of microorganisms. With the
development of powerful microscopes, scientists discovered many single-celled organisms that didn’t fit into any of Linnaeus’
kingdoms. As a result, a new taxon, called the domain, was added to the classification system.
The domain is even broader than the kingdom

Species – Genus – Family – order – class – phylum – kingdom – domain – Life

Comparison of the three domains of life

Trait Archaea Bacteria Eukarya

Multicellularity No No Yes except for many protists

Yes Without Yes for plants, fungi, and some protists

peptidoglycan Yes No for animals and other protists
Cell Wall
With peptidoglycan

Cell Nucleus (DNA inside a

No No Yes
membrane)

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Cell Organelles (other
structures inside No No Yes
membranes)

How Should Viruses Be Classified?

This question was posed at the beginning of the chapter. Should viruses be placed in one of the three domains of life? Are
viruses living things? Before considering these questions, you need to know the characteristics of viruses.

• A virus is nothing more than some DNA or RNA surrounded by a coat of proteins.

• A virus is not a cell.

• A virus cannot use energy, respond to stimuli, grow, or maintain homeostasis.

• A virus cannot reproduce on its own. However, a virus can reproduce by infecting the cell of a living host.
Inside the host cell, the virus uses the cell’s structures, materials, and energy to make copies of itself.

• Because they have genetic material and can reproduce, viruses can evolve. Their DNA or RNA can change through
time. The ability to evolve is a very lifelike attribute.
Many scientists think that viruses should not be classified as living things because they lack most of the defining traits of living
things. Other scientists aren’t so sure. They think that the ability of viruses to evolve and interact with living cells earns them
special consideration. Perhaps a new category of life should be created for viruses. What do you think?

ROBERT WHITTAKER – an American physician and psychotherapy pioneer family therapist.

Whitaker proposed that organisms should be broadly divided into kingdoms, based on certain characters like the structure of
the cell, mode of nutrition, the source of nutrition, interrelationship, body organization, and reproduction. According to this
system, there are five main kingdoms. They are:
• Kingdom Monera
• Kingdom Protista
• Kingdom Fungi
• Kingdom Animalia Kingdom Plantae
Kingdoms are divided into subgroups at various levels. The following flowchart shows the hierarchy of classification.
Kingdom → Phylum → Class → Order → Family → Genus → Species
Kingdom Monera

These organisms are prokaryotic and unicellular. They do not have a well-defined nucleus and also lack cell organelles. Some
organisms show the presence of cell wall while there are others without a cell wall. Consequently, some organisms are
autotrophic and others are heterotrophic. Examples include Bacteria, Cyanobacteria, and Mycoplasma.

Kingdom Protista

Organisms grouped under Kingdom Protista are all unicellular, but eukaryotic organisms. These are the simplest forms of
eukaryotes that exhibit either autotrophic or heterotrophic mode of nutrition. Some organisms have appendages such as cilia
or flagella or pseudopodia to move around. Some examples are Diatoms, Protozoans like Amoeba, Paramoecium

Kingdom Fungi

Heterotrophic, Multicellular and Eukaryotic organisms are grouped under Kingdom Fungi. Their mode of nutrition is
saprophytic as they use decaying organic matter as food. They have cell walls, which are made up of a substance called Chitin.
Fungi also form a symbiotic association with some blue-green algae. Yeast, Mushroom, Aspergillus are examples of Fungi.

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Kingdom Plantae

These are Eukaryotic, Multicellular organisms with a cell wall that is made up of cellulose. They are autotrophs and
synthesize their own food through the process of photosynthesis. This kingdom includes all plants.
Based on the body differentiation and presence or absence of specialized vascular tissue, Kingdom Plantae is divided into
different divisions, namely Thallophyta, Bryophyta, Pteridophyta, Gymnosperms, and Angiosperms. Examples are
Spirogyra, Ferns, Pines, and Mango Plant etc.

Kingdom Animalia

This Kingdom includes organisms that are Multicellular, Eukaryotic, without the presence of cell wall. They have a
heterotrophic mode of nutrition. They also exhibit great diversity. Some organisms are simple while others have a complex
body with specialized tissue differentiation and body organs.
The Animal Kingdom is divided into many phyla and classes. Some of the phyla are Porifera, Coelenterata, Arthropoda,
Echinodermata, Chordata etc. Examples – Hydra, Starfish, Earthworms, Monkeys, Birds etc.

CARL RICHARD WOESE, American microbiologist who discovered the group of single-cell prokaryotic organisms known
as archaea, which constitute a third domain of life.

The Three Domains of Life

In 1970s, scientists began to find evidence for a previously unknown group of prokaryotic organisms. These organisms lived in
extreme environments - deep sea hydrothermal vents, "black smokers", hot springs, the Dead Sea, acid lakes, salt evaporation
ponds - environments that scientists had never suspected would contain a profusion of life!

Dr. Woese proposed that there should be a new caterogy of classification of life - the Domain, a classification category above
Kingdom.

The Three domains - Some Characteristics:

Bacteria: Domain Bacteria is familiar to most people when associated with human or animal disease. However, most bacterial
species do not (and cannot) cause disease. Many species even play beneficial roles by producing antibiotics and food. The soil
teems with free-living bacteria that perform many essential functions in the biosphere, e.g. nitrogen fixation. Our bodies are
covered with bacteria that make up our normal flora.

Fun Fact: There are more bacteria in one person's mouth than there are people in the world. Many are decomposers,
some are photosynthesizers, and a few cause disease. Most bacteria cause disease by producing exotoxins that harm
human cells, while others cause illness as a result of glycoproteins found on the outside of their capsules. There are many
shapes that bacteria can come in, but three of the main ones are cocci (spherical), bacilli (rods) and spirochete (spiral
bacteria).

At least 5 major Phyla:

1. Proteobacteria: Enteric bacteria like E. coli, Salmonella typhus, Legionella, Heliobacter pylorii (cause of many ulcers),
Neisseria gonorrhea (cause of gonorrhea). These bacteria are very closely related to eukaryotic mitochondria.

2. Cyanobacteria: Photosynthetic ‘blue-green’ bacteria = produce O2 gas. Over 2 billion years ago, these bacteria made the O2
rich atmosphere in which we live.These bacteria are very closely related to eukaryotic chloroplasts.
3. Eubacteria: Clostridium (tetanus, botulism), Bacillus, mycoplasma (walking pneumonia).

4. Chlamydias: Parasites: Giardia, Chlamydia (STD)

5. Spirochaetes: Spiral bacteria: cause syphilis, Lyme disease

To read more about bacteria we don't like, see the "Bad Bug Book".
Archaea: Life's Extremists...!

1. Methanogens: “methane-makers”
Use only CO2, H and N to produce energy to live, and as a result give off methane gas. [Image]. Live in
swamps, marshes, gut of cattle, termites, etc. Methanococcus jannaschii, isolated from the deep sea Alvin
probe, was the first Archaean whose genome was sequenced. Methanogens are decomposers; and can be
used in sewage treatment. Methanogens may someday be used to produce methane as fuel!

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2. Extreme Halophiles: “salt lovers”
Require an environment as salty or even 10x saltier than ocean water. Some prefer up to 30%
salt concentrations! These bacteria live in the Dead Sea, the Great Salt Lake, salt evaporation
ponds.

3. Extreme Thermophiles: “heat / cold lovers”

Prefer temperatures above 60C (up to 110C for hyperthermophiles!) or near or below freezing. (Some thermophiles will die at
roon temperature).
Thermophiles Live in hot sulfur springs, Yellowstone Park, deep sea hydrothermal vents “black
smokers”, geothermal power plants. Also live in ocean waters around Antarctica, under the polar
ice caps, etc. Thermus aquaticus and Pyrococcus furiosis and two species.

Extremophiles - Scientific American 1997 (PS. Written by Barry Marrs - but no relation!)

Eukarya

1. Protista – Single celled eukaryotes – Euglena, Amoeba, Paramecium etc

Protists can be found on land, in water, or living inside other organisms. Some protists are photosynthetic,
like "phytoplankton", and produce more oxygen than all land plants put together. Other protists are parasites
or predators. The protozoan Trypanosoma brucei causes African Sleeping Sickness. This parasite it transmitted
to man by the bite of the tsetse fly. Another
protozoan, Entameba histolytica is a parasite of the stomach which kills cells and drinks blood (but do not
actually kill their host). The protozoan Plasmodium vivax causes malaria, carried by female
mosquitos. Most protozoans move by means of pseudopodia ("false feet") or by cilia (little hairs). [Quote]

2. Fungi – Mushrooms, bread molds, water molds, yeasts ,etc

The Kingdom Fungi includes some of the most important organisms on Earth. By breaking down
dead organic material, they cycle nutrients through ecosystems. Other fungi provide drugs such
as penicillin and other antibiotics, foods like mushrooms, truffles and morels, and the bubbles in
bread, champagne, and beer.

Fungi also cause plant and animal diseases: in humans, ringworm, athlete's foot, and several
more serious diseases are caused by fungi. Plant diseases caused by fungi include
rusts, smuts, and leaf, root, and stem rots, and may cause severe damage to crops. However, a number of fungi, in
particular the yeasts, are important "model organisms" for studying problems in genetics and molecular biology.

3. Plantae – Flowering plants, gymnosperms (conifers), ferns, mosses, etc

Kingdom Plantae includes all land plants - an amazing range of diverse forms with more than 250,000 species. Plants first
appeared on Earth in the Ordovician period approximately 510 million years ago. The most striking, and important, feature of
plants is their green color, the result of a pigment called chlorophyll. Plants use chlorophyll to capture light energy, which fuels
the manufacture of food—sugar, starch, and other carbohydrates. [Quote]

4. Animalia – [There is so much to say about this Kingdom

First appeared on Earth ~650 million years ago.

Includes sponges, jellyfish, corals, fish (etc etc) and a special
mention to: Arthropods (includes insects):

"By nearly any measure, the most successful animals on the planet
are the arthropods. They make up over three-fourths of all
currently known living and fossil organisms, or over one million
species in all. Since many arthropod species remain undocumented
or undiscovered, the true number of living arthropod species is
probably in the tens of millions. One recent conservative estimate
puts the number of arthropod species in tropical forests at 6 to 9
million species (Thomas, 1990).

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"Arthropods range in distribution from the deep sea to mountain peaks, in size from the king crab with its 12-foot armspan to
microscopic insects and crustaceans. Despite this unbelievable diversity, the basic body plan of arthropods is fairly constant.
Arthropods have a stiff cuticle made largely of chitin and proteins, forming an exoskeleton. They have segmented bodies to
form integrated units (heads, abdomens, and so on). The phylum takes its name from its distinctive jointed appendages, which
may be modified in a number of ways to form antennae, mouthparts, and reproductive organs." [Quote]

And another special mention to Tetrapods (amphibians, reptiles, birds and mammals):

"Tetrapods were the first vertebrates to truly walk the land. Before tetrapods existed, vertebrates (like fish) were all confined
to living in aquatic habitats. The tetrapods began moving to land in the Paleozoic around 360 million years ago. Tetrapods are
a name that we have given to anything with four feet (tetra=four, pod=feet). Therefore all land dwelling vertebrates can be
considered tetrapods. Tetrapods, whose closest living relatives are lungfish, have two main groups: amphibians and amniotes.
The amniotes in turn have two main groups: the synapsids (including mammals) and the sauropsids (including reptiles and
their fossil relatives).

LYNN MARGULIS - was an American evolutionary theorist and biologist, science author, educator, and popularizer, and
was the primary modern proponent for the significance of symbiosis in evolution

The Endosymbiotic Theory

A theory on the Origins of Eukaryotic Cells: Mitochondria and Chloroplasts
There are a great many differences between Eukaryotic cells and Prokaryotic cells in size, complexity, internal
compartments.
However, there is a curious similarity between prokaryotic cells and the organelles of eukaryotic cells.
Some of these similarities were first noted in the 1880s, but were largely ignored for almost a century!
Chloroplasts of
Mitochondria of Photosynthetic
Prokaryotes Eukaryotes
Eukaryotic cells eukaryotes

1 single, circular Multiple linear chromosomes 1 single, circular 1 single, circular

DNA chromosome compartmentalized in a nucleus chromosome chromosome

Binary Fission Binary Fission Binary Fission

Replication (1 cell splits into 2) Mitosis (1 cell splits into 2) (1 cell splits into 2)

Ribosomes "70 S" "80 S" "70 S" "70 S"

Not found in the plasma membrane

Electron Found in the plasma around cell (found only in the cell's Found in the plasma Found in the plasma
Transport membrane around mitochondria and chloroplasts) membrane around membrane around
Chain cell mitochondrion chloroplast

Size
(approximate) ~1-10 microns ~50 - 500 microns ~1-10 microns ~1-10 microns

Appearance on Anaerobic bacteria: ~1.5 billion years ago

Earth ~3.8 Billion years ago ~1.5 billion years ago ~1.5 billion years ago

Photosynthetic bacteria:
~3.2 Billion years ago
Aerobic bacteria:
~2.5 Billion years ago

Endo = "within"
Endocytosis = (cyto = cell) a process of 'cell eating' - cells are engulfed, but then usually digested as food.

Endosymbiosis = cells are engulfed, but not digested...cells live together is a mutually benefitting relationship, or symbiosis

Her hypothesis originally proposed that:

mitochondria are the result of endocytosis of aerobic bacteria
chloroplasts are the result of endocytosis of photosynthetic bacteria
• in both cases by large anaerobic bacteria who would not otherwise be able to exist in an aerobic environment.
• this arrangement became a mutually beneficial relationship for both cells (symbiotic).

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Margulis' original hypothesis proposed that aerobic bacteria (that require oxygen) were ingested by anaerobic bacteria
(poisoned by oxygen), and may each have had a survival advantage as long as they continued their partnership.

SIMILARITIES AND DIFFERENCES OF PROKARYOES AND EUKARYOTES

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