Concepts in Botany

Introduction

Botany is the scientific study of plant life. As a branch of biology, it is also called plant science(s), phytology, or
plant biology. Botany covers a wide range of scientific disciplines that study plants, algae, and fungi including:
structure, growth, reproduction, metabolism, development, diseases, and chemical properties and evolutionary
relationships between the different groups.

The study of plants and botany began with tribal lore, used to identify edible, medicinal and poisonous plants,
making botany one of the oldest sciences. From this ancient interest in plants, the scope of botany has increased
to include the study of over 550,000 kinds or species of living organisms.

Scope and importance of botany

As with other life forms in biology, plant life can be studied from different perspectives, from the molecular,
genetic and biochemical level through organelles, cells, tissues, organs, individuals, plant populations, and
communities of plants. At each of these levels a botanist might be concerned with the classification (taxonomy),
structure (anatomy and morphology), or function (physiology) of plant life.

Historically, botany covers all organisms that were not considered to be animals. Some of these "plant-like"
organisms include fungi (studied in mycology), bacteria and viruses (studied in microbiology), and algae
(studied in phycology). Most algae, fungi, and microbes are no longer considered to be in the plant kingdom.
However, attention is still given to them by botanists, and bacteria, fungi, and algae are usually covered in
introductory botany courses.

The study of plants has importance for a number of reasons. Plants are a fundamental part of life on Earth. They
generate the oxygen, food, fibres, fuel and medicine that allow higher life forms to exist. Plants also absorb
carbon dioxide through photosynthesis, a minor greenhouse gas that in large amounts can affect global climate.
It is believed that the evolution of plants has changed the global atmosphere of the earth early in the earth's
history and paleobotanists study ancient plants in the fossil record. A good understanding of plants is crucial to
the future of human societies as it allows us to:

* Produce food to feed an expanding population

* Understand fundamental life processes
* Produce medicine and materials to treat diseases and other ailments
* Understand environmental changes more clearly
Human nutrition
All foods eaten come from plants, either directly from staple foods and other fruit and vegetables, or indirectly
through livestock or other animals, which rely on plants for their nutrition. Plants are the fundamental base of
nearly all food chains because they use the energy from the sun and nutrients from the soil and atmosphere and
convert them into a form that can be consumed and utilized by animals; this is what ecologists call the first
trophic level.

Botanists also study how plants produce food we can eat and how to increase yields and therefore their work is
important in mankind's ability to feed the world and provide food security for future generations, for example
through plant breeding.

Botanists also study weeds, plants which are considered to be a nuisance in a particular location. Weeds are a
considerable problem in agriculture, and botany provides some of the basic science used to understand how to
minimize 'weed' impact in agriculture and native ecosystems. Ethnobotany is the study of the relationships
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between plants and people.

Fundamental life processes

Plants are convenient organisms in which fundamental life processes (like cell division and protein synthesis for
example) can be studied, without the ethical dilemmas of studying animals or humans. The genetic laws of
inheritance were discovered in this way by Gregor Mendel, who was studying the way pea shape is inherited.

What Mendel learned from studying plants has had far reaching benefits outside of botany. Additionally,
Barbara McClintock discovered 'jumping genes' by studying maize. These are a few examples that demonstrate
how botanical research has an ongoing relevance to the understanding of fundamental biological processes.

Medicine and materials

Many medicinal and recreational drugs, like tetrahydrocannabinol, caffeine, and nicotine come directly from the
plant kingdom. Others are simple derivatives of botanical natural products; for example aspirin is based on the
pain killer salicylic acid which originally came from the bark of willow trees.[2] There may be many novel
cures for diseases provided by plants, waiting to be discovered. Popular stimulants like coffee, chocolate,
tobacco, and tea also come from plants. Most alcoholic beverages come from fermenting plants such as barley
malt and grapes.

Plants also provide us with many natural materials, such as cotton, wood, paper, linen, vegetable oils, some
types of rope, and rubber. The production of silk would not be possible without the cultivation of the mulberry
plant. Sugarcane, rapeseed, soy and other plants with a highly-fermentable sugar or oil content have recently
been put to use as sources of biofuels, which are important alternatives to fossil fuels, see biodiesel.

Environmental changes

Plants can also help us understand changes in on our environment in many ways.
• Understanding habitat destruction and species extinction is dependent on an accurate and complete catalog of
plant systematics and taxonomy.
• Plant responses to ultraviolet radiation can help us monitor problems like the ozone depletion.
• Analyzing pollen deposited by plants thousands or millions of years ago can help scientists to reconstruct past
climates and predict future ones, an essential part of climate change research.
• Recording and analyzing the timing of plant life cycles are important parts of phenology used in climate-
change research.
• Lichens, which are sensitive to atmospheric conditions, have been extensively used as pollution indicators.
In many different ways, plants can act a little like the 'miners canary', an early warning system alerting us to
important changes in our environment. In addition to these practical and scientific reasons, plants are extremely
valuable as recreation for millions of people who enjoy gardening, horticultural and culinary uses of plants
every day.

Historical Evolution of Botany

History

Early examples of plant taxonomy occur in the Rigveda, that divides plants into Vrska (tree), Osadhi (herbs
useful to humans) and Virudha (creepers). which are further subdivided. The Atharvaveda divides plants into
eight classes, Visakha (spreading branches), Manjari (leaves with long clusters), Sthambini (bushy plants),
Prastanavati (which expands); Ekasrnga (those with monopodial growth), Pratanavati (creeping plants),
Amsumati (with many stalks), and Kandini (plants with knotty joints). The Taittiriya Samhita and classifies the
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plant kingdom into vrksa, vana and druma (trees), visakha (shrubs with spreading branches), sasa (herbs),
amsumali (a spreading or deliquescent plant), vratati (climber), stambini (bushy plant), pratanavati (creeper),
and alasala (those spreading on the ground).

Manusmriti proposed a classification of plants in eight major categories. Charaka SamhitÄ ﾁ and Sushruta
Samhita and the Vaisesikas also present an elaborate taxonomy.

Parashara, the author of Vrksayurveda (the science of life of trees), classifies plants into Dvimatrka
(Dicotyledons) and Ekamatrka (Monocotyledons). These are further classified into Samiganiya (Fabaceae),
Puplikagalniya (Rutaceae), Svastikaganiya (Cruciferae), Tripuspaganiya (Cucurbitaceae), Mallikaganiya
(Apocynaceae), and Kurcapuspaganiya (Asteraceae).

Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by
Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books
constitute the most important contribution to botanical science during antiquity and on into the Middle Ages.
The Roman medical writer Dioscorides provides important evidence on Greek and Roman knowledge of
medicinal plants.

In ancient China, the recorded listing of different plants and herb concoctions for pharmaceutical purposes
spans back to at least the Warring States (481 BC-221 BC). Many Chinese writers over the centuries contributed
to the written knowledge of herbal pharmaceutics.

There was the Han Dynasty (202 BC-220 AD) written work of the Huangdi Neijing and the famous
pharmacologist Zhang Zhongjing of the 2nd century. There was also the 11th century scientists and statesmen
Su Song and Shen Kuo, who compiled treatises on herbal medicine and included the use of mineralogy.

Important medieval works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of
Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

In 1665, using an early microscope, Robert Hooke discovered cells in cork, and a short time later in living plant
tissue. The German Leonhart Fuchs, the Swiss Conrad von Gesner, and the British authors Nicholas Culpeper
and John Gerard published herbals that gave information on the medicinal uses of plants.

In 1754 Carl von Linné (Carl Linnaeus) devided the plant Kingdom into 25 classes. One, the Cryptogamia,
included all the plants with concealed reproductive parts (algae, fungi, mosses and liverworts and ferns).

Modern botany

Considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis
thaliana. This weedy species in the mustard family was one of the first plants to have its genome sequenced.
The sequencing of the rice (Oryza sativa) genome and a large international research community have made rice
the de facto cereal/grass/monocot model. Another grass species, Brachypodium distachyon is also emerging as
an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses.

Other commercially-important staple foods like wheat, maize, barley, rye, pearl millet and soybean are also
having their genomes sequenced. Some of these are challenging to sequence because they have more than two
haploid (n) sets of chromosomes, a condition known as polyploidy, common in the plant kingdom.
Chlamydomonas reinhardtii (a single-celled, green alga) is another plant model organism that has been
extensively studied and provided important insights into cell biology.

In 1998 the Angiosperm Phylogeny Group published a phylogeny of flowering plants based on an analysis of
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DNA sequences from most families of flowering plants. As a result of this work, major questions such as which
families represent the earliest branches in the genealogy of angiosperms are now understood. Investigating how
plant species are related to each other allows botanists to better understand the process of evolution in plants.
Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by
Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books
constitute the most important contribution to botanical science during antiquity and on into the Middle Ages.
The Roman medical writer Dioscorides provides important evidence on Greek and Roman knowledge of
medicinal plants.

In ancient China, the recorded listing of different plants and herb concoctions for pharmaceutical purposes
spans back to at least the Warring States (481 BC-221 BC). Many Chinese writers over the centuries contributed
to the written knowledge of herbal pharmaceutics.

There was the Han Dynasty (202 BC-220 AD) written work of the Huangdi Neijing and the famous
pharmacologist Zhang Zhongjing of the 2nd century. There was also the 11th century scientists and statesmen
Su Song and Shen Kuo, who compiled treatises on herbal medicine and included the use of mineralogy.

Important medieval works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of
Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

In 1665, using an early microscope, Robert Hooke discovered cells in cork, and a short time later in living plant
tissue. The German Leonhart Fuchs, the Swiss Conrad von Gesner, and the British authors Nicholas Culpeper
and John Gerard published herbals that gave information on the medicinal uses of plants.

In 1754 Carl von Linné (Carl Linnaeus) devided the plant Kingdom into 25 classes. One, the Cryptogamia,
included all the plants with concealed reproductive parts (algae, fungi, mosses and liverworts and ferns).

A considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis
thaliana. This weedy species in the mustard family was one of the first plants to have its genome sequenced.
The sequencing of the rice (Oryza sativa) genome and a large international research community have made rice
the de facto cereal/grass/monocot model. Another grass species, Brachypodium distachyon is also emerging as
an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses.

Other commercially-important staple foods like wheat, maize, barley, rye, pearl millet and soybean are also
having their genomes sequenced. Some of these are challenging to sequence because they have more than two
haploid (n) sets of chromosomes, a condition known as polyploidy, common in the plant kingdom.
Chlamydomonas reinhardtii (a single-celled, green alga) is another plant model organism that has been
extensively studied and provided important insights into cell biology.

In 1998 the Angiosperm Phylogeny Group published a phylogeny of flowering plants based on an analysis of
DNA sequences from most families of flowering plants. As a result of this work, major questions such as which
families represent the earliest branches in the genealogy of angiosperms are now understood. Investigating how
plant species are related to each other allows botanists to better understand the process of evolution in plants.

Forest Ecosystem
Forestry is the art, science, and practice of studying and managing forests and plantations, and related natural
resources. Silviculture, a related science, involves the growing and tending of trees and forests. Modern forestry
generally concerns itself with: assisting forests to provide timber as raw material for wood products; wildlife
habitat; natural water quality regulation; recreation; landscape and community protection; employment;
aesthetically appealing landscapes; biodiversity management; watershed management; and a 'sink' for
atmospheric carbon dioxide. A practitioner of forestry is known as a forester.
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Forest ecosystems have come to be seen as one of the most important components of the biosphere, and forestry
has emerged as a vital field of science, applied art, and technology.

Activities

Foresters may be employed by industry, government agencies, conservation groups, urban parks boards,
citizens' associations, or private landowners. Industrial foresters are predominantly involved in planning the
timber harvests and forest regeneration. Other foresters have the specific jobs which include a broad array of
responsibilities. For example, urban foresters work within city environments to enhance urban trees with their
unique needs.

Some foresters work in tree nurseries growing seedlings for regeneration projects. Others are involved with tree
genetics or developing new building systems as forest engineers. The profession has expanded to include a wide
diversity of jobs, typically requiring a college bachelor's degree up to the PhD level for highly specialized areas
of work.

Traditionally, professional foresters develop and implement "forest management plans". These plans rely on tree
inventories showing an area's topographical features as well as its distribution of trees (by species) and other
plant cover. They also include roads, culverts, proximity to human habitation, hydrological conditions, and soil
reports ecological sensitive areas. Finally, forest management plans include the projected use of the land and a
timetable for that use.

Plans for harvest and subsequent site treatment are influenced by the objectives of the land's owner or
leaseholder (for instance, a timber company that holds cutting rights to a given tract of land, or the government
in the case of state-owned forests). There is an increasing trend to consider the needs of other stakeholders (e.g.,
nearby communities or neighborhoods, or rural residents living within or adjacent to the forest tract). Plans are
developed with the prevailing forest harvest laws and regulations in mind. They ultimately result in a
prescription for the harvest of trees, and indicate whether road building or other forest engineering operations
are required.
Activities

Traditional forest management plans are chiefly aimed at providing logs as raw material for timber, veneer,
plywood, paper, wood fuel or other industries. Hence, considerations of product quality and quantity,
employment, and profit have been of central, though not always exclusive, importance.

Foresters also frequently develop post-harvest site plans. These may call for reforestation (tree planting by
species), weed control, fertilization, or the spacing of young trees (thinning of trees that are crowding one
another).

While other duties of foresters may include preventing and combatting insect infestation, disease, forest and
grassland fires, there is an increasing movement towards allowing these natural aspects of forest ecosystems to
run their course, where possible, usually excepting epidemics or risk of life or property. Foresters are specialists
in measuring and modelling the growth of forests (forest mensuration). Increasingly, foresters may be involved
in wildlife conservation planning and watershed protection.

Today

Today a strong body of research exists regarding the management of forest ecosystems, selection of species and
varieties, and tree breeding. Forestry also includes the development of better methods for the planting,
protecting, thinning, controlled burning, felling, extracting, and processing of timber. One of the applications of
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 modern forestry is reforestation, in which trees are planted and tended in a given area.

In many regions the forest industry is of major ecological, economic, and social importance. Third-party
certification systems that provide independent verification of sound forest stewardship and sustainable forestry
have become commonplace in many areas since the 1990s. These certification systems were developed as a
response to criticism of some forestry practices, particularly deforestation in less developed regions along with
concerns over resource management in the developed world. Some certification systems are criticised for
primarily acting as marketing tools and lacking in their claimed independence.

In topographically severe forested terrain, proper forestry is important for the prevention or minimization of
serious soil erosion or even landsliding. In areas with a high potential for landsliding, good forestry can act to
prevent property damage or loss, human injury, or loss of life.

Public perception of forest management has become controversial, with growing public concern over perceived
mismanagement of the forest and increasing demands that forest land be managed for uses other than pure
timber production, for example, indigenous rights, recreation, watershed protection and preservation of
wilderness and wildlife habitat. Sharp disagreements over the role of forest fires, logging, motorized recreation
and others drives debate while the public demand for wood products continues to increase.

Horticulture

Horticulture is the art and science of the cultivation of plants.

Horticulturists work and conduct research in the fields of plant propagation and cultivation, crop production,
plant breeding and genetic engineering, plant biochemistry, and plant physiology. The work particularly
involves fruits, berries, nuts, vegetables, flowers, trees, shrubs, and turf. Horticulturalists work to improve crop
yield, quality, nutritional value, and resistance to insects, diseases, and environmental stresses.

The study of horticulture

Horticulture involves six areas of study, which can be grouped into two broad sections - ornamentals and
edibles:

* Arboriculture the study and selection, planting, care, and removal of individual trees, shrubs, vines, and other
perennial woody plants.
* Floriculture (includes production and marketing of floral crops),
* Landscape horticulture (includes production, marketing and maintenance of landscape plants).
* Olericulture (includes production and marketing of vegetables).
* Pomology (includes production and marketing of fruits)
* Postharvest physiology (involves maintaining quality and preventing spoilage of horticultural crops).

Horticulturists can work in industry, government or educational institutions or private collections. They can be
cropping systems engineers, wholesale or retail business managers, propagators and tissue culture specialists
(fruits, vegetables, ornamentals, and turf), crop inspectors, crop production advisers, extension specialists, plant
breeders, research scientists, and of course, teachers.

Disciplines which complement horticulture include biology, botany, entomology, chemistry, mathematics,
genetics, physiology, statistics, computer science, and communications, garden design, planting design. Plant
science and horticulture courses include: plant materials, plant propagation, tissue culture, crop production,
post-harvest handling, plant breeding, pollination management, crop nutrition, entomology, plant pathology,
economics, and business. Some careers in horticultural science require a masters (MS) or doctoral (PhD)
6
degree.

Horticulture is practised in many gardens, "plant growth centres" and nurseries. Activities in nurseries range
from preparing seeds and cuttings to growing fully mature plants. These are often sold or transferred to
ornamental gardens or market gardens.

Paleobotany

Paleobotany, also spelled as palaeobotany (from the Greek words paleon = old and "botany", study of plants), is
the branch of paleontology or paleobiology dealing with the recovery and identification of plant remains from
geological contexts, and their use for the biological reconstruction of past environments, and the evolution of
both the plant kingdom and life in general. A synonym is paleophytology. Paleobotany includes the study of
terrestrial plant fossils, as well as the study of prehistoric marine photoautotrophs, such as photosynthetic algae,
seaweeds or kelp. A closely-related field is palynology, which is the study of fossilized and extant spores and
pollen.

Paleobotany is important in the reconstruction of ancient ecological systems and climate, known as
paleoecology and paleoclimatology respectively; and is fundamental to the study of green plant development
and evolution. Paleobotany has also become important to the field of archaeology, primarily for the use of
phytoliths in relative dating and in paleoethnobotany,

Overview of the Paleobotanical Record

Macroscopic remains of true vascular plants are first found in the fossil record during the Silurian Period of the
Paleozoic era.. Some dispersed, fragmentary fossils of disputed affinity, primarily spores and cuticles, have been
found in rocks from the Ordovician Period in Oman, and are thought to derive from liverwort- or moss-grade
fossil plants (Wellman et al., 2003).

An important early land plant fossil locality is the Rhynie Chert, an Early Devonian sinter (hot spring) deposit
composed primarily of silica found outside the town of Rhynie in Scotland. The Rhynie Chert is exceptional
due to its preservation of several different clades of plants, from mosses and lycopods to more unusual,
problematic forms. Many fossil animals, including arthropods and arachnids, are also found in the Rhynie
Chert, and it offers a unique window on the history of early terrestrial life.

Plant-derived macrofossils become abundant in the Late Devonian and include tree trunks, fronds, and roots.
The earliest tree is Archaeopteris, which bears simple, fern-like leaves spirally arranged on branches atop a
conifer-like trunk (Meyer-Berthaud et al., 1999). Widespread coal swamp deposits across North America and
Europe during the Carboniferous Period contain a wealth of fossils containing arborescent lycopods up to 30
meters tall, abundant seed plants, such as conifers and seed ferns, and countless smaller, herbaceous plants.

Angiosperms (flowering plants) evolved during the Mesozoic, and flowering plant pollen and leaves first appear
during the Early Cretaceous, approximately 130 million years ago.
Palynology

Palynology is the science that studies contemporary and fossil palynomorphs, including pollen, spores,
dinoflagellate cysts, acritarchs, chitinozoans and scolecodonts, together with particulate organic matter (POM)
and kerogen found in sedimentary rocks and sediments. Palynology does not include diatoms, foraminiferans or
other organisms with silicaceous or calcareous exoskeletons.

Palynology is an interdisciplinary science and is a branch of earth science (geology or geological science) and
biological science (biology), particularly plant science (botany). Stratigraphical palynology is a branch of
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micropalaeontology and paleobotany which studies fossil palynomorphs from the Precambrian to the Holocene.

Methods of study

Palynomorphs are broadly defined as organic-walled microfossils between 5 and 500 micrometres in size. They
are extracted from rocks and sediment cores both physically, by wet sieving, often after ultrasonic treatment,
and chemically, by using chemical digestion to remove the non-organic fraction.

Chemical Preparation

Chemical digestion follows a number of steps. Initially the only chemical treatment used by researchers was
treatment with KOH to remove humic substances; defloculation was accomplished through surface treatment or
ultra-sonic treatment, although sonification may cause the pollen exine to rupture.[4] The use of hydrofluoric
acid (HF) to digest silicate minerals was introduced by Assarson and Granlund in 1924, greatly reducing the
amount of time required to scan slides for palynomorphs.

Palynological studies using peats presented a particular challenge because of the presence of well preserved
organic material including fine rootlets, moss leaflets and organic litter. This was the last major challenge in the
chemical preparation of materials for palynological study. Acetolysis was developed by Gunnar Erdtman and
his brother to remove these fine cellulose materials by dissolving them. In acetolysis the material is treated with
acetic anhydride and sulfuric acid, dissolving cellulistic materials and providing better visibility for
palynomorphs.

Some steps of the chemical treatments require special care for safety reason, in particular the use of HF which
diffuses very fast through the skin and could cause severe chemical burns. Other treatment include kerosene
flotation for chitinous materials.

Major Areas of Research in Botany

Biotechnology

Agronomists use biotechnology to extend and expedite the development of desired characteristics listed in the
Plant Breeding section. Biotechnology is is often a lab activity requiring field testing of the new crop varieties
that are developed.

In addition to increasing crop yields, reducing crop vulnerability to environmental stresses, improving health
and taste of foods, and reducing the need for field applied chemicals, agronomic biotechnology is increasingly
being applied for novel uses other than food. For example, oilseed is at present used mainly for margarine and
other food oils, but it can be modified to produce fatty acids for detergents, substitute fuels and petrochemicals.

Soil Science

Agronomists study sustainable ways to make soils more productive. They classify soils and reproduce them to
determine whether they contain substances vital to plant growth. Such nutritional substances include
compounds of nitrogen, phosphorus, and potassium. If a certain soil is deficient in these substances, fertilizers
may provide them. Agronomists investigate the movement of nutrients through the soil, and the amount of
nutrients absorbed by a plant's roots. Agronomists also examine the development of the roots and their relation
to the soil.

Soil Conservation

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In addition, agronomists develop methods to preserve the soil and to decrease the effects of erosion by wind and
water. For example, a technique called contour plowing may be used to prevent soil erosion and conserve
rainfall. Researchers in agronomy also seek ways to use the soil more effectively in solving other problems.
Such problems include the disposal of human and animal wastes; water pollution; and the build-up in the soil of
chemicals called pesticides, which are used to kill insects and other pests. No-tilling crops is a technique now
used to help prevent erosion. planting of soil binding grasses along contours can be tried in steep slopes. For
better effect, contour drains of depths up to 1 metre may help retain the soil and prevent permanent wash off.

Agroecology

Agroecology is the management of agricultural systems with a strong emphasis on ecological and
environmental perspectives.[5] This area is closely associated with work in the areas of Sustainable Agriculture,
Organic Agriculture, and the development of alternative cropping systems.

Bryology

Bryology is the branch of botany concerned with the scientific study of bryophytes (mosses, liverworts, and
hornworts).
Bryophytes were first studied in detail in the 18th century. The German botanist Johann Jacob Dillenius (1687-
1747) was a professor at Oxford and in 1717 produced the work "Reproduction of the ferns and mosses." The
beginning of bryology really belongs to the work of Johannes Hedwig, who clarified the reproductive system of
mosses (1792, Fundamentum historiae naturalist muscorum) and arranged a taxonomy.

Areas of research include bryophyte taxonomy, bryophytes as bioindicators, DNA sequencing, and the
interdependency of bryophytes and other plant and animal species. Among other things, scientists have learned
that certain species of mosses are carnivorous.

Ethnobotany

Ethnobotany is the study of the relationship between plants and people: From"ethno" - study of people and
"botany" - study of plants. Ethnobotany is considered a branch of ethnobiology. Ethnobotany studies the
complex relationships between (uses of) plants and cultures. The focus of ethnobotany is on how plants have
been or are used, managed and perceived in human societies and includes plants used in food, medicine,
divination, cosmetics, dyeing, textiles, constuction, tools, currency, clothing, literature, rituals, and social life.

Beginning in the 20th century, the field of ethnobotany experienced a shift from the raw compilation of data to a
greater methodological and conceptual reorientation. This is also the beginning of academic ethnobotany. The
founding father of this discpline is Richard Evans Schultes.

Today the field of ethnobotany requires a variety of skills: botanical training for the identification and
preservation of plant specimens; anthropological training to understand the cultural concepts around the
perception of plants; linguistic training, at least enough to transcribe local terms and understand native
morphology, syntax, and semantics.

Native healers are often reluctant to accurately share their knowledge to outsiders. Schultes actually apprenticed
himself to an Amazonian shaman, which involves a long term commitment and genuine relationship. In Wind in
the Blood: Mayan Healing & Chinese Medicine by Garcia et. al. the visiting acupuncturists were able to access
levels of Mayan medicine that anthropologists could not because they had something to share in exchange.
Cherokee medicine priest David Winston describes how his uncle would invent nonsense to satisfy visiting
anthropologists.

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 Genetics: Introduction concepts

Inheritance Patterns

Mendel was the first scientist to develop a method for predicting the outcome of inheritance patterns. He
performed his work with pea plants, studying seven traits: plant height, pod shape, pod color, seed shape, seed
color, flower color, and flower location. Pea plants pollinate themselves. Therefore, over many generations, pea
plants develop individuals that are homozygous for particular characteristics. These populations are known as
pure lines.

In his work, Mendel took pure-line pea plants and cross-pollinated them with other pure-line pea plants. He
called these plants the parent generation. When Mendel crossed pure-line tall plants with pure-line short plants,
he discovered that all the plants resulting from this cross were tall. He called this generation the F1 generation
(first filial generation). Next, Mendel crossed the offspring of the F1 generation tall plants among themselves to
produce a new generation called the F2 generation (second filial generation). Among the plants in this
generation, Mendel observed that three-fourths of the plants were tall and one-fourth of the plants were short.

Mendel's laws of genetics

Mendel conducted similar experiments with the other pea plant traits. Over many years, he formulated several
principles that are known today as Mendel's laws of genetics. His laws include the following:

1. Mendel's law of dominance: When an organism has two different alleles for a trait, one allele dominates.

2. Mendel's law of segregation: During gamete formation by a diploid organism, the pair of alleles for a
particular trait separate, or segregate, during the formation of gametes (as in meiosis).

3. Mendel's law of independent assortment: The members of a gene pair separate from one another independent
of the members of other gene pairs. (These separations occur in the formation of gametes during meiosis.)

Genetics Part-I

DNA replication, transcription and translation.

In very general terms, what does a chromosome contain?

• Information, genetic information to carry out the characteristics of life -- precise self replication, ability to
exchange energy with the environment, etc.

In very general terms, what are the two related functions of DNA?

• Information storage

o DNA replication

• Information transfer

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o DNA transcribed into RNA

o DNA's function in information transfer

What is the Central Dogma associated with information storage and retrieval?

• Central Dogma:
DNA-->RNA-->unfolded protein-->native, folded protein

What are the three processes of the central dogma?

How does DNA function as an information molecule?

• replication, DNA --> DNA

• transcription, DNA --> RNA

• translation, RNA --> unfolded protein --> folded protein

In terms of molecular conformation, what occurs through the central dogma?

• Translation of linear information, a sequence of nucleotides, into 3-D information, the structure of a protein.

What are the differences between DNA and RNA?

• base composition: RNA = AGCU, DNA = AGCT

• carbohydrate: RNA = ribose, DNA = deoxyribose

• structure: RNA = single stranded, DNA = double helix

RNA

o usually single stranded

o linear polymer of ribonucleotides.

o Some secondary and tertiary structure but often ill-defined.

What are the different types of RNA?

What are the functions of the different types of RNA?

• messenger RNA = mRNA, information transfer

• transfer RNA = tRNA, information transfer

• ribosomal RNA = rRNA, structural

• small nuclear RNA = snRNA, ribozymes, RNA processing.

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What is replication?

Transfer of genetic information from one generation to the next.

DNA-directed DNA synthesis: replication of the genome.

What is the structural basis for the precise duplication of the genome?

• The Watson-Crick structure of DNA: the strands are complementary, the nucleotide sequence in one
automatically specifies the other.

• The enzyme, DNA polymerase III, is very accurate: it has proof reading capabilities.

Is replication conservative or semi-conservative? What does that mean?

• Is the parental genome of double stranded DNA fully conserved in the parental cell or is it split equally (semi-
conserved) between two daughter cells?

Replication is semi-conservative.

Genetics Part-II

What is the evidence for semi-conservative replication?

Classical experiments of Meselson and Stahl. Label DNA with *heavy isotope* N15 and allow replication in
light N14: distinguish heavy, light and hybrid DNA by centrifugation.

Results: after 1 generation, each genome contains a hybrid N15-N14 DNA; after 2 generations, there are 2
hybrid and 2 light (N14-N14) genomes.

• Each strand of DNA serves as a template for the synthesis of its complement.

• The strands separate and each is used as a template for the synthesis of a daughter strand.

• The two new double helices each contain half the parental DNA.

• This process produces a replication fork

Is replication uni-directional or bi-directional?

• Bi-directional

• Two replication forks proceeding from the origin.

DNA replication, transcription and translation.
What is the major replication enzyme?

DNA polymerase III, a DNA-directed DNA polymerase

• Synthesis is 5'-->3'

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• Substrates are deoxynucleoside triphosphates (to make deoxyribonucleic acid)

• Proof reading , errors removed by 3'--5' exonuclease

• Processivity is very high (the ability of the enzyme to replicate a large tract of DNA before *falling* off)

• Replication requires DNA unwinding by enzymes termed helicases: these enzymes unwind the DNA helix
before the replication fork and wind it up again afterwards.

There are large numbers of different enzymes and proteins involved at the replication fork in the replisome.

DNA damage by UV radiation or chemicals is repaired by other DNA polymerases. UV-damage results in
adjacent T residues in one strand becoming covaletly linked to each other, producing a thymine dimer. This
causes the double helix to become distorted -- kinky. Xeroderma pigmentosa is a genetic disorder in which
patients cannot carry out UV-radiation repair. They are very prone to skin cancer from an early age.

What is Transcription?

• Copying a gene as RNA

• DNA-directed RNA synthesis from a gene

What is a gene?

• There is no good definition of a gene!

• A sequence of DNA that is transcribed from specific start to specific stop base sequences.

• Beadle and Tatum, working with the eukaryote mold Neurospora crassa, concluded that one gene codes for
one protein.

• But what about genes that code for RNA's like rRNA and tRNA?

• A gene is a sequence of DNA that is transcribed into a single RNA as defined by specific start and stop
sequences of bases.

• Note the circularity of the argument!

• But the single RNA may be polycistronic!

What does that mean?

• A cistron is synonymous with a gene.

• A polycistronic RNA results from the transcription of an operon.

DNA replication, transcription and translation.
What's an operon?

• A genetic unit containing several genes with related functions: the bacterial operon for lactose (milk sugar)
metabolism contains 3 genes coding for 3 different proteins.

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• An operon is transcribed as a single unit, a polycistronic messenger RNA (mRNA) that codes for more than
one gene product.

Name 4 types of RNA. What are their functions?

• mRNA, messenger RNA that is translated into protein

• rRNA, ribosomal RNA that, together with ribosomal proteins, forms a structural scaffold for the translation of
mRNA, the ribosome

• tRNA, transfer RNA, a specific carrier of amino acids

• snRNA, small nuclear RNA involved in processing of mRNA in the nucleus

What is the major transcription enzyme?

RNA polymerase, a DNA-directed RNA polymerase

• RNA synthesis is 5'-->3'

• substrates are ribonucleoside triphosphates ( to make ribonucleic acid)

• begins at the promoter, 5' end of the gene

• processivity is very high, proceeds to 3' end of gene without stopping or falling off the gene

• proof reading by precise Watson-Crick base pairing, A=U and G=C

Regulation of transcription of a gene is at the 5'-end of the gene at region(s) termed operators

• Transcription of some genes is constitutive = housekeeping genes

• Transcription of other genes is in response to a stimulus = inducible genes

Genetics Part-III

What are exons and introns?

• exons are coding regions, and

• introns are non-coding regions of the mRNA transcript

• exons and introns are found in most, but not all, eukaryote genes

• introns have to be spliced out before the mRNA is translated

• splicing is by snRNA's acting as enzymes, or ribozymes, an example of the catalytic function of RNA
DNA replication, transcription and translation.
Translation

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• Synthesis of a linear polymer of amino acids from a linear polymer of nucleotides

Where does it occur?

On the ribosome, a rRNA-protein complex that provides:

• a scaffold for mRNA

• sites for the docking of tRNA charged with a specific amino acid

• an enzyme for peptide bond synthesis between amino acids

• an enzyme for translocation of the mRNA through the ribosome

What is the function of tRNA?

• Carrier of a specific amino acid during translation

What is the structure of tRNA?

• secondary structure has some base-pairing --> cloverleaf

• information transfer at the anti-codon loop, complementary to the codon

• note the importance of H-bonds in the genetic code

• tertiary structure is L-shaped which places the amino acid far from the codon-anticodon site

• degeneracy of the code produces wobble

What is the genetic code?

A sequence of 3 nucleotides forms a codon

• unambiguous, each codon specifies an amino acid, or start, or stop

• degenerate, some amino acids have multiple codons

• 2-letters often sufficient, specifiy hydrophobic and hydrophillic amino acids

What is the enzyme that charges tRNA with an amino acid?

An aminoacyl-tRNA synthetase

• it has proof reading capabilities through the precise fit of amino acid and tRNA

• energy provided by ATP: energy for the formation of aminoacyl-tRNA and for proof reading

• there are at least 20 synthetases, isoaccepting for the tRNA's coding for a single amino acid

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What is the mechanism of translation?

• mRNA forms a large complex with the ribosome and protein factors

• together they guide in the correct aminoacyl-tRNA

• correct amino acid specified by codon-anticodon base pairing (H-bonds)

• protein factors have proof reading capability--energy provided by GTP

• an enzyme catalyzes polymerization of two amino acids, peptide (amide)bond formation between two amino
acids

• an enzyme catalyzes movement of mRNA through the polymerization site: energy provided by GTP

• mRNA translated from 5'--> 3', same direction as it is synthesized

Reprise:

• Flow of information: central dogma

• DNA--> RNA-->linear amino acid sequence --> 3D-conformation of protein

But some viruses have only RNA as their genome: no DNA.

How do they carry out information transfer? How do they get around the unidirectional flow of
information in the central dogma?

• Use an enzyme called reverse transcriptase to transcribe RNA into DNA.

• Example: HIV, a retrovirus

• Then, use central dogma.

• For HIV:

RNA-->DNA--> mRNA --> linear amino acid sequence --> 3D-conformation of protein.

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