[Draft] BOT 1 Notes

7/31/2019 [Draft] BOT 1 Notes

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BOT 1 Lecture Notes by F5XS

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Science is a systematized knowledge derived from observation andexperiment carried on in order to determine the principles underlying what isbeing studied.

Biology (bios, life + logos, discourse or study) is the branch of sciencethat deals with the study of living organisms; scientific study of life. botany deals with plants zoology deals with animals

Branches of Botany(Basic Plant Sciences)

morphology external appearance, formation (phenotype)

anatomy internal structures & arrangement physiology processes and functions ecology distributions, abundance of plants and their plants and environment

[plant] geography spatial distribution of plants [plant] paleontology study of plant fossils

paleontology study of plant fossils

ethnobotany (economic botany) uses of plants

Branches of Botany (Applied Plant Sciences) based on the purposes forwhich the plants are grown

agronomy science and practice of growing field crops forestry managing and harvesting trees for building materials and other

products

horticulture growing, processing and marketing fruits, vegetables and

ornamental plants; landscaping

Principles of Plant Biology characteristics that unify all living things

order hierarchical level of organization simple to complex structural organization components of biomolecules

have genes (hereditary units) metabolism: nothing lives without energy

energy is the capacity to do work

metabolism generates energy for growth, survival and reproduction

growth and development growth is the irreversible increase in size while development is the change

in the complexity of the organism

reproduction

plants give rise to new plants of the same type by either sexual or asexualreproduction

responsiveness: sensing and responding

detects specific forms of stimuli (external and internal glands)

adaptation

a trait that gives the individual an advantage in survival or reproduction,under a given set of circumstances

evolution


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Advances in Plant Science plant biology has changed dramatically over thelast few decades

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970 Sharp boundaries between biochemistry, genetics, physiology and ecology

1980

boundaries between physiology and molecular biology began todisappear

absolute need to use molecular techniques in physiology andphysiological ecology became evident

microarrays and gene sequencing have become common techniques

what is true for plant biology before is no longer valid for plant biologytoday and in the next decades

molecular tools will further increase in importance

integrated approach to further plant biology is being realized

Theories on the Origin of Life

Biblical Theory

Spontaneous Generation Theory

Comet (Panspermia) Theory

Chemosynthetic Theory

Chemosynthetic Theory has four stages:1] abiotic synthesis of simple organic molecules (monomers)2] polymerization of monomers3] aggregation of abiotically produced molecules into droplets4] origin of heredity

Stage 1: Abiotic synthesis of monomers

proposed by Al Oparin and JBS Haldane in 1920s; conditions of primevalEarth favored chemical reactions that synthesized compounds

the earth had a reducing atmosphere

life most likely emerged under high-temperature conditions

exact conditions are unknown

ample availability of hydrogen atoms very little oxygen

high radioactivity and ultraviolet radiation

lightnings and volcanic eruptions were very frequent

the Miller-Urey Experiment was the supporting evidence for Oparin andHaldanes hypothesis

first to show that amino acids and other organic molecules could have beengenerated on a lifeless Earth

Stage 2: Polymerization of Monomers

protenoids theory (microspheres: first proteins) proposed by Sidney Fox

formed in clays

many surfaces for protein formation

many positive and negative charges for protein formation

iron and zinc served as metal catalysts


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Stage 3: Protobiont formation

abiotically produced molecules aggregate into droplets

formed from polypeptides, nucleic acids, carbohydrates

membrane-bound

incapable of reproduction but multiplies by budding or fission

Stage 4: Origin of heredity

RNA fragments were the first replicating system

RNA act like enzymes to assemble new RNA molecules called ribozymeswhich might have constituted the primordial self-replicating system Thomas Cech, 1980

synthesized simple organic molecule that act as a template to producecopies of itself

nucleic acid genes were preceded by simpler hereditary systems

Amino Adenosine (AA) + Ester (E) Amino Adenosine Triacid Ester(AATE)

The Cell Theory

all living things are composed of one or more cells

cells are the basic units of structure and function in an organism

cells come only from preexisting cells

Cells are diverse both in size, shape and internal organization.

Cells are small to promote: transport cell volume to surface area ratios favor small size

control nucleus to cytoplasm consideration metabolic requirements

All cells have:

plasma membrane (plasmalemma)

genetic material

cytoplasm

ribosomes

Fluid Mosaic Model

conceived by SJ Singer and Garth Nicolson in 1972

fluid because of its hydrophobic integral components such as lipids and others mosaic because it is made up of many different parts or kinds of

macromolecules

plasma membrane is a lipid bilayer

provides a barrier between internal and external environment of the cell

allows certain molecules to go through which makes it semi-permeable

made up of phospholipid bilayer with proteins embedded that allow for neededpassage of macromolecules

Ribosomes(protein factories)

sites of protein synthesis

are made of rRNA and protein

cells with high rates of protein synthesis have many ribosomes

Note: The genus Mycoplasma hasthe smallest bacteria that are from0.1m to 1m


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Cell Types

prokaryotes eukaryotes

Genetic Control of the Cell

nucleus genetic control of the cell chromosomes location of inherited DNA and programs cells and programs

cells synthesis of proteins

nucleolus production of ribosomes

Cell Wall

structural support

provides defense against invading pathogens

provides pathways for communications between cells

composed of cellulose, pectin, proteins and hemicellulose (glue that hold thecellulose fibers together)

Growing plant cells produce a primary cell wall which stretches as the cellgrows. A secondary cell wall may then be produced inside the primary cell wall.

Meristems

regions of cell division

main difference between plants and animals

makes possible to grow a new plant from cutting

Apical Meristems

found at the tips of roots and shoots

increase the length of a plant

gives rise to three primary meristems

ground meristem gives rise to ground tissues

protoderm gives rise to skin coverings procambium gives rise to the plumbing of the plant

Other Meristems: Lateral Meristems

secondary growth

add girth (width) by producing wood and bark

ApicalMeristem

Protoderm DermalEpidermis

ParenchymaPeriderm

Procambium Vascular

Xylem

Vessels

Tracheids

ParenchymaFibers

Phloem

Sieve tube members

Companion cells

Fibers

Parenchyma

Ground Meristem

Parenchyma

Collenchyma

SclerenchymaSclerids

Fibers


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Other Meristems: Intercalary Meristem

why grass keeps growing back after you cut it

grasses and related plants do not have lateral meristems

intercalary meristems add to the plants length

Chromista

photosynthetic

source of alginates

Kelp (Alginates)

viscous substance extracted from kelp

used in paper production, toothpaste and in ice cream

Archaeozoa no mitochondriaProtista dumping groundChromista implies pigmentation

Eubacteria

could be either photosynthetic or heterotrophic

with peptidoglycan cell wall

antibiotic sensitive

Archaea

live in extreme environmental conditions

Protista

eukaryotes that do not fit in the other three eukaryotic kingdoms

generally unicellular; some algae are multicellular

photosynthetic or heterotrophic

Fungi

eukaryotic heterotrophs

absorptive type of nutrition

Animalia

eukaryotic multicellular

ingestive mode of nutrition

Plantae

eukaryotic multicellular

autotrophic/photosynthetic

Taxonomy is the science of classifying and identifying plants.

Scientific Names are names understood by all scientists; common namediffers in different parts of the world. Latin is the language usually used forscientific classification.

A taxonomist is a person who identifies names and classifies organisms.


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Aristotle classified organisms based on qualities such as shape, color, abilityto do harm and the place where it is found.

John Ray defined species as organisms capable of interbreeding and

producing fertile species.

Karl Von Linne (Carolus Linnaeus) developed binomial classificationscheme wherein two latin words are put together to indicate the genus and thespecies.

Writing Scientific Names

the first word is the generic name (genus) and the second word is the specificepithet (species)

if there are additional words, they indicate the variety or cultivar

scientific names are followed by author (unitalicized)

usually italicized or underlined

The generic name of an organism is placed first and begins with a large letterand has more common with each other than they have with the members of othergroups.

A species can be defined as a group of organisms that are alike in almostevery feature and consistently produce like organisms.

The hierarchy of biological classifications eight major taxonomic ranks:Life Domain Kingdom Phylum Class Order Family Genus Species

Tagalog English Scientific

SingkamasMexican Turnip

JicamaPachyrrhizus erosus

Talong Eggplant Solanum melongenaSigarilyas Winged Beans Psolocarpus tetragonolobus

Mani Peanuts Arachis hypogaeaSitao String Beans Vigna sisquepedalisBataw Hyacinth Bean Dolichos lablab

Patani Lima Beans Phaseolus lunatusKundol Winter Gourd Benincasa hispadaPatola Sponge Gourd Luffa acutangulaUpo Bottle Gourd Lagenaria siceraria

Kalabasa Squash Cucurbita maximaLabanos White Radish Raphanus sativusMustasa Mustard Brassica integrifolaSibuyas Onion Allium cepaKamatis Tomato Lycopersicon esculentumBawang Garlic Allium sativum

Luya Ginger Zingiber officinaleLinga Sesame Sesamum orientale


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Junctions are special proteins that connect cells.

animals

tight junctions

adherens junctions

gap junctions desmosomes

for plants, plasmodesmata are microscopic openings in the cell wall

The cell membrane has a unique architectural design

Two basic types of embedded proteins:

intrinsic/integral proteins are proteins bound within the plasma membrane extrinsic/peripheral proteins are proteins that do not penetrate the

membrane

Membrane proteins based on functions

transport/transmembrane proteins

channels are proteins that act as selective pores carriers bind molecule on one side of membrane and release it on the other

side

pumps is a term for carriers if transport is active

enzymes speed up biochemical reactions by lowering activation energy

receptor proteins transmit information and induce changes marker proteins give cell identity and are important in cell recognition process adhesion and attachment proteins

adhesion of neighboring cells through intercellular connections or junctions attachment of cytoskeletons

Diffusion

higher to lower concentration

uses kinetic energy of themolecules

molecules move down aconcentration gradient (downhill)

will stop once equilibrium isreached

Transport processes regulated byplasma membrane

passive

no energy required

simple diffusion

mass/bulk flow

osmosis

active

requires energy coupled channel (symport and

antiport)

proton (H+) pump

phagocytosisNote: Aquaporin is a transmembraneprotein that facilitates the movementof water

ACTIVE TRANSPORT


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Diffusion in three types of osmotic environmentPremise: Water is the one that moves freely

isotonic

[SO]=[SI]

water moves into and out of the cell at equal rates net movement of water is zero

no change in cell volume

hypotonic

the solution has a lower concentration of solutes and a higher concentrationof water than inside the cell

[SO][SI]

water moves out of the cell

cell shrinks; cell volume decreases; the cell might undergo plasmolysis,shriveling of the cell

Endocytosis is a process in which organisms or fragments of organisms areengulfed by cells.

phagocytosis(Gk. phagein, to eat; cytos, cell)

cell eating cells engulf large particles (organic matter)

pinocytosis (Gk. pinein, to eat; cytos, cell)

cell drinking

Exocytosis

wastes or secretions are expelled from the cell using small sacs/vesicles

vesicles fuse with membrane and ejects contents

[Draft] BOT 1 Notes

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