[notes] bot1 - introduction to plant sciences

7/31/2019 [Notes] BOT1 - Introduction to Plant Sciences

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BOT 1 Notes by F5XS Introduction to Plant Science

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

being 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 for which 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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iron and zinc served as metal catalysts

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 ribozymes which 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

Note: The genus Mycoplasma has

the smallest bacteria that are from0.1µm to 1µm




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Ribosomes (―protein factories‖)

sites of protein synthesis

are made of rRNA and protein cells with high rates of protein synthesis have many ribosomes

Cell Types

prokaryotes

eukaryotes

Genetic Control of the Cell

nucleus – genetic control of the cell

chromosomes – location of inherited DNA and programs cells and programscell’s 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)

Ribosomes

protein factories of the cell repetition → transcription → translation

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

A

picalMeristem

Protoderm DermalEpidermis

ParenchymaPeriderm

Procambium Vascular

Xylem

Vessels

Tracheids

Parenchyma

Fibers

Phloem

Sieve tube members

Companion cells

Fibers

Parenchyma

Ground Meristem

Parenchyma

Collenchyma

SclerenchymaSclerids

Fibers




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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

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




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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 for scientific classification.

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

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 andproducing 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 letter and has morecommon witheach other than

they have withthe members of other groups.

A species can be definedas a group of organisms thatare alike inalmost everyfeature and

consistentlyproduce likeorganisms.

The hierarchy of biologicalclassification’s

Tagalog English Scientific

SingkamasMexican Turnip

JicamaPachyrrhizus erosus

Talong Eggplant Solanum melongena Sigarilyas Winged Beans Psolocarpus tetragonolobus

Mani Peanuts Arachis hypogaea Sitao String Beans Vigna sisquepedalis Bataw Hyacinth Bean Dolichos lablab Patani Lima Beans Phaseolus lunatus Kundol Winter Gourd Benincasa hispada Patola Sponge Gourd Luffa acutangula Upo Bottle Gourd Lagenaria siceraria

Kalabasa Squash Cucurbita maxima

Labanos White Radish Raphanus sativus Mustasa Mustard Brassica integrifola Sibuyas Onion Allium cepa Kamatis Tomato Lycopersicon esculentum Bawang Garlic Allium sativum

Luya Ginger Zingiber officinale Linga Sesame Sesamum orientale




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eight major taxonomic ranks:Life → Domain → Kingdom → Phylum → Class → Order → Family → Genus

→ Species

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 themembrane

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 attachmentproteins

adhesion of neighboring cellsthrough intercellular connectionsor junctions

attachment of cytoskeletons

Diffusion

higher to lower concentration

uses kinetic energy of themolecules

molecules move down aconcentration gradient (―downhill‖)

will stop once equilibrium is

reached

Transport processes regulated byplasma membrane

passive

no energy required

simple diffusion

ACTIVE TRANSPORT




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mass/bulk flow

osmosis

active requires energy coupled channel (symport and

antiport)

proton (H+) pump

phagocytosis

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 into the cell

cell swells; cell volume increases; the cell might undergo cytolysis, bursting

of the cell hypertonic

the solution has a higher concentration of solutes and a lower 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 are

engulfed 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

Metabolism

biochemical reactions

meditated by enzymes

releases energy

Note: Aquaporin is a transmembraneprotein that facilitates the movementof water




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Two Types of Metabolic Reactions

anabolism

buildup (synthesis) chemistry consumes energy

catabolism

breakdown chemistry releases energy

Energy is the capacity to do work. Forms:

potential – stored energy

kinetic – energy in motion

ATP (Adenosine Triphosphate)

type of nucleotide

nitrogenous base, adenine, the sugar ribose, and a chain of three phosphategroups

bonds between phosphate groups can by hydrolyzed

hydrolysis of the end phosphate group forms ADP and releases 7.3kcal of energy per mole of ATP under standard conditions

Enzymes: biological catalysts; agents of life

globular proteins

catalysts – speed up chemical reactions by lowering the activation energy

activation energy – energy that must be applied to destabilize and breakchemical bonds

high catalytic power

Properties of Enzymes

high specificity

usually acts on single substrate

high efficiency

108

to 1025

times more efficient than uncatalyzed reaction

exhibits reversibility of reaction

Factors affecting enzymatic activity

temperature

pH

concentration of the substrate or enzyme

inorganic or organic molecules as helpers

cofactor: inorganic molecule (mineral)

coenzyme: organic non-protein molecule (vitamin)

Enzyme Inhibition: Types of inhibition:

competitive – another ―look-alike‖ molecule compete with the substrate for the

active site noncompetitive – molecule binds to the enzyme but not at the active site but

the allosteric site; has two types: allosteric and feedback/endpoint inhibition

Allosteric Inhibition

allosteric means ―other site‖




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when an inhibitor molecule binds to the allosteric site, substrate cannot fit intothe active site

Endpoint/Feedback Inhibition

the first step (controlled by E A) is often controlled by the end product (F)

negative feedback is possible

the end products control their own rate of production

there is no buildup of intermediates

Cellular Respiration

main metabolic pathway of releasing energy in the form of ATP from food

overall equation for cellular respiration is opposite that of photosynthesis:C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy

glucose is oxidized and releases 686kCal

oxygen is reduced to water

Two main energy releasing pathways aerobic respiration (produces the most ATP)

anaerobic respiration (fermentation)

alcohol (ethanol) fermentation

lactic acid fermentation

Occurs in three series of reactions1] glycolysis2] citric acid / tricarboxylic acid / Krebs cycle3] electron transport chain

Glycolysis is the ―breaking of sugar‖. One molecule of glucose is split into twomolecules of pyruvate. It is universally found in all organisms and likely evolvedbefore the Krebs cycle and the electron transport chain.

Event 1: energy investment phase

two phosphates added to glucose

requires ATPEvent 2: splitting (cleavage)

6-carbon glucose splits into two 3-carbon moleculesEvent 3: production of ATP and NADH

H

+

released binds to NAD

+

to produce NADH NADH delivers hydrogen to electron transport chain if O2 is available

ADP is phosphorylated to become ATP

two molecules of pyruvic acids are producedIf O2 is not available:

electron transport chain cannot accept NADH

pyruvic acid will be converted to lactic acid

C D E F




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Transition reaction (an oxidation reaction):

connects glycolysis to the citric acid cycleo pryuvate is connected to a 2-carbon

compound: acetyl CoAo CO2 is releasedo NAD

+is converted to NADH + H

+

occurs twice per glucose

occurs in the mitochondrial matrix

Krebs/Cirtric Acid/Tricarboxylic Acid Cycle

named after German-born British physician and chemist, Sir Hans Adolf Krebs

completes the breakdown of sugar

yields 6 CO2, 2 ATP, 8 NADH, and 2 FADH2

Electron Transport Chain

H+

ions (or a pair of e-) are transported from one carrier to another and are

finally used to reduce oxygen to water

energy is released which is in the form of ATP

thylakoids are staked in a granium which is joined to other grania by the

stroma lamella

Composition of chlorophyll extract:

chlorophyll a

universal pigment

twice as more than chlorophyll b in most plants

bluish-green in color

chlorophyll b

found in higher plants and green algae

yellow-green in color

carotene (C40

H56

) – yellow-orange in color

xanthophyll (C40H50O2) – yellow in color

(Plant) Fluorescence is the re-emission of red wavelength.

Excitation of chlorophyll by light – when a pigment absorbs light, it goes from aground state to an unstable excited state

the colors red and blue are mostly used inphotosynthesis

the action and absorption spectra coincide

in blue and red wavelengths

Two interrelated reactions of photosynthesis

light-dependent photochemical reactions

electron flow (photosystems I and II)

electron transport system; two-scheme

occurs in the thylakoid membrane

Input Output

glucose 2 pyruvate2 NAD+

2 NADH2 ATP 2 ADP

4 ADP + 2P 2 ATP (net gain)

Note: Most organelles that are linedwith double membrane, like the

nucleus, mitochondria, and thechloroplast, have their own geneticmembrane.

Chlorophyll absorption maximaBlue Red

C. A 430 nm 662 nm

C. B 453 nm 642 nm




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photosynthetic carbon reduction reactions

carbon fixation reactions

C3 or Calvin Cycle C4 or Hatch & Slack Pathway

CAM or Crassulacean Acid Metabolism

occurs in the cytosol

Non-cyclic electron flow – primary pathway of energy transformation in thelight reactions; produces NADPH, ATP, and O2

the first stable compound of the C3 pathway is phosphoglycerate

the first stable compound of the C4 pathway is oxaloacetate

The three phases of Calvin cycle1] carbon fixation2] reduction3] regeneration of CO2 acceptor (RuBP)

the whole process is a cycle, meaning that it goes back to step one after step3

the enzyme that regenerates RuBP is RuBisCO (Ribulose BisphosphateCarboxylase/Oxygenase)

the enzyme that is highly involved in C4 pathway is PEPc (Phosphoenol

Pyruvate Carboxylase)

CAM plants open their stomata at night, incorporating CO2 into organic acids

Adaptive values

C3 photosynthesis

more efficient under normal light, temperature, and moisture

C4 photosynthesis

photosynthesizes faster under higher light/heat and moisture

CAM photosynthesis

better water use efficiency

Cells divide for growth, development, and repair.

Basic to these are two important features

to transmit complete copy of DNA

to transmit materials necessary for the cell to survive

Cell cycle

proposed by Howard and Pelc (1953)

time from the formation of the initiating cell to form new derivative cells

Cyclins are proteins that regulate passage of the cell through cell cyclecheckpoints.

before a cell starts dividing, the chromosomes replicate producing sister chromatids joined together at the centromere




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the centromere holds the two chromatids together

the kinetochore is a protein that encloses the centromere

Mitotic cell division

division of reproductive(somatic/body) cells

a single cell divides into two identicaldaughter cells (cellular reproduction)

functions for growth, maintenance, repair of body tissues

forms the basis of asexual reproduction

Meiosis

the first phase of meiosis is called reductional division while the second

phase is called equational division cellular events in gamete/gametophyte production

comprised of two consecutive cell divisions

Central dogma of molecular biology

DNA can be copied to DNA by replication

DNA information can be copied into mRNA by transcription

proteins can be synthesized from mRNA as a template by translation

Structure of Nucleic Acids

composed of nucleotides which is composed of a sugar, phosphate group anda nitrogenous base

linked by phosphodiester bond

RNA has ribose as a sugar and A, G, C, and U as nitrogen bases

DNA has deoxyribose as a sugar and A, G, C, and T as nitrogen bases

Chargaff’s Rule

adenine must pair with thymine with two hydrogenbonds

guanine must pair with cytosine with three hydrogen bonds

the bases form weak hydrogen bonds

Characteristics of DNA

has two strands that are antiparallel to each other

hydrogen bonds hold the two strands in a double helix structure

bases are always A to T and C to G

bases are complementary

at 3’ end, a hydroxyl group (OH) is attached while a phosphate group (PO4) isattached to the 5’ end

Steps involved

unwinding of the DNA strands (helicase, SS binding proteins, gyrase) priming of templates (DNA polymerase II)

excision of primers and their replacement with DNA nucleotides (DNApolymerase I)

sealing or joining of breaks (ligase)

o helicase unwinds and separates double helix by breaking hydrogen bonds

Plants Animals

Centrioles

✗ ✓

Cytokinesiscell plateformation

cleavagefurrow

Pairs withPurine A T

Pyrimidine G C




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o single strand binding proteins keep the strands apart; prevent reannealingo gyrase – relaxes twisting tension on the DNA moleculeo

RNA primers – before new DNA strandso primase is an enzyme that polymerizes the RNA primer o DNA polymerase II – with a primer in place, DNA polymerase catalyzes the

synthesis of a new DNA strand in the 5’ to 3’ direction o DNA polymerase I – digests RNA primers through its exonuclease activity;

replaces the exised RNA nucleotideso ligase is a linking enzyme that catalyzes th

e formation of a covalent bond fromthe 3’ to 5’ end of joining strands

plant reproduction may be sexual or asexual

natural vegetative propagation – growing of now plants from parts of aparent plant such as underground stems, roots, and leaves

tuber, corm, rhizome, runner/stolon, offset or ―bulb‖

some ways of asexual vegetative propagation: cutting, layering, grafting,budding, marcotting, and cloning

Benefits of asexual reproduction

true traits of the parents

maintains genetic purity with 100% replication of parent plant

no seed

some plants do not produce a seed or the seeds are too small to work with accelerates time it takes to set a new plant to the market

Pollination is the process of transferring pollens from the male anther to thefemale stigma. Vectors vary from wind, water, animals, insects, to humans. Theimportances of pollination are evolution and production of variable offspring.

Pollen

the shape and form of pollen is related to its method of pollination

insect-pollinated species have sticky, barbed pollen grains

wind-pollinated species are lightweight, small and smooth

Coevolution – interactions between two different species as selective forces oneach other, resulting in adaptations that increase their interdependency.

Plant mimicry – some plants take advantage of the sex drive of some insects

certain orchids look like female wasps, and even smell like them

males try to mate with them, and in the process they pollinate the plant

Plant sexuality and flower diversity

complete flower – contains all four flower organs (sepals, petals, stamen, and

carpels) incomplete flower – lack one or more of the flower parts

perfect flower (bisexual flower) – flowers containing both stamen andcarpels

imperfect flower (unisexual flower) – has either stamens and carpels

monoecious flower – with male and female flowers on the same plant

dioecious flower – with male and female flowers on the different plants




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Double Fertilization First Sperm + Egg = Zygote

Second Sperm + Two Polar Nuclei = Endosperm

the ovule becomes the seed

the zygote becomes the embryo

the seed stockpiles starch, oil, and protein

the ovary becomes the fruit

the ovary wall becomes the pericarp

the pulp of the fruit surrounds the seed and acts as an enticement to animals

so it can be eaten and the seeds spread

Within the ovule, the zygote undergoes mitosis producing two cells:

basal cell gives rise to the suspensor

the suspensor is a column of cells that pushes the embryo into theendosperm

terminal cells which gives rise to the proembryo and most of the embryo…other subsequent stages:

globular stage – cell division of the proembryo

heart-shaped stage – further division of the globular stage produces bilateralsymmetry and two cotyledons forming the heart-shaped embryo

torpedo stage – cotyledons elongate

the mature embryo has large bent cotyledons; the endosperm is depleted andfoot is stored in the cotyledons

Dormancy – temporary suspension of growth and development of the seed

primary dormancy – physiological factors hinder the growth of the seed

secondary dormancy/quiescence – environmental factors hinder the growthof the seed

Seed Germination – resumption of growth of the embryonic plant; involvesseries of physical and biochemical processes

imbibition – taking in of water due to osmosis

hydration

entry of oxygen

activation of enzymes

radical emergence

shoot tip breaks through the soil surface

seedling development

Types of germination epigeal wherein the cotyledons arise with the epicotyl

hypogeal wherein the cotyledons remain underground while the epicotylarises

Different examples of tropism

phototropism (reaction to light)




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geotropism/gravitroprism (reaction to gravity)

thigmotropism (reaction to touch)

hydrotropism (reaction to water/moisture) heliotropism/solar tracking (reaction to the direction of the sun)

auxin (plant hormone) plays a key role in phototropism, gravitropism, andapical dominance

Nastic movements: non-directional respons

es to stimuli

movement can be due to changes in turgor or changes in growth

nastic movements differ from tropic movements in that the direction of tropicresponses depends on the direction of the stimulus, whereas the direction of nastic movements is independent of the stimulus

o nyctinasty – movements at night or in the darko thigmonasty/seismonasty – response to toucho epinasty – bending downwardso hyponasty – bending upwards

both epinasty and hyponasty are promoted by auxin

Plant Hormones (Phytohormones)

phytohormones are endogenous (naturally synthesized)

synthesized in one part of the plant and transported into other part then there

will be a response action effective in very low concentration

Plant Growth Regulators (PGRs) are hormones that include natural andsynthetic forms.

Five classes of phytohormones

auxins

giberelins

cytokinins

ethylene

abscissic acid

Auxin

―the rooting hormone‖

encourage root development in cuttings

plays a key role in:

apical dominance – presence of a terminal but inhibits the growth of axillarybuds

phototropism

gravitropism

fruit development

Gibberellins

―height promoting hormone‖

able to revert genetic dwarfism

can induce parthenocarpy and fruit enlargement

able to promote seed germination




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arctic tundra

located between the north pole and the taiga region

extremely cold temperatures and land remains from year-round alpine tundra

occurs at high elevations

no underlying permafrost

plants are low cushions or mats as in arctic tundra

Reindeer Moss (Cladonia rangiferina

) a species of lichen and the chief winter food of reindeer, moose, and caribou

taiga / coniferous forest / boreal forest

cool and dry, with coniferous trees

forest

temperate rainforest

found on the temperate region

also called deciduous forest

tropical rainforest

found on the tropical region

grasslands/prairie/steppe/pampes/etc.

savanna

desert

chaparral/scrub/shrubland/heathland

[notes] bot1 - introduction to plant sciences

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