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Introduction to biodiversity

Biodiversity: the number and variety of species and ecosystems on Earth

Species: all organism with a similar shape and structure that are capable of breeding freely with each other under natural conditions

Speciation: the evolutionary process in which populations evolve to become distinct species

Hybridization: cross breeding of two different species, plants occasionally do this 

• Other plants, fungi, microorganisms reproduce asexually

Morphology: physical appearance and characteristics of an organism, scientific study of physical characteristics

Heterotrophs: organisms that obtain energy-rich nutrients by consuming other living or dead organisms

Autotrophs: organisms that create their own energy-rich nutrients (using light, chemical reactions, etc.)

Evolutionary changes that occurs in an entire population, usually over a long period of time

Species can have different trait among them = individual variability 

• Species may change over time/space/generations

Biodiversity and taxonomy

Biosphere: the part of Earth where life exists, living organisms and the environment they live in

Ecosystem: a community of living things interacting with non-living things

Organism: any living thing

Cell: The smallest unit of life

Atoms: smallest component of an element

What are organelles made of?

• Carbohydrates

• Lipids

• Proteins

• Nucleic acid (DNA, RNA)

Two types of cells: 

Domains of the tree of life

1. Bacteria 

   1. Consists of all the eubacteria 

2. Archaea 

   1. Consists of all of the archaeabacteria

3. Eukarya

   1. Consists of protists, animals, fungi, plants 

Kingdoms of Life

1. Animals 

2. Plants ex. Ferns, flowering plants, mosses

3. Fungi ex. Mushrooms, yeasts, moulds 

4. Protista - most diverse group of organisms ex. Amoeba, slime molds, algae 

5. Eubacteria - bacteria ex. Salmonella, e. Coli, streptococci 

6. Archaea ex. Extreme thermophiles, extreme halophiles  

• prokaryotic and difficult to distinguish due to small size and lack of internal structure

• most prokaryotes unicellular but some many cells joined together (cluster)

• Found in extreme environments - no oxygen or extreme acidic environments

Taxonomy

Taxonomy: the science of naming organisms and assigning them to groups 

Systematics: the study of biodiversity and the relationships among organisms

Linnaeus System of Classification

• swedish naturalist, developed binomial nomenclature

• Two parts;

  • Genus (first letter capitalized, italicized)

  • Species name (lowercased, italicized)

• Groupings start general with kingdoms, all through the the seven taxa, to species 

Seven taxonomic categories:

• Kingdom

• Phylla

• Class 

• Order

• Family

• Genus

• Species

Phylogeny: reconstruction of evolutionary relationships, family tree style

Dichotomous key

Dichotomous key: series of branching, two-part statements used to identify organisms 

Clade: a taxonomic group that includes a single common ancestor and all its descendants

Nodes – where the main line meets the other

The International Barcode of Life Project

• Ultimately researchers in the field will be able to use a handheld device to immediately identify any species from a tiny sample of DNA

• can be a very useful tool for controlling the traffi cking in products made from endangered species.

• DNA barcoding technology may allow for very low cost routine sampling and monitoring of species diversity in entire ecosystems.

Archaeabacteria and Eubacteria

• Live in/on other organisms, in water, soil, hot springs, ice

What do prokaryotes do?

• They can be pathogens 

• Work in the ecosystems: decomposition, producers, nutrient cycling

• Gut health, produce vitamin B12 and K in the large intestine = mutualism because the bacteria benefit from living in the intestine and people benefit from the healthy bacteria 

• Commercial use: antibiotics, food (cheese, yogurt)

• Biotechnology

Eubacteria 

6 major groups of bacteria:

• Proteobacteria:

  • Some are photosynthetic, others use a different process of photosynthesis

  • Ancestors of mitochondria

  • Nitrogen fixing

  • Ex. bubonic plague, gonnerhea 

• Green bacteria

  • Do a different version of photosynthesis

  • Found in saltwater or hot springs 

• Cyanobacteria (blue-green algae)

  • Does a similar version to photosynthesis

  • Ancestors of chloroplasts

  • Major role with nitrogen fixing and producing in aquatic ecosystems

  • Form symbiotic relationships with fungi

  • Can double population in one hour

  • create algal blooms robbing water of oxygen/killing organisms including fish

• Gram-positive bacteria

  • Used in food production

  • Some have lost their cell wall

  • Mycoplasma = smallest known cells 

  • Ex. anthrax, strep throat, bacteria pneumonia, meningitis 

Thick layer of peptidoglycan = gram +, purple stain

Thin layer of peptidoglycan = gram -, pink stain

• Spirochetes

  • Spiral shaped flagellum embedded in their cytoplasm

  • Move with a corkscrew motion

  • Symbiotic spirochetes in termite intestines ingest wood fibres 

  • Ex. syphilis

• Chlamydias: 

  • Parasites that live within other cells 

  • Ex. chlamydia, trachoma

Parts of a bacterial cell

• Flagella: for movement 

• Cell wall & cell membrane

• Single loop of DNA in the nucleoid 

• Pili: hairlike structures for attachment

• Ribosomes: protein production

• Plasmid: small loop of DNAcoding for a few genes

• Capsule: outer layer on bacteria 

Peptidoglycan: a strong, mesh-like material made of sugars and amino acids that forms the cell wall of most bacteria. It gives the cell shape and protects it from breaking.

Prefix 

• Stepto = chain

• Stapylo = group

• Diplo = two

+

Bacteria shape

• Cocci = spherical shape

• Bacili = rods

• Spirilla = spiral

Metabolism

Autotrophic: 

• Photoautotrophs: use light as energy (O₂,H₂S)

• Chemoautotrophs: une inorganic chemicals as energy (abiotic)

Heterotrophic:

• Saprotrophic: decompose dead organic material

• Mutualism/commensalism: rely on other organisms and use their byproducts (ex. methanogens in the guts of cows – use gases produced to make methane gas)

Binary fission: 

- division of one parent cell into two genetically identical daughter cells

-form of asexual reproduction

-each cell receives exact copy of genetic material from parent cell (chromosome and plasmids)

- mutate 1000 times faster than eukaryote, mutations occur

Step 1: chromosomes duplicate and copies get separated 

Step 2: cell elongates and copies of chromosomes move to the poles 

Step 3: cell divides into two daughter cells

Genetic recombination = genetic diversity

• Transduction: virus enters and picks up DNA from chromosome or plasmid & transfers it to another cell

• Conjugation: plasmid becomes a line when moving between cells because it is transferred through hollow pillus (tube)

• Transformation: dead bacterium ruptures releasing DNA, live bacteria picks it up and incorporates it

Endospore: a dormant structure that forms inside certain bacteria in response to stress; protects

the cell’s chromosome from damage

Bacterial Diseases

• Some cause disease by releasing toxins

  • Ex. botulism food poisoning is caused by toxin released by bacterium Clostridium botulinum  

• Other bacteria contain toxic compounds that are not released till cell dies 

  • Ex. E coli O157:H7 (severe food poisoning and water contamination) 

• Antibiotics kill bacteria by releasing toxins 

• Prokaryotes and fungi produce antibiotics as chemical warfare because they are competing for resources 

Medical antibiotics: compounds used specifically to harm or kill bacteria 

• Specific to the type of bacteria

• Inhibit cell’s ability ot turn glucose into energy/inhibit construction of a cell wall = death of bacterium, only affect certain parts of the cell

• Don’t work on infections caused by viruses

Archaebacteria 

• Oldest of all kingdoms, 

• Can inhabit extreme climates & environments

Own kingdom because:

1. Chemical properies in their cell membranes and walls  are different from Eubacteria  -  unique chemical makeup and most lack peptidoglycan

2. Out of 1700 genes, more than 50% are different from Eubacteria  

Ex. 

• Thermophiles: mainly live in the guy of animals, or at the bottom of marshs = how methane gas is produced

• Halophiles: live in extremely salty conditions ie. the dead sea

• Anaerobic methanogens: can tolerate very hot temperatures and acidic conditions

Protista

Endosymbiosis: a relationship in which a single-celled organism lives within the cell(s) of another organism; recent findings suggest this may be very common

• Protista developed from the folding of the cell membrane of an ancient prokaryotic cell which formed membrane bound organelles

• Mitochondria and chloroplasts were once prokaryotic but then were engulfed by early eukaryotic organisms and incorporated in

Evidence for mitochondria and chloroplasts being added in:

1. Present day mitochondria and chloroplasts have two membranes

2. Inner membrane = similar to ancient prokaryotes, outer membrane = similar to eukaryotes

3. Both, present day, have their own internal chromosomes

4. These chromosomes are very similar to prokaryote chromosomes and contain genetic information used by the organelle

5. Both reproduce through binary fission as prokaryotes do

• Protista can be multicellular or unicellular

• Can be heterotrophs or autotrophs

• Reproduce asexually with some exchange of DNA 

• Live in moist environments 

• Move using pseudopods, cilia, or flagella 

  •  Euglena – use flagellum 

  • Paramecium – use cilia

  • Amoeba – use pseudopods 

Protist groups: 

1. Plant-like

• Contain chloroplasts to carry out photosynthesis

• Asexually and sexually reproduction (through binary fission and conjugation)

• Live in wet and moist environments

• Ex. phytoplankton, euglena

2. Animal-like

• Many are parasitic

• Autotrophs - cannot make their own food, must move to find food

• Lives in water/animal bodily fluids

• Ex. amoeba and plasmodium

3. Fungi-like 

• Cannot make their own food

• Most are decomposers - absorb nutrients from other living organisms

• Reproduce asexually through spores

• Prefer cool, shady, moist places

• Slimy trails as they move 

• Ex. slime molds, water molds

Connection:

• Can cause some serious diseases = malaria, african sleeping sickness

• Algae = healthy aquatic ecosystems, food for humans, fertilizers, provide ⅔ of the world’s oxygen, makes agar

•  Plasmodium causes malaria = mosquitos carry spores and injects them into humans when the bite, travel from liver through bloodstream, multiply and change form, causes RBC to burst, mosquitoes spread by new ones biting into humans that have malaria 

Fungi

• Can be multicellular or unicellular

• Eukaryotes (have membrane bound organelles and a nucleus)

• Heterotrophs = NO PHOTOSYNTHESIS BECAUSE NO CHLOROPLASTS

• Have cell wall made up of chitin

• Main functions: reproduction and absorption of nutrients

• Fungus is from the mycelium (the branching structure)

• The above ground is the reproductive structure (fruiting body)

Ex. ringworm, athlete’s foot, eating wild mushrooms

Fungi are important because:

• They are decomposers 

• Consist of yeast: used to make wine, bread, beer

• Can be eating or be used as ingredients

• Can be used to make antibiotics (pennicilin)

Plants

• Plants use photosynthesis to convert solar radiation to chemical energy

• Carbohydrate: molecule that contains only atoms of carbon, hydrogen, and oxygen in a 1:2:1 ratio

• Main source of chemical energy, plants use carbohydrates for maintenance, growth, and development

• Plants adapt to obtain more sunlight → ex. Adjust position of leaves to reach towards sunlight 

• Plants are food sources for many organisms like herbivores

  • Developed adaptations for protections → toxic/bad smelling substances, tough, prickly, hairy

• Plants need specific nutrients which they absorb from water (Mycorrhizal fungi in roots help)

  • Nitrogen

  • Phosphorus 

  • potassium

• Plants need water for growth and repair 

• Plants need to exchange gases (for most vascular plants, this happens in leaves)

• Plants need to reproduce through asexual and sexual reproduction (male + female gametes = zygote)

* = natural movement from areas of high concentration to low concentration 

3 main non-reproductive organs 

• Stem

• Roots

• Leaves 

Vascular tissue: herbaceous stems arranged in distinct vascular bundles in ground tissue 

• Herbaceous: describes plants with stems that do not have wood

• Vascular bundles: arrangement of long continuous strands of vascular tissue that contain xylem and phloem that run from roots to leaves 

Xylem: tissue that transports water, located closer to the inside of the stem

Phloem: tissue that transports sugars and other minerals, located closer to the outside of the stem 

Phylogeny of vascular plants 

2 systems:

Root system

• Anchor the plant 

• Absorb water and minerals

• Sometimes used for food storage

Shoot system

• Support the plant

• Transfers water and glucose from roots to leaves 

• Leaves (and stems) make sugars through photosynthesis 

Leaves:

• Primary site of photosynthesis

• Gas exchange (CO2 and O2)

• Protection

Stems:

• Hold leaves up to the sunlight (structural support)

• Transports and conducts various substances between the roots and the leaves 

• Food storage (water and sugar)

• Protection (e.g. thorns on roses) 

Parts of a woody stem 

• Bark: outermost layer of stems and roots in woody plants, protection from herbivores, and from low temperature forest fires 

  • Cork, cork cambium, phloem 

    • Cork cambium: meristematic layer in woody plant that produces cork 

    • Cork: tough outer layer that prevents water loss from stem

Spring wood: vascular cambium grows rapidly (water/sun) producing large xylem cells with thin walls → light coloured wood

Summer wood: fewer xylem produced and have thicker cell walls that form layer of darker coloured wood

Heartwood: the older, central core of a woody plant's stem or trunk, made up of dead xylem cells that no longer actively transport water and nutrients, but provide structural support and decay resistance.

Sapwood: the living, outer layer of wood that facilitates water and nutrient transport from the roots to the rest of the tree

Leaves: 

Roles of leaves: photosynthesis, gas exchange, prevent dehydration, storage, protection from predators 

Parts of a leaf

• Chloroplast: an organelle, the site of photosynthesis within a plant cell 

  • Photopigment: in chloroplasts, chemicals that undergo a physical or chemical change with light (e.g. chlorophyll, absorb red/blue light of visible spectrum and reflect green light)

  • Accessory pigments: absorb light wavelengths not absorbed by chlorophyll (e.g. carotenoids)

• Blade: flat part of a leaf

• Petiole: stalk that attaches the blade to the plant stem → 1 blade or several leaflets 

• Venation: arrangement of veins within a leaf

• Cuticle: wax, waterproof, outermost layer  

• Upper epidermis and lower epidermis: single layer of transparent cells, few chloroplasts

• Palisade mesophyll: closely packed, elongated cells, contain the most chloroplasts

• Spongy mesophyll: loosely packed cells, that aids with gas exchange and a few chloroplasts

• Vascular bundle: xylem and phloem, run continuous strands through spongy mesophyll

•  Stomata: Tiny pores in the epidermal cells of leaves and stems; most numerous on the undersides of the leaves; gas exchange

• Guard cells: Pairs of cells surrounding the stomata, or pores, on a leaf or stem

• Swelling or shrinking of the guard cells opens or closes the stomata. When dry = flaccid, when humid = swell

Roots 

Function:

•  anchor and support plants

• to absorb and conduct (move) water and minerals

• to store products of photosynthesis (plant made sugars)

• to control soil erosion

• Aid in creating more plants

Root cap: 

• Produces lubricant 

• Produces carbonic acid

• Protects apical meristem

Root meristem: rapidly dividing undifferentiated cells (growth)

Zone of elongation: newly formed cells undergo growth

Zone of maturation: cells begin to differentiate and take on different roles to form different tissues 

Root hairs: act to increase surface area of root that sits in soil to help contact more water and minerals

Epidermis: outer layer of cells

Root hair: cite of water and mineral uptake 

Endodermis: waxy layer of cells 

Casparian strip: Surrounds endodermis cells, prevents water and minerals from just flowing into root. 

Cortex: region of cells beneath the epidermis, stores carbohydrates and help transport water from epidermis to the xylem 

How does water flow? Water enters the roots through the process of osmosis, using the vascular tissues

Osmosis: movement of water molecules across a semipermeable membrane from an area of low solute concentration to an area of high solute concentration, aiming to balance concentrations on both sides.

Two types of roots

Transport in Plants

Transport into the root

• Water enters root cell via osmosis - the cytoplasm of plant cells have a lower concentration than soil water, 

• Nutrients enter via active transport (energy required) - the cytoplasm of plant cells higher concentration than soil water, 

• Sap into leaves via transpiration - the evaporation of water  from plant leaves when stomata are open, Water molecules pull each other like a chain and move up 

TRANSPIRATION IS AFFECTED BY:

• Humidity of the air

• Temperature of the air

• Strong wind 

• light

1. Enter cell and move into the endodermis 

2. From there enter the vascular cylinder

3. Once inside, nutrients are actively pumped across cell membranes into xylem 

4. Once water/nutrients pass Casparian strip, the liquid is now xylem sap

5. The substances in the xylem sap then move up root toward stem

6. Root pressure moves sap up (osmosis and active transport = capillary action: the tendency of liquid to rise or fall because of attractive forces between the liquid molecules (and the sides of tube/cell wall)

7. Water dries up in leaves due to transpiration and root pressure, capillary action and osmosis push it all to the leaves - MOST CONTRIBUTING FACTOR

Water is drawn up the xylem in the stem by three factors:

1.  Root pressure

2.  Capillary action

3.  Transpiration pull

Transport of sugars 

• Sugars produced by photosynthesis or broken down from storage organs aka tubers

Source: A plant cell with a high concentration of sugars and other solutes, such as a leaf cell 

Sink: plant cell with low concentration of sugars; may convert sugars to starch for storage or used rapidly for energy or building blocks for other carbohydrates ex. cells that are rapidly growing, roots, buds, stems, seeds, fruits

• Sugars can move up and down a plant, depends on location of source cells relative to sink cells (In general, source to sink – connected by column of phloem cells)

• storage structures may be either sources or sinks – may change during the year or plant’s development 

• Seeds are also sinks – store carbohydrates for the plant embryo (why fruits taste sweet) 

• When a plant is producing seeds or fruits, it is still photosynthesizing 

• Sugars must move from source cells in shoot to sink cells that are also in shoot 

Direction of sugar transport

Winter = plants are dormant (no growing/no photosynthesis)  

Spring = plant depends on carbohydrates stored in roots/stems (usually starch), As it begins to grow, the plant breaks down the starch into sugars,  root/stem are sources and top of plant (leaves) are sinks

•  **Water and dissolved sugars (phloem sap) move UP in phloem

Summer = leaves are photosynthesizing and sugars produced are stored in roots/stems

• Top of plant are sources and phloem sap moves DOWN  

3 stages of sugar transport 

1. From Source cells to phloem cells - high sugar concentration in phloem = active transport but water drawn in eventually to phloem through osmosis = increasing turgor of phloem cells near source cells

2. Through the phloem 

3. From phloem to the sink cells - phloem molecules reach sink cells = leave phloem bc sink cells = less sugar concentration via passive transport = phloem becomes low sugar = low turgor of phloem cells near sink cells + water from phloem goes back into xylem

Plant reproduction

• Gymnosperm: a vascular plant that produces seeds in special structures called cones (e.g. conifers: pines, spruce, cedars etc…)

• Angiosperm: a plant that produces flowers; 90% of all modern plant species (e.g. roses)

Pollen grains: waterproof capsules that contain the male gamete

Ovule: structure that contains the female gamete 

Pollination: occurs when a pollen grain fertilizes the ovule and the embryo becomes a seed

Seeds: made up of embryo, food supply and seed coat

Benefits of sexual reproduction:

• More genetic diversity

• Seeds can remain dormant until it has suitable conditions for germination = better survival

• Seeds can move away from parent plant so seedlings have less competition for resources 

Gymnosperms - conifers 

• Male cones = pollen, female cones = eggs 

• Pollination occurs through wind

• When an egg is pollinated and fertilized in a female cone, an embryo develops in a seed in the cone

Angiosperms - flowering plants 

• Reproductive structure called flowers 

• Stamen = male flowering part, anther (produces pollen grains) + filament (raises anther) = stamen

• Carpel = female flowering part, stigma (sticky surface for pollen grains to land on) + style (tube-like structure that leads to ovary) + ovary (contains ovule) = carpel

• Pollination through wind or by animals that transfer pollen 

Cross pollination: transfer of pollen grains from one plant to another

Self-pollination: transfer of pollen grains from one flower to another on the SAME plant

Fruit: mature ovary, fruit development begins when an ovule is fertilized in the ovary and it swells to help protect and disperse the seed

Animals 

• Heterotrophic

• Diploid

• Multicellular

Order of development that created different phyla

• Development of nerve cells

• Radial symmetry - an organism’s body is arranged like a wheel — parts are organized around a central axis

• bilaterally symmetry - an organism can be divided into two mirror-image halves — a left and a right side

  • Cephalization: development of a head region in animals, where structures like the brain, eyes, and other sensory organs are concentrated

• Development of germ layers

• Ectoderm (outer layer): gives rise to skin and nervous system

• Mesoderm (middle layer): gives rise to circulatory, reproductive, excretory, muscular systems

• Endoderm (inner layer): gives rise to inner lining of the gut and respiratory system

• Coelom

• Development of a body cavity (coelom) to surround and contain internal organs and digestive tract, from mesoderm

• Protosomes: bilaterally symmetrical, the mouth forms before the anus e.g. earthworms

• Segmentation becomes apparent 

• Jointed appendages for quicker movement 

• Deuterostomes: bilaterally symmetrical, the anus forms before the mouth e.g. humans

• Development of a large dorsal (back) notochord to help coordinate nervous system function

• Development of a backbone to protect the dorsal nerve cord