Biodiversity - The variety and number of life forms on earth

Scientific Naming

Taxa

• Taxonomy - The branch of biology that identifies, names, and classifies species based on natural features

  • Popularized by Carolus Linnaeus

• Classification - The grouping of organisms based on a set of criteria that helps to organize and indicate evolutionary relationships

• Hierarchical Classification - The method of classifying organisms in which species are arranged in categories from most general to most specific

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

• Rank - A level in a classification scheme, such as phylum or order

• Taxon - A named group of organisms such as phylum Chordata or order Rodentia

Binomial Nomenclature

• The system of giving a two-word Latin name to each species, where the first word is the genus, and the second word is the species

  • The first word is capitalized, and both words should be either italicized or underlined

  • Ex. Homo sapiens

  • It can become flawed when species at lower taxonomic ranks shared the same name

Identifying Species

• Species - A group of organisms that can interbreed in nature and produce fertile offspring

• Species concepts are various definitions of species

  • Morphological Species Concept - The comparison of measurements and descriptions of organisms, accounting for variation, to determine if they belong to the same species

    • Morphology - The branch of biology that deals with the structure or form of organisms

    • It is a simple concept, but determining the acceptable amount of variation can hinder the understanding of a species

  • Biological Species Concept - The ability of organisms to interbreed and produce viable, fertile offspring

    • A widely used concept, but it cannot be applied to species that are separated geographically, fossils, and asexually reproducing organisms

  • Phylogenetic Species Concept - The closeness of organisms, as shown by branches in evolutionary relationships

    • Phylogeny - The evolutionary history of a species

    • It can be applied to extinct species, and DNA analysis can provide evidence, but not all species have a known evolutionary history

• Dichotomous Key - An identification tool consisting of a series of two-part choices that lead the user to a correct identification

  • It can only identify the species, not its evolutionary history

Evolutionary History

• If two species share much of the same evolutionary history, it means they share a common ancestor

  • Ancestor - An organism from which other groups of organisms descended

• The three types of of evidence used to determine the relatedness of species are anatomical, physiological, and DNA

  • Anatomical Evidence - The comparison of the form of species to determine how they are related through evolution

    • Ex. The Oviraptor and cassowary share similar bones and feathers

    • Anatomy - The branch of biology that deals with structure and form, including internal systems

    • Anatomy changes over time to adapt to specific purposes

  • Physiological Evidence - The comparison of proteins among species to determine the degree of genetic similarity

    • Ex. Guinea pigs have insulin so different from other rodents that they were placed in a separate category

    • Physiology - The branch of biology dealing with the physical and chemical functions of organisms, including internal processes

    • Proteins are especially studied, as they indicate information about the organism’s genetics

  • DNA Evidence - The comparison of nucleotides of specific genes to determine the relatedness of organisms

    • Ex. The Turkey Vulture is closer in genetic relation to storks, rather than other vultures

    • Phylogenetic Tree - A branching diagram used to show the evolutionary relationships among species

      • The tree branches from a common ancestral population/gene pool based on new/unique characteristics

      • Clade - A taxonomic group that includes a single common ancestor and all its descendants

        

• Evolutionary history can help narrow down a certain group of species to be used in medicine, understanding disease, agriculture, and animal conservation

• Primitive Traits - An inherited trait from a distant ancestor

• Derived Trait - A recently appeared trait in the most recent ancestor forming a new branch

Domains and Kingdoms

• The structural diversity of Earth’s species is incredibly large, so there are large ranks of domains and kingdoms to classify them

  • Structural Diversity - A type of biological diversity that is exhibited in the variety of structural forms in living things, from internal cell structure to body morphology

• The study of cell types and genes led to the creation of the domain rank, after the creation of kingdom

• The three domains are Bacteria, Archaea, and Eukarya

• The six kingdoms are Bacteria, Archaea, Protista, Plantae, Fungi, and Animalia

• Autotroph - An organism that captures energy from sunlight or non-living substances to produce its own energy-yielding food

• Heterotroph - An organism that cannot make its own food and gets its nutrients and energy from consuming other organisms

Cell Types

• Unicellular - An organism made of only one cell

• Multicellular - An organism made of more than one cell

• Prokaryotic Cell - A smaller, simple type of cell that does not have a membrane-bound nucleus

  • “before the nucleus”

  • Circular DNA, not bound by a membrane

  • Genome made of a single chromosome

  • No organelles

• Eukaryotic Cell - A larger, complex type of cell that does have a membrane-bound nucleus

  • “true nucleus”

  • Have bound organelles

  • Genome made of several chromosomes

• Cellular reproduction includes mitosis (cell division) and meiosis (egg and sperm)

• Hypertonic Solution - There is a greater concentration outside of the cell, so water moves out and the cell shrinks

• Isotonic Solution - There is an equal concentration inside and outside of the cell

• Hypotonic Solution - There is a greater concentration inside of the cell, so water moves in and the cell grows

Bacteria

• Bacteria - An individual prokaryotic cell or a single species that is in the domain Bacteria

• Bacteria can be named by their aggregations and shapes

  • Diplo- - The prefix used for bacteria that aggregate in pairs

  • Strepto- - The prefix used for bacteria that aggregate in chains

  • Staphylo- - The prefix used for bacteria that aggregate in clusters

  • Coccus - A micro-organism whose overall morphology is spherical

  • Bacillus - A micro-organism whose overall morphology is rod-shaped

  • Spirillum - A micro-organism whose overall morphology is spiral-shaped

• Can be aerobic or anaerobic, and usually mesophiles

  • Autotrophic Bacteria - Bacteria that produce their own food

    • Photosynthetic Bacteria - Bacteria that use chemical energy to convert CO2 and water into carbohydrates

      • Some bacteria, such as cyanobacteria, are autotrophs due to the photosynthesis that they can perform from the chlorophyll they contain

        • They are abundant in fresh and salt water, and account for much of the atmospheric oxygen on Earth

        • They are believed to be the first to photosynthesize, which changed the composition of the atmosphere

    • Chemosynthetic Bacteria - Bacteria that use chemical energy from inorganic molecules, such as hydrogen sulfide, to produce organic compounds

      • Do not use sunlight, but instead derive energy from chemical reactions

      • Often found in deep-sea vents or sulfur-rich springs

  • Heterotrophic Bacteria - Bacteria that consume other organisms for energy

    • Saprophytic Bacteria - Decomposers that feed on dead organic matter and act as agents of decay

    • Parasitic Bacteria - Bacteria that obtain food from living cells and fully depend on the host cells for nutrition

  • Aerobic Respiration - Oxygen is required to break down organic matter and produce energy

    • Obligate Aerobe - Bacteria that need oxygen and cannot survive without it

    • Ex. Mycobacterium tuberculosis live in lung tissue

  • Anaerobic Respiration - Energy is produced by breaking down organic matter in the absence of oxygen

    • Obligate Anaerobes - Bacteria that cannot grow in the presence of oxygen

    • Ex. Clostridium botulinum, which germinate in anaerobic conditions

  • Facultative Bacteria - Bacteria that live in either anaerobic or aerobic conditions

  • Mesophile - An organism that lives in habitats characterized by moderate conditions

• Bacteria can reproduce through binary fission, conjugation, transformation, and transduction

  • Binary Fission - The asexual form of reproduction used by most prokaryotes, in which a cell divides into two genetically identical cells of organelles

    • A cell will make a copy of its chromosome and it grows

    • When it reaches a certain size, it elongates and separates itself with a septum

    • This creates two identical daughter cells with a copy of the original DNA

  • Conjugation - A process in which there is a transfer of genetic material involving two cells

    • This occurs in unfavourable conditions where new genetic combinations offer a better chance of survival

    • One donor cell links to a recipient cell through a sex pilus, where it transfers genetic material

    • This results in new genetic content

  • Transformation - The transmission of genetic material where a DNA segment is picked up by a living bacteria, which can now perform the function of the DNA

    • DNA contains genes

    • Bacteria can be given foreign DNA from another organism and make new proteins

    • In order for artificial transformation to work, the plasmid must be advantageous to the new cell, and selectable markers must be present to identify if the transformation works

    • Ex. Cutting out the gene for human insulin and turning bacteria into insulin “factories”

  • Transduction - The transmission of genetic material when a virus infects one cell, and then another, which receives the new DNA

• Plasmid - A small loop of DNA that is separate from the main chromosome, and contains different genes from the chromosome

  • They can join the chromosome or be transferred to another cell, making them an important part of genetic recombination

• Endospore - A dormant bacterial cell able to survive for long periods during extreme conditions

  • These are hard-walled structures that can protect bacteria from heat, radiation, and toxic chemicals

• Bacterial growth starts with a lag phase (acclimatization), then grow under favourable conditions until they plateau at the carrying capacity, where they die due to a build up of waste and a shortage of food

• Bacteria have a glycocalyx in the form of either a capsule or slime layer

• Bacteria have fimbriae, which allow it to attach

• Gram Stain - A stain that separates bacteria into Gram positive and Gram negative, based on the cell wall’s response to the stain

  • Gram-positive bacteria have a thick protein layer of peptidoglycan on their cell wall and stain purple

  • Gram-negative bacteria have a thin protein layer of peptidoglycan and a bilayered membrane and stain pink

    • More resistant to chemicals, so they are more threatening

• Bacteria can be decomposers, nutrient-recyclers, and producers of oxygen

• In every ocean, there are bacteria that can degrade oil and emit CO2

  • Natural bacteria are so far the most efficient at this, as they are adapted to oil spills and the environment

  • Dead zones may result in deep water due to a lack of circulation of oxygen

  • However, it’s a very slow process to be cleaned

Archaea

• Archaea - An individual prokaryotic cell or a single species that is in the domain Archaea

• Methanogenesis - A biological or chemical anaerobic process that produces methane as a by-product, unique to Archaea

• Extremophiles - An organism that lives in habitats characterized by extreme conditions

  • Archaea are normally found in extreme conditions such as heat, acid, and salt

  • Thermophile - A species that can survive extreme heat conditions, such as hot springs

  • Acidophile - A species that can survive extremely acidic environments, such as volcano craters

  • Halophile - A species that can survive extremely salty environments, such as the Dead Sea

• Archaea’s heat-resistance enzymes can be used in biotechnology processes, such as the replication of DNA through polymerase chain reactions.

• Archaea have ribosomes more similar to animals than bacteria

Protists

• Protist - A eukaryotic organism, usually unicellular, that is not a fungus, plant, or animal

  • They are grouped together because they do not fit into other kingdoms

  • Evolved approximately 1.5 to 2 billion years ago through endosymbiosis

    • Endosymbiosis - One prokaryotic cell engulfs a different type of prokaryotic cell forming a symbiotic relationship and functioning like one cell

  • Algae is multicellular

• There are three types of protists: animal-like, fungus-like, and plant-like

• Animal-like protists (protozoa) are heterotrophic, and sometimes parasitic

  • Parasite - An organism that benefits by living in or on another organism at the expense of that organism

  • Phylum Cercozoa

    • Have a cell membrane, but no wall, and use pseudopods for movement

    • Pseudopod - A temporary cytoplasmic extension that amoebas use for feeding and movement

    • Ex. Amoeba

  • Phylum Ciliophora

    • Have many short, hair-like projections called cilia

      • Cilia - A short, hair-like projection that functions in cell movement and particle manipulation when coordinated with other cilia

    • Have an oral groove and gullet which leads to the food vacuole

    • Ex. Paramecia

    • Balantidium coli is the only human parisite ciliate

  • Phylum Zoomastigina

    • Use flagella for movement, and have a hard outer layer to protect their membrane

      • Flagella - A long, hair-like projection extending from the cell membrane that propels the cell using a whip-like motion

  • Phylum Sporozoa

    • Alternate between sexual and asexual reproduction

    • Alternate between two hosts

    • They are all parasitic

      • Ex. Plasmodium which causes malaria in humans and mosquitoes

• Fungus-like protists are heterotrophic, and feed on living organisms, dead matter, and waste

  • They produce spores like fungi, but they have different cell walls

  • Plasmodial slime moulds are visible to the unaided eye as slug-like organisms that creep over decaying organisms, and feed by engulfing food into their cytoplasm

  • Cellular slime moulds exist as individual cells and ingest bacteria or yeast cells

  • Water moulds are filamentous and live on dead organic matter or as parasites, where they release digestive enzymes and absorb the resulting nutrients

• Plant-like protists contain pigments in their chloroplasts which carry out photosynthesis

  • Also known as algae

    • Algae - A unicellular or multicellular photosynthetic, aquatic protist

  • Some are unicellular

    • Phylum Chrysophyta

      • Ex. Diatoms, a type of phytoplankton, are single-celled organisms that are a source of food for larger organisms

        • They have rigid walls of silica, which is common in sand and glass

        • Usually reproduce asexually

    • Phylum Pyrrophyta

      • Dinoflagellates have two flagella at right angles

      • They reproduce very quickly to create algae blooms

        • Red Tide - A coastal phenomenon in which dinoflagellates that contain red pigments are so concentrated that the sea water has a distinct red colour

      • Some, such as Symbiodinium, live in coral reefs, and exchange the benefits of photosynthesis for nitrogen from the coral

        • Coral bleaching is the expulsion of these flagellates

    • Phylum Euglenophyta

      • They have chloroplasts, but can also absorb nutrients

      • Euglena have a light-detecting eyespot

  • Some are multicellular, known as seaweeds

    • Phylum Rhodophytes (Red Algae)

      • The first multicellular organism, approximately 1.5 billion years ago, and the most abundant large algae

      • It contains the pigment phycoerythrin, which allows light waves to reach greater depths of the ocean

    • Phylum Phaeophytes (Brown Algae)

      • Ex. Kelp

      • Can grow dense enough to form forests

      • Have many specialized tissues, including a holdfast, stipe, and blades

    • Phylum Chlorophytes (Green Algae)

      • Mostly aquatic in fresh water

      • Their cell walls contain cellulose, and they have chlorophyll, and store food in the form of starch, like plants

      • They can be unicellular or multicellular

      • Believed to be the closest evolutionary relatives of land plants

Plants

• Plant - A multicellular photosynthetic eukaryote with cellulose-based cell walls

• Reproduce using embryos

  • Embryo - An organism’s early pre-birth stage of development

• Tracheophytes have vascular tissue, which allows for the transport of nutrients

• Bryophytes have non-vascular tissue

• Includes seedless plants and gymnosperms and angiosperms

• Autotrophs that create energy using chloroplasts through photosynthesis

  • Photosynthesis - 6CO₂ + 6H₂O + Sunlight → 6O₂ + C₆H₁₂O₆

Fungi

• Fungi - A stationary, heterotrophic eukaryotic organism whose cell walls contain chitin

  • There are over 100,000 species of fungi

  • They feed by releasing digestive enzymes into their surroundings, and then absorbing the digested nutrients into their cells

  • Closer in relation to animals than plants

• Some fungi, such as yeast, are unicellular

• Most fungi are multicellular

  • Hypha - A multicellular, thread-like filament that makes up the basic structural unit of a fungus

    • Densely packed in a tight mass and difficult to see as separate structures'

  • Mycelium - A complex, net-like mass made of branching hyphae

    • Live in soil and other nutritious substances, such as living or decaying organisms

  • Fruiting Body - The spore-producing reproductive structure in fungi

    • This part can be seen above ground

      

• Fungi digest food first, and then consume it

  • They release enzymes that externally break down food

  • They then absorb nutrients through the cell membranes

  • Parasitic Fungi - Fungi that absorb nutrients from the living cells of a host organism, often living inside of it

    • Ex. Cordyceps invades an insect body

  • Predatory Fungi - Soil fungi whose mycelia have special structures for trapping prey

    • Ex. Arthrobotrys traps nematodes in the soil

  • Mutualistic Fungi - Fungi with partnerships with other organisms, often plants or protists, where mycelia covers the roots of a plant

    • Ex. Mycorrhiza increases the absorptive surface of the plant roots, allowing the plants to take up more nutrients, while receiving sugar from the plant

  • Saprobial Fungi - An organism that feeds on dead organisms or organic wastes, which decomposes dead or decaying matter, where it can absorb nutrients and recycle them into the ecosystem

• Fungi have both asexual and sexual methods of reproduction

  • Asexual reproduction methods

    • Spore production

    • Budding, where smaller cells develop while attached to the parent cell, and the smaller cell is eventually pinched off

    • Fragmentation, where a piece of mycelium breaks and forms a new individual

    • Single-celled spores are produced in the trillions by fruiting bodies

      • They have a protective cell wall, and can be carried to a new life-supporting location to grow

  • Sexual reproduction

    • Under unfavourable conditions, two mycelia will sexually produce spores

      • Zygospore - A diploid structure that develops after two haploid hyphae of opposite types combine and fuse their nuclei

    • Two mating types form a spore-bearing asci

      • Asci - A small finger-like structure in which sac fungi develop spores

• Fungi are classified by reproduction and the structure of the fruiting body

  • Phylum Deuteromycota - Fungi Imperfecti

    • The phylum for fungi that do not reproduce sexually

    • They are diverse, but lack sexual structures, so taxonomists are not certain if they are related to each other

    • Ex. Penicillium, which grows on mouldy fruit and produces penicillin

    • Cyclosporine is obtained from imperfect fungus in soil, which is given to patients after transplant surgery to suppress their immune systems

    • It can also be used to produce cheese

  • Phylum Chytridomycota - Chytrids

    • Mostly unicellular

    • Aquatic, in marine and freshwater ecosystems

    • Their spores have a flagella

    • They can be parasites or live on decaying plants or insects

    • Ex. Synchytrium endobioticum, a parasitic fungus that lives in soil and infects potato plants

Animals

• Animal - A eukaryotic, heterotrophic, multicellular organism

  • They do not have cell walls

  • They are mobile in at least one stage of their life

  • They reproduce sexually with an embryo

  • Diploid - An organism with two sets of chromosomes

• Heterotrophs use cellular respiration to refine materials into useable energy

  • Cellular Respiration - 6O₂ + C₆H₁₂O₆+ Usable Energy → 6CO₂ + 6H₂O

• There are many characteristics that can be used to classify an animal

  • Backbones

    • Invertebrate - An animal that does not have a backbone

      • About 95% of all animals across 34 of 35 phyla

    • Vertebrate - An animal with an internal skeleton and a backbone

  • Levels of organization

    • All animals have cells, and, except for sponges, have tissues, which form organs and organ systems

    • The level of complexity can classify animals

  • Number of body layers

    • All animals besides sponges and Cnidaria have three layers of cells

      • Ectoderm - The outer layer of cells

        • Ex. The skin, nervous tissue, and some sense organs

      • Mesoderm - The middle layer of cells

        • Ex. The muscles, blood, kidneys, and reproductive organs

      • Endoderm - The inner layer of cells

        • Ex. Produces the lungs, liver, pancreas, bladder, and stomach lining

  • Symmetry and body plans

    • Asymmetrical - A body plan with an irregular shape

      • Ex. Sponges

    • Radial Symmetry - A body plan that can be divided along any plane, through a central axis, into roughly equal halves

      • Ex. Cnidarian

    • Bilateral Symmetry - A body plan that can be divided along one plane, through the central axis, into equal halves

      • Ex. Turtles

  • Body cavity

    • Coelom - A fluid-filled body cavity that provides space for the development of organs

      • Coelomates include some worms, molluscs, and vertebrae

      • Coelom gives the body rigidity and something for muscles to brace against

      • It also gives more space for the organs to grow, as they can fold back on themselves

      • In more complex organisms, the coelom is divided into separate categories such as thoracic and abdominal

  • Segmentation

    • Segmentation - The division of multicellular bodies into a series of repetitive parts

      • A single segment can be damaged, but the other segments can function properly

      • Segments allow the body to have complex patterns of movement

  • Movement

    • All animals have body forms that can move in at least one stage

    • Some, such as sponges and sea anemones, are sessile as adults

  • Reproduction

    • Most animals reproduce using gametic reproduction, where a zygote forms from an egg and sperm

    • This can form by internal or external fertilization

    • Species such as aphids can reproduce asexually

Animal Phyla

• Phylum Rotifera

  • Small, sessile, planktonic aquatic forms

  • They have a wheel of cilia on the head used for feeding and locomotion

  • Ex. Brachionus plicatilis

• Phylum Porifera

  • Found in marine and freshwater environments

  • Asymmetrical body plans and no tissue

  • Two layers of cells that are very independent

  • Sessile as adults, and trap food particles that passes through the water

  • Ex. Red toxic finger sponge, Negombata magnifica

• Phylum Cnidaria

  • Includes freshwater hydras, marine jellyfish, and sea anemones and corals

  • Have two layers of cells and tissues, including muscle and nervous systems

  • They can capture prey using stinging tentacles around the mouth opening, which is digested in the gastrovascular cavity

  • Cnidarians have radial symmetry and two body forms

    • Polyp - The tube-shaped sessile body form of cnidarians

    • Medusa - The umbrella-shaped, free-swimming body form of cnidarians

      • Use passive currents or body contractions to move

    • They can switch between body forms during their life cycle

  • Ex. Moon jellyfish, Aurelia aurita

• Phylum Platyhelminthes

  • Flatworm acoelomates with three layers of cells

  • They have simple nervous systems with a brain-like concentration

  • Unsegmented, flattened body shape

  • Ex. Beef tapeworm, Taenia saginata

• Phylum Annelida

  • Worm coelomates with segmented bodies and several organ systems, such as the circulatory system, digestive system, and nervous system

  • Have bilateral symmetry

  • Ex. Earthworm

• Phylum Nematoda

  • Unsegmented roundworms

  • Have a very simple digestive track

  • Ex. Hookworms

• Phylum Mollusca

  • The second most diverse animal species

  • They have bilateral symmetry, three layers of cells, a coelom, and two body openings

  • Many have shells

  • Includes classes bivalves, gastropods, and cephalopods

  • All have a mantle that surrounds the internal organs that are a part of digestive, circulatory, respiratory, excretory, reproductive, and nervous systems

    • Mantle - A membrane that surrounds a mollusc’s internal organs

  • Ex. File clam, Limaria fragilis

• Phylum Echinodermata

  • Includes sea stars, sea urchins, sea cucumbers, and sand dollars

  • Marine animals with radial symmetry, spiny endoskeletons made of calcium carbonate, and tube feet

    • Endoskeleton - An internal skeleton that protects organs and provides support for muscle attachment

  • Use a water vascular system, involving a series of fluid-filled tubes, to extend tube feet

  • Ex. Common sea star, Asterias Rubens

• Phylum Arthropoda

  • The largest animal phylum, including spiders, scorpions, crustaceans, and insects

    • Class Arachnida includes spiders and mites, and have a cephalothorax and abdomen

    • Class Myriapoda include millipedes and centipedes, and have one or two pairs of legs per segment

    • Class Crustacea includes crabs and lobsters, and have five pairs of jointed appendage, two pairs of antennae, and an exoskeleton

    • Class Insecta includes ants and butterflies, and have a head, thorax, and abdomen, and three pairs of legs

  • Have legs made of movable sections connected by joints

  • Have a segmented body and hard exoskeleton

    • Exoskeleton - An external skeleton that protects organs, provides support for muscle attachment, and protects against water loss and predation

  • Ex. Goliath birdeater, Theraphosa blondi

• Phylum Chordata

  • All have a notochord and a dorsal nerve chord

    • Notochord - A flexible, rod-shaped structure found in chordate animals; during vertebrate development it is replaced by the spine

  • Almost all Chordata are vertebrates, where the notochord forms in the embryo, and later becomes the brain and spinal chord

  • Includes mammals, birds, fish, reptiles, and amphibians

  • Ex. Pumpkinseed fish, Lepomis gibbosus

Chordata Classes

• Fish make up half of all vertebrate species

  • Agnatha - Fish without jaws that do not have paired fins, which use suction to hold onto food

    • Ex. Pouched lamprey, Geotria australis

  • Gnathostomata - Fish with paired fins and jaws

    • Chondrichthyes - Sharks and rays with a skeleton made of cartilage

      • Ex. Great white shark, Carcharodon carcharias

    • Osteichthyes - Fish with skeletons made of bone, and also have swim bladders to rise and sink

      • Ex. Atlantic bluefin tuna, Thunnus thynnus

• Class Amphibia - Ectothermic vertebrates with moist skin that inhabit wet ecosystems

  • The first tetrapods to appear and live partially on land were amphibians

    • Tetrapod - A vertebrate with two pairs of limbs; an amphibian, reptile, bird, or mammal

  • They use their moist skin for gas exchange

  • Includes Order Anura (frogs and toads), and salamanders (Order Urodela)

  • Juveniles may have gills

  • Ex. Pumpkin toadlet, Brachycephalus ephippium

• Class Reptilia - Land-dwelling chordates that have scales and lay amniotic eggs

  • Includes orders of lizards and snakes, turtles, and crocodilians

  • They use their body scales to prevent dehydration

  • They use their lungs for gas exchange

  • Fertilization is internal, which creates an amniotic egg with several layers of membranes to prevent it from drying out

  • The incubation temperature can determine the sex of the offspring

  • Teeth are the same type

  • Ectothermic - The reliance on environmental heat for determining internal body temperature

  • Have a three-chambered heart

  • Ex. Arabian sand boa, Eryx jayakari

• Class Aves - Endothermic, calcareous egg-laying vertebrates that have feathers, hollow bones, a toothless skull, and a compact body

  • Endothermic - The use of metabolic heat to maintain a high, constant body temperature

  • Related to at least one group of dinosaurs by nature of their wings and scales

  • Birds have a four-chambered heart, high body temperature, and unique respiratory system that promotes the one-way movement of air

  • Many birds have distinctive songs and calls

  • Ex. Budgerigar, Melopsittacus undulatus

• Class Mammalia - Endothermic vertebrates with mammary glands in females, hair, hearts with four chambers, and highly developed brains

  • Mammals also have different kinds of teeth and an external ear

  • Mammary Gland - A mammalian gland that produces and secretes milk for nourishing and developing young

  • Monotremes - Egg-laying mammals

    • Ex. Duck-billed platypus, Ornithorhynchus anatinus

  • Marsupials - Pouched mammals that have a short gestation period

    • Ex. Red kangaroo, Osphranter Rufus

  • Placental Mammals - Mammals with a placenta

    • Placenta - An organ in the pregnant uterus that exchanges nutrients and oxygen between the mother and developing offspring

    • Ex. Polar bear, Ursus maritimus

Viruses

• Virus - A structure that contains strands of DNA or RNA surrounded by a protective protein coat; it cannot live independently outside of cells

  • Viruses create no waste, produce no energy, and have no membranes, organelles, or cytoplasm

  • Viruses are dormant outside of living host cells

    • Host cells are incubators for DNA/RNA and protein synthesis

    • They are infectious, meaning they pass this DNA from cell to cell

  • Can only reproduce inside of a host cell

  • They are not made of cells

• Classifying viruses

  • Size and shape

    • Capsid - The outer protein coat of a virus that surrounds the genetic material, and can be spherical, crystaline, cylindrical, etc.

  • Types of diseases they cause

    • Viruses have differing genetic material

    • The replication method can either be a DNA virus or an RNA Retrovirus

    • Replication - The fundamental process of all cells, in which the genetic material is copied before the cell reproduces

• Viruses are host-specific and only become active once it has entered the cell

  • Ex. Bacteriophage - infects bacterial cells by injecting DNA into bacterium

• Central Dogma of Biology - DNA in the nucleus, through transcription, creates mRNA which leaves the nucleus, finds ribosomes, and makes proteins

• DNA Viruses

  • Attachment - Virus attaches to the surface of the host cell

  • Insertion - Viral DNA released into host cell and deactivates mRNA of host

    • Viral genetic material intercepts the host’s process to create mRNA

  • Replication - Viral mRNA uses host cell machinery to translate viral mRNA and create viral proteins

  • Assembly - New virus proteins are assembled

  • Lysis - Cell lyses (bursts), releases viral proteins

  • Examples:

    • Epstein-Barr Virus - Mononucleosis

    • Herpes Varcilla-zoster - Chicken pox/shingles

    • Papillomavirus - Warts

    • Adenovirus - Respiratory infection

    • Monkeypox Virus - Monkeypox

    • Variola Virus - Smallpox

• RNA Retroviruses

  • Retroviral RNA inserted into host

  • Reverse Transcriptase (enzyme) activated, and converts retroviral RNA into DNA

  • New retroviral DNA splices into host chromosome and becomes dormant

  • Dormancy period of a variable length, before the virus is triggered

  • Retroviral DNA is spliced out of the host DNA and becomes active

  • Host mRNA is deactivated, and retroviral mRNA is made using the host cell machinery

  • Host ribosomes read retroviral mRNA and produce retroviral proteins

  • Cell lyses and releases new virus proteins

  • Goes against the central dogma of biology

  • Examples:

    • Rubella Virus - German measles

    • HIV - AIDS (attacks Helper T-lymphocytes)

    • Poliovirus - Polio

    • Rhinovirus - Common cold

    • Rabies virus - Rabies

    • SARS-CoV-2 - COVID-19

• Virus Cycles

  • Lytic Cycle - The replication process in viruses in which the virus’s genetic material uses the copying machinery of the host cell to make new viruses

    • Attachment and insertion - the proteins on the surface of the virus bind to protein receptors on the cell’s membrane

    • DNA/RNA Replication

    • Virus assembly

    • Lysis - viruses are released

  • Lysogenic Cycle - The replication process in viruses, in which the viral DNA enters the host cell’s chromosome; it may remain dormant and later activate and instruct the host cell to produce more viruses

    • Attachment and insertion

    • Provirus formation - insertion with host chromosome

      • Provirus - A virus which can invade a cell, but does not kill it

    • Lysogeny

    • Provirus separation, virus replication and assembly

    • Lysis - viruses are released

    • Examples:

      • Herpes, warts, viral pneumonia, HIV

  • Temperate Virus - A virus that replicates using the lysogenic and lytic cycle, where the virus lays dormant, and cell lyses is not immediate

  • Virulent Virus - A virus that replicates using the lytic cycle, where cell lyses is immediate

• Viruses can be transmitted through the air, physical contact, and insect bites

  • Power of a Virus - How easily a virus can be transmitted

  • Epidemic - A large-scale transmission confined to a geographical area

  • Pandemic - A large-scale transmission that is global

• Vaccines - Mixtures containing weakened versions of a dangerous virus

  • The antigen triggers the immune system (B Plasma Cells) to produce specific antibodies

  • Antibodies will recognize foreign substances and mark them for destruction by other immune cells

  • When real viruses enter the body, immune system will remember the specific antibody to produce

  • Vaccines can prevent and eradicate viruses

• SARS-CoV-2

  • Uses spike proteins to gain entry into epithelial cells via a receptor called ACE2

  • The virus tricks the cell into swallowing it through endocytosis

  • ACE2 becomes occupied and does not perform its regular function

• Prion - An infectious particle that causes damage to nerve cells in the brain, and that appears to consist mostly or entirely of a single protein

  • Only known disease agents to lack genetic material

  • They convert from normal proteins to harmful particles with different molecular shapes

  • Causes brain diseases, such as Creutzfeldt-Jakob Disease, scrapie, and bovine spongiform encephalopathy

• Viruses can be used by genetic engineers by injecting genes into a virus, which then replicates inside of a host cell

Types of Diversity

• Species Diversity - The variety and abundance of species in a given area

• Genetic Diversity - The variety of heritable characteristics (genes) in a population of interbreeding individuals

  • Genes - The genetic material that controls the expression and inheritance of traits and the production of protein

  • Gene Pool - All the genes of all the individuals in a population

  • Population - A group of individuals of the same species in a specific area at a specific time

  • The genetic diversity is usually greater within a species, rather than a population, because separated populations will have combinations of genes best suited towards their environment

  • Genetic diversity provides resistance to disease and changing environments, as individuals with genes best suited to resist a challenge can interbreed with the population

  • Genetic diversity supports conservation biology, as species can be introduced to an area to establish a greater genetic diversity

• Ecosystem Diversity - The variety of ecosystems in the biosphere

  • There is a variety of biotic and abiotic factors around the earth, including populations, altitude, climate, and light levels

    • Ecosystems become richly diverse as a result

Ecosystem Services

• Ecosystem Services - The benefits experienced by organisms, including humans, which are provided by sustainable ecosystems, and the benefits an ecosystem experiences provided by organisms.

  • Ex. Forests take up carbon dioxide and maintain soil fertility

  • Includes climate regulation, water supply, pollination, habitats, food production, raw materials, recreation, genetic resources, and nutrient recycling.

• Ecosystems with greater species diversity provide reliable services and resilience

  • Inertia - The ability for an ecosystem to resist disturbance

  • Resilience - The ability of an ecosystem to remain functional and stable in the presence of disturbances to its parts

  • Keystone Species - A species that is more influential in an ecosystem than others in the stability of the system

  • A large amount of diversity is required to fulfill ecological niches and keep other species numbers in check

• When humans introduce new species to an area, it can create competition, which causes an altered food web and reduced population diversity

Symbiotic/Composite Organisms

• Lichen - An organism that results from a mutualistic relationship between a fungus and a photosynthetic plant or alga

  • They are an example of a composite organism

  • They are an important food source for many animals

  • Lichen also emit enzymes, which break down matter and play an important role in primary succession

• Rhizobium Bacteria - Bacteria found on roots that turn atmospheric nitrogen into useable ammonia for other organisms

• Mycorrhizae - A fungus that grows on plant roots, where it receives sugar from the plant, and gives the plant phosphorus from the soil

Biodiversity Crisis and Evolution

• As humans continue to interfere with ecosystems at an unprecedented rate, the Earth’s ecosystems are in a crisis

• The current rate of extinction among species is high enough to match historical mass extinctions, known as a biodiversity crisis

  • Mass Extinction - A large-scale dying out of a large percentage of all living organisms within an area over a short time

  • Biodiversity Crisis - The current decline in genetic, species, and ecosystem diversity that may represent a mass extinction

  • Modelling is used to make predictions about future climates and impacts on ecosystems

    • Modelling - A scientific method in which an idea about a mechanism is formulated, and real-life data are then used to see if the data fit the model

• Warmer climates have increased plant growth and limited lichen growth, which has been detrimental for caribou foraging for lichen in the winter

  • As well, plants begin growing earlier in the year, so caribou have a harder time finding food at peak nutritional value

• Ecosystems formed in high altitudes as suffering as the suitable land for growth continues to move towards a higher, smaller area

  • As well, plant populations can become isolated, leading to a lack of biodiversity

• Reptiles, such as Ontario turtles, that rely on temperature sex determination are suffering, as increasingly warmer temperatures are producing increasingly more females

  • Temperature Sex Determination - A system in which the sex of offspring is determined by incubation temperature rather than by genes

• Warmer temperatures have caused pollination relationships to lose their matched timing, so that pollinators emerge too early and starve, and plants no longer have surviving pollinators to help the species to survive

• An increase in aquatic system temperature caused invertebrate population densities to decrease, and reduced the growth of fish

Aspects of an Experiment

• A control group proves the viability of the experiment, and serves as a base for comparison

  • Positive controls prove that something is working

  • Negative controls prove that nothing happens when there should not be anything happening

• An independent variable is what gets changed

  • There should only be one

• A dependent variable is the effect of the independent variable