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Unit I - Biodiversity 

Ch 1.1 -Biodiversity - an introduction

What is a species

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

Species: all organisms capable of breeding freely with each other under natural conditions

Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics

Evolutionary change: a change that occurs in an entire population, usually occurs over a long period

A species is defined as a group whose members can freely breed among themselves under natural conditions → biological species concept

Species are defined based on a set of physical characteristics/morphology when the traditional species definition does not apply

Physical and behavioral changes that occur in the entire population of a species are referred to as evolutionary change


Biodiversity

Genetic diversity: the genetic variability among organisms, usually referring to the individual of the same species

Different species vary in behaviors, habitats, ecological niches and abundance, and genetic makeup as well


Diversity in Ecology

Heterotroph: an organism that obtains energy by consuming living/dead organisms

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<aside> ✨ Autotroph: an organism that uses sources of energy to produce nutrients from the water, gases, and/or minerals

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<aside> ✨ Species diversity: a measure of diversity that takes into account the quantity of each species present, as well as the variety of different species present

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<aside> ✨ Structural diversity: the range of physical shapes and sizes within a habitat/ecosystem

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Diversity is influenced by the total number of individuals present in an ecosystem → ecosystem with many large populations is considered more diverse

The range of physical sizes, shapes, and distribution of the individual, as well as habitats and communities in an ecosystem is referred to as structural diversity

→ greater structural diversity can support a greater diversity of species as it has a great biodiversity

Food supply - between species and their food

  • eg.1 - boneworms feed exclusively on bones of dead whales

  • eg.2 - the photosynthetic micro-organism performs photosynthesis and supplies the coral animals and clams with a steady supply of food

Protection - for shelter and protection

  • eg.1 - hermit crabs use the shells of dead snails for a protective home

  • eg.2 - Cecropia trees provide shelter for a certain species of ants, and the ants protect the tree by biting and stinging herbivores

Transportation - move from place to place with the help of another species

  • some flower mites climb onto the bills of hummingbirds moving from flower to flower

  • many seed have hooks that allow them to stick to passing animals → carried long distances before they fall off and begin growing

Reproduction - depends on other species for their own successful reproduction

  • trilliums produce seed with fleshy tissues that attack ants and dispersed on them

  • many bird species build their nests in the abandoned tree cavities made by woodpeckers on their own nests

Hygiene - help maintain the health of another species

  • coral reefs have “cleaning stations” where large fish come to have external parasites removed by small fish and shrimp

  • the bacteria that lives on our skin protect us from other bacterial and fungal infections

Digestion - living within digestive tracts are essential for food digestion

  • a variety of bacteria and other micro-organisms lives within the termites’ guts to digest the wood

  • bacteria living in the large intestines of humans produce vitamins that are absorbed into the circulatory system


Biodiversity at risk

loss of biodiversity affects humans:

  • threatens food supply when entire species and plant varieties are lost

  • eliminates sources of natural medicines and potential new medicines

  • has a significant economic impact on tourism and forestry when accompanied by habitat destruction

  • has the potential to cause serious disruptions in biogeochemical cycles such as the carbon cycle

A change in climate may make conditions too hot/cold, too wet/dry for species adapted to the original climatic conditions

Human actions result in a rapid loss of natural habitats due to agriculture, forestry, urban expansion, the introduction of invasive species, over-harvesting of wild populations and serious water and air pollution

  • production of greenhouse gases → human-caused climate change


Ch 1.2 - The Nature of Classification

<aside> ✨ Biological classification: the systematic grouping of organisms into biological categories based on physical and evolutionary relationships, include producers, herbivores, carnivores, and scavengers

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Taxonomy - Developing a Classification System

<aside> ✨ Taxonomy: the science of classifying all organisms, classify both living and fossil species

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Observing the morphology, behavior and even geographic location can be used to identify organisms

→ similarity in form, or evolutionary change challenges this way of identification


Early Biological Classification Systems

<aside> ✨ Botanist: specializing in the study of plants

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Carl Linnaeus

<aside> ✨ Genus: a taxonomic level consisting of group of similar species

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<aside> ✨ ********************************************************************************************************************************************************************************************Binomial nomenclature: the formal system of naming species whereby each species is assigned a genus name followed by a specific name

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Before Carl Linnaeus, it was common for species to be given one/more long descriptive names → Carl Linnaeus assign a binomial short name using binomial nomenclature

Traditional Taxonomic Levels

<aside> ✨ Taxon: a category used to classify organisms

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<aside> ✨ Kingdom: the highest taxonomic level of the traditional Linnaean system of classification

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<aside> ✨ Species → Genus → Family → Order → Class → Phylum → Kingdom

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<aside> ✨ Each level of a taxonomic level → Taxon

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Dichotomous Key

<aside> ✨ Dichotomous key: a series of branching, two-part statements used to identify organisms

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A dichotomous key is a structure in which a large set of items is broken down into smaller subsets → leading to the smallest available classification unit

  • provides an easy method of identifying a species


Ch 1.3 - Phylogeny and Modern Taxonomy

<aside> ✨ Evolution: the scientific theory that describes changes in species over time and their shared ancestry

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The theory of evolution states that all living things are descended from a common ancestor

Taxonomy - the classification, identification, and naming of organisms - aims to group organisms according to how closely related they are to each other


Phylogeny

<aside> ✨ Phylogeny: the study of the evolutionary relatedness between, and among, species

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<aside> ✨ Phylogenetic tree: a diagram depicting the evolutionary relationships between different species/groups

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<aside> ✨ Clade: a taxonomic group that includes a single common ancestor and all its descendants

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Phylogeny is the science that deals with evolutionary relationships between and among species → tracks relationships between entire species presented in a phylogenetic tree

A clade is a taxonomic group that includes a single ancestor species and all its descendants

  • the tips of a branch on a phylogenetic tree can represent a particular species/an entire group of species


Taxonomy Today

Phylogenetic analysis can uncover the evolutionary relatedness of organisms → group into different-sized clades



Ch 1.4 - Kingdoms and Domains

<aside> ✨ Prokaryote: a single-celled organism that does not contain membrane-bound organelles

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<aside> ✨ Eukaryote: any organism whose cells contain organelles, some are single-celled while others are multicellular

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<aside> ✨ Protist: organisms that contain a nucleus and other organelles but show a diversity of shapes, sizes, and life cycles

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Kingdom of Life

Kingdoms - Animals, Plants, and Fungi, Eubacteria, (eukaryotic) Protists\

Eubacteria

  • prokaryotic, cell walls contain peptidoglycan + unique compounds, and vary in shape and size

  • can be photosynthetic, chemotrophic/heterotrophic, can reproduce asexually

  • eg - Escherichia coli, Salmonella, Nitrogen-fixing bacteria

Archaea

  • prokaryotic, cell walls and cell membranes contain peptidoglycan and have a unique structure, most are extremely small

  • some are extremophiles, live in the digestive tracks of mammals and marine environments, and all can reproduce asexually

  • eg - extreme thermophiles, methanogens

Protista

  • eukaryotic, cells have extreme diversity of cellular structure, some have chloroplasts and cell walls

  • may be heterotrophic/photosynthetic/both, have variable forms of movement, usually live in aquatic/other moist environment, reproduce sexually and asexually

  • eg - amoeba, kelps, algae

Fungi

  • eukaryotic, the cell wall is composed of chitin, most are multicellular, no not have chloroplasts

  • all are heterotrophic, most are terrestrial, and reproduce asexually and sexually

  • eg - mushrooms, yeast, molds

Plants

  • eukaryotic, all are multicellular, cell walls are composed of cellulose, and possess chloroplasts

  • autotrophic and photosynthetic, most are terrestrial, reproduce sexually and asexually

  • eg - mosses, ferns, conifers, flowering plants

Animals

  • eukaryotic, all are multicellular, cells do not have cell walls or chloroplasts

  • all are heterotrophic, most reproduce sexually, live in terrestrial and aquatic environments

  • eg - elephants, sponges, corals, insects, snails, birds, humans

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Domains of Life

<aside> ✨ Domains: the highest taxonomic level, there are three domains of life

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In 1996, Carl Woese revealed that all organisms could be classified into three domains with different genetic makeups

  • Domain Eubacteria → Kingdom Eubacteria

  • Domain Archaea → Kingdom Archaea

  • Domain Eukaryotes → Kingdom Protista, Animals, Plants, and Fungi


Ch 2.1 - The Prokaryotes: Eubacteria and Archaea

<aside> ✨ Domain Eubacteria and Archaea are prokaryotes, single-celled, and lack membrane0bound organelles

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Why Prokaryotes Are Important

<aside> ✨ Pathogen: a disease-causing agent, often a virus or micro-organism

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<aside> ✨ Mutualism: a relationship between two species that live in very close association with each other, whereby benefitting each other from the association

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<aside> ✨ Antibiotics: a substance that can kill/weaken micro-organisms, natural antibiotics are produced by bacteria/fungi, whereas synthetic antibiotics are manufactured

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Bacterial diseases: cholera, leprosy, typhoid fever, strep throat, salmonella, poisoning, and tuberculosis

Many bacteria (and some archaea) are decomposers and others are producer

  • recycle nutrients and are vital to biogeochemical cycles

  • fix/convert atmospheric nitrogen into compounds → photosynthetic bacteria are the major producers

  • humans rely on bacteria in the large intestine to produce needed vitamins K and B12 → mutualism

  • essential to the production of cheese, yogurt, soy sauce, and chocolate

  • bacteria also produced antibiotics → destroy and inhibit the growth of other micro-organisms

  • modified to produce medically valuable compounds - insulin and human growth hormone


Domain Eubacteria

Proteobacteria (Purple bacteria)

  • some used a different form of photosynthesis

  • ancient forms of the bacteria were the likely ancestors of eukaryotic mitochondria

  • some are nitrogen fixing

  • responsible for the bubonic plague, gonorrhea, dysentery, and some ulcers

Green Bacteria

  • use a form of photosynthesis that differs from other eukaryotes

  • usually found in salt-water environments/hot springs

Cyanobacteria (Blue-green algae)

  • uses a form of photosynthesis similar to plants and other eukaryotes

  • ancient forms of these bacteria were the likely ancestors of eukaryotic chloroplasts

  • play a major role as producers and nitrogen fixers in aquatic ecosystems

  • form a symbiotic relationship with fungi

Gram-positive bacteria

  • cause many diseases such as anthrax, strep throat, bacterial pneumonia, and meningitis

  • used in food products such as yogurt and probiotic products with lactobacillus

  • some lost their cell walls

Spirochetes

  • their spiral-shaped flagellum is embedded in their cytoplasm

  • move with a corkscrew motion

  • cause syphilis

  • symbiotic spirochetes in termite intestines digest wood fiber

Chlamydias

  • all are parasites that live within other cells

  • cause chlamydia, an STI

  • cause trachoma, the leading cause of blindness

Characteristics

<aside> ✨ Plasmid: a small loop of DNA often found in prokaryotic cells, usually containing a small number of genes

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<aside> ✨ Capsule: an outer layer on some bacteria that provide some protection for the cell

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<aside> ✨ Bacterium shapes: Coccus (sphere), Bacillus (rod), Spirillum (spiral)

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<aside> ✨ Bacterium groupings: Mono (one), Diplo (two), Strepto (in a chain), Staphylo (cluster)

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  • chromosome is a single loop of DNA (deoxyribonucleic acid) found in the nucleoid

  • ribosomes used in protein synthesis are scattered throughout the cytoplasm

  • have one/more flagella for movements and pili → pili are made of stiff proteins that help the cell attach to other cells/surface

  • have one/more plasmid in the cytoplasm → a small loop of DNA that carries a small number of genes → not essential to the function but give antibiotic resistance

  • have complex cell walls composed primarily of peptidoglycan → the cell wall become strong and rigid when the chains cross-linked

  • some have a sticky capsule → reduce water loss, resists high temperatures and helps keep out antibiotics and viruses

Metabolism

<aside> ✨ Inorganic chemical: a chemical that as an abiotic origin, some simple substances that are produced by organisms are also inorganic

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<aside> ✨ Organic chemical: any chemical that contains carbon and is produced by a living thing (except CO2)

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<aside> ✨ Obligate aerobe: an organism that can’t survive without oxygen

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<aside> ✨ Facultative aerobe: an organism that can live with/without oxygen

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<aside> ✨ Fermentation: an anaerobic process that releases chemical energy from food

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<aside> ✨ Obligated anaerobe: an organism that can’t survive in the presence of oxygen

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Autotrophic bacteria make their own food → assemble complex C molecules from simple inorganic chemicals (eg. H2O, CO2, and minerals)

Heterotrophic bacteria get their nutrients from C containing organic chemicals found in other living organisms/their remains

The primary sources of energy for living things are sunlight and chemical

  • organic molecule - sugar, fats, proteins

  • inorganic molecule - H2, sulfur, and iron compounds

Obligated aerobes - animals and plants → need oxygen obtained by respiration to get energy from food

Facultative aerobes → perform aerobic respiration in the presence of oxygen and anaerobic respiration/anaerobic fermentation when oxygen is absent

Obligated anaerobes → can’t live in an environment where oxygen is present

Reproduction

<aside> ✨ Binary fission: the division of one parent cell into two genetically identical daughter cells, a form of asexual reproduction

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<aside> ✨ Conjugation: a form of sexual reproduction in which two cells join to exchange genetic information

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<aside> ✨ Transformation: a process in which a bacterial cell takes in and uses pieces of DNA from its environment

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<aside> ✨ Horizontal gene transfer/lateral gene transfer: any process in which one species gets DNA from a different species

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<aside> ✨ Endospore: a dormant structure that forms inside certain bacteria in response to stress, protects the cell’s chromosomes from damage

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Binary Fission

  • produce two daughter cells with identical genetic material (chromosomes and plasmids)

  • cell elongates and DNA is replicated → cell wall and plasma membrane begins to divide → cross-wall forms completely around divided DNA → cell elongates

  • copying begin error result in mutation/changes in the genetic makeup → increase the genetic diversity

Conjugation

  • a bacterial cell passes a copy of a plasmid to the nearby cell through a hollow pillus → may benefit the nearby cell

  • considered sexual reproduction

Horizontal gene transfer

  • transformation occurs when a cell picks up a loose fragment of DNA from its surroundings and uses it → DNA fragment came from a different species

Some bacteria produce a highly resistant structure that forms around the chromosome called an endospore

  • withstand extreme conditions and remain dormant until conditions improve

Bacterial Diseases

some infectious bacteria can cause diseases by producing and releasing toxins

  • botulism food poisoning - toxin released by Clostridium botulinum → cause muscle paralysis

  • severe food poisoning - the releasing of toxin after E. coli cells die → water contamination (a case of horizontal gene transfer)

Antibiotics and Antibiotic Resistance

Antibiotic substances are produced by prokaryotes and fungi as a form of chemical warfare

Overuse of antibiotics can cause bacteria to adapt and become resistant

  • resistant bacteria is most likely to survive and reproduce when exposed to antibiotics → resistant bacteria make up more of the population → bacteria become more resistant and make the antibiotics ineffective

Gram Stain

most bacterial cell walls contain peptidoglycan

  • a polymer composed of modified sugars cross-linked by short polypeptides

  • archaeal cell walls contain polysaccharides and proteins but no peptidoglycan

→ Gram Stain test can classify bacterial species as Gram-positive and Gram-negative

Gram +

Gram -

positive result in the test

negative result in the test

take up crystal violet stain

alcohol degrades cell wall allowing crystal violet stain to wash away

look purple under the microscope

take up the counter stain and appear pink

have thick peptidoglycan layer that retains the stain

thin peptidoglycan layer

more receptive to antibiotics

less receptive due to outer membrane


Domain Archaea

  • have unique chemical makeup in their cell membranes and walls and lack peptidoglycan

  • many inhibits extreme environments as the cell membranes and cell walls are more resistant to physical and chemical disruption

Methanogens

  • live in low-oxygen environment such as sediments of swamps and lakes, digestive tracks

  • generate energy by converting chemical compounds into methane gas which is released into the atmosphere

Halophiles

  • salt-loving organisms that can live in highly saline environment such as the Dead Sea

  • most are aerobic and get organic food molecules

  • some uses light as a secondary energy source

Extreme thermophiles

  • live in extremely hot environments including hot springs and hydrothermal vents

  • optimal temperature range for growth is 70 - 95C

Psychrophiles

  • cold-loving organisms found mostly in the Antarctic and Artic oceans

  • optimal temperature range for growth is -10 to -20C


Ch 2.2 - Viruses, Viroids, and Prions

Viruses

<aside> ✨ Virus: a small infectious particle containing genetic material in the form of DNA/RNA within a protein capsule

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<aside> ✨ Capsid: a protein coat that surrounds the DNA/RNA of a virus

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<aside> ✨ RNA (ribonucleic acid): a nucleic acid found in all cells and some viruses, usually carries genetic information that provides instruction for synthesizing protein

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  • small, non-living particles

  • consists of genetic materials surrounded by a capsid made of protein

  • do not have cytoplasm

  • can’t grow/reproduce on their own

  • don’t produce/use energy

  • don’t create waste

  • contain DNA/RNA that carry information that provides instructions for synthesizing protein molecules

  • infectious and are passed from cell to cell → control the cell of the host cell

Why viruses are important

<aside> ✨ Epidemic: a large a large-scale outbreak of disease, usually confined to a limit geographic region

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<aside> ✨ Pandemic: an epidemic that occurs over a widespread geographic area, often globally

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Viral diseases include

  • mild symptoms: common cold, chicken pox

  • serious/deadly symptoms: AIDs, cholera, rabies

  • easy transmission: influenza virus

DNA virus

  • hepadnavirus → hepatitis B

  • herpesvirus → cold sores, genital herpes, chicken pox

  • adenovirus → respiratory infections, tumors

RNA virus

  • paramyxovirus → measles, mumps, pneumonia, polio, common cold

  • retrovirus → HIV/AIDS

  • rhabdovirus → rabies

Classification and Phylogeny

<aside> ✨ Bacteriophage: a virus that infects bacteria

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  • classified into orders, families, genera, and species

  • most can infect only one singular host species/closely related host → might infect only one organ system/single tissue/cell type

  • eg.1 Human Immunodeficiency Virus (HIV) - only infect certain immune system cells

  • some can infect many species → rabies can infect all mammals and birds

  • bacteriophage → inject DNA into the bacterium while the protein capsule remains outside

Origin and Characteristics of Viruses

  • originated as small infectious cells and lost their cytoplasm and ability to reproduce outside a living cell over time

  • suspected that viruses originated as “escaped” fragments of DNA/RNA molecules

  • all consist of an RNA/DNA molecule surrounded by a capsid, and some are surrounded by an envelope→ envelop is created when a virus leaves a host cell and part of the host cell membrane wraps around the virus

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Infectious Cycle

<aside> ✨ Lysis: the rupturing of a cell, can occur when newly made viruses are released from a host cell

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<aside> ✨ Lysogeny: a state of dormancy in which viral DNA may remain within a host cell’s chromosome for many cell cycle generations

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<aside> ✨ Transduction: a type of gene transfer in which a virus transfer DNA from one bacterium to another

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Lytic Cycle

  1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm

  2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle

  3. the viral DNA constructs the cell to make and assemble new viral DNA and capsids

  4. lysis occurs as the host cell bursts

Lysogenic Cycle

  1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm

  2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle

  3. the viral DNA gets inserted into the bacterial chromosomes

  4. the viral DNA has replicated along with the bacterial DNA every time the cell divides

  5. the viral DNA separates from the bacterial chromosome when activated

  6. the viral DNA constructs the cell to make and assemble new viral DNA and capsids

  7. lysis occurs as the host cell bursts

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Vaccination and Human Health

Vaccines are mixtures that contain weakened forms/part of a virus → trigger a response by the immune system without causing infection after injecting into the body → creates a chemical “memory” that allows the immune system to react quickly if the individual comes in contact with the real virus

→ reduce human suffering and save lives

→ some diseases like AIDS is not suitable for developing effective vaccines → structure and characteristics of the infection/constant changes that makes it ineffective the next year

Putting viruses to work

<aside> ✨ Gene therapy: a method of treating diseases in which genes are introduced into cells to replace, supplement/repair a defective gene

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  • using a virus capsule to deliver a drug → used to deliver drugs to targeted cells in the body - eg. deliver chemotherapy drugs to cancer cells

  • using a virus to insert a new copy of a gene → used to insert corrective genes into individuals who suffer from genetic disorders

  • using a virus to insert a gene taken from one species into another species → used to create genetically modified organisms, used in GMO crops


Viroids and Prion

<aside> ✨ Viroid: a small infectious piece of DNA responsible for diseases in plants

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<aside> ✨ Prion: an abnormally shaped infectious protein responsible for some brain diseases of mammals

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Viroids

  • small, infectious pieces of RNA

  • smaller than viruses and do not have a capsid

  • RNA does not code for protein

  • plant pathogens

  • may interfere with the normal formation and functioning of RNA within the host cell

Prions

  • proteinaceous infectious particles

  • found in the brain and nervous tissues of an infected animal

  • enter the bloodstream and go to the brain → interact with normally shaped protein → cause those proteins to change the shape and become abnormal and infectious → brain full of spongy holes


Ch 2.3 - Protists

Most are aquatic but are terrestrial


Why Protists are Important

Protists perform photosynthesis along with some prokaryotes → major producers in the world’s ocean

  • non-photosynthetic protists are important consumers

Many protists are parasites → do not harm host organisms, but can cause serious diseases

  • eg.1 - Plasmodium (single-celled protist) - causes malaria

  • eg.2 - sleeping sickness and amoebic dysentery

  • eg.3 - Giardia lamblia (intestinal parasite of humans) - causes giardiasis → causes abdominal pain, diarrhea, and chronic inflammation of the gut


The Origins of Eukaryotes

<aside> ✨ endosymbiosis: a relationship in which a single-celled organism lives within the cell of another organism

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protists were the first eukaryotes → have nucleus and organelles bound by membranes

  • developed from the folded cell membrane of ancestral prokaryotes → increase cell surface area allowing a better exchange of materials

Mitochondria and chloroplasts are thought to have originated from endosymbiosis → once a prokaryotic organism that was engulfed by an early anaerobic eukaryotic cell

  • each has two membranes

  • inner membranes are similar to those of the ancestral prokaryote, and outer membranes match the cell membranes of eukaryotes

  • have their internal chromosomes similar to prokaryote chromosomes and contain genetic information used by the organelles

  • reproduce independently within eukaryotic cells by binary fission

→ mitochondria were believed to be aerobic prokaryotes relating to modern proteobacteria

→ chloroplasts were believed to be photosynthetic prokaryotes relating to modern cyanobacteria


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Characteristics

  • eg.1 - Heterotrophic paramecia

  • macronuclei → control the metabolism and are responsible for the normal functioning of cells

  • micronuclei → responsible for controlling reproduction, genetic reorganization during conjugation, and production of macronuclei

  • contractile vacuoles → contract to eliminate excess water

  • gullet → taking in food

  • cilia → moving

  • trichocysis → release long fibers for defense

Euglenoids - photosynthetic autotrophs

  • unicellular

  • two flagella for moving

  • outer surface covering consist of stiff proteins

Cilliates - heterotrophs

  • unicellular

  • complex internal structures

  • have cillia for movement but no cell walls

Apicomplexa - heterotrophs

  • unicellular

  • no cell wall

  • parasites

Diatoms - photosynthetic autotrophs

  • unicellular

  • move by gliding

  • covered by glass-like silica shells

Amoebas - heterotrophs

  • have hard outer skeletons

  • move by extensions of the cytoplasm called pseudopods

Slime Molds - heterotrophic decomposers

  • have unicellular and multicellular stages

  • move with flagella/pseudopods

Red algae - photosynthetic

  • almost all are multicellular

  • no cilia/flagella

  • cell walls are made of cellulose


Interactions in Ecosystems

Protists play key roles are producers/consumers

  • eg.1 - green, red, and brown algae (seaweeds) - gas-filled bladder help produce energy through photosynthesis → primary producers in aquatic food webs

Climate change is affecting many protists

  • eg.1 - the rising temperature in oceans and lakes, and water is becoming acidic → affect protists’ ability to produce outer protective shells and the increase in some species → may not survive → may damage the food chain

  • eg.2 - the zooxanthellae lose their green chlorophyll pigment when the corals are stressed by pollution/warm temperature → coral appears bleach white → die


Life Cycle

<aside> ✨ Haploid: cell containing half the usual complement of chromosomes (n)

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<aside> ✨ Diploid: cell containing two copies of each chromosome (2n)

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<aside> ✨ Zygote: cell formed by the fusion of two sex cells, diploid (2n)

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Single-celled protists reproduce asexually and sexually

  • asexual: binary fission - cell divides into two genetically identical daughter cells → macronucleus elongates and divides → all organelles are divided equally between the daughter cells

  • sexual: conjugation - cells align and exchange genetic materials (some involve the exchange of special micronuclei)

  • sexual: formation of zygote - the haploid sex cells fuses together

<aside> ✨ Sporophyte: a diploid organism that produces haploid spores in an alternation of generation life cycle

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<aside> ✨ Spore: a haploid reproductive structure, usually a single cell. capable of growing into a new individuals

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<aside> ✨ Gametophyte: a haploid organism that produces haploid sex cells in an alternation of generation life cycle

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<aside> ✨ Alternation of generations: a life cycle which diploid individuals produce spores that create haploid individuals, the haploid individuals reproduce sexually, producing sporophyte individuals and completing the cycle

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  1. Diploid sporophytes produce and release single-celled haploid spores

  2. find and attach to a surface and begin dividing and growing into multicellular haploid gametophytes

  3. produce haploid sperm and eggs

  4. becomes a diploid zygote and grows into a multicellular sporophyte

→ asexual and sexual reproduction are needed to complete a full cycle of alternation of generation

  • eg.1 - hydra - can reproduce through sexual reproduction or diploid reproduction with buds that resemble the original adult

  1. Plasmodium zygote pass through the gut wall and develop into oocysts that produce many haploid sporozoites by meiosis

  2. injected into the blood which will be carried to the liver

  3. sporozoites reproduce asexually in liver cells containing merozoites

  4. merozoites enter the blood stream and invade red blood cells, reproducing asexually → ROC die and release merozoites → cause chills and fever

  5. some merozoites in RBC develop into immature male and female gamete cells which are released into the bloodstream

  6. female mosquito ingest blood from an infected human and the gamete matures in the mosquito’s gut, and then fuse to form zygote


Ch 3.2 - Plants

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

What is a Species?

Species: all organisms capable of breeding freely with each other under natural conditions

Hybridization: the cross-breeding of two different species

Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics

A species is a group whose members can freely breed among themselves under natural conditions → biological species concept

Species are defined based on a set of physical characteristics/morphology


Variation over Time and Space

Evolutionary change: a change that occurs in an entire population, usually occurs over a long period


Biodiversity

Genetic diversity: the genetic variability among organisms, usually referring to individuals of the same species

Species vary in their behavior, habitats, ecological niches, and abundance

  • genetically diverse


Diversity in Ecosystem

Heterotroph: an organism that obtains nutrients by consuming living / dead organisms

Autotroph: an organism that uses sources of energy to produce nutrients from the water, gases, and/or minerals

Species diversity: a measure of diversity that takes into account the quantity of each species present, as well as the variety of different species present

Structural diversity: the range of physical shapes and sizes within a habitat/ecosystem

Diversity of Interactions

The important activities and processes of one species may depend entirely on another species for success → contribute to the stability and productivity of their ecosystem

Diversity is influenced by the total number of individuals present in an ecosystem

→ ecosystem with many large populations is considered more diverse

Diversity of Habitats

The range of physical sizes, shapes, and distribution of individuals, as well as habitats and communities in an ecosystem → structural disversity

Unit I - Biodiversity 

Ch 1.1 -Biodiversity - an introduction

What is a species

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

Species: all organisms capable of breeding freely with each other under natural conditions

Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics

Evolutionary change: a change that occurs in an entire population, usually occurs over a long period

A species is defined as a group whose members can freely breed among themselves under natural conditions → biological species concept

Species are defined based on a set of physical characteristics/morphology when the traditional species definition does not apply

Physical and behavioral changes that occur in the entire population of a species are referred to as evolutionary change


Biodiversity

Genetic diversity: the genetic variability among organisms, usually referring to the individual of the same species

Different species vary in behaviors, habitats, ecological niches and abundance, and genetic makeup as well


Diversity in Ecology

Heterotroph: an organism that obtains energy by consuming living/dead organisms

</aside>

<aside> ✨ Autotroph: an organism that uses sources of energy to produce nutrients from the water, gases, and/or minerals

</aside>

<aside> ✨ Species diversity: a measure of diversity that takes into account the quantity of each species present, as well as the variety of different species present

</aside>

<aside> ✨ Structural diversity: the range of physical shapes and sizes within a habitat/ecosystem

</aside>

Diversity is influenced by the total number of individuals present in an ecosystem → ecosystem with many large populations is considered more diverse

The range of physical sizes, shapes, and distribution of the individual, as well as habitats and communities in an ecosystem is referred to as structural diversity

→ greater structural diversity can support a greater diversity of species as it has a great biodiversity

Food supply - between species and their food

  • eg.1 - boneworms feed exclusively on bones of dead whales

  • eg.2 - the photosynthetic micro-organism performs photosynthesis and supplies the coral animals and clams with a steady supply of food

Protection - for shelter and protection

  • eg.1 - hermit crabs use the shells of dead snails for a protective home

  • eg.2 - Cecropia trees provide shelter for a certain species of ants, and the ants protect the tree by biting and stinging herbivores

Transportation - move from place to place with the help of another species

  • some flower mites climb onto the bills of hummingbirds moving from flower to flower

  • many seed have hooks that allow them to stick to passing animals → carried long distances before they fall off and begin growing

Reproduction - depends on other species for their own successful reproduction

  • trilliums produce seed with fleshy tissues that attack ants and dispersed on them

  • many bird species build their nests in the abandoned tree cavities made by woodpeckers on their own nests

Hygiene - help maintain the health of another species

  • coral reefs have “cleaning stations” where large fish come to have external parasites removed by small fish and shrimp

  • the bacteria that lives on our skin protect us from other bacterial and fungal infections

Digestion - living within digestive tracts are essential for food digestion

  • a variety of bacteria and other micro-organisms lives within the termites’ guts to digest the wood

  • bacteria living in the large intestines of humans produce vitamins that are absorbed into the circulatory system


Biodiversity at risk

loss of biodiversity affects humans:

  • threatens food supply when entire species and plant varieties are lost

  • eliminates sources of natural medicines and potential new medicines

  • has a significant economic impact on tourism and forestry when accompanied by habitat destruction

  • has the potential to cause serious disruptions in biogeochemical cycles such as the carbon cycle

A change in climate may make conditions too hot/cold, too wet/dry for species adapted to the original climatic conditions

Human actions result in a rapid loss of natural habitats due to agriculture, forestry, urban expansion, the introduction of invasive species, over-harvesting of wild populations and serious water and air pollution

  • production of greenhouse gases → human-caused climate change


Ch 1.2 - The Nature of Classification

<aside> ✨ Biological classification: the systematic grouping of organisms into biological categories based on physical and evolutionary relationships, include producers, herbivores, carnivores, and scavengers

</aside>

Taxonomy - Developing a Classification System

<aside> ✨ Taxonomy: the science of classifying all organisms, classify both living and fossil species

</aside>

Observing the morphology, behavior and even geographic location can be used to identify organisms

→ similarity in form, or evolutionary change challenges this way of identification


Early Biological Classification Systems

<aside> ✨ Botanist: specializing in the study of plants

</aside>

Carl Linnaeus

<aside> ✨ Genus: a taxonomic level consisting of group of similar species

</aside>

<aside> ✨ ********************************************************************************************************************************************************************************************Binomial nomenclature: the formal system of naming species whereby each species is assigned a genus name followed by a specific name

</aside>

Before Carl Linnaeus, it was common for species to be given one/more long descriptive names → Carl Linnaeus assign a binomial short name using binomial nomenclature

Traditional Taxonomic Levels

<aside> ✨ Taxon: a category used to classify organisms

</aside>

<aside> ✨ Kingdom: the highest taxonomic level of the traditional Linnaean system of classification

</aside>

<aside> ✨ Species → Genus → Family → Order → Class → Phylum → Kingdom

</aside>

<aside> ✨ Each level of a taxonomic level → Taxon

</aside>


Dichotomous Key

<aside> ✨ Dichotomous key: a series of branching, two-part statements used to identify organisms

</aside>

A dichotomous key is a structure in which a large set of items is broken down into smaller subsets → leading to the smallest available classification unit

  • provides an easy method of identifying a species


Ch 1.3 - Phylogeny and Modern Taxonomy

<aside> ✨ Evolution: the scientific theory that describes changes in species over time and their shared ancestry

</aside>

The theory of evolution states that all living things are descended from a common ancestor

Taxonomy - the classification, identification, and naming of organisms - aims to group organisms according to how closely related they are to each other


Phylogeny

<aside> ✨ Phylogeny: the study of the evolutionary relatedness between, and among, species

</aside>

<aside> ✨ Phylogenetic tree: a diagram depicting the evolutionary relationships between different species/groups

</aside>

<aside> ✨ Clade: a taxonomic group that includes a single common ancestor and all its descendants

</aside>

Phylogeny is the science that deals with evolutionary relationships between and among species → tracks relationships between entire species presented in a phylogenetic tree

A clade is a taxonomic group that includes a single ancestor species and all its descendants

  • the tips of a branch on a phylogenetic tree can represent a particular species/an entire group of species


Taxonomy Today

Phylogenetic analysis can uncover the evolutionary relatedness of organisms → group into different-sized clades



Ch 1.4 - Kingdoms and Domains

<aside> ✨ Prokaryote: a single-celled organism that does not contain membrane-bound organelles

</aside>

<aside> ✨ Eukaryote: any organism whose cells contain organelles, some are single-celled while others are multicellular

</aside>

<aside> ✨ Protist: organisms that contain a nucleus and other organelles but show a diversity of shapes, sizes, and life cycles

</aside>


Kingdom of Life

Kingdoms - Animals, Plants, and Fungi, Eubacteria, (eukaryotic) Protists\

Eubacteria

  • prokaryotic, cell walls contain peptidoglycan + unique compounds, and vary in shape and size

  • can be photosynthetic, chemotrophic/heterotrophic, can reproduce asexually

  • eg - Escherichia coli, Salmonella, Nitrogen-fixing bacteria

Archaea

  • prokaryotic, cell walls and cell membranes contain peptidoglycan and have a unique structure, most are extremely small

  • some are extremophiles, live in the digestive tracks of mammals and marine environments, and all can reproduce asexually

  • eg - extreme thermophiles, methanogens

Protista

  • eukaryotic, cells have extreme diversity of cellular structure, some have chloroplasts and cell walls

  • may be heterotrophic/photosynthetic/both, have variable forms of movement, usually live in aquatic/other moist environment, reproduce sexually and asexually

  • eg - amoeba, kelps, algae

Fungi

  • eukaryotic, the cell wall is composed of chitin, most are multicellular, no not have chloroplasts

  • all are heterotrophic, most are terrestrial, and reproduce asexually and sexually

  • eg - mushrooms, yeast, molds

Plants

  • eukaryotic, all are multicellular, cell walls are composed of cellulose, and possess chloroplasts

  • autotrophic and photosynthetic, most are terrestrial, reproduce sexually and asexually

  • eg - mosses, ferns, conifers, flowering plants

Animals

  • eukaryotic, all are multicellular, cells do not have cell walls or chloroplasts

  • all are heterotrophic, most reproduce sexually, live in terrestrial and aquatic environments

  • eg - elephants, sponges, corals, insects, snails, birds, humans

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Domains of Life

<aside> ✨ Domains: the highest taxonomic level, there are three domains of life

</aside>

In 1996, Carl Woese revealed that all organisms could be classified into three domains with different genetic makeups

  • Domain Eubacteria → Kingdom Eubacteria

  • Domain Archaea → Kingdom Archaea

  • Domain Eukaryotes → Kingdom Protista, Animals, Plants, and Fungi


Ch 2.1 - The Prokaryotes: Eubacteria and Archaea

<aside> ✨ Domain Eubacteria and Archaea are prokaryotes, single-celled, and lack membrane0bound organelles

</aside>


Why Prokaryotes Are Important

<aside> ✨ Pathogen: a disease-causing agent, often a virus or micro-organism

</aside>

<aside> ✨ Mutualism: a relationship between two species that live in very close association with each other, whereby benefitting each other from the association

</aside>

<aside> ✨ Antibiotics: a substance that can kill/weaken micro-organisms, natural antibiotics are produced by bacteria/fungi, whereas synthetic antibiotics are manufactured

</aside>

Bacterial diseases: cholera, leprosy, typhoid fever, strep throat, salmonella, poisoning, and tuberculosis

Many bacteria (and some archaea) are decomposers and others are producer

  • recycle nutrients and are vital to biogeochemical cycles

  • fix/convert atmospheric nitrogen into compounds → photosynthetic bacteria are the major producers

  • humans rely on bacteria in the large intestine to produce needed vitamins K and B12 → mutualism

  • essential to the production of cheese, yogurt, soy sauce, and chocolate

  • bacteria also produced antibiotics → destroy and inhibit the growth of other micro-organisms

  • modified to produce medically valuable compounds - insulin and human growth hormone


Domain Eubacteria

Proteobacteria (Purple bacteria)

  • some used a different form of photosynthesis

  • ancient forms of the bacteria were the likely ancestors of eukaryotic mitochondria

  • some are nitrogen fixing

  • responsible for the bubonic plague, gonorrhea, dysentery, and some ulcers

Green Bacteria

  • use a form of photosynthesis that differs from other eukaryotes

  • usually found in salt-water environments/hot springs

Cyanobacteria (Blue-green algae)

  • uses a form of photosynthesis similar to plants and other eukaryotes

  • ancient forms of these bacteria were the likely ancestors of eukaryotic chloroplasts

  • play a major role as producers and nitrogen fixers in aquatic ecosystems

  • form a symbiotic relationship with fungi

Gram-positive bacteria

  • cause many diseases such as anthrax, strep throat, bacterial pneumonia, and meningitis

  • used in food products such as yogurt and probiotic products with lactobacillus

  • some lost their cell walls

Spirochetes

  • their spiral-shaped flagellum is embedded in their cytoplasm

  • move with a corkscrew motion

  • cause syphilis

  • symbiotic spirochetes in termite intestines digest wood fiber

Chlamydias

  • all are parasites that live within other cells

  • cause chlamydia, an STI

  • cause trachoma, the leading cause of blindness

Characteristics

<aside> ✨ Plasmid: a small loop of DNA often found in prokaryotic cells, usually containing a small number of genes

</aside>

<aside> ✨ Capsule: an outer layer on some bacteria that provide some protection for the cell

</aside>

<aside> ✨ Bacterium shapes: Coccus (sphere), Bacillus (rod), Spirillum (spiral)

</aside>

<aside> ✨ Bacterium groupings: Mono (one), Diplo (two), Strepto (in a chain), Staphylo (cluster)

</aside>

  • chromosome is a single loop of DNA (deoxyribonucleic acid) found in the nucleoid

  • ribosomes used in protein synthesis are scattered throughout the cytoplasm

  • have one/more flagella for movements and pili → pili are made of stiff proteins that help the cell attach to other cells/surface

  • have one/more plasmid in the cytoplasm → a small loop of DNA that carries a small number of genes → not essential to the function but give antibiotic resistance

  • have complex cell walls composed primarily of peptidoglycan → the cell wall become strong and rigid when the chains cross-linked

  • some have a sticky capsule → reduce water loss, resists high temperatures and helps keep out antibiotics and viruses

Metabolism

<aside> ✨ Inorganic chemical: a chemical that as an abiotic origin, some simple substances that are produced by organisms are also inorganic

</aside>

<aside> ✨ Organic chemical: any chemical that contains carbon and is produced by a living thing (except CO2)

</aside>

<aside> ✨ Obligate aerobe: an organism that can’t survive without oxygen

</aside>

<aside> ✨ Facultative aerobe: an organism that can live with/without oxygen

</aside>

<aside> ✨ Fermentation: an anaerobic process that releases chemical energy from food

</aside>

<aside> ✨ Obligated anaerobe: an organism that can’t survive in the presence of oxygen

</aside>

Autotrophic bacteria make their own food → assemble complex C molecules from simple inorganic chemicals (eg. H2O, CO2, and minerals)

Heterotrophic bacteria get their nutrients from C containing organic chemicals found in other living organisms/their remains

The primary sources of energy for living things are sunlight and chemical

  • organic molecule - sugar, fats, proteins

  • inorganic molecule - H2, sulfur, and iron compounds

Obligated aerobes - animals and plants → need oxygen obtained by respiration to get energy from food

Facultative aerobes → perform aerobic respiration in the presence of oxygen and anaerobic respiration/anaerobic fermentation when oxygen is absent

Obligated anaerobes → can’t live in an environment where oxygen is present

Reproduction

<aside> ✨ Binary fission: the division of one parent cell into two genetically identical daughter cells, a form of asexual reproduction

</aside>

<aside> ✨ Conjugation: a form of sexual reproduction in which two cells join to exchange genetic information

</aside>

<aside> ✨ Transformation: a process in which a bacterial cell takes in and uses pieces of DNA from its environment

</aside>

<aside> ✨ Horizontal gene transfer/lateral gene transfer: any process in which one species gets DNA from a different species

</aside>

<aside> ✨ Endospore: a dormant structure that forms inside certain bacteria in response to stress, protects the cell’s chromosomes from damage

</aside>

Binary Fission

  • produce two daughter cells with identical genetic material (chromosomes and plasmids)

  • cell elongates and DNA is replicated → cell wall and plasma membrane begins to divide → cross-wall forms completely around divided DNA → cell elongates

  • copying begin error result in mutation/changes in the genetic makeup → increase the genetic diversity

Conjugation

  • a bacterial cell passes a copy of a plasmid to the nearby cell through a hollow pillus → may benefit the nearby cell

  • considered sexual reproduction

Horizontal gene transfer

  • transformation occurs when a cell picks up a loose fragment of DNA from its surroundings and uses it → DNA fragment came from a different species

Some bacteria produce a highly resistant structure that forms around the chromosome called an endospore

  • withstand extreme conditions and remain dormant until conditions improve

Bacterial Diseases

some infectious bacteria can cause diseases by producing and releasing toxins

  • botulism food poisoning - toxin released by Clostridium botulinum → cause muscle paralysis

  • severe food poisoning - the releasing of toxin after E. coli cells die → water contamination (a case of horizontal gene transfer)

Antibiotics and Antibiotic Resistance

Antibiotic substances are produced by prokaryotes and fungi as a form of chemical warfare

Overuse of antibiotics can cause bacteria to adapt and become resistant

  • resistant bacteria is most likely to survive and reproduce when exposed to antibiotics → resistant bacteria make up more of the population → bacteria become more resistant and make the antibiotics ineffective

Gram Stain

most bacterial cell walls contain peptidoglycan

  • a polymer composed of modified sugars cross-linked by short polypeptides

  • archaeal cell walls contain polysaccharides and proteins but no peptidoglycan

→ Gram Stain test can classify bacterial species as Gram-positive and Gram-negative

Gram +

Gram -

positive result in the test

negative result in the test

take up crystal violet stain

alcohol degrades cell wall allowing crystal violet stain to wash away

look purple under the microscope

take up the counter stain and appear pink

have thick peptidoglycan layer that retains the stain

thin peptidoglycan layer

more receptive to antibiotics

less receptive due to outer membrane


Domain Archaea

  • have unique chemical makeup in their cell membranes and walls and lack peptidoglycan

  • many inhibits extreme environments as the cell membranes and cell walls are more resistant to physical and chemical disruption

Methanogens

  • live in low-oxygen environment such as sediments of swamps and lakes, digestive tracks

  • generate energy by converting chemical compounds into methane gas which is released into the atmosphere

Halophiles

  • salt-loving organisms that can live in highly saline environment such as the Dead Sea

  • most are aerobic and get organic food molecules

  • some uses light as a secondary energy source

Extreme thermophiles

  • live in extremely hot environments including hot springs and hydrothermal vents

  • optimal temperature range for growth is 70 - 95C

Psychrophiles

  • cold-loving organisms found mostly in the Antarctic and Artic oceans

  • optimal temperature range for growth is -10 to -20C


Ch 2.2 - Viruses, Viroids, and Prions

Viruses

<aside> ✨ Virus: a small infectious particle containing genetic material in the form of DNA/RNA within a protein capsule

</aside>

<aside> ✨ Capsid: a protein coat that surrounds the DNA/RNA of a virus

</aside>

<aside> ✨ RNA (ribonucleic acid): a nucleic acid found in all cells and some viruses, usually carries genetic information that provides instruction for synthesizing protein

</aside>

  • small, non-living particles

  • consists of genetic materials surrounded by a capsid made of protein

  • do not have cytoplasm

  • can’t grow/reproduce on their own

  • don’t produce/use energy

  • don’t create waste

  • contain DNA/RNA that carry information that provides instructions for synthesizing protein molecules

  • infectious and are passed from cell to cell → control the cell of the host cell

Why viruses are important

<aside> ✨ Epidemic: a large a large-scale outbreak of disease, usually confined to a limit geographic region

</aside>

<aside> ✨ Pandemic: an epidemic that occurs over a widespread geographic area, often globally

</aside>

Viral diseases include

  • mild symptoms: common cold, chicken pox

  • serious/deadly symptoms: AIDs, cholera, rabies

  • easy transmission: influenza virus

DNA virus

  • hepadnavirus → hepatitis B

  • herpesvirus → cold sores, genital herpes, chicken pox

  • adenovirus → respiratory infections, tumors

RNA virus

  • paramyxovirus → measles, mumps, pneumonia, polio, common cold

  • retrovirus → HIV/AIDS

  • rhabdovirus → rabies

Classification and Phylogeny

<aside> ✨ Bacteriophage: a virus that infects bacteria

</aside>

  • classified into orders, families, genera, and species

  • most can infect only one singular host species/closely related host → might infect only one organ system/single tissue/cell type

  • eg.1 Human Immunodeficiency Virus (HIV) - only infect certain immune system cells

  • some can infect many species → rabies can infect all mammals and birds

  • bacteriophage → inject DNA into the bacterium while the protein capsule remains outside

Origin and Characteristics of Viruses

  • originated as small infectious cells and lost their cytoplasm and ability to reproduce outside a living cell over time

  • suspected that viruses originated as “escaped” fragments of DNA/RNA molecules

  • all consist of an RNA/DNA molecule surrounded by a capsid, and some are surrounded by an envelope→ envelop is created when a virus leaves a host cell and part of the host cell membrane wraps around the virus

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Infectious Cycle

<aside> ✨ Lysis: the rupturing of a cell, can occur when newly made viruses are released from a host cell

</aside>

<aside> ✨ Lysogeny: a state of dormancy in which viral DNA may remain within a host cell’s chromosome for many cell cycle generations

</aside>

<aside> ✨ Transduction: a type of gene transfer in which a virus transfer DNA from one bacterium to another

</aside>

Lytic Cycle

  1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm

  2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle

  3. the viral DNA constructs the cell to make and assemble new viral DNA and capsids

  4. lysis occurs as the host cell bursts

Lysogenic Cycle

  1. the virus binds to the surface of the host cell and inserts its DNA into the cell’s cytoplasm

  2. the viral DNA forms a loop and may enter the lysogenic/lytic cycle

  3. the viral DNA gets inserted into the bacterial chromosomes

  4. the viral DNA has replicated along with the bacterial DNA every time the cell divides

  5. the viral DNA separates from the bacterial chromosome when activated

  6. the viral DNA constructs the cell to make and assemble new viral DNA and capsids

  7. lysis occurs as the host cell bursts

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Vaccination and Human Health

Vaccines are mixtures that contain weakened forms/part of a virus → trigger a response by the immune system without causing infection after injecting into the body → creates a chemical “memory” that allows the immune system to react quickly if the individual comes in contact with the real virus

→ reduce human suffering and save lives

→ some diseases like AIDS is not suitable for developing effective vaccines → structure and characteristics of the infection/constant changes that makes it ineffective the next year

Putting viruses to work

<aside> ✨ Gene therapy: a method of treating diseases in which genes are introduced into cells to replace, supplement/repair a defective gene

</aside>

  • using a virus capsule to deliver a drug → used to deliver drugs to targeted cells in the body - eg. deliver chemotherapy drugs to cancer cells

  • using a virus to insert a new copy of a gene → used to insert corrective genes into individuals who suffer from genetic disorders

  • using a virus to insert a gene taken from one species into another species → used to create genetically modified organisms, used in GMO crops


Viroids and Prion

<aside> ✨ Viroid: a small infectious piece of DNA responsible for diseases in plants

</aside>

<aside> ✨ Prion: an abnormally shaped infectious protein responsible for some brain diseases of mammals

</aside>

Viroids

  • small, infectious pieces of RNA

  • smaller than viruses and do not have a capsid

  • RNA does not code for protein

  • plant pathogens

  • may interfere with the normal formation and functioning of RNA within the host cell

Prions

  • proteinaceous infectious particles

  • found in the brain and nervous tissues of an infected animal

  • enter the bloodstream and go to the brain → interact with normally shaped protein → cause those proteins to change the shape and become abnormal and infectious → brain full of spongy holes


Ch 2.3 - Protists

Most are aquatic but are terrestrial


Why Protists are Important

Protists perform photosynthesis along with some prokaryotes → major producers in the world’s ocean

  • non-photosynthetic protists are important consumers

Many protists are parasites → do not harm host organisms, but can cause serious diseases

  • eg.1 - Plasmodium (single-celled protist) - causes malaria

  • eg.2 - sleeping sickness and amoebic dysentery

  • eg.3 - Giardia lamblia (intestinal parasite of humans) - causes giardiasis → causes abdominal pain, diarrhea, and chronic inflammation of the gut


The Origins of Eukaryotes

<aside> ✨ endosymbiosis: a relationship in which a single-celled organism lives within the cell of another organism

</aside>

protists were the first eukaryotes → have nucleus and organelles bound by membranes

  • developed from the folded cell membrane of ancestral prokaryotes → increase cell surface area allowing a better exchange of materials

Mitochondria and chloroplasts are thought to have originated from endosymbiosis → once a prokaryotic organism that was engulfed by an early anaerobic eukaryotic cell

  • each has two membranes

  • inner membranes are similar to those of the ancestral prokaryote, and outer membranes match the cell membranes of eukaryotes

  • have their internal chromosomes similar to prokaryote chromosomes and contain genetic information used by the organelles

  • reproduce independently within eukaryotic cells by binary fission

→ mitochondria were believed to be aerobic prokaryotes relating to modern proteobacteria

→ chloroplasts were believed to be photosynthetic prokaryotes relating to modern cyanobacteria


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Characteristics

  • eg.1 - Heterotrophic paramecia

  • macronuclei → control the metabolism and are responsible for the normal functioning of cells

  • micronuclei → responsible for controlling reproduction, genetic reorganization during conjugation, and production of macronuclei

  • contractile vacuoles → contract to eliminate excess water

  • gullet → taking in food

  • cilia → moving

  • trichocysis → release long fibers for defense

Euglenoids - photosynthetic autotrophs

  • unicellular

  • two flagella for moving

  • outer surface covering consist of stiff proteins

Cilliates - heterotrophs

  • unicellular

  • complex internal structures

  • have cillia for movement but no cell walls

Apicomplexa - heterotrophs

  • unicellular

  • no cell wall

  • parasites

Diatoms - photosynthetic autotrophs

  • unicellular

  • move by gliding

  • covered by glass-like silica shells

Amoebas - heterotrophs

  • have hard outer skeletons

  • move by extensions of the cytoplasm called pseudopods

Slime Molds - heterotrophic decomposers

  • have unicellular and multicellular stages

  • move with flagella/pseudopods

Red algae - photosynthetic

  • almost all are multicellular

  • no cilia/flagella

  • cell walls are made of cellulose


Interactions in Ecosystems

Protists play key roles are producers/consumers

  • eg.1 - green, red, and brown algae (seaweeds) - gas-filled bladder help produce energy through photosynthesis → primary producers in aquatic food webs

Climate change is affecting many protists

  • eg.1 - the rising temperature in oceans and lakes, and water is becoming acidic → affect protists’ ability to produce outer protective shells and the increase in some species → may not survive → may damage the food chain

  • eg.2 - the zooxanthellae lose their green chlorophyll pigment when the corals are stressed by pollution/warm temperature → coral appears bleach white → die


Life Cycle

<aside> ✨ Haploid: cell containing half the usual complement of chromosomes (n)

</aside>

<aside> ✨ Diploid: cell containing two copies of each chromosome (2n)

</aside>

<aside> ✨ Zygote: cell formed by the fusion of two sex cells, diploid (2n)

</aside>

Single-celled protists reproduce asexually and sexually

  • asexual: binary fission - cell divides into two genetically identical daughter cells → macronucleus elongates and divides → all organelles are divided equally between the daughter cells

  • sexual: conjugation - cells align and exchange genetic materials (some involve the exchange of special micronuclei)

  • sexual: formation of zygote - the haploid sex cells fuses together

<aside> ✨ Sporophyte: a diploid organism that produces haploid spores in an alternation of generation life cycle

</aside>

<aside> ✨ Spore: a haploid reproductive structure, usually a single cell. capable of growing into a new individuals

</aside>

<aside> ✨ Gametophyte: a haploid organism that produces haploid sex cells in an alternation of generation life cycle

</aside>

<aside> ✨ Alternation of generations: a life cycle which diploid individuals produce spores that create haploid individuals, the haploid individuals reproduce sexually, producing sporophyte individuals and completing the cycle

</aside>

  1. Diploid sporophytes produce and release single-celled haploid spores

  2. find and attach to a surface and begin dividing and growing into multicellular haploid gametophytes

  3. produce haploid sperm and eggs

  4. becomes a diploid zygote and grows into a multicellular sporophyte

→ asexual and sexual reproduction are needed to complete a full cycle of alternation of generation

  • eg.1 - hydra - can reproduce through sexual reproduction or diploid reproduction with buds that resemble the original adult

  1. Plasmodium zygote pass through the gut wall and develop into oocysts that produce many haploid sporozoites by meiosis

  2. injected into the blood which will be carried to the liver

  3. sporozoites reproduce asexually in liver cells containing merozoites

  4. merozoites enter the blood stream and invade red blood cells, reproducing asexually → ROC die and release merozoites → cause chills and fever

  5. some merozoites in RBC develop into immature male and female gamete cells which are released into the bloodstream

  6. female mosquito ingest blood from an infected human and the gamete matures in the mosquito’s gut, and then fuse to form zygote


Ch 3.2 - Plants

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

What is a Species?

Species: all organisms capable of breeding freely with each other under natural conditions

Hybridization: the cross-breeding of two different species

Morphology: the physical appearance and characteristics of an organism, the science of the study of these physical characteristics

A species is a group whose members can freely breed among themselves under natural conditions → biological species concept

Species are defined based on a set of physical characteristics/morphology


Variation over Time and Space

Evolutionary change: a change that occurs in an entire population, usually occurs over a long period


Biodiversity

Genetic diversity: the genetic variability among organisms, usually referring to individuals of the same species

Species vary in their behavior, habitats, ecological niches, and abundance

  • genetically diverse


Diversity in Ecosystem

Heterotroph: an organism that obtains nutrients by consuming living / dead organisms

Autotroph: an organism that uses sources of energy to produce nutrients from the water, gases, and/or minerals

Species diversity: a measure of diversity that takes into account the quantity of each species present, as well as the variety of different species present

Structural diversity: the range of physical shapes and sizes within a habitat/ecosystem

Diversity of Interactions

The important activities and processes of one species may depend entirely on another species for success → contribute to the stability and productivity of their ecosystem

Diversity is influenced by the total number of individuals present in an ecosystem

→ ecosystem with many large populations is considered more diverse

Diversity of Habitats

The range of physical sizes, shapes, and distribution of individuals, as well as habitats and communities in an ecosystem → structural disversity