Monday February 22 – Viruses (17-1) Thursday February 25 – Kingdom Monera Part 1 (17-2) Friday February 26 – Microscopes
Week 2
Monday February 29 – Kingdom Monera Part 2 (17-2) Tuesday March 1 – Kingdom Protista Introduction (18-1) Wednesday March 2 – Kingdom Protista cont’d (18-2; 18-3) Thursday March 3 – Kingdom Protista – Animal-like Protists (18-2) Friday March 4 – Kingdom Protista – Animal-like Protists (cont’d) VIRUS/BACTERIA/PROTIST QUIZ
Week 3
Monday March 7 – Kingdom Protista – Plant-like Protists (18-3) Tuesday March 8 – Kingdom Protista – Fungi-like Protists (18-3) Wednesday March 9 – Study day Thursday March 10 – Unit Test Friday March 11 – Gallery Walk
Explain how structure, function, environment and cost-benefit are related (Game)
Explain the current theory on how Protists evolved from Monerans
Identify and Label the generic Protist structure
Identify the structure and functions of Paramecium parts
Describe reproduction of Paramecium
Compare and contrast the Protist Phyla
Provide examples of Protist Phyla
Kingdom Protista is a group created by exclusion. Historically, taxonomists and biologists alike had much trouble classifying these organisms. The reason for this difficulty is that members of Kingdom Protista have characteristics not unlike Animalia, Plantae or Fungi. Unlike the other four kingdoms (Animalia, Plantae, Fungi and Monera), which are relatively clear cut, members in Kingdom Protista are very diverse and share little in common. Lynn Mangulis, the scientist who came up with the endosymbiont hypothesis, wrote that the Kingdom Protista
“is defined by exclusion: its members are neither animals…, plants…, fungi …, nor prokaryotes.”
Perhaps a more scientifically sound definition: “unicellular (single-celled) organisms that are eukaryotic”. As you will recall from our taxonomy unit, Prokaryotes are organisms without a nucleus or membrane-bound organelles, and Eukaryotes are organisms with a nucleus and membrane bound organelles. (Ribosomes are organelles, but are not membrane-bound)
Therefore, a protist is simply a unicellular organism with:
Nucleus containing DNA
Membrane bound organelles
Which about sums up all that these organisms have in common.
But where did these organisms come from? Where did they evolve from?
Several observations seemed to provide some clues as to how it happened.
Mitochondria and Chloroplasts, organelles that exist in eukaryotic cells, have their own DNA. The DNA is completely separate from the DNA of the eukaryotic cell itself.
Some Protists have organelles that can be removed, without ill effect on the Protist. Some of these organelles can even grow on their own!
Some of the Eukaryotic cell’s organelles are structurally, very similar to Prokaryotes
Noticing these characteristics, Lynn Margulis proposed the Endosymbiont Hypothesis. The hypothesis states that organelles are actually descended from prokaryotes that lived inside another prokaryote in a symbiotic relationship. Each benefited the other. For example, a blue-green bacteria that lived in a bigger moneran had shelter, while the bacteria provided the host cell with sugars and nutrients. At some point, the blue-green bacteria may have lost their independence, and became the precursors to the organelles we see today.
A creative way of explaining Endosymbiosis.
Paramecium sp.(Phyla: Ciliophora)
Paramecium is a model organism for protists. Like most model organisms, it has been studied extensively and is easily cultivated (grown). However, a model organism is not necessarily representative of the group it comes from. Just as a lab rat is not necessarily representative of all mammals, or even all rodents, so we should not assume that Paramecium is a perfect representation of Protists.
Movement |Paramecium sp. is classed in Phylum Ciliophora, a protist phylum characterized by cilia.
Feeding | Paramecium sp. feeds on small organisms, such as bacteria. The cilia first sweep the food toward the oral groove, a small opening where food is trapped. The oral groove leads to the gullet, which produces food vacuoles, a small sac where food is stored. the food vacuole then contacts lysosomes, organelles containing digestive enzymes. These digestive enzymes then break down the food, and the wastes are expelled from the anal pore.
Water Balance | Paramecium sp. live in freshwater environments. Because the Paramecium sp. has a higher solute concentration than the freshwater around it, water tends to move inside the cell. Therefore, excess water must be expelled from the Paramecium sp. from the cytoplasm to the contractile vacuole.
Reproduction | Paramecium sp. is able to reproduce via binary fission (asexual reproduction). The micronuclei are duplicated, and the macronucleus is split apart. The split occurs lengthwise, like pulling silly putty apart. During conjugation, however, two paramecium arrange side by side and exchange genetic information.
No new daughter cells result from conjugation, therefore it is not a form of reproduction. However, the exchange in genetic information does lead to an increase in genetic diversity amongst the population. An increase in genetic diversity leads to more diverse traits, and having more traits means there’s a greater chance that at least a few of the cells may have the correct traits to survive, even thrive, in the environment.
Therefore, asexual reproduction occurs more often in stable, unchanging environments. Under these conditions, because Paramecium sp. are likely to survive and thrive, energy is better invested in increasing population numbers. However, all offspring will be genetically identical. Conjugation occurs more often in unstable, changing environments that are stressful. Even if Paramecium sp. numbers increase, because the genetic diversity is low, there is less likely to be individuals that have the gene combination to help them survive in the environment. therefore, it is much more beneficial for Paramecium sp. to invest their energy in conjugation, where gene combinations are reshuffled.
(Binary Fission)
(Conjugation)
Kingdom Protista Phyla
We cover nine Protist phyla in this course: 4 animal like, 3 plant like and 2 fungi like.
Animal-like Protists (Heterotrophic)
Plant-like Protists (Autotrophic)
Fungi-like Protists (Heterotrophic)
Ciliophora
Zoomastigina
Sporozoa
Sarcodina
Euglenophyta
Pyrrophyta
Chrysophyta
Acrasiomycota
Myxomycota
Phyla
Picture
Distinguishing Characteristics
Examples
Ciliophora
“Ciliates”
(“Cilia-bearer”)
Animal like protist with cilia
Paramecium sp.
Stentor sp.
Vorticella sp.
Zoomastigina
“Zooflagellates”
Animal like protist with flagella
Trypanosoma
Trichonympha
Sporozoa
Non-motile, spore producing animal like protist
Plasmodium
Sarcodina
Pseudopods
Some produce silicon shells (SiO2)
Ameba
Heliozoans
Foraminifers
Radiolarians
Euglenophyta
Flagellum
Chloroplasts and red eyespot
Structurally similar to zoomastiginan
Phototrophic Heterotrophs
Euglena sp.
Pyrrophyta
Dinoflagellates
(“fire-plant”)
2 flagellum, one wrapped around like a belt.
Thick plates, armored appearance
Named for bioluminescence in some members of this phyla.
Gonyaulax polyhedron (Red tide)
Chrysophyta
(“golden plant)
Beautiful silicon shells
Cell walls made out of pectin
Stores food as oil rather than starch to stay afloat.
Diatoms
Acrasiomycota
Cellular Slime Molds
Lives part of life as amoeba
Individuals aggregate (group together) into one mass and migrate when food runs low.
Produces fruiting bodies that spread spores.
Myxomycota
Acellular slime molds
Life part of life as amoeba.
Produces plasmodiums, a large single celled, multinucleate mass that may stretch a few centimeters.
Compound microscopes are a basic tool of biology. They are standard for a number of fields, including health care, research, toxicology, and many many more.
They are also just really cool in general.
Parts of a Microscope
Ocular Lens – has a power of 10x
Objective Lens(es) – a set of lenses with three or four different powers
Low power (4 x)
Med power (10 x)
High power (40 x)
Stage – where the slides are placed
Diaphragm – a dial that can be turned to control the amount of light coming through
Coarse focus knob – shifts the height of the stage to help focus. As the name suggests, the coarse adjustment knob shifts the stage faster and should be handled with caution
Fine focus knob – shifts the height of the stage to help focus, but very very slightly.
Light
Total Power
The total magnifying power of a microscope is calculated like this:
Ocular Lens Power x Objective Lens Power = Total Lens Power
In the case of our microscopes, the magnifying power of the ocular lens is 10x. The magnifying power of the objective lens vary (4 x, 10 x, 40 x).
Therefore, the total magnifying power at all levels is:
Low 10 x 4 = 40 x
Med 10 x 10 = 100 x
High 10 x 40 = 400 x
Creating a Wet Mount
Obtain a clean slide and coverslip (be very careful when handling these as both are glass)
Put your specimen flat onto the slide.
Put a drop of water onto your specimen
Put the coverslip on. Make sure to put it down at a 45 degree angle. This pushes out the air to reduce air bubble formation
If there is too much water on your slide, gently dab away with a paper towel.
Calculating size of specimen based on the field of view
Suppose you saw this flea under your microscope. How could you figure out how large it really is? One critical piece of information is just how wide is the field of view?
When we are looking at low power, the field of view will be wider than if we are looking at high power, since we are now focused on a smaller area.
At Low Power, the field of view is about 4.2 mm, or 4200 um (1 mm = 1000 um)
At Med Power, the field of view is about 4.2 mm, or 1680 um (1 mm = 1000 um)
At High Power, the field of view is about 4.2 mm, or 420 um (1 mm = 1000 um)
So how do we calculate the field of view? Suppose we were looking at the cells above at medium power and I was trying to figure out how big the cell is.
I know that the diameter of the field of view is 1680 um. And I estimate that about 6 cells fit across the diameter.
Therefore
1680 um / 6 = 280 um
This means that the cells are about 280 um across.
Identify and label structures of a generic Moneran
Identify and Describe the four criteria through which Moneran are classified
Describe the ways in which Moneran obtain/metabolize energy
Describe the three ways Moneran reproduce
Kingdom Monera is a large, diverse and wholly under-appreciated group of organisms. They perform many critical functions in the ecosystem, such as detritivores. They are used in the food industry for production of foods, such as milk or cheese. They are also responsible for many human diseases, such as the black plague that destroyed a third of the European population in the 14th century.
Members of this kingdom are also called bacteria.
Generally, bacteria all share some common features.
Structure of generic Monera
All Monera are unicellular and prokaryotic
No nucleus. DNA or RNA and ribosomes floating in cytoplasm.
Cell membrane made of lipids
Cell wall made of peptidoglycan to protect cell
Flagellum (plural: flagella) to move
Ways to classify a Moneran
Because of their small size, bacteria are very hard to observe under the microscope. Even when their individual shape or form can be seen, many look far too alike to definitively classify. Thankfully, we do have ways to classify Monera.
Shape – Almost all Monera fit into one of three shapes: round and spherical (cocci), long and rod shaped (bacilli) and spiral shaped (spirilla). Cells can also be classified based on their clustering behavior. Some cluster into colonies and strings, while others are primarily solitary.
Gram stains – because bacteria are for the most part, transparent to the naked eye, they must be stained to be properly observed under the microscope. When Hans Christian Gram, a Danish bacteriologist was staining bacteria with crystal violet, he realized that some bacteria retained the stains and became purple, while some did not and became pink. As it turns out, this has to do with the thickness and structure of the peptidoglycan cell wall. Generally, a thicker cell wall will retain more of the crystal violet, while thin ones will not.
Bacteria movement – some bacteria have flagella, whip like projections, that allow them to move. Some bacteria secrete slime to move along like a slug. Still others don’t move at all.
DNA/RNA Sequencing – the most specific way to identify a bacteria is probably through DNA/RNA sequencing. We do so by identifying the genes of the bacteria, which is probably fairly specific to each species. This method has become more common in recent years as the cost of genome sequencing decreases.
Ways Moneran get their energy
It should be noted that the following terms describe where organisms (any organism, not just bacteria) get their energy from.
Phototrophic Autotroph: organisms that derive their energy from the sun
Chemotrophic Autotroph: organisms that derive their energy from inorganic chemicals (chemicals that are not derived from living things)
Chemotrophic Heterotroph: (aka heterotrophs) are organisms that derive their energy from organic chemicals (chemicals that are derived from living things)
Phototrophic Heterotroph: are organisms that derive their energy from organic chemicals or the sun, depending on which source is available
————- (End of Thursday, February 25) ——————-
Ways Monerans Metabolize their energy
Depending on whether the Moneran uses one or both of the following
1. Cellular Respiration – a series of chemical reactions that uses sugars and oxygen to produce energy.
2. Fermentation – a series of chemical reactions that converts sugars to acids, gases or alcohol, and produces energy. It occurs without oxygen.
we classify monerans as follows.
Obligate Aerobes: Monerans that need oxygen in order to produce energy (aerobic respiration). These Monerans mainly use cellular respiration.
Obligate Anaerobes: Monerans that will die in the presence of oxygen, as oxygen is toxic to these monerans. These Monerans mainly use fermentation.
Facultative Anaerobe: Monerans that can produce energy in oxygen (cellular respiration), but switch to fermentation if there is no oxygen.
Ways Monerans Reproduce
Binary fission – where the cell replicates its DNA, and splits into two daughter cells, where each daughter cell gets one set of DNA
Conjugation – the bacterial form of sexual reproduction. Involves the exchange of genetic information.
Spore Formation – strictly speaking, not a form of reproduction. Occurs when a bacterium produces a hard covering (spore) and becomes metabolically inactive to preserve itself in adverse environments.
https://www.youtube.com/watch?v=EtxkcSGU698
Bacteria Research Mini-Project – One page fact sheet on an assigned bacterium – DUE TUESDAY FEBRUARY 1st
Identify the structures of bacteriophages and retroviruses
Describe the life cycle of (1) Lytic and (2) Lysogenic viruses
Describe the body’s defence mechanisms against a viral/bacterial infection
What are Viruses?
Viruses are defined as “noncellular particles made up of genetic material and protein that can invade living cells”. They do not belong to any of the five kingdoms of organisms. It isn’t even clear whether viruses are living or non-living. While they do evolve in so much as only successful viruses can propagate their genetic information, they do not have cells, do not grow or reproduce, and do not use energy the way living things do. They also cannot live independently of cells, as they depend on cells to replicate.
Nevertheless, viruses are fascinating tiny machines of nature that have been used and studied for a variety of purposes, such as in genetic engineering, combatting cancer, and to destroy harmful bacteria in foods. Some viruses are also responsible for some of the most debilitating diseases known to man, including HIV (Human immunodeficiency virus) leading to AIDS, mono, shingles, herpes and chickenpox.
Identifying Viruses
Viruses come in many shapes, sizes and life cycles. There are two specific groups of viruses we will focus on here.
Bacteriophages
Retroviruses
Bacteriophages have a distinct shape and structure.
There are two distinct parts: a head and a tail. The head is composed of a protein capsid or coat. It contains the DNA information. The tail and fibers at the base are used to attach the virus to bacteria, where it can then inject its genetic information into the cell.
Retroviruses are named for their ability to insert their genetic material into the existing genetic information of the host cell.
Normally DNA is “transcripted” to RNA (nucleic acid made of a single chain of nucleotides, in contrast to two strands in DNA). However, the genetic information in retroviruses are made up of RNA.
When the RNA enters the host cell, enzymes attach the piece of RNA to the DNA of the cell. Complementary nucleotides then attach to the RNA, making it double stranded and indistinguishable from host cell genome.
Just like the head of bacteriophages, made of a protein capsid coat with genetic information inside, retroviruses a protein capsid with RNA. However, they are also surrounded by a lipid membrane (membrane envelope) and often antigens.
Antigens are structures on the outside of the virus, toxins or proteins. The antigens act like the face of a virus, which can be recognized by the body and targeted by the body.
DNA Replication
DNA do not techninically reproduce the way living organisms do. However, they do invade host cells, causing them to create more copies of viruses. There are two ways that this happens.
Lytic Cycle
Lysogenic Cycle
Virus attaches to host cell
DNA information is injected into the cell
Cell reads the virus’s genetic information (it cannot tell the difference between its own DNA and viral DNA)
Cell replicates viruses inside itself
Viruses become very numerous until the cell eventually bursts releases the viruses
NOTE: Bacteriophages can also replicate through the lysogenic cycle. Retroviruses almost always replicate through the lysozenic cyccle.
1, Virus attaches itself to host cell
2. DNA/RNA information is injected into the cell |
3. Virus Genetic information is incorporated into the host cell’s genetic information, where it remain dormant for many years.
4. As the cell goes through cellular respiration, each daughter cell will also contain virus genetic information
5. At some point, the viral genes are activated, and replication begins.
6. Again, the viruses become very numerous until the cell bursts.
Thankfully, the human body also has some ways of protecting ourselves against viruses, at different levels of specificity.
Primary Line of Defense:
These forms of defense are non-specific, as in, it is to protect against any form of pathogen, virus, bacterial, protist, etc.
– Skin
– Oil and Sweat
– Hairs and cilia in mouth and nose
– Stomach (acids)
– Saliva, sweat and tears (lysozyme)
Secondary Line of Defense:
These forms of defense are also non-specific, but are generally activated only when pathogens have invaded.
– Inflammatory response: white blood cells
– Fever
Tertiary Line of Defense
The most specific form of defense. These forms of defense are activated specifically to target the pathogen.
This is usually done through antibodies that are produced based on the antigens on the surface of the pathogen. The antibodies can then target the pathogens.
–Interferons : produced by cells to interfere with virus replication
– Antibody production: white blood cells produce antibodies
