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Eubacteria (true bacteria) Notes

True Bacteria Notes:

Part One: Unity and Diversity

 

Ways to classify bacteria

  • Shape and size
  • Gram positive and Gram negative
  • Metabolism (include respiration and food source)

A. Size and Shape

  • Bacteria were first described by Leeuwenhoek in 1677 after he had invented the compound microscope.

 

  • Bacteria range in size from about 1 to 10 um long by about 0.2 to 0.3 um across (1 um = .001 mm).

 

Most bacteria come in one of three different shapes:

 

(1) Rod shaped:                             Bacillus(i)     [filaments or single].

 

(2) Spherical shaped:                    Coccus(i)     [pairs, chains, groups or single].

 

(3) Spiral shaped:                         Spirillum(a)     [seldom in colonies]

 

Some bacteria tend to form groups:

 

Diplococci                                        are pairs of spherical shaped bacteria

 

Streptococci                                    are chains of spherical shaped bacteria

 

Staphylococci                                 are clusters of spherical shaped bacteria

B: Gram positive and Gram negative

The term gram positive or negative, refers to both a staining proccess and specific structure of bacterial cell membranes or wall. The gram staining method is one of the more important techniques in microbiology. Yet one has to realize that this technique is not 100 percent fool proof. Differences in results can be due to type of stains and age of bacteria.

 

  • The staining process follows the following protocal:
  1. Heat fix bacteria to slide
  2. Stain with purple dye (crystal violet), rinse with distilled water
  3. Stain with with iodine (marker), rinse with water
  4. Rinse with alchol wash, functions as a decolorization process in which negative lose colour.
  5. Stain with safranin (red stain) which is counter stain for gram negative

 

 

 

 

In regards to cell membrane structures:

  • Gram positive bacteria have cell walls composed of peptidoglycan (murein) and teichoic acid. ( basically a sugar based structure combined with amino acids)
  • Gram negative bacteria also have cell walls composed of a peptidoglycan ( in small amounts) but this layer is surrounded by a lipopolysaccharide outer membrane.

 

Comparison of Characteristic of Gram + and Gram –

Characteristic Gram Positive Gram Negative
Gram Reaction Stain dark violet or purple Stain pink
Ratio RNA to DNA 8:1 1:1
Nutritional requirements More complex Less complex
Susceptability to penicillin Marked Less marked
Susceptability to streptomycin and tetracycline Much less Marked
Susceptability to anionic detergents Marked Less marked
Resistance to sodium azide Marked Less marked

 

C: Metabolism and Nutrition

 

Cell Metabolism:

Nutrients are ingested and then:

  1. broken down by enzymes within cell
  2. further breakdown of material is done to produce energy
  • Energy is absorbed by biochemical ADP (adenine di phosphate)
  • Energy is released by biochemical ATP ( adenine tri phosphate)

 

Energy can be produced with or without oxygen

  1. Anearobic: are bacteria that do not need oxygen for cell metabolism

 

  1. Areorobic: are bacteria that require oxygen for cell metabolism

 

  1. Facualtative: are bacteria that can metabolize with or without oxygen

 

  • Obligate Aerobes are those which must have oxygen
  • Obligate Anaerobes are bacteria which cannot tolerate

 

There are many types of nutrition found among bacteria:

 

Autotrophic Nutrition:

 

  1. Some are photosynthetic (use sunlight energy to produce their own food)

.

  1. Some are chemosynthetic (oxidize inorganic compounds to obtain their

energy to produce their own food).

  • These organisms are known as Photoautotrophs and Chemoautotrophs in that they manufacture their own food.

 

Heterotrophic Nutrition.

They must obtain their energy and nutrients from other sources.

For example:

  • Saprophytic bacteria : digest materials in their environment by releasing   powerful digestive enzymes. They then absorb the digested nutrients.

 

  • Parasitic bacteria : rely on other organisms to provide the digested nutrients directly.

Part Two: Interactions

Bacteria can exist everywhere there is life this includes:

in the air

in the water

in the earth

on plants

in organism

  • without bacteria, we as humans could not exist
  • bacteria are the most primitive form of life because they:
  1. a) grow and reproduce ( as often as one time every 15 minutes)
  2. b) they use nutrients to survive
  3. c) they have simple cell structures
  • it is possible to see bacteria through a light or electron microscope
  • Bacteria are both helpful and harmful
  • To preserve or stop bacteria metabolism they can be:

chilled

dried out

frozen

heated

 

Dangerous bacteria are called pathogens because they cause diseases.

 

  • to control pathogenic bacteria you can remove bacteria by:

removing all bacteria using extreme heat

wash with antiseptic soaps

use antibiotics

specific immunization for specific bacteria proteins

 

  • Some bacteria can become resistant to antibodies by altering protein coat or structure of cell wall.

 

  • Bacteria can change into dormant forms called spores, which allow the bacteria to stop metabolism in extremely harsh environments

 

Useful Bacteria

Most bacteria are not pathogenic — include decomposers, nitrogen

fixing bacteria, vitamin producing bacteria, bacteria used to make

insulin and growth hormone, bacteria used in dry cleaning, tanning,

cheese, yogurt

 

Essential Bacteria:

Bacteria can be helpful because:

  • they help plants absorb nutrients from the soil ( specifically nitrogen)
  • they are used to make milk products such as yogurt, cheese and butter
  • they can be used to manufacture antibiotics
  • they can alter biproducts from sewage treatments into non toxic waste
  • they can be used to produce specific gases such as methane
  • they are used for fermentation

 

 

Escherichia coli                              Gram – rod shape   (bacilli)

Sarcina lutea                                    Gram + round shape (cocci)

Bacillus subtilis                               Gram + rod shape   (bacilli)

Bacillus cereus                                Gram + rod shape   (bacilli)

Serratia marcescens                      Gram – rod shape   (bacilli)

Rhodospirillum rubrum                 Gram – spiral shape (spirilla)

 

Harmful Bacteria

 

Harmful bacteria can cause disease (Pathogenic) by interfering with the host’s normal routine, by destroying cells and tissues, by producing endotoxins and exotoxins, and by eliciting an immune response.

  • An endotoxin is a toxin within the bacterium that is only released when the bacterium dies and it breaks down.
  • An exotoxin is a toxin released by living bacteria.

 

Koch’s Postulates: –

used to prove that an organism is responsible for a particular disease.

 

  1. must be shown that the organism in question is always present in

the diseased hosts.

 

  1. microbe must be isolated from the host and grown in a pure

culture.

 

  1. microbe from pure culture must be capable of producing the

disease symptoms in a new healthy host.

 

  1. microbes isolated from the newly infected host must be grown in a

pure culture and compared to the original micro-organism.

 

Examples:

 

  1. a) Respiratory Tract: Strep throat, Rheumatic fever, Scarlet fever;

Pneumonia, Whooping cough, Diphtheria,                                                                    Tuberculosis…

 

  1. b) Skin: Staph (pimples and boils), Leprosy, Gas gangrene…

 

  1. c) Nervous System: Tetanus, Botulism, Meningitis…

 

  1. d) Digestive System: Typhoid fever, Cholera, Dysentery; (food

poisoning) Salmonella, Botulism, Staph…

 

  1. e) Venereal Diseases: Gonorrhea, Syphilis…

 

Infection by bacteria

 

There are three lines of defence through which bacteria must

penetrate:

 

  1. a) through the strong epidermal tissue (skin).. .in wounds, pores,

openings.

  1. b) phagocytic white blood cells which engulf foreign materials including
  2. c) antibodies produced by other white blood cells.

 

Active Immunity

Is slow acting (because the body is taking time to produce antibodies against the infection); but long lasting (because the body produces “memory cells” which “remember” how to produce these specific antibodies again).

 

Normally produced by actual initial infection (chicken pox), or by using a vaccine (polio, smallpox). The vaccine consists of either weakened (attenuated) bacteria, dead bacteria, or artificial products which resemble the actual foreign invader ( biological antigen).

 

Passive Immunity

This is fast acting (because the person is injected with antiserum containing the necessary antibodies or antitoxin); but short-lived (because the person does not actually produce the antibodies – hence no memory cells for the future!). The protein antibodies are often provided from the blood of a larger animal such

as a horse! (Tetanus, Rabies). New techniques have been designed so that bacteria can produce specific antibodies. Newborns initially have Passive Immunity through the passage of antibodies across the placenta, and in the Mother’s milk. In some cases, injection of Toxoids stimulate the production of natural antitoxins.

 

Antibiotics a biological substance which will kill or slow (inhibit) the growth

of an organism.

e.g.                             Penicillin, Tetracycline, Bacitracin, Ampicillin,

Erythromycin…

 

  1. a) must be bacteria-specific.
  2. b) some people are allergic to certain antibiotics.
  3. c) some could kill off useful bacteria.
  4. d) may reduce the competitive pressure and allow

harmful bacteria to survive.

  1. e) may cause resistant strains to develop.

 

Other biocides include: Sulfur Drugs, antitoxins, various

bacteriocides, disinfectants…

 

Part Three: Changes with time

Reproduction

 

  1. Bacteria reproduce mostly asexually by a process called BinaryFission. In this method, the circular ring of DNA replicates, and then the cell divides into two daughter cells — each with its own DNA.

 

  1. Some bacteria can also undergo sexual reproduction by a process called Conjugation. In this method, the “male” is connected to the “female” by a tube called a Pilus. The DNA from the “male” then travels through the tube to the “female”. Here, it recombines with the “female” DNA and the “female” bacterium then divides.

 

  1. Some bacteria can be Transformed into a different cell by absorbing fragments of DNA of other cells. In another method of producing recombined bacterial DNA, bacteriophages (viruses) carry portions of the bacterial DNA from one cell to another. This process is called Transduction.

 

  1. When environmental conditions are not favourable, some bacteria are capable of forming highly resistant thick-walled Endospores until conditions once again return to normal.

Part Four Form and Function

Cell Structure: A bacteria cell has the following structures:

  • Nuclear material      in the form of DNA to pass on genetic information
  • Cell membrane:      which controls the flow of material in and out of a cell
  • Ribosome:                which assist in making cell proteins
  • Cell wall
  • Flagella
  • Endospores

 

Response to Stimulus:

 

Bacteria Lab Questions:

 

  1. Why must you always use sterile technique when working with

bacteria?

 

  1. What does “pathogenic” mean?

 

  1. What is an “inoculum”?

 

  1. List three general rules for handling bacteria.

 

  1. When is the Pour Plate Method of culturing bacteria used?

 

  1. Why must you be careful in regulating the temperature of the melted agar in the Pour Plate Method?

 

  1. In procedure 7 in each of the labs, why did you have to flame the mouths of the test tubes?

 

  1. What is the reason for using the streak plate method?

 

 

  1. What is the reason for using the Pour plate method?

 

 

Designing an experiment.

 

  • From these biological facts, could you design a lab to test a simple hypothesis?
  • After you have a simple hypothesis…design a simple lab that can be done in less than one week. It should include both quantitative and qualitative data.

 

 

 

 

 

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes,Microbio and have No Comments

Inquiry into Bacteria

Inquiry into Bacteria:

 

Topic One:    Myths and Monera

 

Prior to doing this assignment consider what comes to your mind when you hear or read the term bacteria?

 

Some questions you may want to consider while reading the text:

  • Where are bacteria found?
  • Are most bacteria harmful?
  • How are bacteria related to other organisms?
  • What is the difference between a prokaryote and eukaryote
  • How are the activities of life useful in examining how bacteria interact with other species?

 

Topic Two:    The problems of classification

 

Here is the first thing to consider:

  • What was the original system to classify organisms?
  • What properties or observations did this system use for classification?
  • Can these observations be used to classify microscopic organism?
  • What techniques could be used to establish observational criteria?
  • What are some limitations of classifying organism based upon structures?

 

 

Topic Three:             Metabolic Perspectives

Now we have gone molecular, so how can metabolic pathways provide a new way to classify organism?

 

           Consider the following

 

  • How do organism get or make their energy?
  • How do organisms feed themselves?
  • How is the environment related to metabolism?

 

 

Topic Four    Interactions with Humans

 

           Positive Interactions

 

  • What are the top ten positive interactions with bacteria?

 

 

           Negative Interactions

 

  • How is metabolism and structure related to negative interactions?
  • How are negative interactions prevented?

(from a macrobiotic to molecular perspectives)

 

 

Topic Five:    Playing with critters!

 

  • What is the criteria for sanitary technique?
  • How can metabolic activities be used make observations about bacteria?
  • What simple tests and ideas can we create?

Topic Six:      Creating a testable experiment!

  • You will be responsible for creating an experiment!

 

Refernces for all these questions can be found in:

Bacteria Notes

 

 

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes,Microbio and have No Comments

Biology 11 Top Ten Virus Question

Mr. C’s Top Ten Questions About Virus

 

Question One: Are Virus living things?

 

 

Non living Characteristics Living Characteristics
they do not respire they do have DNA or RNA
there is no cellular structure they do have proteins and enzymes
they do not grow they have the potential to make other cells make copies of themselves, this is more like duplication than reproduction
they can be crystallised due to harsh environments virus show diversity associated with the hosts they infect
they cannot reproduce on their own * this is a great table for a test question….

 

Question Two: What are virus and where did they come from?

 

  • Virus may be linked to the original entity of life as a noncellular ancestor of cells
  • Their means of existence may imply that they were once primitive organisms that loss cell structures in order to assist parasitic lifestyle.
  • The genetic material within a virus is only a fragment of an original genome.

 

Question Three:

What is the structure of a virus and how is it associated with its lifestyle.

  • Most virus are composed of a protein coat which surrounds a small fragment of DNA or RNA.
  • Most virus are only visible with electron microscopes ranging in size from .015 to .45 microns.
  • Some of the protein coats are specialised for the host that the virus infects.
  • The shape of the protein coat may vary from spherical shapes to bacteriophage which have additional structures to add attachment to host.
  • Shapes are usually spherical, rod shaped or tadpole shaped.

 

Question Four: How are virus classified?

  • Virus are classified by the host they infect
  • Plant virus: ( example tobacco mosaic virus)
  • Animal ( by class: Aves : Bird, Insecta: insects) virus
  • Bacteria virus or Bacterio phage

 

Question Five: How are virus transmitted?

  • In plants: virus can be transmitted from contact with insects, direct contact between plant seeds, leaves or stems.

 

  • In animals: virus can be transmitted from coughing, sneezing, talking, direct contact and insects.

 

Question Six: How do virus infect host

A general infection follows the following pattern.

  1. The virus comes in contact with host cell and attaches to host cell.
  2. Viral Protein coat is either removed after absorption by host or virus injects nucleic material into host.
  3. Viral DNA or RNA is replicated by the host cell.
  4. Replicated viral DNA or RNA is translated into proteins for viral enzymes and protein coat.
  5. New virus are assembled within host cell from replicated and translated material.
  6. Virus either remain in host or host cell breaks due to too many virus within cell.

 

Specialised infections:

Bacteriophage: Virus that infect bacteria

In this type of infection there is the possibility of two events

  1. a) A lytic cycle
  1. Virus attaches to host bacteria, an enzyme eats away the host’s cell wall and   viral nucleic material is injected into host
  2. Viral nucleic material is incorporated into host nucleic material
  3. Viral nucleic material begins to replicate and translate its code, this takes over the bacteria normal cellular functions.
  4. As many as 100 or more copies of the original virus are made by host bacteria
  5. The host bacteria burst and virus is release to the environment. The word lytic comes from the Latin which means to burst open

 

  1. b) A lysogenic cycle.

Much like the lytic cycle the host bacteria is infected by the virus, however lyses of the bacteria does not happen immediately. Bursting of the cell only occurs when the bacteria become weakened or there is a change in the environment.

 

 

Retrovirus Infections:

  • A retrovirus is a RNA virus which infects the host in a unique fashion.
  • The viral RNA serves as a template for the host cell to make a segment of DNA.
  • This DNA is then encoded into the host’s genetic material.
  • The cell does not die but changes due to the new encoded material.
  • The mechanisms of this type of infection are still being researched.

Question Seven: Are all infections the same?

The answer is no. There are at least three possible outcomes from an infection:

Results of viral infection can be:

  1. A virulent infection:
  • This is when the virus causes a lytic cycle and the host cell dies

 

  1. A latent infection:
  • This is when the virus either becomes part of host genome or remains dormant until changes in host cell and or external environment.

 

  1. Tumour producing infection:
  • This is when the host cell is not destroyed but mutated causing the host cell to divide and produce cluster of cells that have changed from the original cell. If these cells remain dormant they are said to be benign and show themselves as a wart or tumour), if these cells become mobile, they are said to be malignant.

 

Question Eight: What diseases are caused by viral infections?

  • Some common viral infections are:

viral pneumonia,            the common cold,   influenza,       mumps,         measles, German measles         polio                           shingles      chickenpox    smallpox, AIDS virus                       hepatitis                    warts              yellow fever   cold sores hoof and mouth disease      Ebstein Barr virus                mosiacs in plants

 

  • May be associated with some cancers, leukaemia’s, and autoimmune disorders
  • Some lethal viruses: Ebola (95% fatality rate)
  • Most publicised virus: HIV

 

 

Question Nine: Is there a way to treat or cure viral infections?

  • One of the first methods of preventing infection by virus was done by the Chinese, who rubbed other individuals with skin scabs from those individuals who survived a viral infection such as small pox.
  • Edward Jenner, created a process called vaccination ( from the Latin origin vaca for cow : another famous cow story!) by exposing individuals to cowpox virus, which he noted prevented them from being infected from a more virulent virus for small pox.
  • It is useless to treat a viral infection with antibiotics however people treated with a killed strain of virus or viral proteins may create their own antibodies to attack onto viral proteins.

 

Question Ten: How were virus discovered?

 

  • Discovery of virus were initially related to nature of infection of hosts
  • Actual viral material viral material was not purified until 1933 by Stanley. This particular material was crystallise tobacco mosaic.
  • Identification of viruses has improved with the increased efficiency of electron microscopes.
  • Because viral DNA/RNA interacts with host nucleic material, viruses are continue to change and evolve.

 

If you have any further questions you wish to explore

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes,Microbio,Microbio and have No Comments

Biology 11 DNA,Taxonomy and Evolution Review

Taxonomy, Evolution and DNA Review

DNA

1.   What are the building blocks of DNA?

2.   How is DNA similar and different from RNA?

3.   What is a “nucleotide”?

4.   How do nucleic acid base pairs match up?

5.   Which nucleic acid base is not found in DNA?

6.   What is the sequence of converting information from DNA to a protein?

 

The code of a strand of DNA can be “transcribed” and “translated”

7.   What does transcribe mean?

8.   How do you translate the DNA code?

9.   What is a “triplet”?

10.        What is a complementary strand?

11.        Can you translate a strand of mRNA given a table that includes mRNA triplets? (See worksheet)

 

Evolution

1.   What is the distinction between direct and indirect proof?

2.   How is convergent and divergent evolution linked to types of proof of evolution?

3.   How can fossils be linked both to gradual and punctuated rates of changes of evolution?

4.   What is a trait from Darwin or Lamarcks point of view?

5.   How are traits linked to populations and gene frequency?

6.   What is speciation and how is it linked to isolation mechanisms?

7.   What is  the significance of gentic drift, gene flow, and non random mating linked to evolution ( Clue please look at chapter on DNA and Evolution)

 

Chapter Three Quiz feedback

 

1)   Darwin verse Lamarack

·      Lamarack proposed a law of use and disuse

·      Lamarack proposed that a trait produced by use and disuse was an acquired characteristic

·      The example of the length of the giraffes neck  was used to show that the length got longer to access food.

·      The individual organism changes due environmental needs

 

 

In comparison

 

·      Darwin proposed that changes in living things was due to a process which he called natural selection

·      Like farmers select specific traits in agriculture, Darwin said that “Nature” was selecting the traits in living things in the wild. He referred to the selection by humans as call “Artificial selection” and the selection of traits by nature as “natural selection”.

·      Darwin used a two part premise to explain how nature selected a trait

·      His first “proof” was to show that there was some mechanism that was keeping populations from over populating. Using economist Malthus’s ideas, he proposed that populations do not over populate due to “a struggle for existence”. Put simply, population size was being affected by something.

·      His second “proof” was to state that within any population of species, there is a wide range of traits. He did not know the source of these traits but he did notice a diversity in traits. He noted that organisms with survived and were able to pass these traits on were those organism that had a trait that  was able to adapt to what was occurring in the natural environment. This idea of competition and survival of the fittest was similarly proposed by Wallace who spoke about traits allow species to compete and survive and then pass along traits.

·      Put simply, Darwin said that species do not over populate because there is something limiting that growth, The factor that seemed to limit growth was a Natural Selection of traits that allowed the species to survive and pass those traits onto the next generation. The key point is…nature..the environment is doing the selection.

 

Using the Galpagos Islands and Finches

 

So here is how the story should go…

 

A population of original finches arrives at a new location. In this case an island.

The island is able to support the population both with food, water, and habitat. So the population is able to survive, reproduce and grow. In addition, there are no predators to limit the growth of the population. So the population grows but does not over populate. So there must be a reason why.

 

Within this population is a diversity in shapes of beaks. Those birds with beaks that are able to eat the food on that island are more likely to survive. Nature is selecting a specific trait. Those who do not have that trait migrated. This introduces the idea of “gene flow” (yes..this is on the test!!!)..something Darwin did not know about.

 

Those birds who did not have the right beak shape for a specific island could fly to another island. Again..migration and gene flow. On the new island was a different habitat. The species which had a trait that allowed the species to survive and populate on the new island was now being selected by a natural source. Aha..natural selection!

 

What are the implications of this statement?

The reason why things change with time is governed by a mechanism in which nature is doing the selection. The organism that has the trait that allows it to adapt to a small change in the environment will pass that trait to the next  generation. Notice that two key words are being used: survive and adapt.

 

DNA and Darwin and Lamarck

 

The theory of Natural Selection was able to propose a feasible explanation as to how and why species change with time. It proposed that “nature” was selecting traits that improved the chance for survival and therefore reproduction.

 

The idea of a characteristic or a trait was a means to show an adaptation had occurred. The actual source of that adaptation was hidden until the mechanisms of how DNA was discovered.

 

Mutations are a change in the sequence of nucleic bases within DNA. Mutations can also occur due to missing or extra chromosomes or sequences of DNA changing. Put simply..the source of variation is within the code of DNA.

 

An example of a favoured mutation is the change in colour of English peppered Moths.  When the DNA, which mutated created a black pigmented Moth, the population of black moths increased when predators could not find the moth on dark, charcoal coated trees. When the soot in the air decreased due to cleaner burning of coal, the trees now could show their natural white colour. Those moths that had not adopted the changed DNA were able to now increase their population.

This change in expression of traits lead to a more definitive definition of evolution within biology in respect to a change in allele frequency within a population.

 

 

Evidence, mechanisms, rates of change and forming new species.

 

1.   If a population is isolated due to morphology, geography, behavior or ecology it is forming a new species due to an isolation mechanism. Notice that there is now a ..that in singular ..species being formed. So we notice that isolation mechanism is linked to the term speciation.

2.   If one species crosses the isolation mechansim, then a new species can be formed. If that product of reproduction is not able to reproduce, it is some times called a hybrid. A hybrid is something new due to mixing two species.

3.   Darwin proposed that Nature is selecting traits and this is what is going on to create new species. He did not come up with the term “adaptive radiation”.

4.   After the mechanism of how DNA works was discovered and explored, there was now a valid source to explain things like mutations and traits. It has been proposed  that a specific segment of DNA is responsible for making a specific protein. This segment has been called “a gene” and the theory is that for one gene there is a specific protein. Introducing this idea into evolution, now we can talk about Gene Flow, Gene Pool, Genetic Drift all linking to a change in populations due to the presence or lack of genetic material.

5.   The idea of a gene is now being challenged because it has been discovered that several pieces of DNA code may be involved in making a protein. It is also being proposed that expression of sequences of DNA can also be regulated. So..once again..the reason why things change with time is a theory and subject to scientific inquiry.

 

Rates of change

 

There are several examples where Darwin’s mechanism also showed a gradual change in time. This created a group of folks who proposed that things change gradually and the theory put forth was called Gradualism.

 

In 1972, a new theory was proposed to explain gaps in fossil records and quick changes in evolution. The idea was that a population quickly adapts to adapt and then reaches equilibrium. Think about cell phones and you get the idea real fast. One product sets the pace and others hurry to catch up. If you graph this rapid change you have a line with a large slope followed by a flat horizontal line where there is equilibrium.

 

Mention equilibrium and the physicist and chemist get all excited. Some physics folks suggested that energy within the system was being used up to a point where there was none left for those who could adapt. Chemist jumped for joy and started getting involved with metabolic rates, equilibrium constants and meanwhile, the biologist knew that all things are connected. Lets think of this as the Three Bear Theorem. Too hot, too cold and then..just right.

 

Now the question is…is anyone reading these notes. It is a dark and stormy afternoon in Vancouver. The heat has been turned off in my room. I am wearing a sweatshirt and hidden underneath it is  a snoopy t shirt that says “dazed and confused”. I am exhausted, cold and my head is full of phlegm. It is Friday and the class before me is taking a physics pre test. A population of fruit flies is now invading my room and some inspired student decided to  submerge an electric heating element in one of my fish tanks. Five fish gave their lives two days after remembrance day. Poppies do not grow in aquariums. As predicted, several students did not read my notes and so their quiz marks are less than stellar. If any one can remember what the t shirt I am wearing says, then I will give bonus marks on the next evaluation.

 

 

 

 

 

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posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes,Evolution and have No Comments

Bio 11 Darwin Top Ten Assignment

Mission Number One:

 

Go on line and find 10 unknown facts about Darwin.

 

Mission Number Two

 

From the following ten locations find the following:

 

  1. At least 8 definitions for evolutions

 

  1. A discussion of Lamarack verses Darwin

 

  1. A discussion comparing Wallace to Darwin

 

  1. A discussion on Darwin’s struggles and life

 

  1. A discussion on creationism verse Natural Selection

 

  1. A discussion able the pros and cons of Darwin’s theory

 

  1. A discussion about evolution of aquatics ecosystems and biomes

 

  1. A discussion on how evolution is used in the work place or as a job.

 

  1. 24 myths about evolution

 

  1. Criteria to be a human

 

 

 

http://www.nuffieldfoundation.org/science-society/weblinks-evolution

 

http://glencoe.mheducation.com/sites/0078675642/student_view0/unit5/chapter15/web_links.html

 

http://www.dynamicearth.co.uk/learning/earth-explored/evolution-extinction/web-links

 

http://biology.jbpub.com/hall/evolutionprinciples/web_links.aspx

 

http://www.ck12.org/biology/Theory-of-Evolution-by-Natural-Selection/web/Changes-in-the-Environment/

 

http://mygeologypage.ucdavis.edu/cowen/historyoflife/evolutionlinks.html

 

http://www.cengage.com/resource_uploads/static_resources/0495112860/16117/Ch13.html

 

http://humanorigins.si.edu/

 

http://www.nsta.org/evolution/

 

http://evolution.berkeley.edu/evolibrary/home.php

 

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes and have No Comments

Evolution of the Blank Project

Biology Eleven

Evolution Project: Evolution of the _________.

 

The purpose of this activity is to find an item within your life that you can examine and explore ideas related to the concept of evolution. For example; how has a particular toy changed since you were a child? How has the fashion of shoes changed? What about the evolution of “Barbie” or GI Joe? Has there been a change in sporting items such as: skis, snowboards; baseball gloves and golf clubs?

 

  • Part One: Selecting an item ( 4 marks)

Select an item within your life that you have been interested in since your were a child. This item can be a type of toy, a sporting item, an article of clothing or another category that you wish to present. Once you have selected an item, please consult with me and sign up to insure no duplication of projects.

 

What are you looking for?

  1. In reference to your item, find and provide evidence of a minimum of four stages of structural alterations that have occurred.
  2. Show these stages with a diagram, drawing or rich written description.

 

  • Part Two: Describing your item ( 8 marks)
  1. By observing and describing qualitative and quantitative observations of your item, describe how the features of your item have changed with time.
  2. Using the biological vocabulary listed in your vocabulary sheet, describe changes of your items in biological terminology.
  3. Cite evidence of items that may have been ancestors to your item.
  4. Make a family tree of your item
  5. On your family tree show possible convergence and divergence, and any other patterns of inheritance.

 

 

 

Part Three: Mechanisms of change and your item                           total:   (8 marks)

Describe mechanisms that caused the change

  1. Using Lamarack’s and Darwin’s ideas to explain why or how your item changed with time                   ( 4 marks).
  2. Use your family tree to describe and label possible mechanisms of change.

( 2 marks)

  1. Compare two other non-biological mechanisms or causes for changes of your items, ( For example: Consumerism, Media and advertising, Fads and economics). ( 2 marks)

 

Presentations of assignment:

You can present your information in one of the following choices:

  1. A web page ( on a disk or on line)
  2. A written report with diagrams ( in a duotang binder)
  3. A poster board with a written explanation of the content on the board.

 

  • You will be judged not on the amount of content but the quality of content. So please do not attempt to publish a book!
  • Content will be marked both on quality of presentation ( please type out material) and effort shown while working on project

 

  • Complete prior to consultation:
You first item choice second choice
Stages of development Stages of development
1. 1.
2. 2.
3. 3.
4. 4.
Possible ancestor Possible ancestor
Confirmation of consultation Confirmation of consultation

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes and have No Comments

Chapter 3 Nelson Review Questions Answers

Nelson Text Review Questions   : Chapter 3

 

  1. The modern view of evolution is based on scientific evidence which combines both genetic information and the theory of natural selection. It implies a change over time. Earlier beliefs were based on opinion and nonscientific evidence. This earlier view held that living things had been “fixed” since the beginning, and were unchangeable.

 

  1. The variety (adaptation) of beak types displayed by the islands’ finch species made the greatest impression on Darwin.

 

  1. Survival of the fittest means that individuals with traits best suited for and environment are better able to compete, survive, and reproduce. Adaptation is the basis through which natural selection can occur, with those individuals that are best adapted to particular environments becoming the most successful reproducers. The direction of evolution is determined by the adaptation.

 

 

  1. Lamarck offered and explanation for the mechanism of evolution – that species change over time, and that the environment is a factor n that change. He showed that evolution is adaptive and that the diversity of life is the result of adaptation (see pages 91- 93).

 

  1. Buffon’s theory indicated that the creation of a species did not occur in a single place at a single time and that a species was not created in a perfect state. Later he wondered if certain species might develop from a common ancestor. Darwin accepted Buffon’s ideas and went on to provide an explanation for the manner in which species change over time.

 

 

  1. Structural, physiological, and biochemical are the three types of adaptation.

 

  1. The moths adapted a color (pigmentation) change from light-colored to predominantly dark-colored (melanic) forms in response to the environmental changes caused by the industrial fumes of the mid-1800s.

 

Applying the Concepts

 

  1. The study of genetics has shown that acquired characteristics cannot be passed on to offspring, so Lamarck’s ideas have been proven incorrect.

 

  1. a) Lamarck would have suggested that the zebra wanted to avoid the annoying bite of the tsetse fly and developed the striped to do this.

 

 

  1. b) Darwin or Wallace would have suggested that some zebras were striped more than others. Tsetse flies bit those that had few stripes, or had pale stripes. These zebras got the parasite and died, and the striped zebras, which were bitten less frequently, reproduced and passed the stripes to their offspring.

 

  1. c) Answers can vary.

 

  1. Human activities can affect evolution by isolating populations of organisms in different areas. Small organisms are less likely to cross roads to find a mate, so the road can become an effective barrier. Bridges can bring two isolated populations together, stopping their speciation.

 

  1. Lamarck had recognized the impact of environmental factors on the course of evolution. He recognized that the mechanism for evolution was natural selection through adaptation. This became the basis for Darwin’s theory of evolution.

 

 

  1. The traditional and widely accepted model for the rate of evolutionary change holds that change occurs slowly or gradually within populations of organisms. The peppered moth case (and others mentioned in the test) demonstrated that certain changes (e.g., coloration in moths) can take place rapidly.
  • Some populations (e.g., mosquitoes exposed to insecticides) show wide fluctuations in number, indicating the loss (or gain) of tremendous numbers of individuals, but the species continues (although it may evolve in the process).

 

  • The loss of individuals may reduce the gene pool and modify the population, but the species continues.

 

  • The life span of individuals is trivial in comparison to the “life span” of species. Hence, specific individuals contribute very little to the survival of the species. On the other hand, if the species does not survive, there will of course be no more individuals.
  1. Adaptation to environment is a very complex process and very difficult to study in the natural environment. It is impossible, for example, to devise and experiment to show the effect on a caribou population of another ice age. Adaptation also takes a very long time, and may not be suitable for direct study (e.g., even an adaptation taking hundreds of years would be difficult to study directly). Carefully constructed computer models mimic the response of organisms in the “real world,” and allow scientists to run simulations that show, in minutes, the effects of environmental changes that might take years of real time. They can also vary different aspects of the environment and look at their effects on populations. Supercomputers allow such models to contain far more complexity and to be more realistic. Examples will be various.
  2. Answers will vary, and might include some of the following:

 

  • Roads can be a barrier to some species, and their construction can subdivide populations. Each smaller population may experience slightly different selection pressures, and it may contain a slightly different gene pool than the original, continuous, population.

 

  • Hydroelectric dams cause extensive flooding and disruption of natural populations, creating new sets of selection pressures which can affect the direction and rate of evolution. Some major projects have even been stopped because they would cause the extinction of a specific organism found only in the area that would be disrupted by the dam.

 

  • The building of navigable waterways connecting previously unconnected (or poorly connected) bodies of water allows the spread of species beyond previous limits, and alters community composition and selection pressures (e.g., the lamprey entering the Great Lakes).

 

  • Pumping of wasted water from ships’ bilges has been implicated in the introduction the zebra mussel to the Great Lakes, introducing a new and fast-growing grazer to the community, with implications both for existing species and for our use of the waterways.

 

  1. High reproductive capacity is normally linked with high egg number and short development time (e.g., many species of fish and insects). Where there are many young, there will be many different combinations of parental genes, increasing the chance that there will be some combinations that are better able to withstand a particular selection pressure. Such populations can also respond more rapidly to sudden pressures. (Compare the response of humans, which have a nine-month gestation period and approximately 20 years between generations, with the response of flies, which may have only days between successive generations.)

 

Critical-Thinking Questions

  1. Answers will vary. When humans are domesticating animals and plants, they choose traits that they (the humans) want to propagate. They do not allow “nature to take its course.” For example, animals many thousands of miles apart can parent an offspring by artificial insemination; this would not occur naturally.

 

  1. answers should recognize that, in the Galapagos, similar populations of organisms invaded a series of islands on which there were different selection pressures. It is almost the type of situation a researcher might set up if she were interested in evolution in natural situations, and if she had hundreds (perhaps thousands) of years to observe the results. Answers should include the idea of isolation one island population from populations on other islands and /or the mainland.

 

  1. If a Lamarckian explanation of evolution were to be endorsed, then evolutionary changes in an organism would be interpreted as meeting the needs of the individual organism.

 

  1. Answers will vary, but may be evaluated in relation to the literature used to research them.

 

posted by Marc Bernard Carmichael in Biology Eleven,Biology Eleven Notes and have No Comments

Biology 11 Chapter 3 Lecture Notes

Chapter Three: Mechanisms of Change

Some notes to stimulate your appetite to think about the mechanisms of change and how to prepare for chapter three quiz.
In chapter two, we are introduced to evidence regarding showing change with time. The premise is this, from direct and indirect evidence; there are observations that show a change with time. This process of change with time can be shown in adaptations in populations of organisms. We have noted that this process can be shown using concepts such as speciation and isolation mechanisms. Basically, keep one species away from another and allow mating only to occur within this population, the chances are that a unique species will evolve. In chapter three, we begin to hypothesize about the mechanism that causes this change.

Historical note:

Though some philosophers have suggested that we learn nothing from observing history, the case is not the same for observing fossils. We begin with the notion that all species are fixed. No that does not mean neutered but that all species were put on the earth at a specific time and in a specific place. From a western philosophical point of view, those folks that were busy classifying nature never challenged this idea. Biologists were in fact part of a field of inquiry known as natural history and sometimes grouped with natural philosophers. For many years, “Naturalists” were quite content to just identify and classify and to create some universal means to classify all living things. Then the inquiry into how things worked began. The scientific method created a method of thinking to examine the world. Forces such as gravity and energy became the field of inquiry for scientists. From this inquiry came “laws” and interpretations of chemical and physical forces. As naturalist began to observe more history of organisms upon the earth, the inquiry began to follow the same pattern of questioning. What was going on? Why did organisms become extinct? Why were animals different? Were there unknown forces within nature, like the forces of gravity and Newtonian physics?

So lets look into the text to answer the following:

Who started asking questions about the fixity of species and how could this questioning affect how people perceived fossils?

Once a question is asked, more will follow.

So who proposed the idea of adaptations, the law of use and disuse?

Why do you suppose he used a term such as “law”?

Let’s make a few observations such as”: a heron has long legs, some insects are resistant to insecticides,and some organisms have thick skin or fur.

How could we explain these adaptations from Lamarck and Darwin’s point of view?

Now lets get logical and examine some of the ideas proposed by both Lamarck and Darwin.

Here are some statements, can you identify ones that Darwin would support or Lamarck would support?

Which Statements can be used with the other to create an argument?

Many types of variations exist within a species
Members of a species tend to increase in a geometric ration from generation to generation (example 2:4:8:16: 32)
Some variations have more survival value than others
Organisms in a population reproduce, but the population tends to remain constant
There is a struggle for survival
Organisms are able to adapt to their environment when they inherit variations that have been developed by their parents through use and disuse of certain organs
How would Darwin use some of these statements to support his mechanism of change?

With both Darwin and Lamarck, we have a key problem to consider: Does the environment affect how an organism evolves, or does the organism have a means to adapt to the environment?

One of the key issues is the notion of choice. If we accept the idea that the environment is selecting species, then does the notion of “free will” and “choice” have a place in human thought?

So let’s look outside the realm of the human mind. Organisms on the planet have genetic material. This material allows organisms to display traits. This information, first shown by an inventive monk named Mendel remained unknown to both Lamarck and Darwin. While both were looking for a source of change, either within the organism or due to the environment, neither of them knew about the origin and transmission of variation.

Darwin did consider domestic animal breeding and noted how humans could artificially select traits, but he still didn’t know about the source of these traits. He did suggest that through artificial breeding of animals, humans could “select” a desirable trait. However he was still in a muddle about the origins of traits or why some organisms produced infertile young. For example, the notion of a “hybrid”…which is a product of a cross of two species and in some cases can be infertile such as a donkey and horse was a mystery to Darwin. Darwin did note the formation of species, and the multiplication of species or speciation. He suggested that this process was gradual with time. Yet the more evidence that was brought forth challenged this portion of his idea. Can you define and show examples of the idea known as “punctuated equilibrium”?

Now here is the challenge…

Darwin suggested that his observations about finches in the Galapagos islands was an example of the process of evolution and that by noting this process, the mechanism for natural selection could be illustrated

First of all…who offered the idea of a struggle for existence and natural selection to Darwin?
Now by using some of the terminology such as:

Isolation mechanisms

Speciation

Hybrid

Competition

Predators

Can you describe what occurred with the finches and why they changed with time? Remember to break up you explanation into two parts…the observations that showed a process and the concepts that explain the mechanism.

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Chapter Two Notes for Bio 11

Chapter Two Notes

 

Big Ideas in Biology: Change with Time

 

What is the significance of a change with time? How do we define evolution? What are some patterns of evolution and how can we prove that a change actually occurred. How are species formed or changed with time? These are the primary questions in chapter two.

 

Evolution is:

  • an explanation for the increase in biological diversity.

 

  • a theory that describes how current species are descendants of species of previous generations.

 

  • is a process by which populations show change (gradual or punctual) over several generations.

 

  • a basic definition of evolution is a gradual change of species with time.

 

First of all, a change within a species of organisms can be noted by a change in structure, habitat or even behaviour. This change can be refered to as an adaption.

 

When is a population of organisms considered to be adapted to it’s environment?

( this is a great question to remember..)

 

  • Even though the environment may change to a small degree, successive generations of offspring thrive.

 

  • The most desirable adaptations are those which give an organism a advantage to survive.

 

A way of showing a longer duration of change with time is to examine remnants of previous generations. These remnants can be actual bones or imprints of organisms. This preserved bits of structural or imprinted information are refered to as fossils.

Ø  Fossil records provide the most direct evidence of evolution

  • Most fossils are found in sandstone and limestone.
  • Problems with fossils:

There are gaps in fossil records

  • due to movement of the earth
  • no know record of organism in that time period
  • one organism eating another at one location and then depositing the remnant at another location

 

Some specimens are not complete organisms

 

The process of fossilization requires a specific type of soil

 

Some specimens are too soft to make a fossil

  • for example a shelled organism would make a better imprint than a worm)

 

With the advent of genetic research and cell biology, there are now new ways to establish indirect proof of a change with time:

 

  1. Embryology:
  • Examining the stages of development of an embryo in a variety of species, there appears to be some similarities. This similarity was noted by …who said “     “. Basically, the development of an embryo shows the species phylogenic or family history.

 

  1. Examining structures

There are three terms relative to structures that are useful for comparing species.

 

This table may be helpful for comparing homologous to analogous structures.

Structure type and example Structure Function
Homologous similar different
Analogous different similar
Vestigial present no function

 

  1. Physiology

 

  1. Biochemistry

 

Pattern of Evolutions:

 

Convergence

If an organisms develops similar structures due to living in similar environments but they are separated due to being geographically isolated, this is an example of convergent evolution. Basically two distinct species show a similarity, although they are not genetically link. The term converge means to come together.

 

Divergence

If an organism is separated by geographic barriers, then it will not be able to reproduce with other species. This population will diverge from the original species that it was separated from.

 

Sources of change

 

The concept of speciation

 

The term “speciation” refers to the formation of new species. New species are formed when one population of the same species is separated from another and there is no exhange of genetic information between the two populations.

 

what can cause speciation?

 

Isolating mechanisms that may lead to speciation

( remember diagram in class about sea snails)

  • geographic
  • ecological
  • behavioral
  • morphology
  • genetic

 

While many of these isolation mechanisms may be crossed, for example a snail may adapt from one ecological environment to another. The one barrier that cannot not be crossed in natural situations is the reproductive or genetic barrier.

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Magnification and Microscope

Microscopes and Magnification

“I have got the power”

 

One of the tools that biologist use is the microscope. It function is to view a world that the normal eye cannot see. Stop for a moment and Imagine the first time some one saw moving matter under the lens. If you were that person, would you be afraid or full of wonder? This is a loaded question simply because now it is common to see magnified images of virus and bacteria in TV commercials. Perhaps the novelty is gone but the usage of the microscope remains a basic skill of any one studying biology.

 

Concept One:           Power

“You’ve got the power…”, nope-wrong idea, but here is the scope. Power means the ability to make something bigger. End of story. The larger the power, the smaller the object you can view. The smaller the power, then you are already looking at organisms that are relatively large. The compound microscope enlarges images through a series of lens and mirrors. By illuminating the image, a reflection of that image passes through the lens to the eye. Starting with the eye is the ocular lens. This lens is used for viewing and is the lens that is adjusted to focus on an object. The objective lens is next to the object and remains stationary while viewing. So how much bigger is the object? Well if you take the ocular lens magnification (on the side of the lens) and multiply that number times the objective lens magnification ( on the side of the lens) you have the total magnification or power that the microscope enlarges the object. Here is the catch. Magnification in this context, is how many times larger is the object your are looking at. For example, at low power on a microscope, the ocular lens is let’s say (10x). This means that the lens will make the actual object 10 times larger. The objective lens is perhaps 5X. So the actual object will now appear ( 5×10) or 50 times larger than it is in real life.

 

So what!

Well if we are looking at objects under the microscope, we have to realize that the tool, the microscope, is altering what is actualy occurring under the lens. All that we view is now larger than life and just to keep things interesting, all images are inverted and upside down. So if you are looking at an organism swimming to the left of your field of view, it is actually upside down and swimming the opposite way. This may be helpful to remember the next time you are trying to draw a moving organism.

 

So how do we draw these critters? Well let’s use the worksheet to explain…

 

Prior to answering questions, lets come up with a strategy to organize our work. This will make life and marking a lot easier.

 

How to lay out your work: (save this as a template!)

 

Record facts                        Do work or calculations                           Answer

here                                                    here

 

Write formulas

here

 

 

Problems..

 

 

Record facts                        Do work or calculations                           Answer

three lens                                                                  5 x 2                =          10   low power

2x                                                                                5 x 20             =          100 medium power

20x                                                                              5 x 200           =          1000 high power

200x

ocular=5x

 

Write formulas

ocular times objective = total power

 

Record facts                        Do work or calculations                           Answer

field of diameter = 10 mm             10 mm/ 4 =                                       2.5 mm

 

Write formulas

field of diameter/ # of object = actual size

 

 

Record facts                        Do work or calculations                           Answer

none                                                   use micrometer slide to measure

field of view

remember on average

low power     field diameter

 

Write formulas

 

4.

Record facts                        Do work or calculations                           Answer

high power diameter                      .45 mm / 20 seconds         =                      mm/sec

equals .45 mm                                always include units

 

Write formulas

field diameter (distance)

divided by time equals speed

 

5.

  1. the source of light is actually quite good and can be focused to level of magnification, as you increase power, you need more light. The amount of light can be adjusted by using the diaphragm.
  2. the organism may or may not be dead. If alive and you are using a slide with a concave depression in the slide, the critter is going to move up and down through the water. So you need to adjust focus as the critter moves. Correct answer
  3. Usually the microscope remains at the same level of magnification. This may change not with time but with who is looking down the lens. Always remember to start with low power, switch to the next objective power and slowly adjust the fine tuning knob.

 

6.

Trick question…it depends on the type and size of cells. At low power, you would be able to see the largest field of view, so more distance. This is the obvious answer. However you may not be able to focus on small images and so you may have to move up to the next power to see these images. Don’t worry I don’t like trick questions either.

 

 

 

 

 

 

 

 

Questions

 

 

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