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Archive for December, 2015

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:


dried out




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



  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.




  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



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


  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,



  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



  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



  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 Dec 14

Biology 11 Lesson Outline                                      Date Dec 14th



Last lessons Objective



Quiz on immune system and virus vocab

Today’s Objectives  

1.   Introduction to Bacteria

2.   Gap notes

3.   Analogy project (discussion)



Number One


Common misconceptions about bacteria

·      They are all bad ( will need to know 10 reasons why this is false)

·      https://www.youtube.com/watch?v=qCn92mbWxd4




Number Two

Gap notes handed out in class.

You can confirm answers by referring to green binder.



Number Three

Creating your own analogy.

See class hand out

Please contact Mr C regarding your choice before Winter Break.

You need to sign up in green binder!

Text book Reference


Chapter Eight: Bacteria

True Bacteria Notes on Blog

You tube Reference UC Berkeley and link to evolution


Microbiology on line (from the UK)


Micro facts that may make you feel dirty


Bacteria and virus






Take Home Message ·      Germs is just a general term for a misunderstood living thing!




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

Bio 12 Enzyme Lab Dec 14th

Biology 12 Lesson Outline                                      Date Dec 14th



Last lessons Objective




Introduction to enzymes

Today’s Objectives  

1.   Inquiry based enzyme lab

2.   Lab quiz on Thursday lunch or Friday

3.   Exam on Wednesday (DNA,RNA and Enzymes)



Number One


You are provided with three protein powders, labeled as A, B, and C.


You are told that two of the powders are enzyme diastase, amylase and the third powder is a non-enzyme protein.


In two stages, you need to design a lab to decide which is the non-enzyme and then, which is the amylase and diastase.


You also need to have a control.


The substrate you are using is starch.


Your indicator is Benedicts solution that turns yellow when there are monosaccrides.


You should write up the lab using the outline in section two



Number Two








Procedure (in point form)


Results Table



To include:

·      Identify each powder and explain why

·      Discuss evidence and facts about denaturing due to   temperature

·      Discussion of possible experimental error

·      Discussion about the activity of amylase verse diastase



To include:

·      Hypothesis of lab verses results

·      Experimental error

·      Next variable to check



Number Three

Online References


Enzyme Lab



Amylase Lab



Amylase lab



Distinct questions to answer in your discussion

·      What is the difference between using Iodine verses Benedicts solution?

·      Which enzyme would be subject to denaturing and why?


Text book Reference


Chapter 6
posted by Marc Bernard Carmichael in Biology 12,Biology 12 Lesson Outline and have No Comments