Assignment 1 - MCB2004 Summer 2020 PDF

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MCB2004 Summer 2020

Assignment 1 (Chapters 1,3,4,5,6)

CHAPTER 1 1. List the possible definitions for microorganisms – in terms of size, cellular structure, culturability and their ability to cause diseases. Bacteria:  

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Size: about 10x smaller than Eukaryotes; measured in microns (Average size 1 micron) Cellular Structure: peptidoglycan in cell walls and circular chromosomes, lack organelles. All bacteria contain a cell membrane, nucleoid, ribosomes, and cytoplasm. Some bacteria however can contain structures such as flagella for locomotion, plasmids for additional genetic information, etc. Culturability: take about 24 hrs. to culture Ability to cause disease: Bacteria that develop endospores can develop diseases because of the resistance and endurance of these spores. Examples include Clostridium tetani which can cause the disease known as ‘lockjaw’ and Clostridium difficile which can cause nosocomial infections. Archaea:

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Size: about 10x smaller than Eukaryotes Cellular Structure: single celled organisms; although they share may characteristics as bacteria, the ribosomal sequence present made them distinct from bacteria. No presence of peptidoglycan in their cell walls Culturability: many archaea are unculturable. most of the culturable and well-investigated species of archaea, however, include two main phyla: Euryarchaeota and Crenarchaeote Ability to cause disease: No definitive virulence gene or facts ; nevertheless, can have opportunity to cause disease with characteristics of having access to host and capabilities of long-term colonization and coexistence with endogenous flora in a host

Eukaryotes:  

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Size: Larger cells measured in mm Cellular Structure: contain double membrane-bound organelles; contain a true nucleus (double membrane bound) ; Endosymbiotic (larger precursor cells consumed smaller prokaryotic cell which then developed a specialized function) Culturability: in the mammalian class of the animalia kingdom, cells can be isolated from tissues for ex vivo culture in several ways. Only white cells are capable or growth in culture. Culture of non-mammalian cells such as plant cells and insect cells are also possible Ability to cause disease: Fungi can cause diseases in humans through accidental contact with soil, water, or dust. Community-acquired infections can be caused by environmental pathogens // Protozoan pathogens are also present, such as Trypanosoma brucei known as African Sleeping Sickness.

List the different eukaryotic groups: Protozoa, Fungi, Helminths, Algae, Animals, Plants

MCB2004 Summer 2020 3.

Assignment 1 (Chapters 1,3,4,5,6)

Which group of microorganisms may be described as being cellular and acellular? Viruses can be described as being acellular and cellular. Acellular as viruses only contain nucleic acid, and its protein shell (capsid). They also contain no ribosomes, however, when they infect a cell, they ‘hijack’ its’ ribosomes which allows it to increase its numbers.

4.

5.

What are the different categories of Microbiology (as a subject) and describe the functions of each category? 

Medical Microbiology: Deals with microbes that cause diseases in humans and animals

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Public Health Microbiology and Epidemiology: Monitor and control the spread of diseases in communities USPHS, CDC, WHO

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Immunology: Complex web of protective substances and cells produced in response to infection Includes vaccination, blood testing, and allergy Role of the immune system in cancer and autoimmune diseases

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Industrial Microbiology: Safeguards our food and water Biotechnology Microbes used to create amino acids, beer, drugs, enzymes, and vitamins

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Agricultural Microbiology: Relationships between microbes and domesticated plants and animals Plant specialists , animal specialists

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Environmental Microbiology Study the effect of microbes on the earth's diverse habitats Aquatic, Soil, Geomicrobiology, Astrobiology

List the benefits of microorganisms in helping to shape planet earth. Most microbes are deeply involved in the flow of energy and food through the earth’s ecosystems. Photosynthetic microorganisms such as bacteria and algae account for more than 70% of earth’s oxygen productio n. Decomposition of dead matter and wastes are also carried out by bacteria and fungi. Humans also use microorganisms for thousands of years to improve life and even shape civilizations ( yeast for production of bread, wine, beer ; fungi penicillium for anti-biotic // Biotechnology, Genetic Engineering, Recombinant DNA Technology, Bioremediation)

MCB2004 Summer 2020

6.

Assignment 1 (Chapters 1,3,4,5,6)

How did the earth’s atmosphere get majority of its oxygen? The earth’s atmosphere got majority of its oxygen from bacteria and algae in the ocean. These bacteria and algae are photosynthetic organisms, which means that they produce oxygen as an end product of their food synthesis. They account for about 70% of the 21% of oxygen found on earth’s atmosphere

7.

How did Bacteria, Archaea and Eukarya evolve and when did representative cells from each group appeared on planet earth? Bacteria, Archaea and Eukarya evolved from the last universal common ancestor (LUCA). Microbes were first adapting to the environment about 3.5 billion years into the creation of the Earth. Bacteria and archaea have not really evolved; while eukaryotes have developed membranes and evolved significantly (insects forming first, followed by reptiles, mammals, then humans)

8.

Compare and contrast the characteristics of Bacteria and Archaea? Bacteria and archaea both have nuclear material that is free in their cytoplasm. They also have no membrane-bound organelles present. However, the cell wall makeup of bacteria and archaea differs. Bacteria cells wall is made up peptidoglycan while archaea is comprised of unique membrane lipids, and pilin proteins. The ribosomal RNA sequence in archaea is also distinct from bacteria

9.

What critical genetic component of microorganisms helped to categorize them into Bacteria, Archaea and Eukarya. The critical component of microorganisms that help to categorize them into Bacteria, Archaea and Eukarya are their nucleus composition. Eukaryotes contain a true nucleus that has a doublemembrane layer while Prokaryotes such as Bacteria and Archaea contain a false nucleoid that is free. Bacteria and Archaea differ however in their genetic information, so are classified differently

MCB2004 Summer 2020

Assignment 1 (Chapters 1,3,4,5,6)

CHAPTER 3 10.

What is an axenic medium? Axenic: a sterile that such as a pure culture; an axenic animal is born and raised in a germ-free environment. This medium is free of other living things except the one being studies

11.

Describe the different media types based on their physical, chemical, and functional properties: 

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Physical o Liquid: water-based solutions that do not solidify at different temperatures (Nutrient Broth) o Semisolid: exhibit clot-like consistency at room temperature. Contain enough gelatin or agar to thicken but produce a firm surface. At high temperatures, Agar mixture can turn to liquid, and when cooled back down to room temperature, can return to solid form (Nutrient Agar) o Solid: provides a firm surface upon which cells can form discrete colonies ; used to isolate bacteria and fungi. Chemical o Synthetic: all chemical properties in the media are known. Percentages and every basic details of the recipe are defined o Complex: certain portions of the media are not known ; extracts of animals, plants, or yeasts (Blood, serum, meat extracts, yeast extracts, etc. EXTRACTS) Functional o General Purpose: support just about any growth of a wide spectrum of microorganisms; contains mixture of ingredients that support a wide variety of microbial life o Enriched: contains complex organic substances (blood, serum, hemoglobin or special growth factors including specific vitamins or amino acids that fastidious bacteria require for growth) o Selective: contains one or agents that inhibit the growth of certain microbes while simultaneously encouraging the growth of select microorganisms ; important in primary isolation of a certain type of microorganism from a mixed sample o Differential: allow multiple types of microorganisms to grow, but displays visible differences (HALOs) among them; designed for special microbial groups

What are the five I’s of studying microorganisms?  Inoculation  Incubation  Isolation  Inspection  Identification

MCB2004 Summer 2020

13.

Assignment 1 (Chapters 1,3,4,5,6)

What processes are involved in the microbial Identification process? Biochemical Testing: determine fundamental chemical characteristics such as nutrient requirements, products given off during growth, presence of enzymes and mechanisms for deriving energy o

Other analytical and diagnostic tools include genotypic testing (detects microbes based on their DNA), immunologic testing (tests the isolate against known antibodies), and inoculation of suitable laboratory animals

Microbial profiles are determined through combining: (1) Phenotypic testing, (2) Genotypic testing, (3) Immunologic testing, (4) macroscopic analysis, (5) microscopic analysis

14. What are the properties of a solid medium? Solids mediums can either turn into liquids at certain high temperatures then convert back to solid form at room temperatures (Examples include Agar which is a red algae which is a solid media at room temperature, but when exposed to temperatures above 100C it begins to liquify). Other solid media cannot be liquified, however, and provide a firm surface upon which cells can form discrete colonies, used to isolate fungi and bacteria.

15. What are the characteristics of selective and differential media? Selective Media: contains one or more agents that inhibit the growth of certain microbes while encouraging select microbes to grow. This media is important in primary isolation of a certain type of microorganism from a mixed sample Differential Media: allows multiple types of microorganisms to grow but display visible differences ( or Halo’s) between colonies due to the metabolism of certain ingredients that cause a color change. 16. Describe the parts and functions of a typical compound microscope? A typical compound microscope consists of two lenses: the objective lens, and the ocular lens. The objective lens can have variations to determine the magnification (4x, 10x, 40x, 100x are examples) and the ocular lens which are binocular in nature and have their own magnification (10x for example). In typical compound microscopes there is a lamp in the base which serves the function of illuminating the specimen/source on the stage. A condenser is used to focus light onto the specimen and helps to gather stray/diffused light from the illumination source

MCB2004 Summer 2020

17.

Assignment 1 (Chapters 1,3,4,5,6)

What is the sequence of magnification in a typical compound light microscope – with regards to the order of lenses participating in the magnification process? Light leaves the light source > passes through the condenser lens > light rays strike the specimen then pass through the objective lens (real image in this section) > from the objective lens the image flips forming a virtual image then passes through the ocular lens for additional magnification > light then finally strikes the eye and the image is processed in our brain

18.

Describe the different properties of a microscope as it relates to contrast, magnification, refraction, and resolution. Contrast: 

the difference in light intensity between the image and the adjacent background intensity. A minimum contrast of 0.02 is needed by the human eye to distinguish differences between the image and its background Magnification:

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Results from a complex interaction between visible light waves and the curvature of a lens; a clear, glass sphere can magnify most objects Refraction:

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The bending or changing in the angle of light rays as it passes through a medium, such as a lens ; the greater the difference between the two substances, the greater the refraction Resolution:

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19.

Also known as resolving power, it is the capacity of an optical system to distinguish/separate two adjacent objects or points from one another It is determined by a combination of characteristics of the objective lens and the wavelength of light being used to illuminate the sample (optical microscopes use visible light)

How can a clearer image be achieved with a compound light microscope? You can obtain a cleared image with a compound light microscope by using a light source with a lower wavelength (such as violet). This short wavelength provides increased energy which allows you to obtain a clearer image. Inverse proportionality: wavelength of light decreases = resolution increases ; wavelength of light increases = resolution decreases

MCB2004 Summer 2020

Assignment 1 (Chapters 1,3,4,5,6)

20. List and describe the different types of light microscopy. 

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Bright Field: most widely used light microscope ; forms image when light is transmitted through the specimen. The specimen will produce an image that is darker than the surrounding brightly illuminated field. Multipurpose instrument used for both live, unstained material and preserved, stained material Dark field: can be formed form a bright-field microscope by adding an accessory called a stop to the condenser. The stop blocks all light from entering the objective lens – except peripheral light that is reflected off the sides of the specimen itself, which results in a brightly illuminated specimen surrounded by a dark (black) field. Most effective in visualizing living cells that would be distorted by drying or heat or that cannot be stained with the usual methods

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Phase-Contrast: uses phase plates; kind of lens system that arranges/manipulates rays of light in phases and as such helps to project images based on the qualities of the refractive indices of the internal materials of the cell ; every cell has intracellular organelles which have the capability of refracting light rays ; each has refractive indices which allow image to be interpreted vividly based on these qualities. Denser cell parts (e.g. organelles) alter the pathway of light more than less dense regions (cytoplasm). Provides 2-dimensional imaging

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Interference: works similar to phase-contrast microscope but has additional lens system that provides ability of 3-D imaging.

21. What is the purpose of staining in microscopy? Staining in microscopy creates contrast and makes inconspicuous features stand out. Staining allows scientists to prepare specimens based on what they want to observe/evaluate specifically

22. What are the differences between simple and differential staining? Simple: requires one dye to create color or contrast; an uncomplicated procedure Differential: uses two differently colored stains to clearly contrast cell types or cell parts; is a complicated staining technique

23. List specific examples of certain types of differential staining techniques?  Gram Stain: used to differentiate major categories based on color reaction of cells ( GramPositive bacteria stain purple ; Gram-Negative bacteria stain pink  Endospore stain: used to distinguish endospores from vegetative cells (detects endosporemembers of the genera Bacillus and Clostridium.

MCB2004 Summer 2020 

Assignment 1 (Chapters 1,3,4,5,6)

Acid-Fast Stain: differentiates acid-fast bacteria from nonacid-fast bacteria by detecting mycolic acid ( Acid-fast bacteria stain pink ; nonacid-fast bacteria stain blue // detects the agents of tuberculosis and leprosy

CHAPTER 4 & 5 24.

In a typical Bacterial cell, list the different cellular structures and their functions.

Typical Bacterial cell contain the following:  Cell membrane : an essential component that control activity and what goes in and out of the cell  Nucleoid: contains blueprint of life; genetic coding/DNA of bacteria  Ribosomes: allow protein synthesis  Cytoplasm: houses all internal structures such as the nucleoid and ribosomes; is 80% water 25. Which parts of a typical pathogenic Bacteria may interact with the host in the establishment of a disease? External structures of Bacteria may interact with the host in the establishment of a disease, specifically the fimbriae. Fimbriae are small bristle-like fibers sprouting off the surface of certain species of bacteria (E.g. Neisseria gonorrhoeae) 26.

How can sterility be achieved? Sterility can be achieved through various means including heat, radiation, chemicals, highpressurization, and filtration. An autoclave is often used in microbiology to achieve sterility. It is a device that uses steam to sterilize equipment and other objects. This process inactivates all bacteria, viruses, fungi, and spores.

27. What are the major differences between a Gram positive and a Gram-negative Bacteria? Gram stains have the purpose of differentiating two different types of bacteria, where differences lie in the structure of the cell envelope: Gram-Positive and Gram-negative: Gram Positive:  Composed of a thick cell wall composed of peptidoglycan (20-80 nm thick)  contain an inner cytoplasmic membrane  when stained; produces a blue/purple color Gram Negative:    

Have an outer membrane Composed of a thin cell wall (1-3 nm thick) Contain inner cytoplasmic membrane When stained; produces a pink/red color

MCB2004 Summer 2020

Assignment 1 (Chapters 1,3,4,5,6)

28. What are the differences between a hypertonic and a hypotonic solution? Hypertonic: contains a higher concentration of solutes compared to another solution Hypotonic: a solution that has a lower solute concentration compared to another solution 29. What happens to a cell when it is placed in a hypertonic, hypotonic or an isotonic environment?  A cell placed in a hypertonic solution will shrivel , as the water in the cell will want to move towards the high concentration in order to attempt to bring about osmosis // Hypertonic Solution = cell shrivels up, plasmolysis  A cell placed in a hypotonic solution will swell up and become full of fluid until lysed as the water solute will want to move into the area with a higher concentration of solute to bring about equality. // Hypotonic Solution = cells swell up, cytolysis  A cell in an isotonic solution will have an equal amount of solute and water so there is no major difference brought about. Cell can resume normal live. 30. How did the chloroplast and mitochondrion develop in eukaryotic cells? It is believed that organelles such as chloroplast and mitochondrion developed in eukaryotic cells through the theory of endosymbiosis. It is believed that a large precursor cell consumed smaller prokaryotic cells which then developed a specialized function (such as providing photosynthetic abilities or protein synthesis) 31. Compare and contrast the characteristics of Bacteria and eukaryotic cells. Bacteria contain a naked nucleus (nucleoid) while Eukaryotic cells contain a double membrane bound nucleus. Bacteria shapes can be categorized into three general types such as Coccus, Bacillus, and Vibrio while Eukaryotes contain a cytoskeleton with the three main types...