Cell Biology: Structure, Function, and Microbial Applications, Study notes of Microbiology

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Unit 1: Introduction to Microbiology and Microscopes

Microbiology- EXAM 1

-Recognizing historical advances in microbiology-

-Vocabulary Terms-

1. Cell theory - Cells are the fundamental component of life and cells give rise to other

cells.

2. Simple microscope - Light passes through a single lens.

3. Compound microscope - Light passes through two sets of lenses.

4. Spontaneous generation - Theory that life arises from nonliving matter.

5. Biogenesis - Generation of living matter from other living matter.

6. Symbiotic relationship - Close physical relationship between two or more dissimilar

organisms.

Cell theory has 3 tenets-

1. Living organisms are made up of one or more cells.
2. Living cells arise from pre-existing cells.
3. Cells are the fundamental unit of structure and function of living organisms.

Each Scientists & their contribution-

1. Hooke- first observed cells

2. Virchow- popularized cell theory

3. Van Leeuwenhoek- first to view microbes

Statements that are apart of cell theory-

1. Living matter comes from other living matter

2. Cells are the fundamental structural and functional units of an organism

3. Living organisms are made up of one or more cells

-Spontaneous generation-

One of the oldest explanations was the theory of spontaneous generation. Aristotle and other early scientists observed what appeared to be life forms appearing from nonliving matter such as maggots growing on rotting meat and frogs appearing on muddy riverbanks.

4. Virus - Acellular microbe made of proteins and genetic material, either DNA or RNA, never both.
5. Viroid- Virus-like containing only a short strand of circular RNA that can self-replicate.
6. Prion - An infectious protein.
7. Prokaryote -Microorganism with no membrane bound nuclei or organelle.
8. Eubacteria - Single cell prokaryotic microorganism. <True= bacteria.
9. Archaea - Unicellular prokaryotic organism without peptidoglycan in the cell wall. None are known human pathogens.
10. Eukaryote - Microorganisms that have membrane bound nuclei and organelles.
11. Algae - Unicellular or multicellular photosynthetic eukaryote with cell walls made out of cellulose.
12. Fungi - Unicellular or multicellular eukaryote with cell walls made with chitin and are not photosynthetic.
13. Protozoa - Eukaryotic single cell organism. This group is very diverse usually categorized by mode of motility.
14. Helminth- Multicellular, eukaryotic parasitic worm that are visible by the naked eye but involve microscopic eggs and larvae.

-Binomial Nomenclature-

• Binomial nomenclature is a system in which each species of animal or plant receives a name in which the first term identifies the genus to which it belongs and the second the species itself.
• Haloquadratum walsbyi – The genus describes the saltwater environment and arrangement of the organism. Halo is Greek for salt. Quadratum represents a square arrangement of the bacteria. These bacteria were discovered by Anthony Edward Walsby.

1. Which part of the bacteria Escherichia coli represents the genus name_?_

• Escherichia

2. The current 8 levels of classification from largest to smallest are:

• Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

3. What is the purpose of the binomial nomenclature system?

• To provide a consistent way to name species.
• To ensure that each species has a different and unique name.
• To avoid confusion that can occur when using common names.

-Three Domains of Life-

Living organisms are divided into three large groups called domains. Microorganisms are found in each of the three domains of life:

• Archaea - contains prokaryotic organisms
• Bacteria - contains prokaryotic organisms
• Eukarya - contains eukaryotic organisms; this domain is further divided into Kingdoms

NOTE: Some microorganisms, such as viruses, do not fall within any of the three domains of life.

-Three domains of life-

Archaea: are prokaryotes that resemble bacteria but are different from them in their genetic makeup and certain aspects of their cell structure, such as the pseudopeptidoglycan in their cell walls. They are unicellular prokaryotic cells with significant differences in genetics, metabolic pathways, and the composition of their cell walls and membranes.

Bacteria : are prokaryotes that differ from archaea. Their cell wall is made up of peptidoglycan/lipopolysaccharide and can also form spores, unlike archaea. They are prokaryotic because their genetic material is not housed within a true nucleus, and they do not have membrane-bound organelles.

Eukarya : contains all unicellular and multicellular eukaryotic organisms: algae, fungi, protozoa, and helminths. Eukaryotes have a true nucleus and membrane-bound organelles.

-Major Groups of Microorganisms and Biodiversity-

Acellular Microbes - Microorganisms differ from each other in size, in structure, habitat,

metabolism, and many other characteristics. Some microbes, such as viruses, viroid9s, and prions, are acellular (not composed of cells).

Different types of Acellular Microbes-

1. Viruses are acellular microbes. They are not made up of cells and not alive. They can be active or inactive and cannot replicate on their own. They require a host cell, which will provide all the mechanics for viral replication. Made up of proteins and nucleic acids 3 DNA or RNA, never both.
2. A viroid is an acellular particle that consists only of a short strand of circular RNA capable of self-replication. Example: Potato spindle tuber viroid
3. Prion is an infectious protein. It is acellular, do not contain DNA or RNA. It is a misfolded rogue form of a healthy protein or a misfunctioning protein. Remember the 3- D configuration of a protein determines its function. If it is not folded correctly, it cannot function correctly. Example: Mad cow disease

-Prokaryotic Microbes-

• Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus). o Archaea are prokaryotes that resemble bacteria but are different from them in their genetic makeup and certain aspects of their cell structure, such as the pseudopeptidoglycan in their cell walls. It is a unicellular prokaryotic cell.

The endosymbiotic theory states that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host.

The endosymbiotic theory is supported by the finding of non-nuclear DNA in which of the following organelles?

• Mitochondria and chloroplast

-Recognizing the importance of microbiology-

-Vocabulary Terms-

1. Chemotherapy - Treatment of disease by using chemical substances.
2. Antibiotic - Chemicals produces naturally by bacteria or fungi to act against other microorganisms.
3. Synthetic drugs - Chemotherapeutic agents prepared from chemical in a laboratory.
4. Pathogen - Disease causing microorganism.
5. Pure culture - A population of cells or multicellular organisms growing in the absence of other species or types.
6. Isolate - Refers to the separation of a strain from a natural, mixed population of living microbes. Example: isolate pathogen from normal microbiota.
7. Normal microbiota - Population of microorganism found in and on a host animal or environment that normally cause no harm.

-Important scientists and their contributions-

1. Ignaz Semmelweis - connected hand washing to the transmission of disease
2. Joseph Lister - used surgical antiseptic
3. Robert Koch - connected a specific pathogen to cause a disease
4. Alexander Fleming - Discovered Penicillin
5. Paul Ehrlich - looked for antimicrobial chemical that cause the least harm to patients
6. Sahachiro Hara - discovered compound 606 3 which works against Treponema Pallidum , the causative agents of syphilis agents in humans.

-The germ theory of disease-

The germ theory of disease, states that many diseases may result from microbial infection. The work of several scientists and physicians contributed to the germ theory of disease linking microbes to the spread of disease.

Germs cause these types of diseases:

• Infectious

What statement best reflects the Germ Theory of Disease?

• Most diseases are caused by microorganisms.

-Koch's Postulates-

Koch9s postulates are based on the idea that the cause of a specific disease could be

attributed to a specific microbe.

1. object.
2. Total magnification - The produce of the ocular magnification and objective magnification. Example: Ocular = 10x, Objective = 5x, Total magnification 3 10x5= 50x.
3. Resolution - The ability of lenses to distinguish fine detail and structure.
4. Diffraction - The bending of light scatterings as it touched the edges of an object.
5. Contrast - The darkness of the background relative to the specimen.
6. Fluorescence - The ability of an object to absorb ultra-violet light and give off visible. Being illuminated against a dark background.
7. Antibodies - Molecules that are produced by humans and many animals in reaction to a foreign substance.
8. Micrometer - One millionth of a meter 1/1,000,
9. Nanometer - One billionth of a meter 1/1,000,000,

-Microbial Staining-

-Vocabulary terms-

1. Stain - Coloring a microorganism with a dye to make some structures visible.
2. Simple stain - A single basic dye.
3. Fixation - Using heat or c chemical to kill and adhere microorganisms to the microscope slide.
4. Mordant - Used in some cases to improve bonding between the stain and organism.
5. Smear - A thin film of material used for microscopic examination.
6. Differential stain - Differentiate bacteria according to their reactions to stains.
7. Virulence - The degree to with a pathogen can cause disease
8. Capsule - A gelatinous covering that is a means to determine that organism9s virulence.
9. Endospore - A special resistant, dormant structure formed within cell that protects a bacterium from adverse environmental conditions.
10. Flagella - Structures of locomotion to small to be seen with a light microscope without staining.

-Microscopy Techniques and their Uses-

• Magnification - Most microscopes use the series of lenses and properties of light to magnify small objects. Magnification is the ability of a lens to enlarge an object compared to the real size of the object. Example: A cell's actual size is 10 um. If we magnify it 100x (100 times), it will appear to be 10,000 um (10 mm).

• Crystal violet- Primary dye, stains all cells initially
• Iodine- Mordant, intensifies the stain
• Alcohol- Decolorizes cells with lipopolysaccharides in the cell wall
• Safranin- Counter stain, visualize decolorized cells

-Acid-fast stain-

The acid-fast stain is an important diagnostic tool. It is able to differentiate two types of gram- positive cells: those with a waxy mycolic acid in their walls and those that do not.

Mycolic acid is found in Mycobacterium leprae and Mycobacterium tuberculosis the causative agents of leprosy and tuberculosis respectively.

- The steps for Acid Fast Staining-

o STEP 1- Carbolfuchsin: Primary Stain

▪ Carbolfuchsin is applied to a fixed smear, and the slide is gently heated. The heating enhances penetration and retention of the dye. Then the slide is cooled and washed with water to remove the excess dye.

o STEP 2- Decolorization

▪ The slide is then treated with alcohol to decolorize or remove the red stain from the bacteria that are not acid-fast. The acid-fast microorganisms retain the red. These are the bacteria with mycolic acid in their cell walls. In the non-acid-fast bacteria, whose cell walls lack the lipid components, the carbolfuchsin is rapidly removed during decolorization.

• Methylene Blue: Counterstain o The slide is then stained with methylene blue counterstain. Non-acid-fast cells appear blue after the counterstain is applied.

-Capsule stain-

The capsule is a gelatinous covering found on some bacteria. The presence of a capsule is directly related to an organism9s virulence. Virulence is the degree to which a pathogen can cause disease. This is a valuable diagnostic tool.

Capsule staining is more difficult than other differential stains because capsular materials are water-soluble and may be dislodged or removed during the rigorous washing. Capsules do not

accept most biological dyes, such as safranin, and there for a halo appears around each stained bacterium.

-Endospore Stain-

Endospores are a resistant, formant structure formed within a cell that protects a bacterium from adverse environmental conditions. They are uncommon in most bacterial cells. They cannot be stained by ordinary methods such as simple staining or Gram staining because the dyes don9t penetrate the endospore9s wall.

-Flagella Staining-

Flagella are structures of locomotion too small to be seen with a light microscope without staining. Flagella, while not always clinically important, are used to identify bacteria in a mixed sample. It is a tedious process of using mordant and carbolfuchsin to build the diameter of the flagellum until it is visible.

Unit 2: Prokaryotic and Eukaryotic Cell Structure

Microbiology- EXAM 1

-PROKARYOTIC CELL STRUCTURES-

1. Cytoplasm - Gel-like substance within the plasma membrane.
2. Ribosome - Internal structure- Where protein synthesis occurs. Prokaryotic cells have 70s ribosome.
3. Nucleoid - Internal structure- Area of cell where the chromosome is located.
4. Plasmid - Internal structure- Small, circular, double-stranded DNA molecules.
5. Endospore - Internal structure- Internal structure- Protects the genome in a dormmate state- created when environmental conditions are unfavorable.
6. Plasma membrane - Internal structure- Lipid bilayer made of phospholipids- selective permeable.
7. DNA - Internal structure- Circular, singular chromosome.
8. Cell wall - Main function is to protect the cell- Major component is peptidoglycan.
9. Fimbriae - External structure- Short projections- enables a cell to attach to surfaces.
10. Pili - External structure- Long proteins appendages that aid in attachment- sex pilus.
11. Flagella - External structure- Used for movement.
12. Capsule - External structure- Aids in attachment and evasion of host immune response.

70 Ribosome Pili Fimbriae Endospore Capsule

DNA

Flagella Cell wall Cytoplasm Plasma membrane

80 Ribosome Nucleus Mitochondria Membrane bound organelles

The word morphology refers to the shape of the cell.

• Coccus - round sphere
• Bacillus - rod
• Vibrio - curved rod
• Coccobacillus - short rod
• Spirochete - long helical spiral

Bacterial cells of the same species can assume special arrangements.

• Diplo coccus - pair of cocci
• Tetrad - a group of 4 cells arranged in a square
• Strepto coccus - chain of cocci
• Staphlyo coccus - cluster of cocci
• Strepto bacillus - chain of rods

Eukaryotic cells are generally larger in size than prokaryotic cells and include examples such as animal, fungal, and plant cells.

Organelles found in eukaryotic cells:

• Nucleus
• Plasma membrane
• Cell Wall
• DNA
• Mitochondria
• Cytoplasm
• Membrane-bound organelles

SIMILARITIES & DIFFERENCES:

Prokaryotic: Both: Eukaryotic:

Vocabulary Terms for Gram-negative and Gram-positive cell walls

1. Peptidoglycan - Only found in bacteria- unique meshwork found in the cell wall of gram- positive and gram-negative cells
2. Cell wall- Protects the cell from harsh conditions
3. Gram Positive- Contain many layers of peptidoglycan
4. Outer membrane- External to the peptidoglycan layer, contains the LPS
5. Gram negative- More complicated cell wall with a thin layer of peptidoglycan between the plasma membrane and the outer membrane
6. Lipopolysaccharide (LPS)- Found in gram negative cells ONLY- functions as an endotoxin

Gram-positive cells have a cell wall that contains many layers of peptidoglycan. Some well- known Gram-positive bacteria include Staphlyo - and Streptococcus species. Note the many layers of peptidoglycan that make up the cell wall of gram-positive cell walls. The peptidoglycan of gram-positive cells is the target of many antibiotics.

Gram-negative cells have a more complicated cell wall compared to gram-positive cells. From the figure below, you can see that the peptidoglycan layer is thinner than in the gram-positive cell wall.

Similarities : Plasma membrane & Presence of peptidoglycan

Differences : Thick vs thin layer of peptidoglycan. Gram-negative cells have the following additional cell wall components.

1. Outer membrane
2. Periplasmic space
3. Lipopolysaccharide (LPS) a. Lipid A = endotoxin

-Identifying Atypical cell walls- Vocabulary terms-

1. Mycobacterium- Genus of bacteria that contain acid in their cell walls.

2. Mycoplasmas- Lack a cell wall.

3. Mycolic Acid- Waxy substance in the cell wall of myobacterium

4. Acid fast stain- Differentiates between cells that have mycolic acid in their cell walls

and those who do not.

5. Pleomorphic- Take on a variety of shapes- no rigid cell wall to main shape.

-Vocabulary Terms-

1. Facilitated diffusion - The diffusion of solutes through a protein channel; a passive transport. 2. Simple diffusion - The passive movement of molecules down their concentration gradient. 3. Active transport - The transport of molecules across a membrane that requires energy. 4. Passive transport - The movement of molecules across a membrane down their concentration gradient. Does not require energy. 5. Osmosis - The movement of water down its concentration gradient 6. Hypertonic solution - Solution containing a higher concentration of solutes compared to the inside of the cell. Results in water rushing out of the cell = Plasmolysis. 7. Hypotonic solution - Solution containing a less concentration of solute as the inside of cells results in water rushing inside the cell = Osmotic lysis. 8. Isotonic solution - Solution containing an equal concentration of solutes as the inside of cells = no net movement of water. 9. Plasma membrane - Selective permeable membrane surrounding the cell. Allows some molecules to enter and leave the cell. 10. Endocytosis - Type of membrane transport- brings substances inside the cell.

11. Exocytosis - Type of membrane transport- allows substances to move outside of the cell.

Plasma Membrane

The plasma membrane surrounds the cell and creates a barrier separating the inside of the cell from the outside environment. With this separation, however, we do want to allow some molecules , such as water , ions , and other molecules, to move across the membrane. Because of this, mechanisms exist to allow some molecules in while keeping others out. This is called selectively permeable.

Passive Transport

The plasma membrane is selectively permeable , meaning that the membrane allows some molecules to pass while keeping others out.

Passive transport mechanisms include:

• Simple Diffusion
• Facilitated Diffusion
• Osmosis

NOTE: These mechanisms are passive because they do not require energy.

Simple diffusion is the movement of small, uncharged molecules across a semipermeable membrane such as the plasma membrane. Molecules will flow down their concentration gradient from areas of high concentration to lower concentrations. Simple diffusion does not require energy or help from protein channels.

Facilitated diffusion is another example of passive transport because no energy is required. Large and/or charged molecules cannot simply diffuse through the plasma membrane. They need help via a protein channel. Protein channels embedded within the plasma membrane allow these molecules to move across the membrane.

Osmosis is the movement of water. It is a passive event because it does not involve energy. There are three types of solutions that we are going to consider and learn about how they affect cells.

• Isotonic Solution - This type of solution has an equal number of solutes inside of the cell as outside. This means that water moves in and out of the cell at the same rate. There is no change in the cell shape or function.

Unit 3: Metabolic Diversity of Microorganisms

and Metabolism

-Distinguish organic molecules, structure, and function-

-Vocabulary Terms-

1. Organic - A molecule containing both carbon and hydrogen
2. Dehydration- A reaction where water is removed to form a bond between two smaller molecules
3. Inorganic - A molecule that is missing either carbon or hydrogen
4. Monomer - A single repeating sub-unit is a larger molecule
5. Hydrolysis- A reaction where water is added to break a bond in a larger molecule
6. Polymer - A larger molecule made of monomers
7. Macromolecules - Large organic molecules used is large quantities by living organisms
8. Hydrophilic - A molecule that likes to be in water
9. Amphipathic - A molecule that has a hydrophilic and a hydrophobic portion
10. Gene -A portion of DNA that codes for a functional product, usually a protein
11. Hydrophobic - A molecule that does not mix with water
12. Isomer - Molecules that have the same formula but are arranged differently

-Structure of Carbohydrates-

Carbohydrates include sugars, starches, and polysaccharides. They are all made of carbon, hydrogen and oxygen in a [CH2O]n formula.

• Monosaccharides- are simple sugars or monomers. The simple sugars include hexoses ( carbons) like glucose, pentoses (5 carbons) like ribose or deoxyribose. Notice sugars end in-ose.
• Disaccharides- is formed through a dehydration synthesis reaction between two monosaccharides and a glycosidic bond is formed. They can be broken apart by a hydrolysis reaction back into the monosaccharides. Some important disaccharides are: Maltose, Lactose, and Sucrose.
• Polysaccharides- Hundreds of monosaccharides strung together form polymers or polysaccharides. There are many glycosidic bonds holding the chain together.
• Types of Polysaccharides o Starch - plants storage of glucose o Glycogen - animal storage of glucose o Cellulose - cell wall component of plants and algae o Peptidoglycan - cell wall of bacteria (sugar + amino acids) o Chitin - cell wall of fungi and exoskeleton of insects o Beta-glucans - cell wall of fungi, algae and plants

-Functions of Carbohydrates-

Carbohydrates have many different functions such as food sources, structural components, and source of energy storage.

• Energy- Short term energy is derived from simple sugars and stored energy from polysaccharides.
• Structure- Carbohydrates are found in cell walls of many organisms and cell membranes as glycoproteins.
• Genetic information- Carbohydrates such as 5 carbon ribose and deoxyribose sugars form the backbone of DNA and RNA, so they play a role in transmitting genetic information.

-Carbohydrate functions transcript-

Carbohydrates are a source of quick energy. Many bacteria can use sugars for energy and also use them before fermentation to make many products. Stored energy can be found in starch in plants and glycogen in animals. These storage molecules can be broken down quickly and used as an energy source.

Larger carbohydrates can be used as structural molecules. Plants use cellulose to build their cell wall and bacteria has peptidoglycan in their cell wall. Fangio use chitin and beta glucans for cell walls.

Five carbon sugars ribose and deoxyribose are found in RNA and DNA respectively and make the backbone of nucleic acids. In this role the sugars are part of the genetic information of the cell.

• Carbohydrates contain which elements? o Carbon, hydrogen, and oxygen.

-Structure of Lipids-

Lipids (fats) contain mostly carbon and hydrogen and little oxygen, so unlike other macromolecules, lipids are hydrophobic. Examples of lipids are triglycerides and fatty acids , phospholipids , and sterols.

• Fatty acids are long-chain hydrocarbons and can be saturated or unsaturated. An unsaturated fatty acid has one or more double bonds which will create a bend in the chain. A saturated fatty acid has all single bonds, full of hydrogen.