Microbiology Ch.1-5 Exam

What is metabolism? Anabolism? Catabolism? Which one requires energy and which one produces energy?

Metabolism is the sum of all chemical processes carried out by a living organism. Anabolism is a reaction that requires energy to synthesize complex molecules from simpler ones. Catabolism is a reaction that releases energy by breaking complex molecules into simpler ones.

What is the one molecule required for all life as we know it?

H2O

3D shape! 3D shape! 3D shape! How do temperature and pH affect this?

High temperature and pH (low-acidic) can denature proteins, altering their shape and destroying their function.

What is the main function of DNA? What are the 3 functions for RNA?

DNA stores the cells genetic info and transmits it to offspring RNA is an intermediary in conveying genetic instructions, structural components, and regulating gene function

Why does an electron microscope give better resolution than a light microscope?

Light microscopes can't resolve objects less than .2 micrometers away from each other. The EM uses electron beams rather than light and electromagnets rather than glass lenses to focus the beam.

Which scientist came up with the term "cell"? Who was the first scientist to use a microscope to observe and sketch what we now know are bacteria?

Robert Hooke coined the term cell. Leeuwenhoek was the first to observe microorganisms using lenses.

Typically, what are the first two steps in any staining procedure (before stains are added)? What are the purposes for these two steps?

Smear (spreads organism on slide) Fix (kills and keeps organism in place)

What are the two components that make up a fat molecule?

glycerol + 3 fatty acids

What's the difference between a saturated and an unsaturated fat?

saturated fat = fat molecule with no double bonds (i.e. butter in solid state) unsaturated fat = fat molecule with 1 or more double bonds (i.e. oil in liquid state)

What's the difference between a monosaccharide, a disaccharide, and a polysaccharide?

mono - 1 sugar di - 2 sugars poly - more than 2 sugars

Which class of macromolecule cross links the sugar chains together to make peptidoglycan?

polypeptides (short proteins) form a lattice

What are chemotaxis and phototaxis? Remember they can be both positive and negative.

(+) Chemotaxis = going TOWARD something (+) Phototaxis = going TOWARD light (-) Chemotaxis = going AWAY from something (-) Phototaxis = going AWAY from light All help with motility/sensing things

What are the steps of a Gram stain and what are the chemicals used? What colors are Gram positives and Gram negatives? What cell structure is the biological basis for us seeing Gram positive versus negative? What's arguably the most critical step?

1. heat fix, smear. 2. primary stain: crystal violet 3. mordant: iodine 4. decolorize: alcohol 5. counterstain: safranin Gram positive is purple, gram negative is pink. The cell wall is responsible for gram positive vs negative The most critical step is decolorizing with alcohol because it dehydrates the cell.

What are the steps of an endospore stain? What's the primary stain? What's the mordant step in the procedure? What is the feature of a spore that necessitates this step?

1. heat fix, smear. 2. primary stain: malachite green. 3. steam heat for dye penetration to spores (mordant step) 4. rinse: water removes dye except from spores 5. counterstain: safranin The feature of a spore that necessitates this step is its strong resistance to adverse conditions

What are the 4 steps of Koch's postulates? What are 2 reasons we can't always fulfill these postulates for every disease?

1. isolate bug from all cases of disease 2. grow bug in pure form in lab 3. inoculate healthy host 4. reisolate the same bug #2/3 cannot always be done for physical and ethical reasons

What are the 3 basic shapes for bacteria? What is diplo? Strepto? Staphylo?

3 basic shapes: coccus (spheres), bacillus (rods), spiral Diplo - in pairs Strepto - in chains Staphylo - in clusters

What's pathway feedback inhibition?

A reversible noncompetitive inhibition that regulates the rate of many metabolic pathways

What's a mordant?

A second chemical that increases the intensity of the primary staining dye

What is the difference between a simple stain and a differential stain?

A simple stain colors an organism just so you can see basic cell shapes and arrangements. A differential stain uses two or more dyes and colors two different organisms or parts of an organism.

How many chromosomes in a typical bacterial cell? To which other cell structure are bacterial chromosomes attached?

A single chromosome are in a typical bacterial cell. They're attached to the cell wall.

Remember that all viruses are parasites and are considered bad from a biomedical point of view. What's a prion as compared to a virus?

A virus is an acellular entity consisting of nucleic acids and proteins, a prion is also acellular but only contains protein

What are the 3 parts of ATP? Where's the energy?

Adenosine Ribose sugar 3 phosphates The energy is released when a phosphate is removed

What are the subunits that make up proteins? What is the general structure of these subunits? What are a couple of functions for proteins in a bacterial cell?

Amino acids. Structure, enzymes, transport

What is an enzyme and how do enzymes fit the definition of catalysts? Key feature - recycling. What are substrates, products, and active sites?

An enzyme is a protein that acts as a catalyst. It speeds up reactions without being used up. Substrates are the substance on which the enzyme acts, products are the result of an enzymatic reaction, and active sites are areas on an enzyme that allow the substrate(s) to bind to it

Why are we seeing new diseases emerging and spreading quickly across the globe?

Bacteria can change their nature via DNA and can cause new diseases or new forms of old diseases

What are the parts of a modern brightfield microscope? How do you calculate total magnification?

Base, condenser (converges light beam), iris diaphragm (controls amount of light), coarse and fine adjustment knob, stage, objective lens (magnifies image before passing it through the body tube), body tube, ocular lens (further magnifying the image). Total magnification is objective power times ocular power

What's the basic structure of a cell membrane? What is the function of the cell membrane?

Basic structure = phospholipid bilayer w/ associated proteins. Hydrophobic tails, hydrophilic heads. Function = selective permeability: controls what gets in and out of the cell

What are the 4 classes of macromolecules?

Carbohydrates Lipids Proteins Nucleic acids

What is the element which defines an organic molecule?

Carbon

What are the 2 main elements which form lipids? What is the feature of phopholipids which give them the ability to form cell membranes?

Carbon and Hydrogen Mostly oil so they're hydrophobic

What is the name for the group of 3 nucleotides which identify which amino acid to insert into a growing protein chain?

Codon

Enzyme inhibitors: competitive vs allosteric (non-competitive). What's the difference? You can have reversible and irreversible kinds for both.

Competitive - a molecule similar in structure to a substrate can bind to an enzyme active site and prevent that other substrate from attaching Noncompetitive - a molecule can attach to an allosteric site on the enzyme (a site other than the active site) and change its shape, ultimately preventing the other substrate from attaching

What are the 3 differences in structure and components between DNA and RNA?

DNA - double stranded, T=Thymidine, Deoxyribose RNA - single stranded, U=Uracil, Ribose

What is the term used to describe the loss of 3D structure (and function) of a protein?

Denaturation

What is an endospores? Which two big genuses of bacteria make spores? Why do they do it? Why do we care about spores from a medical point of view?

Endospore = dormant, tough, non reproductive structure produced by some bacteria, made by certain Gram (+) bacteria in response to environmental stress. They do it to protect the seeds so they can survive. From a medical point of view, they are hard to get rid of. We use an autoclave to sterilize things enough to destroy spores. Genuses that make spores = clostridium and bacillus

What do you need to make active transport happen? What molecule provides this?

Energy is needed, ATP provides this

What extra component is required for facilitated diffusion (versus simple diffusion)?

Facilitated diffusion requires a transport protein

What are the two microscopic observations about flagella on a bacterial cell that help us to identify the cell?

Flagellum are polar is there is either one at one end or one at each end (no more than one at an end). They can be monotrichous (one flagellum), amphitrichous (one at each end), lophotrichous (two or more at one or both ends), petritrichous (all over the surface), or atrichous (none).

What's the function of a ribosome? What are they made of? Targets of a lot of antibiotics.

Function - making proteins. They are made of 2 subunits known as 50S and 30S which combine to make a complete 70S (not 80S) ribosome. Antibiotic targets such as streptomycin and erythromycin.

What are the two big differences between the Gram positive and Gram negative cell wall?

G(+) = up to 40 layers, 90% of cell wall is peptidoglycan G(-) = 1 layer, 5-20% of cell wall is peptidoglycan

What does the word glycocalyx mean? What are the two big functions for it?

Glyco - sugar Calyx - coat Glycocalyx - sugarcoat If it is organized and firmly attached to the bacterium, it's a capsule. If it is disorganized and loosely attached, it is a slime layer that protects from phagocytosis and aids in attachment

What kinds of ideas that we take for granted about diseases were proposed by some ancient scholars such as Hippocrates, Thucydides, Varro and Lucretius?

Hippocrates - disease can be transmitted Thucydides - people who have had a disease & recovered didn't get it again Varro - the existence of tiny invisible animals caused disease Lucretius - seeds of disease

What are the 3 elements needed to form a monosaccharide?

Hydrogen Oxygen Carbon

What's hypertonic vs isotonic vs hypotonic? What happens to a cell when you place it in each of those kinds of solutions?

Hypertonic = less solvent than solute. Cell will shrivel and shrink because water is exiting the cell Isotonic = equal solvent and solute. Cell remains homeostatic Hypotonic = more solvent than solute. Cell will swell and burst because water is entering the cell

What step in cell wall synthesis does penicillin stop?

In Gram (+) it blocks formation of peptide crossbridges. In Gram (-) it blocks formation of bond between tetrapeptides.

What is a coenzyme and what kind of nutrients often serve as coenzymes?

It is a nonprotein organic molecule bound to or loosely associated with an enzyme. Many are synthesized from vitamins.

How's an antibiotic officially defined? What's the fundamental idea behind the use of antibiotics to treat diseases in people or animals?

It is an agent that inhibits bacterial growth, "kill the bug not the person"

How is the wavelength of light defined? What is the relationship between wavelength and the energy carried by the light?

It is the length of a light ray, the distance between two adjacent crests. The shorter the wavelength, the higher the energy.

What is refractive index and how does immersion oil work to help us achieve better resolution in our brightfield microscopes?

It is the measure of the speed at which light passes through material. Light refracts every time it passes from one medium to another. Immersion oil (replacing air) has the same refractive index as glass, therefore it eliminates the refraction of light as it passes from the slide to the objective lens.

What's LPS? What's the L stand for and what does it do to us? What is the PS and how do we use it?

LPS = Gram (-) cell outer membrane = Lipopolysaccharide. L = Lipid, A = its an endotoxin and is toxic in blood or GI tract, released by dying bacteria, causes fever and vasodilation. PS = polysaccharide - provides antigenic specificity, for example E. Coli

What is lysozyme and what does it do to help us fight infections?

Lysozyme is an enzyme found in tears, mucous, and saliva. It cleaves the bond between NAM and NAG in the disaccharide backbone of peptidoglycan. It basically cuts apart cell wall bonds.

What is the "Germ Theory" of disease?

Microorganisms can invade other organisms and cause disease

Are there more bacteria or cells in your body? How many times is the difference between the number of cells and the number of bacteria?

More bacteria, 10x

What are the smallest free-living bacteria? Do they have cell walls?

Mycoplasma. They do NOT have cell walls

What are the two sugars which make up the sugar chains in peptidoglycan?

NAG NAM

How does a negative stain differ from a regular simple stain?

Negative stains are used because a simple stain is incapable of penetrating the bacteriums capsule. The difference is that the background is stained a dark color. A second simple stain can be used to show the cell inside its capsule.

Are all microbes bad? What is the big difference between the bacteria and the Archea?

No. Archea like to live in extreme conditions, where bacteria couldn't survive. Also archea have not been proven to cause disease.

What is the general structure of the subunits of nucleic acids? What are the 3 parts of each subunit? Where is energy stored in these structures for use by cells?

Nucleotides nitrogen-containing base, ribose, triphosphate ATP stored in TP

Where are the fimbriae on a cell? How many? What's their big function? What's the function of a sex pilus? How many on a cell?

Outside of cell, few to hundreds per cell. They're like velcro that help attach to other cells. Function of pilus = used during transfer of DNA between cells. 1-2 pili per cell but longer than the fimbriae (similar structure).

What does an image from a darkfield microscope look like? What kinds of medically important bacteria are typically observed using darkfield? Do you have to stain specimens? Why might this help with your observations using darkfield?

Only the organism is illuminated, allowing you to see the bright organism more clearly on a dark background. Live spirochetes (that can cause syphilis) are viewed using this technique. Stains do not have to be applied.

What's an example of simple diffusion into/out of a cell and why does it work?

Osmosis = passive diffusion for water = high water concentration (low solute) to low water concentration (high solute)

What are oxidation and reduction? Coupled?

Oxidation is the loss or removal of electrons. Reduction is the gain of electrons. A coupled oxidation reduction is when one substance loses electrons while another one gains them.

What's the difference between a passive process and an active process?

Passive (simple facilitated) = molecules diffuse across membrane until equilibrium is reached, follows gradient, no ATP needed. Active = a protein, usually specific for the substance being moved, moves molecules across the membrane, energy (ATP) is needed because it is moving AGAINST the gradient.

Which way do the concentration gradients go in passive vs active processes?

Passive = follows gradient Active = against gradient

What modification is made to a typical fat molecule so that it can be used to make a cell membrane? What is the structure that lipids spontaneously form to make membranes?

Phosphorus binds to it. Phospholipid bilayer

What's a plasmid compared to a chromosome? Do plasmids and chromosomes replicate in a coordinated manner? Why do we care about plasmids?

Plasmids are small circular DNA molecules that can replicate independently from the main chromosome. We care about plasmids because they cause antibacterial resistance.

What are the 4 structures (primary etc) for proteins and what is the general definition of each?

Primary structure: sequence of amino acids Secondary structure: orientation of protein in space due to hydrogen bonding Tertiary structure: overall FINAL shape due to formation of many bonds and hydrophilic and hydrophobic interactions Quaternary structure: shape of 2 or more proteins associated for a function

Who were the 3 scientists we talked about in reference to spontaneous generation and briefly, what did each do? Which one is considered to have done the experiments that ended the idea of spontaneous generation?

Redi (covered rotten meat to prevent maggots), Spallozani (boiled broth and sealed it to prevent maggots) and Pasteur ended the idea of spontaneous generation with Swan-necked flasks

What are a couple of functions for the cell wall?

Shape and osmotic stress

What's the typical order of size for viruses, bacteria and human cells?

Smallest to largest, in that order

What's the only human disease that has been completely eradicated from the planet?

Smallpox

What was Semmelweis' contribution to modern sanitary practices? Lister's?

Suggested washing your hands before delivering a baby, to prevent childbirth fever

How is resolution defined? What is the relationship between wavelength and resolution?

The ability to see two objects as separate and distinct. Wavelength and resolution are inversely proportional.

What are the steps of an acid-fast stain? What's the primary stain? What's the mordant step in the procedure? What bacteria are the targets of acid-fast staining and what is it about them that makes them hard to stain?

They are the same steps as gram staining, except the primary stain is carbolfuchsin and the mordant is heating the slide for penetration of cells. Mycobacteria are the targets of acid fast staining. They are hard to stain because of the high lipid content in the cell wall.

How are enzymes named?

They are usually named by adding the suffix -ase to the end of the substrate on which they act

What is the extra structure that Gram negatives have outside the wall? What's one function for it?

They have an outer lipopolysaccharide (LPS) membrane. Its strong negative charge helps evade phagocytosis and complement-mediated cell lysis. It provides a barrier to some substances like penicillin and detergents. Gram (-) are harder to kill

Chemical pathways: D → E - what's D and what's E?

They're both enzymes, D activates E and then E activates another

What is a typical use for phase-contrast microscopy in biomedical work?

To observe unstained, alive microorganisms

What are the two types of electron microscopes and what is the difference in the image between the two of them? What kinds of lenses are used to focus an EM?

Transmission and scanning EM. Transmission is more for viewing internal structures and transmission gives a clear 3D view of the object. Electromagnetic lenses are used

What are the basics for how fluorescence works? Which kind of light is used to "excite" the fluorescent molecule and what kind of light is emitted from it so we can see it? What is the most typical use for fluorescence microscopy in the biomedical field?

Ultraviolet light is used to excite molecules so they release light of a longer wavelength, producing bright shades of orange, yellow, or yellow green. The most typical use of this is fluorescent antibody staining, which determines whether an antigen is present.

What are the two kinds of techoic acids that are a unique component of the Gram positive cell wall? Remember - a lot of negative charge.

Wall techoic acids Lipotechoic acids

What are the 3 parts of a flagellum? Do all bacteria have them? What is the version of them called inside spirochete bacteria? What swimming motion do spirochetes exhibit? What's one disease caused by a spirochete?

Whip or filament (long outer part), hook (wider part outside cell), basal body (anchor to the cell wall and membrane). Spirochete's version is called axial filament, corkscrew movement; Lyme Disease. Not all bacteria have flagellum

How do you do chemical reactions at room temp? What's activation energy?

You can do chemical reactions at room temperature with the help of enzymes. Enzymes lower the activation energy (amount of energy required for a reaction to occur)