
Chemicals have properties. Biochemicals have both properties and ways of interacting with other chemicals eg. Fats vs. Carbohydrates. Fats form monolayers in water. Cell parts and Cells are the basic unit of life. They have attributes: Reproduction, metabolism, storage, transport, movement. We will look at a Prokaryotic cell from the outside in with an eye toward relating cell part properties to the biochemicals which compose them.
1. External Structures:
a. Glycocalyx or Capsule (computer slides)
1. Slime formation prevents dehydration.
2. allows for colony stability under adverse circumstances. Can be a big problem with biofilm development in catheters or industrial pipes. Dangerous source of infection in hospitals which is not readily removed by disinfection.
3. Non pathogenic organisms also have a capsule. Alcaligenes viscolactis is one of them.
4. Capsule can interfere with immune defenses of the host. It can interfere with phagocytosis. It swells during an infection, in many cases (Quellung reaction base of serological testing).
5. Streptococcus mutans sticks to teeth due to a capsule. Plaque becomes tartar if not removed.
6. Alcaligenes Viscolactis in milk.
b. Flagella--protein = flagellin. Anchored through the cell wall to a series of rings which rotate. Flagella is rigid and works more like an outboard motor than a whip. Must rotate thousands of times a minute in order to push cells with all that surface through water. 4mm to 6 mm per minute in E.coli. Flagella can rotate at 2500 rpm. All spirilla have flagella (axial filaments or endoflagella) about 1/2 of the bacilli and a few cocci.
DEFINITIONS:
4. Polar, lophotrichous, amphitrichous, peritrichous.
5. Runs and tumbles. Taxis, chemo, photo, thermo, magneto.
When a stimulus is present tumbles are inhibited and the flagella turns counterclockwise constantly toward the stimulus. This is positive taxis. When a substance initiates tumbles the cell's flagella go clockwise and the cell tumbles, resuming its run in another direction.
c. cell walls (exceptions--Mycobacterium, mycoplasma, archaebacteria, L-forms, spheroplasts, protoplasts.
1. Surrounding, encasing molecule is peptidoglycan. Visual.
2. Examine differences between Gram + and Gram - cell walls.

To the left is a gram stain of Staphylococcus epidermis done in our lab. The spherical cocci are tiny and are gram positive because they retain the primary stain crystal violet.
Below is a gram stain of a mixed culture of Micrococcus luteus (box like arrangements of cocci) with Escherishia coli. Micrococcus is gram positive while E.coli is gram negative. E. coli consists of very small delicate rods seen pink because they lose the primary stain as they are gram negative.
The gram negative cell wall of E. coli is much thinner than the wall of Micrococcus. Coli's cell wall also contains less peptidoglycan and more lipopolysaccharide.
3. Explain LPS and its role as an endotoxin and fever producer.
4. Also mention Spheroplasts and Protoplasts, L forms. Chlamydia and Rickettsia.
d. pili and fimbriae: Structures that allow sticking to surfaces---important in pathogenesis eg. UTI'"s, biofilms, teeth, glass, rocks (Pellicle formation in culture). Some Pili specialized. Sex pilus. 1946 experiment with minimal media showed genes transfered requiring contact. Define: auxotroph, prototroph, mutation rate. Minimal media (Glucose salts media). Mating types. F+ and F- (movie) e. other structures:
1. Chromatin Body--Long cirucular piece of DNA. Couple of thousand genes. It is haploid and relatively easy to manipulate eg...stick other genes into using bioengineering techniques.
2. Plasmids---small cirucular pieces of DNA (F factor is on a plasmid, Antibiotic resistance carried on plasmids). They are easily transferred from one cell to another. During sexual transfer recipient becomes F+.
3. Ribosomes---70s----50 + 30. Two parts. e. Mesosomes, endospores, fat globules, polyphosphate, Sulphur granules, magnetosomes, photosynthetic structures.
BIOCHEMICAL REACTIONS AND ENZYMES
I. Structure supports function. Function is physiology and metabolism. Metabolism is the sum of the biochemical reactions inside a cell. Lets take a closer look at how biochemical reactions or just ordinary chemical reactions occur.
A. Collision theory: This makes sense as an explanation of how two molecules may interact to form bonds. One bangs into another. If the collision is energetic enough--we see this as the reaction mixture being hot enough---or as Activation Energy---and if the vulnerable parts of the molecules are the ones that get hit, we get bonds breaking and new bonds forming.
H2O2 + I- ----> IO- + H2O IO-
+ H2O2 ----> O2 + H2O + I-
Two points should be made about the above reaction. It takes two steps to happen. I- is not used up in the reaction. The reaction occurs due to contact with I- where bonds are broken and new bonds formed. What bond is broken and what new bond forms? Also, I- is an inorganic small ion. Small inorganic species that speed reactions are called catalysts.
ENERGY DIAGRAM WITH AND WITHOUT A CATALYST
Define: Activiation Energy, catalyst (two examples), exergonic reaction, endergonic reaction. Show hydrogen peroxide and Iodide catalyst and catalase reaction. Explain how catalase identifies organisms Staph and Strep.

ENZYME ATTRIBUTES
1. Large protein molecules at approx 40,000 amu, Glucose substrate about 180 amu.
2. Denatured by heat--cooked potato vs. raw potato. Catalyst versus enzyme.
3. Lowers Activation energy by substrate binding at special place on the enzyme called the "Active Site"! There are other important sites on the enzyme but the active site is most important for catalysis.
4. Cofactors which bind and release from the Active site are often required (not always)...Vitamins and minerals act as cofactors. B vitamins often needed for energy reactions.
5 Efficient and able to process thousands of substrates per second. So only a small amount of enzyme needed to do reactions.
6. Can be interfered with. Example: Penicillin combines with an enzyme which is needed to put peptide cross links in cell wall material (Why is penicillin more active against gram positives?)
7. Delicate in that environmental conditions for use are narrow---pH, Temperature, Osmotic pressure, concentrations of substrates must be withing proper limits. Extremes can denature and kill cells.
FACTORS THE AFFECT THE ACTIVITY OF ENZYMES
1. TEMPERATURE
2. PH
3. CONCENTRATION OF SUBSTRATE
4. CONCENTRATION OF ENZYME
GRAPH THE AFOREMENTIONED VARIABLES AGAINST REACTION RATE..
ENZYME INHIBITION
1. Competitive Inhibition: Show succinic to fumaric acid and malonic acid inhibitor.
Succinic Acid Ž Fumaric Acid

Malonic Acid Inhibits the above reaction
2. Show structure of folic acid and PABA:
All inhibitors act at the active site. The inhibition is reversible by adding more substrate. New drugs are made which retain the properties of the inhibitor but which have new properties, like remaining in the urine longer etcetera.
When an inhibitor "looks like" the substrate of an enzyme it can inhibit it either reversibly or irreversibly. In irreversible inhibition the contact usually occurs in a place by covalent bonding and not just by stearic reactions.
Feedback Inhibition, Allosteric Inhibition, Endproduct Inhibition. Precursor Activation, Energy link control. Positive and Negative Feedback. All involve ligands and receptor.
INHIBITION AT THE LEVEL OF THE GENE.
FIRST DISCOVERED WAS THE LACTOSE ARRAY OF GENES THAT E.COLI HAS.
CALLED THE LAC OPERON--JACOB AND MONOD WORKED OUT THE MODEL: Wavy line made at R is repressor protein from R = repressor gene. I is the Incucer gene and a, b, c, and d are structural genes (make enzymes for lactose fermentation. Inducer can bind with repressor protein and "shut off".
I----a------------b--------------c--------------d-----------R------------> /\/\/\/\/\/\/\/
Structural genes for lactose
metabolism & repressor
(protein always on)(constitutive enzyme)
Another graphic with a promoter gene, which must be activated to turn system on:
LITHOTROPHS
PHOTOTROPHS
ORGANOTROPHS BREAK TO:
1. HETEROTROPHS (PARASITES, SAPROPHITES, Holotrophs)
2. Also Mutualistic bacteria and Commensals.
Metabolism is all reactions, break to:
A. Catabolic Reactions
B. Anabolic Reactions.
Example of catabolism is Glycolysis:
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