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Microbial Metabolism

-the sum of all biochemical reactions carried out by a living organism
-reactions that break down complex molecules into simpler ones, releasing energy
C6H12O6-->6 Co2
-motility (flagella)
-active transport across membranes
-anabolism (biosynthesis), which requires input of energy
-reactions that build complex molecules from simpler ones
-requires an input of energy (sunlight)
e.g. building new DNA polymers from nucleotides (replication)
-energy must first be input to break bonds and rearrange atoms (activation energy)
-enzymes function to lower the activation energy of a biochemical reaction, thus increasing the rate of reaction

little nudge-activation energy-required for breaking of two diff. twigs
-most are proteins, some are RNA's (ribozymes)
-increase reaction rates
-many enzymes couple two reactions, such as the release of energy and the performance of work
-end in "ase"
-non-protein molecule that is required for the enzyme to function
e.g. vitamins and minerals
-enzyme WITHOUT a cofactor
-contains the whole enzyme;active
Important enzymes and cofactors
-NAD+ (nicotinamide adenine dinucleotide)
-NADP+ (NAD and phosphate)
-FAD (flavin adenine dinucleotide)
-CoA (co-enzyme A)
-metal ions such as Mg2+, Fe2+, and Cu2+
Temperature and PH dependence pf enzymes
-enzyme activity is a function of protein 3D confirmation which is sensitive to PH and temp.
Enzyme Inhibition
reversible when protein binds with weak enzyme, but
irreversible when protein covalently bonds with an enzyme; it may also destroy the 2(secondary) and 3 (tertiary) structure
Competitive vs noncompetitive enzymes (with respect to active site)
-competitive-resemble the natural substrate and compete for the active site

-noncom.-alter protein conformation by binding to allosteric site
Examples of diff. types of inhibitors
1. Arsenic (V)--a phosphate analog that inhibits is COMPETITIvE..reversible.. but a person may die if not treated right away
causes a person to lose energy bc ATP stores are depleted and the system shuts down

2.Arsenic (III)-binds sulfhydryl groups of amino acids, disrupting protein tertiary structures (unfolding)
irreversible-break apart proteins;undo their structure
1000 times more lethal than arsenic V
Catabolism: energy-yielding metabolism
-reactions that break down complex molecules into simpler ones, releasing energy

carbs, lipids, proteins, and nucleic acids are used for energy
Aerobic Respiration
-used in carbohydrate catabolism
-requires oxygen
-high-energy electrons are stripped off a substrate molecule and used to generate ATP e.g. C-H bonds->high energy
-glycolysis (Embden-Meyerhof Pathway)
-Kreb's cycle
-Electron Transport Chain
Anaerobic Respiration
-functions w/out oxygen
Process of aerobic respiration
-high energy e- are stripped from substrate molecules, electron donors, and shuttled to O2, a terminal electron acceptor

Organic C + O2-> CO2 +H2O+ ATP
-the organic oxygen is oxidized to carbon dioxide and dioxide is reduced to water

exergonic-releasing energy
Oxid/redox reactions
oxidation involves losing e-

reduction involves gaining e-
10 step metab pathway; each step requires a diff. enzyme
-first 5 steps-energy investment phase
steps 6-10 energy conserving phase
products: 2 ATP and 2 pyruvate molecules
-requires an initial input of ATP
Substrate-level phosphorylation
an enzyme takes a phosphorylated molecule and removes it from another, and sticks it onto another molecule

it has to be an organic molecule that the enzyme takes the phosphorylated molecule from
Alternatives to glycolysis: pentose phosphate pathway
1. Pentose phosphate (phosphlogluconate) pathway
-glucose molecule broken down into 1 ATP and 2 NADPH

-ribose-5-phosphate (nucleotide synthesis)
-erythrose-4-phosphate (amino acid synthesis)
alternatives to glycolysis: enter-doudoroff pathway
glucose broken up into 1 ATP and 2 NADPH
-you end up with unique anabolic precursors and 2 pyruvate molecules
Kreb's cycle
aka citric acid cycle or TCA (tricarboxylic acid cycle)
-involv. 8 steps in which 2 carbons are completely oxidized in acetate (their e- are stripped) and become attached to dioxide forming carbon dioxide
-oxaloacetate is a carrier
-citrate (6carbon molecule)
-regenerates process back to oxaloacetate so that cycle can begin again
-end up with 3 NADH and 2 NAD+

there are 4 high-energy e- carriers per oxaloacetate group
originak cabon molecule is gone
-cycle occurs twice w/glucose splitting into 2 pyruvates
Electron transport chain
-majority of ATP produced here
-periplasm helps drive oxidative phosphorylation
-NADH donates e- to the first carrier, who passes it down the chain
-at each step a little bit of energy is lost
-the last protein carrier hands e- to oxygen , forming water
if there wasn't an e- acceptor at the end, the chain would stop

34 ATP per molecule are produced
FAD or FADH2 are the only ones that can donate e- in electron transport chain
measures the proton concentration
-the inside of the periplasm can be three levels off from the outside
-ATP synthase (an enzyme)/ ATPase helps push the H+ against the concentration gradient; it snaps ADP and phosphate molecule together
Anaerobic environments
mouth (contains biofilms), urethra, vagina, intestinal tract*, overexerted muscles
*some bacteria (like feces) take and require alot of oxygen, leaving less oxygen for intestinal tract

puncture wounds are often anaerobic-clostridium tentinum, a strict anaerobe
Anaerobic terminal electron acceptors (TEA)
-Mn (IV)
-Fe II
-So4 2-
-leads to spoilage of food by microorganisms
-production of alcoholic beverages or acidic dairy products (cheese)
-only anaerobic energy-yielding process that doesn't make use of electron microscope
the building up of new molecules
Where does the carbon come from in order for biosynthesis to function?
a. preformed organic compounds (heterotroph)-humans

b. Co2 (autotroph)-self feeders such as plants, algae, and bacteria
Where does the carbon molecule's
energy come from?
a. light (phototroph)

b. chemical (chemotrophs)

most heterotrophs are chemotrophs and most autotrophs are phototrophs
Where do the carbon molecules get their electrons from?
a. preformed organic compounds (organotrophs)

b. inorganic compounds (lithotrophs_
What classification are humans?
hetero, chemo, organotrophs
How can we classify E-Coli nutritionally?
E-Coli can live off glucose alone
-chemoorganohetertroph->energy from chemicals, electrons and carbon from organic compounds
What do the cells make sure there is present (or not present) before they replicate?
cells ask:
-are there enough nutrients around?
what can promote or hinder replication?
Binary fission
1. DNA replication
2. Cell Elongation and chromosome separation
3. septum formation
4. daughter separation

daughter cells that don't separate are streptococci, staphylococci, diplococci, and streptobacili
Exponential growth
-def: entire pop. doubles
at best conditions, one cell becomes two in about 20 min
e.g. Tuberculosis doubles every couple of months due to its thick peptidoglycan wall
Growth rates
generation time-aka doubling time; time required for one cell to become two
-can be as low as 20 min but is typically 1-3 hrs.
Bacterial growth stages: lag phase
1. Lag phase-
cells sense their environment and gear up to take advantage of available resources
-can last as little as a few minutes or days, or months, even years depending on conditions
Bacterial growth: exponential phase (logarithmic)
cells are optimized for growth under the environmental conditions present
-numbers increase by a constant, normalized (per cell basis) rate, but at an ever increasing absolute rate--sheer numbers are increasing faster
-cells are most susceptible to antibiotics in this phase
Bacterial growth: stationary phase
no net increase or decrease in cell number
-cells continue to function
-growth is limited/halted because of either:
a. resource availability or
b. waster accumulation or both

-this phase can last a long time; resources are limited, there aren't many nutrients to build new cells "closed system" e.g. mostly human body

in open system, new nutrients are being brought in and wastes are discarded properly e.g. our bloodstream is the closest we have to an open system aka sepsis->prone to infections
Fastidious microbes
-picky microbes; only grow when specific nutrients are met..fresh sheep blood agar is good nutrient for them
Bacterial growth:death phase
death rate is greater than division rate
-resources may still be available
-waste accumulates and becomes limiting
Chemical requirements for microbial growth
1. Macronutrients and electron donors- carbon, nitrogen, sulfur, and phosphorus

2. Micronutrients- trace elements, growth factors that are required when the cell can't build its own vitamins

3. Electron acceptors-oxygen for aerobic processes
Macronutrients and electron donors
-sources of CARBON (carbs, lipids, proteins), NITROGEN (nucleotides, amino acids), PHOSPHORUS (ADP to ATP, phospholipids can limit overall growth when they run out), and SULFUR (disulfide bridges and acts as cofactor) are essential for the biosynthesis of the cell
most often the carbon source is also the energy source (i.e. electron donor)
-used in electron transport chain and oxidative phosphorylation
Micronutrients: trace elements (minerals)
-mostly act as cofactors for enzymes
apoenzyme+enzyme cofactor->holoenzyme (whole enzyme)
Respiratory (aerobic) terminal electron acceptors
-oxygen (O2)
-nitrate/nitrite (no3-/no2-)
-carbon dioxide
Classification according to oxygen requirements
1. Obligate aerobes-oxygen is required O2
2. Facultative aerobes- oxygen is preferred, but other e- acceptors or fermentation can be employed
3. Obligate anaerobes- acceptor other than oxygen is required; it is often toxic to these organisms; can be fermentative

4. Microaerophiles- oxygen is required, but in low concentrations; oxygen is often toxic to these organisms

5.Aerotolerant anaerobes-acceptor other than oxygen is required; oxygen is not toxic to these organisms
Bordetella Pertussis
whooping cough
-strickly aerobic, non-motile, gram negative, bacillus (rod)
-found in upper respiratory tract because there isn't any oxygen in lower intestinal tract
Vibrio cholerae
-faculatively anaerobic, gram negative
Clostridium botulinum
-obligately anaerobic, gram positive, bacillus, non-invasive-does poor job invading our host cells
spores aren't sensitive to oxygen even when host cell dies
our muscles contain it, it bubbles over, producing oxygen when hydrogen peroxide is added to a cut
Physical requirements for microbial growth
1. temp
2. PH
3. Salinity
all these denature proteins, make them lose their functions
-any chemical reaction, including enzyme-catalyzed reactions will increase with increasing temperature
-enzyme-catalyzed reactions are limited by the stability of the protein catalyst
-proteins are stable at low temperatures and denature at higher temp.
e.g. pepsin and trypsin break down proteins in stomach-enzymes fold at an optimum pH
increasing temp= a change in pH and salinity
-optimum is in pH and salinity and after that optimum, the protein denatures (higher)-irreversible-
colder (lower)-slows down chemical reaction, reversible
-generation time shortens as temp increases
high sugar or salt content-cell loses water; drawn out of the cell and proteins denature...hypertonic

isotonic-equal sugar or salt;free exchange of water

hypotonic-low sugar or salt;cell gains water

tonicity=dissolved substances content
-bacteria and other microorganisms attached to a solid surface and embedded in a contiguous layer of EPS
2.growth by binary fission
3.dispersal (in time organisms escape, looking for other food surfaces)
bacteria shed flagellum when they enter biofilms
What do biofilms do?
-give persistent infections
-show the inefficacy of antimicrobials and disinfectants/detergents
-impede tissue repair as long as biofilm is present
-direct and continue tissue damage
e.g. an open wound can contain a biofilm that won't go away so that surgery/amputation are the only way to get rid of it;antibiotics won't kill it
Where do biofilms form?
-urinary catheters
-heart valves and other indwelling devices including prostheses
-superficial wounds
-periodontal disease (plaque, cavities, gingivitis)
-otitis media
-cystic fibrosis pneumonia->most patients die from biofilms in lungs