micro exam 2

MRSA

methicillin resistant Staph. aureus

macrophage

white blood cell, phagocytic, fights infection

diderm

gram negative cells that have two membranes

CheA

sensor kinase

Filament

projects from cell surface, composed of protein flagellan (H antigen)

Basal Body

embedded in the cell surface, consists of a rod and several rings, a circular rotor

Hook

short, curved segment joining the filament to the basal body

Monotrichous

1 flagellum at 1 end of cell

Amphitrichous

2 flagella, 1 at each end

Lophotrichous

tuft of flagella at one or both ends

CheY

response regulator

siderosphores

bind to iron and bring to transporter

hemophore

gets iron from hemoglobin

types of work

mechanical, chemical, and transport

mechanical work

flagella rotation

chemical work

ATP synthase

transport work

proton pump

1st law of thermodynamics

Energy is conserved. It can be transferred, but not created or destroyed

2nd law of thermodynamics

Systems spontaneously evolve towards thermodynamic equilibrium, the state of maximum entropy

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catabolism

degradative reactions, compounds broken down to smaller molecules, energy liberated

anabolism

synthesis reactions, smaller molecules combined, energy consumed

oxidation

removal of electrons from a compound

reduction

addition of electrons to a compound

dehydrogenase/oxidoreductase

enzymes that catalyze REDOX reactions

oxidizing agents

remove electrons from a compound, reducing themselves

reducing agents

donate electrons to compounds, oxidizing themselves

standard redox potential (E’o)

* the more negative, the more likely to give up electrons
* the more positive, the more likely it will accept electrons

REDOX tower

compounds at the top are very reduced and good energy sources, compounds at the bottom are very oxidized and good electron acceptors

Co-Enzymes: the electron carriers

* NAD: nicotinamide adenine dinucleotide
* NADP: nicotinamide adenine dinucleotide phosphate
* FAD: flavin adenine dinucleotide
* CoQ: ubiquinone
* cytochromes

NAD

* can transfer 2 electrons
* shuttles electrons from glycolysis/TCA cycle to electron transport system (ETS)

NADP

* can transfer 2 electrons
* reduced form donates electrons to power synthetic reactions

FAD

* can transfer one or two electrons
* derived from riboflavin
* enzyme bound prosthetic group donates electrons to ETS

CoQ

* lipid soluble
* can transfer 2 electrons to ETS

Cytochromes

* membrane bound proteins
* easily oxidized or reduced to move electrons down the ETC

Heat unit of energy

1 cal = 4.84 J

Toxins that cleave NADH

* C. difficile toxin


* Diphtheria toxin
* Pertussis toxin
* Cholera toxin

C. difficile toxin

* actin
* requires fecal transplant

Diphtheria toxin

* EF-2
* protein synthesis

Pertussis toxin

* Gia
* inhibits adenylate cyclase

Cholera toxin

* Gsa
* activates adenylate cyclase
* treatment: water and IV antibiotics

Biological catalysts (enzymes)

* speed up reaction by lowering energy of activation
* example: nitrogenase can fix nitrogen (N2 + H2 = NH3) at ambient temp and only 1 atm, while industry uses 400 atm to produce ammonia

Catalytic cycle

1. enzymes contain an active site that has a high affinity for specific substrates
2. the substrate binds to the enzyme to form an enzyme-substrate complex
3. the binding of the substrate and enzyme causes bond change of the substrate (can make or break bonds)
4. products are then released and the enzyme is free to bind to other substrates

Competitive inhibition

enzyme inhibition where binding of the inhibitor to the active site on the enzyme prevents binding of the substrate (example: sulfa drugs have a higher affinity for DHPS than the substrate)

Non-competitive inhibition

inhibitors reduce the activity of the enzyme and bind equally well to the enzyme, whether or not it has already bound the substrate. Inhibitor has a different binding site than substrate (allosteric site)

allosteric activators

enhance enzyme activity

allosteric inhibibitors

decrease protein activity

feedback inhibition

an enzyme catalyzes a product, and once that product accumulates to a certain level, the product inhibits the enzyme to regulate the levels of product

metabolism

the sum of all chemical reaction in a cell (catabolism and anabolism)

EMP/Glycolysis

1. Phosphorylation of extracellular glucose by phosphoenolpyruvate (PEP) carbohydrate phosphotransferase system to form glucose 6-phosphate. Consumes 1 ATP.
2. Glucose-6-phosphate is converted to fructose-6-phosphate by phosphohexose isomerase (isomeration reaction because fructose is an isomer of glucose).
3. \*Regulatory step!!! Fructose-6-phosphate is phosphorylated to fructose-1,6-diphosphate by phosphofructo-kinase (PFK-1). 1 ATP is consumed. Irreversible pathway, so a different pathway must be used to do the reverse conversion during gluconeogenesis. Rate-limiting step.

Activator: Magnesium ADP

Inhibitor: PEP


4. Fructose-1,6-diphosphate (6C) is split by fructose bisphosphate aldolase into dihydroxyacetone phosphate (3C) and 2-glyceraldegyde-3-phosphate (3C).
5. Triose phosphate isomerase isomerizes dihydroxyacetone phosphate into 2 glyceraldehyde 3-

phosphate.


6. 2 glyceraldehyde-3-phosphates are dehydrogenated and organic phosphate is added to them via glyceraldehyde-3-phosphate dehydrogenase to make 2 1,3-bisphosphoglycerate. The hydrogen is used to reduce 2 NAD+ to make 2 NADH + 2H+.
7. 2 1.3-diphosphoglycerates have a phosphate group removed and transferred to ADP by phosphoglycerate kinase to form 2 ATP and 2 3-phosphoglyerate. At this step, ATP consumed = ATP made. This reaction is substrate level phosphorylation
8. 2 3-phosphoglycerate are transformed into 2 2-phosphoglycerate by phosphoglycerate mutase.
9. 2 2-phosphoglycerates are transformed into 2 phosphoenolpyruvates. 2 H2O are produced.
10. 2 phosphoenolpyruvate are substrate-level phosphorylated into 2 molecules of pyruvate and 2 ATP by the enzyme pyruvate kinase.

EMP/Glycolysis yield

* 2 ATP per glucose
* 2 NADH + H+ per glucose
* 2 pyruvate per glucose

EDP Pathway

* yields 1 ATP, 1 NADH, 1 NADPH per glucose
* not used in eukaryotes, only pathway for cyanobacteria
* major pathway in N. gonorrhea, Pseudomonas, and Streptococcus
* minor pathway for E. coli

PPP Pathway

* yields 2 NADPH per glucose
* produces erythrose 4-P and ribose 5-P

cw rotation

cell tumbles

ccw rotation

cell runs

macronutrients

carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur

micronutrients

potassium, magnesium, calcium, and iron in small amounts

autotroph

produce organics from inorganics

heterotroph

requires organic compounds

organotroph

obtain nutrients from organic compounds

lithotroph

obtain nutrients from inorganic compounds

phototroph

obtain nutrients from light

chemotroph

obtain nutrients from chemical reactions of compounds (litho and organo are both chemotrophs)

primary active transport

* use energy from ATP hydrolysis to move substances across a chemical gradient
* uniporters move a single molecule at a time
* ATP binding cassette transporters are primary active transporters

secondary active transport

* cotransporters move two molecules at a time
* the two substances are the ion powering the gradient
* powered by chemiosmosis

aquaporins

integral membrane proteins, allows water to flow more rapidly than regular diffusions

symport

when ion and molecule move in the same direction

antiport

when the ion moves in the opposite direction as the molecule

quorum sensing

regulatory process that ensures there is a sufficient cell density before a specific gene product is made

covalent modification

Covalent modification is a chemical process that involves the covalent attachment or removal of functional groups to or from a protein, DNA, or other biomolecules. This process can alter the activity, stability, or localization of the biomolecule, and is often used as a regulatory mechanism in biological systems. Examples of covalent modifications include phosphorylation, acetylation, and glycosylation.

oxidative decarboxylation of pyruvate

* enzyme complex: pyruvate dehydrogenase multienzyme complex
* 5 steps: 1. pyruvate decarboxylation 2. HETPP TPP lipoamide 3. transfer acetyl to coenzyme A 4. FAD and FADH 5. NAD, NADH and H+
* LINK BETWEEN GLYCOLYSIS AND KREBS CYCLE
* products per pyruvate: acetyl coA, NADH, H+, and CO2

Krebs Cycle/TCA Cycle/Citric Acid Cycle

* net yield: 2 CO2, 3 NADH, 1 FADH2, 1 GTP per 1 acetyl CoA
* regulated step: isocitrate hydrogenase (kinase= inactive, phosphotase= active)

electron transport functions

1. establish and maintain a steep hydrogen ion gradient across membrane
2. re-oxidize coenzymes (NADH, NAD+)
3. dispose of low energy electrons to final electron acceptor

proton motive force (PMF)

* ATP synthesis
* flagella rotation
* active transport

substrate level phosphorylation (SLP)

produces ATP by transferring a phosphate group from a high energy substrate directly to ADP

Glycolysis ATP yields

* oxidative phosphorylation: 2 NADH, 5 ATP
* substrate level phosphorylation: 2 ATP

Pyruvate decarboxylation ATP yields

* oxidative phosphorylation: 2 NADH, 5 ATP

Krebs cycle ATP yield

* oxidative phosphorylation: 6 NADH, 15 ATP, 2 FADH2, 3 ATP
* substrate level phosphorylation: 2 ATP (GTP)

Total ATP yields

32 ATP

fermentation

* organics (such as pyruvate) serve as final electron acceptor
* energy yield per glucose: 2 ATP
* main function: bacteria must generate NAD+ from NADH

Pasteur Effect

* anaerobic conditions: low growth rate, high glucose consumption
* aerobic conditions: high growth rate, low glucose consumption

homolactic fermenter

reduce most of the pyruvate generated by glycolysis into lactate

heterolactic fermenter

form lactate and other end products like ethanol and CO2; more than one fermentation pathway

mixed acids fermentation

* ATP yield: 2.5 per glucose

2,3 butanediol fermentation

* yields butanediol, ethanol, and lactic acid

fermentation’s role in nature

degrade complex organic material like cellulose

anaerobic respiration

* inorganic other than O2 serve as final electron acceptor: nitrate, sulfate, carbon dioxide

anapleurotic reactions

restore to optimal level of OAA (keeps oxidative phosphorylation high)

C4 Pathways

* Wood-Workman reaction
* Pyruvate + CO2 + NADPH
* Gluconeogenesis

Wood-Workman reaction

PEP + CO2, OAA + Pi

enzyme: pep carboxylase

Pyruvate + CO2+ NADPH reaction

enzyme: malic enzyme

Gluconeogenesis

* pyruvate + CO2+ ATP, OAA + ADP + Pi
* enzyme: pyruvate carboxylase

C3 Pathway

* first step in dark reactions of photoynthesis
* ribulose 1,5-bip
* enzyme: RUBISCO

Nitrogen fixation

* catalyzed by nitrogenase
* inhibited by O2
* uses H+ as electron donor and ATP as energy source

aminations

* amino group is introduced into an organic molecule; used to synthesize amino acids

transaminations

* reaction between an amino acid and keto acid where amine and keto groups are switched

The first step in nitrogen assimilation is:

the conversion of N2 to NH3

Nitrogen cycle

HN4+ + NO2- yields N2 + 2 H2O

Penicillin

* the first antibiotic
* discovered by Fleming in 1928

Beta-Lactams

* penicillins (fungus product)
* cephalosporins (fungus product)
* monobactams (bacterial products)
* carbapenems (Streptomyces product)

Beta-Lactam Characeristics

* broad spectrum
* all contain a lactam ring
* especially effective against Gram + organisms
* cell wall synthesis inhibitor