Term
Regulation of cAMP
*When glucose is available
**When glucose is unavailable |
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Definition
*Enzyme system transfers phosphate to glucose
** Enzyme system transfers phosphate to adenyl cyclase and cAMP is made |
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Term
| What controls level of cAMP? |
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Definition
□ Get it by getting rid of 2 phosphates from ATP, which adenyl cyclase does
□ Adenyl cyclase |
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Term
Adenyl cyclase
*increase
**decrease |
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Definition
| ® Increase of glucose than adenyl cyclase decreases ® Decrease of glucose than adenyl cyclase increase |
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Term
| Catabolite activator protein (CAP) |
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Definition
Also called cyclic AMP receptor protein (CRP)
Exists in 2 forms
- Active form when cAMP is bound
- Inactive form when free of cAMP
• The only way lac operon is active is when there is lactose and no glucose so cAMP can bind to CAP and transcription will occur, the repressor will be inhibited from lactose and adenyl cyclase will make cAMP. |
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Term
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Definition
| cyclic adenosine monophosphate - It activates CAP |
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Term
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Definition
When you use one carbon source for growth than switch to another allowing for a short stationary phase between the 2
*Catabolite repression plays a role in this pattern of growth |
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Term
Porin protein functions
OmpC?
OmpF? |
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Definition
OmpC is smaller porin protein
- Dominant when e coli is in high osmolarity intestinal tract
- Lower levels of diffusion
OmpF is larger porin protein
- Dominant when e coli is in dilute environment
- Allows more diffusion on solutes |
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Term
Phosphorelay system of porin proteins
envZ?
ompR? |
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Definition
*Regulate expression of porin proteins (ompC and OmpF) depending on osmolarity
• env Z (sensor kinase)
- Autophosphorylates in high osmolarity
•ompR (response regulator)
- Phosphorylated and regulates transcription |
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Term
| 2 component regulatory system |
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Definition
• 2 proteins govern pathway
- Sensor kinase
- Response-regulator protein |
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Term
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Definition
• Extracellular receptor for metabolite
• Intracellular communication pathway |
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Term
| Response-regulator protein |
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Definition
• Activated by sensor kinase
• DNA binding protein
□ Activator-enhances transcription when needed
□ Repressor-inhibits transcription unless needed |
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Term
| Mechanisms used for global regulation |
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Definition
Global regulatory systems often use many types of regulation such as :
- Two component signal transduction systems
- Phosphorelay systems
- Regulatory proteins
- Alternative sigma factors |
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Term
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Definition
- Has gene X that is only produed under certain environmental conditions.
- Gene x has a transcriptional control
- Molecule x outside the cell binds to the receptor on the membrane which send a signal to a functional molecule inside the cell that send a signal to gene x |
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Term
| Global regulatory systems |
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Definition
• Affect many genes and pathways simuoltaneously
• Regulon
- Genes or operons controlled by a common regulatory protein.....Ex) CAP
• Modulon
- Operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators |
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Term
| Regulation of translation by small RNA molecule |
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Definition
small (sRNAs) or noncoding (ncRNAs) RNAs
- Some (antisense RNAs) are complementary to mRNA and function by base pairing
- May inhibit or enhance translation |
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Term
| Regulation of Translation |
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Definition
• SD--- shine delgardo sequence--->binding spot for the ribosome
• Ligand is a molecule that binds something
• Riboswitches in gram-negative bacteria regulate translation of mRNA
- Effector binding elements at the 5' end alters mRNA leader folding pattern
• Translation initiation can also be controlled by some small RNA molecules |
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Term
Riboswitches
(sensory RNAs found on mRNA) |
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Definition
• A specialized of transcription attenuation
• Riboswitches in gram positive bacteria function in transcriptional termination |
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Term
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Definition
• Transcriptional control by a protein (AraC) that acts both positively and Negatively
- Activity depends on environmental
conditions
- Inactive when arabinose present
- Active when arabinose absent |
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Term
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Definition
Regions
1:2--> stem loop
3:4-->stem loop (terminator)
2:3-->stem loop antiterminator
Region 1 is part of the leader peptide (trpL)
-has 2 adjacent trp codons |
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Term
| Regulation by attenuation |
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Definition
• Controlling of transcription termination
• First demonstrated with trp operon
• More recently riboswitches have been demonstrated to
also play a regulatory role |
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Term
| The tryptophan (trp) operon |
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Definition
• Consists of 5 structural genes
• Negative repressible genes by trp repressor
• Operon only functions in the absence of tryptophan |
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Term
| Positive control of the lac operon |
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Definition
• Regulated by Catabolite activator protein (CAP)
- Allows for preferential use of glucose |
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Term
| regulation of the lac operon by the lac repressor |
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Definition
• Cis acting elements
- DNA sequences where regulatory proteins binds
- In area of the gene
• Trans acting elements
- Regulatory proteins that bind to Cis-acting elements |
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Term
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Definition
• Tetramers of repressor form and bind to the three operator sites (O1, O2, O3)
• Allolactose is inducer |
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Term
| negative control of lactose (lac) operon |
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Definition
• Inducible genes
- Three structural genes
- Lac repressor (lacl) binds operator
• Inhibits transcription
• Enzymes normally not produced unless lactose present |
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Term
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Definition
• Codes for genes needed to breakdown lactose
• Under positive and negative control
- Negative control
• Lac repressor which binds to operator
- Positive control
Catabolite activator protein (CAP) which binds to CAP site |
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Term
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Definition
• Genes under coordinate regulation
- Share promoters
- Share operators and other regulatory regions |
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Term
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Definition
• Modified by small effector molecules
- Non-covalently bind regulatory proteins
- Interactions between effector and regulatory protein affect transcription |
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Term
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Definition
| • Activator protein at a regulatory region stimulates transcription |
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Term
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Definition
• Repressor protein at regulatory site (operator)
• Repressor proteins
- Stop transcription
- Exist in active and inactive (aporepressor) forms
- Inducers and corepressors affect activity of repressor |
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Term
| Control of transcription initiation by regulatory proteins |
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Definition
• Turned on happens in different ways and requires regulatory proteins
- Induction
- Repression
• Inhibit transcription (negative control)
• Promote transcription (positive control)
**Regulated by inducers, corepressors and inhibitors |
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Term
| Control of transcription initiation by regulatory proteins |
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Definition
• Induction and repression occur because of the activity of regulatory proteins and DNA binding domains
• These proteins either inhibit transcription (negative control) or promote transcription (positive control) |
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Term
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Definition
• Enzymes that function usually in an anabolic pathways
• Present unless the end product turns them off |
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Term
| Inducible genes B-galactosidase enzyme |
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Definition
• Inducible enzyme usually functions in a catabolic pathway
• Require presence of inducer or effector molecule |
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Term
Regulation of transcription initiation
(CRI) |
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Definition
• Replacement of degraded enzymes
• Constitutive genes (house keeping genes)
- Always on
• Inducible genes
- Gene is off until you turn it on
• Repressible genes
- Gene is on until you turn it off |
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Term
| 2 approaches to regulation |
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Definition
• Regulation of gene expression
• Alter activity of enzymes and proteins |
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Term
| Type V protein secretion pathway |
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Definition
• Recently discovered
• Need sec-dependent pathway
• Can form a channel in outer membrane through which they transport themselves; hence they are called autotransporters |
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Term
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Definition
- Secrete proteins
- Secrete DNA from donor to recipient bacterium during conjugation
- Found in both gram + and gram - |
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Term
| Type III protein secretion pathway |
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Definition
• Secretes virulence factors of gram-negative bacteria
• Across both plasma membrane and outer membrane, and into host
• Some type III secretion machinery is syringe-shaped
- Forms injectisomes |
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Term
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Definition
• Bacteria and some archaea
• Moves across plasma membrane
• "twin" arginine residues in their signal sequence
• Works with type II secretion system |
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Term
| Type II protein secretion pathway |
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Definition
• Plant and animal pathogens (gram negative)
• Periplasmic across outer membrane
• Observed in some gram-negative bacteria, including some pathogens
• Complex systems consisting of up to 12-14 proteins |
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Term
| Type I protein secretion pathway |
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Definition
- Related to ABC transport systems
- Gram-positive/gram-negative bacteria, and archaea
- Secretion of toxins, proteases(gelatinase) , other proteins |
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Term
| protein secretion pathway that are sec-dependent and sec-independent |
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Definition
Type I and III are sec-independent
Type II, V, IV are sec-dependent(only across the outer membrane and not periplasmic space |
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Term
| Protein secretion in gram-negative bacteria |
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Definition
• Six proteins secretion systems identified
• Types I and IV also in gram positives
• Types II, III, and V are unique to gram-negatives
○ Most secrete virulence factors |
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Term
Sec-dependent pathway
(A.K.A general purpose pathway) |
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Definition
• Translocates proteins from cytoplasm to or from the plama membrane
• Secreted proteins synthesized as preproteins having amino-terminal signal peptide
• secY, secE, and secG form a channel in the membrane
• secA translocates preprotein through the plasma membrane. When preprotein emerges from plasma membrane a signal peptidase removes the signal peptide |
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Term
| Common Translocation and Secretion systems |
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Definition
• Sec-dependent pathway
- The major pathway for all bacteria for transporting proteins across the plasma membrane
• Gram negative bacteria
- May use sec system
- Also must cross the outer membrane using types I,II,III,IV,V systems
• All pathways require energy |
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Term
| Protein translocation and secretion in bacteria |
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Definition
• Numerous protein secretion pathways have been identified
- Some reside in all 3 domains
- Some unique to bacteria and archaea, gram negative cells, and gram positive cells
• Translocation
• Secretion |
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Term
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Definition
- Movement of proteins from cytoplasm to plasma membrane or periplasmic space
§ Include transport proteins, ETC proteins, proteins involved in chemotaxis and cell wall synthesis, enzymes |
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Term
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Definition
- Movement of proteins from the cytoplasm to external environment
§ Hydrolytic enzymes for nutrient break down |
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Term
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Definition
• Removal of part of polypeptide before folding
• Inteins-get rid of
• Exteins-keep |
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Term
| Protein folding and molecular chaperones |
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Definition
• Molecular chaperones
- Proteins that aid the folding of nascent poly peptides
- Protect cells from thermal damage
§ Eg. Heat-shock protein
- Aid in transport of proteins across membranes
. DnaJ prevents the dna from folding abnormally |
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Term
| Amino-acyl tRNA synthases |
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Definition
• Very accurate and error Rate is very tiny
• "charge" tRNA |
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Term
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Definition
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Term
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Definition
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Term
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Definition
• Genotype--gene sequence
• Phenotype--physical features
- Produce lactose |
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Term
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Definition
-the site of RNA polymerase binding --RNA polymerase holoenzyme
• Core polymerase and sigma factor(necessary for binding the promoter) |
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Term
| 3 major groups of chemolithotroph |
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Definition
• Have ecological importance
• Several bacteria and archaea oxidize hydrogen
• Sulfur-oxidizing microbes
- Hydrogen sulfide (H2S), sulfur(So), thiosulfate (S2O3^2-)
• Nitrifying bacteria oxidize ammonia to nitrate |
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Term
| Fermentation (pyruvate pic ) |
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Definition
• Homolactic fermenters-make lactic acid
• Heterolactic fermenters-- makes lactic acid primarily
• Food spoilage
• Alcoholic fermentation---alcoholic beverages and bread
• Mixed acid fermentation... Ex.) E. coli
Acetyl-CoA can be fed into Krebs cycle |
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Term
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Definition
• Oxidation of NADH produced by glycolysis
• Pyruvate or derivative used as endogenous electron acceptor
• Substrate only partially oxidized
• Oxygen not needed
• Oxidative phosphorylation does not occur
• ATP formed by substrate-level phosphorylation |
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Term
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Definition
○ Loosing useful nitrogen
○ Reduction of nitrate to nitrogen gas
○ In soil, causes loss of soil fertility |
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Term
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Definition
• Branched
○ Low aeration-bd branch
○ High aeration-bo branch
• Complex I and complex IV no complex III and II |
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Term
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Definition
• Facultative, soil bacterium
• Extremely versatile metabolically
• Can do aerobic respiration
- Similar to process in mitochondria
- Protons transported to periplasmic space
- Can use one carbon molecules instead of glucose
Can use methanol
• Can denitrify |
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Term
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Definition
• uncouple ATP synthase from electron flow.
• Make the membrane permeable to protons.
• Stop PMF and the making of ATP
- Ex.) Dinitrophenol DNP |
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Term
| Bacterial and Archaeal ETCs |
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Definition
• Plasma membrane
• Some resemble mitochondrial ETC, but many are different
• Different electron carriers
• May be branched
• May be shorter
• May have lower P/O ratio |
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Term
Theoretical vs. actual yield of ATP
* What could affect ATP yield? |
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Definition
- Bacterial ETCs are shorter and have lower P/O ratios
- Environmental conditions
- PMF in bacteria and archaea is used for other purposes
Biosynthesis precursor need |
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Term
| ATP yield during aerobic respiration |
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Definition
• Maximum ATP yield can be calculated
• If P/O is 2.5 for NADH and 1.5 for FADH2,
- Actually probably lower
- ~32 ATP for total |
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Term
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Definition
• Complex I
• Complex II'
• Complex III
• Complex IV (electropositive) |
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Term
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Definition
(electronegative)
- Electrons from NADH get donated and H+ get pumped out |
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Term
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Definition
- Gets e-from FADH2 and gives e- to CoQ
- CoQ gets an e- from complex I |
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Term
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Definition
| - Gets e- from CoQ and proton get pumped across |
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Term
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Definition
electropositive)
- Get e- from complex III and protons get pumped across
- Gives e- to O2 to form H2O |
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Term
| ***cyanide--why is it so lethal? |
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Definition
- Because it effects and prevents the e- from going to oxygen
- Stops fermentation. Irreversible enzyme inhibitor |
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Term
| Electron transport system and formation of ATP |
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Definition
- Electron carrier proteins are located in the cell membrane space
- Elecctrons travel down the chain and protons are transported across the membrane with coenzyme Q
- Pair electron with O2 to form water |
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Term
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Definition
• Diffusion of protons back across membrane (down gradient) drives formation of ATP
• ATP synthase
- Uses PMF catalyze ATP synthesis
- 2 parts
§ F0-membrane region
§ F1--is the synthase where ATP is made |
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Term
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Definition
• For oxidative phosphorylation
- Protons move outward from the mitochondrial matrix as e- are transported down the chain
- Proton expulsion during e- transport results in the formation of a concentration gradient of protons and a charge gradient
- The combined chemical and electrial potential difference make up the proton motive force (PMF) |
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Term
| Oxidative phosphorylation |
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Definition
| • Process by which ATP is synthesized as the result of electron transport driven by the oxidation of a chemical energy source |
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Term
| The breakdown of glucose to pyruvate |
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Definition
• 3 common routes
○ Embden-meyerhof pathway
○ Pentose phosphate pathway
○ Enter-duodoroff pathway |
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Term
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Definition
Glucose + 2adp + 2Pi + 2NAD+
2 pyruvate + 2ATP + 2NADH + 2H+ |
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Term
| Summary of pentose phosphate pathway |
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Definition
Glucose-6-P + 12NADP+ + 7H2O
6CO2 + 12 NADPH + 12H+Pi |
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Term
| The tricarboxylic acid cycle |
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Definition
| • Also called TCA, Citric Acid Cycle, and Kreb's Cycle |
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