Exam 2 Flashcards
What are the two pathways for chemoorganotrophic fueling?
Respiration and Fermentation
Aerobic Respiration
O2 is the electron acceptor
Anaerobic respiration
Electron acceptors include NO3-, SO4 2-. CO2, Fe3+, and SeO4 2-
What process includes the electron transport chain leading to a proton motor force (PMF) that is used to synthesize ATP
oxidative phosphorylation
which pathway requires an electron transport chain to generate Proton Motive Force (PMF)?
Respiration
Is there PMF involvement in Fermentation?
no, the electrons go directly to endogenous acceptors
What is an example of an endogenous electron acceptor?
Pyruvate
How many carbons does Pyruvate have?
3
What are the three stages of aerobic respiration?
- Large nutrient molecules broken down to their constituent parts
- constituent parts further oxidized/degraded
- Partially oxidized products are fully oxidized to CO2 to produce NADH, FADH2, and a large yield of ATP
Organizing principles of Respiration
- A wide variety of molecules get funneled into a few metabolic intermediates
- The product of one reaction serves as substrate for the next
- Catabolic pathways degrade many nutrients to a few metabolic intermediates
- Reversibility in the system enables macromolecular synthesis
What is an example of reversibility in the system
Amphibolic pathways can be used catabolically or anabolically
What occurs in glycolysis?
sugars get broken down into pyruvate and related intermediates
What are the three major pathways of glycolysis considered by Prescott?
- Embden-Meyerhof (most common)
-Hexoses to pyruvate - Pentose phosphate/hexomonophosphate (also common)
-Generally used for biosynthesis - Entner-Doudoroff (microbial)
-Alternative hexose to pyruvate
Substrate level phosphorylation turns what into what?
it phosphorylates ADP into ATP
How many pyruvate and ATP does the Ebden-Meyerhof pathway yield?
2 pyruvate and 2 ATP
Why does Pyruvate make additional NADH and FADH in the Elden-Meyerhof pathway?
ATP
What is the Tricarboxylic Acid Cycle also known as?
The Citric Acid Cycle or the Krebs Cycle
Can the Krebs cycle/TCA cycle/Citric acid cycle run in reverse for biosynthesis?
Yes
How many ATP does aerobic respiration generate?
38
How many ATP does fermentation generate?
2
where does the TCA/Citric Acid cycle/Krebs cycle occur in eukaryotes?
The Mitochondria
Where does the TCA cycle/Krebs cycle/citric Acid cycle occur in prokaryotes?
the cytoplasm
Describe the structure of the Kreb’s cycle in regards to Carbons
- Pyruvate gets decarbobxylated and goes from 3 carbons to 2
- The 2 carbons combine with the 4 carbons of oxaloacetate and creates citrate, a 6 carbon molecule
- citrate changes arrangement and become isocitric acid (still 6 carbons)
- Another carbon is removed creating alpha-ketoglutarate, 5 carbon precursor metabolite. NADH is also formed
- The last carbon of glucose is released and NADH is used. The carbon precursor metabolite succinyl-CoA (4 carbon chain) is formed
- CoA is cleaved from succinyl-CoA to form GTP, with can be used to make ATP
- Succinct is oxidized to fumarate. FAD serves as the electron acceptor
- Fumerate reacts with H2O to form maleate
- Malate is oxidized, generating more NADH and regenerating oxaloacetate, which is needed to accept the 2 carbons from acetyl-CoA and continue the cycle
When is most ATP made?
When NADH and FADH2 are themselves oxidized by the ETC
Where is the ETC localized in prokaryotes vs. eukaryotes?
- Prokaryotic: plasma membrane
- Eukaryotic: mitochondrial membrane
What it’s he best electron acceptor?
Oxygen
what is the number of ATP from the TCA?
1
how does ATP synthase work in the mitochondrial ETC?
It spins to grab ATP and phosphate and turns it into ATP
How many times per second does the central rotor turn during ATP synthesis?
150
what does the E. coli transport chain depend on?
The concentration (low or high)
- the number of protons is different
if something says aerobic, what should we assume?
That the ETC is used
Why does anaerobic respiration yield less energy?
Because the E0 of final electron acceptor is generally less positive than E0 of O2
Is the final electron acceptor in fermentation endogenous or exogenous?
Endogenous
What causes glycolysis to stop in fermentation?
If NAD+ is not available
Does fermentation have a TCA cycle?
No, ATP is formed only by substrate-level phosphorylation, no oxidative phosphorylation occurs
What does the bacterial cell wall do?
- provides ridigity
- protection from osmotic lysis (bursting)
- protection from toxic substances
- pathology factor
- increased ability for microbe to function as a pathogen
- is an important antibiotic target
Synthesis of peptidoglycan
Nucleoside diphosphate involvement
- UPD-NAM
- UDP-NAG
the three compartments in peptidoglycan synthesis
- Cytoplasmic
- Membrane
- Periplasmic
Which two carriers “ferry” intermediated in peptidoglycan synthesis?
- UDP
- Bactoprenol
What inhibits L-Ala and D-Ala?
Cycloserine
What is required in Cytoplasmic synthesis I? What is not?
ATP is required, tRNA and ribosomes are Not
What is lipid I in cytoplasmic synthesis?
Bactoprenol-P-P-NAM-pentapeptide
Bactoprenol is a __-carbon alcohol
55
UDP-NAG + Lipid I —> ________+ _____
Lipid II + UDP
What is lipid II in cytoplasmic synthesis?
Bactroprenol-P-P-NAM (pentapeptide)-NAG
Bactoprenol transfers what across the membrane?
The completed peptidoglycan repeat unit [NAG-NAM (pentapeptide)]
peptide cross-linking causes peptidoglycan to become _________
Insoluble
Without cross-linking, the matrix lacks the strength to maintain _______
Righty
What is the smallest amino acid and is very flexible
Cystine
What inhibits transpeptidation in both gram + and gram - in E. coli traanspeptidation?
Penicillins
The removal of what occurs in both gram + and gram - E. coli?
The removal of D-Ala
What is a reason that “there may be a danger in underdosage” in administering penicillin?
Because exposing his microbes to non-lethal quantities of the drug makes them resistant
What is the central dogma?
DNA, RNA, and Protein
Nucleotides polymerize in which direction?
3’-5’
How many H-bonds are between A & T
2
How many H-bonds are between G & C?
3
In all Arcahea and most bacteria, DNA is in what double helix shape?
Circular
Is DNA more or less organized in eukaryotic chromatin?
More
DNA synthesis is in what direction?
5’ - 3’
What three things do standard DNA polymerases require?
- Template
- Primer
- Deoxynucleotide triphosphate
What direction is the leading strand in?
5’-3’
what direction is the lagging strand in?
3’-5’
Primosome
Primate that makes short RNA primer and accessory proteins
What does RNA primer recruit?
DNA polymerase
When do Catenanes form?
When two circular daughter chromosomes do not separate
What temporarily breaks the DNA molecules so that the strands can separate?
Topoisomerase
What is the flow of genetic information?
DNA -> RNA -> protein
What are the three classic types of RNA?
- messenger RNA
- ribosomal RNA
- transfer RNA
What are the newly discovered classes of RNA in eukaryotes?
- siRNA (small interfering RNA)
- microRNA
- lnc RNA (long noncoding RNA)
What are the three stages of transcription?
-Initiation
-elongation
-Termination
Initiation
Binds RNA polymerase to the promoter region near the beginning of the gene
Elongation
Then occurs generating a complementary RNA copy
Termination
The final step of transcription when the RNA polymerase releases the newly formed RNA molecule
What is the definition is Gene
A protein-coding open reading frame (Start codon to stop codon)
What determines the amount of protein transcribed?
The amount of RNA transcribed
Holoenzyme = core enzyme + ________ factor
Sigma
Only what type of enzyme can begin transcription
Holoenzyme
in an Rho (p)-independent
- transcribed RNA contains a hairpin (multiple GC base-pairs) followed to as a stem
- polymerase pauses at the hairpin, and U-stretch paired with A in template is too weak an interaction to keep polymerase on the template
Rho (p)-dependent
- terminator region pauses transciption at a stem-loop (no
