Exam 2 Flashcards
What are the major elements of the human body?
Carbon, oxygen, hydrogen, nitrogen, and trace sulfur, iron, phosphorous, and potassium
What are the four major macromolecules?
Protein, RNA, DNA, lipids, carbohydrates
Who are Miller and Urey? What did they do?
They demonstrated that organic compounds may have originated naturally from inorganic compounds by replicating the environment of the early earth
Describe a synthesis reaction (ex: building sugars)
requires ATP and releases water
How do sugars preform different functions?
they branch differently
branched glucose is starch, branched cellulose for granules, lines of cellulose for fibers
Describe MacConkey Media
bacteria that metabolize lactose show up pink, media selects against gram positive
Describe Hektoen Media
indicates lactose fermentation and H2S production, selects against gram positive
Describe photoautotrophs
light and CO2
Describe photoheterotrophs
light and organic C
Describe chemoautotroph
inorganic C and CO2
Describe chemoheterotroph
organic C
What does obligate mean in terms of metabolism?
cannot choose method of metabolism
What does facultative mean in terms of metabolism?
can choose method of metabolism
What is fermentation?
The production of acids and alcohols as a way to partially oxidize glucose
A process that uses an organic molecule (pyruvate) as its final electron acceptor to regenerate NAD from NADH so that glycolysis can continue
What is respiration?
the ability to use an external electron acceptor to fully oxidize glucose and generate further ATP from oxidative phosphorylation
What is redox potential?
The tendency for a molecule to acquire electrons and become reduced; electrons flow from molecules with lower redox potentials to those with higher redox potentials
What is substrate level phosphorylation?
Direct method of ATP production in which a high-energy phosphate group is removed from an organic molecule and added to an ADP molecule
What is chemiosmosis?
The flow of hydrogen ions (proton motive force) across the membrane that powers ATP synthesis
metabolism
primarily about carbon, energy, and electrons
contains both anabolism and catabolism
catabolism
break things down and release energy
anabolism
use energy to build things
What are the three steps of glycolysis?
preparation (Glucose is split, investment of 2 ATP), redox reactions (investment of inorganicP, reduction of NAD+ to NADH), and substrate level phosphorylation (4ADP to 4 ATP)
Summarize glycolysis
requires 2 ATP and glucose, produces 2 NADH, 4 ATP, and 2 pyruvate
Summarize fermentation (typical)
pyruvate is reduced to lactate, NADH is oxidized to NAD
Summarize respiration
pyruvate is converted to acetyl CoA, producing CO2/NADH/FADH/ATP
How do you calculate the delta G naught of a reaction?
Delta G0 = Sum of Delta G0f (products) - Sum of Delta G0f (reactants)
What does exergonic mean? What does endergonic mean?
Negative Delta G0 is exergonic (release energy) and positive Delta G0 is endergonic (absorbs energy)
Summarize the Krebs/TCA cycle
Acetyl-CoA + 3 NAD+ + FAD + GDP + P → 2 CO2 + 3 NADH + FADH + ATP
Why can’t bacteria use the Krebs/TCA cycle?
They have an incorrect ratio of pyruvate to NADH (can only reoxidize so many NADH per pyruvate)
Bacteria cannot use this cycle because they cannot use the extra NADH/FADH because that would require a different ratio of pyruvate to NADH
What is the electron transport chain?
A series of oxidation/reduction reactions linked to generation of a proton motive force and ending with reduction of a terminal electron acceptor
Where are the proteins that are involved in electron transport?
Proteins involved in electron transport are in the cell membrane (innermost membrane of mitochondria)
What is oxidative phosphorylation?
The creation of ATP by linking electron transfer reactions to ATP synthesis. Oxidative phosphorylation uses chemiosmosis.
How do electrons move in the electron transport chain? From molecules with ________ to molecules with ___-
Electrons flow from electron donors (with a more negative Eh/oxidation potential) to electron acceptors
What is ATP synthase / ATPase? What drives it?
ATP synthase (or ATPase) is a multisubunit complex that can make ATP from ADP and P or break down ATP to ADP and P Driven by the return of protons to the cytoplasm across their gradient (proton motive force)
How do purely fermenting bacteria use ATP synthase / ATPase?
Reverse direction creates H+ gradient (soley fermenting cells cannot create a gradient on their own, which is needed to acidify a vesicle or create a lysosome)
Define anaerobic respiration
Not using oxygen as terminal electron acceptors
NAD+, FAD+, FMN+, Cytochrome C, Iron-Sulfur protein, Quinone, Menaquinone, Chlorophyll, Cytochrome b, Cytochrome c. Which transfer electrons only?
Iron-Sulfur protein, Cytochrome b, Cytochrome c
NAD+, FAD+, FMN+, Cytochrome C, Iron-Sulfur protein, Quinone, Menaquinone, Chlorophyll, Cytochrome b, Cytochrome c. Which transfer both electrons and protons?
NAD+, FAD+, FMN+, Quinone, Menaquinone
NAD+, FAD+, FMN+, Cytochrome C, Iron-Sulfur protein, Quinone, Menaquinone, Chlorophyll, Cytochrome b, Cytochrome c. Which transfer protons only?
None
Where is there a need for an iron source?
Electron transport chain
Where are protons pumped across the membranes in the electron transport chain?
3 locations, NADH reductase, Cytochrome Reductase, Cytochrome Oxidase.
Put the following in order for glycolysis:
ATP, Glucose, Pyruvate, Fructose-6-Phosphate, Glyceraldehyde-3-Phosphate, Fructose-1,6-diphosphate, Phosphoenolpyruvate(PEP), , Glucose-6-Phosphat, 3-Phosphoglycerate, 2- Phosphoglycerate, 1,3-Disphosphate
Glucose + ATP-> Glucose-6-Phosphate -> Fructose-6-Phosphate + ATP -> Fructose-1,6-diphosphate ->
Glyceraldehyde-3-Phosphate (production of NADH) -> 1,3-Disphosphate (production of ATP) 3-Phosphoglycerate -> 2- Phosphoglycerate -> Phosphoenolpyruvate(PEP) (production of ATP -> Pyruvate (production of NADH)
Put the following in order for the TCA Cycle:
Citrate, Malate, Oxaloacetate, a-ketoglutarate, NADH, succinyl-CoA, ATP, Succinate, FADH2, Fumarat, Isocitrate
Fumarate-> Malate-> NADH-> Oxaloacetate-> Citrate-> Isocitrate-> NADH-> a-ketoglutarate-> NADH-> succinyl-CoA-> ATP-> Succinate-> FADH2
SFMOCI
If the electron transport chain was stopped, ATP synthesis would ….
stop
If ATP synthase was stopped, the electron transport chain would…
slow down due to buildup of protons
If a proton permeable pore was added to a microbe, ATP synthesis would… and the electron transport chain would …
stop, be unaffected
What is proteomics?
all of the proteins that a microbe can make
What is transcriptomes?
all of the messenger RNA a microbe can make
How are genome sequences assembled?
Break genome into small segments, use algorithms/bioinformatics to look for overlapps and create a contiguous sequence, do detailed work with additional sequences to fill in gaps
How are genes found in DNA sequences?
ORF: Open reading frame
Look for start codon (ATG) then go codon by codon to find possible stop codons, narrow down by minimum amino acids, look for RBS, look for codon bias
What is genome annotation?
Computer goes through first and matches genes to similar genes in other organisms, then humans go through and check/add
Describe transformation
Some cells are naturally competent and can take up DNA from their environment and incorporate it into its chromosome
Describe the two subtypes of transduction
Virus mediated
Sometimes virus accidentally packages chromosomal DNA
Generalized
Virulent/temperate phages, host cell DNA, any gene
Specialized
Temperate phages, phage+host DNA, genes close to insertion site
Describe conjugation
Requires cell-cell contact
F plasmid wants to spread, enables its host to exchange DNA
DNA can be plasmid or chromosome (with plasmid inside)
Usually low efficiency unless plasmid is permanently part of the chromosome and brings along beneficial genes (F plasmid has no beneficial parts on its own)
High frequency recombination
How can conjugation be used in genetics?
Can be used to map chromosome, genes are transferred in the order they are in the chromosome
What is a prototroph?
Organism can grow on minimal medium without any supplements
What is a auxotroph?
A mutant strain which requires a specific supplement to grow on a minimal medium
Oxidation is the …. of electrons while reduction is the … of electrons
removal, addition
If glucose was only fermented, how many ATP would be produced?
2
Pyruvate is (oxidized/reduced) in normal respiration to acetyl CoA
oxidized
When pyruvate is fermented, it is (oxidized/reduced)
reduced (so that NADH can be oxidized to NAD)
What are the three methods of horizontal gene transfer?
conjugation, transduction, transformation
When glucose is converted to CO2, it is being (oxidized/reduced)
oxidized
What typically generates more ATP, substrate-level phosphorylation or chemiosmosis?
Chemiosmosis (during oxidative phosphorylation) is the movement of ions down their gradient. This includes the electron transport chain, which produces by far the most ATP
What is the fate of pyruvate in a microbe that uses respiration?
It is oxidized in the Krebs cycle
How is DeltaE(o) related to DeltaG(o)?
DeltaG(o) = -nFE(o)
inversely related
Cellular membranes can become energized due to the formation of a proton motive force, what ways can bacterial cells use this potential energy?
produce ATP, create lysosomes, power flagella, pair with ion transport (Na+H+ antiporter), store partial energy (can produce 1.5 ATP instead of 1, because the other half is stored as protons)
List some basic differences and similarities between fermentation and respiration using glucose as the carbon and energy source
fermentation: does not produce additional ATP during regeneration of NAD, does not require oxygen, can be used to produce a variety of products, pyruvate is final e- acceptor
(common) respiration:produces additional ATP, produces only CO2 and H2O, O2 is final e- acceptor, electron transport chain and citric acid cycle, oxidative phosphorylation
both: use pyruvate, regenerate NAD, redox reactions, include substrate-level phosphorylation
