Lecture 6 - Metabolism Flashcards
what is the definition of metabolism?
the sum total of all chemical reactions in a cell
what is the importance of metabolism?
metabolism is important because it helps with the identification of unknowns. this is because each bacterium has a unique metabolic signature (like a fingerprint) that can be used to identify it.
what is another reason for the importance of metabolism?
we can use the knowledge of unique metabolic processes that we can:
- Exploit commercially (example: oil degradation, making fermented products like cheese, and biofuel like ethanol.
- Use metabolism as antimicrobial “targets” to kill bad microbes.
what are the two categories of metabolism?
-Catabolism
-Anabolism
what is catabolism/catabolic pathways?
Catabolic pathways:
-Break down large molecules into small ones.
-Releases energy.
Example: catabolism of glucose
(hint: catabolism = cut)
what is anabolism/anabolic pathways?
Anabolic pathways:
-Build larger molecules from small ones.
-Requires energy.
Example: photosynthesis (building of glucose)
what links the two processes of catabolism and anabolism?
Energy and precursor metabolites (small molecules)
-(Catabolic processes harvest the energy that is released during the breakdown of molecules and uses it to make ATP. Catabolic pathways also produce precursor metabolites used in biosynthesis (which is anabolism)).
-(Anabolic processes (biosynthesis) synthesize and assemble subunits of macromolecules that make up the cell structures. Anabolic pathways also use the ATP and precursor metabolites produced in catabolism).
we store energy released from catabolic reactions and store it as what?
ATP
what is the function of ATP?
it is the energy currency of the cell
what is the potential energy of ATP?
it has high potential energy
why do we use ATP/why is it important?
because it:
-is an instantaneous source of energy.
-it is flexible (you can use less/more of it).
-is it rechargeable.
what is the structure of ATP?
adenosine triphosphate with 3 phosphates.
(adenine, ribose (sugar), and phosphate groups)
what does ATP become? what is it converted to?
ADP
adenosine diphosphate.
(adenine, ribose (sugar), and phosphate groups)
when energy is inputted into ATP, what does it become? when energy is taken out?
When energy is put in, it becomes ATP.
When energy is taken out of ATP, it becomes ADP + Pi. (This cycle goes on)
(Energy is released as a phosphate group and is ejected from ATP)
metabolic pathway:
A series of chemical reactions are catalyzed by _____ that convert substrate(s) into product(s)?
Enzymes
what are enzymes?
they are the macromolecules (proteins) to help start a reaction
what are in between the substrate and end products in a metabolic pathway?
intermediates
what is the function of enzymes? What is the role in metabolism?
they help catalyze (initiate and accelerate) chemical reactions.
Catabolism of glucose into smaller molecules like carbon dioxide and water releases
energy and electrons.
a. How is the energy stored in the cell?
b. what happens to the electrons?
a. How is the energy stored in the cell? The energy is stored in the cell as ATP.
b. What happens to the electrons? The electrons are first dumped onto empty dump trucks (NAD+ and FAD) to form loaded dump trucks (NADH and FADH2). Ultimately NADH and FADH2 dump electrons onto the terminal electron acceptors.
what is the structure of enzymes? what type of macromolecule are they?
protein
Enzymes bind to the reactant or ____ in a pocket called the ____ _____.
Substrate; active site
Enzymes catalyze a reaction to form a product that is then ejected from where?
from the active site
do enzymes change?
no they remain UNCHANGED at the end of the reaction
what is the requirement for enzymes to be attached to a substrate?
they just have to be really specific for the substrate
what are factors that affect enzyme activity?
temperature, pH, concentration, salt, regulators (activators and inhibitors), etc.
chemical reactions need an input of energy called _____ _____ to break the bonds between the atoms of the reactants?
activation energy
how do enzymes contribute to the activation energy?
enzymes lower the activation energy of reactions
what is the catabolism of glucose?
it is the breakdown of glucose that is the universal metabolic pathway
what is the purpose of the catabolism of glucose?
to get energy
in the catabolism of glucose, is it energy rich? what is the part that is energy rich?
yes it is, glucose is an energy rich energy source.
what are two ways that the catabolism of glucose breaks glucose down into simpler molecules?
- Respiration
- Fermentation
both respiration and fermentation involve what coenzymes that carry what?
-They both involve coenzymes NAD+ or FAD which carry electrons (e-) and protons (H+) as NADH and FADH2
both respiration and fermentation have what acceptor?
terminal electron acceptor
both respiration and fermentation create what sort of energy?
ATP
do respiration and fermentation create end-products?
yes
what are the three stages of respiration?
- Glycolysis
- Transition steps and Krebs cycle
- Electron transport chain
why is glycolysis called “sugar splitting”?
because it starts with 1 glucose that has 6 carbons (in the cytoplasm) and then produces 2 pyruvates that are 3 carbons each.
what is the net ATP and NADH in glycolysis?
2 ATP and 2 NADH
is oxygen required for glycolysis?
no
why do we need to make NADH during glycolysis?
Because we need to carry high-energy electrons released from the breakdown of glucose.
what do we have to input for glycolysis?
1 glucose, 2 ATP, 2 NAD+
where does glycolysis occur?
in the cytoplasm
what happens within the transition step?
both pyruvates are broken down to create 2 acetyl coa molecules.
when the pyruvates are broken down, what is released PER pyruvate? (transition step)
2 CO2, 2 NADH, 2 Acetyl-CoA
where does the transition step occur?
in the cytoplasm
each pyruvate that comes out of glycolysis becomes what, and which enters what?
each pyruvate that comes out of glycolysis becomes Acetyl CoA, which enters the Krebs cycle.
in total, after 2 turns of the cycle in the transition step, what is produced?
6 CO2
2 ATP
8 NADH
2 FADH2 (from both transition and krebs)
i think its:
4 CO2
2 ATP
6 NADH
2 FADH2
just from krebs
when acetyl coA goes into the Kreb’s cycle, what happens?
2 Acetyl CoA go into the Kreb’s cycle -
4 CO2, 6 NADH, 2 FADH, and 2 ATP are produced. (per both pyruvates/both acetyl coA’s)
what is the step after the Kreb’s cycle?
Electron Transport Chain
what is the electron transport chain a series of?
a series of e- carriers in the plasma membrane
what does the ETC receive?
it receives high energy e-‘s from the 10 NADH and 2 FADH2
what does the ETC pass along?
it passes e-‘s along carriers in the chain
where does the ETC occur?
in the plasma membrane
what is inputted for the ETC?
O2
10 NADH
2 FADH2
in the ETC, electron carriers do what 2 things?
- They extract energy from the high-energy electrons.
- Other electron carriers pump protons (H+) to outside the cell, using this energy to form a proton gradient (against conc. gradient, so it’s active transport)
in the ETC, energy of the electrochemical gradient is called what?
energy of the electrochemical gradient is called proton motive force (potential energy)
what is ATP synthase in the ETC? what does it do?
it is an enzyme that allows protons to reenter the cell down the concentration gradient. it then harvests the energy of the proton motive force to make ATP.
how does ATP synthase make the ATP? what is this process called?
it makes the ATP from ADP and Pi; this is called chemiosmosis.
what is the output produced after the ETC?
34 ATP and H2O
what is the formula of the respiration?
C6H12O6 + O2 —–> 6 CO2 + 6 H2O + 38 ATP
compare the location of where the following occurs in Prokaryotes vs Eukaryotes:
Glycolysis, Transition step, Kreb’s cycle, ETC
Prokaryotes:
Glycolysis- cytoplasm
Transition- cytoplasm
Kreb’s- cytoplasm
ETC- plasma membrane
Eukaryotes:
Glycolysis- cytoplasm
Transition- mitochondrial matrix
Kreb’s- mitochondrial matrix
ETC- mitochondrial inner membrane
in which stage do you get the maximum energy?
the electron transport chain
which stage is the glucose completely broken down in?
the Kreb’s cycle
what is aerobic respiration?
-Using O2 as the terminal electron acceptor
what is the end product in aerobic respiration?
H2O
how many ATP’s are made in aerobic respiration?
38 ATP’s in prokaryotes
what is anaerobic respiration?
-using no O2
what organisms use anaerobic respiration?
only bacteria
instead of using O2 as the terminal electron acceptor, what is used in anaerobic respiratin?
it uses another inorganic molecule such as nitrate or sulfate as the terminal e- acceptor
what are the end producs of anaerobic respiration?
nitrite and hydrogen sulfide
how many ATP’s are made in anaerobic respiration?
the ATP yield varies per organism, but less than 38 ATP’s are made
if E. coli had to choose between aerobic respiration, anaerobic respiration, and fermentation, which would it choose and why?
it would choose aerobic respiration because it makes the most ATP
what is fermentation? does it require O2?
no it does not require O2
is fermentation the same as anaerobic respiration?
NO
what does fermentation start with?
Glycolysis
does fermentation have the Kreb’s cycle or the ETC?
no, neither
fermentation uses ____ as a derivative as a terminal electron acceptor?
pyruvate
what does fermentation produce? (hint- how many ATP?)
a net of 2 ATP
Fermentation starts with a 6-carbon glucose molecule. It is split into 2 (3-carbon) pyruvate molecules. What are those pyruvate molecules converted into? Why?
They are converted into lactic acid by extracting NADH.
This happens because there is nowhere to dump the NADH (no O2, nitrate, or sulfate), so we dump the NADH on the pyruvate and get lactic acid.
what are the end products of fermentation?
-Lactic acid
-Ethanol + CO2
-Others (we get a variety of end-products)
In what 2 ways is fermentation useful?
Many end-products of fermentation are useful in:
1. The industry (food, beverages, solvents, etc.)
and
2. The microbiology lab to identify unknown bacteria.
If an organism had its choice of any metabolic pathway, which one would it prefer?
Aerobic respiration because it yields the most ATP. E. coli can do all 3, but again it prefers aerobic.
The most common starting pathway for the breakdown of sugars is:
Glycolysis
Enzymes act on _________ to produce _________
Substrates; products
In chemiosmosis, ATP is generated when:
Protons move across the membrane through ATP synthase
The transition step and Krebs cycle:
1. Produces 5 ATP
2. Produces 2 NADH
3. Produces 6 CO2
4. Produces 8 FADH2
5. Produces 6 H2O
- Produces 6 CO2
In fermentation, ATP is produced:
1. By glycolysis only
2. By glycolysis and the Krebs cycle
3. By glycolysis, Krebs cycle and electron transport chain
4. By anaerobic respiration
5. By catabolizing fats
- By glycolysis only
Escherichia coli can use three metabolic pathways to gain energy—aerobic respiration, anaerobic respiration and fermentation. How does it choose which one to use at any given time? Which one is the most efficient and why?
In order to use a particular metabolic pathway, the organism must have the necessary components for that pathway (enzymes, electron transport chain, etc.). E. coli has the machinery to run all three pathways. In addition, the appropriate terminal electron acceptor must be present. In aerobic respiration, oxygen must be present. In anaerobic respiration, an inorganic molecule such as nitrate or sulfate must be present. In fermentation, pyruvate is used as a terminal electron acceptor. The most efficient pathway is aerobic respiration because it yields 38 ATP. E. coli will use this pathway preferentially if oxygen is present. If oxygen is absent, E. coli can use the other two pathways as long as the terminal electron acceptors are present. The next most efficient pathway is anaerobic respiration, yielding less than 38 ATP (but more than two). The least efficient pathway is fermentation which only yields two ATP. Under the latter two pathways, E. coli will grow more slowly.
What is the order of preference for a bacterium to obtain energy? 1 - Fermentation, 2 - Aerobic Respiration, 3 - Anaerobic Respiration
2, 3, 1
Which metabolic pathway is unaffected by the availability of oxygen?
1. Transition step
2. Aerobic electron transport chain
3. Kreb’s cycle
4. Glycolysis
- Glycolysis
Which stage of aerobic respiration yields the maximum ATP?
Electron transport chain
The terminal electron acceptor during fermentation is:
Pyruvate
Which of the following organisms can derive energy using fermentation?
Prokaryotic and Eukaryotic cells
what is Salmonella enterica?
Salmonella enterica is a Gram negative, rod-shaped bacterium. When it infects the small intestine, an inflammatory response is mounted by our immune system to fight off the bacterium. During this response, tetrathionate is produced. Out of the numerous bacteria in our intestine, only S. enterica can use tetrathionate for anaerobic respiration. The rest of the bacteria have to resort to fermentation to make energy in this anaerobic environment. Because respiration makes more energy than fermentation, S. enterica can outcompete the intestinal microbiota causing infection.
In the tetrathionate broth, Salmonella uses tetrathionate as the terminal electron acceptor for anaerobic respiration. State one similarity and one difference between aerobic and anaerobic respiration.
Aerobic and anaerobic respiration both use glucose as their substrate and perform glycolysis to break it down. However, the terminal electron acceptors differ between aerobic and anaerobic respiration. Aerobic respiration uses O2 as its terminal e- acceptor, whereas anaerobic respiration uses inorganic materials such as nitrate or sulfate as its terminal e- acceptor.
Apart from turtles, name a food item that commonly carries Salmonella
Alfalfa sprouts
Apart from Salmonella, name another common bacterial intestinal pathogen
Campylobacter
what are other options of catabolism other than glucose?
Protein/carb/lipid metabolism
what pathways do the Protein/carb/lipid metabolism use to catabolize?
they use the same pathways as mentioned before (glycolysis, TS, Krebs, ETC)
when do we use Protein/carb/lipid metabolism?
when we don’t have glucose
what are exoenzymes?
they use their enzymes to break up the polymers into monomers.
they can create subunits for pathways (ex: the catabolism of starch into glucose)
what are examples of exoenzymes?
-Gelatinase and protease (converts proteins to amino acids)
-Amylase and cellulase (converts carbs to sugars)
-Lipase (converts lipids to glycerol and fatty acids)
anabolism requires the input of ____?
energy
anabolism includes photosynthesis in plants, algae, and cyanobacteria. what is the formula?
6 CO2 + 12 H2O + light energy —> C6H12O6 + 6 H2O + 6 O2
anabolism includes the synthesis of carbohydrates. what are some examples? the synthesis of these examples uses what taken from existing catabolic pathways?
glycogen, proteins, lipids, and nucleic acids. this is synthesized using precursor metabolites taken from existing catabolic pathways.
precursor metabolites uses ____ to build bigger molecules (polymers)
intermediates
what are amphibolic pathways?
when both catabolism and anabolism use the same pathways (like glycolysis, TS, Krebs, ETC) but the direction depends on the cellular needs.
what does “amphi” mean?
both or two
glycolysis is seen in:
1. respiration
2. fermentation
3. anabolism
4. all of the above
- all of the above
O2 is required for which stages of respiration?
In aerobic: TS, Krebs, and ETC. (all of these stages will NOT happen without O2).
*only glycolysis can occur without O2
what are the stages involved in the following:
-Aerobic respiration
-Anaerobic respiration
-Fermentation
Aerobic respiration:
- Glycolysis
- Transition Step
- Kreb’s Cycle
- Electron Transport Chain
Anaerobic respiration:
- Glycolysis
- Transition Step
- Kreb’s Cycle
- Electron Transport Chain
Fermentation
- Glycolysis
what are the terminal electron acceptors in the following:
-Aerobic respiration
-Anaerobic respiration
-Fermentation
-Aerobic respiration: O2
-Anaerobic respiration: inorganic mol.
-Fermentation: Pyruvate
what are the end products in the following:
-Aerobic respiration
-Anaerobic respiration
-Fermentation
-Aerobic respiration: 38 ATP
-Anaerobic respiration: less than 38 ATP (varies w/ organism)
-Fermentation: 2 ATP
which type of organism performs the following:
-Aerobic respiration
-Anaerobic respiration
-Fermentation
-Aerobic respiration: all organisms
-Anaerobic respiration: only bateria
-Fermentation: Bacteria, and even our muscle cells.
What is the overall purpose of respiration for an organism?
To make energy (ATP)
What is the overall reaction equation for respiration? Where do the reactants
come from? Where do the products go?
C6H12O6 —–> 6 CO2 + 6 H2O + 38 ATP
The reactants come from the product of photosynthesis. The CO2 diffuses out of the cell, the water stays in the cell and ATP is used in the cell to do work.
Glycolysis:
i. Where in the cell does it take place?
ii. It produces __ ATP and __ NADH.
iii. Does it require oxygen?
i. The cytoplasm
ii. 2 ATP and 2 NADH
iii. No
Transition step:
i. Where in the cell does it take place?
ii. It produces __ ATP and __ NADH.
iii. Does it require oxygen?
i. The cytoplasm
ii. 0 ATP and 2 NADH
iii. Yes
Krebs cycle:
i. Where in the cell does it take place?
ii. It produces __ ATP and __ NADH and __ FADH2
iii. Does it require oxygen?
i. The cytoplasm
ii. 2 ATP 6 NADH 2 FADH2
iii. Yes
Electron transport chain
i. Where in the cell does it take place?.
ii. It produces __ ATP and __ NADH.
iii. Does it require oxygen?
iv. Electrons flow from the electron donor _____ and ____ to the terminal electron acceptor ___.
i. The plasma membrane
ii. 34 ATP and 0 NADH
iii. Yes
iv. NADH and FADH2; O2
What is the proton-motive force? Explain how the downhill flow of electrons generates this force?
The proton-motive force is the energy of the electrochemical gradient. The downhill flow of electrons generates the proton-motive force by carriers actively pumping the protons outside of the cell. This creates a proton gradient.
How is proton motive force used to make ATP by chemiosmosis?
Protons move down the concentration gradient and through ATP synthase to reenter the cell. This harvests the energy of the proton-motive force to make ATP from ADP and Pi.
Which respiration stage produces the maximum NADH?
The Krebs cycle.
What is fermentation? Why do organisms undergo fermentation? How is it different
from respiration?
Fermentation produces ATP without O2, but it is not the same as anaerobic respiration. It is different from respiration because its’ end products are lactic acid, ethanol + CO2, and others.
Similarity - both use glycolysis
Differences - terminal electron acceptor and end product different
What is an amphibolic pathway? Give an example.
An amphibolic pathway is when catabolism and anabolism use the same pathways (glycolysis, TS, Krebs cycle, and ETC) but the direction depends on what the cellular needs are.
An example is: During the Krebs cycle, there is catabolism of carbohydrates and anabolic precursors for amino-acid synthesis.
A pet turtle’s stool can be shown to have the presence of Salmonella enterica. How was this tested?
A stool sample from the child was submitted to the clinical laboratory. One of the tests performed on the sample - a tetrathionate broth test - confirmed the presence of the bacterium Salmonella enterica. Turtles can carry Salmonella and have been often linked to disease outbreaks. In fact, the sale of tiny pet turtles has been banned in the US since 1975 because of the number of illnesses they cause and the risk to children.
In the tetrathionate broth, Salmonella uses ______ as the terminal electron acceptor for anaerobic respiration.
tetrathionate
State one similarity and one difference between aerobic and anaerobic respiration.
Aerobic and anaerobic respiration both use glucose as their substrate and perform glycolysis to break it down. However, the terminal electron acceptors differ between aerobic and anaerobic respiration. Aerobic respiration uses O2 as its terminal e- acceptor, whereas anaerobic respiration uses inorganic materials such as nitrate or sulfate as its terminal e- acceptor.
Apart from turtles, name a food item that commonly carries Salmonella
Alfalfa sprouts and eggs
Apart from Salmonella, name another common bacterial intestinal pathogen
Campylobacter
what type of bacteria is Salmonella enterica?
Salmonella enterica is a Gram negative, rod-shaped bacterium
what happens when Salmonella enterica infects the small intestine?
When it infects the small intestine, an inflammatory response is mounted by our immune system to fight off the bacterium.
During the response after Salmonella enterica entering the small intestine, what is produced?
Can Salmonella only us this certain bacteria for anaerobic respiration?
How do the rest of the bacteria make energy?
During this response, tetrathionate is produced. Out of the numerous bacteria in our intestine, only S. enterica can use tetrathionate for anaerobic respiration. The rest of the bacteria have to resort to fermentation to make energy in this anaerobic environment. Because respiration makes more energy than fermentation, S. enterica can outcompete the intestinal microbiota causing infection.
