Ch. 8: Microbial metabolism Flashcards
enzymes are mostly composed of :
proteins
what do enzymes speed up?
rate of cellular reactions
[they lower activation energy required]
metabolism
all the biochemical reactions that occur in a cell or organism
anabolism
-forming covalent bonds
-usually with energy/ATP
Ch 8: definition- AKA biosynthesis; larger molecules are built from smaller ones, which results in formation of cell structure
catabolism
chemical breakdown of complex compounds into simpler units to be used in cell metabolism
[larger molecules are degraded or broken down into smaller molecules, usually with release of energy].
enzyme
a protein biocatalyst that facilitates metabolic reactions
[a catalyst- chemical that increases rate of a chemical reaction without becoming part of the products or being consumed in the reaction].
substrate
the specific molecule upon which an enzyme acts
active site
the specific region on an apoenzyme that binds substrate; the site for reaction catalysis. [catalytic site]
holoenzyme
[conjugated enzyme]
an enzyme complete with its apoenzyme and cofactors
-fully assembled, conjugated enzyme
apoenzyme
the protein part of a conjugated enzyme (as opposed to nonprotein or inorganic cofactors)
-the biggest part of an enzyme
-has primary, secondary, tertiary, sometimes quaternary structure
Cofactors
an enzyme accessory; the NON protein part of conjugated enzyme
-can be organic like coenzymes
or organic like: Fe2+, Mn2+, Zn2+, or other metallic ions
exoenzymes
an extracellular enzyme chiefly used to hydrolyze nutrient macromolecules that cannot readily enter the cell; this enzyme is secreted into the environment, where it may function in saprobic decomposition of organic debris or support the invasion of tissues by pathogens
endoenzymes
an intracellular enzyme that functions primarily within the cell compartment, as opposed to enzymes that are secreted
constitutive enzyme
An enzyme present in bacterial cells in constant amounts, regardless of the presence of substrate
ex) enzymes of the central catabolic pathways
labile
molecules or compounds that are chemically unstable in the presence of environmental changes
-sensitive
denature
the loss of normal characteristics (shape, configuration) resulting from some molecular alteration; used in reference to loss of normal activity by proteins when their 3D structure has been altered by heat or chemicals
condensation reaction
type of chemical reaction in which two molecules are combined to form a single molecule
[forming a glycosidic bond between 2 glucose molecules to generate maltose- requires the removal of a water molecule]
hydrolysis reaction
a reaction in which one molecule breaks apart to form multiple smaller molecules.
[breaking a peptide bond between 2 amino acids requires a water molecule that adds OH to one amino acid and H to another].
rate-limiting step
the slowest step out of all the steps that occur for a given chemical reaction
redox reactions
reactions that involve the transfer of electrons from one species to another.
electron carrier
small organic molecules involved in the transfer or shuttling of electrons from one molecule to another
substrate-level phosphorylation
a mechanism of ATP formation involving the transfer of a phosphate from a donor molecule to ADP to form ATP.
oxidative phosphorylation
uses the energy derived from a series of redox reactions to drive an enzyme called ATP synthase [enzyme that makes ATP]
ATP synthase-final culminating enzyme and aerobic and anaerobic cellular respiration— Respiratory chain
Using ATP synthase to make ATP from free floating ADP in an organic phosphate
proton motive force
the force that promotes movement of protons across membranes downhill the electrochemical potential.
metal ions are-
single atoms
transient carrier
temporary carrier ; temporarily holding things like protons, hydrogen atoms, functional groups, etc…
-important for transferring molecules from reactant to another
regulated enzymes
their levels of production in cell change based on if they are needed
ex) DNA replication related enzymes
A constitutive exoenzyme is :
made all the time & secreted outside the cell
what are the 2 mechanisms for enzyme regulation?
- competitive inhibition: similarly shaped molecule competing against substrate
-similar enough to bind to active site, but not similar enough for the chemical reaction; competitor molecule can block reaction if it wins
ex) antibiotics - non-competitive/ allosteric inhibition: has active and allosteric site; When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed slightly so that they work less well.
ex) feedback inhibition
repressed gene expression
VS
induced gene expression
slowing production down / reducing amount of gene being used/expressed
make more of the enzyme/more gene expression
—-slow, takes longer, also longer lasting
the reduced version of a molecule—
has more energy
more electrons
usually more hydrogen atoms
than oxidized versions
photophosphorylation
used in photosynthesis
Similar to oxidative phosphorylation BUT
uses ATP synthase which gets its energy to form ATP from photons (sunlight)
aerobic respiration
Pathways involved
final electron acceptor
products
primary pathway found in
pathways involved: glycolysis, TCA [krebs] Cycle, electron transport
final electron acceptor: O2
products: ATP, Co2, H2o
primary pathway found in: aerobes; facultative anaerobes
anaerobic metabolism
-Fermentative-
Pathways involved
final electron acceptor
inputs & products
primary pathway found in
pathways involved: glycolysis
final electron acceptor: organic molecules
input: 1 glucose
products: Lactic acid
OR ethanol + Co2
2 ATP made in glycolysis
primary pathway found in: facultative, aerotolerant, strict anaerobes
anaerobic metabolism
-respiration-
Pathways involved
final electron acceptor
products
primary pathway found in
pathways involved: glycolysis, TSA [krebs] cycle, electron transport
final electron acceptor: various inorganic ions (No3-, so42-, Co33-)
products: highly varied; can include Co2, ATP, organic acids, H2S, CH4. N2.
primary pathway found in: anaerobes; some facultative and aerotolerants
which organisms use the respiratory chain?
obligate aerobes, obligate anaerobes, facultative anaerobes
where does aerobic respiration occur?
mitochondrion in eukaryotes
-electron transport takes place in the cristae
[cytoplasm in prokaryotes]
transition step
[of aerobic respiration]
2nd step of aerobic respiration
-pyruvic acid turned into acetyl CoA
OUTPUTS:
2 NADH
2 CO2
PER GLUCOSE.
Where does glycolysis step take place?
cytoplasm of every kind of cell
In bacterial cells, aerobic respiration takes place in:
cytoplasm
& plasma membrane
In eukaryotic cells, aerobic respiration after glycolysis and before respiratory chain takes place in:
mitochondrion (matrix)
Outer>inner membrane > matrix
difference of ATP burning during aerobic respiration for eukaryotic VS prokaryotic cells
Eukaryotic cells burn 2 extra ATP as they must pump pyruvic acid into the mitochondria matrix
So eukaryotes can make up to 36 ATP while prokaryotes can make 38 since all steps take place in the cytoplasm
Glycolysis
1st step of aerobic respiration
-process of breaking down glucose in half to make 2 new molecules of pyruvic acid C3H3O3.
-glucose becomes phosphorylated 2x using ATP [priming the glucose]
INPUT: 1 Glucose & 2 ATPs
OUTPUT:
2 ATPS
2 NADH
2 pyruvic acids
takes place in the cytoplasm
TCA cycle
[AKA Krebs cycle]
3d step of aerobic respiration
Starting compound: acetyl CoA that enters TCA cycle
1st reaction is coenzyme A molecule dropping off the acetyl group and transferring it to OAA Oxaloacetic acid to form citric acid
-2 turns per glucose
Input: ACETYL-COA
OUTPUTS:
2 ATP
2 FADH2
4 CO2
6 NADH
-3 NADH form per TCA cycle (because 2 turns of cycle per glucose)
-1 FADH2 per TCA cycle (total 2 per glucose)
-2 CO2 released per TCA cycle (total of 4)
-1 ATP made per TCA cycle (total 2 per glucose)
Where does cell use ATP?
wherever it needs
respiratory chain
2 main steps
inputs & outputs
3d major metabolic pathways of aerobic cellular respiration [prep step doesn’t count as major step]
2 main steps
-Electron transport chain— NO ATP MADE
protein complexes that couple redox reactions, creating an electrochemical gradient that leads to the creation of ATP in a complete system named oxidative phosphorylation
-Oxidative phosphorylation
inputs: 2 FADH2, 6O2, 10NADH
OUTPUTS:
34 ATP
6 H2O
in prokaryotic cell, where does electron transport take place?
plasma membrane
chemiosmotic theory
describes component of aerobic respitation- respiratory chain and how it works
-during electron transport, some carriers actively transport protons across the cristae membrane and into the intermembrane compartment of the mitochondrion. This sets up concentration gradient of hydrogen ions called the proton motive force PMF.
fermentation general steps
-Glycolysis
specialized Fermentation pathway= incomplete oxidation of glucose
fermentation- formation of alcohol– ethanol + lactic acid
input: glucose
OUTPUTS
ethanol
lactic acid
maximum ATP made- 2 ATP
which step in fermentation is the only step where ATP is formed?
glycolysis
why do cells prefer aerobic respiration VS fermentation
up to 36 ATP made with aerobic respiration
only 2 ATP made with fermentation
& with fermentation, 2 toxic products are made: alcohols and lactic acid
oxidative phosphorylation produces the most ________.
ATP
[34 max ATP with prok. and euk. cells]
chloroplast structure
3 membranes
-inner membrane
-outer membrane
-thylakoid membrane- GRANUM–stack of thylakoids
Stroma- fluid filled space; contains ribosomes & DNA. between thylakoid and inner membrane
Photosynthesis—-2 types of reactions
inputs & outputs for both
where do they take place?
light dependent reaction
-input is sunlight and water [water undergoes lysis, releasing:
-output is o2 oxygen gas, released bc toxic to cell
-another output in the cell – ATP and NADPH
-takes place in thylakoid membrane
light independent reaction
-input is ATP and NADPH, + Co2 from outside
-product/ only output is glucose/sugar
-takes place in stroma
Where on an enzyme does the substrate bind?
active site
Metabolic pathways that regenerate their starting point are called ________ pathways.
cyclic
Which cofactor is most commonly used as a transient carrier?
coenzymes
What is the protein part of a holoenzyme?
An apoenzyme
metallic ions. are a type of:
cofactor
Vitamins are an important part of:
coenzymes
Allosteric enzymes are always used in:
noncompetitive inhibition
Enzymes that are only produced when substrate is present are termed
induced enzymes.
NAD+.
NADP.
FAD.
These are all :
electron carriers
True or False: Glycolysis takes place in the same place in prokaryotic cells as it does in eukaryotic cells.
true
Substrate-level phosphorylation occurs in
glycolysis and TCA cycle.
During which of the phases of cellular respiration is the majority of ATP formed?
the respiratory chain
How many carbon dioxide molecules are produced by the complete aerobic breakdown of one glucose molecule?
6
Which of the following is not a process that regenerates ATP?
substrate-level phosphorylation
reductive phosphorylation
oxidative phosphorylation
photophosphorylation
reductive phosphorylation
In bacterial cells, when glucose is completely oxidized by all the pathways of aerobic cellular respiration, what is the maximum number of ATP generated?
38 ATP
The formation of citric acid from oxaloacetic acid and an acetyl group begins in what step
the TCA cycle.
The redox carriers that comprise most of the electron transport chain and are responsible for accepting and donating electrons are
the cytochromes.
In which stage of aerobic respiration is water produced?
electron transport system
As the electron transport carriers shuttle electrons, they actively pump ________ into the intermembrane compartment setting up a concentration gradient called the proton motive force.
hydrogen ions
The reactions of the specialized fermentation pathways function to regenerate ________ molecules for use in glycolysis.
NAD+
[NADH becomes NAD +]
Considering the entire fermentation pathway starting with glucose, what is the net production of ATP from one glucose molecule?
2 ATP
In which pathway is the most NADH generated?
[respiration]
the TCA cycle
If you trace what happens to the carbon in aerobic respiration, what happens to the carbon atoms from the sugar and fat in your food or from the fat burned from your body as you lose weight?
you breathe it out as CO2
What is the energy source that drives ATP synthase?
The proton motive force
what is sunlight captured by in photosynthesis?
chlorophyll molecule
where is the chlorophyll molecule found?
embedded within thylakoid membrane
what are the 2 components of the chlorophyll molecule?
porphyrin head
hydrocarbon tail
how is sunlight trapped by a plant?
photons will be absorbed by the porphyrin head of the chlorophyll molecule
in photosynthesis, carbon dioxide is taken in through pores of the leaf called:
stomata
where do light-dependent reactions take place?
thylakoid membrane of plants (euk, algae), and cyanobacteira (prok.)
how many chlorophyll molecules are in a chloroplast?
millions
in photosynthesis, the electron transport chain is a series of:
cytochromes
in photosynthesis, The cytochromes will pump _________________________
protons across membrane/ into the thylakoid lumen space to create a proton concentration gradient: the proton motive force
the proton motive force can be used to drive the enzyme ATP synthase to ___________________________________
take ADP and inorganic phosphate and make ATP
The light-driven production of ATP from ADP and inorganic phosphate is called:
photophosphorylation.
light-independent reactions takes place in:
stroma
What are the steps of light-independent reactions
- Carbon fixation
-Co2 enters the stroma and binds to RuBP > - reduction & synthesis
-reduction - adding energy in hydrogen atoms from NADPH
-synthesis of sugar molecules - regeneration
-regenerate RuBP to re-start process
in light-independent reactions, which enzyme is responsible for joining and binding Co2 to RuBP is:
RuBisCO
[may be most important enzyme on the planet bc it makes organic molecules for almost all life on earth]
How much ATP is made per glucose molecule in glycolysis?
2 ATP
What is the purpose of NAD + (NADH) in cellular respiration?
electron carrier used to temporarily store energy during cellular respiration
Why is the TCA cycle considered a cycle?
Starting compound is regenerated at the end of cycle, so it will go around again
— oxaloacetic acid (oxaloacetate) is the exact molecule needed to accept an acetyl-CoA molecule and start another turn of the cycle.
What are the possible products of fermentation?
the most common are ethanol, lactic acid, carbon dioxide, and hydrogen gas (H2).
What is the purpose of NADH dehydrogenase?
Complex I (NADH dehydrogenase) is the first enzyme in the respiratory chain. It catalyses the electron transfer from NADH to ubiquinone that is associated with proton pumping out of the matrix.
what is the purpose of ATP synthase?
catalyzes the synthesis of ATP from ADP and phosphate
Name the molecule in phototrophs designed to capture photons.
chlorophyll
Photolysis
[process in light-dependent reaction in photosynthesis]
This part of photosynthesis occurs in the granum of a chloroplast where light is absorbed by chlorophyll; a type of photosynthetic pigment that converts the light to chemical energy. This reacts with water (H2O) and splits the oxygen and hydrogen molecules apart
[ the light reactions that use energy from sunlight to split water molecules ]
what does a chlorophyll molecule look like?
Porphyrin head with a central magnesium atom
hydrocarbon tail
How much ATP is made per glucose molecule in fermentation?
2
In each transfer of an electron through the Electron transport system, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions (H+) across a membrane. In prokaryotic cells, H+ is pumped to the : __________________________
periplasmic space
Name the 6 electron carriers in aerobic respiration in order:
complex I
complex II
Coenzyme Q or ubiquinone
Complex III
Cytochrome
Complex IV
Electron carrier complex I
consists of NADH dehydrogenase
[receives NADH from glycolysis and TCA cycle]
Electron carrier coenzyme Q
mobile carrier that picks up electrons from complex I and II and donates them to complex III
Electron carrier: cytochrome c
mobile carrier that shuttles electrons between complex III and IV
What are the major steps in order of light-dependent reactions?
PS II reaction
electron transport
PS I reaction
ATP synthase & photophosphorylation
In photosynthesis, _________ acts as the final acceptor of the photosynthetic electron transport chain
NADP+
what are the inputs and outputs of glycolysis?
Input: 1 glucose and 2 ATP
Output: 2 ATP, 2 NADH, 2 pyruvic acids
What are the inputs and outputs of the TCA cycle?
Input: 1 ACETYL-COA per TCA cycle; 2 Acetyl CoA per glucose
Output:
2 ATP
2 FADH2
4 CO2
6NADH
(cut in half for per turn)
What are the inputs and outputs of the respiratory chain?
Input: 2 FADH2, 6 O2, 10 NADH
Outputs: 34 ATP, 6 H2O
What are the inputs and outputs of fermentation?
Input: 1 glucose
Output: ethanol & Co2 OR lactic acid… + 2 ATP
What are the major metabolic pathways in an obligate aerobic and an obligate anaerobic organism?
Glycolysis
TCA cycle
Respiratory chain
What are the major metabolic pathways in a facultative anaerobe?
Glycolysis
TCA cycle
Respiratory chain
Fermentation when no oxygen
How much ATP is made per glucose molecule in glycolysis?
2 ATP
(1 per turn)
How much ATP is made per glucose molecule in the TCA cycle?
2
(1 per turn)
How much ATP is made per glucose molecule in the respiratory chain?
34 (solely in oxidative phosphorylation, electron transport only makes water).
How much ATP is made per glucose molecule in fermentation?
2 NET ATP
What is the final electron acceptor for aerobic organisms?
O2
What is the final electron acceptor for anaerobic organisms?
Inorganic ions/ salts-
Where does each step of respiration take place in the prokaryotic cell?
Glycolysis- cytoplasm
TCA- cytoplasm
Electron transport- plasma membrane
Where does each step of respiration take place in the eukaryotic cell?
Glycolysis- cytoplasm
TCA- mitochondrial matrix
Electron transport- mitochondrion cristae
What are the total inputs and outputs for aerobic metabolism?
C6H12O6 + 602 > 6CO2 + 6H20 + 36 - 38 ATP
which metabolic step produces the most ATP in our body?
oxidative phosphorylation
What are the common products of fermentation?
2 ATP, lactic acid, OR carbon dioxide & ethanol
What is the purpose of ATP synthase? How does it function and what does it need to function?
catalyzes the synthesis of ATP from ADP and phosphate
-it needs proton motive force to function, uses proton motive force and spins; creates covalent bond between ADP and inorganic phosphate
after photolysis, where do the electrons released from the splitting of water go? Where do the protons go? Where do the oxygen atoms go?
electrons- resupply the chlorophyll
protons- pumped across the membrane into thylakoid space > creates a proton concentration gradient (proton motive force)
oxygen atoms- released out bc toxic to cell
Carbon fixation in photosynthesis takes place during:
light-independent reactions
At what step is oxygen made in photosynthesis?
light-dependent reaction – in photolysis
