Microbial metabolism Flashcards
what is metabolism
chemical reactions inside the cell
what are exergonic reactions
reactions that are spontaneous and release energy
what are endergonic reactions
reactions that require energy
what is anabolism
endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, fuels by the use of cellular energy
what is catabolism
exergonic pathways that break down complex molecules into simpler ones
what pathway releases energy stored in complex molecules
catabolic pathways
what are autotrophs
organisms that convert inorganic carbon dioxide into organic carbon compounds
what are examples of autotrophs
plants and cyanobacteria
what are heterotrophs
organisms that rely on organic compounds such as nutrients from autotrophs
what is energy derived from
the transfer of electrons
what are phototrophs
organisms that get their energy from light
what are chemotrophs
organisms that obtain energy for electron transfer by breaking chemical bonds
what are orgnotrophs
chemothrophs that get energy from organic compounds
what are lithotrophs
chemotrophs that get energy from inorganic compounds, including hydrogen sulfide and reduced iron
example of inorganic carbon chemoautotrophs
hydrogen
sulfur
iron
nitrogen
carbon monoxide oxidizing bacteria
chemoheterotrophs examples
all animals, most fungi, protozoa, and bacteria
photoautotroph examples
all plants, algae, cyanobacteria, green and purple sulfur bacteria
Photoheterotrophs examples
Greenland purple non sulfur bacteria, heliobacteria
What are oxidation reaction
reactions that remove electrons from donor molecules, leaving them oxidized
what are reduction reactions
reactions that add electrons to acceptor molecules leaving them reduced
what is a redox reaction
oxidation and reduction reactions happening in tandem
how is the energy released from the breakdown of chemical bonds within nutrients stored
either electron carriers or in ATP
what are electron carriers
molecules that bind to and shuttle high-energy electrons between compounds in pathways
where do the principle electrons carrier come from
the B vitamin group
what is the most common mobile electron carrier
NAD+/NADH
what is NAD+
the oxidized from of nicotinamide adenine dinucleotide
what is NADH
the reduced form of NAD+
what is NADP+
nicotine adenine dinucleotide phosphate the oxidized from of an NAD+ that contains an extra phosphate group
what is NADP+ when reduced
NADPH
what is FAD
the oxidized form of flavin adenine dinucleotide
what is the reduced form of FAD
FADH2
what are NAD+/ NADH and FAD/FADH2 used in
energy extraction from sugars during catabolism in chemoheterotrophs
what are NADP+/NADPH used for
anabolic reactions and photosynthesis
what are FADH2, NADH and NADPH referred to
as having reducing power due to their ability to donate electrons to various chemical reactions
What molecule is at the heart of ATP
AMP- adenosine monophosphate
what is AMP composed of
an adenine molecule bonded to a ribose molecule and a single phosphate group
what is ribose
a five carbon sugar found in RNA
what is AMP a nucleotide of
RNA
what does a second phosphate group added to MAP form
ADP-adenosine diphosphate
what does the addition of a 3rd phosphate group added to MAP result in
ATP
why is phosphorylation
adding a phosphate group to a molecule
how do phosphate groups act in series
they are negatively charged and repel each other
what does phosphate repelling each other do to ADP and ATP
it makes them inherently unstable
what are the bonds in ADP and ATP called
high-energy phosphate bonds
what happens when high-energy bonds are broken to release phosphate
dephosphprylation, energy is released to drive endergonic reactions
what is a catalyst
a substance that helps speed up a chemical reactions
why are catalysts reusable
they are to used or changed during chemical reactions
what are enzymes
proteins that serve as catalysts for biochemical reactions inside cells
how do enzymes function
by lowering the activation energy of a chemical reaction in the cell
what is activation energy
energy needed to form or break a chemical bond and convert reactants to products
how do enzymes lower activation energy
by binding to the reactant molecules and holding them in such a way as to speed up the reaction
what are substrates
the chemical reactants to which an enzyme binds
what is an active site
the location within the enzyme where the substrate binds
what is the match between an enzyme and substrate like
a jigsaw puzzle
what happens when an enzyme binds to its substrate
the enzyme structure changes slightly to find the best fit between the transition state and the active site
what is induced fit
active-site modification in the presence of substrate with simultaneous formation of the transition state
what conditions influence enzymes
PH
substrate concentration
temperature
what happens to enzymes when environmental temperature is increased
reaction rate increases, they eventually denature and lose 3d structure and function
what happens to enzymes outside the suitable temperature range
chemical bonds in the active site are affected making them less well suited to bind substrates
what happens to enzymes at higher concentrations of substrates
activities increase at higher concentrations until ir reaches saturation and no longer bind
at what temperature to human pathogen enzymes work best
37C
what are the two helper molecules
cofactors and coenzymes
what are cofactors
inorganic ions such as iron and magnesium that help stabilize enzyme conformation and function
what enzyme requires bound zinc ion to function
DNA polymerase
what are coenzymes
organic helper molecules that are required for enzyme action
what are the most common sources of coenzyme
dietary vitamins
are coenzymes reusable
yes
what does coenzyme a do
binds to the enzymes active site aiding in the transition of a substrate to a product
what is an apoenzyme
an enzyme lacking a necessary cofactor or coenzyme and is inactive
what is a holoenzyme
an Enzyme with the necessary associated cofactor or coenzyme and is active
what are other coenzymes that provide high-energy electrons or phosphate groups to bind enzymes
NADH and ATP
what is a competitive inhibitor
a molecule similar enough to a substrate that it can compete with the substrate and bind to an active site by blocking the substrate from binding
what is required for a competitive inhibitor be effective
the inhibitor concentration needs to be approximately equal to the substrate concentration
how do sulfa drugs work
they bind to the active site of an enzyme within bacterial folic acid synthesis pathway prevention folic acid synthesis and bacterial growth
what does a noncompetitive inhibitor do
binds to the enzyme at an allosteric site to block substrate binding to the active site
how does a noncompetitive inhibitor block substrate
by inducing conformational change that reduces the affinity of the enzyme for its substrate
what concentration is needed for noncompetitive inhibitors
lower than substrate concentration
what does an allosteric activator do
binds to an enzyme away from the active site inducing conformational change, increasing the affinity of the enzymes active site for its substrate
what is feedback inhibition
the use of a pathway product to regulate its own further production
What is glycolysis
the most common pathway for the catabolism of glucose for bacteria, eukaryotes and archaea
What does glycolysis do
produces energy, reduced electron carriers and precursor molecules for cellular metabolism
does glycolysis use oxygen
no
where does glycolysis take place
the cytoplasm of cell
what does glycolysis begin with
6-carbon glucose molecule
what does glycolysis end with
two molecules of a three carbon sugar called pyrubate
what does glycolysis using the emp pathway consist of
energy investment phase
energy payoff phase
what happens in the energy investment phase of the EMP pathway
energy from two atp molecules modify a glucose so the 6 carbon sugar can be split evenly into two phosphorylated three carbon molecules called glyceraldehyde 3 phosphate
what happens during the energy payoff phase of EMP
energy is extracted by oxidizing G3P to pyruvate producing four ATP moleculsing and reducing 2 molecules of NAD+ to two molecules of NADH using electrons from original glucose
what do the ATP molecules produced during the energy payoff phase of glycolysis formed by
substrate-level phosphorylation
what happens during substrate level phosphorylation
a phosphate group is removed group is removed from an organic molecule and is directly transferred to an available ADP molecule producing ATP
what is the net gain from a single glucose molecule during glycolysis
2 ATP
2 NADH
2 pyruvate
what is the main glycolysis pathway
EMP pathway, used by animals and many bacteria
what is the alternate glycolytic pathway used by many prokaryotes
ED pathway
what is the 3rd type of glycolytic pathway that occurs in all cells
PPP
what is considered the most ancient universal glycolytic pathway
PPP
what are the intermediates from the PPP used for
biosynthesis of nucleotides and amino acids
when will the PPP pathway be preferred
when nucleic acid or protein synthesis is needed
what must happen for pyruvate to be further oxidized
it must first be decarboxylated
what enzyme is required o decarboxylate (transition reaction) pyruvate
pyruvate dehydrogenase
describe pyruvate dehydrogenase
a two carbon acetyl group
what must pyruvate dehydrogenase attach to
coenzyme a
where doe the transition reaction occur
the mitochondrial matrix of eukaryotes and cytoplasm of prokaryotes
what does the Krebs cycle do
transfers remaining electrons from the acetyl group produced during the transition reaction to electron carrier molecules reducing them
where does the Krebs cycle take place in prokaryotes
cytoplasm
what makes the Krebs cycle different from glycolysis
it is a closed loop,
what happens in the last step of the Krebs cycle
the compound using in the first step is regenerated
what does the kern cycle do
a series of chemical reactions that capture the 2 carbon acetyl group and adds them to a four carbon intermediate producing a 6 carbon intermediate citric acid
What does the Kreb cycle produce
2 CO2
1 ATP
3NADH
1 FADH2
what can be produced using the Krebs cycle
glucose metabolism
amino acids
chlorophylls
fatty acids
nucleotides
is the Krebs cycle anabolic or catabolic
both
when does oxidative phosphorylation occur
during cellular respiration
how is most ATP generated
oxidative phosphorylation
