Metabolism Flashcards
what is metabolism?
the sum of all chemical reactions in the body/the making and breaking of all molecules
what is metabolic pathway?
begins with a specific molecule which is altered in a series of intermediate steps, each catalyzed by a specific enzyme resulting in a product
catabolic pathways
release energy by breaking down molecules
anabolic pathways other name?
biosynthetic pathways
anabolic pathways
consume energy to build complex molecules
what is the capacity to cause change?
energy
kinetic energy
energy of motion
thermal/heat energy
kinetic energy due to the random motion of atoms or molecules
light/solar energy
radiant energy of electromagnetic waves in the visible portion of electromagnetic spectrum
potential energy
stored energy that matter possesses as a result of its location or spatial arrangement
chemical energy
potential energy available in molecules for release in a chemical reaction
closed systems
systems that are unable to exchange energy or matter with their surroundings
open systems
systems that allow energy and matter to move between the system and the surroundings
first law of thermodynamics
energy of universe being constant
only changes into different forms
second law of thermodynamics
energy transfers increasing the entropy/disorder of the universe
what is the entropy in life and organisms? what are they called?
have low entropy as they are very organized
“islands of low entropy” in an increasingly random universe
spontaneous process
a process that occurs without the inapt of energy / energetically favorable
can be harnessed to perform work
exergonic reactions
proceed with a net release of free energy
a downhill reaction
-delta G
endergonic reactions
require free energy to drive a reaction and are not spontaneous
uphill reaction
+delta G
when a chemical system is an equilibrium, what can it not do?
cannot do work
a cell at metabolic equilibrium is dead
one of defining features of life is disequilibrium
ATP
adenosine triphosphate stores the potential energy to react with water and powers cellular work
what does ATP mediate?
coupling - using exergonic processes to drive endergonic ones
how does ATP work?
when a hydrolysis reaction breaks an inorganic phosphate group off from ATP.
why are the products ADP (adenosine diphosphate) and inorganic phosphate, more stable than ATP?
the 3 phosphate groups are negatively charged and repeal each other like a compressed spring
what type of reaction is ATP to ADP?
exergonic/spontaneous reaction
Can ADP be broken down?
AMP (adenosine monophosphate)
characteristic of ATP
weak bonds
unstable
more stored potetntial energy
ADP + Pi (inorganic phosphate group)
stronger bonds
more stable
less stored potential energy
what is ATP made up of?
3 negatively charged phosphate groups
adenine
ribose
what is required to break bonds?
energy
what is phosphorylated intermediate?
enzymes take the detaches inorganic phosphate and attach it to another molecule
atp’s exergonic energy is coupled to another endergonic reaction
when reaction is complete, the inorganic phosphate is released and can reattach to ADP forming ATP once again
what type of transport work can ATP be used for?
to phosphorylate the movement of solutes across the cell membrane from where there are few solutes to many solutes (low to high concentration)
what type of mechanical work can ATP be used for?
to motor proteins like kinesin to “walk” along microtubule (a component to the cytoskeleton of a cell) tracks while transporting an organelle
what does ATP do to be reused?
it can recycle and is a renewable resource
~ 10 million ATP molecules consumed and regenerated per second
cellular respiration creates the most ATP
what is an enzyme?
a macromolecule that acts as a catalyst without being consumed
be aware that not all enzymes are proteins`
examples of enzymes that are not proteins
ribozyme
what are ribozymes eviddence for?
like a prehistoric cooler, ribozymes are the missing piece of evidence that modern life might have evolved from a primitive “RNA world”
doing the job of DNA, RNA could carry genetic information and then doing the job of proteins(enzymes), ribozymes could catalyze the replication of that info to be passed on to future generations
what is Gibb’s Free energy?
energy available to do work in a cell
what is Ea?
activation energy - the amount of energy needed to contort the reactants so the bonds break in this reaction
when is the energy the highest in the system?
at the summit of the energy profile hill called the transition state where the reactants are most unstable
since the products are lower in energy than the reactants what does this mean?
that the formation of new bonds release more energy than was invested in the breaking of old bonds
what does the addition of an enzyme do to the reaction?
lowers Ea
what is a substrate?
the reactant that acts on an enzyme
what is an enzyme-substrate complex?
when the enzyme binds to a substrate
how does an enzyme and substrate interact?
the enzyme binds to a substrate, forms a complex, then it converts the substrate into a product and is available to be used again
what does the unique 3d conformation of enzymes enable for binding?
allows them to bind to a specific substrate only
fit together like lock and key
where does the substrate bind to in ana enzyme?
active site - a pocket/groove on the surface of an enzyme where catalysis occurs
are enzymes rigid? what happens?
no- induced fit
what is induced fit?
when the substrate bids to the enzyme’s active site this causes the enzyme to change its shape slightly to form a snug fit with the substrate like a clasping handshake
how strong are the bonds between a substrate and active site?
weak interactions - H bonds or ionic bonds
what does the enzyme do after the substrate attaches?
the enzyme catalyzes the conversion of the substrates to products that then leave the active site freeing the enzyme up to take on more substances
are metabolic pathways reversible?
most of them are, so the reaction can go backwards or forwards
rate is typically 1000 substrate molecules per sec
how does environmental factors affect the efficiency of enzymes?
enzymes have optimal conditions that it works better under
how does temp affect enzymes?
increasing temp speed up the rate of an enzyme-catalyzed reaction, but too high a temp can denature it
what is the optimal temp for most human enzymes?
35-37 C
optimal ph for humans?
6-8
how do concentration of substrate molecules affect the reaction rate?
the more substance available, the more frequently they access the active site of the enzymes/the faster the reaction
what does it mean for enzymes to be saturated?
all enzymes will be bound to substrates
what happens when enzymes are saturated?
to increase rate of product formation, more enzymes are created prompting the cell to perform protein synthesis of a particular enzyme
what are cofactors?
inorganic molecules that bind to the active site of an enzyme before the substrate binds and are necessary for that particular enzyme to function
Zinc, iron, copper
what are coenzymes?
organic molecules that bind to the active site of an enzyme such as vitamins
competitive inhibitors
molecules that mimic the substrate and compete for admission to the active site of the enzyme
CO compete with O2 in binding to iron/heme groups in hemoglobin
why is competitive inhibition reversable?
bonds are weak
strong bonds are not irreversible
how does nerve gas work?
blocks the enzyme that breaks down neurotransmitters, so muscles stay permanently contracted
how does aspirin work?
- injury/headache
- arachidonic acid - substrate
aspirin bonds irreversibly here to active sit COX 1/2 - cyclooxygenase (COX-1)
- thromboxane A2
what are irreversible inhibiters?
bind covalently to the active site of an enzyme blocking its functions and as name implies, are irreversible since the bonds are strong
herbicides, pesticides, nerve gas to apsirin
what are irreversible inhibiters?
bind covalently to the active site of an enzyme blocking its functions and as name implies, are irreversible since the bonds are strong
herbicides, pesticides, nerve gas to aspirin
how does the first antibiotic discovered called penicillin work?
penicillin binds to the active site of the enzyme involved in building bacterial cell walls/acts as an irreversible inhibitor
are antibiotics effective against viruses, bacteria, or both?
bacteria
is active site binding the only mode of action antibiotics works?
no, there are many different mechanisms antibiotics destroy bacteria
block protein synthesis/nucleic acid synthesis
noncompetitive inhibitors
bind to another part of the enzyme and in doing so change the shape of the enzyme that the active sute becomes less effective at catalyzing substrate product.
is noncompetitive inhibition reversible?
yes, bonds are weak
allosteric regulation
“other solid”
used to describe any case in which an enzyme function can oscillate bw being in the active or inactive form by the binding of a regulatory molecule to a location other than the allosteric site/regulatory site
what is the allosteric site?
enzyme’s active site
what can a binding to the allosteric site result in?
activate or inhibit enzyme’s activity
what are allosteric enzymes made if?
2+ subunits and they typically shift between 2 diff forms
how does each intermediate step in a metabolic pathway occur?
due to a different specific enzyme
how does a metabolic pathway know when enough product is made and to stop forming products?
feedback instruction - the turning off of a metabolic pathway by the end product binding to an allosteric site in an enzyme early in the pathway
what does feedback inhibition do?
changes shape of the enzyme so that the substrate no longer binds to the active site
shuts down metabolic pathway temporarily to prevent cell from wasting chemical resources/energy and making more products than necessary
