biochem Flashcards
what are enzymes
biological catalysts that kinetically increase the rate if a reaction without being consumed
what does the catalyst not affect?
- – gibbs energy
- – reactants
- – products
hydrolase def
hydrolyzes chemical bonds (includes ATPases— breaks down ATP into ADP and into a phosphate group– , proteases, and others)
*isomerase def
rearranges bonds within a molecule to form of an isomer
kinase def
adding phosphate groups from a high energy carrier to other groups
ex: growth hormone, platelets, insulin
due to having a cascade
what causes denaturation of amino acids?
- high temp
- presence of high metals
- acidosis / alkalinosis
chymotrypsin
is the enzyme that selects for the aromatic amino acids: phenylalanine, tryptophan, and tyrosine at the carboxyl part
bulky belongs to longer part
trypsin
is the enzyme that selects for the basic amino acids: lysine and arginine at the carboxyl part
what causes protein building to become favorable
ATP coupling
difference of in vivo and in vitro being spontaneous
the cells in body are naturally more favorable bc it has ATP on the sidelines waiting to participate with atp coupling
however in vitro is a lab setting so it introduces an enzyme to an unfavorable reaction to take place and speed up rxn (kinetic)
why are enzymes more globular shaped than anything else
its easier for them to work bc they resemble a protein with a globular shape that has the active site better available for the substrate (reactant ) to bind to
to stabilize a charge do u need a similar charge or an opp charge?
u need an opp charge to stabiliz bc the same charge will just make it more reactive
lysisne will stabilize glutamate
do enzymes act or produce the transition state
produce
can a certain reactant or product be favorable at all times?
no bc it depends on the given time and what it has more of it … chetlatier principle always comes into play
what configurations are found in animals
L for AA (think of aLLLlanine) and D for sugars
recognition pocket
part of the enzymes structure near the active site that attracts certain aa residues to come along
why does a protein denature
the temp is too high and the protein starts to lose affinity for the substrate and the globular structure breaks
cofactors vs coenzymes
Cofactors serve the same purpose as coenzymes, as they regulate, control, and adjust how fast these chemical reactions would respond and take effect in our body. The big difference is that coenzymes are organic substances, while cofactors are inorganic
cofactors vs coenzymes ex
cofactors can be vitamins
coenzymes can nad and fad bc main function is to accept and store electrons within proteins.
saturation
even if u add more substartes there aren’t enough enzymes to bind to each one so the vmax will reach a horizontal slope and not increase
tense vs relaxed cooperativity
tense means u are not cooperative and can remain inactive not helping others to join whereas relaxed is active and will cause more to join
investment part of glycolysis
use 2 atp to make 2 PGAL (3 carbons attached to a phosphate group)
in glycolysis, each pgal produces 3 things
2 atp
pyruvate
NADH
structure of pyruvate
3 carbon molecule
how can aa make glucose
through oaa (oxaloacetate)
hpw is OAA made from pyruvate? pyruvate carboxylase which adds another carbon to make 4 that oaa should have
if there is too much amp then …
not enough atp so gluconeogen will be halted bc that requires a lot of atp
what is a slow regulator and may takes hour to days
anything that halts transcription
is atp consumed or produced for the pentose pathway
no
chylomicron
type of lipoptoeins (carries triglycerides and cholesterol) found in the small intestine once bile emulsifies fats into smaller particles
lacteal
lymphatic capillary that have larger pores that can carry the chylomicrons to different parts of the body especially to thoracic ducts
ischemia
restricted blood flow which can lead to decreased amount of o2
what happens when there isn’t enough glucose being made
there will be less pyruvate being made (glycolytic pathway) which in turn will cause less pyruvate to be moved to ether lactate (fermentation) or to krebbs …
so less pyruvate as well
main enzyme involved in leactic acid fermentation of pyruvate to lactate is
lactate degyhrogenase (LDH)
why is there an increase in ammonia when the body undergoes muscle fatigue
it is looking for its next fuel which will come from breaking down amino acids which will have byproduct of urea
embolism
blood clot or air bubble
edema
excessive fluid
ischemia
reduced blood flow
when does glycogenesis occur and what hormone stimulates it
mostly in the liver or muscles during the fed state and insulin helps it because it wants to put glucose into the cells
alpha sugar vs beta sugar
beta has oh groups on same side whereas the alpha has the oh groups on opp sides like diff axial positions (one is up and the other one is down)
the first carbon of the carbohydrate
is the reducing end and can take off the H so that the O can form a glycosidic linkage
most important starting material for glycogenesis
udp - glucose (which to make is an endergonic reaction) but can be coupled by phosphatase energy
glycogenin
has a specific tyrosine that attracts the udp-glucose
has autoglyocsylation
autoglycosylation
when it comes to glycosidic linkages, no specific enzymes are needed
basic process for glycogenesis
use the phosphatases for energy to get have udp as a byproduct and make aoutoglycosylation linkages with glucose to glycosidic bonds to have END PRODUCT OF GLYCOGEN
two enzymes involved in glycogenesis
glycogen synthetase:
makes the line of 1-> 4 bonds
can also add once the branching enzyme makes the first branch
branching enzyme :
-break the 1 -> 4 bond to make branches that are part of the 1 -> 6 bonds
why does glycogenlysis occur
the blood glucose is low
fasting state
hormones in charge of glycogenlysis?
glucagon
epinephrine
neriephrine
growth hormone
glycogen phosphorylase involved with glycogenlysis?
glycogen phosrylase cuts the glucose bond and adds phosphate group to individ glucose but cannot go to the glucose that are close to the 1-6 bond and has to wait for the debranching
debranching enzyme involved in glycogenlysis
debranches the 1-6 glucose bond and transfers 3 glucose molecules to the 1 4 bond
which hormones use gcpr pathway
glucagon
N.E.
epineph.
anterograde vs retrograde
ante is fwd
retro is reverse
protein kinase a
made from camp and can inhibit glycogenesis and promote glycogenolysis to get fatty acids
where does gluconeogenesis occurs
liver and kidneys (proximal convoluted tubule)
pyruvate carboxylase
adds co2 of pyruvate to make OAA
special about malate from krebbs
PUSHED OUT OF MATRIX , converted back into OAA , then PEP (step b4 making pyruvate in glycolysis)
enxyme that makes the oaa into pep is pepck (phosphor enol pyruvate carboxy kinase)
pep is 3 carbons
fructo bis phosphatase
rds for gluconeogenesis that make fructo 6 phosphate
relationship btwen smooth er and glucose6 phosphatase
enzyme (glucose 6 phosphatase) take off phosphate off of glucose so it can leave and enter blood
when glycerol has a phosphate what happens
it turns into DHAP of glycolysis
when it comes to disulfide bonds and agents, tell me what is going on
OPP OF WHAT U THINK
reducing agents are the ones that are reduced so they are breaking the disulfide bonds by putting h
oxidizing agents are the op they are building the disulfide bonds
usually has to do with cysteine amino acid
when it comes to beta oxidation, how many fadh2 and nadh are made from a 14 carbon going to acetyl coA (2 carbons)
14/2 - 1 = 6 for each coenzyme
when it comes to atomic atoms that are closed shells and half shelled, would s or d sublevel be more stable?
closed d sublevel
which hormone is responsible for fatty acid synthesis
insulin because to promote the synthesis, there needs to be high blood glucose and a fed state
why would too much atp cause fatty acid synthesis
because if u have too much atp u don’t want to keep breaking down products. u will start the neg feedback and now do synthesis
what does citrate lyase do
changes citrate back into OAA and aceyl COA
then OAA turns into malate and then malate turns into pyruvate by producing NDAPH
acaetyl co A carboxylase
carries biotin(coenzyme) and adds in another carbon in the form of co2 onto the acetyl coA to make the acetyl coA (2 carbons) into malonyl coA (3 carbons)
keep in mind that the coA of the malonate will then be transferered by tranactylase to a fatty acid
types of regulation for acetyl coA carboxylase
citrate which will promote
long fatty acids with coA that will inhibit because they are coming from oxidation
insulin will promote
cortisol, glucagon, epi/norepi will inhibit
active and inactive form of acetylco A carboxylase
dimers is inactive form and the polymerization (when the dimers are all in a group) will be the active form
fatty acid oxidation vs synthesis
oxidation breaks down the fatty acids
what is the role that protein kinase A have on acetylk co A carboxylase
it phosphorylates the ACC which causes it to back into the dimer inactive form which will then need a phosphatase to remove the phosphate if it ever planned to become active again
carnitine acytle transporter I vs II
keep in mind that these are actually 16 fatty acids called palmitoil
I brings the fatty acids into mitochrondria for oxidation while the II is already in mitochrondria
if I is inhibited it cant bring fatty acids into the mitcondria so the fatty acids will just go on to synthesis
acetyl I transacetylase
taking up actyl coA and turning it into acetate and move the acetate group onto the cystine group
overall steps for fatty acid synthesis
Location: cytosol of cell
1-Citrate leaves mitochondrial matrix, crosses double membrane layers, to cytosol
2-Citrate converted to acetyl CoA + OAA via enzyme citrate lyase
3-Acetyl CoA (2C) gets converted to malonyl CoA (3C) via enzyme ACC (acetyl CoA carboxylase)
4-Malonyl CoA gets lengthened 2 C at a time via enzyme fatty acid synthase
5-Regulation: high insulin triggers fatty acid synthesis
6-Fatty acid + glycerol = triglycerides (stored in adipocyte cells)
ACC is the rate-limiting step. It also needs NADPH (which we get from PPP). Malonyl-CoA from FA synthesis inhibits beta oxidation by inhibiting carnitine acyltransferase I (@ outer mitochondrial membrane), part of the transport system that lets activated FA back into the mitochondria. (thus FA synth and beta ox are antagonistic pathways like glycolysis and gluconeo)
hydride
one h proton with 2 electrons
why are free fatty acids not sent off to rbc or blood brain barrier
FFA enter blood and are transported by albumin to other cells (mostly liver and muscle). They don’t get transported to RBCs or the brain because RBCs don’t have mitochondria, and FFA can’t pass the blood-brain barrier.
What is the basic order of events in the digestion and mobilization of dietary fats?
Dietary fats are insoluble in aqueous solution, and cannot be absorbed by the intestinal mucosa.
Hint #2
2 / 5
Bile is secreted from the gallbladder to emulsify dietary fat particles to form finely dispersed, soluble micelles.
Hint #3
3 / 5
The formation of micelles allows for intestinal lipases to degrade the dietary particles so that they may be absorbed and used to form TAGs.
Hint #4
4 / 5
The triacylglycerols are incorporated with cholesterol and apolipoproteins within the intestinal mucosa.
Hint #5
5 / 5
The correct order is: emulsified by bile→ degradation by lipases→ absorption and conversion into triacylglycerols→ incorporation into chylomicrons.
upregulate vs downregulate activity usually done by transcription factors
upregulate is good and will promote the activity
downregulate is bad bc it will decrease the activity
upreg incr # of receptors so more sensitivity
downred decr # of receptors so less sensitivity and can be a problem like insulin reg in type 2 diabetes
replication vs transcription
replication really has to do only with the dna strand.. transcription has to do with regulating activity effects
methionine vs cysteine
Disulfide bonds in proteins are formed between the thiol groups of cysteine residues by the process of oxidative folding. The other sulfur-containing amino acid, methionine, cannot form disulfide bonds.
refractory period
due to the hyperpolarization that occurs after the action potential due to the K+ voltage gated channel allow too much K+ to exit the cell during depolarization.
relationship btwn depolarization, action pot, and potassium
no relationship bc needs sodium
folding of proteins happen in what organelle
rer
diff btwn locations of the protron gradient and etc
etc is across inner membrame and protron gradient is inside the inner
acetyl coA structure
two carbons and S-CoA
two carbons are the methyl group and the carbonyl
