Shared Flashcard Set

Details

Biochem Enzymes and Heme
KYCOM Block 2
222
Biochemistry
Graduate
09/24/2012

Additional Biochemistry Flashcards

 


 

Cards

Term
what is the job of a catalyst
Definition
increse the rate of a reaction without being changed itself
Term
why do we need enzymes
Definition
reactions would be too slow
Term
what are enzymes made of
Definition
usually protine, sometimes ribozymes
Term
what is the reactant called in an enzyme reaction
Definition
substrate
Term
what are some of the common ways to name enzymes
Definition
"substrate"-ase, "substrate + reaction description"-ase, "random other common name"
Term
describe the systemic way to name enzymes
Definition
"systemic name"-ase, "substrate: substrate systemic category"-ase
Term
what does a one way arrow in an enzyme reaction indicate
Definition
under normal human conditions the reaction goes in that direction, it could go the other way in reality but it isnt likley
Term
what does a double sided arrow in an enzyme reaction indicate
Definition
under normal human conditions, the reaction can go in either direction
Term
what is the active site
Definition
pocket of an enzyme that binds a substrate with amino acid compliments to it
Term
what is the ES
Definition
enzyme substrate complex: enzyme bound to substrate in a new conformation to facilitate catalysis
Term
what is the EP
Definition
enzyme product: dissociates into enzyme and product
Term
what is a way we can measure the catalytic efficiency
Definition
turn over number
Term
what is the turn over number
Definition
number of molecules of substrate converted to product per enzyme per second
Term
what is the abreviation for turn over number
Definition
Kcat
Term
how do enzymes display specificity
Definition
they only allow one or few substrates (similar structure), only do one type of reaction
Term
what is a holoenzyme
Definition
enzyme and its non-protein component
Term
what is an name for an active enzyme
Definition
holoenzyme
Term
what is an apoenzyme
Definition
enzyme without its non protein component
Term
what is a name for an inactive enyme
Definition
apoenzyme
Term
what is a cofactor
Definition
non-protein component of an enzyme made of metal
Term
what is a coenzyme
Definition
non-protein component of an enzyme made of organic molecules
Term
how are coenzymes made
Definition
vitamins
Term
what are some examples of coenzymes
Definition
niacin makes NAD+, riboflavin makes FAD
Term
what is the point of the non-protein component of an enzyme
Definition
some enzymes need these (cofactor, coenzyme) to work
Term
how are enzymes regulated
Definition
activated or inhibited based on cell need
Term
what is the energy barrier
Definition
energy difference between that of reactants and a high energy intermediate that occurs during the formation of the product
Term
what does a high free energy of activation mean
Definition
slower reaction
Term
what do enzymes do to the free energy of activation
Definition
lower it, NOT change it. it accelerates the rate of the reaction but does not change the equlibruim
Term
desctibe the location of enzymes
Definition
specific subcellular compartments near organells, isolating substrates and products from competing reactions, organizes them into purposeful pathways
Term
what does it mean when we say that an enzyme "stabilizes the transition state"
Definition
holds substrate in conformation of high energy between substrate and product, increasing the concentration of the transition state and making it more likley that it will turn into product but giving chemical groups that participate in reaction to substrate and facilitate the form of the transition state
Term
what is the enzyme velocity
Definition
number of substrate that turns to product per unit time
Term
what is the normal units for enzyme velocity
Definition
micro mol / product / min
Term
what is maximal enzyme velocity
Definition
rate of enzyme catalization of a reaction with increasing substrate concentration until it reaches a max, all binding sites full, enzyme is saturated
Term
what is the hyperbolic curve
Definition
curve most enzymes follow.
Term
what are the axies of the hyperbolic curve
Definition
initial velocity (Vo) vs concentration of substrate
Term
what is the name of the principal that outlines the governing of the hyperbolic curve
Definition
michaels-menten kinetics
Term
what does increasing the temperature around an enzyme do
Definition
increases velocity until a peak then decreases it making the molecules more high energy to breach activation energy until the peak which denatures
Term
what happens when an enzyme is denatured
Definition
ionic bonds dissociate
Term
what is the normal temperature good for human enzymes
Definition
37-40 deg C
Term
how does pH affect enzymes
Definition
enzyme substrate needs certian groups protonated or unprotonated to form a catalytic enivornment, changes in pH can change protonation and ionic interactions denaturing the enzyme
Term
what is the optimum pH for an enzyme
Definition
varies for each
Term
what is the reaction model in michaels menten reactions (word explination)
Definition
enzyme reversably combines with substrate to make complex that yields product and the free enzyme
Term
what is the reaction model in michaels menten reactions (reaction explination)
Definition
E + S <-> ES -> E + P
Term
what is k1
Definition
the rate constant of the forward reaction in a michaels menten reaction when enzyme combines with substrate
Term
what is k-1
Definition
the rate constant of the reverse reaction in a michaels menten reaction when enzyme dissociates from substrate
Term
what is k2
Definition
the forward only reaction where enzyme and substrate complex make enzyme and product in a mimchaels menten reaction
Term
in general, what does the michaels menten equation describe for us
Definition
how reaction velocity varies with substrate concentration at a given enzyme concentration
Term
what do we need to assume to make the michaels menten reaction work
Definition
amount of substrate bound by the enzyme at a given time is a small percentage of the total substrate aviable to drive the reaction forward and initial veolcity is used so there is no appreciable back reaction from product to substrate
Term
what is km
Definition
characteristic of an enzyme and particular substrate that relfects affinity of an enzyme for that substrate
Term
what is km equal to
Definition
1/2 max velocity
Term
what does a small km indicate
Definition
high affinity, so it takes a low concentration of substrate to reach 1/2 max velocity
Term
what does a big km indicate
Definition
low affinity, it takes lots of substrate to reach 1/2 max velocity
Term
how are max velocity and enzyme concentration related
Definition
they are directly proportional
Term
if we double enzyme concentration, what happens to max velocity
Definition
it doubles
Term
if we half enzyme concentration, what happens to max velocity
Definition
it is half
Term
what does first order mean
Definition
when [S] < km, velocity is proportional to the substrate concentration and first order describes the rate
Term
what does zero order mean
Definition
when [S] > km, velocity is approx constant and equal to max velocity and independent of [S] making it zero order in respect to the substrate
Term
what is a lineweaver burk plot
Definition
inverse of michaelis menten
Term
what are the axis of a lineweaver burk plot
Definition
1/Vo vs 1/[S]
Term
what is the shape of a lineweaver burk plot
Definition
line
Term
what can we directly determinie from a lineweaver burk plot
Definition
Km and Vmax
Term
why do we need the lineweaver burk plot
Definition
because of the parabolic nature of the michaiels menten plot, Vmax is difficult to percisley determine
Term
what is the X axis on a lineweaver burk plot
Definition
-1/Km
Term
what is the y axis on a lineweaver burk plot
Definition
1/Vmax
Term
in addition of Km and Vmax, what is a lineweaver burk plot useful for
Definition
determining mechanisms of action of enzyme inhibitors
Term
what happens in Km or Vmax increases to a linweaver burk plot
Definition
they will be closer to 0
Term
what happens in Km or Vmax decreases to a linweaver burk plot
Definition
they will get further from 0
Term
what is an inhibitor
Definition
any substance that can diminish the velocity of an enzyme catalyzed reaction
Term
what does an irreversible inhibitor do
Definition
binds to enzymes through covalent bonds irreversibly
Term
what does a reversible inhibitor do
Definition
usually binds with non-covalent bonds and possibly covalent as long as the enzyme can be recovered
Term
what are the two types of reversible inhibitors
Definition
competitive and noncompetitive
Term
what does a competitive inhibitor do
Definition
binds reversibly to the same site that the substrate would normally occupy
Term
how does a competitive inhibitor affect Vmax, why
Definition
the effect of a competitive inhibitor can be overcome with lots of substrate so it does not affect Vmax because we assume there is unlimited substrate
Term
how does a competitive inhibitor affect Km, why
Definition
it increases the Km because most substrate is needed to achieve 1/2Vmax so the apparent affinity is lower
Term
on the graph for competitive inhibitors, what happens to the 1/Vmax point
Definition
it stays the same
Term
on the graph for competitive inhibitors, what happens to the -1/Km point
Definition
it becomes more negative (closer to zero)
Term
what is an example of a competitive inhibitor
Definition
statin drugs
Term
explain how statin drugs do competitive inhibition, what is the biological significance
Definition
statin is a structural analog to HMG CoA reductase which is involved in cholesterol synthesis so it competes for its active site, lowering cholesterol
Term
how does a noncompetitive inhibitor work
Definition
inhibitor binds reversibly to a site other than the substrate binding site, it can bind wether the substrate is bound or not
Term
how do noncompetitive inhibitors affect Vmax, why
Definition
they cannot be overcome by increasing substrate so they lower the Vmax
Term
how do noncompetitive inhibitors affect Km
Definition
they do not interfere with the binding of the substrate so it does not change the affinity, no affect
Term
what happens to the point -1/km on the graph due to a noncompetitive inhibitor
Definition
it stays the same
Term
what happens to the point 1/Vmax on the graph due to a noncompetitive inhibitor
Definition
it increases in Y value, it gets further from zero
Term
what is an example of a noncompetitive inhibitor
Definition
ferrochelatase
Term
explain how ferrochelatase does noncompetitive inhibition
Definition
it inserts Fe into the protophoryin which makes heme, fe noncompetitivly inhibits ferrocheletase by binding its sulfhydril groups on cystine stopping Fe getting into heme
Term
why is the rate of enzymes in the body affected by the concentration of the substrate
Definition
because physiological substrate is near the range of Km so an increase will prompt proportional increase in rate and vice verse.
Term
how a allosteric enzymes regulated
Definition
by effectors
Term
how do effectors work
Definition
they bind to sites other than the active site on enzymes altering their affinity to substrate (affect Km) or the catalytic activity (Vmax) or both
Term
what is a negative effector do
Definition
inhibit allosteric enzyme activity, decrease Vmax or increase Km
Term
what does a positive effector do
Definition
increase allosteric enzyme activity, increase Vmax or decrease km
Term
what is a homotrophic effector
Definition
when the substrate itself serves as an effector, most often positivly. alters the other binding sites of the enzyme changing their Km or Vmax
Term
what is another name for homotrophic effectrs actions
Definition
cooperitivity
Term
what type of curve demonstrates cooperitivity
Definition
sigmoidal
Term
what is an example of coopertivity
Definition
Hb O2 binding
Term
what is a heterotrphic effector
Definition
effector is different than the substrate, possibly a product inhibiting the rate limiting step, binding the enzyme at a site other than the active site
Term
what is an example of a heterotrphic effector
Definition
PFK-1 is the rate limiting step in glycolysis, citrate from the TCA cycle can shut this step down if it builds up making the sythesis of glycogen vs glucose
Term
what is the most common form of enzyme regulation
Definition
covalent modification usually via phosphorlyation or dephosphorlyzation of the SER, ThR, or TYR -OH group
Term
what does a kinase do
Definition
phosphorlyates enzymes
Term
what does a phosphatase do
Definition
dephosphorlyates enzymes
Term
what does fasting cause in metabolic enzymes
Definition
activates phosphorlyating kinases, activates catabolism and inhibiting anabolism
Term
what does a well fed state do to metabolic enzymes
Definition
inhibits phosphorylzation, deophsphorlyzation activated. activates anabolism and inhibiting catabolism
Term
explain how induction or repression can control enzymes
Definition
you can alter their synthesis by controling their gene expression or their degredation by controling other genes
Term
what qualifies an enzyme to be regulated by induction or repression of expression
Definition
it usually needs to be under specific physiological conditions and not in constant use
Term
how long does it take for gene alteration to control enzymes
Definition
hours to days
Term
how long does it take for covalent measures to change enzyme activity
Definition
seconds to minutes
Term
why are steroids not immediatly effective
Definition
because they control gene expression not covalent modifications to enzymes
Term
describe the normal enzyme component of the blood
Definition
there are a small amount for things like coagulation and a teeny bit because of cell lysis and turn over
Term
why is having some enzymes from cell lysis and turn over in the blood ok
Definition
because they are normally removed
Term
when is having some enzymes from cell lysis and turn over in the blood a problem, what does this cause, what is it caused by
Definition
when they are not removed and build up, tissue damage, disease
Term
how can you determine the extent of tissue damage using plasma and where it came from
Definition
count the levels of enzymes from lysed cells, cells have specific enzymes so can you look at the type to see where they lysed from
Term
what are isoenzymes
Definition
caralyze the same reaction but are a different on the amino acid level, they may also have different quatrentary subunits
Term
how can you find isoenzymes vs enzymes in the lab
Definition
electrophoreses, different amino acids give different weights
Term
why are isoenzymes useful
Definition
different organs have specific ones and can indicate the location of disease
Term
What type of effector is a homotroohic effector
Definition
Positive
Term
How does a homotroohic effector work
Definition
Substrate itself is the effector
Term
What does a homotroohic effector do to Vmax and Km
Definition
Increases Vmax and decreases Km of other substrate binding sites
Term
What is the shape of a curve for homotroohic effectors
Definition
Sigmoidal when Vo vs substrate concentration
Term
What type of effector shows cooperatively
Definition
Homotrophic
Term
How does a heterotrophic effector work
Definition
Effector is different than the substrate
Term
Is a heterotrophic effector positive or negative
Definition
Both
Term
What does heterotrophic effectors show is going on in the reaction
Definition
Feedback inhibition
Term
What is feedback inhibition
Definition
Accumulation of product inhibits rate limiting step at a location other than a binding site for the substrate
Term
What is an example of feedback inhibition
Definition
PFK-1 is rate limiting step in glycolysis, citrate from the CAC can inhibit this step changing from production of glucose to glycogen
Term
How is covalent modification of enzymes done
Definition
Phosphorlyation or desphosphorlyation of -OH of ser, the, and tyr
Term
What does kinase do
Definition
Phosphorlyates
Term
What does phosphatase do
Definition
Dephosphorlyation
Term
Does phosphorylation turn on or off genes
Definition
Either depending on the situation
Term
When fasting what enzyme is being inhibited, what enzyme is activated
Definition
Anabolic pathways were inhibited, kinases activated
Term
When well fed what pathway is inhibited, what enzyme is activated
Definition
Catabolism is inhibited, desphosphorlyation enzymes are activated
Term
What are ways other than phosphorylation we can regulate enzymes
Definition
Control transcription, control mRNA, altering gene expression (control synthesis or degration),
Term
What limits when we. An alter gene expression to control enzymes
Definition
You cannot do it for enzymes that are used all the time to make energy
Term
Way is the difference between the timing of covalent and genetic alterations to enzymes
Definition
Covalent takes minutes, genetics take hours
Term
What are the reasons enzymes are in the blood
Definition
Fragments due to cell lysis, normal blood enzymes like for clotting
Term
Why are the enzymes due to cell lysis in the blood medically significant
Definition
Normally the enzymes are removed so an increase in level can indicate tissue damage in the tissue that enzyme correlates to
Term
What is an isoenzyme
Definition
Enzyme that catalyzes the same reaction but uses different amino acids to do it and may have a different quaternary structure
Term
How can you identify isoenzymes from other enzymes
Definition
If you do electrophoresis they will be a different weight due to their difference in size t the enzyme they are like
Term
What is heme
Definition
A prosthetic group tightly bound to a protein
Term
What is a prosthetic group
Definition
Coenzyme permeability associated with the enzyme or another protein and is returned to original form
Term
What does heme do in cytochromes
Definition
Electron carrier function, lots in ETC
Term
What does heme do in catalyase
Definition
Proximal enzyme. Breaks down hydrogen peroxide to water and oxygen
Term
What is the shape of a heme called
Definition
Prophyrin
Term
What a thte bonds in the iron of heme bound to
Definition
4 nitrogens bind to iron, 1 to hb or myoglobin on r group of HIs of globin, binds oxygen
Term
Where is myoglobin found in the body
Definition
Cardiac and skeletal muscle
Term
What is the function of myoglobin
Definition
Binds oxygen very tight, only releases oxygen if the body is very low in it, it's high affinity can change the rate of diffusion in the cell
Term
Describe the structure of myoglobin
Definition
One chain similar to aha or beta, interior non polar site with his that binds 1 oxygen and a his that binds iron of heme, polar amino acids on surface
Term
what is HbA
Definition
adult hemoglobin
Term
how many oxygen does a hemoglobin transport
Definition
4
Term
how many oxygen does a myoglobin transport
Definition
1
Term
what kinds of molecules can a hemoglobin transport
Definition
oxygen, CO2, H+, 23-BPG, bicarbonate
Term
what mechanism regulates the oxygen binding site on heme
Definition
allosteric
Term
describe the quaternary structure of hemoglobin
Definition
alpha beta dimer
Term
what is the state of the hemoglobin in the T form
Definition
deoxygenated, lower oxygen affinity, rigid
Term
dscribe the bonds of a hemoglobin in the T form
Definition
strong hydrophobic bonds between the alpha and beta chains. weak ionic and hydrogen bonds between the two alpga beta dimers
Term
what is the state of hemoglobin in the R form
Definition
oxygenated, high oxygen affinity, relaxed
Term
describe the bonds of a hemoglobin in the R form
Definition
the bonds within the dimers will be the same but the ionic and hydrogen ones between the dimers will lessen
Term
when looking at a hemoglobin curve, what location in the body does the left side indicate
Definition
the tissues
Term
when looking at a hemoglobin curve, what location in the body does the right side indicate
Definition
the lungs
Term
what is the shape of a hemoglobin curve
Definition
sigmoid
Term
what is the shape of a myoglobin curve
Definition
hyperbolic
Term
what are the axis on a hemoglobin coopertivity graph
Definition
partial pressure of o2 (mmHg) vs degree of saturation of O2
Term
what is the P50
Definition
partial pressure of oxygen to achieve half the saturation in the atmosphere
Term
what does a low P50 indicate
Definition
high affinity
Term
what does a high P50 indicate
Definition
low affinity
Term
in general, what does it mean if a Hb curve is shifted left
Definition
binds oxygen with higher affinity
Term
in general, what does it mean if a Hb curve is shifted right
Definition
more oxygen is released, less is bound to Hb. less degree of saturation in the lungs
Term
what shift of a Hb curve is generally more benificial
Definition
shift right
Term
myoglibin P50 is usually _____. why?
Definition
low, because of the higher affinity it has for oxygen
Term
what are two important examples of cooperative biniding
Definition
hemoglobin and allosteric enzymes
Term
what is the heme-heme interaction
Definition
interaction on one site of Hb makes other sites increase their affinity for Hb allowing more oxygen to be delivered to the tissues in response to small changes in pO2
Term
what does the pO2 in the tissues allow
Definition
unloading
Term
what does the pO2 in the lungs allow
Definition
saturation of Hb
Term
what is the bohr effect
Definition
Hb has less affinity for oxygen at lower pH values shifting the curve right, unloading more oxygen. a greater pO2 is needed to achieve the same oxygen saturation
Term
what can cause lower blood pH and this the bohr effect
Definition
lactic acid, CO2
Term
what activity of Hb is favored at a low pH
Definition
unloading
Term
what activity of Hb is favored at high pH
Definition
loading
Term
what is the bicarbonate reaction
Definition
CO2 + H2O -> H2CO3 -> HCO3 + H+
Term
why does the Hb assume the T state without oxygen
Definition
because the pKa of his shifts without O2 so it cannot bind proteins as well, this stabilizes the T state leading to less oxygen affinity
Term
when in the T state, which way is the curve shifted
Definition
right
Term
how and where is 2,3-BPG made
Definition
product of glycolysis in RBC
Term
what does 2,3-BPG bind do
Definition
deoxyhemoglobin
Term
what function does 2,3-BPG play
Definition
stabilizes the T form of Hb, decreasing oxygen affinity
Term
how does 2,3-BPG bind Hb
Definition
at picket between B globin chains to positive amino acids because they are negative
Term
what happens to 2,3-BPG when oxygen binds a Hb
Definition
it is expelled from the Hb
Term
what does 2,3-BPG do to the Hb curve
Definition
shifts right
Term
what action does 2,3-Bpg help the Hb do
Definition
unload oxygen into tissues
Term
what diseases can cause the body to make more 2,3-BPG
Definition
chronic hypoxia, COPD, emphysima, high altitudes, anemia, hypoxia
Term
what do lung function decreasing diseases do to 2,3-BPG and the Hb curve
Definition
cause the body to make more of it, shifting it right
Term
when someone gets a blood transfusion, why for ~6 hours do they have problems letting their O2 go into the tissues
Definition
the transfused blood had the 2,3-BPG mostly deteroirate, after about 6 hours it builds back up. initially, the transfused blood will not release oxygen well
Term
what does the curve look like when someone has just had a blood transfusion, does it shift?
Definition
it is more like myoglobin, it is only slightly sigmoidal, shifts left
Term
how does CO2 bind to Hb
Definition
it travels in the form of bicarbonate and when attached is a carbamate on the N terminal of AA of Hb turning the Hb into carbaminohemoglobin
Term
what is the equation for CO2 Hb interaction
Definition
Hb-NH2 + CO2 -> Hb-NH-COO` + H+
Term
what effect does CO2 have on the structure of Hb
Definition
stabilizes the T form
Term
what does CO2 do to the Hb curve
Definition
shifts right
Term
what does CO2 do to the Hb affinity
Definition
less affinity for oxygen
Term
what does Hb have a higher affinity for: O2, CO2, 2,3-BPG, or CO
Definition
CO
Term
where does CO bind to Hb
Definition
at the oxygen binding site
Term
when CO attaches to Hb what physical changes does it cause
Definition
Hb goes into the R state, now has a higher affinity for oxygen or CO, whatever, less unloading
Term
what does CO do to the Hb curve
Definition
shift left
Term
describe the structure of fetal Hb, what does this cause
Definition
gamma chains lack some of the AA that interact with 2,3-BPG so low affinity for it provides a higher oxygen affinity allowing baby to steal O2 from mom
Term
what is the function of HbA2
Definition
unknown
Term
what is another name for HbA1c
Definition
modified adult hemoglobin
Term
how is HbA1c made
Definition
over time, adult Hb is glycosylated non enzymatically to an extent in proportion to the sugar around the RBC in their 120d
Term
what can HbA1c test for
Definition
it someone has been following their diabetes diet or it it isnt working
Term
what percent of Hb is FHb, HbA2, and HbA1c in an adult
Definition
<2, 2-5, 3-8
Term
what is the most common inherited blood disorder
Definition
sickle cell anemia
Term
when do the symptoms for sickle cell appear, why
Definition
around 6 mo old because the issue is with beta globin and you dont replace gamme globin with beta until then
Term
what are the symptoms of sickle cell
Definition
apisodes or crises (pain), chronic hemolytic anemia, increased susceptability to infection
Term
how long does a sickle cell live
Definition
20d
Term
what is the exact mutation inoved in sickel cell, mutated to what
Definition
glutamate is replaced with valing going from negative to neutral
Term
how can you seperate sickle cell Hb and normal
Definition
electrophoresis because they are different weights
Term
what does the chance in amino acid in sickle cell cause structurarly
Definition
makes a pocket in b globin so it can bind to another Hb making Hb fibrils causing the cell to sickle only when the cell is deoxygenated
Term
why do sickled cells cause problems
Definition
they dont flow normally and stick to eachother and the walls, they cannot pass through small capilaries due to their rigidity
Term
what causes crises
Definition
pain from trying to smoosh sickle cells through capillaries
Term
what can increase severity of sickling in sickle cell anemia
Definition
anything that puts Hb in the deoxy state: high altitudes, flying in a non-pressurized plane, increasing CO2, decreasing pH, increasing 2,3-BPG
Term
what does dehydration do to someone with sickle cell
Definition
decreases blood flow causing less movement of oxygen and more Hb unloading, more Hb will be in deoxy form increasing sickling
Term
what can exercise to do someone with sickle cell
Definition
decreases pH / CO2 and causes more sickling
Term
what are some treatments for sickle cell
Definition
hydration, analgesic, antibiotic therapy, blood transfusion, hydroxyurea
Term
what does hydroxyurea do
Definition
increase fetal hb
Term
what mutation happens in Hb C disease
Definition
lysine is substituted for glutamate (in the same spot as sickle cell)
Term
what are the symptoms of homozygous HbC disease
Definition
mild chronic hemolytic anemia, no infractive crises, no specific therapy
Term
what mutation happens in Hb SC disease
Definition
patient inherits one copy of HbS and one of HBC
Term
what are the symptoms of Hb SC disease
Definition
symptoms are more variable and between severe sickle cell and HbC disease. less frequent sickling leading to less frequent and severe crisis
Supporting users have an ad free experience!