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119 Cards in this Set

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What does it mean that Hb is cooperative?
-Meaning that binding of each O2 molecule to the tetramer increases the affinity with which the next O2 can bind.
-Likewise, with each removal, the affinity decreases. This is important deep in tissues where Hb has the ability to release O2.
1. How does lower pH affect Hb O2 affinity?
2. CO2?
3. 2,3-Diphosphoglycerate (DPG)?
1. low pH decreases Hb affinity for O2
2. CO2 decreases affinity for O2 (makes sense, in tissues where CO2 is high, you want O2 coming off Hb)
3. DPG allows Hb to adapt to hypoxia by releasing O2 more easily.
Describe the mutation that causes sickle cell disease. What does this do phenotypically?
A mutation in the B-globin gene causing a change from Glu to Val at position 6 on Chromosome 11. Presence of Val at position 6 allows deoxyHbS to polymerize into microfibrils that distort RBC shape and cause both hemolysis and vaso-occulsive disease.
What chromosome is Alpha-globin and Beta-globin on?
1. Alpha-globin: Chromosome 16
2. B-Globin: Chromosome 11
Describe embryonic a-globin's expression through the life cycle. What is the Greek letter assigned to this?
It occurs only briefly during development (0-6 wks) and then adult form dominates through fetal growth and into adulthood. Greek = Zeta
How many alpha-globin genes do most people have? How many are active?
Four - two on each chromosome 16. They're all active each contributing about 1/4 of the total alpha expression.
Describe embryonic B-globin's expression through the life cycle. What is the Greek letter assigned to this?
Similar to Zeta - it drops off quickly between 0-6 weeks as it is replaced by gamma--globin which doesn't disappear until after birth. Greek = Epsilon
How many forms of adult Hb are there? What are they and describe relative percentages.
HbA (alpha2beta2) and HbA2 (alpha2gamma2). HbA2 accounts for only a few percent of adult Hb
Of the alpha and beta globins, which is more likely to cause clinical problems?
Beta globins because each chromosome 11 has only one functional B-globin gene.
RBCs contain an enzyme to help get rid of CO2 - what is it and what does it do?
Carbonic Anhydrase. Hydrates CO2 to carbonic acid (H2CO3). This spontaneously dissociates to bicarbonate HCO3- and H+ - both of which are highly soluble in plasma.
Iron exists in hemoglobin as two forms - which can/cannot bind O2?
Ferrous form (Fe2+) can bind O2 and Ferric (Fe3+) cannot. Ferric iron is found in an inactive form of hemoglobin called "methemoglobin"
What is P50?
It is the partial pressure of oxygen yielding 50% saturation of binding
In regard to the partial pressure curves of Hb and Mb, describe their overall shape. Which one gives up O2 less easily?
Hb is sigmoidal and Mb is hyperoblic. Myoglobin gives up O2 much less easily.
Hb has a P50 at around a pO2 of 25mmHg. Why is that good?
25mmHg is roughly the pO2 of resting/working tissues. At this point, Hb readily gives up its oxygen.
Discuss how the affinity for Hb changes depending on the subunit composition and what this means for fetal Hb
Fetal Hb (alpha2-gamma2) has a higher affinity for O2 than adult Hb - that means the fetus' circulation can draw O2 from maternal blood at the low pO2 of the placenta.
Hemoglobin exhibits sequential co-operativity for oxygen binding. Define.
Binding of oxygen to one subunit induces a conformational change that is partially transmitted to adjacent subunits. The transmission of the partial conformational change induces an increased affinity for oxygen by these adjacent subunits.
Describe the Taut of Hb
Taut Hb the DEOXY form and has constrained movement of its polypeptide chains that inhibits O2 from entering and binding complex. It thus has a low affinity for O2 and more likely to give it up than the Relaxed form.
Describe the Relaxed form of Hb.
Relaxed Hb is the result of oxygen binding that causes rupture of some of the iconic and hydrogen bonds giving Hb more freedom of movement. This form has a high affinity for O2 and less likely to give it up than Taut.
Discuss the equilibrium between T and R states.
With no O2 bound, the T state is favored. Once O2 starts binding, the equilibrium begins to shift toward favoring R. When 2 O2 are bound, T and R are in equilibrium. Once 3 and 4 O2 are bound, R state is heavily favored.
In essence, what does cooperative binding accomplish?
It increases Hb binding of O2 in O2-rich areas (i.e. lungs) while increasing the release of O2 in deoxy areas where it is needed most (i.e. deep tissues).
How does O2 binding change the conformation of the Hb subunit?
Without O2 bound, heme Fe2+ is pulled away from the plane of porphyrin ring. When O2 is bound, it pulls Fe2+ back into the plane of the ring, causing other Hb subunits to shift relative to one another into an arrangement that favors the R-conformation.
Define allosteric regulator or effector. What are allosteric regulators for Hb? How do they affect affinity for O2?
A molecule that can bind to a protein and induce a conformational change that alters the affinity for substrate at some other site. Hb allosteric regulators are CO2, DPG, and H+. They all bind to Hb and reduce its affinity for O2.
Including DPG, H+, and CO2, summarize the allosteric regulation in hemoglobin.
DPG--HHb--CO2 +O2 <---> HbO2 + CO2 + DPG + H+
Describe how the equilibrium of the allosteric regulation of Hb shifts according to where it's at in the body.
In lungs where O2 is abundant, equil is shifted to the right where HCO3+ is converted to CO2 and DPG is released. In tissues, where CO2 and H+ is high and O2 is low, the eq is shifted to the left, causing O2 to be released from Hb and CO2 and H+ bind and removed from tissue.
How does decreasing the pH affect the pO2 of Hb? Figure it out using the HbO2 equilibrium equation and plotting a graph % Saturation vs pO2. Do the same for CO2.
See pg 22 lecture.
H+ and CO2 are Heterotropic Negative Allosteric effectors. Why are they: 1) Heterotropic 2) Negative 3) Allosteric? 4) What would O2 be classified as?
1. Heter bc they are not O2
2. Negative bc they decrease the affinity for O2
3. Allosteric bc they bind to a site other than the O2 sites.
4. Is a Positive Homotropic Allosteric effector.
Describe the regulatory classification of O2 in regard to H+ and CO2 binding to Hb
O2 is a negative allosteric effector of H+ and CO2.
Where does DPG bind in Hb and is it a positive or negative effector? Binding is through...?
It binds in a central cavity between the B subunits. It is a negative allosteric effector. Binds through ionic interactions.
What does DPG essentially do? Why is this important?
It fine-tunes the affinity of Hb for O2 in response to changes in metabolism and environment. DPG obviates the need for RBC to synthesize different isoforms of Hb - especially since it doesn't have that ability.
In terms of T and R states, what does DPG do? And therefore what affect does it have on Hb's affinity for O2?
It stabilizes the T state and therefore decreases Hb's affinity for O2.
What would you regarding DPG concentration in RBC between an high altitude dweller vs low? Why?
High altitude dweller would have higher DPG concentration. DPG stabilizes the T form Hb letting O2 release easier in the low O2 enviro of high altitudes.
How would the Bohr effect shift with higher temp? How is this useful physiologically?
It would shift to the right. Useful during elevated metabolic rates associated with fever.
What is the genetic inheritability of SCD? What causes it?
1. Homozygous recessive. 2. Caused by point mutation in the adult B-globin gene that causes substitution of Valine for Glutamic Acid at amino acid 6.
What is HbS?
It is the SC variant where the Hb contains two normal alpha su's and two defective adult beta-globulin su's.
How does the sickle cell shape form?
Normally, Glu is a hydrophilic residue on the water surface of a B-chain. Val is a hydrophobic residue that creates a sticky patch on the globin when it is substituted. This leads to polymerization of Hb tetramers into long chains - causing the sickle cell shape and reduced deformability of the RBCs.
Besides the vaso-occlusive manifestations of sickle cell disease, what are two other sxs of SCD?
Shorter erythrocyte half-life and chronic hemolytic anemia.
What four independent factors affect the rate and extend of polymer formation in circulating SS RBCs?
1. Degree of deoxygenation (affected by changes in pH, ionic strength, and temp)
2. Intracellular hemoglobin concentration.
3. Relative amount of HbF present - it prevents polymerization
4. Hydration - scRBC tend to be dehydrated which increases sickle cell shape and stickiness.
What is the most common therapy for SC? How does the drug work?
Hydroxyurea - an antitumor drug. It increases the percentage of HbF and therefore decreases sickling.
Based on charge, what is more negative - Hb or HbS?
Hb - the mutation substitutes Glu to Val. Glu is neg charged and Val is neutral. Thus, wt has more negative charge.
How is RFLP used to diagnose SC?
DNA is restricted and run on a gel. MstII enzyme specifically cuts at CCTNAGG - however, in SS pts, the sequence CCTNTGG is no longer recognized. This results in a longer fragment of DNA compared to wt that runs slowly on a gel.
Name the embryonic, fetal and adult Alpha-globulins
Embryonic: Zeta
Fetal: Alpha
Adult: Alpha
Name the embryonic, fetal and adult Alpha-globulins
Embryonic: Epsilon
Fetal: Gamma
Adult: Sigma and Delta
Where does heme Fe2+ get all six of its protons to satisfy its electron requirements?
4 from the Nitrogens in the protoporphyrin ring. 1 from a His residue that's part of the protein and 1 from the Oxygen
What is the primary role of myoglobin?
As a store for O2. Also, in muscle, it may facilitate diffusion of O2 down concentration gradient.
What has greater affinity for Hb - O2 or CO? What is the consequence of this in terms of T and R states and re O2 delivery?
CO. CO "locks" Hb in R state. Even if just one CO is bound, the other 3 O2 on Hb cannot be released to tissues.
Define the Bohr effect.
The ability of protons to modulate Hb's affinity for oxygen. See p. 23 lecture notes.
What is the problem in Thalassemia?
Failure to produce a B- and/or A-globulin. I.e. there's an imbalance between a- and b-chains.
Sickle cell pts are most susceptible when?
Whenever they're Hb is deoxygenated (exercise, fever, COPD). Deoxygenated Hb is what polymerizes.
Which Thalassemia is more common? Why?
Beta. Bc there are two alpha genes / chromosome vs one beta gene / chromosome. Having two messed up alpha genes is less likely.
What is the difference between B-zero and B-plus thalassemia?
B-zero makes no B-globin and therefore no functional RBCs.
B-plus makes chain but it is dysfunctional - it's not as severe as B-zero.
What happens in hereditary persistence of fetal hemoglobin?
For unknown reasons, large deletions in gamma and beta genes result in turning on of fetal genes. Pt usually doesn't realize they have it - favorable consequence for high altitude dwellers.
What is HbC? What are the clinical consequences of this? How does it affect people who are heterozygous for HbS (i.e. they're Hb SC)
It a mutation Glu --> Lys where a neg charge is substituted for a pos charged residue. It's not as severe as the Val substitution but it still doesn't function properly. It's a less severe form of Thalassemia and if complexed with HbS, then a mild form of sickle cell.
What is HbA1c and what is its clinical consequence?
Hemoglobin is often glycosylated permanently throughout its 120 day life cycle. Normally, a low amount is glycosylated but if unregulated blood sugar levels, as in diabetics, this is higher. A good way to evaluate the long term control of blood glucose levels.
Specifically, what do enzymes do? What do they don't do?
They reduce the free energy of activation of the reaction. THEY DO NOT CHANGE Keq!
What is Keq? Define it relative to product A and product B. Can a catalyst affect it?
It is the energy difference between the two - think of the free energy diagram. Catalysts cannot change Keq (draw the E diagram to prove it to yourself).
What is the rate constant (Kr)? Can a catalyst affect it?
Kr is the free energy required to activate a rxn to make products. Catalyst can lower the energy required.
Know that there is a group commissioned to formally/systematically name enzymes. How many classes are there?
6
Before a reaction can happen, reactants A and B must diffuse into each other. They are typically surrounded by tightly bound water molecules...why is that?
Because the functional groups are typically charged or polar.
When reactants diffuse into each other, what happens in terms of the water molecules surrounding them and subsequent interactions?
The water molecules form a cage where the molecules experience about 150 collisions before diffusing away (at RT).
For a reaction to occur within the reaction sphere, what three things must occur?
1. Reactants must collide with enough energy to exceed activation energy.
2. Reactants must collide with correct orientation.
3. During collision, water molecules within the hydration sphere must be physically moved away.
What is the proximity effect of enzymes?
It is the ability of enzymes to bring substrates together, line them up, and increase chances of right collision for rxn.
In terms of transition state, how do enzymes increase the rate of rxn?
Enzymes typically have a part of the rxn pocket that stabilizes the transition state. Usually it binds more tightly than the initial reactant. This has been useful for drug design - e.g. anti-HIV protease inhibitor.
Possible exam Q: If you were to design a drug to inhibit a rxn, what would you target?
Design a molecule that closely resembles the transition state molecule.
What are the three most common aa found in active sites of enzymes? Why is that?
Glutamate, Aspartate, Histidine. They can act as general acids/bases - i.e. proton donors or acceptors. Since physiological pH is very narrow, these aa provide the right proximal pH for rxns to occur.
In terms of polarity, what is the microenvironment for enzymes at its active site? Why is this beneficial? What can the microenvironment do in terms of pKa?
It is typically hydrophobic. It excludes solvent molecules from getting in the way, and if the transition state is less polar than the substrate or product, this microenvironment stabilizes it and lowers the energy of activation. In terms of pKa, it can alter the pKa's of aa to either more easily protonate or deprotonate. (see p34)
Briefly discuss the example used re the two-step protease and peptidase catalysis rxns and their microenvironment. (see pg 35)
Step 1: Polarization of peptide carboxyl group to form an oxyanion similar to transition state.
Step 2: proximity of a nucleophile to attack the carbonyl carbon - which ultimately removes peptide bond. This rxn requires a Zn2+ to create carboxy anion. (see pg 35)
The example he used re Ribonuclease, demonstrates what? Particularly about His and its special ability. (p35)
How enzymes can function as a general acid and/or base. Histidine can function as both an acid and a base in the same enzyme. (p35)
Describe "induced fit". How does it reduce the energy required to cause a rxn?
It is a conformation change that enzymes cause to distort the shape of a substrate into one that resembles the transition state. Bc the enzyme favorably binds to substrates this way, it reduces the amount of energy required to make this required conformational change.
What? Review pg 37. 9/13 lecture at 58:00 and earlier.
What? Review pg 37. 9/13 lecture at 58:00 and earlier.
Know "catalytic triad" mechanism at 1:00:00 on 9/13
Know "catalytic triad" mechanism at 1:00:00 on 9/13
What is covalent catalysis?
It is when a covalent enzyme-substrate intermediate is formed during the course of a rxn.
What are the residues in the catalytic triad?
Asp102, His 57, Ser195.
What role does Asp102 in the triad?
It forms a low-barrier H-bond with H57, turning it into a powerful base.
What role does H57 have in the triad after it is converted to a base by Asp102? (see pg 37)
His57 deprotonates Ser195
What role does Ser195 play in triad once it has been deprotonated?
It acts as a nucleophile and attacks the carbonyl carbon of the peptide - forming a covalent bond
Catabolism vs Anabolism?
Catabolism breaks down to yield energy. Anabolism takes in energy to build new molecules.
In what molecules is energy stored (5 - 3 of which are co-factors)
ATP, GTP, NADPH, NADH, FADH2
Which energy molecules are used to drive anabolic pathways?
ATP and NADPH
Define substrate level phosphorylation.
The metabolic process that generates high energy molecules directly - either GTP or ATP
Although you can get more energy out of splitting ATP at this P bond, it's irreversible. Bn which P bond is this? Bn which bond is it not irriversible?
Between the alpha and beta. Between beta and gamma.
Why is the hydrolysis of the pyrolphosphatase from ATP irriversible?
B/c pyrophosphatse immediately cleaves pyrolphosphate.
What is the role of phosphoreatine? What enzyme mediates the rxn?
It stores a high energy phosphate bond that can be used to quickly convert ADP to ATP when the cells need a burst of energy. Creatine Kinase mediates this rxn.
NADH is another way to store energy. How does it do it?
NAD+ captures two high energy electrons in the form of hydride ion (H with 2e) to form NADH. Reoxidation by O2 in mitochondria yields 2.5 ATP.
You know that NADH can accept a hydride ion to store energy - does NADP+ do the same?
No. NADP+ accepts hydride ions to produce NADPH but it has biosynthetic and antioxidant defense system roles - not ATP synth role.
On pg 44, note subtle difference between NAD+ and NADP+ - at the 'OR' group in the figure, R is either H or P
On pg 44, note subtle difference between NAD+ and NADP+ - at the 'OR' group in the figure, R is either H or P
Similar to NADH, how does FAD capture/release energy?
It can capture two high energy electrons to form FADH or FADH2. It can be oxidized by O2 in mitochondria to yield 1.5 ATP.
Prof wants use to know where "business end" of each energy storing molecule is. Review that:
Creatine: bottom right p 43
NADH: upper right p 44
FAD: bottom half p44
Prof wants use to know where "business end" of each energy storing molecule is. Review that:
Creatine: bottom right p 43
NADH: upper right p 44
FAD: bottom half p44
Note how Acetyl-CoA is a high energy species that can transfer acetyl groups to other bio molecules or water. p45
Note how Acetyl-CoA is a high energy species that can transfer acetyl groups to other bio molecules or water. p45
Name the four high energy storage molecules and the two low energy molecules.
High energy: Creatine, FADH2, NADH, Acetyl-CoA.
Low energy: Glycogen, Triglyceride (Fat)
When intake of energy exceeds needs, how does the body store it? Is there a storage means from protein?
Glycogen and triglyceride are energy stores. No storage unit for protein - must degrade own tissues if necessary.
Review general properties of metabolic pathways on pg 45
Review general properties of metabolic pathways on pg 45
How do you determine the reaction order?
It's based on how many reactants there are. If there are two, it's 2nd order. If one, it's first order.
What is usually the limiting step in enzyme mediated rxns? What is usually the fastest?
The conversion to products is usually the slowest. Binding to the enzyme is usually the fastest. (Review graph on p51)
What is the Michaelis-Menton Equation? What are the two assumptions here?
vo = (vmax[s])/(Km + [s])
Assumptions:
1. [s] is equal to the initial amount added and there is no product yet
2. The concentration of [ES] is nearly constant as P is being formed.
(see p. 52)
You know the Michaelis-Mention equation - but what does Vmax equate to? Knowing this, you should know what effect increasing the [E] should be on vo.
Vmax = k2[E], so by increasing the [E], you'll increase the vo.
What does Km equate to? It is defined as the substrate concentration at which the rxn rate is half of Vmax. However, remember that it defines the average K for the entire rxn and derivation involves using each K.
Km = (k-1 + k2)/k1
When considering the Michaelis-Menton equation, what does it reduce to when [S]<<Km or when [S]>>Km?
1. [S]<<Km
What is a competitive inhibitor?
Binds to same enzyme form as the substrate.
How is the Vmax affected by a competitive inhibitor?
It is not. See p55.
Go over the various inhibitors and their features:
1. Competitive
2. Non-competitive
3. Uncompetitive
4. Irreversible I
p 53-8
Go over the various inhibitors and their features:
1. Competitive
2. Non-competitive
3. Uncompetitive
4. Irreversible I
p 53-8
Recall how the activity of Phosphofructiokinase changes according to the presence of ATP and AMP and how this is typical of allosteric enyzmes. p58
Recall how the activity of Phosphofructiokinase changes according to the presence of ATP and AMP and how this is typical of allosteric enyzmes. p58
review how inactive/active enzyme equilibrium is dependent on concentration of inhibitor and/or substrate. p58.
review how inactive/active enzyme equilibrium is dependent on concentration of inhibitor and/or substrate. p58.
This is important for carbohydrate nomenclature: What is the most reduced carbo and what is the most oxidized?
Most reduced: CH4
Most oxidized: CO2
Monosaccharides can only be classified as two things...?
aldose (has aldehyde group) and ketose (has ketone group)
How do you determine the chirality of a CHO?
You start with the chiral C furthest from the carbonyl end. and look at the OH. If it is on the left side, it is L- on the right side it is D-.
What is the difference between isomers and epimers?
Isomers have a chiral C and have groups that differ around that C. Epimers are sugars with more than one chiral carbon and differ only by the configuration about a single carbon. (Think about L- vs D- glucose. If you flip only one OH group, it's an epimer)
What are the four most biologically important hexoses? And what is their relations to each other regarding epimers and isomers?
A. Remember GalGMF
1. Galactose
2. Glucose
3. Mannose
4. Fructose
B. Draw out to help with relations:
1. Galactose and Glucose are C4-epimers
2. Glucose and Mannose are C2-epimers
3. Glucose and Fructose are isomers
Isomers that exist as mirror image molecules are termed...?
Enantiomers
in bio systems, where are sugars oxidized?
At C1 or C6
Sugars (aldohexoses) oxidized at C6 have what suffix?
Sugars oxidized at C1 have what suffix?
C6 = -uronic acid or uronate
C1 = -conic acid or conate
What is common table sugar? It is composed of what two monosaccharides?
Sucrose is F-ing Good:
Fructose
Glucose
1. When hexose sugars cyclize, what is this rxn called? (there's two types).
2. When the new ring forms and the -OH is above the ring, it is a _a_? Below the ring it is _b_?
1. hemiacetalisis or hemiketalisis
2. a. Above is Beta anomeric
b. Below is Alpha anomeric
What are the subunits that make up lactose and maltose?
Lactose: Galactose and Glucose
Maltose: 2x Glucose
Know that: Humans can digest alpha 1,4 (amylose) and alpha 1,6 linkages (amylopectin, glycogen) but cannot digest beta 1,4 linkages (cellulose). p 68-9
Humans can digest alpha 1,4 (amylose) and alpha 1,6 linkages (amylopectin, glycogen) but cannot digest beta 1,4 linkages (cellulose). p 68-9
What is a Schiff base?
A double bond between a N and C.
Alpha-amylase is present in __a__ and __b__. It attacks the internal alpha 1,4 glycosidic bonds of __c__ and __d__.
a. saliva
b. pancreatic juice
c. starch
d. glycogen
Lactase is relatively non-abundant. How can lactose become a problem in the digestive system?
If not digested, it remains a disaccharide and cannot be absorbed. In the large intestine, it functions as an osmotic molecule where it pulls water in and causes diarrhea. It can also be a food to microbes and cause cramping and gas.
How can you ID the carina in a radiograph?
Find the aortic knob...it's medial to the base of that.
In radiograph, what forms the right side boarder of the heart? What about the left? Why is the right
R = R atrium
L = L ventricle