Biochem Block Iii - Week 2

Front 1

Hb binds O2 at a _______ pH level (lungs) and releases O2 at a ______ pH level (tissues)

Why?

Back 1

Higher

Lower

Lower, acidic pH strengthens the ionic interactions in the T-state (histidine gets protonated)

Front 2

Heme is comprised of ...? (2)

Back 2

1. Protoporphyrin IX ring

2. Ferrous (2+) iron

Front 3

What are the six bonds that Fe2+ forms in a heme?

Back 3

4 to the protoporphyrin ring

1 to a histidine side chain from helix F

1 to O2

Front 4

What is the main secondary structure found in Mb and Hb?

Back 4

alpha-helix

Front 5

Lower Kd = ______ tightly bound ligand to protein

Back 5

more tightly bound

Front 6

In which state is the Fe+ of heme evenly situated in the plane of the protoporphyrin ring?

Higher or lower O2 binding affinity?

Back 6

Relaxed

Higher

Front 7

How many ionic bonds are present in the T-state of Hb? How many interchain / intrachain?

Back 7

8

6/2

Front 8

How does the concentration of CO2 affect binding affinity of O2 to Hb?

Back 8

Higher concentrations = lower O2 binding affinity

Lower concentrations = higher O2 binding affinity

Front 9

How does the concentration of CO affect binding affinity of O2 to Hb?

Back 9

Higher concentrations = higher O2 binding affinity

Lower concentrations = lower O2 binding affinity

Front 10

What protein is a strong regulator of O2 binding affinity, decreasing the affinity of Hb for O2?

Back 10

2,3-bisphosphateglycerate (BPG)

Front 11

How does carbon dioxide lower Hb affinity for O2? (2)

Back 11

1. 23% of Co2 forms a non-covalent adduct (carbaminohemoglobin) with Hb

2. The conversion of CO2 to HCO3 and H+ acidifies the system, decreasing O2 binding affinity

Front 12

How does CO poisoning affect Hb?

Back 12

CO binds Hb 250x more tightly than O2 and stabilizes the R-state, making it harder for Hb to offload CO2

Front 13

What disease state is caused by the oxidation of Fe2+ to Fe3+?

What can cause it?

Back 13

Methemoglobinemia

-Exogenous oxidizing drugs (benzocaine, dapsone), compounds containing nitrates or well water contaminated by nitrates

Front 14

What happens to the tissue BPG levels at high altitude?

Back 14

They increase to increase the release of bound O2 in the tissues

Front 15

What is the difference on the structural level between gamma Hb and beta Hb subunits?

Back 15

In gamma: 2 serine residues replace 2 histadine residues in the BPG binding pocket of the B subunit. Therefore, HbF has a lower affinity for BPG and higher affinity for O2

Front 16

What genetic defect leads to sickle cell disease?

Back 16

Glu6 -> Val6 in B-globin chain of hemoglobin

Front 17

What defect is seen in Hemoglobin C disease?

More or less severe than sickle cell?

Back 17

Glu6 -> Lysine

Less severe

Front 18

What are HbS prone to that HbA are not? Under what conditions?

Back 18

They self-assemble into strands and fibers

Caused by conditions that promote the deoxy form: exercise, high altitudes, hypoxic conditions

Front 19

What drug is used to treat sickle cell?

Mechanism?

Back 19

Hydroxyurea

Promotes the expression of fetal Hb, which replies the abnormal HbS B-globin allele in some hemoglobin molecules. HbF cannot self-assemble into strands/fibers, and prevents the formation of sickle cells

Front 20

What are the 2 types of alpha-globin genes? When are they seen?

Back 20

alpha and zeta

Alpha: almost always

Zeta: only in embryonic Hb

Front 21

What are some genetic causes of Methemoglobinemia?

Back 21

-Mutations in NADH-cytochrome B5 reductase

-Mutations in a- and b-globin chains near the heme iron

Genetic deficiencies of enzymes that reduce the levels of NADH in the cell (pyruvate kinase)

Front 22

What is a treatment for Methemoglobinemia?

Back 22

IV infusion of methylene blue

Front 23

What is the genetics of thalassemias?

Back 23

Autosomal recessive

Front 24

Which Thalassemia is most common in Mediterraneans?

Back 24

Beta

Front 25

On which chromosomes are the alpha and beta-globin genes clustered?

Back 25

16 (alpha)

11 (beta)

Front 26

Expression of globin genes is regulated by what?

Back 26

LCRs

Locus control regions

Front 27

A complete absence of B-globin expression is known as?

About 50% absence?

Back 27

Complete = B0-thalassemia

Half = B+-thalassemia

Front 28

What can cause B+-thalassemia?

Back 28

Being het for a mutation in the B-globin locus, or having a mutation in the control region

Front 29

What is the result of a-thalassemia(-) with no a-globin expression?

Back 29

Still births

Front 30

What is thrombosis? (2)

Back 30

1) aggregation of platelets

2) formation of an insoluble fibrin clot

Front 31

What does the blood clotting cascade require?

Back 31

Ca++

Front 32

What cross links fibrin?

Back 32

Factor XIII

Front 33

What is the initiator of the clotting response (released from the damaged sub endothelial layer of blood vessels)?

Back 33

von Willebrand Factor

Front 34

What forms fibrin by cleaving fibrinogen?

Back 34

Thrombin

Front 35

What residues in the coagulation factors bind phospholipids on platelet membranes to localize the clotting?

Back 35

y-carboxyglutamate

Front 36

What is the first platelet integrin to bind the injury? What does it bind?

The second? What does it bind?

Back 36

1st: GPIa/IIa, binds collagen

2nd: GPIIb/IIIa, binds vWF and fibrinogen

Front 37

Platelet activation releases what factors from the cell?

Back 37

1. ADP (stimulates platelet aggregation)

2. BCC factors: Factors V and XIII and fibronigen

3. Ca++

4. Platelet factor 4: binds heparin

5. Growth factors (initiate migration and proliferation of wound healing cells)

6. Serotonin (vasoconstrictor)

Front 38

Platelet activation stimulates synthesis of ________, which is a vasoconstrictor & activates GPIIb/IIIa on cell surface.

What drug inhibits this?

Back 38

Thromboxane A2

low dose aspirin

Front 39

Where does vWF come from? What are its 2 major roles?

Back 39

-vWF is present in the subendothelial space and secreted from platelets

1. Activates platelets via the GP1b R in the sub endothelial space

2. stabilizes Factor VIII in circulation

Front 40

Hemophilia A is characterized by lack of what?

Back 40

Factor VIII

Front 41

What is a zymogen?

The zymogens of the BCC become...

Back 41

A polypeptide chain that only displays biological activity after it has been chemically altered, usually by proteolytic cleavage

-Serine proteases & protein cofactors

Front 42

Which factors are serine proteases that are activated by cleavage?

Back 42

VII, XI, IX, X, prothrombin, Protein C

(all have a after once activated)

Front 43

What is the associated factor for Factor VII?

Back 43

Tissue Factor (Factor III)

Front 44

What is the associated factor for Factor IXa?

Back 44

Factor VIIIa

Front 45

What is the associated factor for Factor Xa?

Back 45

Factor Va

Front 46

What is the associated factor for Factor IIa (thrombin)?

Back 46

Thrombomodulin

Front 47

What is the associated factor for Protein Ca?

Back 47

Protein S

Front 48

What is the extrinsic pathway for the BCC?

Back 48

Damaged tissues present Tissue Factor III to circulating factor VII -> autocatalyzes to factor VIIa -> activates factor X to Xa

VIIa -> activates IX to IXa in the intrinsic pathway

Front 49

What is the intrinsic pathway for the BCC?

Back 49

XI to XIa -> IX to IXa -> activates X to Xa

Front 50

What is the result of X activation to Xa?

Back 50

Thrombin activation

Front 51

How can thrombin augment its own activation?

Back 51

By converting factors V, VIII, and XI into activated cofactors

Front 52

What is the common pathway?

Back 52

X to Xa + Va -> prothrombin to thrombin

Front 53

How does thrombin cross-link fibrin?

Back 53

Thrombin activates Factor XIII to XIIIa

XIIIa catalyzes a transamidation reaction between Glutamine and Lysine side chains

Front 54

Which coagulation factors are post-translationally modified with y-carboxyl groups to increase their ability to bind calcium?

Back 54

Factors II, VII, IX, X, and Protein C

Front 55

What is a required cofactor for y-carboxylation?

Back 55

Vitamin K

Front 56

What contributes to the thromboresistance of normal vascular endothelium? (3)

Back 56

1. Endothelial cells are highly negatively charged

2. They synthesize Prostaglandin I2 and NO (vasodilators and inhibitors of platelet aggregation)

3. They synthesize thrombomodulin and heparin sulfate, which inhibit thrombin

Front 57

What can reversibly inhibit Factor Xa? What does it also inhibit?

Back 57

Tissue Factor Pathway Inhibitor (TFPI)

TFPI-Xa complex can inhibit FVIIa-TF complex

Front 58

What naturally occurring inhibitory proteins are present in the plasma at high concentration? They inhibit serene proteases

Back 58

Serpins

Front 59

What serpin controls the activity of Thrombin and other serine proteases?

Back 59

Antithrombin III (ATIII)

Front 60

How does heparin accelerate the rate of Thrombin inactivation?

Back 60

BInds lysine residues on ATIII and accelerates its rate of Thrombin binding by making its arginine residue more readily available for interaction with thrombin

Front 61

What is the pathway of thrombin's anti-thrombotic effects?

Back 61

Thrombin binds the endothelial cell R thrombomodulin -> alters function of Thrombin and allows Thrombin to activate Protein C -> protein Ca & cofactor Protein S suppress the BCC by cleaving & deactivating Factor VIIIa and Va by proteolytic cleavage

Front 62

Protein Ca stimulates endothelial cells to increase secretion of ________, which reduces platelet aggregation

Back 62

prostaglandin PGI2

Front 63

What type of factor Va is resistant to inactivation by Protein Ca/Protein S? What is the result?

Back 63

Factor V Leiden

Hypercoagulability

Front 64

What serine protease degrades the fibrin in a clot?

Back 64

Plasmin

Front 65

What protein converts plasminogen to plasmin? What proteins inhibits plasmin?

Back 65

Activators:

tPA: tissue plasminogen activator

scu-PA (urokinase)

Streptokinase: bacterial protein

Inhibitors:

-alpha-2-antiplasmina: inhibits plasmin activity

-Plasminogen activator inhibitor (PAI-1): inhibits tPA

Front 66

What cells produce immunoglobins?

Back 66

B cells

Front 67

What is a foreign molecule that is selectively bound by antibodies?

Back 67

Antigen

Front 68

What is the molecule that induces antibody production?

Back 68

Immunogen

Front 69

What is the small region of a larger molecule that elicits the production of a specific antibody?

Back 69

Antigenic determinant / epitope

Front 70

What types of bonds hold the heavy chains to each other, and heavy to light chains?

Back 70

Disulfide

Front 71

What domains exist within the heavy chains?

Back 71

CH1-CH3 (constant), VH (variable)

Front 72

What are the 2 types of light chains?

What domains exist within light chains?

Back 72

Lambda or kappa

CL (constant) and VL (variable)

Front 73

Where is the antibody cleaved by papain?

Back 73

Between CH1 and CH2 (cleaves the V from the Y), into Fc (heavy only) and Fab (light chain and heavy chain VH and CH1)

Front 74

What is the basic shape of an IgA?

Heavy chain?

Back 74

Dimer

Alpha

Front 75

What is the basic shape of an IgM?

Heavy chain?

Back 75

Pentamer

u (mu)

Front 76

Each individual constant and variable domain in an antibody is an example of ________

Back 76

Supersecondary structure

Front 77

Antibodies are comprised mostly of what type of secondary structure?

Back 77

B-sheet/ B-sandwich

Front 78

What is the arrangement of beta strands in the constant domains?

What is the arrangement of beta strands in the variable domains?

Back 78

4-3

5-4

Front 79

What are the specific antigen binding sites within the variable domain? How many are there?

Back 79

Complementarity Determining Regions (CDRs)

3/variable region, 12 total

Front 80

What proteins other than antibodies have an immunoglobin fold structural motif?

Back 80

Fibronectin and cell adhesion molecules (CAMs), T-cell receptor and MHCs

Front 81

What antibody-based technique is used to investigate the interactions between protein and DNA in the cell?

Back 81

ChIP

Front 82

What is a cancer from a plasma cell called? What are the symptoms?

Back 82

Myeloma

CRAB: Ca++, renal failure, anemia, bone lesions

Front 83

What is used to select for fused mouse spleen/myeloma cells in culture?

Back 83

HAT medium: only cells with HGPRT enzyme (from spleen cells) can grow

Front 84

What type of antibody has a variable domain from mouse with the remainder from human origin?

Suffix?

Back 84

Chimeric

Ends in -ximab

Front 85

What type of antibody has the CDRs from mouse with the remainder from human origin?

Suffix?

Back 85

Humanized

Ends in -zumab

Front 86

What type of antibody is entirely human?

Suffix?

Back 86

Fully human

Ends in -mumab

Front 87

What is the suffix for a fully mouse antibody?

Back 87

-momab