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Biochemistry > Chapter 5 > Flashcards

Chapter 5 Flashcards

1
Q

Oxygen transport proteins

A
  • myoglobin and hemoglobin are part of a large family of oxygen transport proteins
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2
Q

Ligand

A

a molecule that reversibly binds a protein

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3
Q

Globin family of proteins

A
  • present in all branches of life (archae, bacteria, eukaryotes, prokaryotes)
  • defined by the highly conserved globin fold - example of a structural motif
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4
Q

Why do we need proteins to transport O2?

A
  • O2 cannot easily diffuse in mammals
  • O2 is a diradical (reactive), leads to reactive oxygen series and damage biomolecules
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5
Q

What is the function of myoglobin?

A
  • binds O2
  • facilitates diffusion of O2 into muscle
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6
Q

What is the function of Hemoglobin?

A
  • binds O2
  • transports O2 through the body in blood
  • picks up O2 from lungs and disperse to tissues
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7
Q

Structure of Myoglobin

A
  • monomeric (1 chain, 1 subunit)
  • 1 heme
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8
Q

Structure of Hemoglobin

A
  • tetrameric (heterotrimer)
  • 4 hemes
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9
Q

Prosthetic Group

A

non amino acid group that is bound to the protein
- many proteins contain prosthetic groups that support their function

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10
Q

What is the prosthetic group in myoglobin/ hemoglobin?

A

Heme group

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11
Q

What does a heme group do?

A
  • A heme group is permanently bound to each globin domain and is responsible for O2 binding and the red color of Mb/Hb
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12
Q

When is a heme group added?

A

the heme group is added to Mb/Hb post-translationally and is responsible for binding O2

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13
Q

What does a heme group contain?

A
  • a protoporphyrin ring
  • Fe 2+ atom
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14
Q

What are the six bonds that “coordinate” iron?

A

-four nitrogens in the porphyrin ring, - one nitrogen in the proximal Histidine, and the O2

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15
Q

What is the ligand for myoglobin/hemoglobin?

A

oxygen

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16
Q

What binds iron?

A

The proximal histidine

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17
Q

What hydrogen bonds to the O2?

A

the distal histidine

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18
Q

Carbon monoxide poisoning

A
  • CO bind to hemoglobin 40-times more tightly than O2
  • O2 has a non linear bond while CO has a linear bond which is strongest allowing CO to outcompete O2
  • Poisoning is a result of CO outcompeting O2
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19
Q

Equilibrium expression that describes the reversible binding of a protein (P) to a ligand (L)

A

P+L ⇌ PL
Ka=[PL]/[P][L]

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20
Q

Kd: Dissociation Constant

A

= 1/ Ka = [P][L]/[PL]
- smaller Kd= tighter binding

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21
Q

Fractional Saturation Y

A
  • Y= [PL]/[P]+[PL]
    = (bound active sites)/(total active sites)
  • Y= [L]/[L]+[Kd] ; form of a rectangular hyperbola
    [L]=pO2 (partial pressure of O2)
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22
Q

What determines binding affinity?

A

chemical bonds and the intermolecular forces between ligand and its binding site

23
Q

What are the pros/cons of high affinity binding?

A
  • If binding is to high then it can’t unbind to complete its function
  • we want reversible binding
  • we need it to bind tight enough to do its job
24
Q

Subunit Composition of Hemoglobin

A

-Hemoglobin tetramer: α2β2
-multiple globin genes
- fetal hemoglobin: α2γ2 (binds more tightly to oxygen)

25
Q

fetal hemoglobin

A
  • α2γ2
  • binds more tightly to oxygen so that babies can get oxygen from their mother
26
Q

What is the benefit of more subunits?

A
  • allows for more regulation
  • “communication” between the subunits allows for more cooperative binding of O2
27
Q

Cooperativity

A

binding of one ligand increasing the affinity for binding subsequent ligands
- O2 binding at one subunit of Hb must change the other binding sites ( increasing affinity)

28
Q

What are the two distinct conformations or state of hemoglobin?

A
  • R-State: oxyhemoglobin (~active) O2 bound
  • T-State:deoxyhemoglobin (~inactive) unbound
29
Q

What influences the balance between the R and T state of hemoglobin?

A

O2 and effectors

30
Q

What stabilizes the T state?

A

stabilized by subunit interface interactions

31
Q

What happens to Fe 2+ when O2 binds?

A

the iron atoms shrinks

32
Q

What happens of the protoporphyrin ring when O2 binds?

A

concave shape —> flattens out

33
Q

What happens to the helix attached to histidine F8 (proximal) when O2 binds?

A

shifts the whole alpha helix/ causes conformational change throughout

34
Q

What is low O2 associated with?

A

low-affinity/T-State

35
Q

What is high O2 associated with?

A

high-affinity/R-State

36
Q

Homotropic modulator

A
  • O2 binding favors R state
  • O2 is the ligand
37
Q

Heterotrophic modulators

A
  • Heterotropic= not the ligand
  • H+ and CO2 regulate and are all transported by Hb
  • both favor the T state
38
Q

Bohr Effect

A

the effect of pH and CO2 on the binding and release of O2 by hemoglobin

39
Q

How is H+ carried?

A

“carried via protonation of His146 (β) (as well as other His residues)

40
Q

How is CO2 removed?

A

its covalently attached to the N-terminus of each chain
- both alpha and beta subunits
- NH3+ converted to carbamate
- carried to lungs and removed

41
Q

2,3-Biphosphoglycerate (BPG)

A
  • produced in respiring tissues
  • binds the central cavity of hemoglobin, stabilizing the T state
42
Q

What are antibody functions inside the body?

A
  • involved in the immune response (humoral and cellular)
  • recognize and bind foreign agents and recruit immune cells
43
Q

How are antibodies made by the body?

A
  • produced in B lymphocytes or B cells
  • one B cell produces one kind of antibody
  • antibodies make up 20% of your total blood protein
  • at anytime there are 100,000,000 different antibodies circulating
44
Q

Variable regions

A

antigen binding sites are created by random shuffling of the immunoglobulin genes
- is what gives rise to different types of antibodies

45
Q

5 Classes of Immunoglobulins in Vertebrates

A
  • characterized by heavy chain
    1. alpha for IgA: mucus, tears, saliva
    2. delta for IgD: on B cell receptors
    3. epsilon for IgE: allergies
    4. Gamma for IgG: late defense
    5. mu for IgM: early defense
46
Q

Immunoglobulin G Structure

A
  • two heavy chains and two light chains
  • antigen binding site varies
  • bottom part binds to receptors on b-cells
  • Top part: (FAB) fragment that does antigen binding
  • Bottom part: (FC) constant fragment
47
Q

Antibody/Immunoglobulin/Ig

A

A protein generated against, and capable of binding specifically to, an antigen

48
Q

Antigen

A

A molecule capable of eliciting the synthesis of a specific antibody in vertebrates

49
Q

Epitope

A

An antigenic determinant; the particular chemical group or groups in a macromolecule (antigen) to which a given antibody binds

50
Q

Induced fit

A

ligand binds and binding site form fits around ligand (hand and glove)

51
Q

What influences antigen binding/ affinity?

A

IMFs between the epitope and antigen binding site on IgG

52
Q

Polyclonal Antibody

A

population of B cells that produce a bunch of IgG against 1 antigen
- strong but less specific binding

53
Q

Monoclonal Antibody

A

1 B cell that makes 1 antibody
- weaker binding but very specific

54
Q

Examples of antibodies in research

A
  • Western blots
  • ELISAs
  • Immunoprecipitation

Biochemistry (8 decks)

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