Lecture 1 - Protein Structure/Function (Hemoglobin Molecule)

Question 1

3/1 Letter abbreviation of: Glycine

Answer 1

Gly, G - small molecule

Question 2

3/1 Letter abbreviation of: Alanine

Answer 2

Ala, A - small molecule

Question 3

3/1 Letter abbreviation of: Serine

Answer 3

Ser, S - nucleophilic

Question 4

3/1 Letter abbreviation of: Threonine

Answer 4

Thr, T - nucleophilic

Question 5

3/1 Letter abbreviation of: Cysteine

Answer 5

Cys, C - nucleophilic

Question 6

3/1 Letter abbreviation of: Valine

Answer 6

Val, V - hydrophobic

Question 7

3/1 Letter abbreviation of: Leucine

Answer 7

Leu, L - hydrophobic

Question 8

3/1 Letter abbreviation of: Isoleucine

Answer 8

Ile, I - hydrophobic

Question 9

3/1 Letter abbreviation of: Methionine

Answer 9

Met, M - hydrophobic

Question 10

3/1 Letter abbreviation of: Proline

Answer 10

Pro, P - hydrophobic

Question 11

3/1 Letter abbreviation of: Phenylalanine

Answer 11

Phe, F - aromatic

Question 12

3/1 Letter abbreviation of: Tyrosine

Answer 12

Tyr, Y - aromatic

Question 13

3/1 Letter abbreviation of: Tryptophan

Answer 13

Trp, W - aromatic

Question 14

3/1 Letter abbreviation of: Aspartic Acid

Answer 14

Asp, D - acidic, pKa = 3.9

Question 15

3/1 Letter abbreviation of: Glutamic Acid

Answer 15

Glu, E - acidic, pKa = 4.07

Question 16

3/1 Letter abbreviation of: Asparagine

Answer 16

Asn, N - amide

Question 17

3/1 Letter abbreviation of: Glutamine

Answer 17

Gln, Q - amide

Question 18

3/1 Letter abbreviation of: Histidine

Answer 18

His, H - basic, pKa = 6.04

Question 19

3/1 Letter abbreviation of: Lysine

Answer 19

Lys, K - basic, pKa = 10.79

Question 20

3/1 Letter abbreviation of: Arginine

Answer 20

Arg, R - basic, pKa = 12.48

Question 21

AA are linked by?

Answer 21

• Peptide bonds which are formed by ribosomes
• Water is released in formation of the bond
• Most side chains are in a trans configuration
• Peptide bonds are non-rotatable due to partial double bond resonance and can only rotate around phi and psi angles

Question 22

What are the forces which stabilize protein tertiary structure? (In order of strongest to weakest)

Answer 22

1) Disulphide bonds - covalent bond between Cysteine side chains when they become oxidized, primarily in extracellular proteins
Weak, non-covalent forces
2) Electrostatic forces - H bond between positively and negatively charged side chains
3) H bonds - FON
4) Van der Waal attractions - fluctuating charges of non polar side chains in a small area allows for some attraction

Question 23

Why do proteins fold?

Answer 23

deltaG = deltaH - T(deltaS)

• deltaG must be negative for a spontaneous process to occur
• Hydrophobic effect drives energy for folding of a protein
• Low entropy environment has ordered water around surface exposed hydrophobic AA (clathrate cages)
• Non-polar/hydrophobic side chains are then buried to the core and the hydrophilic/polar residues make up the outside because they can form H bonds to the water –> burying hydrophobic AA releases caged water and increases deltaS

Question 24

Myoglobin vs Hemoglobin

Answer 24

Mb - monomer located in muscle cells which is very good at storing O and releasing it when needed but not at transporting it
Hb - tetramer (2 alpha, 2 Beta globulin chains) found in RBC which transports O2
*AA sequences of the alpha and beta globulins are identical

-Both adopt a globin fold with each chain binding a central Heme molecule

Question 25

Describe the structure of Heme

Answer 25

• There is a central core of Fe within a porphyrin ring

* Plants have a central Mg instead of this

Question 26

T vs R state of Hb

Answer 26

T (“tense”) state = deoxyHb, decreased O2 affinity

• assumes a donut shape with 2,3-BPG in the center
• Has 0.4 angstrom puckering of central Fe out of porphyrin ring

R (“relaxed”) state = oxyHb, increased O2 affinity
*O2 binding Fe causes electronic rearrangement and allows heme to smooth out + interacts closer with Histidine F8, pulling on the alpha helix

Question 27

How can proteins bind tightly to O2 in lungs and effectively release it in respiring tissue?

Answer 27

1) Cooperative binding - 1st O2 is difficult to load but O2 affinity increases every time another binds
2) Allosteric effectors - 1st O2 binding causes conformational changes in other subunits

Question 28

2,3-BPG

Answer 28

• Negative heterotropic effector of O2 binding, favoring T state
• Required for cooperative O2 binding and is responsible for Hb-O binding curve
• W/o it, this curve assumes a shape similar to MMb
• Glycolysis byproduct
• At sea level = 5 mM
• [BPG] increase –> downward O dissociation curve
• [BPG] decrease –> upward shift towards Mb curve

Question 29

Fetal Hb and pregnant women

Answer 29

• Fetal Hb = 2alpha, 2gamma –> gamma chain is similar to adult Beta chain but lacks a 2,3-BPG binding residue, therefore favoring movement of O2 from maternal RBC –> fetal RBC
  
  • doesn’t stabilize T state and doesn’t bind BPG
• Pregnant women have increased BPG –> increase O2 offloaded to fetus

Question 30

How do humans adapt to high altitudes?

Answer 30

1) Initially at regular 5 mM of BPG, the lungs pick up less O2 due to less available, but try to deliver the same amount to the tissues (30% efficiency)
2) Cells increase [2,3-BPG] to ~ 8 mM
3) Picks up less O2 in lungs due to T state favored but able to unload more O2 to the tissues (37% efficiency vs normal 38%)

Question 31

At what torr does Hb give off half of its Oxygen?

Answer 31

P50 = 26 torr

Question 32

Negative heterotropic effectors of O2 binding

Answer 32

• stabilizes T state
  1) increased [2,3-BPG]
  2) decreased pH - protonation of globin residues –> release of O2 from Hb (Bohr Effect)
  3) increased CO2 - modifies globin N-terminal amino groups –> carbamino-terminal residue so it can be transported
  4) increased temperature - increased respiration and therefore increased CO2 production
• All cause right O dissociation curve shift –> decrease O2 affinity
  
  • left shift caused by the opposite

Question 33

Bohr Effect

Answer 33

• Negative heterotropic effector of O2 binding - right O dissociation curve shift
• H+ released upon CO2 hydration (respiration) in tissues and then this is used to protonate globin residues of Hb –> readily release O2
• decreased pH –> release of O2
• If BetaHistidine HC3 is protonated –> forms salt bridge with BetaAspartate FG1 - stabilize conformation –> betaHistidine HC3 C-terminus forms bonds with alphaLys C5 –> stabilization of deoxyHb conformation

Question 34

CO Poisoning

Answer 34

• CO binds tightly to Hb and outcompetes O2 to bind to Hb
• Binding 1 CO forces Hb into tightly bound conformation, not allowing O2 to be released
• decreased O2 binding capacity (downward shift) and left shift - O2 remains bound even at pO2 found in tissues
• No cure, can only put patient on 100% O2