Lecture 1 - Protein Structure/Function (Hemoglobin Molecule) Flashcards
Protein Structure/Function (Hemoglobin Molecule)
3/1 Letter abbreviation of: Glycine
Gly, G - small molecule
3/1 Letter abbreviation of: Alanine
Ala, A - small molecule
3/1 Letter abbreviation of: Serine
Ser, S - nucleophilic
3/1 Letter abbreviation of: Threonine
Thr, T - nucleophilic
3/1 Letter abbreviation of: Cysteine
Cys, C - nucleophilic
3/1 Letter abbreviation of: Valine
Val, V - hydrophobic
3/1 Letter abbreviation of: Leucine
Leu, L - hydrophobic
3/1 Letter abbreviation of: Isoleucine
Ile, I - hydrophobic
3/1 Letter abbreviation of: Methionine
Met, M - hydrophobic
3/1 Letter abbreviation of: Proline
Pro, P - hydrophobic
3/1 Letter abbreviation of: Phenylalanine
Phe, F - aromatic
3/1 Letter abbreviation of: Tyrosine
Tyr, Y - aromatic
3/1 Letter abbreviation of: Tryptophan
Trp, W - aromatic
3/1 Letter abbreviation of: Aspartic Acid
Asp, D - acidic, pKa = 3.9
3/1 Letter abbreviation of: Glutamic Acid
Glu, E - acidic, pKa = 4.07
3/1 Letter abbreviation of: Asparagine
Asn, N - amide
3/1 Letter abbreviation of: Glutamine
Gln, Q - amide
3/1 Letter abbreviation of: Histidine
His, H - basic, pKa = 6.04
3/1 Letter abbreviation of: Lysine
Lys, K - basic, pKa = 10.79
3/1 Letter abbreviation of: Arginine
Arg, R - basic, pKa = 12.48
AA are linked by?
- 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
What are the forces which stabilize protein tertiary structure? (In order of strongest to weakest)
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
Why do proteins fold?
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
Myoglobin vs Hemoglobin
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
Describe the structure of Heme
- There is a central core of Fe within a porphyrin ring
* Plants have a central Mg instead of this
T vs R state of Hb
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
How can proteins bind tightly to O2 in lungs and effectively release it in respiring tissue?
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
2,3-BPG
- 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
Fetal Hb and pregnant women
- 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
How do humans adapt to high altitudes?
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%)
At what torr does Hb give off half of its Oxygen?
P50 = 26 torr
Negative heterotropic effectors of O2 binding
- 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
Bohr Effect
- 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
CO Poisoning
- 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
