Biochem Sept. 17th

(Topic 4)

Whats a Ligand?

A molecule that binds to a protein. Can be a small molecule, a peptide, or another protein

Explain the Dissociation constant

• PL ⇌ L + P in equilibrium

• Kd = [P][L]/[PL]

• The higher the affinity for the ligand, the lower the dissociation constant (Kd).

What are the common units?

• Millimolar - m 10^-3 M

• Micromolar - µ 10^-6 M

• Nanomolar - n 10^-9 M

  (many protein-protein interactions lie in the micromolar to nanomolar range)

What is myoglobin?

• oxygen binding protein in muscle cells

• Consists of 8 alpha helices

• Contains a heme prosthetic group, which is essential for binding oxygen

How does O2 bind to myoglobin?

• the central Fe II is coordinated by 4 N atoms of the ring and 1 N atom from one side chain of Histidine

• O2 can bind reversibly to form the 6th coordination bond

• His E7 forms a H bond to the bound O2

What is the Fractional Saturation of Binding formula?

• Y = Concentration of protein with ligand bound / total protein concentration

• or [PL] / [P] + [L]

• Can also express as Y = [L] / Kd + [L]

What is the formula for when asked “How much of O2 is bound to myoglobin?”

• YO2 = pO2 / K + pO2

• O2 is a gas, therefore its concentration can be expresses as its partial pressure, pO2

What is the p50?

• The p50 is the partial pressure of oxygen at which myoglobin is 50% saturated with oxygen. It is an important measure of oxygen affinity in myoglobin

• K = p50

What is Hemoglobin?

• Hemoglobin is a oxygen-transport protein in red blood cells

• 2 alpha subunits (blue)

• 2 beta subunits (red

• With heme groups shown as white 

Are Hb and Mb similar? How?

• yes, Hb and Mb are similar in their secondary and tertiary structures

• But, Hb and Mb are only ~18% identical in primary sequence

Describe the O2 binding differences between Hb and Mb

• Hemoglobin:

  • O2 binding affinity of Hemoglobin is lower than that of Myoglobin because it needs to release O2 to tissues

  • At low pO2, Hemoglobin exhibits low oxygen affinity but as the pO2 increases, the affinity increases; binding of first O2 increases the affinity of the remaining binding sites

  • Sigmoidal = affinity lower at tissues (to release it) and higher at lungs

• Myoglobin:

  • has a higher O2 binding affinity, which makes it ideal for holding oxygen until muscle cells need it

  • Hyperbolic = affinity always high

What happens when O2 binds to Hb?

• Hb undergoes a conformational change when O2 binds (T-state —> R-state) 

• It changes for T to R to increase the affinity for the next O2

• T-state = tense = low affinity (Deoxy)

• R-state = relaxed = higher affinity (Oxy)

What is the Bohr Effect?

• Describes the phenomenon where if the pH decreases, (acidity increases) the oxygen-binding affinity of hemoglobin decreases, promoting oxygen release in tissues

• This occurs due to certain ionizable groups in Hb become acidic and release protons (H+) upon binding O2

  • This means increasing pH favours O2 binding

How does BPG effect Hb and O2 affinity?

• BPG (2,3-bisphosphoglycerate) reduces the O2 affinity of hemoglobin by stabilizing the T-state, facilitating oxygen release in tissues.

  • BPG is an allosteric effector that decreases Hb O2 affinity

• Increased BPG levels promote the release of O2, particularly under conditions of high altitude or exercise.

What is Collagen?

• A structural protein found in connective tissues, providing strength and support to skin, bones, tendons, and ligaments.

• Collagen is essential for maintaining the integrity of various tissues in the body.

• Every 3rd residue is a glycine

• Contains many repeating triplets Gly-Pro-Hyp (hydroxyproline)

• Quite hydrophobic

Why is collagen so strong?

• Due to its cross-linking between chemically modified lysine residues in collagen

• Its triple helix structure

• Many proline and glycine residues contributing to stability and strength

  • because proline is has a rigid ring structure that can force chains into a fixed angle

  • and glycine is the smallest so it packs tightly

What are some collagen related diseases?

• Scurvy 

  • lack of vitamin c in diet (needed for enzyme that hydroxylates proline)

• Osteogenesis imperfecta

  • due to the replacement of glycine with another amino acids