CHAPTER 5 (Picture)

CHAPTER 5 (Picture) - David L. Nelson and Michael M. Cox...

Info iconThis preview shows pages 1–12. Sign up to view the full content.

View Full Document Right Arrow Icon
Lehninger Principles of Biochemistry Fourth Edition Chapter 5: Protein Function David L. Nelson and Michael M. Cox
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Reversible binding of a protein to a ligand: Oxygen-binding proteins Oxygen can be bound to a heme prosthetic group Protoporphyrin Porphyrin ring Myoglobin has a single binding site for oxygen
Background image of page 2
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 4
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
6 Protein - Ligand Definitions. Ligand – A molecule bound reversibly to. by a protein. Bind site –site on a protein that ligand binds Induced fit – structural adaptation that occur between protein and ligand. Substrate – molecule acted upon by enzymes Catalytic site or active site –substrate binding site on an enzyme. i. Protein – ligand interactions Consider reversible bind of a protein (P) to a ligand (L) at equilibrium is P + L = PL Ka = [PL]/[P][L], Ka = association constant Rearrangement Ka[L] = [PL]/[P] If [L] >>> L-binding site the L remains constant. θ = fraction of ligand-binding site (PL) on the protein that are occupied θ =(binding site)/(total binding area) = [PL]/[PL] + [P], substitute Ka[L][P] for [PL] θ = Ka[L][P]/Ka[L][P] +[P] = Ka[L]/Ka[L] +1 = [L]/[L] +1/Ka Ka can be obtained by plotting θ vs [L] ( Fig 5-4a ) - The fraction of the ligand-binding sites occupied approaches saturation asymptotically as [L] increases . - The [L] at which half of the available ligand-binding site are occupied ( = 0.5) correspond to 1/Ka or Kd.
Background image of page 6
7 Protein - Ligand Kd = [P][L]/[PL] [PL] = [P][L]/Kd θ = [L]/[L] + Kd When [L] = Kd, one-half of the ligand-binding sites are occupied. Note : Tighter binders require low [L] and hence lower Kd value ( TABLE 5-1 ). Binding Oxygen: θ = [O 2 ]/[O 2 ] + Kd If Kd = [O 2 ] 0.5 . Then, θ = [O 2 ]/[O 2 ] + [O 2 ] 0.5 . Concentration of volatile substance in solution is proportional to its partial pressure of the gas phase above. θ = PO 2 /PO 2 + P 50
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 8
ii. Protein structure and ligand binding Binding of the ligand to protein depend on the protein structure and the accompanied conformational change . For example : CO binds to free heme molecules 20,000 times better than O 2 does, but binds only 200 times better when heme is bound to myoglobin. WHY? Steric hindrance (Geometry of hydride orbitals) ( Fig 5-5a, 5-5b ). Free oxygen is positioned at an angle and CO is straight. In Myoglobin, oxygen interacts with HisE7 while CO cannot ( Fig 5-5c ). Breathing effect Rapid molecular flexing of amino acid R groups produce transient cavities in protein structure to allow oxygen but not CO.
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 10
11 Protein - Ligand iii. Hemoglobin and oxygen transport (Fig. 5-6) Hemoglobin transport oxygen throughout the body. Myoglobin being insensitive to small changes in concentration of
Background image of page 11

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 12
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 40

CHAPTER 5 (Picture) - David L. Nelson and Michael M. Cox...

This preview shows document pages 1 - 12. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online