BC 351 Lecture Notes - Cooperative Binding, Conformational Change, Myoglobin

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lemondog142

5 Aug 2014

School

CSU

Department

Biochem + Mole Biology

Course

BC 351

Professor

Aaron Sholders

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Document Summary

A ligand is any molecule that has a reversible interaction with a protein. A section of dna: tata-box (dna element) and tata-binding protein. Dissociation constant kd: the reciprocal of the ka for a protein:ligand interaction. The fraction bound ( ) (y) is the fraction of binding sites occupied by a. Kd ligand concentration where 50% protein is bound. At the tertiary level, myoglobin is similar to any of the subunits of hemoglobin. True for both myoglobin and and subunits of hemoglobin. Subunit: does not have d helix, skips directly to e. Loops termed based on helices they connect (ab loop connects a and b helices) In subunit there is a ce loop. Na loop starts at n-terminus till a helix. Hc loop starts at h helix till c-terminus. Amino acids named: a10 10th amino acid in a helix or residue 12. His f8 or his93 in myoglobin, his87 in subunit of hb, his92 in subunit of hb.

Related Questions

Answer the bold text. Briefly explain answer.

2. What is the dissociation constant or Kd? How does the Kd relate to the affinity of a protein for its ligand? Does the number of sites occupied by a ligand increase linearly with the [L]? What is fraction or percent bound? How does percent bound relate to the Kd? When I say that the Kd is 20uM what does this mean in terms of [L] and occupied binding sites? How is Kd affected by the rate constants governing the ligand binding event? What is the relationship between Kd and changes in free energy? What changes in free energy would you expect to see for a protein with a high affinity for its ligand?

I want to find the Kn value of Cu(II) and EDTA. I was given the formula kn= [ML4]/[ML3][L]. 12.3 ml of edta was used to tritrate 0.1194 grams of Copper in 50 ml of water. The indicator used was murexide.

At the core of general acid-base theories, there is the concept of âtransferâ of one entity to another. In the case of BrÃ¸nsted-Lowry acid base theory, the transferred entity is the proton, and their transfer processes are widely exploited in chemical methods. In addition to proton transfer, electron pairs can also be donated/shared between donors and acceptors. In this case, an atom/molecule, which can accept a pair of electrons, is referred to as a Lewis acid while the entity donating the pair of electrons is referred to as a Lewis base. The most prevalent Lewis acid-base systems involve metal complexes with vacant nd-orbitals, as well as electron deficient systems including B, Si, Ge, etc. The Lewis acid base theory is also known as the Hard-Soft acid base theory (HSABT) with âhardnessâ defined as small highly charged species that are weakly polarizable (Lewis acids). In contrast, âsoftnessâ is described by species that are larger and highly polarizable species with low charge (Lewis bases).
In the case of metal chemistry, Lewis acid-base theory provides a means to describe the ability of âligandsâ to coordinate to metal ions as well as the stability of metal-ligand complexes. Recall that coordination bonds are the donation/acceptance of lone pairs of electrons to empty metal orbitals to another atom; the definition of Lewis acid-base chemistry! The stability of Lewis acid-base complexes can be described through the stability constant which is analogous to the Ka that describes BrÃ¸nsted-Lowry acidities. Many metal ions can coordinate (bind) many Lewis base ligands in a step-wise fashion according to:
M + L = ML K1 = [ML]/[M][L] Eq. 1
ML + L = ML2 K2 = [ML2]/[ML][L] Eq. 2
ML2 + L = ML3 K3 = [ML3]/[ML2][L] Eq. 3
MLn-1 + L = MLn Kn = [ML4]/[ML3][L] Eq. 4
and for which the free energy for this dissociation reaction is given by:
ÎG0 = -RTLnKn Eq. 5.
where R is the gas constant and T is the temperature in Kelvin.
Figure 1: Left- EDTA. Right- Typical EDTA-transition metal complex.
The ethylene diamine tetraacetic acid ligand (EDTA, a Lewis base) provides a mechanism to probe the Lewis acid strength of various metal complexes (Figure 1). This multi-dentate ligand (multiple Lewis base sites on a single ligand) forms complexes with metals of the form:
Mn+ + Y4- = MYn-4 Eq. 6
K = [MYn-4]/[Mn+][Yn-4] Eq. 7
where Y4- is the EDTA ligand.
In this experiment, the Lewis acid strength for two different metals will be examined by measuring the stability constants for the metal-EDTA complex. Of specific interest is the how the Lewis acid strength of the metal ion correlates with:
1) atomic/ionic radii, 2) oxidation state, 3) electron configuration, and 4) polarizability.
You will determine the stability constants of both a Cu2+- and Zn2+-EDTA complexes as well as the corresponding free energy. Using these data, you will compare the relative Lewis acidities of both metals and describe differences in terms of the metal ion properties described above.
.
Chemicals
CuSO4
ZnSO4
EDTA
Murexide
Instruments
Buret
Experimental
You and your group will determine the concentration and ultimately the free energy of Cu(II) and Zn(II) using the hexadentate chelating ligand, EDTA.
You will be given a ~100 mM standardized solution of EDTA (check the label for exact concentration prior to beginning). You will need to weigh ~0.1 g per metal salt sample. Dissolve the metal salt into 50 mL of DI water. Add 2-3 drops of murexide to your metal. After properly preparing your buret with EDTA, titrate your metal with EDTA. Repeat for a total of 3 titrations per metal.
1. Approximately how much EDTA will you need for each titration assuming the metal-saltsâ masses are accurate?
2. What type of indicator is murexide and what color will its endpoint be?
Post-Lab Questions
1.
a) Using the equations given in the introduction and your titration results, what are the Kn of the EDTA-Copper complex? Show calculations.
b) Using the equations given in the introduction and your titration results, what are the Kn of the EDTA-Zinc complex? Show calculations.
2. What are the corresponding ÎG values for the EDTA-metal complexes? Show your calculations
3. Would copper be considered a hard or soft lewis acid? What about zinc? Describe what makes these metals hard or soft.
4. What trends would you predict for EDTA-metal complex Kn and ÎG values when:
a) going down a row of transition metals of the same oxidation state?
b) of the same transition metal with increasing oxidation state? (For example, Iron can exist as Fe(II), Fe(III), Fe(IV), and higher oxidation states)
5. Discussion (formal report style): Compare and contrast the concepts of Lewis and BrÃ¸nsted-Lowry acids and bases. Support these concepts with your data over the last two weeks and with research. Cite your sources.

BC 351 Lecture Notes - Cooperative Binding, Conformational Change, Myoglobin

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