Chapter 5 - Biochemistry

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Section 1

Question Answer
The conversion of hemoglobin from the T to the R form involves breaking C-terminal______.ion pairs
An increase in pCO2 causes hemoglobin's affinity for oxygen to ______.decrease
Hemoglobin's subunits bind oxygen in a ______ mannerpositively
The absence of 2,3-BPG causes hemoglobin's affinity for oxygen to________.increase
Sickle cell hemoglobin does not form fibers in the ______ form.R
When unstable hemoglobins are degraded, the products often cause cell lysis, leading to a condition called ______.hemolytic anemia

Section 2

Question Answer
When oxygen binds to heme, the oxygen forms a hydrogen bond with _______.His E7
Mutations that favor the oxidation fo the heme iron to the +3 oxidation state can cause ______.cyanosis
Most of myoglobin's secondary structure is in the form of _______alpha helicies
Myoglobin's physiological role is to facilitate oxygen________.diffusion
In sickle cell anemia, the negatively charged Glu has been replaced with the neutral _____.Val

Section 3

Question Answer
Describe the concept of "induced fit" in ligand-protein binding.It refers to the structural modifications that occur when a ligand binds to a protein. This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.
Explain why most multi-cellular organisms use an iron-containing protein for oxygen binding proteins.Heme-bound iron is less reactive in the formation of reactive oxygen species (e.g. superoxide ions) that can damage biological structures.
Why is carbon monoxide (CO) toxic to aerobic organisms?It binds to heme with a higher affinity that oxygen, and thus prevents oxygen from binding to Hb.
For the binding of a ligand to a protein, what is the relationship between the Ka, the Kd, and the affinity of the protein for the ligant?Ka = 1/Kd. The larger the Ka, the higher the affinity of the protein for the ligand
How does BPG binding to hemoglobin decrease its affinity for oxygen?BPG binds to a cavity between the beta subunits. It binds Hb in the low affinity T state, thereby stabilizing that conformation
What is the effect of pH on the binding of oxygen to hemoglobin? (b) Briefly describe the mechanism of this effectThe affinity decreases with decreasing pH. (b) At lower pH (higher hydrogen ion concentration) there is increasing protonation of protein residues such as histidine, which stabilizes the low affinity conformation of the protein subunits
Why is it likely that the immune system can produce a specific antibody that can recognize and bind to any specific chemical structure?As a result of genetic recombination mechanisms, antibody-producing B cells are capable of producing different antibodies with different binding specificities.

Section 4

Question Answer
What is the role of the Major Histocompatibility Complex (MHC) in the immune response?MHC proteins are present on the surface of specialized immune system cells. MHC plays a role in the ability of the immune system to discriminate between self and non-self.
Describe briefly the basic structure of an IgG protein molecule.An IgG protein contains two heavy chains (Mr 50,000) and two light chains (Mr 25.000). The chains are arranged in a Y-shaped structure. Disulfide bonds link the heavy chains to one another and to the light chains.
What properties of antibodies make them useful biochemical reagents?The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association
Explain why globin alone or heme alone is not effective as an oxygen carrier.Globin lacks an oxygen-binding group and therefore cannot bind O2. The iron ion in heme alone is easily oxidized to Fe3+ and then cannot bind O2. The bound heme gives a protein such as myoglobin the ability to bind O2. In turn, the protein helps prevent oxidation of the heme iron.
Highly active muscle generates lactic acid by respiration so fast that the blood passing through the muscle experiences a drop in pH from about 7.4 to about 7.2. Under these conditions, hemoglobin releases about 10% more O2 than it does at pH 7.4. Explain.The increased O2 release is the result of the Bohr effect. The increase in [H+] promotes the shift from the oxy to the deoxy conformation of hemoglobin. The decrease in oxygen affinity improves oxygen delivery to the muscle, where it is needed.
Explain why the amino acid substitution found in hemoglobin from individuals afflicted with sickle cell anemia causes the mutated hemoglobin to polymerizeThe subsitution of the nonpolar Val for the negatively charged Glu results in a non polar patch on the surface of the mutated Hb S protein._-This nonpolar Val fits into a hydrophobic pouch on the surface of a neighboring Hb S; thus the Hb S molecules clump together. The hydrophobic pouch is only present on only in the T conformation, of Hb; thus when the hemoglobin is in the oxygenation form, polymerization does not occur

Section 5

Question Answer
The interactions of ligands with proteinsare usually transient
A prosthetic group of a protein is a non-protein structure that ispermanently associated with the protein
When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied byone O2 molecule and one amino acids atom
Myoglobin and the subunits of hemoglobin havevery similar tertiary structures, but different primary structures.
An allosteric interaction between a ligand and a protein is one in whichbinding of a molecule to a binding site affects binding properties of another site on the protein.
In hemoglobin, the transition from T state to R state (low to high affinity) is triggered byoxygen binding
The fundamental cause of sickle-cell disease is a change in the structure ofhemoglobin
An individual molecular structure withing an antigen to which an individual antibody binds is as aneptitope

Section 6

Question Answer
The proteins of the Major Histocompatibility Complex (MHC) bind and displayantigen fragments
Which of the following parts of the IgG molecule are not involved in binding to an antigen?Fc
A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodiesare synthesized by a population of identical, or "cloned" cells.
Which of the following generalizations concerning motor proteins is correct?They convert chemical energy into kinetic energy
The predominant structural feature in myosin molecules isan alpha helix
The energy that is released by the hydrolysis of ATP by actin is used foractin filament assembly
During muscle contraction, hydrolysis of ATP results in a change in theconformation of myosin