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Biochemistry Exam 3
Terms in this set (36)
A prosthetic group that is a small molecule with a tetrapyrole ring system. Protoporphyrin IX is the prosthetic group and is called a heme when oxygen is bound to it.
Planar molecule with six ligands. Four ligands are Nitrogen atom while the fifth is a proximal histidine. Sixth ligand is vacant in deoxymyoglobin and is occupied in oxymyoglobin.
Steric hindrance prevents free heme from oxidizing to form metmyoglobin which does not bind to oxygen. This is due to the distal histidine which forces oxygen to bind at 30 degrees, preventing formal oxidation.
Discussion of Oxygen Binding to Myoglobin.
The binding of oxygen to myoglobin depends on the partial pressure of oxygen. A plot of the portion of myoglobin sites occupied to the partial pressure of oxygen is called a BINDING CURVE. This curve is HYPERBOLIC. Myoglobin has a HIGH AFFINITY at ALL PRESSURES because the partial pressure at half saturation is so low. Binding is FAST AND SIMPLE.
A small protein where 3/4 of amino acids are in eight alpha helices connected by short random coils.
A protein or QUATERNARY structure composed to 4 PROTEIN SUBUNITS. With two identical alpha subunits and two identical beta subunits. Both alpha and beta subunits contain RANDOM COILS. Each subunit contains a heme, hemoglobin can BIND FOUR OXYGEN molecules. TETRAHEDRAL arrangement with cavity in center. SALT BRIDGES, H-BONDING, and LONDON FORCES between subunits mostly between ALPHA and BETA.
Discussion of Oxygen Binding to Hemoglobin
The binding of oxygen to involves four subunits that act INDEPENDENTLY, binding oxygen and the same time. A plot of the occupied hemoglobin sites to the partial pressure of oxygen is SIGMOIDAL. Indicates that the binding of oxygen to heme facilitates binding of additional oxygen to other heme grounds which is known as POSITIVE COOPERATIVITY. At low oxygen pressure binding is weak and hemoglobin resists binding, as pressure increases a THRESHOLD is reached where rapid binding occurs.
Tells the degree of cooperativity between the subunits. Tells the minimum number of subunits with binding sites in the protein. (h=1) Subunits are non-cooperative and behave independently. (h=binding sites) Cooperative and completely interacting.
Rates for 1st and second Binding Sites of Hb.
k1 = 0.133 (M ^ -1) k4 = 40 (M ^ -1)
Physiological function of Mb and Hb
Myoglobin has the HIGHER AFFINITY for oxygen at all partial pressures of oxygen. In the LUNG where the partial pressure of oxygen is high hemoglobin is SATURATED, and in the TISSUES where the pressure of oxygen is low hemoglobin binding is weak and oxygen is TRANSFERRED to myoglobin because MYOGLOBIN has a HIGHER AFFINITY for oxygen than HEMOGLOBIN.
Allosteric interactions occur when a specific small molecules bind to a protein and modulates it's activity. The small molecules are called ALLOSTERIC EFFECTORS and may be ACTIVATORS or INHIBITORS of the protein.
Binding Curve for Hemoglobin
Binding Curve for Myoglobin
Affinity Constant for Myoglobin
Affinity Constant for Hemoglobin
Reaction of Oxygen Binding to Myoglobin
Reaction of Oxygen Binding to Hemoglobin
Portion of Occupied Hemoglobin Binding Sites
Portion of Occupied Myoglobin Binding Sites
Hill Plot Equation
Two Models for Allosteric Interactions in Hemoglobin
SEQUENTIAL MODEL which allows for a series of changes in the CONFORMATION of the the subunits for the ligand. Allows for NEGATIVE COOPERATIVITY. CONCERTED MODEL which features an OLIGOMERIC protein that is neither tense (binding of the ligand is difficult) or relaxed (binding of the ligand is easy). When the ligand binds to the T state a concerted conformation change occurs in the protein leading to an R state. NO INTERMEDIATES.
Two factors affecting the allosteric changes in hemoglobin.
1. Oxygen binding produces a conformational change that is ELECTRONIC and STERIC. 2. ALLOSTERIC EFFECTORS.
Describe the electron conformational change associated with oxygen binding.
Electronic change is due to the ferrous ion in the heme group. In deoxy Hb the ferrous ion is in high spin (PARAMAGNETIC) state. In oxyHb the ferrous ion is in a low spin (DIAMAGNETIC) state. When Oxygen bind to ferrous ion, the ion shifts from a HIGH to LOW spin state, causing the PROXIMAL histidine bond to SHORTEN. This causes the histidine to become PERPENDICULAR to the HEME changing the heme from a DOME shape to a PLANAR shape. This brings the heme within VAN DER WAALS radius of a nearby VALINE.
Describe the steric conformational change associated with oxygen binding.
When the heme moves within the VAN DER WAALS radius of the VALINE the REPULSION is relieved by breaking a HYDROGEN BOND between valine and a nearby TYROSINE. This causes a complex of hydrogen bonds and SALT BRIDGES to be broken to relive strain in the conformation which results in a change in the CONFORMATION from deoxyHb to oxyHb.
Four Allosteric Effectors
Bohr Effect. Carbon Dioxide Transport. Chloride Ion. 2,3-Bisphosphoglycerate.
The Bohr Effect (equation)
Defined by the response of Hb to a CHANGE in pH. A decrease in pH lowers the affinity of Hb for oxygen which means deoxy Hb is FAVORED at the TISSUE LEVEL. The binding curve shifts to the right.This occurs because pH affects SALT BRIDGES and some H-BONDS. The Bohr effect permits efficient UNLOADING of oxygen from Hb to Mb at the tissue level.
Carbon Dioxide Transport (equation)
Transportation of carbon dioxide is PASSIVE. One mechanism is the formation of BICARBONATE. A second mechanism is to react with the N-terminal group on each of the 4 SUBUNITS of Hb. The binding curve shifts to the right. Deoxy Hb is favored. More efficient transfer occurs because p50 is higher for oxygen transfer to Mb.
To maintain charge neutrality, chloride ions are exchange for bicarbonate in RED BLOOD CELLS. Chloride binds to deoxy Hb between N-terminal Valine and side-chain ARG. The presence of chloride ion promotes PROTONATION of the N-terminal. In oxyHb, chloride ions and protons are RELEASED. Enhances the Bohr Effect. Binding curve shifts to the right, deoxy Hb is favored.
Present in blood at a concentration of 4.5 mM. BPG LOWERS the AFFINITY of Hb for oxygen. BPG sits in the CENTRAL CAVITY of the 4 subunits by IONIC INTERACTIONS. BPG stabilizes the conformation of deoxyHb and therefore LOWERS the AFFINITY of Hb for oxygen. BPG cannot bind to the oxyHb. Binding curve shifts further to the right.
Combined Effect of Allosteric Effectors
The combination of these effects allows transfer of oxygen between Hb and Mb to occur at higher p50 for oxygen. All about efficient transfer.
Eukaryotic Gene Structure (Pathway)
INTRONS are noncoding regions of DNA. EXONS are coding regions of DNA.
Mutation of DNA
MUTOGENIC Agents benzo[a]pyrene, nitrous acid, aflatoxin, UV. NATURAL MISTAKES.
Three Natural Mistakes
BASE REPLACEMENT -> silent mutation where the same amino codes for a different base but NO EFFECT or missense mutation where different base is coded for. NONSENSE MUTATION -> base replacement leads to stop codon, protein is too short. FRAMESHIFT MUTATION -> base insertion or base deletion changes protein sequence.
Definition of Carbohydrates
Polyhydroxy aldehydes and ketones.
Three classes of Carbohydrates
MONOSACCHARIDES - single sugars freely soluble in water. OLIGOSACCHARIDES - short chains of single sugars covalently linked together, forming the core structure of N-linked CHO moieties. POLYSACCHARIDES - long chains made of hundreds to thousands of single sugars covalently linked together.
Two families of Monosaccharides
Aldose -> contains Aldehyde function group. Ketose -> contains ketone functional group.
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