Principle Of Biochemistry

Front 1

Molecular Chaperones?

Back 1

These are proteins that interact with partially folded polypeptides or improperly folded polypeptides facilitating correct pathways in which folding can occur.

Front 2

Chaperonins

Back 2

These are elaborate protein complexes required for the folding of a number of cellular proteins that do not fold spontaneously.

Front 3

Protein folding in cells probably involves multiple pathways?

Back 3

Initially, regions of secondary structures may form followed by folding into supersecondary structures. Large ensemble of folding are rapidly brought to a single native conformation.

Front 4

What is a Ligand?

Back 4

A molecule bound reversibly by a protein is called a ligand.

Front 5

Structural adaptation that occurs between protein and ligand?

Back 5

Protein function often entails interactions with other molecules. A protein binds a molecule, known as a ligand, at its binding site. Proteins may undergo conformational changes when a ligand binds, a process called induced fit. In a multisubunit protein, the binding of a ligand to one subunit may affect ligand binding to other subunits. Ligand binding can be regulated.

Front 6

What is Heme Composition?

Back 6

Heme consists of a complex organic ring structure, protoporphyrin IX, with a bound iron atom in its ferrous (Fe2+) state.

Front 7

Heme

Back 7

In multicellular organisms—especially those in which iron, in its oxygen-carrying capacity, must be transported over large distances—iron is often incorporated into a protein-bound prosthetic group called Heme.

Front 8

What happens when oxygen binds?

Back 8

When oxygen binds, the electronic properties of Heme iron change; this accounts for the change in color from the dark purple of oxygen-depleted venous blood to the bright red of oxygen-rich arterial blood.

Front 9

What are Myoglobin's?

Back 9

Myoglobin is a single polypeptide of 153 amino acid residues with one molecule of Heme. It is typical of the family of proteins called globin's, all of which have similar primary and tertiary structures. The polypeptide is made up of eight alpha-helical segments connected by bends.

Front 10

Functions of Myoglobin?

Back 10

As a transport protein, it facilitates oxygen diffusion in muscle. Myoglobin is particularly abundant in the muscles of diving mammals such as seals and whales, where it also has an oxygen- storage function for prolonged excursions undersea.

Front 11

Protein and Ligand-Binding and Biological Consequences?

Back 11

The biological consequence is that there will be A reduction in CO binding which is physiologically important, because CO is a low-level byproduct of cellular metabolism.

Front 12

Fraction of binding site occupied by Heme?

Back 12

Myoglobin contains a Heme prosthetic group, which binds oxygen. Heme consists of a single atom of Fe2 coordinated within a porphyrin. Oxygen binds to myoglobin reversibly; this simple reversible binding can be described by an association constant Ka or a dissociation constant Kd.

Front 13

What's an Allosteric Protein?

Back 13

An allosteric protein is one in which the binding of a ligand to one site affects the binding properties of another site on the same protein.

Front 14

Modulator for Allosteric Protein?

Back 14

The modulators for allosteric proteins may be either inhibitors or activators. When the normal ligand and modulator are identical, the interaction is termed homotropic. When the modulator is a molecule other than the normal ligand, the interaction is heterotropic.

Front 15

What happens in the body tissue when CO2 is not converted to bicarbonate in the tissue.

Back 15

Carbon dioxide is not very soluble in aqueous solution, and bubbles of CO2 would form in the tissues and blood if it were not converted to bicarbonate.

Front 16

Regulation of oxygen binding to hemoglobin by BPG has an important role in fetal development?

Back 16

Because a fetus must extract oxygen from its mother’s blood, fetal hemoglobin must have greater affinity than the maternal hemoglobin for O2. The fetus synthesizes gamma subunits rather than beta subunits, forming alpha2 gama2 hemoglobin. This tetramer has a much lower affinity for BPG than normal adult hemoglobin, and a correspondingly higher affinity for O2. Oxygen-Binding Proteins—Hemoglobin Is Susceptible to Allosteric Regulation.

Front 17

How many Heme does an adult hemoglobin has?

Back 17

Normal adult hemoglobin has four Heme-containing subunits, two alpha and two beta, similar in structure to each other and to myoglobin. Hemoglobin exists in two interchangeable structural states, T and R. The T state is most stable when oxygen is not bound. Oxygen binding promotes transition to the R state.

Front 18

Explain Hill Plot?

Back 18

Oxygen binding to hemoglobin is both allosteric and cooperative. As O2 binds to one binding site, the hemoglobin undergoes conformational changes that affect the other binding sites—an example of allosteric behavior. Conformational changes between the T and R states, mediated by subunit-subunit interactions, result in cooperative binding; this is described by a sigmoid binding curve and can be analyzed by a Hill plot.

Front 19

Two major models have been proposed to explain the cooperative binding of ligands to multisubunit proteins?

Back 19

The concerted model and the sequential model.

Front 20

Oxygen binding to hemoglobin is also modulated by 2,3-bisphosphoglycerate... Explain?

Back 20

Oxygen binding to hemoglobin is also modulated by 2,3-bisphosphoglycerate, which binds to and stabilizes the T state.

Front 21

Sickle Anemia?

Back 21

Sickle-cell anemia is a genetic disease caused by a single amino acid substitution (Glu6 to Val6) in each  chain of hemoglobin.

Front 22

Is myoglobin a motif, a domain, or a complete three-dimensional structure?

Back 22

Myoglobin is all three. The folded structure, the globin fold, is a motif found in all globins. The polypeptide folds into a single domain, which for this protein represents the entire three-dimensional structure.

Front 23

Suggest why molecules with aromatic substituents would disrupt the formation of amyloid.

Back 23

Aromatic residues seem to play an important role in stabilizing amyloid fibrils. Thus, molecules with aromatic substituents may inhibit amyloid formation by interfering with the association of the aromatic side chains.

Front 24

Under appropriate conditions, hemoglobin dissociates into its four subunits. The isolated subunit binds oxygen, but the O2-saturation curve is hyperbolic rather than sigmoid. In addition, the binding of oxygen to the isolated a subunit is not affected by the presence of H, CO2, or BPG. What do these observations indicate about the source of the cooperativity in hemoglobin?

Back 24

These observations indicate that the cooperative behavior—the sigmoid O2-binding curve and the positive cooperativity in ligand binding of hemoglobin arises from interaction between subunits.

Front 25

A team of biochemists uses genetic engineering to modify the interface region between hemoglobin subunits. The resulting hemoglobin variants exist in solution primarily as alpha/beta dimers. Are these variants likely to bind oxygen more weakly or more tightly? Explain your answer.

Back 25

More tightly. BPG-binding site would be disrupted. Oxygen binding would probably be tighter, because the default state in the absence of bound BPG is the tight-binding R state.

Front 26

Some researchers have suggested that a drug used to treat Alzheimer’s disease may also be effective in treating type 2 (adult onset) diabetes mellitus. Why might a single drug be effective in treating these two different conditions?

Back 26

Amyloid is formed in the pancreas in association with type 2 diabetes, as it is in the brain in Alzheimer’s disease. Although the amyloid fibrils in the two diseases involve different proteins, the fundamental structure of the amyloid is similar and similarly stabilized in both, and thus they are potential targets for similar drugs designed to disrupt this structure.

Front 27

What are coenzymes?

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Coenzymes acts as transient carriers of specific functional groups.

Front 28

What are prosthetic group?

Back 28

This is when enzymes are covalently bound to a metal ion or coenzymes.

Front 29

What is holoenzyme?

Back 29

A complete catalytic enzymes together with its bound coenzymes or metal ion.

Front 30

What are Substrates?

Back 30

The molecule that is bound in the active site and acted upon by the enzymes.

Front 31

Does enzymes affect the equilibra of reactions?

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Enzymes affect the rate of reaction and catalyst do not affect reaction equilibra.

Front 32

What do you understand by the word activation energy?

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The difference between the transition state and the ground state at the energy lever is called Activation Energy.

Front 33

What is transition state?

Back 33

Transition state can be defined as the fleeting molecular moment in which events such as bond breakage, bond formation and charge development have proceeded to the precise point at which decay to substrate or product is equally likely.

Front 34

A higher activation energy correspond to a slower reaction; why?

Back 34

This is because catalyst enhance reaction rates by lowering activation energies.

Front 35

What is a Reaction Intermediate?

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A reaction intermediate is any species on the reaction pathway that has finite chemical lifetime.

Front 36

What is a Rate-Limiting Step?

Back 36

The rate-limiting step is the highest energy-point in
the diagram for interconversion of S and P.

Front 37

What is Binding Energy?

Back 37

Binding energy is defined as the major source of free energy used by enzymes to lower the activation energies of reaction.

Front 38

How does an enzyme use binding energy to lower the
activation energy for a reaction?

Back 38

Enzymes are structurally complementary of their substrates so that makes them fit together like lock and key.

Front 39

The distinguishing feature of an enzymes-catalyzed reaction?

Back 39

Substrate binding occurs in a pocket on the enzyme called the active site.

Front 40

What is an Enzymes Specificity?

Back 40

The ability to discriminate between a substrate and a competing molecule.

Front 41

Consider what needs to occur for a reaction to take
place, the prominent physical and thermodynamic factors contributing to G‡, the barrier to reaction?

Back 41

1) Entropy
2) Distortion of substrates.
3) Proper alignment of catalytic functional groups on the enzyme.
4) The solvation shell of hydrogen-bonded water.

Front 42

What do you understand by the word general acid-base catalysis?

Back 42

This refers to as proton transfer mediated by other classes of molecules

Front 43

What do you understand by Pre-Steady State and State of an enzyme-substrate complexes?

Back 43

Pre-steady state is defined at the initial state in which the enzymes-substrate complexes starts to build up while the Steady state can be said to be when the enzyme-substrate complexes reaction is reached over time and it's balanced.