Protein Structure and Function

What is a motif?

A motif is a recognizable folding pattern involving two or more elements of secondary structure folds. Motifs are only a small part of a protein and usually represent a structural unit.

What is a domain?

A domain is a part of a polypeptide chain that is independently stable. Domains usually act as functional units.

What are the characteristics of myoglobin?

Myoglobin is contained in muscle cells and delivers oxygen when needed. Myoglobin has a very high affinity for oxygen and is better for keeping oxygen in tissues than hemoglobin.

What are the characteristics of hemoglobin?

Hemoglobin is made up of four subunits that are similar to myoglobin. It is located in red blood cells and is better for transporting oxygen than myoglobin.

What is cooperativity?

Cooperativity occurs when substrate binding at one site promotes binding at another site.

How does cooperativity affect the function of hemoglobin?

Cooperativity causes hemoglobin to release oxygen more freely than myoglobin, making it ideal to bind to oxygen in the lungs and release it in the tissues.

Describe the T-state

The T-state, or tense state, occurs when a protein is not bound to its substrate.

Describe the R-state

The R-state, or relaxed state, occurs when a protein is bound to its substrate.

What is the molecular mechanism of cooperativity?

Oxygen binding at one site triggers a transition from T to R, increasing binding at other sites. Unloading works the same way. Oxygen dissociation at one site triggers a transition from R to T, increasing dissociation at other sites.

What is the effect of 2,3-BPG on hemoglobin?

2,3-BPG stabilizes the T-state, making it more energetically favorable for hemoglobin to release its bound oxygen than it would be otherwise.

What is the Bohr’s effect?

1. Free protons stabilize the T-state, meaning that during lactic acid production (exercise), hemoglobin affinity for oxygen is reduced (and more oxygen is released).

2. Carbon dioxide stabilizes the T-state by reacting with an amino group. The reaction releases a proton (further stabilizing the T-state) and allows hemoglobin to transport carbon dioxide back to the lungs.

What causes sickle cell disease?

Glu6 in beta chain is mutated to Val

What determines binding specificity of antibodies?

Complementarity between antigen and binding sites. This can be achieved by specific amino acid residues and by conformational changes (induced fit).