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Flashcards in Binding and Conformational Change Deck (12):

What is a ligand?

A ligand is a substance that can bind to a protein and change the conformation of the protein.


What allows the ligand to bind to the binding-site perfectly?

The R group/ligand-binding site on the surface of the protein has complementary shape and chemistry (charge, polarity) to the ligand which allows a perfect fit.


Why is ligand binding important?

Ligand binding is important because the binding pulls the polypeptide in towards the ligand which causes a conformational change. Because a proteins structure is crucial to its function, a conformation change will also cause a functional change. Therefore, conformatinal changes regulate the activity of proteins.


How can DNA act as a ligand and how does this allow it to be packaged?

Since the sugar-phosphate backbone is negatively charged it can bind to positively charged proteins. Therefore, DNA can be wrapped around histone proteins to form nucleosomes, which can then be packaged into chromosomes.


How can proteins control gene expression in a cell by regulating the transcription of genes?

Each protein has a binding-site that is specific to a particular base sequence on DNA. When one of these proteins binds to DNA, it can either stimulate transcription by allowing the attachment of RNA polymerase, or inhibit transcription by blocking the attachment of RNA polymerase. Examples of protiens that do this are thyroxine and steriod hormones.


Describe the action of an enzyme binding to its substrate (ligand).

- When the substrate starts to bind to the active site, the small changes in bonding pulls the enzyme towards the substrate and this conformational change is called induced fit.
- Induced fit helps to further increase the binding and interaction between the active site and substrate.
- However, the enzyme is trying to go back to its original conformation and so it is under tension which makes it more likely for the substrate to be broken. This is what lowers the activation energy.


What is an allosteric enzyme?

An allosteric enzyme is an enzyme that change their conformation when they bind to a modulator to regulate their activity.


Where do modulators bind and what effect do they have (positive and negative)?

Modulators bind to an allosteric enzyme at the allosteric site/secondary binding site, which causes a change in the affinity of the active site for its substrate. Positive modulators increase the affinity and so increase the enzyme activity. Negative modulators decrease the affinity and so decreases enzyme activity.


What is cooperativity and what kind of proteins do it?

Proteins with quatenary structure can show cooperativity between their polypeptide subunits. Cooperativity is when the binding of a ligand to one subunit of the protein increases the affinity of the other subunits.


Describe how haemoglobin shows cooperatvity when oxygen binds to one of the subunits.

When an oxygen atom binds to one of the haem groups, it increases the affinity of the remaining haem groups for oxygen. This increases oxygen collection in areas of high oxygen concentration such as in the lungs.


Describe how haemoglobin shows cooperativity when oxygen is released from one of the subunits.

When oxygen is released from one haem group, the affinity for oxygen of the other haem groups is decreased. This increases oxygen release in areas of low oxygen concentration such as in working tissues.


What is the effect of pH and temperature on the affinity to oxygen for haemoglobin?

A low pH and high temperature will decrease haemoglobins affinity for oxygen since heat and acid is released in hard-working tissues to help haemogobin release oxygen. A high pH and low temperature increases haemoglobins affinity for oxygen.