U1-KA2 - PROTEINS - 3)ligand binding/conformation and reversible binding of phosphate + control of conformation

Question 1

What is a ligand

Answer 1

Ligand is a general term for any substance that can bind to a protein.

Question 2

What does the binding of a ligand do to a protein

Answer 2

The binding of a ligand slightly changes the shape of a protein

Question 3

How is ligand binding possible / brought about

Answer 3

-the folding which produces tertiary structure of protein is stabilised by interactions between the R groups , however there are R groups that are not involved in this folding and are exposed to the outer surface of the protein, meaning they can bind to other molecules

Question 4

How does protein folding produce ligand binding

Answer 4

Protein folding produces ligand binding sites on the surface of the protein. These binding sites are clefts on the surface of the protein .

Question 5

How does ligand binding happen

Answer 5

• previous (due to exposed R groups)
• protein folding produces ligand binding sites (previous)
  These ligand binding sites will have have a complementary shape to their ligand , matching like a jigsaw piece.
• they also have complementary chemistry to the ligand. (A binding site may have charged, polar and non polar R groups arranged in it which will match the charged, polar and non polar areas on a ligand. The matched area interact causing ligand to bind to protein)

Question 6

Why is ligand binding important

Answer 6

• the interactions between the ligand and binding site pull the polypeptide structure im towards the ligand , bringing about a change in shape - a conformational change
• the shape of a protein is crucial for its function , so a change in conformation caused functional change to a protein

Question 7

Conformation change is the mechanism used to regulate the ______ of _______

Answer 7

Conformational change is the mechanism used to regulate the activity of proteins

Question 8

What does allosteric mean / what is an allosteric protein and what can they consist of

Answer 8

• Allosteric is a term that means “other shape” and refers to proteins that have interactions between spatially distinct sites on the same protein.
• Many allosteric proteins consist of multiple subunits (have quaternary structure)

Question 9

Explain co-opertivity in binding of allosteric proteins

- why is this of biological importance

Answer 9

• many allosteric proteins consist of multiple subunits (have quaternary structure)
• they may sow coopertivity in binding : where binding at one subunits alters the affinity of the remaining subunits: the binding of a substrate molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.
• this is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in the substrate concentration

Question 10

Allosteric enzymes contain a second type of site called..

Answer 10

Allosteric enzymes contain a second type of site called an allosteric site

Question 11

Modulation of allosteric enzymes

• what do modulators do
• what is the effect of this

Answer 11

• Modulators regulate the activity of enzymes when they bind to the allosteric site
• following binding of a modulators the conformation of the enzyme changes , and this alters the affinity of the active site for its substrate , thereby altering the effectiveness of substrate binding and enzyme activity.

Question 12

What do positive modulators(activators)do ?

Answer 12

• once positive modulators binds, the overall shape of the enzyme changes (making the active suitable for the substrate)
• Positive modulators increase the enzymes affinity for the substrate and so increase the enzyme activity
• some substrates cannot fit into the active site until the positive modulator binds to the allosteric site

Question 13

What do negative modulators(inhibitors)do ?

Answer 13

• The allosteric enzyme is already in their active conformation
• When a negative modulator binds , they reduce the enzymes affinity for the substrate
• the binding of the negative modulator causes a change in the shape of the active site to such an extent that the substrate no longer fits

Question 14

Negative modulation allows the cell to ____ a particular reaction

Answer 14

Negative modulation allows the cell to slow a particular reaction

Question 15

Cooperativity in haemoglobin - why is binding of oxygen to haemoglobin known as cooperative binding

Answer 15

Binding of oxygen to haemoglobin is known as cooperative binding because the binding of successive oxygen molecules facilitates the binding of the next

Question 16

Haemoglobin cooperativity explained fully :

Answer 16

• haemoglobin has four polypeptide subunits (each have a haem group capable of binding with oxygen)
• when an oxygen molecule binds to one subunit it changes the conformation of the subunit
• this will change the confirmation of other subunits, increasing their affinity for other subunits for oxygen
• as the o2 affinity of haemoglobin increases further as oxygen binds to each subunit , oxygen collection is maximised when oxygen levels are high (in lungs / gills)

Question 17

How is oxygen collection maximised in areas where oxygen is high ?

Answer 17

as the o2 affinity of haemoglobin increases further as oxygen binds to each subunit , oxygen collection is maximised when oxygen levels are high (in lungs / gills)

Question 18

What happens when haemoglobin subunits release oxygen (the opposite)
- how is oxygen release maximised

Answer 18

• the release of an oxygen molecule from one subunit, decreases the oxygen affinity of the other subunits.
• in low oxygen areas (working tissues) the release of oxygen from each subunit decreased the oxygen affinity of the other subunits , therefore ,maximising the release of oxygen where it is needed.

Question 19

Explain the oxygen disassociation curve

Answer 19

• without co-opertivity the oxygen saturation of haemoglobin would increase in a straight line as the oxygen concentration in the tissue increased
• however the oxygen disassociation curve is S shaped showing that the haemoglobin holds less oxygen in low oxygen surroundings and holds more oxygen in high oxygen surroundings

Question 20

What is the binding of oxygen to haemoglobin influenced by

Answer 20

• Temperature

- pH

Question 21

How does temperature affect binding of oxygen to haemoglobin

Answer 21

• the increase in temperature causes haemoglobin to have a lower affinity for oxygen (curve moves right)
• the decrease causes higher affinity (curve moves left )

Question 22

How does pH affect binding of oxygen to haemoglobin

Answer 22

• The decrease in pH causes the haemoglobin to have a lower affinity for oxygen (curve moves right)
• increase causes higher affinity (curve moves left)

Question 23

What conditions will reducing binding of oxygen to haemoglobin and promote increase oxygen deliver to tissue

Answer 23

Reduced pH and increasing temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue

Question 24

Disassociation curve examples

Answer 24

Look in bio notes

Question 25

Reversible binding of phosphate + control of conformation

Phosphorylation of proteins is a form of _____ _________ _________

Answer 25

Phosphorylation of proteins is a form of post translational modification.

Question 26

A large subset of proteins are inactive when they are first synthesised and require post translational modification to become activated.
What is the most common form of activation ?

Answer 26

The most common form of activation is the reversible addition of phosphate onto particular R groups

Question 27

Reversible addition of a phosphate - what does it do

- why is it important

Answer 27

• The reversible addition/removal of a phosphate from particular R groups can be used to cause reversible conformational changes in proteins which can affect protein activity.
• this is an important method in regulating the activity of many cellular proteins , such as enzymes or receptor molecules

Question 28

Phosphorylation can ________ some proteins and _________ others.

Answer 28

Phosphorylation can activate some proteins and deactivate others

Question 29

Adding a phosphate group adds a ________ charge , what can this do ?

Answer 29

Adding a phosphate group adds a negative charge,which can disrupt ionic interactions in the unphosphorylated protein and new ones can be created.

Question 30

How is the addition and removal of a phosphate from a protein carried out

Answer 30

The addition and removal of phosphates from a protein is carried out by enzymes.

Question 31

The protein that carries out phosphorylation

- what catalyses the reverse reaction

Answer 31

• protein kinases carries out phosphorylation , which is the transfer of a phosphate group from ATP to other proteins
• there are over 500 protein kinases in the human proteome
• as shown in the diagram (bright red page 29) the terminal phosphate of ATP is transferred to specific R groups creating ADP as well as phosphorylated protein.
• protein phosphotases catalyse the reverse reaction

Question 32

The protein that carries out dephosphorylation

Answer 32

• protein phosphatases catalyses dephosphorylation which is the removal of a phosphate from a molecule , and the reverse reaction of the protein kinase
• there are about 150 protein phosphatases in the human proteome.

Question 33

Some proteins are _________ by phosphorylation whilst others are ________.
- give an example

Answer 33

• some proteins are activated by phosphorylation whilst others are inhibited.
• for example : phosphorylation of the enzyme glycogen phosphorylase b converts it to the active glycogen phosphorylase a ; while phosphorylation of another metabolic enzyme called glycogen synthase inactivated the enzyme.

Question 34

Most protein kinases are dephosphorylated and inactive. How are they activated ?

Answer 34

They are activated by phosphorylation- by another kinase.

• this reversibility of kinase phosphorylation is important in signal transduction cascades , where kinases activate other downstream kinases to amplify a signal.

Question 35

Kinases and phosphatases are crucial in the control of the ____ _____

Answer 35

Ki oases and phosphatases are crucial in the control of the cell cycle

Question 36

ATPases hydrolyse ATP

Answer 36

ATPases are a group of transmembrane enzymes that hydrolyse ATP and use the phosphate to phosphorylate themselves, rather than their substrate.

• the phosphate binding changes their conformation and so alters their function.
• the conformational change moves substances across the membrane
• all transmembrane ATPases are involved in active transport of ions across the membrane , and the sodium potassium pump (Na/K ATPase) s an important example of this type of enzyme.

Question 37

An enzyme controlled reaction is taking place at optimum conditions. There is a large surplus of substrates. How can product yield be increased?

Answer 37

• adding a positive modulator

- increasing enzyme concentration