AH Biology: Unit 1 Proteomics and Protein

Structure 4Reversible Binding of Phosphate

and Control of Conformation

Think

• What conditions are affected by the permanent activation of specific proteins?

• What is the charge on a phosphate group?

• What effect does phosphate have on protein?

• How is ATP generated by a cell?

• How is ATP used by a cell?

Kinase

• Kinase is often responsible for the phosphorylation of other proteins through ATP.

Kinase

• A phosphate group is highly charged, altering the position of charged bonding in the three-dimensional structure of the protein and as a result causing a conformational change.

Kinase

• Kinase animation 1

• Kinase animation 2

Kinase • Control of the cell cycle through cyclin dependent kinase Cdks.

• Cyclins build up during the separate phases of the cell cycle and drive the cell into mitosis through the activation of different Cdks.

• Each Cdk phosphorylates different target proteins in the cell.

• Four classes of cyclin-Cdk:

1. G1-Cdk2. G1/S-Cdk3. S-Cdk4. M-Cdk + mitosis promoting factor (MPF)

• Control of cell cycle game

Kinase

• Now read this article:

– Knight JDR, Qian B, Baker D, Kothary R (2007) Conservation, Variability and the Modeling of Active Protein Kinases. PLoS ONE 2(10): e982. doi:10.1371/journal.pone.0000982

– Use Proteomics Tutorial 1 and answer the targeted questions in relation to this article.

Phosphatase

• Phosphatase catalyses dephosphorylation of other proteins by the hydrolysis of phosphate from the protein molecule.

• This again changes the conformation of the protein as a result of charge interactions of the R groups in the protein.

• The cell cycle is finally pushed into the M phase by the phosphatase Cdc25. This removes an inhibitory phosphate from MPF, activating mitosis.

Phosphatase and glycogen metabolism

• Gluconeogenesis:

– Glucose-6-phosphatase is an important enzyme involved in the dephosphorylation of glucose-6-phosphate produced from the metabolism of glycogen.

– This generates glucose, which is then available for excretion from the cell or directly for respiration.

Phosphatase and glycogen metabolism

Glucose-6-phosphatase system deficiencies

Signal transduction• Extracellular hydrophilic signalling molecules are involved in

the activation of extracellular receptor proteins that then interact with intracellular proteins through a series of kinases and phosphatases.

• This cascade of phosphorylation and dephosphorylation quickly activates intracellular events.

• Insulin and the blood sugar level are controlled in this way, as is cell death (apoptosis).

• G-protein-coupled signal transduction

• Cyclic AMP signalling

Kinase cascade

Sodium potassium pump

ATPases

• Sodium potassium pump animation

• Glucose co-transporter animation

Mitochondria

Aerobic respiration

Regeneration of ATP

• ATP is regenerated in respiration.

• Most respiration takes place in the mitochondria via oxidative phosphorylation.

• This creates a proton gradient that is used to drive the membrane-bound enzyme ATP synthase and thus produce ATP.

Skeletal/striated muscle and contraction using ATP

Transmission electron microscope image: human striated muscle

Sarcomere

Sarcomere

• A muscle contracts as the actin and myosin filaments slide past each other.

• The distance between the Z lines decreases during muscle contraction and as a result the muscle shortens.

• This can be seen in the muscle as the A bands remain the same length but the I band and H zone get shorter during the contraction.

• Sarcomere contraction animation

Muscle contraction via ATPase

• Myosin has heads that act as cross bridges as they bind to actin at specific binding sites and allow the muscle to contract.

Muscle contraction via ATPase

• Breakdown of ATP and cross-bridge movement animation.

• Actin and myosin animation

• Actin and myosin animation: Harvard BioVisions in detail

Protein interactions in the cell

• The following animations illustrate the importance of protein in the control of the cell’s activities:

– The Inner Life of the Cell: protein interactions

– pathways to cancer animation

– apoptosis animation

– cell signals animation

Think

• What conditions are affected by the permanent activation of specific proteins?

• What is the charge on a phosphate group?

• What effect does phosphate have on protein?

• How is ATP generated by a cell?

• How is ATP used by a cell?