BIOMG 1350 Lecture Notes - Lecture 4: Binding Energy, Phosphorylation, Threonine
18 Dec 2016
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Quote of the Day: “He who seeks rest finds boredom. He who seeks work finds rest.” - Dylan
Thomas
Lecture 4: Proteins in Action
● Proteins perform functions in the cell because they have the ability to bind to other
proteins or chemicals in the cell
○ Ligands: anything that binds to the protein
○ Ligands determines the function
■ Binding of the ligands are very specific
■ Binding dependent on noncovalent bonds (hydrogen, van der waals, etc)
● Needs to have many bonds because NC bonds are generally
weak
○ Folds: Binding sites form when AA side chains fold together and form a pocket
for the ligand
■ Side chains form a surface for binding to the ligands
Proteins as Enzymes
● Many Functional Classes of proteins
○ Enzymes: Catalyze covalent bonds
■ Biological catalysts
■ Active site: pocket that has the right AA side chains for the substrate
■ Enzymes increases the rate of chemical reactions (reduces the energy
needed)
■ Enzymes are not changed by the reaction, can be recycled
■ Enzymes catalyze reactions by lowering the activations energy barrier
■ Enzymes can encourage a reaction in several ways
● Binds to 2 substrate molecules and orients them precisely to
encourage reaction to occur between the 2 substrates
● Binding of substrate to rearrange electrons, creating positive and
negative charges to favor a reaction
● Strains the bound substrate molecule, to force it toward a
transition state to favor a reaction
○ Example: Lysozyme servers bacterial cell wall
polysaccharides
○ Binding energy is used to distort the substrate so it more
closely resemble the transition state
○ AA side chains are perfectly positioned to participate in
reaction
■ Reaction Coupling: Enzymes can “couple” two reactions together to drive
an energetically unfavorable reaction
■ ATP is most widely used energy source in the cell
● Example of Coupling Reaction: energy can be used to drive
energetically unfavorable reaction
find more resources at oneclass.com
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Document Summary
Quote of the day: he who seeks rest finds boredom. He who seeks work finds rest. - dylan. Proteins perform functions in the cell because they have the ability to bind to other proteins or chemicals in the cell. Ligands: anything that binds to the protein. Binding of the ligands are very specific. Binding dependent on noncovalent bonds (hydrogen, van der waals, etc) Needs to have many bonds because nc bonds are generally weak. Folds: binding sites form when aa side chains fold together and form a pocket for the ligand. Side chains form a surface for binding to the ligands. Active site: pocket that has the right aa side chains for the substrate. Enzymes increases the rate of chemical reactions (reduces the energy needed) Enzymes are not changed by the reaction, can be recycled. Enzymes catalyze reactions by lowering the activations energy barrier. Enzymes can encourage a reaction in several ways.
