2. Proteomics, protein structure, binding and conformational change

Question 1

What is the proteome?

Answer 1

• The entire set of proteins expressed by a genome.
• The proteome is larger than the number of genes, particularly in eukaryotes, because more than one protein can be produced from a single gene as a result of alternative RNA splicing.

Question 2

How are genes expressed in a cell?

Answer 2

• Not all genes are expressed as proteins in a particular cell type.
• The set of proteins expressed by a given cell type can vary over time and under different conditions.

Question 3

How are membranes structured in eukaryotes?

Answer 3

Eukaryotic cells have a system of internal membranes, which increases the total area of membrane.

Question 4

What is the endoplasmic reticulum?

Answer 4

• The ER forms a network of membrane tubules continuous with the nuclear membrane.
• Rough ER has ribosomes on its cytosolic face while smooth ER lacks ribosomes.

Question 5

What is the Golgi apparatus?

Answer 5

• The Golgi apparatus is a series of flattened membrane discs.
• The discs are connected allowing molecules to move within the Golgi apparatus.
• The Golgi apparatus is adjacent to the endoplasmic reticulum.

Question 6

What are lysosomes?

Answer 6

Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates.

Question 7

What are vesicles?

Answer 7

• Vesicles transport materials between membrane compartments.
• They consist of an aqueous solution enclosed by a lipid bilayer.

Question 8

Where are lipids and proteins synthesised?

Answer 8

• Lipids and proteins are synthesised in the ER.
• Lipids are synthesised in the SER and inserted into its membrane.
• The synthesis of all proteins begins in cytosolic ribosomes
• The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol.

Question 9

What are transmembrane proteins?

Answer 9

• Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER
• Translation continues after docking, and the protein is inserted into the membrane of the ER.

Question 10

Describe movement of proteins between membranes

Answer 10

• Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.
• As proteins move through the Golgi apparatus they undergo post-translational modification.
• Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack, as they move post-translational modifications take place.
• The addition of carbohydrate groups is the major post-translational modification.

Question 11

What is the role of vesicles in the movement of proteins?

Answer 11

• Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.
• Vesicles move along microtubules to other membranes and fuse with them within the cell.

Question 12

Describe the secretory pathway.

Answer 12

• Secreted proteins are translated in ribosomes on the RER and enter its lumen
• The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
• These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
• Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins

Question 13

What are proteins?

Answer 13

• Proteins are polymers of amino acid monomers.
• A monomer is a molecule that may bind chemically to other molecules to form a polymer.

Question 14

What is the structure of amino acids?

Answer 14

• Amino acids are linked by peptide bonds to form polypeptides.
• Amino acids have the same basic structure, differing only in the R group present.
• The wide range of functions carried out by proteins results from the diversity of R groups.

Question 15

How are amino acids classified?

Answer 15

Amino acids are classified according to their R groups:
* basic (positively charged) - hydrophylllic
* acidic (negatively charged) - hydrophyllic
* polar - hydrophyllic
* hydrophobic - non-polar

Question 16

What is primary structure?

Answer 16

The primary structure is the sequence in which the amino acids are synthesised into the polypeptide.

Question 17

What is secondary structure?

Answer 17

• Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure
• These regions are either alpha helices, parallel or anti-parallel beta-pleated sheets, or turns.
• beta-sheets are parallel or antiparallel depending on their N and C termini.

Question 18

What is tertiary structure?

Answer 18

• The polypeptide folds into a tertiary structure
  This conformation is stabilised by interactions between R groups:
• hydrophobic interactions
• ionic bonds
• London dispersion forces
• hydrogen bonds
• disulfide bridge

Question 19

What is quaternary structure?

Answer 19

• Quaternary structure exists in proteins with two or more connected polypeptide subunits.
• Quaternary structure describes the spatial arrangement of the subunits.
• A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.

Question 20

How do pH and temperature affect proteins?

Answer 20

• Interactions of the R groups can be influenced by pH and temperature.
• This is why pH and temperature will affect the structure (and function) of a protein.
• Increasing temperature disrupts the interactions that hold the protein in shape
• As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost,

Question 21

Describe ligand binding.

Answer 21

• A ligand is a substance that can bind to a protein
• R groups not involved in protein folding can allow binding to ligands
• Binding sites will have complementary shape and chemistry to the ligand
• As a ligand binds to a protein-binding site the conformation of the protein changes
• This change in conformation causes a functional change in the protein

Question 22

What are allosteric interactions?

Answer 22

• Allosteric interactions occur between spatially distinct sites.
• Many allosteric proteins consist of multiple subunits.
• Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits
• Allosteric enzymes contain a second type of site, called an allosteric site
• Modulators regulate the activity of the enzyme when they bind to the allosteric site
• Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

Question 23

How does binding in haemoglobin demostrate cooperativity?

Answer 23

• Haemoglobin demonstrates quaternary structure in that is made up of four polypeptide subunits, each of which contain a haem group capable of binding a molecule of oxygen.
• When one of the subunits binds a molecule of oxygen, the second binds more easily, and the third and fourth easier still.
• This process is known as cooperativity; the ligand binding to one subunit of the protein has increased the other subunits’ affinity for the ligand.

Question 24

How do temperature and pH affect haemoglobin’s ability to bind to oxygen?

Answer 24

• As temperature increases, affinity for oxygen decreases
• As pH decreases, affinity for oxygen decreases.

Question 25

How are phosphates used in post-translational modification?

Answer 25

• Phosphorylation of proteins is a form of post-translational modification.
• The addition or removal of phosphate from particular R groups can be used to cause reversible conformational changes in proteins which can affect a protein’s activity.

Question 26

What is the role of kinase proteins in phosphorylation?

Answer 26

• Protein kinases catalyse the transfer of a phosphate group to other proteins.
• The terminal phosphate of ATP is transferred to specific R groups creating ADP as well as a phosphorylated protein.
• Protein phosphatases catalyse the reverse reaction.

Question 27

How does phosphorylation affect protein activity?

Answer 27

• Phosphorylation brings about conformational changes, which can affect a protein’s activity.
• The activity of many cellular proteins, such as enzymes and receptors is regulated in this way.
• Some proteins are activated by phosphorylation while others are inhibited.