Proteins

Question 1

Explain what is meant by the proteome.

Answer 1

The proteome is the entire set of proteins expressed by a genome.

Question 2

Which is larger, the number of genes or the proteome, and why?

Answer 2

The proteome because more than one protein can be produced from a single gene as a result of alternative RNA splicing, in which introns are removed from RNA transcripts and exons are retained.

Question 3

What is the name for genes that do not code for proteins?

Answer 3

Non-coding RNA genes and these include those that are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes.

Question 4

State some of the factors that affect the proteins being expressed.

Answer 4

• the metabolic activity of the cell
• cellular stress
• the response to signalling molecules
• diseased versus healthy cells

Question 5

Do eukaryotic cells have small or large surface area to volume area?

Answer 5

Small

Question 6

What do eukaryotic cells have to increase the total area of membrane.

Answer 6

A system of internal membranes.

Question 7

What is the Golgi apparatus?

Answer 7

A series of flattened membrane discs.

Question 8

Where are lipids synthesised?

Answer 8

In the smooth endoplasmic reticulum and they’re inserted into its membrane.

Question 9

What is the difference between rough and smooth reticulum?

Answer 9

RER has ribosomes on it’s cytosolic face, while smooth ER lacks ribosomes.

Question 10

Where does the synthesis of all proteins begin?

Answer 10

In cytosolic ribosomes.

Question 11

Explain the process of the synthesis of cytosolic ribosomes.

Answer 11

The synthesis of cytosolic proteins is completed in the cytosolic ribosomes and then remain in the cytosol.

Question 12

Explain the process of the formation of transmembrane proteins.

Answer 12

Synthesis begins in a cytosolic ribosome. Transmembrane proteins carry a signal sequence that 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. 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 they move through the Golgi apparatus, they undergo post-translational modification. Vesicles that leave the Golgi apparatus take transmembrane proteins to the plasma membrane and lysosomes. Vesicles fuse with them within the cell.

Question 13

Explain what happens in the Golgi apparatus.

Answer 13

As the proteins move through the Golgi apparatus, they undergo post-translational modification. Molecules move through the Golgi discs in vesciles that bud off from one disc and fuse to the next one in the stack. Within the Golgi apparatus, enzymes catalyse the addition of various sugars (carbohydrates) in multiple steps to form glycoproteins.

Question 14

Breifly explain the synthesis of secretory proteins.

Answer 14

Proteins for secretion are translated in ribosomes on the RER and enter its lumen. Peptide hormones and digestive enzymes are examples of proteins for secretion. The proteins move through the Golgi apparatus and are then packaged into secretory vesicles. Secretory vesicles move to, and fuse with, the plasma membrane, releasing the proteins out of the cell.

Question 15

What is proteolytic cleavage and give an example of a secreted protein that requires it.

Answer 15

Proteolytic cleavage is another tyoe if post-translational modification. Digestive enzymes are one example of secreted proteins that require proteolytic cleavage of inactive precursors to become active. If digestive enzymes were synthesised in active form, they could digest the tissues in which they were synthesised.

Question 16

Explain the structure of amino acids.

Answer 16

Amino acids have amine groups (NH2) , carboxylic acid groups (C, double bond O, OH) and R groups.

Question 17

State the different types of R groups.

Answer 17

• basic
• acidic
• polar
• hydrophobic

Question 18

What does the range of functions carried out by proteins result from?

Answer 18

The diversity of R groups.

Question 19

Explain what is meant by the primary structure.

Answer 19

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

Question 20

What do regions of secondary structure come from?

Answer 20

Hydrogen bonding, when weak positive charges on hydrogen atoms are attracted to weak negative charges on oxygen or nitrogen atoms and occurs along the backbone of the protein strand.

Question 21

State the types of hydrogen bonding.

Answer 21

• alpha helices
• parallel or anti-parallel beta-pleated sheets
• turns (usually join different secondary structures together or allow changes of direction in the polypeptide, causing folding to create compact molecules)

Question 22

How are tertiary structure stabilised?

Answer 22

By interactions between R groups.

Question 23

State the different types of tertiary structures.

Answer 23

• hydrophobic interactions
• ionic bonds
• London dispersion forces
• hydrogen bonds
• disulfide bridges (strong covalent bonds between R groups containing sulfur)

Question 24

When does quaternary structure exist?

Answer 24

In proteins with two or more connected polypeptide subunits. The quaternary structure describes the spatial arrangement of the subunits.

Question 25

What is a prosthetic group and give an example of one.

Answer 25

A non-protein unit tightly bound to a protein and necessary for its function. The ability of haemoglobin to bind with oxygen is dependent on the prosthetic haem group.

Question 26

Explain what effect increasing temperature has on R group interactions.

Answer 26

Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.

Question 27

Explain how R group interactions are affected by pH.

Answer 27

The charges on acidic and basic R groups are affected by pH- as pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.

Question 28

What is a ligand?

Answer 28

A ligand is a substance that can bind to protein R groups that are not involved with protein binding.

Question 29

Explain the process of ligand binding.

Answer 29

Binding sites have a complementary shape and chemistry to the ligand. As a ligand binds to a protein-binding site, the protein conformation changes - this change causes a functional change in the protein.

Question 30

What happens when a substrate molecule binds to one active site of an allosteric enzyme and why is this important?

Answer 30

It 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 substrate concentration.

Question 31

What do proteins with multiple subunits show? Explain what is meant by this.

Answer 31

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.

Question 32

What is the name for the second type of site on an allosteric enzyme?

Answer 32

Allosteric site.

Question 33

What are modulators?

Answer 33

Modulars regulate the activity of the enzyme when they bind to the allosteric site.

Question 34

Explain what happens once a modular has binded.

Answer 34

Following the binding of a modulator, the conformation of the enzyme changes, which alters the affinity of the active site for the substrate. Positive modulators increase the enzyme’s affinity for the substrate; negative modulators reduce the enzyme’s affinity.

Question 35

Explain co-operativity in haemoglobin.

Answer 35

The binding and release of oxygen at one subunit alters the affinity of the remaining subunits for oxygen.

Question 36

What is the name of the shape of the graph that shows oxygen levels vs oxyhaemoglobin saturation?

Answer 36

Sigmoid

Question 37

Explain what happens to the binding of oxygen to haemoglobin when pH is decreased or temperature is increased

Answer 37

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced ( right shift in the graph).

Question 38

What is the name of the protein which catalyses the transfer of a phosphate group to other proteins?

Answer 38

Protein kinases.

Question 39

What does protein phosphatase do?

Answer 39

It catalyses the removal of phosphate from a protein.

Question 40

What does phosphorylation do to proteins?

Answer 40

Phosphorylation brings about conformational changes, which can affect a protein’s activity.

Question 41

What charge does adding a phosphate group add?

Answer 41

Negative charges.

Question 42

What can phosphates do to proteins?

Answer 42

Ionic interactions in the unphosphorylated protein can be distributed and new ones created.