Key Area 2

Question 1

The proteome is…

Answer 1

The entire set of proteins expressed by a genome.

Larger than the number of genes since more than one protein can be produced from a single gene due to alternative RNA splicing.

Question 2

Non-coding RNA genes:

Answer 2

Transcribed to produce:
- tRNA
- rRNA
- Other RNA molecules that control gene
expression.

Question 3

Factors affecting proteins expressed by cell.

Answer 3

Metabolic activity of the cell.

Cellular stress.

The response to signalling molecules.

Diseased versus healthy cells.

Question 4

Eukaryotic cells have:

Answer 4

A system of internal membranes.

A large total area of membrane.

Relatively small surface area to volume ratio.

Question 5

What does the endoplasmic reticulum (ER) do?

Answer 5

Forms a network of membrane tubules continuous with the nuclear membrane.

Synthesises lipids and proteins.

Question 6

The Golgi apparatus

Answer 6

A series of flattened membrane discs.

Question 7

Lysosomes

Answer 7

Membrane-bound organelles.

Contains a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates.

Question 8

Vesicles

Answer 8

Transports materials between membrane compartments.

Question 9

Rough ER (RER)

Answer 9

Has ribosomes on its cytosolic face.

Question 10

Smooth ER (SER)

Answer 10

Lacks ribosomes.

Synthesises lipids and inserts them into its membrane.

Question 11

Cytosolic Ribosomes

Answer 11

Where synthesis of all proteins begins.

Where synthesis of cytosolic proteins is completed.

Question 12

Transmembrane proteins:

Answer 12

Carry a signal sequence that halts translation.

Directs the ribosome synthesising protein to dock with the ER to form RER.

Translation continues after docking and protein is inserted into ER membrane.

Question 13

Signal sequence:

Answer 13

A short stretch of amino acids at one end of the polypeptide.

Determines the eventual location of a protein in a cell.

Question 14

After proteins are inserted into ER membrane:

Answer 14

They are transported by vesicles from the ER to fuse with the Golgi apparatus.

Question 15

As proteins move through the Golgi apparatus:

Answer 15

They undergo post-translational modification:

Molecules move through the Golgi discs in vesicles.

Enzymes catalyse the addition of various sugars to form the carbohydrates.

Question 16

What is a major modification?

Answer 16

The addition of carbohydrate groups.

Question 17

When vesicles leave the Golgi apparatus:

Answer 17

They take proteins to the plasma membrane and lysosomes.

Vesicles move along microtubules to other membranes and fuse with them in the cell.

Question 18

Secreted proteins:

Answer 18

Synthesised as inactive precursors, proteolytic cleavage is required to produce active proteins.

Translated in ribosomes on the RER and enter its lumen.

E.g. Peptide hormones and digestive enzymes.

Question 19

Secreted proteins in Golgi Apparatus:

Answer 19

Move through the Golgi apparatus and are then packaged into secretory vesicles.

The vesicles then move fuse with the plasma membrane, releasing the proteins out of the cell.

Question 20

Proteolytic cleavage:

Answer 20

Type of post-translational modification.

E.g. Digestive enzymes require proteolytic cleavage to become active.

Question 21

What are proteins?

Answer 21

Polymers of amino acid monomers.

Question 22

How are amino acids linked?

Answer 22

By peptide bonds to form polypeptides.

Question 23

R Groups:

Answer 23

Differentiate amino acids.

Allow proteins to carry out a wide range of functions.

R-groups vary in:
- Size
- Shape
- Charge
- Hydrogen bonding capacity
- Chemical reactivity

Question 24

Amino acids

Answer 24

Classified according to their R groups:
- Basic (positively charged)
- Acidic (negatively charged)
- Polar
- Hydrophobic

Question 25

Primary structure:

Answer 25

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

Question 26

Secondary structure:

Answer 26

Result of hydrogen bonding along the backbone of the protein.

Types:
- Alpha helices.
- Parallel or anti- parallel beta-pleated sheets.
- Turns.

Question 27

Tertiary structure:

Answer 27

Polypeptide folds.

This conformation is caused by interactions between R groups, e.g:
- Hydrophobic interactions
- Ionic bonds
- London dispersion forces
- Hydrogen bonds
- Disulfide bridges

Question 28

Disulphide bridges:

Answer 28

Covalent bonds between R groups containing sulphur.

Question 29

Quaternary structure:

Answer 29

Spatial arrangement of the subunits.

Exists in proteins with two or more connected polypeptide subunits.

Question 30

Prosthetic group:

Answer 30

A non-protein unit that’s tightly bound to a protein and necessary for its function.

E.g. The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.

Question 31

Effect of temp on R-groups interactions:

Answer 31

Increasing temperature:
- Disrupts the interactions that hold the protein
in shape
- Protein begins to unfold, and becomes
denatured.

Question 32

Effect of pH on R-groups interactions:

Answer 32

Affects acidic based R-groups.

As pH increases or decreases from the optimum: - Normal ionic interactions between charged
groups are lost.
- Changes the conformation of the protein until it
becomes denatured.

Question 33

What is a ligand?

Answer 33

A substance that can bind to a protein

Question 34

Ligand Binding:

Answer 34

R groups not involved in protein folding can bind to ligands.

Binding sites have complementary shape and chemistry to the ligand.

Question 35

Conformational changes by ligands:

Answer 35

The conformation of the protein changes when ligand binds to a protein-binding site.

Change in conformation causes a functional change in the protein.

Question 36

Allosteric interactions:

Answer 36

Binding of a substrate to an active site of an allosteric enzyme increases the affinity of the other active sites.

The activity of allosteric enzymes can vary greatly with small changes in substrate concentration.

Question 37

Allosteric enzymes:

Answer 37

Multiple subunits (quaternary structure).
Contain a second type of site, called an allosteric site.

Question 38

Cooperativity in allosteric enzymes:

Answer 38

Changes in binding at one subunit alter the affinity of the remaining subunits.

E.g. Binding/release of oxygen in haemoglobin.

Question 39

Modulators:

Answer 39

Regulate the activity of the enzyme when they bind to the allosteric site.

Changes the conformation of the enzyme which alters the affinity of the active site for the substrate.

Question 40

Positive modulators:

Answer 40

Increase the enzyme’s affinity for the substrate.

Question 41

Negative modulators:

Answer 41

Negative modulators reduce the enzyme’s affinity.

Question 42

Binding/release of oxygen in haemoglobin:

Answer 42

Example of cooperativity.

Binding/releasing oxygen at one subunit alters the affinity other subunits have for oxygen.

Question 43

Effect of temp/pH on oxygen binding/release in haemoglobin.

Answer 43

Increase in temperature and decrease in pH:
- Lowers the affinity of haemoglobin for oxygen.
- Binding of oxygen is reduced.
- Reduces binding of oxygen to
haemoglobin, increasing oxygen delivery to
respiring tissue.

Question 44

Conformational change by phosphate:

Answer 44

Addition or removal of phosphate can cause reversible conformational change in proteins.

Common form of post-translational modification.

Question 45

What does the enzyme kinases catalyse?

Answer 45

Phosphorylation.

Question 46

Phosphorylation:

Answer 46

The transfer of a phosphate group to other proteins.

Terminal phosphate of ATP is transferred to specific R groups.

Causes conformational change, affecting the protein’s activity. (This is how the activity of enzymes, receptors, etc. are regulated)

Question 47

What does the enzyme phosphatases catalyse?

Answer 47

Dephosphorylation.

Question 48

Activation and inhibition by phosphorylation:
Adding a phosphate group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created