Proteins

Question 1

What is proteomics

Answer 1

The study of sets of proteins and their properties

Question 2

What is the proteome ?

Answer 2

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

Question 3

Why is the proteome larger than the number of genes ?

Answer 3

Particularly in eukaryotes, because more than one protein can be produced from a single gene as a result of alternative RNA splicing

Question 4

What are non-coding RNA genes

Answer 4

-Not all genes are expressed as proteins in a particular cell type.

-Genes that do not code for proteins are called non-coding RNA genes

This includes genes that are transcribed to produce;
-tRNA
-rRNA
-RNA molecules that control the expression of other genes.

Question 5

Why can the set of proteins expressed by a given cell type vary ?

Answer 5

-The set of proteins expressed by a given cell type can vary over time and under different conditions.

Some factors affecting the set of proteins expressed by a given cell type are:
-Metabolic activity of the cell
-Cellular stress
-Response to signalling molecules
-Diseased versus healthy cells

Question 6

Why do Eukaryotic cells have a system of internal membranes ?

Answer 6

-Because of their size, eukaryotes have a relatively small surface area to volume ratio. The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes

-Increases total area of membrane.

Question 7

What is the endoplasmic reticulum ?

Answer 7

-The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane.

-Lipids and proteins are synthesised in the ER

Question 8

What is the Golgi apparatus ?

Answer 8

The Golgi apparatus is a series of flattened membrane discs.

Question 9

What are lysosomes ?

Answer 9

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

Question 10

What do vesicles do ?

Answer 10

Vesicles transport materials between membrane compartments.

Question 11

Where are lipids synthesised ?

Answer 11

Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane.

Question 12

What are the types of endoplasmic reticulum ?

Answer 12

Rough ER (RER) has ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes.

Question 13

Where does the synthesis of all proteins begin ?

Answer 13

The synthesis of all proteins begins in cytosolic ribosomes

Question 14

Where are cytosolic proteins synthesised ?

Answer 14

The synthesis of cytosolic proteins is completed there (the cytosol), and these proteins remain in the cytosol

Question 15

What are proteins produced by ribosomes bound to the ER generally destined for ?

Answer 15

-Insertion into a membrane

-Secretion from the cell

Question 16

What are examples of secreted proteins ?

Answer 16

Peptide hormones and digestive enzymes are examples of secreted proteins.

Question 17

What type of post-translational modification do many secreted proteins require ?

Answer 17

-Proteolytic cleavage is another type of post-translational modification.

-Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins.

-Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.

Question 18

What is the role of the Golgi apparatus ?

Answer 18

As proteins move through the Golgi apparatus they undergo post-translational modification.

Post-translational modification is that a protein’s structure may become modified by adding chemical groups, such as;
-Carbohydrate groups (major modification)

Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates

Question 19

Describe the production of transmembrane proteins

Answer 19

1) Synthesis begins in the cytosolic ribosomes

2) Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER

3) A signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.

4) Translation continues after docking, and the protein is inserted into the membrane of the ER

Question 20

Describe the movement of proteins (transmembrane) between membranes

Answer 20

1) Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.

2) As proteins move through the Golgi apparatus they undergo post-translational modification

3) Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates. The addition of carbohydrate groups is the major modification.

4) Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.

5) Vesicles move along microtubules to other membranes and fuse with them within the cell.

Question 21

Describe the production of secretory proteins.

Answer 21

1) Synthesis begins in the cytosolic ribosomes

2) Presence of a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER

3) A signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.

4) Translation continues after docking, secreted proteins are translated in ribosomes on the RER and enter its lumen

Question 22

Describe the secretory pathway

Answer 22

1) Once the secretory proteins are in the RER lumen, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.

2) The proteins move through the Golgi apparatus, undergoing post-translational modification, and are then packaged into secretory vesicles.

3) Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates. The addition of carbohydrate groups is the major modification.

4) These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell.

Question 23

What are and what determines the structure of proteins ?

Answer 23

-Proteins are polymers of amino acid monomers

-Amino acid sequence determines protein structure

-Amino acids are linked by peptide bonds (CONH) to form polypeptides

Question 24

Describe the structure of an amino acid

Answer 24

-Amino acids have the same basic structure, differing only in the R group present.

-R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.

-The wide range of functions carried out by proteins results from the diversity of R groups

Question 25

What are the classes of amino acids ?

Answer 25

Amino acids are classified according to their R groups: -Basic (positively charged) -Acidic (negatively charged) -Polar -Hydrophobic

Question 26

What is the primary structure ?

Answer 26

The primary structure is the sequence in which the amino acids are synthesised into the polypeptide (Determines the final shape of the protein, due to different amino acids having different properties)

Question 27

What is the secondary structure ?

Answer 27

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure. These secondary structural arrangements include; -Alpha helices -Parallel beta-pleated sheets -Anti-parallel beta-pleated sheets -Turns

Question 28

What is the tertiary structure ?

Answer 28

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 bridges -Disulfide bridges are covalent bonds between R groups containing sulfur.

Question 29

What is quaternary structure ?

Answer 29

-Quaternary structure exists in proteins with two or more connected polypeptide subunits. -Quaternary structure describes the spatial arrangement of the subunits.

Question 30

What is a prosthetic group ?

Answer 30

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

Question 31

What can interactions of R groups be affected by ?

Answer 31

Interactions of the R groups can be influenced by temperature and pH.

Question 32

How does temperature affect interactions of R groups ?

Answer 32

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

Question 33

How does pH affect the interactions of R groups ?

Answer 33

-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 34

What are ligands ?

Answer 34

-A ligand is a substance that can bind to a protein.

Question 35

How do ligands bind to proteins and what affect does this have ?

Answer 35

-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, causing a functional change in the protein.

Question 36

What are allosteric interactions ?

Answer 36

-Allosteric interactions occur between spatially distinct sites -The binding of a substrate molecule to one active site of an allosteric enzyme 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 37

What are allosteric proteins

Answer 37

-Allosteric proteins have multiple ligand-binding sites and many consist of multiple subunits (quaternary structure) -These 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.

Question 38

What are modulators ?

Answer 38

Modulators regulate the activity of the enzyme when they bind to the allosteric site. There are positive and negative modulators

Question 39

How do modulators work ?

Answer 39

Following binding of a modulator, the conformation of the enzyme changes and this 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 40

Give an example of a protein showing co-operativity

Answer 40

The binding and release of oxygen in haemoglobin shows co-operativity Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen.

Question 41

Describe the influence and physiological importance of temperature and pH on the binding of oxygen

Answer 41

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.

Question 42

Describe the reversible binding of phosphate and the control of conformation

Answer 42

The addition or removal of phosphate can cause reversible conformational change in proteins. -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; Adding a phosphate group adds negative charges, ionic interactions in the unphosphorylated protein can be disrupted and new ones created. -This is a common form of post-translational modification

Question 43

Which enzymes are involved in the phosphorylation and dephosphorylation of proteins ?

Answer 43

-Protein kinases catalyse the transfer of a phosphate group to other proteins: the terminal phosphate of ATP is transferred to specific R groups -Protein phosphatases catalyse the reverse reaction

Question 44

What are the types of post-translational modification ?

Answer 44

-The addition of carbohydrate groups (major modification) -Proteolytic cleavage -The addition or removal of phosphate groups and the associated conformational change