2 - proteins

Question 1

what is the proteome?

Answer 1

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

Question 2

Explain why the proteome is larger than the number of genes in an organism

Answer 2

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 3

Not all genes are expressed as proteins in a particular cell type, give examples

Answer 3

Genes that do not code for proteins are called non-coding RNA genes and include those that are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes.

Question 4

What affects the set of proteins expressed by a given cell type?

Answer 4

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

Question 5

Give examples of factors which affect the set of proteins expressed by a given cell

Answer 5

Some factors affecting the set of proteins expressed by a given cell type are the metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells.

Question 6

What cells have a system of internal membranes, which increase the total area of the membrane?

Answer 6

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

Question 7

Describe the role of vesicles

Answer 7

Vesicles transport materials between membrane compartments.

Question 8

Describe the structure of the endoplasmic reticulum (ER), Golgi apparatus and lysosomes

Answer 8

• The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane.
• The golgi apparatus is a series of flattened membrane discs.
• Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates.

Question 9

Where are lipids and proteins synthesised?

Answer 9

Lipids and proteins are synthesised in the ER

Question 10

What is the difference between the Rough ER (RER) and smooth ER (SER)?

Answer 10

Rough ER has ribosomes of its cytosolic face while smooth ER lacks ribosomes.

Question 11

Where are lipids produced?

Answer 11

Lipids are synthesised in the smooth ER and inserted into its membrane.

Question 12

Where are cytosolic proteins produced?

Answer 12

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

Question 13

describe the location of transmembrane protein production

Answer 13

Transmembrane proteins are produced in the ER

Question 14

What happens once proteins are in the ER?

Answer 14

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

Question 15

What happens to proteins as they move through the Golgi apparatus?

Answer 15

As proteins move through the Golgi apparatus they undergo post-
translational modification and the addition of carbohydrate groups is the major modification.

Question 16

Where do vesicles that leave the golgi apparatus take proteins?

Answer 16

vesicles that leave the Golgi apparatus take proteins to the plasma
membrane and lysosomes.

Question 17

What do vesicles move along to get to other membranes?

Answer 17

vesicles move along microtubules to other membranes and fuse with them within the cell.

Question 18

What is the location of translation of proteins which are secreted from the cell?

Answer 18

Secreted proteins are translated in ribosomes on the RER and enter its lumen.

Question 19

Describe the secretory pathway

Answer 19

• The proteins move through the golgi apparatus and are them packaged into secretory vesicles
• These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell.

Question 20

What are many secreted proteins synthesised as?

Answer 20

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

Question 21

What is an example of a secreted protein that requires proteolytic cleavage to become active?

Answer 21

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

Question 22

What does amino acid sequence determine?

Answer 22

Amino acid sequence determines protein structure. proteins are polymers of amino acids

Question 23

Name the bonds which link amino acids together in proteins and recognise its chemical structure.

Answer 23

Amino acids are linked together by peptide bonds to form polypeptides.

Question 24

Describe the basic structure of an amino acid.

Answer 24

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

Question 25

Classify amino acids according to the R group present.

Answer 25

Amino acids are classified according to their R groups: basic (positively charged); acidic (negatively charged); polar; hydrophobic

Question 26

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

Answer 26

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

Question 27

Describe the primary sequence of a protein.

Answer 27

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

Question 28

Describe the secondary sequence of a protein including alpha helices, parallel oranti-parallel beta-pleated sheets, or turns.

Answer 28

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure - alpha helices, parallel or antiparallel beta-pleated sheets, or turns.

Question 29

What structure do polypeptides fold into?

Answer 29

The Polypeptide folds into a tertiary structure

Question 30

Describe the interactions between R groups which stabilise tertiary structure

Answer 30

The tertiary structure in polypeptides is stabilised by interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges.

Question 31

What exists in proteins with two or more connected polypeptide subunits?

Answer 31

Quaternary structure exists in proteins with two or more connected polypeptide subunits.

Question 32

What is a prosthetic group?

Answer 32

A prosthetic group os a non-protein unit tightly bound to a protein and necessary for its function, the heam group of haemoglobin is an example

Question 33

How can interactions of the R groups be influenced by temperature and pH?

Answer 33

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

Define the term ligand

Answer 34

A ligand is a substance that can bind to a protein

Question 35

What do R groups not involved in protein folding allow?

Answer 35

R groups not involved in protein folding can allow binding to ligands

Question 36

state

Answer 36

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 37

Describe how allosteric interactions occur between spatially distinct sites

Question 38

state

Answer 38

Many allosteric proteins consist of multiple subunits (have quaternary structure)

Question 39

Describe the process of cooperativity

Answer 39

Allosteric proteins with multiple subunits show cooperativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits.

Question 40

state

Answer 40

Allosteric enzymes contain a second type of site, called an allosteric site and modulators regulate the activity of the enzyme when they bind to this site.

Question 41

Describe the effect the binding of a modulator may have on a protein

Answer 41

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

Question 42

Describe cooperativity in terms of the binding and release of oxygen from haemoglobin.

Answer 42

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

Question 43

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

Answer 43

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 repairing tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.

Question 44

What can the addition or removal of phosphate cause?

Answer 44

The addition or removal of phosphate can cause reversible conformational change in proteins and this is a common form of post-translational modification.

Question 45

Describe the role of protein kinases.

Answer 45

Protein kinases catalyse the transfer of a phosphate group to other proteins.

Question 46

Describe the use of ATP in phosphorylation reactions.

Answer 46

The terminal phosphate of ATP is transferred to specific R groups

Question 47

Describe the role of protein phosphatases.

Answer 47

Protein phosphatase catalyse the reverse reaction.

Question 48

state

Answer 48

Phosphorylation brings about conformational changes, which can affect a protein’s activity and the activity many cellular proteins, such as enzymes and receptors, is regulated in this way

Question 49

state

Answer 49

Some proteins are activated by phosphorylation while others are inhibited

Question 50

What adds negative changes and ionic interactions in the unphosphorylated protein can be disrupted and new ones created.

Answer 50

Adding a phosphate group adds negative charges and ionic interactions in the unphosphorylated protein can be disrupted and new ones created.