Cells and Proteins

Question 1

What is the proteome?

Answer 1

The entire set of proteins that is, or can be, expressed by a genome, cell tissue, or organism at a certain time

Question 2

Why is the proteome greater than the number of genes?

Answer 2

Because more than one protein can be produced from a single gene as a result of alternative RNA splicing.

Question 3

Are all genes expressed as proteins?

Answer 3

No, genes that do not code for proteins are called non-coding RNA genes.

Question 4

How can protein expression in a given cell type vary?

Answer 4

Protein expression can vary over time and under different conditions e.g. metabolic activity of the cell, cellular stress, the response to signalling molecules, diseased versus healthy cells.

Question 5

What do eukaryotic cells have that increases the total area of the membrane?

Answer 5

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

Question 6

What does the endoplasmic reticulum form?

Answer 6

The ER forms a network of membrane tubules continuous with the nuclear membrane.

Question 7

What is the golgi apparatus?

Answer 7

The golgi apparatus is a series of flattened membrane discs.

Question 8

What are lysosomes?

Answer 8

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

Question 9

What do vesicles do?

Answer 9

Vesicles transport materials between membrane compartments.

Question 10

Where are lipids and proteins synthesised?

Answer 10

Lipids and proteins are synthesised in the endoplasmic reticulium.

Question 11

Where exactly are lipids synthesised?

Answer 11

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

Question 12

Where does the synthesis of all proteins begin?

Answer 12

The synthesis of proteins begins in the cytosolic ribosomes.

Question 13

What happens after cytosolic proteins have been synthesised in the cytosolic ribosomes?

Answer 13

the cytosolic proteins remain in the cytosol.

Question 14

What happens to transmembrane proteins after synthesis in the cytosolic ribosomes?

Answer 14

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

Question 15

What happens after docking at the ER?

Answer 15

Translation continues and the protein is inserted into the membrane of the ER.

Question 16

What happens after the protein has been inserted into the ER?

Answer 16

The protein is transported by vesicles that bud off from the ER and fuse with the golgi apparatus.

Question 17

What happens at the golgi apparatus?

Answer 17

The proteins move through the golgi apparatus and undergo post-translational modifications.

Question 18

What is the major modification that happens in the golgi apparatus?

Answer 18

The addition of a carbohydrate group.

Question 19

What happens after modifications at the golgi apparatus?

Answer 19

Vesicles that leave the golgi apparatus take proteins to the plasma membrane and lysosomes.

Question 20

What happens to the vesicles after proteins have been taken to the plasma membrane or lysosomes?

Answer 20

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

Question 21

What happens to secreted proteins after synthesis in the cytosolic ribosomes?

Answer 21

They have a signal sequence which halts translation and docks at the ER. Translation continues in ribosomes on the RER and it enters its lumen.

Question 22

What happens after the secreted proteins enter the lumen?

Answer 22

The proteins move through the golgi apparatus and are then packaged into secretory vesicles.

Question 23

What happens after secreted proteins are out into secretory vesicles?

Answer 23

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

Question 24

Why do many secreted proteins require proteolytic cleavage?

Answer 24

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

Question 25

What are proteins?

Answer 25

Proteins are polymers of amino acid monomers.

Question 26

What are amino acids linked by?

Answer 26

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

Question 27

Explain amino acids basic structure.

Answer 27

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

Question 28

How are amino classified?

Answer 28

Amino acids are classified according to their R group: basic (positively charged), acidic (negatively charged), polar and hydrophobic

Question 29

What causes the diversity of amino acid R groups?

Answer 29

The wide range of functions carried out by proteins.

Question 30

What is the primary structure?

Answer 30

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

Question 31

What causes secondary structure regions?

Answer 31

Hydrogen bonding along the backbone of the protein strand.

Question 32

What are secondary structures?

Answer 32

Alpha helix, parallel or anti-parallel beta-pleated sheets or turns.

Question 33

How is a tertiary structure made?

Answer 33

The polypeptide folds into a tertiary structure.

Question 34

What stabilises the conformation if the tertiary structure?

Answer 34

Interactions between R groups such as: Hydrophobic interactions, ionic bonds, London dispersion forces, hydrogen bonds and disulfide bridges

Question 35

Where does a quaternary structure exist?

Answer 35

In proteins with two or more connected polypeptide subunits.

Question 36

What is a prosthetic group?

Answer 36

A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.

Question 37

How can interactions between R groups be influenced?

Answer 37

Temperature and pH

Question 38

How does temperature influence R group interactions?

Answer 38

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

Question 39

How does pH influence R group interactions?

Answer 39

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 40

What is a ligand?

Answer 40

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

Question 41

What can allow binding to ligands?

Answer 41

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

Question 42

What do the binding sites have to bind to a ligand?

Answer 42

The binding site will have complementary shape and chemistry to the ligand.

Question 43

What happens when a ligand binds to a protein-binding site?

Answer 43

The conformation of the protein changes.

Question 44

What happens when the conformation of a protein changes?

Answer 44

Causes the protein to have a functional change in the protein.

Question 45

Where do allosteric interactions happen?

Answer 45

Occur between spatially distinct sites.

Question 46

Do allosteric proteins have subunits?

Answer 46

Many allosteric proteins consist of multiple subunits.

Question 47

What does allosteric proteins with multiple subunits show?

Answer 47

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

Question 48

What do allosteric enzymes contain?

Answer 48

Allosteric enzymes contain a second type of site, called an allosteric site.

Question 49

What do modulators do?

Answer 49

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

Question 50

What happens after a modulator has binded?

Answer 50

The conformation of the enzyme changes and this alters the affinity of the active site for the substrate

Question 51

What does the binding of oxygen in haemoglobin show?

Answer 51

Cooperativity

Question 52

What lowers the affinity of haemoglobin for oxygen?

Answer 52

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

Question 53

Why is reduced pH and an increase in temperature goof (haemoglobin and oxygen)?

Answer 53

Reduced pH and increasing the temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.

Question 54

What can cause reversible conformational changes in proteins?

Answer 54

The addition or removal of phosphate can cause reversible conformational changes in proteins.

Question 55

What is a common post-translational modification?

Answer 55

Addition or removal of a phosphate.

Question 56

What do protein kinases do?

Answer 56

Catalyse the transfer of a phosphate group to other proteins.

Question 57

What phosphate is transferred to specific R groups in a protein.

Answer 57

The terminal phosphate of ARP.

Question 58

What catalyses the reverse reaction? (Removing a phosphate)

Answer 58

Protein phosphatatses

Question 59

What happens during phosphorylation?

Answer 59

Brings about a conformational changes, which can affect a protein's activity. The activity of many cellular proteins is regulated in this way.

Question 60

How does phosphorylation affect a protein?

Answer 60

Some proteins are activated while others are inhibited.