Proteins

Question 1

Define Proteome:

Answer 1

the entire set of proteins expressed by a genome

Question 2

Why is the proteome larger than the number of genes?

Answer 2

because more than one gene can be expressed from a single gene due to RNA splicing

Question 3

What happens during RNA splicing?

Answer 3

different exons can be expressed from one gene or different introns may be retained

Question 4

List some of the factors that affect the set of proteins expressed by a given cell type:

Answer 4

the metabolic activity of the cell
state of cellular stress
response to signalling molecules
state of health or disease

Question 5

What term is used to describe genes that do not code for proteins?

Answer 5

Non-coding RNA genes

Question 6

Describe the endoplasmic reticulum:

Answer 6

an internal system of specialised membranes which forms a network of membrane tubules continuous with the nuclear membrane

Question 7

What is the difference between the rough and smooth ER?

Answer 7

The RER has docked ribosomes on its cytosolic face, while the SER lacks ribosomes

Question 8

Define Golgi apparatus:

Answer 8

A series of flattened membrane discs related to the ER. It has associated vesicles which transport materials between membrane compartments

Question 9

How are Lysosomes formed?

Answer 9

Lysosomes are formed from specialised Golgi vesicles

Question 10

Define Lysosome:

Answer 10

A membrane bound organelle which contains a variety of hydrolases that can digest proteins, lipids, nucleic acids and carbohydrates

Question 11

Describe the structure of the cell membrane:

Answer 11

Main components are phospholipids and proteins. Phospholipids have hydrophobic tail and hydrophilic head. Proteins are either integral or peripheral.

Question 12

Where does the synthesis of all proteins begin?

Answer 12

Cytosolic ribosomes

Question 13

Describe the synthesis of cytosolic proteins:

Answer 13

Begins in cytosolic ribosomes and is completed there. The proteins then remain in the cytosol to carry out their specialised functions.

Question 14

Describe how lipids are synthesised:

Answer 14

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

Question 15

What is transmembrane protein?

Answer 15

A protein which is integral to the membrane and permanently attached there

Question 16

Describe the synthesis of transmembrane proteins:

Answer 16

Begins in the cytosolic ribosomes but is completed when the relevant cytosolic ribosomes dock with the ER to become part of the ER.

Question 17

What is the role of a transmembrane protein?

Answer 17

They carry a signal sequence that will determine the eventual location of that protein in a cell.

Question 18

What is a signal sequence?

Answer 18

A short stretch of 16-30 amino acids at one end of the polypeptide

Question 19

Define peripheral proteins:

Answer 19

Proteins that form weak bonds on the surface of membranes - either with the phospholipid heads or with exposed parts of integral proteins

Only temporarily attached

Question 20

What is the role of a signal sequence?

Answer 20

It halts translation and directs the ribosome to dock with the ER forming RER.

Question 21

What happens after the ribosome docks to form the RER?

Answer 21

After docking, the signal sequence is removed and the protein is inserted into the membrane of the ER

Question 22

What occurs after proteins are inserted into ER membrane?

Answer 22

they are transported in the membranes of vesicles that bud off from the ER and fuse with the Golgi apparatus.

Question 23

What do proteins undergo as they move through the Golgi apparatus?

Answer 23

Post-translational Modification

Question 24

What is the major post-translational modification which takes place?

Answer 24

Addition of carbohydrate groups

Question 25

How are the carbohydrates formed?

Answer 25

Enzymes catalyse sugars in multiple steps to produce the carbohydrates added

Question 26

Carbohydrate groups are added, what else is produced?

Answer 26

Glycoproteins

Question 27

How do molecules move through the Golgi apparatus?

Answer 27

travel in vesicles that bud off from one disc and fuse to the next one in the stack

Question 28

so glycoprotein is also produced, what is it used for?

Answer 28

contains vesicles that can be recruited into other membranes including the plasma membrane

Question 29

how does the synthesis of proteins for secretion differ?

Answer 29

translated in ribosomes but then enter its lumen rather than becoming integrated with lipid components

Question 30

What follows the entry of lumen in the secretory pathway?

Answer 30

they move through the Golgi apparatus and are packaged into secretory vesicles

Question 31

describe the role of secretory vesicles:

Answer 31

leave the Golgi apparatus and take proteins to the plasma membrane for secretion from the cell

Question 32

what is the alternative fate of a secretory vesicle?

Answer 32

some develop into lysosomes that are retained in the cytosol to digest...

Question 33

what do inactive precursors require to produce active proteins?

Answer 33

proteolytic cleavage

Question 34

proteolytic cleavage is important. What would happen if digestive enzymes were synthesised in active form?

Answer 34

they would digest the tissues in which they are synthesised

Question 35

how do amino acids differ from eachother?

Answer 35

R group

Question 36

what are the four R group classifications?

Answer 36

non-polar polar (neutral) acidic (negative) basic (positive)

Question 37

How can the primary structure of a protein be described?

Answer 37

The order of specific amino acids determined by the base sequence on the mature mRNA strand

Question 38

discuss the bonding associated within the secondary structure of proteins:

Answer 38

when hydrogen bonds are formed between weak positive charges on hydrogens and weak negative charges on oxygen and nitrogen atoms.

Question 39

What causes the shape of tertiary structure?

Answer 39

conformation is stabilised by interactions between R groups

Question 39

what are the three features associated with secondary structures?

Answer 39

alpha helices beta-pleated sheets turns

Question 40

five interactions which occur within tertiary structure:

Answer 40

ionic bonds hydrophobic interactions LDF's Hydrogen bonds disulfide bridges

Question 41

what two factors can affect the interactions of R groups and hence the shape of the protein?

Answer 41

temperature and pH

Question 42

how does temperature affect the shape of the protein?

Answer 42

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

Question 43

how does pH affect the shape of proteins?

Answer 43

it affects the charges on the acidic or basic R groups

Question 44

how does pH affect the shape of proteins?(extended)

Answer 44

as pH increases/decreases from optimum, normal ionic interactions between charged groups are lost which gradually changes the conformation of the protein until it becomes denatured

Question 45

what is meant by the quaternary structure?

Answer 45

when two or more polypeptide subunits are connected by bonds or interactions between R groups of different subunits

Question 46

what is meant by a prosthetic group?

Answer 46

non-protein unit tightly bound to a protein and necessary for its specific function

Question 47

Define Ligand:

Answer 47

a substance which can bind to a protein

Question 48

how do ligands bind to proteins?

Answer 48

they can bind to R groups which are not involved in protein folding

Question 49

what happens when a ligand binds to a protein?

Answer 49

conformational change which causes a change in the function of a protein

Question 50

what do allosteric proteins with multiple subunits show?

Answer 50

co-operativity

Question 51

what is meant by co-operativity?

Answer 51

changes in binding at one subunit alters the affinity of the remaining subunits

Question 52

what is an example of co-operativity?

Answer 52

the binding and release of oxygen in haemoglobin

Question 53

describe negative modulation of enzyme action:

Answer 53

negative modulators act as an inhibitor and reduce the enzymes affinity for the substrate

Question 54

describe positive modulation of enzyme action:

Answer 54

positive modulators act as an activator and increase the enzymes affinity for the substrate

Question 55

what is the third example of post-translational change?

Answer 55

phosphorylation

Question 56

describe phosphorylation:

Answer 56

the addition or removal of phosphate from particular R groups which cause reversible conformational changes in proteins

Question 57

which enzyme catalyses the transfer of a phosphate group to other proteins?

Answer 57

prptein kinases

Question 58

which enzyme catalyses the reverse reaction of phosphorylation?

Answer 58

protein phosphatases