Proteonomics

Question 1

What is a genome?

Answer 1

The genome is all of the hereditary information encoded in DNA

Question 2

What is the proteome

Answer 2

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

Question 3

The proteome is larger than the number of genes, particularly in eukaryotes, because of?

Answer 3

Alternative RNA splicing (one gene many proteins)

Question 4

Factors affecting the set of proteins expressed by a given cell type?

Answer 4

metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells

Question 5

What are genes not coding for a protein called? examples?

Answer 5

non-coding RNA genes
tRNA, rRNA and RNA

Question 6

Why do eukaryotic cells have a system of internal membranes?

Answer 6

to increase total area of membranes and provides a larger surface area for vital functions to take place

Question 7

Describe the ER

Answer 7

forms a network of membrane tubules continuous with the
nuclear membrane

Question 8

Describe the Golgi apparatus

Answer 8

series of flattened membrane discs

Question 9

Describe lysosomes and their function

Answer 9

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

Question 10

Role of vesicles?

Answer 10

transport materials between membrane compartments

Question 11

What is synthesised in the ER?

Answer 11

Lipids and proteins

Question 12

Synthesis of lipids?

Answer 12

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

Question 13

Where does the synthesis of all proteins start?

Answer 13

cytosolic ribosomes

Question 14

Pathway of synthesis for cytosolic proteins?

Answer 14

Completed in the cytosolic ribosome and remain in the cytosol

Question 15

Examples of cytosolic proteins?

Answer 15

Nucleus, mitochondria and chloroplasts

Question 16

Pathway of synthesis for transmembrane protein

Answer 16

Cytosolic ribosome
Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER
Translation continues after docking, and the protein is inserted into the membrane of the ER

Question 17

How do proteins travel in the ER

Answer 17

they are transported by vesicles that bud off from the ER
and fuse with the Golgi apparatus

Question 18

What happens as proteins move from the Golgi Apparatus?

Answer 18

they undergo post-translational modification

Question 19

What are examples of post-translational modifications

Answer 19

addition of carbohydrate groups is the major modification
phosphorylation and a disulphide bond

Question 20

Vesicles that leave the Golgi apparatus take proteins where?

Answer 20

plasma membrane and lysosomes

Question 21

How do vesicles travel along a cell?

Answer 21

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

Question 22

Pathway of secreted proteins

Answer 22

Secreted proteins are translated in ribosomes on the RER and enter its lumen
The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell

Question 23

Many secreted proteins are synthesised as inactive precursors and require what to produce active proteins?

Answer 23

proteolytic cleavage

Question 24

Examples of secreted proteins?

Answer 24

insulin and trypsin

Question 25

Amino acids are linked by?

Answer 25

peptide bonds to form polypeptides

Question 26

What four R groups are present on amino acids

Answer 26

basic (positively charged); acidic (negatively charged); polar; hydrophobic

Question 27

Diversity of R groups lead to

Answer 27

The wide range of functions carried out by proteins

Question 28

What is primary structure?

Answer 28

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

Question 29

What is secondary structure and examples?

Answer 29

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

Question 30

Tertiary structure?

Answer 30

folded polypeptide

Question 31

How is tertiary structure stabilised?

Answer 31

R group interactions like hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges

Question 32

What is quaternary structure?

Answer 32

proteins with two or more connected polypeptide subunits

Question 33

What is a prosthetic group?

Answer 33

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

Question 34

How can pH and temperature influence R groups?

Answer 34

Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured. 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 35

What is a ligand?

Answer 35

substance that can bind to a protein

Question 36

What can bind to a ligand?

Answer 36

R groups not involved in protein folding

Question 37

Describe binding site for a ligand?

Answer 37

complementary shape and chemistry to the ligand

Question 38

What happens when a ligand binds?

Answer 38

conformation of the protein changes which causes a functional change in the protein

Question 39

Allosteric interactions occur?

Answer 39

between spatially distinct sites

Question 40

Structure of many allosteric proteins?

Answer 40

consist of multiple subunits (have quaternary structure)

Question 41

Allosteric proteins with multiple subunits show co-operativity in binding which means?

Answer 41

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

Question 42

Allosteric enzymes contain a second type of site called?

Answer 42

an allosteric site

Question 43

Function of modulators?

Answer 43

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

Question 44

What happens when a modulator binds?

Answer 44

conformation of the enzyme changes and this alters the affinity of the active site for the substrate. Negative modulators reduce the enzyme's affinity for the substrate and positive modulators increase the enzyme's affinity for the substrate.

Question 45

Example of protein that shows co-operativity?

Answer 45

haemoglobin

Question 46

Describe structure of haemoglobin?

Answer 46

demonstrates quaternary structure in that is made up of four polypeptide subunits, each of which contain a haem group capable of binding a molecule of oxygen

Question 47

What are the two main factors that affect haemoglobin's ability to bind to oxygen

Answer 47

temperature - as temperature increases, affinity for oxygen decreases, curve shifts right pH - as pH decreases, affinity for oxygen decreases, curve shifts right

Question 48

The addition and removal of phosphate can cause?

Answer 48

reversible conformational change in proteins

Question 49

Function of kinases?

Answer 49

catalyse the transfer of a phosphate group to other proteins

Question 50

the terminal phosphate of ATP is transferred to?

Answer 50

specific R groups

Question 51

Function of phosphotase

Answer 51

catalyses dephosphorylation

Question 52

What does adding a phosphate group do to amino acids?

Answer 52

adds negative charge

Question 53

How to regulate the activity of many cellular proteins, such as enzymes and receptors

Answer 53

Phosphorylation brings about conformational changes, which can affect a protein’s activity

Question 54

What 2 outcomes can happen by phosphorylation of a protein?

Answer 54

Some proteins are activated by phosphorylation while others are inhibited