Proteomics (Key Area 2)

Question 1

What is the Proteome?

Answer 1

The entire set of proteins expressed by a genome

Question 2

Why is the Proteome larger than the genome?

Answer 2

Due to RNA splicing causing more than one protein to be produced from a single gene

Question 3

Why are not all genes expressed as proteins in a particular cell?

Answer 3

Some genes are
non-coding RNA genes which include those that are transcribed to produce tRNA, mRNA and rRNA molecules which control the expression of other other genes.

Question 4

Why do Eukaryotes have a system of internal membranes?

Answer 4

Because they’re smaller, the plasma membrane is too small to carry out all the vital functions meaning a system of internal membranes is needed to increase surface area for cellular functions

Question 5

What are the below structures/What do they do:

.Endoplasmic Reticulum
.Golgi Apparatus
.Lysosomes
.Vesicles

Answer 5

ER- forms a network of membrane tubules continuous with the nuclear membrane

Golgi Apparatus- Series of flattened membrane Discs

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

Vesicles- transport materials between membrane compartments

Question 6

Where are lipids and proteins synthesized?

Answer 6

The endoplasmic reticulum

Question 7

How are lipids synthesized?

Answer 7

They are synthesized in the smooth endoplasmic reticulum (SER) and inserted into its membrane

Question 8

How are proteins synthesized?

Answer 8

.Synthesis of all proteins begins in the cytosolic Ribosomes
. Cytosolic Proteins are synthesized there and remain in the cytosol
.Transmembrane proteins carry a signal sequence, which halts translation and directs the
ribosome synthesizing the protein to dock with the Endoplasmic Reticulum, forming Rough Endoplasmic Reticulum (RER)
.Translation continues after docking, and the protein is inserted into the membrane of the ER

Question 9

How do proteins move between Membranes?

Answer 9

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

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

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

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

Question 10

How does the Secretory Pathway Work?

Answer 10

.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

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

Question 11

What are proteins Polymers of?

Answer 11

Amino acid monomers

Question 12

What does the Amino Acid Sequence determine?

Answer 12

Protein Structure

Question 13

Amino acids have the same basic structure, differing only in the R group present. The wide range of functions carried out by proteins results from the diversity of these R groups. Name the four R groups

Answer 13

.Basic (Positively charged)
.Acidic (Negatively charged)
.Polar
.Hydrophobic

Question 14

What is the Primary Structure?

Answer 14

The sequence in which the amino acids are synthesized into the polypeptide

Question 15

What is Secondary Structure?

Answer 15

Formed from hydrogen bonding along the backbone of the protein strand. Examples are alpha-helices, parallel or anti-parallel beta-pleated sheets, or turns

Question 16

What is the Tertiary Structure?

Answer 16

Formed from the polypeptide folding.

This conformation is stabilized by interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges

Question 17

What is the Quaternary Structure?

Answer 17

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

Question 18

What is a Prosthetic group?

Answer 18

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

Question 19

What can Interactions of the R groups be influenced by?

Answer 19

Temperature and ph

Question 20

What can change the conformation of a protein?

Answer 20

Ligand Binding

Question 21

What is a Ligand?

Answer 21

A substance that can bind to a protein

Question 22

Describe how Ligand Binding causes a functional change in a protein

Answer 22

.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

.This change in conformation causes a functional change in the protein

Question 23

Describe how Allosteric proteins and interactions work

Answer 23

.Allosteric interactions occur between spatially distinct sites

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

.Allosteric proteins with multiple subunits show cooperativity 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

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

.Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate

.The binding and release of oxygen in haemoglobin shows co-operativity

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

Question 24

Describe the process of reversible binding of the phosphate

Answer 24

The addition or removal of phosphate can cause a reversible conformational change in proteins

This is a common form of post-translational modification

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
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