Post-translational modifications of proteins

Question 1

What is a conformer?

Answer 1

A protein that has been folded in different ways

Question 2

Why do there tend to be amino acid variants?

Answer 2

Due to RNA editing of a single gene (different forms are encoded by a single gene)

Question 3

What is the proteome?

Answer 3

It is the entire complement of proteins that is or can be expressed by a cell, tissue or organism

Question 4

In order to get from a polypeptide chain to a functional protein, what must the protein do?

Answer 4

1. fold into unique 3D shapes
2. undergo modifications
3. be sorted into its correct cellular location
4. assemble correctly with other protein subunits with which it functions

Question 5

The information for these proteins modification is ultimately contained within what?

Answer 5

the primary amino acid sequence

Question 6

What are the 5 different post-translational modifications that proteins can undergo ?

Answer 6

1. modification of amino acids
2. modification during folding
3. modification during transport
4. modification required to activate proteins
5. reversable modification that regulate protein activity (not covering here)

Question 7

How many common amino acids are there?

Answer 7

There are 20 common amino acids

Question 8

What are all the different types of modifications proteins can go through after its been produced?

Answer 8

Question 9

What amino acids are most commonly phosphorylated?

Answer 9

Serine, Threonine, Tyrosine

Question 10

What does the phosphorylation of the amino acids tend to change?

Answer 10

The charge of the R-group

Question 11

What amino acid can mimic the switch permanently of phosphorylation and what amino acid can create an unswitchable version?

Answer 11

Aspartate mimics the switch permanently

alanine can create an unswitchable version

Question 12

Give 3 other examples for how amino acids are modified, what they are modified by and then what the modified amino acids are used for ?

Answer 12

1. Conversion of glutamic acid to gamma-caboxyglutamate by vitament K-dependant carboxylase.

This is most commonly used in blood clotting protiens such as Prothrombin (its important because it binds platelets which helps to form clots)

2. Conversion of proline to 4-hydroxyproline in collagen and plant cell wall protein. This is done by enzyme 4-polyl hydroxylase

3. Conversion of lysine to 5-hydroxyline in collagen and 6-N-merthyl lysine in myosin (important for transcription and also structurally). This is done by lysyl hydroxylase enzymes

Question 13

Whats an example of a reversable PTM?

What is it used in?

What does it help stop?

Answer 13

Lysine acetylation is an example of a reversable modification

It is used in transcription control

it also helps stop the interaction between DNA and the histone

Question 14

Whats Ubiquitination? What terminus does it occur through?

Answer 14

an enzyme PTM in which a ubiquitin protein is attached to a substrate protein. This modification occurs through the C- terminus.

Question 15

in Ubiquitination, whats the main function of the proteasome?

Answer 15

to degrade unneeded or damaged proteins by proteolysis

Question 16

What can be used to anchor proteins to membranes?

Give 3 examples of this and where they are bound to on the amino acid?

Answer 16

fatty acids and lipids

examples:

1. Myristoylation (C14 fatty acid to N-terminal glycine)

2. Palmitoylation (C16 fatty acid to internal cysteine)

3. Prenylation (prenyl lipid to cysteins 4 residues from C-terminus)

Question 17

Whats an important function of selenoproteins?

Answer 17

their antioxidant activity

Question 18

What 2 enzyme promote the correct folding of a protein by catalysing modification reactions?

Give the name and what they catalyse

Answer 18

1. Peptidyl prolyl isomerase catalyses proline isomerisation. (proline tends to be in the cis posirtion but would work better in the trans position so this protein helps to change its conformation)

2. Protein disulphide isomerase promotes correct disulphide bond formation

Question 19

Disulphide bond formation occurs through the reaction of the nearest thiol (-SH) group is not always desirable, name a protien that corrects this inappropriate disulphide bond formation during protein synthesis?

Answer 19

Protein disulphide isomerase

Question 20

Whats the most common signal sequence? Give 2 examples of this and where the signals direct the proteins to?

Answer 20

The most common type of signal sequences is an N-terminal peptide

Examples include:

1. Signal peptide (SP) directing proteins to the ER

2. Transit proteins (TP) directing proteins to the chloroplast and the mitochondria

Question 21

In some cases, there can be 2 signal sequences, where do these tend to direct proteins?

Answer 21

They initially direct proteins to the chloroplast and then intot he thylakoid lumen

Question 22

What happens to signal sequences immediately after transport and what is this done by?

Answer 22

Signal sequences are cleaved immediately after transport is complete by a peptidase in the target compartment

Question 23

Protein modifications are required to activate proteins. In what ways is this done (theres 3)

Answer 23

1. Proteolytic cleavage

2. Binding of cofactors

3. Assembly into oligomeric complexes (also important in folding)

Question 24

Give 2 examples of protein modification through proteolytic cleavage?

Answer 24

1. pre-proinsulin –> insulin

Pre-proinsulin (no disulphide bridges) –ER–> proinsulin–Golgi–> insulin

(look up image in lecture 10)

2. Conversion of Zymogens to active enzymes

Zymogens are precursors of enzymes that are activated in a proteolytic cascade after release as granuels into the duodenum

Question 25

Whats meant by a simple enzyme?

Answer 25

an active enzyme that consits of only proteins

Question 26

Whats a coenzyme?

Answer 26

A cofactor that is a small organic molecule such as a vitamin

Question 27

Name the 3 forms of active enzymes and what they are comprised from?

Answer 27

1. Protein- simple enzyme

2. metal ion- enzyme + cofactor

3. Organic molecule (coenzyme)- enzyme + cofactor

Question 28

How many haem groups does myoglobin have?

Answer 28

only 1

Question 29

What type of complex do many proteins need to be assembled in, in order to function?

Answer 29

oligomeric complexes

Question 30

What are the 3 forms of oligomeric complexes?

Answer 30

1. oligomer of identical subunits
2. oligomer of two different subunits
3. large complex comprised of many different protein subunits

Question 31

Whats the purpose of PTM?

Answer 31

1. increase the diversity of the proteome
2. regulate cellular activity
3. occur at distinct amino acids or peptide linkages and are most often mediated by enzyme activity