Languages of cell communication 2

Question 1

Localisation within the cell

Answer 1

Protein localisation can affect their activities

Question 2

Post-translational modifications

• what are they?
• different forms?

Answer 2

= reversible covalent modifications

> addition of small chemical groups 
- phosphorylation ,acetylation etc
> addition of large molecules
- sugars, lipids etc 
> cleavage of proteins
> isomerisation

Question 3

Post-translational modifications

- huge variety

Answer 3

Increases no. of potential molecular states

• > provides versatility
• different proteins can be encoded by 1 gene

expands diversity + dynamic behaviour of proteins encoded by genome

Question 4

Post-translational modification

- consequences

Answer 4

Conformational changes

Altered protein-protein interactions
- promote or prevent protein binding

Subcellular localisation

Proteolytic stability

Question 5

Conformational changes

Answer 5

In polypeptide backbone
OR
in intramolecular arrangement of different folded domains of protein

Question 6

Altered protein-protein interactions

Answer 6

create or destroy a binding site
- due to effects on charge, H-bonding + shape on binding surface

can have secondary effects
- e.g. changes in subcellular localisation or further PTMs

Question 7

Subcellular localisation

Answer 7

PTM alters dynamics of shuttling of proteins between different sub-cellular compartments (aka Protein Trafficking)

Question 8

Subcellular localisation

- example

Answer 8

Lipid modification directs many proteins to stably interact w/ cellular membranes

Question 9

Proteolytic stability

Answer 9

Alters expression of level of a protein

Phosphorylation (often coupled to ubiquitination) can target a protein for proteolytic degradation

Other modifications can stabilise a protein

Question 10

Common PTMs

Answer 10

Addition of simple functional groups

• Phosphorylation
• Methylation
• Acetylation

Addition of large molecules

• glycosylation
• ubiquitination

Proteolysis + isomerisation

Question 11

Phosphorylation

- as a regulatory mechanism

Answer 11

Specific +
Tightly regulated +
Flexible control
… of protein function

Provides points of kinetic control

Question 12

Phosphorylation

- general protein names

Answer 12

Writer enzyme
= protein kinases adding P

Eraser enzyme
= protein phosphatases removing P

Question 13

Kinases

- most common

Answer 13

Ser/Thr + Tyr protein kinases

Question 14

Phosphate group

• charge
• effects

Answer 14

-vely charged

Attracted to +vely charged groups nearby +can disrupt hydrophobic interactions

OR repel -vely charged groups

Question 15

Phosphorylation

- secondary structures

Answer 15

Local disruption 
(steric or electrostatic effects)

= P group disrupts a H bond between an alpha helix + a beta-pleated sheet
-> helix unfolds

Local ordering
(forming new structures)

= P group H-bonds w/ 2 +vely charged residues
-> allows previously unstructured region to fold into alpha helix

Question 16

Phosphorylation

- tertiary + quaternary structures

Answer 16

Long range disruption:

= P group prevents binding of a protein + partner molecule OR another domain of same protein

Long range ordering:

= P group can promote new long-range intramolecular + intermolecular interactions
(creates a docking site)

Question 17

What makes intracellular signals precise + specific?

Answer 17

1. Specificity of interaction between signalling molecules
2. High threshold
   - for signal activation maintained by constitutively active eraser enzymes
3. Back up mechanisms
   - 2 parallel pathways to activate a single downstream target protein
4. Signal integration

Question 18

SRC family kinase

- inactive shape

Answer 18

SH2 binds to phosphate group on C-terminal of tyrosine

Linker domain tightly bound between SH2 + SH3

Question 19

SRC family kinase

- phosphatase acts…

Answer 19

P removal
-> loosens structure

• > activating ligand can bind to SH3 domain
• > conformation change
• > Tyrosine loop phosphorylated = activated
• > moves out of kinase active site

= Active kinase

Question 20

What determines kinase substrate specificity?

- i.e. mechanisms that control which Ser, Thr or Try residues get phosphorylated

Answer 20

Active site
- complementary

Docking sites
- elsewhere in kinase domain

Modular binding domains
- appended to the kinase domain to recruit target substrates

Scaffolds/adaptors
- different proteins stabilise complex between kinase + substrate

Question 21

Phosphorylation coupled w/ ubiquitination

- process

Answer 21

Phosphate attracts ubiquitin

• > recognition signal for proteasome
• > binds + degrades into peptides

Question 22

Phosphorylation coupled w/ ubiquitination

- important e.g.

Answer 22

Cell cycle
- transitions between phases regulated by Cyclin-CDKs

When Cyclin-CDK is required

• > CK inhibitor phosphorylated
• > Cyclin-CDK activated

Question 23

Changes in localisation influence..?

Answer 23

Probability of interaction between molecules

Question 24

Co-localisation of reacting components…?

Answer 24

Drives reactions much more efficiently

Question 25

2 most common cellular translocations involved in signalling

Answer 25

Movement of proteins to + from nucleus

Movement of proteins to + from cell membranes

Question 26

Movement of proteins to + from nucleus

Answer 26

Access to nucleus essential for activity of proteins that act on chromatin
- e.g. chromatin modifiers + TFs

Question 27

Movement of proteins to + from cell membranes

Answer 27

Many signalling proteins + their substrates from only on membranes

Confining molecules to the membrane
-> increases the local concentrations