Regulation of protein activity

Question 1

Cell identity is defined by its

Answer 1

proteome
Different cell types contain the same genome, but they express different RNAs and proteins
gene to mRNA–> alternative promotors, alternative splicing, RNA editing
mRNA to protein –> folding, degradation, co and post translational modification

Question 2

what is proteome?

Answer 2

: a set of proteins produced in an organism, system

or biological context

Question 3

Regulation is effected at multiple levels: name them.

Answer 3

0. Chromatin structure and methylation
1. Transcription regulators
2. RNA processing
3. RNA transport
4. Translation
5. mRNA degradation
6. Protein activity

Question 4

Post-translational Events

Answer 4

As the polypeptide chain forms, it folds into its three dimensional shape
– Some spontaneously
– Some need helper proteins called chaperones
Hydrophobic parts inside

Question 5

What is the role of chaperones?

Answer 5

Assisted folding: the role of chaperones
Chaperones recognize hundreds of different non-native or misfolded polypeptides by their hydrophobic surfaces
Chaperones prevents aggregation of misfolded
or denatured proteins
acts an isolation cell and provides a favorable environment for gentle folding

Question 6

What happens if incorrect folding is not death by the cell and what is the mechanism that deal with it?

Answer 6

protein aggregation —> cell death disease
Protein levels are regulated by targeted degradation: the role of the proteasome
incompletely folded protein and digested by proteasome –> loss of protein

Question 7

The Proteasome

Answer 7

•
The Proteasome
–
cap recognizes and binds polyubiquitinated proteins
–
polyubiquitinated is hydrolyzes , unfolds the proteins
–
degrades the target to peptides 3-25aa long
•
ATP driven
•
Proteolytic activity (processive)

Question 8

Fate of newly synthesized proteins

Answer 8

proteins can move between compartment in different ways

Question 9

What happens if it takes too long for the chaperons to correctly fold the incorrectly folded protein

Answer 9

it’s degraded by proteasome

Question 10

Parts of the proteasome

Answer 10

Cap- recognizes and bind to the polyubiquitinated proteins
Central cylinder (proteas )

Question 11

How can protein move between compartments

Answer 11

cytosol to nucleus –> gated transport (selective gate)
cytosol to ER, mitochondria and etc… –>transmembrane transport (protein translocators)

from ER to the other compartment= vesicular transport
The signal that act as a post code is the amino acid sequence of the protein

Question 12

Signal sequence for import into nucleus

Answer 12

nuclear localization sequence NLS

predominantly Lys —> positively charged

Question 13

Signal for export from the nucleus

Answer 13

Nuclear export (NES)

Question 14

Import into ER

Answer 14

contains many hydrophobic amino acid

Question 15

How do proteins move from Cytosol to ER?

Answer 15

A Signal-Recognition Particle (SRP) Directs the ER Signal Sequence to a Specific Receptor in the Rough ER Membrane

Signal sequence of growing peptide binds to the signal recognition particle
binding of SRP to signal peptide causes a pause in translation
The ribosome-SRP complex binds to the SRP receptor on ER which causes the ribosome to bind to the translocator and translation continue and translocation begins

Question 16

What cleaves the peptides from the ribosome in ER?

Answer 16

signal peptidase

Question 17

What happens to the protein in post-translational modification in ER?

Answer 17

• glycosylated

* stabilised by disulfide bonds

Question 18

glycosylation of the protein in ER

Answer 18

• addition of a common oligosaccharide
• covalently attached to the side chain of an
asparagine residue (N-linked)
• may be required for folding, stability and
function

Question 19

how protein is stabilised by disulfide bonds?

Answer 19

stabilised by disulfide bonds
• covalent bond between 2 cysteine side chains
• intra- or inter-molecular crosslinks
• requires oxidative condition

Question 20

Post-translational activation

Answer 20

• Covalent modifications of proteins after translation may include:
– Proteolysis (cleavage of the protein), e.g. activation of digestive enzyme
– Glycosylation (addition of sugars),e.g. blood group antigens
– Phosphorylation (addition of phosphate groups).e.g. receptor kinase substrate
• Such modifications are often essential to the final functioning of the protein.

Question 21

Examples of chemical modifications of proteins and their function

Answer 21

Acetyl on Lys–> Helps to activate genes in chromatin by modifying histones
Ubiquitin on Lys –> Monoubiquitin addition regulates the transport of membrane proteins in vesicles
Polyubiquitin chain targets a protein for degradation

Question 22

How different addition of Ubiquitin effect the protein?

Answer 22

Monoubiquitylation —> histone regulation
Multiubiquitylation –> endocytosis
Polyubiquitylation–> Proteasome degradation or DNA repair
Ubiquitin– depending on different binding of the molecules to each other their fate can be changed

Question 23

Importance of post-translation modification

Answer 23

important role in regulating protein activity and protein levels
Post-translational modifications forma regulatory protein code

Question 24

Two ways of activating the activity of proteins:

Answer 24

covalent phosphorylation (proteins kinase and proteins phosphatase) 
or non-covalent binding of GTP facilitated by another protein (GEF)( Guanine nucleotide exchange factor  and GTPase activator protein)
protein bound to GTP activated

Question 25

Growth factor

Answer 25

A growth factor can trigger a cell to grow, differentiate, or divide. Many growth factors act by binding to a receptor on the cell’s surface, causing the receptor to initiate a series of events inside the cell that lead to a cellular response, such as cell division. The sequence of molecular events and chemical reactions that lead to a cell’s response is called a signal transduction pathway.

Question 26

Signal transduction in cancer

Answer 26

Signal transduction pathways are by necessity highly regulated. If a pathway triggered by a growth factor cannot turn off, for example, cells may continually divide without regulation—that is, become cancerous.
IN cancer Ras/GTP cannot be converted back to Ras-GDP

Question 27

Growth factor Signal transduction

Answer 27

Binding of Growth factor to surface receptor —> receptor undergoes dimerization which is a form of Oligomerisation
then it is Auto-phosphorylation
Small molecule binding:
o Ras-GTP: on / Ras-GDP: off
• Protein-protein interaction:
o Ras/Raf
• Phosphorylation cascade: protein kinases
• Addressing to specific sub-cellular localisation:
o phosphorylation: MAPk => nucleus

Question 28

How does an epigenetically silenced gene differ from a mutant gene (a null allele of the same gene)?

Answer 28

A gene not expressed due to alteration of its DNA sequence will never be expressed and the inactive form will be inherited generation to generation. An epigenetically inactivated gene may still be regulated. Chromatin structure can change in the course of the cell cycle, for example, when transcription factors modify the histone code. Also, unlike mutational inactivation, epigenetic inactivation may change from generation to generation.

Question 29

Eukaryotic cells can control gene expression by which of the following mechanisms?

a. DNA acetylation
b. Histone acetylation of nucleosomes
c. Repression of operons
d. RNA induced modification of chromatin structure

Answer 29

Histone acetylation of nucleosomes

Question 30

DNA methylation helps regulate:
Select one:
a. how tightly the DNA is bound to histones
b. which genes are turned on or off
c. which environmental influences will be passed on to the next generation
d. how cell division will proceed

Answer 30

which genes are turned on or off

Question 31

In human DNA, which nucleotide base is methylated at the 5’ position?

Select one:

a. Guanine
b. Cytosine
c. Adenosine
d. Thymine

Answer 31

Cytosine

Question 32

A researcher found a method she could use to manipulate and quantify phosphorylation and methylation in embryonic cells in culture. In one set of experiments she succeeded in decreasing methylation of histone tails. Which of the following results would she most likely see?

Select one:

a. Inactivation of the selected genes
b. Decreased binding of transcription factors
c. Decreased chromatin concentration
d. Increased chromatin condensation

Answer 32

Inactivation of the selected genes

Question 33

CG methylation near promoter has what effect?
Select one:
a. It temporarily alters the DNA structure
b. It turns genes ‘on’
c. It turns genes ‘off’
d. It permanently alters the DNA structure

Answer 33

It turns genes ‘off’

Question 34

Which of the following will increase transcription?
Select one:
a. Shielding positive charge of DNA
b. Shielding promoter for polymerase binding
c. Shielding positive charge of histones
d. Shielding termination region

Answer 34

Shielding positive charge of histones