Regulation of protein activity Flashcards
Cell identity is defined by its
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
what is proteome?
: a set of proteins produced in an organism, system
or biological context
Regulation is effected at multiple levels: name them.
- Chromatin structure and methylation
- Transcription regulators
- RNA processing
- RNA transport
- Translation
- mRNA degradation
- Protein activity
Post-translational Events
As the polypeptide chain forms, it folds into its three dimensional shape
– Some spontaneously
– Some need helper proteins called chaperones
Hydrophobic parts inside
What is the role of chaperones?
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
What happens if incorrect folding is not death by the cell and what is the mechanism that deal with it?
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
The Proteasome
• 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)
Fate of newly synthesized proteins
proteins can move between compartment in different ways
What happens if it takes too long for the chaperons to correctly fold the incorrectly folded protein
it’s degraded by proteasome
Parts of the proteasome
Cap- recognizes and bind to the polyubiquitinated proteins Central cylinder (proteas )
How can protein move between compartments
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
Signal sequence for import into nucleus
nuclear localization sequence NLS
predominantly Lys —> positively charged
Signal for export from the nucleus
Nuclear export (NES)
Import into ER
contains many hydrophobic amino acid
How do proteins move from Cytosol to ER?
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
What cleaves the peptides from the ribosome in ER?
signal peptidase
What happens to the protein in post-translational modification in ER?
- glycosylated
* stabilised by disulfide bonds
glycosylation of the protein in ER
• 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
how protein is stabilised by disulfide bonds?
stabilised by disulfide bonds
• covalent bond between 2 cysteine side chains
• intra- or inter-molecular crosslinks
• requires oxidative condition
Post-translational activation
• 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.
Examples of chemical modifications of proteins and their function
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
How different addition of Ubiquitin effect the protein?
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
Importance of post-translation modification
important role in regulating protein activity and protein levels
Post-translational modifications forma regulatory protein code
Two ways of activating the activity of proteins:
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
Growth factor
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.
Signal transduction in cancer
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
Growth factor Signal transduction
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
How does an epigenetically silenced gene differ from a mutant gene (a null allele of the same gene)?
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.
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
Histone acetylation of nucleosomes
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
which genes are turned on or off
In human DNA, which nucleotide base is methylated at the 5’ position?
Select one:
a. Guanine
b. Cytosine
c. Adenosine
d. Thymine
Cytosine
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
Inactivation of the selected genes
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
It turns genes ‘off’
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
Shielding positive charge of histones
