MVU3 PROTEIN FOLDING IN THE CELL -2 Flashcards
what are similar amino acids?
same properties
what does AA sequence similarity indicate?
evolutionary conservation
what does homology suggest?
common structure or function
what are polypeptides if they do not have any sequence similarity?
they are said to be divergent
what are proteins of the same family?
set of proteins or domains that have homologous sequences and structures
often have related functions
organism can have several proteins from same family
proteins from family can be found in different organisms
what interactions can the polypeptide backbone have?
hydrogen bonds and van der waals
what is the importance of post translational modification (PTM)?
can be chemically modified after translation
contribute to proteomic diversity and complexity
essential for regulation and cellular signaling
what are the different types of PTMs?
cleavage into smaller proteins by peptidases (trans membrane proteins)
covalent modification of N terminus
covalent modification of side chains (introducing functional groups to proteins)
what are side chain modifications used for?
can change surface or conformation of a protein
can create or block a binding site for other proteins
used as switches, very fast
what are those PTMs regulated by?
enzymes
regulated and reversible
what are the main types of PTMs?
phosphorylation
methylation
acetylation
glycosylation
sumoylation
ubiquitination
what is the major regulatory mechanism and what proportion of proteins undergo?
phosphorylation
30% of proteins get phosphorylated
what group is phosphorylated?
the hydroxyl group
what are the 3 amino acids that can undergo phosphorylation?
(S, T, Y) serine, threonine and tyrosine
what does adding a phosphoryl group do to an amino acid?
changes the charge (from polar to negatively charged - can now do ionic and electrostatic interactions) and the size (makes it bigger)
what are the enzymes that transfer phosphates from ATP?
kinases
how many different kinds of kinases are there?
50, they are specific for side chain and surrounding peptide sequence
what enzymes remove phosphate groups?
phosphatases
what are the different kinase/phosphatase families?
Ser/Thr kinases/phosphatases
Tyr kinases/phosphatases
dual specificity (Ser/Thr and Tyr) kinases/phosphatases
serine and threonine are together because they have very similar structures
what is acetylation of lysine and its effects
lysine is the only one that can be acetylate
it changes the polarity
done by lysine acetyltransferases (KATs) and deacetylases (KDACs)
used for signaling and metabolic effects
what does histone acetylation mean for DNA transcription?
histone acetylation is a sign of active transcription
what does the methylation of arginine and lysine involve?
addition of 1 or 2 methyl groups to the guanidino group
adds size
what are the different degrees of methylation possible of lysine?
mono, di or trimethylated
what enzymes are involved in the methylation of lysine?
lysine methyltransferases and lysine demethylases
what does PTM binding play an important role in?
transcription regulation and DNA repair mechanisms
provides new binding sites for proteins
what does the folded structure of a protein depend on?
depends on hydrophobic interactions in the interior of the structure
where are polar structures found
found on the outer surface
what is the native conformation?
the completely folded conformation of a protein
when does side chain modification take place?
takes place after folding is complete
what are the interactions that contribute to folding?
hydrophobic interactions, hydrogen bonds, van der waals interactions, ionic bonds, disulfide bonds
what determines the native structure of a protein?
the primary sequence of AA
what is the native structure in terms of free energy?
minimal energy
folding is thermodynamically favoured (negative delta G)
folding is spontaneous but assissted
what is involved between the primary sequence and the native conformation?
intermediates
unfolded domains have no secondary or tertiary structure
what stabilises the native conformation of a protein?
hydrophobic contacts
what do some domains require to be stable?
require a ligand partner (a cofactor or another protein subunit)
what can native states be in equilibrium with?
near native folding intermediates
what is aggregations?
hydrophobic regions prefer to be in contact with other hydrophobic regions
interactions between different unfolded proteins leads to insolubility
neurodegenerative diseases
what can lead to protein misfolding?
genetic mutation
required ligand not available
harmful environment conditions (heat)
aging: decreased efficiency of protein quality control mechanism (loss of protein homeostasis)
what are some genetic mutations that can lead to changes to polypeptide sequences?
AA substitution, insertion, deletion, premature sotp
what can substitution to a similar amino acid lead to?
may lead to little or no effect
what does substitution that greatly changes the AA properties lead to?
can disrupt the folding/function of the protein
what are mutations in the KCNH2 gene and what do they lead to?
Phe to Ser (pathogenic)
Ser to Leu (pathogenic)
Asp to Asn (not pathogenic)
what is protein homeostasis?
extensive network of components that acts to maintain proteins in the correct concentration, conformation and subcellular location, to cooperatively achieve the stability and functional features of the proteome
how many genes encode for chaperones and what happens when you delete a gene?
400 genes
deletion= cell death
what do chaperones recognise?
exposed hydrophobic patches
what do you switch out phospho serine for when you want to see the effects of phosphorylation of serine in a lab?
switch it out for aspartic acid (similar structure to phospho serine)
what do you switch out serine for when you want to see what happens when its not phosphorylated?
switch serine out for alanine (alanine has a similar structure and doesn’t have an OH groups so it will never have a negative charge)
