Protein Synthesis & Folding Flashcards
What is a chaperone?
A large group of proteins whose role is to
- stabilise unfolded proteins
- unfold them for translocation across membranes or for degredation
- assist in their correct folding and assembly
When a protein is unfolded or misfolded it is:
aggregation-prone
protease-sensitive
it binds chaperones
non-functional
in contrast to an unfolded protein, a globular, soluble protein is:
stable and soluble
protease resistant
doesn’t bind chaperones,
functional
Unfolded proteins are prone to aggregation. They may aggregate into ______ ______; amyloid formation is the cause of diseases such as ________, _______ and _________.
toxic amyloid, Alzheimer’s, Parkinson’s, type 2 diabetes
What is a chaperonin?
A protein that provides favourable conditions for the correct folding of other proteins, thus preventing aggregation.
What are the roles of Small Heat Shock Proteins (Hsp)?
- protective role in suppressing protein aggregation in vivo and in vitro.
- bind and stabilise denatured protein under conditions of cellular stress, ageing and degenerative disease.
- do not appear to have unfolding and refolding activity.
- high capacity for protein binding; up to 2 denatured proteins per subunit.
- upregulated under cellular stress, e.g. heat, oxidative stress.
GroES is also known as
Hsp10, chaperonin10 (smaller lid)
GroEL is also known as
Hsp60, chaperonin60 (bigger box)
Hsp10 is also known as
GroES, chaperonin10
Hsp60 is also known as
GroEL, chaperonin60
Hsp70 binds to ______ regions of the protein
hydrophobic
The Hsp70 family protects cells from _____ and _______ stress by preventing protein aggregation
thermal, oxidative
Hsp40 causes Hsp70 to undergo _______
conformational change
Binding and refolding by Hsp40 is driven by _________
ATP hydrolysis
where might you find the GroEL/ES system?
eubacteria, mitochondria and chloroplasts
True or False: a chaperone is a catalyst
True
True or False: a chaperone forms covalent bonds with the protein.
False; it’s a catalyst so forms non-covalent bonds
Outline the chaperone mechanism.
- Small chaperones (e.g. Bip, Hsp70, Hsp40, DnaK) bind transiently to hydrophobic sequences as they come off the ribosome. They reduce the time vulnerable surfaces are exposed to cytoplasmic interactions by cycling on and off the surfaces until they are buried by folding.
- The Anfinsen Cage is made up of the GroEL/ES complex. Single, partly folded chains are encapsulated one at a time, and released when ATP forms ADP
What are the 2 types of post-translational modifications?
- Covalent addition to side chains
2. Cleavage of protein backbone at a specific rate
What are the different possible covalent additions to side chains in post-translational modification?
- Phosphorylation
- Acylation
- Methylation
- S-prenylation
- Glycosylation
- Oxidation
- Transamidation
- Carboxylation of glutamate for Ca binding
- Hydroxylation
Post-translational modification: phosphorylation.
Addition of phosphate group is usually to an OH group (Ser, Thr, Tyr), can occasionally be His/Asp.
Protein is phosphorylated by kinase enzymes (these enzymes are often targeted by drugs).
Can add 1 or 2 negative charges, meaning v strong covalent bonds can be formed.
Protein structure changes after phosphorylation, so function can be switched on and off; phosphorylation can also block access to a binding site, switching off function.
Post-translational modification: Acylation.
Addition of an acetyl group.
Acylation of lysines in histones or PF3 transcription factors control gene expression; when the lysine groups are acylated the gene leaves the histone causing it to be expressed.
N-terminal acylation:
- lysine residues in N terminal of histones can be acylated
- takes place during protein synthesis
- irreversible
- protects against degredation e.g. blocking N-terminus, prevents ubiquitin addition
- N-acylation prevents post-translational translocation through the ER so is useful for trafficking.
Acylation of ______ in _______ or PF3 transcription factors control gene expression; when the ______ groups are acylated the gene leaves the ________ causing it to be expressed.
lysine, histones, lysine, histone
Post-translational modification: Methylation.
Addition of CH3 group
usually on Lys or Arg (often on histone proteins). Histones need to have a positive charge
S-adenosyl methionine co-factor (SAM) carries methyl group. 1 or 2 methyls can be added.
Histones need to have a _______ charge.
positive
What are histones?
Highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation.
what is a nucleosome?
a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones
Post-translational modification: S-prenylation.
C15 or C20 prenyl groups added to Cys.
They are very hydrophobic, so the protein moves to membrane
Post-translational modification: Glycosylation.
Addition of sugars or glycans.
Usually addition to OH
A monosaccharide that’s often added is GlnNAc or Tri/tetrasaccharide
Linear addition, there are lots of OH groups so lots of branching occurs.
O-glycosylation: Usually between GlnNac and Ser, Thr, Tyr. Formed via condensation reaction.
N-Glycosylation: More common, more complex than O-g. takes place in the ER. sugars are attached to Asn in Ser/Thr-X-Asn sequence motif. If they don’t fold properly they get ubiquinated and degraded.
Post-translational modification: Oxidation
formation of disulphide bonds via oxidation reaction.
- Only occurs in CYSTEINE residues as only amino acid that has SH group. It helps to stabilise folded proteins.
Disulphide bonds in the nucleus and cytoplasm are rare because the environments are reducing. Conditions become more oxidising passing through the secretory pathway so more disulphide bonds form.
Reverse reaction requires enzyme Glutathionine reductase and NADPH + H+
Disulphides first form randomly in the ER so usually the wrong Cys side chains pair up. Protein Disulphide Isomerase (PDI) catalyses the random exchange of disulphide bonds. PDI doesn’t know which disulphide bonds to make but the correct ones are most stable so you end up with the native folded protein. It’s also a chaperone enzyme.
Outline N-glycosylation
More common and more complex than O-glycosylation.
Takes place in ER
Sugars are attached to Asn in Ser/Thr-X-Asn motif.
Complex saccharides are added to proteins destined for the ER and Golgi
They interact with the chaperone proteins to help folding.
If they don’t fold properly they get ubiquinated and degraded.
In post-translational modification, oxidation is the formation of _______ _____ via oxidation reaction. It only occurs on ______ residues, because ____________.
disulphide bonds, cysteine, they’re the only amino acids to have a SH group
In post-translational modification, the reverse reaction for oxidation is catalysed by _______
Glutathionine reductase and NADPH + H+
In post translational oxidation, ____________ catalyses the random exchange of disulphide bonds.
Protein Disulphide Isomerase (PDI)
Post-translational modification: Transamidation
Forms cross linked side chains, joins Gln to Lys forming an amide bond
Post-translational modification: carboxylation of glutamate for calcium binding
gamma-carboxy Glu binds 2+ metals tightly - especially Calcium. Common enzymes involved in blood clotting - the reaction to form gamma-carboxy Gly requires vitamin K. Vitamin K deficiency causes uncontrolled bleeding (only seen occasionally in new borns).
Post-translational modification: hydroxylation.
Hydroxylated amino acid residues. Use Fe(II) monoxygenase enzymes to add oxygen. 5-OH Lys usually then glycosylated
Collagen contains ______ amino acids.
hydroxylated
_______ is the main protein in bone, skin, ligaments, cartilage and tendons
Collagen
Collagen is the most abundant protein in _______
vertebrates
Collagen has a ______ helix structure
triple
Conversion of ___ to ___ stabilises collagen ______ helix structure
Pro, Hyp, triple
Lack of _________ causes scurvy
Vitamin C
Symptoms of scurvy include:
malaise, lethargy, spots on skin, bleeding gums, open wounds, loss of teeth, jaundice, fever, (death)
who demonstrated that scurvy can be treated with fresh fruit and veg?
James Lind
Diptheria is caused by toxins released from what?
Corynebacterium diphtheriae
Outline how diptheria affects a cell.
NAD is split to release nicotinamide and a very reactive ribaoxabarbenium ion. The toxin catalyses the conversion of His715 to dipthamide. Dipthamide is then ADP-ribosylated by diptheria toxin. Protein synthesis then stops in the infected cell.
How might you reverse effects of diptheria?
Vitamin B3: ADP-ribosylation of EF-2 is reversed by giving high doses of nicotinamide (a form of vitamin B3), since this is one of the reaction’s end-products, and high amounts will drive the reaction in the opposite direction.
In a gram negative cell, proteins that are to be secreted to the extracellular environment have to cross:
two membranes and a thin cell wall
In a gram positive cell, proteins that are to be secreted to the extracellular environment have to cross:
one membrane and a thick cell wall
Outline Sec-dependent pathway.
It is the most common pathway. Found in both gram negative and positive bacteria.
It can translocate proteins across a membrane, or integrate them into it. The signal peptide at the beginning of the protein shows protein is to be exported. (bacterial proteins usually start with M).
-Chaperones (SecB) bind to pre-protein to keep it from folding too soon.
-Sec A binds to the SecY/SecE complex of proteins and translocates the pre-protein through the plasma membrane. This is driven by ATP hydrolysis.
-Signal peptidase cleaves the signal peptide once the other side of the membrane is reached. The protein then folds into its proper shape and carries out its function.
The _____ of a gram-negative cell lies between the inner and outer membrane and contains important proteins that bind nutrients for transport into the cell and other proteins that carry out enzymatic reactions. Proteins are delivered here by a common pathway involving _____ protein.
periplasm, SecA
There are several steps in the Sec-dependent secretion pathway; First, the protein is _____ in the cytoplasm. The presecretion protein protein is captured by a piloting protein called _____. _____ then binds to the unfolded protein and helps to keep it in an unfolded state, which will make secretion through a membrane much easier than if it has a chance to fold. ____ delivers the protein to ______, a structure peripherally associated with the membrane-spanning ______ translocon - the pore in the membrane through which the protein will be passed. _____ is an ATPase that appears to act like a plunger. it binds to ATP allowing it to insert deep into the ______ channel, pushing through about 20 amino acids. ATP hydrolysis then causes _____ to release the protein and withdraw. At this point, ____ can bind fresh ATP, rebind the target protein, and reinsert, pushing through another 20 amino acids. Immediately following translocation into the periplasm, ____________ such as LepB, snip off the amino-terminal signal sequence of the protein. The mature protein is then released into the periplasm. Periplasmic proteins delivered by the Sec system arrive ______ and ________, so require periplasmic _______ to guide their tertiary folding.
translated SecB SecB SecB SecA SecYEG SecA SecYEG SecA SecA periplasmic signal peptidases unfolded inactive chaperones
Protein secretion: As a ribosome ______ a protein destined for the inner membrane, the first part of the protein to emerge from the ribosome tunnel is a very ________ region called a signal sequence (must consist of 9 or more _______ amino acids). A cytoplasmic structure, called a ________, or SRP, quickly binds to the signal sequence. SRP, which is a complex of ____ and _____, essentially paralyses the ribosome. SRP delivers the stalled ribosome and its _________ to the cell membrane, where SRP binds to a transmembrane protein called ____. Although some proteins spontaneously insert into the membrane, most use a general secretion complex composed of three proteins, collectively called the _______ translocon, embedded in the cell membrane. In this process, SRP dissociates from the complex, prompting ______ to deliver the signal sequence to the translocon.
translate hydrophobic hydrophobic signal recognition particle RNA protein nascent protein FtsY SecYEG
is cystic fibrosis a dominant or recessive disease?
recessive
in cystic fibrosis which gene is affected? and what kind of mutation is it?
F508, deletion mutation: Phe missing
in cystic fibrosis, what are the implications of the deletion mutation?
mutation inhibits transport to the Golgi, instead is degraded by ERAD pathway. It leads to clogging of airways due to mucus build up.
how many amino acids in ubiquitin molecule
76
ubiquitin has a _____ structure
ball on stick
what are the subunits for a ubiquitin molecule?
4 stranded beta sheet with 1 alpha helix
