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BIO315H5- Midterm Exam Guide - Comprehensive Notes for the exam ( 20 pages long!)


Department
Biology
Course Code
BIO315H5
Professor
Jade Atallah
Study Guide
Midterm

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UTM
BIO315H5
MIDTERM EXAM
STUDY GUIDE

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BIO315- HUMAN CELL BIO
Chapter 6 (Lectures 1-3)
Where does the information on how a protein is to fold located?
Located in the gene.
What is required to produce a properly folded protein?
Many different types of chemical reactions.
Why must it fold up?
The process of gene expression is not over when a sequence of amino acids is generated. In order to be
useful to the cell, the new polypeptide must fold up into its unique 3D conformation where hydrophobic
residues are buried in the interior core and is achieved by large numbers of covalent interactions. The
sum of all these energetically favourable arrangements leads to the final folding pattern. All this must
also happen at the correct speed.
When does protein folding occur? What does the protein become in a few seconds 1?
For some proteins, folding begins immediately as each protein domain emerges from the ribosomes
starting from the N terminal. Within a few seconds it forms a molten globule.
What is 1?
1 is a molten globule. It has a compact structure that contains most final secondary feature. It is aligned
in roughly the right conformation and is less highly ordered than the final folded form. It has an
unusually dynamic and flexible state. Basically, it is the starting point for a relatively slow process in
which many side-chain adjustments occur that eventually forms the correct tertiary structure.
How long does it take to synthesize an average size protein?
It takes several minutes to synthesize a protein of average size.
When is most of the folding process complete?
Most of the folding process is complete by the time the ribosome releases the C- terminal end of a
protein.
What does the above process entail?
1) The protein must bind any small molecule cofactors required for its activity (non covalent
interactions)
2) It must undergo covalent modification like protein glycosylation and protein phosphorylation
(kinases) as well as others (over 200 types).
3) The protein must assemble correctly with other protein subunits with which it functions.
Where is the information needed for all steps contained in?
It is ultimately contained in the amino acid sequence.
How has the answer to the above evolved?
Through many million years of selection through evolution. They were selected not only for
conformation but also for the ability to fold rapidly.
Are folding paths always correct?
Not always correct or stable.
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List all discussed examples of off pathway structures.
1) Kinetically trapped
2) Exposed patch of hydrophobic amino acids on the surface
3) Aggregation
These proteins are likely non functionally and are potentially dangerous and require a special class of
proteins called chaperones to fold correctly.
4) Can also occur if:
i) failed to fold correctly after leaving the ribosome (accident due to environment or mutations)
ii) suffered an accident that partly unfolded it at a later time
iii) failed to find its normal partner subunit in a larger protein
What are molecular chaperones? How do they achieve quality control?
Molecular chaperones recognize incorrect off-pathway configurations by using hydrophobic surfaces of
their own to bind to exposed hydrophobic surfaces.
They achieve quality control by carrying out protein repair by giving additional chances to fold and
preventing aggregation.
What are the types of molecular chaperones?
There are several major families of molecular chaperones/ Many molecular chaperones are heat-shock
proteins (hsp) that are synthesized in dramatically increased amounts after elevated temperature. This
is in operation of a feedback system where it is the response to greater amounts of misfolded proteins
that may be due to higher temperature.
Explain the hsp70-like machinery of the molecular chaperone.
1) Act early in the life of many proteins (often before the protein leaves the ribosome)
2) Each monomer binds to ~4-5 hydrophobic amino acids and ATP
3) Uses ATP hydrolysis where the hsp70 undergoes a conformational change that binds the target
tighter
4) Then it releases the protein and gives it a chance to refold.
5) Repeated cycles of hsp binding and release help the target protein to refold.
What are hsp60-like proteins?
Called chaperonins. They act after a protein is fully synthesized. It acts as an isolation chamber so it has
a large barrel shape.
How do hsp60-like proteins work?
1) The misfolded proteins is first captured via exposed hydrophobic entrance to the chamber which
often helps to unfold misfolded proteins.
2) The protein is released into the chamber, which is lined with hydrophilic surfaces
3) The chamber is sealed with a lid (required ATP)
4) The substrate is allowed to fold in solation (no other proteins to aggregate)
5) After ~10 seconds, ATP is hydrolyzed and this weakens the lid
6) The binding of more ATP molecules ejects the cap. The protein is released whether the it is folded or
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