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BIOC 212 Lecture Notes - N-Terminus, Disulfide, Secretion

Course Code
BIOC 212
Thomas Duchaine

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Jason C. Young = Prof
Topics covered
Intro to proteins what they are what they do, Intro to co-chaperones (proteins responsible in
folding of other proteins, how they work in folding and degradation (removal of misfolded proteins)
How proteins can be chemically modified and how they can turn into amyloids.
Next section, membranes, how they are formed, from lipids. How the sercretory.
All organisms need proteins to function. Basic building blocks of cells, bodies, made from AA, made
by ribosomes.
Proteins are functional parts of the cell.
Default: in the cell( means human/mammalian cells) cells are bound by membranes, have
intracellular structures labelled in the diagram. Between these organelles, there’s the cytosol.
Cytosol is full of organelles, intracellular proteins, macromolecules, all essential to performing
processes of life.
Some review: Proteins are the main functional components in cells. Genes are encoded by DNA,
DNA is translated to RNA, RNA transcribed into proteins. Genes are linear, therefore Proteins are
made as linear polypeptide sequences, but they must fold into 3D structures. The structure is what
pferforms function. By folding, it becomes more physically stable internally and it exposes
functional surfaces it needs to interact with other molecules. Remember that sequence determines
structure, which determines function and often localization (where the protein will act within or
outside the cell).
Proteins are composed of 20 amino acids (composed of an amino group, an acidic group and most
importantly a side chain). Side chains have different characteristics: nonpolar (hydrophobic)
uncharged or polar(hydrophilic) uncharged, or polar and charged. Of the polar amino acids, they
can also be acidic or basic. Small or large. (1) non-polar and neutral, (2) polar and neutral, (3) acidic
and polar, (4) basic and polar.
AA are covalently linked into long chains of polypeptides.
Learn the structures, names and abbreviations of all the amino acids.
Polypeptides: Amino acids are polypeptides covalently linked together into polymers. By peptide
bonds, At one end we have an amino terminus (N terminus), Pos charged, at other end, carboxy
terminus, C terminus neg charged. The peptide bonds themselves are not charged though they are
hydrophilic(polar). Peptide bonds themselves do not rotate well, we can get rotation around
central/alpha carbon. But there is limited degree of rotation.
Charge and hydrophobicity of polypeptide is determined by the side chains of AA. All polypeptides
ahve same uncharged backbone, specificity, particular characteristics of proteins are going to
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depend on side chains. In terms of folding, both the side chains and the backbone can form
noncovalent contacts with other amino acids.
Protein folding: Interactions between AA of polypeptides with stabilize the structure of protein and
interactions with other monomers. Types of noncovalent interactions, hydrophobic interactions
(exclusion of water). Hydrogen bonds (where a hydrogen is shared between two polar groups) van
der Waals (transient/temporary dipoles between all atoms which can intereact with each other).
Ionic bonds (charged atoms interacting with each other)
All the noncovalent interactions contribute to structure and folding of proteins. In terms of folding
for proteins, the most important type of interaction is the hydrophobic interactions. The other
types of bonds and the rigidity (ability to rotate the backbone) contribute to the folding of proteins.
Generally speaking, in proteins, polar side chains form the surface and hydrophobic side chains
form the interior.
Proteins with similar sequences, have similar structures, thus similar functions biologically.
On a Cysteine (Cys or C) side chain, there is a sulphur bonded to a hydrogen on one side and a
carbon atom on the other (C-SH) referred to as a sulphyrdryl or thiol. Upon oxidation, the
sulphydryl forms a disulphide bond.
Of the types of bonds, one type of covalent bond that contributes to protein folding is the disulfide
bond. The disulfide bond provides stabilisation for proteins in the secretory pathway(extracellular
proteins and proteins inside the organelles of the secretory pathway). Proteins on the cytosolic side
of secretory membranes (cytosol, nucleus and mitochondria) do not have disulphide bonds.
List of importance for folding (diagram in the slides)
Disulfide bonds are the only covalent bonds that contribute to protein structure, not many of them
Covalent interactions are much stronger than non-covalent interactions.
Strong hydrophobic interactions are not only important for protein structure, but also important
for the formation of biological membranes and how proteins and membranes can interact and form
the structures within of the cell.
Units of protein structure
Primary structure corresponds to the amino acid sequence; encoded by the mRNA,
translated by ribosomes.
Secondary Structure
-local conformation patterns between amino acids.
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