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Lecture

BIOC 212 Lecture 1.docx

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Department
Biochemistry
Course
BIOC 212
Professor
Thomas Duchaine
Semester
Winter

Description
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 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
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