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Anatomy & Cell Biology
ANAT 212
Jason Young

BIOC 212 Lecture 1 Jason Young – Monday January 7 2013 NOTE: This NTC is meant to be used as a study aid to supplement your own class notes. Hence, not all of the text or diagrams contained in the lecture slides will be reproduced here. Announcements:  Professor Young will be teaching for the first half of the course  Lectures slides will be posted at least 2 days in advance  There is no required textbook but you can refer to Molecular Biology of the Cell, Alberts et al. 4th or 5th Ed.  The 4 is available for free online. You cannot download the textbook but the site is searchable: you can search for the topic and read it online  Realistically the books will be out of date so some of the material we cover in class will be from the textbook while some will be more recent things  If it is not on the lecture slides it will not be on the exam *The following lecture corresponds to “Protein Folding” powerpoint #1 on MyCourses* Cellular Proteins  Genes and mRNA are linear in the body o Proteins are translated linearly by cytosolic ribosomes o However, it must fold into a specific 3-dimensional form  This allows them to have physical stability and functional surfaces  It is the primary sequence of a protein that determines its folding pattern, structure and localization Amio Acids  REVIEW: Amino acids have a carboxyl group and an amino group  Attached to the central alpha carbon is a “side chain” which makes the amino acid specific due to its chemical characteristics (ex. Size, polar, charged, hydrophobic, covalent linkages)  Professor Young wants us to learn the names, abbreviations, and structures of all 20 Amino acids as well as their characteristics  It is important to understand and learn the structures of the amino acids because it will provide insight on how proteins fold and function  It is also important to recognize the similarities and differences in the amino acids such as the addition of a 2H when going from Asparagine to Glutamine  Some amino acid side chains are chemically similar to each other o They share characteristics such as being polar, acidity, etc. o They are structurally different by sometimes only an additional 2H from another amino acid Polypeptides + Backbones  The polypeptide backbone becomes uncharged once the peptide bond is formed but remains polar 1  The N- terminus is positively charged and the C terminus is negatively charged  In order to form the structure of a protein both the side chain and the backbone form non covalent contacts  The peptide bond of the back bone cannot rotate because it is planar  The only rotation one can get is around thα C located in the backbone o There are also preferred rotation angles between amino acids  There are alternations of stiff and relaxed portions stretching out over the entire backbone it is not limp like a piece of string Folding  Folding is mainly driven by hydrophobic interactions though other interactions can contribute to the structure of the protein  Non-covalent bonds are very important for the way proteins fold  The following interactions can help the methods by which this folding occurs. o Hydrogen bonding (caused by polar atoms) o Ionic bonds in the protein o Van der Waals interactions (transient dipoles formed between all atoms) o Hydrophobic interactions (goal is to exclude water from hydrophobic residues)  A protein is said to be in its “native state” when it is in its most stable conformation  The protein tends to cluster in a way that leaves the hydrophobic residues in the core of the structure and the polar residues on the exterior of the structure.  If two proteins have similar primary structures (sequences) when they fold, they will have similar native states. Because native states are directly related to the functions of a protein, they could have similar functions as well  Similarities between proteins are important because they assist in discovering their biological functions Disulfide bonds  Covalent disulfide bonds make a great contribution to protein folding, more so than ionic bonds because their strength is much greater  Even though there may be only one or two disulfide bonds present their impact on the folding will be quite large  These are reserved for secretory organelles and are usually stored in the lumen space of the organelle  Cytosolic proteins do not have sulfide bonds o Proteins: cytosol, nucleus, mitochondria Summary of interactions (see figure on the right) Strong hydrophobic interactions are important for protein structure and for membrane formation  There are also several side chains that can participate in hydrogen bonds Protein Structure  Primary structure – defines the amino acid sequence of a protein  Secondary structure –portions of polypeptides that fold in a certain way i.e α-helic
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