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Lecture 3

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Biology 1002B
Denis Maxwell

Lecture 3: Protein Structure and Function 1. Basic structure of an amino acid and what are the different classes of amino acids?  All proteins are polymers of amino acids (residues)  There are 20 different side groups represented by R o Eg. Single hydrogen atom o This side group give them individual properties  Classes of amino acids o Nonpolar amino acids (10) o Uncharged polar amino acids (5) o Negatively charged (acidic) polar amino acids (2) o Positively charged (basic) polar amino acids (3) 2. Chemistry of the peptide bond and how is it formed?  Polypeptide: Chains of covalently peptide bonded amino acids  Protein: polypeptide folded into a specific 3D shape  Formed by dehydration synthesis o Amino group of amino acid (N terminal) + carboxyl group of another amino acid (C terminal) o Amino acids are added ONLY to the carboxyl end 3. The four levels of protein structure.  Primary structure o Unique sequence of amino acids o Forms a polypeptide o Determined by nucleotide sequence coding region  Secondary structure o Alpha helix  Cylinder or barrel  H bonds between top and bottom coil o Beta pleated sheet  Side by side alignment  H bonds between atoms of each strand o Less regular: random coil or loop o Hydrogen bonds between hydrogen (attached to N) and oxygen (attached to C)  Tertiary structure o Folding of secondary structure into 3D shape o Four major interaction between R groups  Ionic bonds (+ amino acid with – oxygen)  Hydrogen bonds  Hydrophobic interactions (nonpolar bonds cluster away from polar aqueous solution  Disulphide bridges (S-S) o Flexible structure allows to undergo into unique conformational changes giving unique function  Quaternary structure o Arrangement of more than one polypeptide chains o Many tertiary structures combine together o E.g. collagen  3 helical polypeptides that aggregate to form a trip helix structure  Major component of connective tissue 4. Cofactors/Prosthetic Groups  Organic or inorganic nonprotein chemical compound that is bound to a protein  Required for the protein to function  E.g. vitamins  E.g. heme o Oxygen-carrying protein hemoglobin has 4 heme molecules o One attached to each globin protein o Each heme contains a central iron atom responsible for binding molecules of oxygen 5. Protein Domains  Large structural subdivisions from folding of polypeptide(s)  Often one domain is connected to another by a segment of random coil  Hinge formed by flexible random coil allows domains to move  Each domain is structurally and functionally distinct 6. Reasons why photosystems have antenna proteins while the eye doesn’t.  In photosynthesis you want to try to gather as much light in one area o Harvest energy  For photoreceptor o Harvest light as information o They produce an image 7. Points of control for regulation of protein abundance.  Genes code for proteins  Regulate transcription (copying DNA into mRNA)  Regulate translation (converting mRNA to protein) 8. Factors affecting mRNA transcript abundance.  Balance of rate of transcription and rate of mRNA decay/turnover 9. Steps in making a Northe
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