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Lecture 3

Biochem - Lecture 3 .docx

12 Pages

Course Code
Psychology 2070A/B
Kelly Olson

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Biochemistry Lecture 3 - By the end of today you will: 1. Be able to calculate net charge of an amino acid with an uncharged side chain. 2. Describe the characteristics of a beta sheet. 3. Define and describe tertiary and quaternary structure. 4. Be able to describe a protein domain’s characteris9cs. 5. Understand the molecular structure of disulfide bonds. 6. Learn how proteins fold and how they become unfolded. 7. Understand the concept of protein families. Amino acid charge problem: alanine Q. What is the net charge of alanine(only has amino and carboxyl group) at pH 5? Given: pKa of α-amino group = 10.0 pKa of α-carboxyl group = 2.0 *We will work this out in class together.  Do it separately then combine Alpha- Amino group NH3+: NH2 is 10^5 :1 Assume 100% NH3+ Therefore, a charge on a alpha-amino group is +1(1)=1 Alpha- Carboxyl Group COOH:COO- is 1:10^3 Assume 100% COO- Therefore, charge on alpha-carboxyl group is -1(1)=-1 Therefore, charge net charge on amino acid is (+1) + (-1)=0 2° structure: Beta sheets  Hydrogen bonds occur between the backbone of two or more polypeptide chains arranged adjacently and in parallel  Side chains project alternately up and down 1 “pleated sheet” 2 Beta sheet (movie)  Anti-parallel form (C-terminus lined up with N-terminus, N with C )  Parallel Beta pleated sheet C-terminus lined up with C, N lines up with N  Hydrogen bonding between these makes the folds in the beta sheet o 2 structure, Summary  Silk fibroin (extremely strong material) consists mostly of β-sheets.  Most proteins have both α-helices and β-sheets, plus turns and other less regular structure.  Primary sequence determines type of structure formed. Human cystatin C Biomarker of kidney function 3 Tertiary Structure  Concerns the 3D arrangement of the polypeptode chain  Stabilized by bonds between side chains or side chains to Backbone  Interactions between residues distant 
in sequence  Gives overall shape of protein “Birds of a feather flock together...”  _Hydrophobic interactions most important  “The tendency of hydrocarbons to form intermolecular aggregates in an aqueous medium” o Something hydrophobic in aqueous medium have tendency to flock together  Hydrophobic side chains 'hidden' from water - Cluster together; exclude water from interior  This causes Charged side chains (which are hydrophilic) are mainly exterior  Long extended polypeptide sequence (filled balls are hydrophobic residues)  all these aggregate together (form in the center)  hydrophilic(not filled balls) stay on the outside Hydrophobic interactions continued 4 Cannabinoid Receptors THC  There is a couple of these receptors and any cannabis plant has many of them  The receptor is made primarily of alpha helices and what binds to this receptor (ligand) is THC  Primary sequence of receptor  Plasma membrane interior is hydrophobic and thus in this AA sequence, hydrophobic residues stick to hydrophobic regions which is the plasma membrane  Hydrophilic residues go to hydrophilic region  Hydrophillicity and hydrophobicity This therefore has impact on function and structure of protein ° 3 structure is stabilized by multiple weak bonds and a very important covalent bond! 5  Weak forces (other than hydrophobic interactions): - Hydrogen bonds 
 - Van der Waals forces 
 - Ionic bonds  However, one type of covalent bond 
 - Disulfide bond
 o Between cysteine residues in distant parts of the protein o Only form in oxidizing environments “weak” bonds -- Panel 2-7 Disulfide bonds Hydrogen bonds can form in many different places!  Disulfide bonds formation depends on state of oxidation and also on the fact they these bonds can Formed between two separate polypeptides or within one polypeptide  Forms intrachain disulfide bond in oxidized state which holds tertiary structure together 6 ° 3 structure: Domains  Domain is distinct region of protein that can fold independently of other regions - A critical concept for larger proteins - Definition: distinct region of a protein o Domain often can fold independently o Domains provide structure and/or function - Many proteins made up of connected domains - Related domains of
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