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BIOCHEMISTRY K384 Week 3 Notes Instructors: Dr. Brenda Blacklock; Dr. Andrew Kusmierczyk 01/23/2018 and 01/25/2018 Highlight = Important Principle or Concept Highlight = Key Term Lecture #5/Biochemistry with Dr. Kusmierczyk Anatomy of Amino Acid -Alpha carbon is Chiral -R group determines functionality “Tools”: Every ‘tool’ of an amino acid allows us to do stuff Protein Zoo → Lego (building blocks) -Conformation: “Structure” a protein can have -Arrangement of atoms in protein -Can have multiple structures -Key Points: -Proteins can have many conformations -Proteins MUST be able to change conformation to do job -Conformation determines stability of protein -Native Protein: Functional Structure folded shape ← Can have several -Non-Native State: Birth state, unfolded ← Cell wants to avoid -4 Levels of Protein Structure: -Primary -Sequence of amino acids -Individual links -Peptide Bond: Polymers of amino acids -C-N Bond: Partial double-bond characters -Rigid, planar, weak dipole, favor trans conformation -Rotation: Bonds connected to alph can rotate. -Flat. Only rotate around alpha carbons -Dihedral Angles -Phi (ɸ): Angle around alpha carbon--amide nitrogen bond -Psi (Ѱ): Angle around alpha carbon--carbonyl carbon bond -In fully extended polypeptide, both phi and psi are 180 degrees -Not all angles allowed! -Steric considerations influence what is allowed
-Ramachandran plot: Can show allowed conformations -Secondary -Local spatial arrangement of polypeptide chain -Certain chain pattern -Dependent on Backbone -Characterized by set of psi and phi values -Alpha helix and Beta sheet are most common -Alpha Helix -Simplest structure of polypeptide -Tightly Wound, no hole in the middle -Backbone on inside (R groups face out) -Right-handed -Pitch: 5.4 Angstroms ← Distance for one full turn every 3.6 amino acids -3.6 Amino Acids per turn of helix -3rd/4th residue will be on same face 5.4/3.6 = 1.5 ← Rise/amino acid Amphipathic Generate properties -Helical Wheel Diagram: Helices with two different properties - “N” Goes towards N-terminus - “O” towards C-terminus -Exist H-bonds between carbonyl “O” of n-th amino acid and amide “H” or (n+4)-th amino acid in helix -Except for near ends, all peptide bonds take part in H-bonds -Very stable structure -Helix has Dipole -Amino acids don’t all have same propensity in alpha helix -Ala = strong helix; Leu = frequent in helices -Other: Long string of Asp or Lys -Pro: Oddball. >4 (high number. Can’t form H-bond) -Gly: 4.6 kJ/mol. -Don’t memorize table on slide 19 -Why are Gly and Pro rarely found in helices? -Hint: Each secondary structure requires amino acids to adopt certain characteristics of phi/psi angles -Beta Sheets: -Made up of strands with beta conformation -More extended than alpha helices -Several strands form sheet -H-bonds occur between strands (don’t in alpha helix) -Parallel and Antiparallel -Difference in H-bond between them, but R groups always on the same side of sheet -Beta Turn -Glycine and Proline Favored -Occur when strands change direction -180 turn is accomplished over 4 amino acids
-Stabilized by H-bond from “O” of n-th redsidue to “H” amide of (n+3)-rd residue -Proline: Position 2 -Glycine: Position 3 -Found at protein surface -Why is Proline Special?- Cis conformation favored -Random Coil -When no clear defined secondary structure - “Undefined”/ “unstructured -Assessing Secondary Structure -Ramachandran plot -Know phi and psi? Can predict secondary structure -Circular Dichroism (CD) -Peptide backbone absorbs far UV light -Conformation determines how well light is absorbed -Measured as a function of wavelength. Gives curve -What to know: -Where on Ramachandran plot helices and sheets are -CD “Shape” of the three curves on Fig. 4-9 (Not the numbers, just shape) -Tertiary: -3D of secondary final structure conformation -Involve interactions between elements far away from each other in primary structure -Stabilized by many interactions -For monomeric proteins, this is final structure -Quaternary -For multisubunit proteins -Two or more polypeptides into bigger structure -Identical subunits within multisubunit Proteins -Two Major Classes Fibrous Proteins: -Insoluble. Made from single secondary structure Globular Proteins -Water-soluble globular proteins -Lipid-Soluble membraneous proteins Collagen -G-X-Y Repeats give left handed alpha chain (CHAIN not HELIX) with 3 aa/turn -Pro and 4-Hyp allow sharp twists of chain -Triple helix: Strong. 3 chains twisted around each other -Chains cross linked together -Gly allows tight packing -Lack of Vit. C = scurvy
Globular Protein -Structure not repeating -Very compact - hydrophobic interior, hydrophilic exterior -Stabilized by H-bonds, ionic interaction, S-S bonds -Diverse structure -Motif: Recognizable folding pattern found in number of proteins -Two or more secondary structure elements -Can be small and simple or large -Could be independently stable -Domain: Independently stable -Self-contained -Folds autonomously -Small proteins have 1 domain -Large protein have several - “Classes” based on motifs Alpha/beta: One part is beta and one is alpha -X-ray Crystallography: -Crystallize protein -NMR -Assign NMR signals Future: -Cryo and cryoEM (just an intro, no details to know) All proteins begin as unfolded/U/Non-native and must reach Native state/N to function Lecture 5 Expectations page Lecture #6/Biochemistry with Dr. Kusmierczyk Review -4 levels of Protein structure: Primary, Secondary, Tertiary, Quaternary -Primary: Amino acids that make up the protien -Secondary: Phi and Psi angles. Backbone -Tertiary: Final 3D structure. Highest level common to all proteins -Quaternary: For multimeric proteins only. How they can be arranged
Intro:-Residue: Individual amino acids in a chain -Unfolded to folded state of proteins. non-native/U to Native/N
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School: Indiana University Purdue University - Indianapolis
Course: Fundamentals of Biochemistry
Term: Spring 2016
Tags: biochemistry, Chemistry, Biology, Lehninger Principles of Biochemistry, and Biochemistry 1
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