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Biochemistry Free For All
Protein Structure Biochemistry Free For All
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From Amino Acids to Proteins
Peptide Bonds Alpha Carboxyl Alpha Amine In Ribosomes
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Primary Protein Structure
Linear sequence of amino acids Joined by Peptide Bonds Translated from mRNA using Genetic Code Synthesis begins at amino end and terminates at carboxyl end Ultimately determines all properties of a protein
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Polypeptides Alternating Orientations of R-groups A simple view
Peptide Bond Free Alpha Amine Free Carboxyl Group Amino Terminus Carboxyl Terminus
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Peptide Bonds Double Bond Behavior Alpha Carbons Usually
Chemical Character Double Bond Behavior Alpha Carbons Usually Trans-oriented
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Proteins Alpha Carbons Trans Interacting Bulky Groups
Separated bulky groups Proteins Alpha Carbons Trans Steric Hindrance Interacting Bulky Groups Alpha Carbons Cis
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Polypeptides Multiple Peptide Bond Planes Free Rotation
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Phi and Psi Angles Peptide Bond Omega Angle Psi Angle Phi Angle
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Ramachandran Plot Bond Angles Primary Angles of Stability
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Secondary Structure Alpha Helix
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Secondary Structure Alpha Helix Hydrogen bonds stabilize structure
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Secondary Structure Anti-Parallel Parallel Hydrogen Bonds
Beta Strands / Beta Sheets Anti-Parallel Parallel
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Beta-Sheet Interactions
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Secondary / Supersecondary Structures
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Ramachandran Plot Labeled
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Secondary Structure Collagen Keratin Fibroin Connective tissue
Fibrous Proteins Collagen Connective tissue Keratin Hair / nails Fibroin Silk
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Partial Sequence Collagen Primary Structure Hydroxyproline
Proline in Helix Abundant Glycine Occasional Lysine
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Keratins Structural Proteins Fibrous 50 in Humans
Intermediate Filaments of Cytoskeleton Hair, nails, horns
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Fibroin Silk Beta sheets Repeating glycines
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Secondary Structure Types
Alpha Helix Beta Strands / Beta Helix Reverse turns (5 types) 310 Helix
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Secondary Structure Tendencies of Amino Acids High Propensity for
Alpha Helices High Propensity for Reverse Turns High Propensity for Beta Strands
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Amino Acid Hydropathy
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Soluble vs. Membrane Bound Proteins
Hydrophobic Amino Acid Bias Inside Hydrophilic Amino Acid Bias Outside Hydrophilic Amino Acid Bias Outside of Bilayer Hydrophobic Amino Acid Bias In Bilayer
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Reverse Turns
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Tertiary Structure Random Coil Turns Beta Strands Alpha Helices
Folding and Turns Beta Strands Alpha Helices Random Coil Turns
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Folding of a Globular Protein
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Unfolding of a Globular Protein
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Forces Stabilizing Tertiary Structure
Hydrogen Bonds
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Forces Stabilizing Tertiary Structure
Disulfide Bonds (Covalent)
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Forces Stabilizing Tertiary Structure
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Denaturing/Unfolding Proteins
Break forces stabilizing them Mercaptoethanol/dithiothreitol - break disulfide bonds Detergent - disrupt hydrophobic interactions Heat - break hydrogen bonds pH - change charge/alter ionic interactions Chelators - bind metal ions
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Denaturing/Unfolding Proteins
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Folding of a Globular Protein
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Energetics of Folding
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Protein Structural Domains
Leucine Zipper Protein Structural Domains Leucine Zipper - Prot.-Prot. and Prot.-DNA Helix Turn Helix - Protein-DNA Zinc Fingers SH2 Domains - Protein-Protein Pleckstrin Homology Domains - Signaling (Membrane) Leucine Zipper Zinc Finger Helix-Turn-Helix SH2 Domain Pleckstrin Domains
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Folding Errors
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Prion Replication Model
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Amyloids and Disease Amyloids - a collection of improperly folded protein aggregates found in the human body. When misfolded, they are insoluble and contribute to some twenty human diseases including important neurological ones involving prions. Amyloid diseases include (affected protein in parentheses) - Alzheimer’s disease (Amyloid β) Parkinson’s disease (α-synuclein) Huntington’s disease (huntingtin), Rheumatoid arthritis (serum amyloid A), Fatal familial insomnia (PrPSc)
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Protein Processing GroEL / GroEL-GroES
Chaperonins - Proper folding - environment for hydrophobic sequences GroEL / GroEL-GroES Proteasomes - Degradation to oligopeptides of about 8 amino acids each
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Role of Ubiquitin Flag for protein destruction by proteasome
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Intrinsically Disordered Proteins
Not all proteins folded into stable structures Intrinsically Disordered Proteins (IDPs) have regions favoring disorder IDP regions tend to lack hydrophobic residues Rich in polar amino acids and proline IDPs may favor adaptation to binding another protein IDPs may favor being modified IDPs may be more involved in signaling and regulation Non-IDPs more involved in catalysis and transport Metamorphic Proteins May adopt more than one stable structure Lymphotactin - monomeric receptor. Binds heparin as dimer
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Protein Structure Primary – Amino Acid Sequence
Secondary / Supersecondary – Repeating Structures – short range forces Tertiary – Folded structures – longer range interactions
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