Amino Acids Proteins Part II Dr Kevin Ahern
- Slides: 44
Amino Acids & Proteins Part II Dr. Kevin Ahern
From Amino Acids to Proteins Peptide Bonds In Ribosomes Alpha Carboxyl Alpha Amine
Primary Protein Structure Linear sequence of amino acids Joined by Peptide Bonds Translated from m. RNA using Genetic Code Synthesis begins at amino end and terminates at carboxyl end • Ultimately determines all properties of a protein • •
Polypeptides Alternating Orientations of R-groups A simple view Peptide Bond Free Carboxyl Group Peptide Bond Amino Terminus Carboxyl Terminus Free Alpha Amine Peptide Bond Alternating Orientations of R-groups
Peptide Bonds Chemical Character Double Bond Behavior Alpha Carbons Usually Trans-oriented
Proteins Alpha Carbons Trans Steric Hindrance Separated bulky groups Interacting Bulky Groups Alpha Carbons Cis Separated bulky groups
Polypeptides Multiple Peptide Bond Planes Free Rotation
Phi and Psi Angles Phi Angle Psi Angle Peptide Bond Omega Angle
Ramachandran Plot Bond Angles Primary Angles of Stability
Secondary Structure Alpha Helix
Secondary Structure Alpha Helix Hydrogen bonds stabilize structure
Secondary Structure Hydrogen Bonds Beta Strands / Beta Sheets Anti-Parallel
Beta-Sheet Interactions
Secondary / Supersecondary Structures
Ramachandran Plot Labeled
Secondary Structure Fibrous Proteins • Collagen • Connective tissue • Keratin • Hair / nails • Fibroin • Silk
Collagen Primary Structure Hydroxyproline Proline in Helix Abundant Glycine Occasional Lysine Partial Sequence
Structural Proteins Keratins Fibrous 50 in Humans Intermediate Filaments of Cytoskeleton Hair, nails, horns
Fibroin Silk Beta sheets Repeating glycines
Secondary Structure Types Alpha Helix Beta Strands / Beta Helix Reverse turns (5 types) 310 Helix
Secondary Structure Tendencies of Amino Acids High Propensity for Alpha Helices High Propensity for Beta Strands High Propensity for Reverse Turns
Amino Acid Hydropathy
Soluble vs. Membrane Bound Proteins Hydrophobic Amino Acid Bias Inside Hydrophilic Amino Acid Bias Outside Hydrophobic Amino Acid Bias In Bilayer Hydrophilic Amino Acid Bias Outside of Bilayer
Metabolic Melody Oh Little Protein Molecule (To the tune of "Oh Little Town of Bethlehem") Oh little protein molecule You're lovely and serene With twenty zwitterions like Cysteine and alanine Your secondary structure Has pitches and repeats Arranged in alpha helices And beta pleated sheets The Ramachandran plots are Predictions made to try To tell the structures you can have For angles phi and psi And tertiary structure Gives polypeptides zing Because of magic that occurs In protein fol-ding Copyright © Kevin Ahern A folded enzyme’s active And starts to catalyze When activators bind into Its allosteric sites Some other mechanisms Control the enzyme rates By regulating synthesis And placement of phosphates And all the regulation That's found inside of cells Reminds the students learning it Of pathways straight from hell So here’s how to remember The phosphate strategies They turn the GPb's to a's And GSa's to b's
Reverse Turns
Tertiary Structure Folding and Turns Beta Strands Alpha Helices Random Coil Turns
Folding of a Globular Protein
Unfolding of a Globular Protein
Forces Stabilizing Tertiary Structure Hydrogen Bonds
Forces Stabilizing Tertiary Structure Disulfide Bonds (Covalent)
Forces Stabilizing Tertiary Structure
Denaturing/Unfolding Proteins Break forces stabilizing them Mercaptoethanol/dithiothreitol - break disulfide bonds Detergent - disrupt hydrophobic interactions Heat - break hydrogen bonds p. H - change charge/alter ionic interactions Chelators - bind metal ions
Denaturing/Unfolding Proteins
Folding of a Globular Protein
Energetics of Folding
Protein Structural Domains Leucine Zipper - Prot. -Prot. and Prot. -DNA Helix Turn Helix - Protein-DNA Leucine Zipper Zinc Fingers SH 2 Domains - Protein-Protein Pleckstrin Homology Domains - Signaling (Membrane) Zinc Finger Helix-Turn-Helix Leucine Zipper SH 2 Domain Pleckstrin Domains
Folding Errors
Prion Replication Model
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 (Pr. PSc)
Protein Processing Chaperonins - Proper folding - environment for hydrophobic sequences Gro. EL / Gro. EL-Gro. ES Proteasomes - Degradation to oligopeptides of about 8 amino acids each
Role of Ubiquitin Flag for protein destruction by proteasome
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
Protein Structure • Primary – Amino Acid Sequence • Secondary / Supersecondary – Repeating Structures – short range forces • Tertiary – Folded structures – longer range interactions
Metabolic Melody My Old Enzymes (To the tune of "Auld Lang Syne") Copyright © Kevin Ahern Whene’er my proteins go kaput If they are past their prime. The cells will act to soon replace All of my old enzymes They know which ones to break apart Ubiquitin’s the sign A marker for pro-TE-a-somes To find the old enzymes These soon get bound and then cut up In pieces less than nine More chopping yields the single ones Building blocks from old enzymes So in a way the cell knows well Of father time it’s true Amino acids when reused Turn the old enzymes to new
- Amino acids are joined together in proteins by
- Kevin ahern biochemistry
- Gene expression:
- Precipitation of proteins by strong mineral acids
- Ahern tractor
- Net charges of amino acids
- Serylglycyltyrosylalanylleucine
- What are enzymes made of
- Amino acid name
- Glucogenic amino acid
- Transdeamination of amino acids
- Quantitative estimation of amino acids by ninhydrin
- Aromatic amino acids
- Amino acids classification
- Adenine thymine cytosine and guanine
- Aromatic amino acids
- Urea cycle definition in biochemistry
- Deamination of amino acids
- Peptide bond dehydration synthesis
- Chemsheets a2 1102 amino acids 2 answers
- Protein amino acids
- What is made of amino acids
- Pvt tim hall
- Difference between hydrophobic and hydrophilic amino acids
- A _________bond joins amino acids together.
- Chirality definition
- Conditionally essential amino acids
- Catabolism of amino acids
- 191 amino acid
- Genetic code wheel
- Diphthamide
- Plp mechanism transamination
- Importance of sulphur containing amino acids
- Transdeamination of amino acids
- 17/35
- How many codons are needed to specify three amino acids?
- Amino acids are building blocks of
- Amino acid structure
- Phenol containing amino acids
- Glucogenesis vs gluconeogenesis
- Two amino acids joined together
- Properties of amino acids
- Optical properties of amino acids
- Protein amino acids
- Wikipedia amino acids