av Eliana Carter 4 år siden
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Significant Cys content
Hair, Claws, Outer Epidermal Layer
Interactions between polypeptide chains
Independently Folding Regions (domains)
Distinct Interactions
Type I occur 2x more frequently than Type II
Hydrogen bond between the peptide bonds of 1st and 4th residues
Type II have Gly in 3rd position
Glycine: small side chain allows for tight corners
Proline are preferred in 2nd position
Proline: conformationally restricted with fixed phi angle keeps turn rigid
Extended chains
Peptide chains align side-by-side
Parallel and Antiparallel
Amide groups Hydrogen bond
Extended peptide anions- pleated geometry
Planar peptide bonds are in the pleat
R-groups alternate (up, down, up, down..)
At Carbons are the apices
Geometry
This allows for helix faces
Charged: helix with a string of similarly charged residues
Amphipathic: hydrophobic face and hydrophilic face
There are 3.6 residues per turn- roughly every 3rd to 4th residue will be on same face
All side chains point outward from core
Very compact structure
Stabilized by intramolecular Hydrogen bonds between peptide bonds
Peptide "backbone" is the core of the coil
R-groups protrude outwards
Right-handed twist
Chain is coiled like a spring
Proteins may fold in one environment, then move to another environment
Other proteins can help fold the protein
Proteins start to fold before they are completely made
Denatured state is less stable
Hydrophobic Interactions: Drive burial of hydrophobics in the protein interior
London Dispersion Forces: Between hydrophobic residues in the protein interior
Ionic Interactions: Acidic and Basic groups (e.g. Asp-Lys)
Hydrogen bonding: Inter- and Intramolecular Hydrogen bonds
They help overcome energy barriers or alter salvation to change the folding landscape
Guanidine
Urea
Enthalpy
Spectral
Fluorescense
Circular Dichroism
Secondary structures are unique arrangements of chiral centers leading to unique spectra
Unique absorption of circularly polarized light
No direct image of protein is obtained, just a series of spatical constraints
Complicated
Only small proteins can be studied
Dynamics of protein-ligand interactions
Motional dynamics of whole molecule
Protein is in solution
Solution conditions are not "native"
Crystal contacts can distort important regions of proteins
Structure is static
Proteins must crystallize; not aqueous structure
Large proteins and protein complexes
Very High resolution - 1.5 A
PolyT
Elution: Free Thymine
Immobilized PolyT
Purpose: mRNA purification
His Tag
Elution: High imidazole in elution buffer
Imidazole chelates Ni 2+ on column, so His-tagged protein sticks on column
Proteins are engineered to have a His6 sequence
Ni 2+ is immobilized on column
Engineered into gene sequence
Cation Exchange
Wash off impurities (-) and neutral impurities
Choose buffer so analyte is (+) charged
Cations stick to (-) charged column
Anion Exchange
Elute analyte with High salt or basic conditions (deprotonates analyte)
Wash off impurities (+) and neutral impurities
Equilibrate column then adsorb analyte to column
Choose buffer so analyte is (-) charged
Anion stick to (+) charged column
Separates based on size
Exchanges buffer components between sample matrix and column buffer
No adhesion to the stationary phase
Large molecules are more often in flow path, so they elute first
Small molecules explore internal space and are out of flow path
Porous particles
Membrane Components
Soluble Proteins
Isopycnic Centrifugation
Takes a sample and the more dense component settles to the botton while the least dense component floats in the center
Differential Centrifugation
Left with pellets containing ribosomes and large macromolecules
Keeps breaking up the materials so that they become soluble proteins
Spins very fast and separates organelles
Water forms cages around hydrophobics (antiparallel orientation of water dipoles); Very LOW Entropy of solvent
Decrease in entropy of water drives the burial of hydrophobic surface area
Hydrophobic groups condense. Preleases trapped water to bulk
Micelle forms. Water released to bulk solvent
Micelle formation: High Entropy of solvent
Biomolecule
Fatty Acid
Micelle
Globular Protein
Hydrophobic amino acids interact in center of proteins
Hydrophobic tails in center of the micelle interact with London Dispersion Forces
Always attractive interactions
Weak, local interactions between the fluffy, deformable electron clouds of hydrophobic groups
Occur in the absence of water
Favorable Interactions between hydrophobic molecules
Critical for folding and function of biological molecules
Like charges attract and opposite charges repel
Charged side chains and Nitrogen and Carbon termini
Water is dipole
Orients Hydrogen toward anions and Oxygen toward cations
Makes ATP and reduced conenzymes
Degradative
Oxidative
More bonds to Oxygen
Reductive
More bonds to Hydrogen
Uses ATP and reduced coenzymes
Eat
Synthetic
Free Energy (delta G)
Excess Energy that can be used as work or heat
Equilibrium
Dynamic interconversion of products and reactants
"How far?"
Heat, work, and energy of chemical reactions
Enzymes Stabilize Transition State conformation
Activation Energy (delta G+)
Energy required to overcome the Activation Barrier
Activation Barrier
Determined by energy of Transition State
Transition State:
Intermediate between substrate and product
Unstable
Distinct conformation
Ice cap on large or moving bodies of water
Temperature of water below ice is buffered from subzero air
Water doesn't freeze through
Terrestrial Animals
Internal water buffers extremes of temperature
Cell wall
Plasma Membrane
Chromatin
Cell Wall --> Cellulose
Plasma Membrane --> Protein
Chromatin --> DNA
Cellulose --> Sugars
Protein --> Amino Acids
DNA --> Nucleotides
~3000 are expressed in all cells
20,000 to 24,000 genes
Peripheral
Integral
Fluid Mosaic Model
Fat Soluble Materials
Signaling Lipids
Receptors
Phosphoglycerides
Phosphate
Glycerol
Noncovalent Bonds
Ionic Interaction
Hydrophobic Interaction
Van der Waals Interaction
Dipole-Dipole Interaction
Ion-dipole Interactions
Hydrogen Bonds
Good Solvent, Bad Solvent
Ice Floats
Polar, Dipole
Cholesterol
Sphingolipids
Phosphoacylglycerol
Lard - TAGs in animals - saturated FAs
Oils - TAGs in plants - unsaturated FAs
Storage in Adipose
FAs esterified to glycerol
Fatty Acids
hemiacetals and acetals
Glycosidic bonds
Monosaccharides
Phosphodiester
Ribophosphate backbone
Nucleotides
Amino Acids
R= side chains
20 common acids
folded complex structures
3 or 4 degrees structures
Glucose
Starch
Ate and Digested
Anabolism
Catabolism
Animals
Synthesis of digestive enzymes
Pro-peptidases/ Peptidases
Pro-elastase/ Elastase
Chymotrypsinogen/ Chymotrypsin
Trypsinogen/ Trypsin
Triacyglycerol
Pancreatic Lipase
Hormones
Bile acid synethesis
Bile Salts
Enzymer
Harvesting
Adsorption of small molecules
Transporters
Intestinal lining
Digestion of Fats
Pancreatic Lipase (+Colipase)
Bile Acids
Liver
Pancreatic Enzymes
Zymogens
Neutralization
Zymogen/Protease
Activation by acid
Protease- Enzyme that hydrolyses peptide bonds (Pepsin)
Zymogen- Inactive precursor protease (Pepsinogen)
Hydrolyze peptide bonds
Pepsinogen/Pepsin
Acidic Conditions
Strong Acid
Activates pepsinogen to pepsin in stomach
Unfolds proteins
Acidifies chewed food entering stomach
Completely dissociates
Cells in stomach lining secrete HCl
Stomach lining epithelium is protected from acid by mucins
Secreted after meal is eaten
Peptide bonds
Amides
Stable polymers folded into complex structures
Purpose
Digestion of Proteins
Homogenization
Acid
Saliva
pH
Enzymes
Amylase
Proteins
Mucopolysaccharides
Antimicrobials
Enzymes that degrade or poison microbes
Teeth
Chewing
