1 survey of biochemistry proteins and biomolecular stability
TRANSCRIPT
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SURVEY OF BIOCHEMISTRY
Proteins and Biomolecular Stability
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Protein Structure
• Primary (1°): amino acid sequence
• Secondary (2°)– Alpha Helix– Beta Sheet
• Tertiary (3°)
• Quaternary (4°)
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Primary and Secondary Structure
Myoglobin - 2V1K Superoxide Dismutase - 1XSO
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Recap
• Structures of 20 amino acids
• pKa and pI
• 1°: Polypeptide Sequence
• 2°: Secondary Structures– Alpha Helices – Beta Sheets
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Recap continued
• Protein Purification Methods– Gel Filtration– Ion Exchange– Affinity
• How to assess purification?– Purity – Yield
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SDS-PAGE
• Electrophoresis: a method for separating molecules based on size and charge when exposed to an electric field.
Name “SDS-PAGE”:
SDS = sodium dodecyl sulfate
PAGE = polyacrylamide gel electrophoresis
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Sodium Dodecyl Sulfate
SDS confers negative charge on proteins and denatures proteins
Sodium Dodecyl Sulfate(Lauryl Sulfate)
CH3(CH2)11OSO3
Amphiphilic
Hydrophilic Hydrophobic
Anionic Detergentin a wide variety of products
Proteins are primarily denatured by boiling them
prior to electrophoresis!
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Buffers maintain pH control Allow gel to fully polymerize
Stacking Gel
0.5M Tris-HCl
pH 6.8
Resolving Gel
1.5M Tris-HCl
pH 8.8
SDS-PAGE Buffers
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Ensure that sample has fully dentured!
Stacking Gel
0.5M Tris-HCl
pH 6.8
Resolving Gel
1.5M Tris-HCl
pH 8.8
In the Gel In the Sample
Laemmli Sample
Buffer
0.5M Tris-HCl,pH 6.8
SDS
Glycerol
Bromophenol Blue
Sample Preparation
Boil Sample for 1-5 min
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Electrophoresis Buffer
H3N-CH2-COOH+
AcidicForm
H3N-CH2-COO+ -
ZwitterionicForm
BasicForm
H2N-CH2-COO -
FullyProtonated
Loss of 1Proton
Loss of 2Protons
Tris Base, Glycine, SDS
Electrophoresis Buffer
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Stacking Gel0.5M Tris-HCl
pH 6.8
Resolving Gel1.5M Tris-HCl
pH 8.8
In the Gel
H3N-CH2-COO
H2N-CH2-COO
+ -
Zwitterion Form
-
Basic Form
SDS-PAGE
Gly lags
Gly leads
Note: Discontinuous SDS-PAGE is depicted here!
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12+
-
Migration in an SDS-PAGE Gel
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Migration in an SDS-PAGE Gel
Stop electrophoresis when dye front reaches
bottom of gel
Stain with Coomassie
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Purity
• Purity is a measure of how undefiled a protein sample is.
Lots of impurities
Pure protein
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Yield
% Yield =Amount of protein recovered
Amount of protein initially
Example:
1
2
3
% Yield = (208 / 358.2) x 100 = 58.1%After 2 steps of purification
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Protein Sequencing
• Separate subunits
• Dansyl Chloride Reaction
• Proteolytic Digestion
• Cyanogen Bromide Cleavage
• Edman Degradation
Read on yourown!
Study how each works!
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How to separate subunits?
Dithiothreitol, DTT 2-Mercaptoethanol
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Proteolytic Digestion
Know this!
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Proteolytic Digestion
How many fragments would result from digestion with trypsin?
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Proteolytic Digestion
Trypsin cleaves after Lys (K) and Arg (R):
16 fragments!
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Protein Structure Classifications
• 1°: amino acid sequence
• 2°: local spatial arrangement of a polypeptide backbone without regard for side chains
• 3°: 3D structure of a protein including its side chains
• 4°: spatial arrangements of subunits
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Tertiary Folds
Alpha Beta
Some proteins only have
alpha helices (plus turns and random coils).
Others only have beta
sheets (plus turns and random coils).
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Alpha/Beta Tertiary Folds
Some proteins have a combination of alpha
helices and beta sheets(plus turns and random
coils).
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Biomolecular Stability
Nucleic acids and proteins are stabilized by the same types of intermolecular forces.
Hydrophobic Effect: the tendency of water to minimize its contact with
hydrophobic groups in molecules.
How does the hydrophobic effect impact proteins and nucleic acids?
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Entropy
Entropy measures the spontaneous dispersal of
energy:
how much energy is spread out in a process
-or- how widely spread out it becomes — at a specific
temperaturehttp://www.entropysite.com
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Entropy & the Hydrophobic Effect
How is entropy increased by the hydrophobic effect?
http://www.cryst.bbk.ac.uk/PPS2/projects/day/TDayDiss/Major.html
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How do bond energies compare?
Type of Bond Bond Strength (kJ/mol)Covalent 348 - 460 Ionic Interaction 86Hydrogen Bond 20Dipole-dipole 9.3London Dispersion 0.3
Table 2-1
Relatively speaking, H-bonds are weak,but they are not nearly as weak as one might expect!
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Why Do Base Pairs Stack?
ENTROPY
Hydrophobic effect induces release of
water “binding” to DNA bp’s such that the hydrophobic ring
systems can stack on top of each other to
minimize contact with water.
Consider the magnitude of stacking
energy…Etc.
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Forces Stabilizing Biomolecule Structure
Proteins Nucleic Acids
Hydrophobic Effect Hydrophobic Effect Globular shape Base Stacking
Disulfide Bonds
H-Bonds H-bonds Alpha Helices Base Pairing Beta Sheets
Ionic Interactions Ionic Interactions Salt Bridges Metal Ions