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109 Cards in this Set
- Front
- Back
Glucose - two forms
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B(beta)-form = CELLULOSE
a(alpha)-form = starch Beta means up position; axial Alpha means down posit; equatorial |
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Nucleic acids
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Backbone: sugar-phosphate-sugar-phosph..
Differentiation: comes from bases |
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Lipids
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have a block-like sturcutre
Nonpolar Fatty Acid chains (hydrocarbs) Polar Phospholipids together, form a bilayer w/ nonpolar tails directed away from water. |
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Years ago Earth was formed
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4.5 Billion
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Years ago Microorganisms formed
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3.5 billion
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Eukaryotes formed
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2.25 billion yrs ago
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Oxygen atmosphere formed
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1.5-2 billion yrs ago
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Early steps in Evolution
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-Prebiotic Synthesis of Molecules
-Biosynthetic Cycles began -Energy transformation/collection -Replication ---CELLULAR LIFE (the RNA world?) |
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Urey-Miller Experiment
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Illustrated that simple, prebiotic conditions can generate amino acid products.
-Reducing Atmsphere of NH3, H2, CH3, H2O -Spark -Generated Amino Acid products |
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Hammerhead Ribozyme
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-Discovery suggests that catalytic RNA molecules could have played fundamental roles in evolution of life.
-Makes plausible the idea of an early "RNA WORLD"; lifeforms depended on RNA for heredity, info storage, promotion of specific reactions. |
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Imino acid
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proline
-3 carbon cyclic side chain -still non-polar -only amino acid with side chain bonded to amino group. |
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2 Ways to make a Buffer
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Mix an Acid with its salt to get desired pH.
Mix weak acid or base w/ strong base or acid. |
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Nonpolar amino acids
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Glycine, Alanine, valine, leucine, isoleucine, methionine, proline
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only non-chiral amino acid
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glycine; not L or D
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aromatic amino acids
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phenylalanine, tyrosine, tryptophan
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Special features of Tyrosine/Tryptophan
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-kind've polar - Hydroxyl/NH groups.
-Aromatic rings contain delocalized electrons that strongly absorb UV lite. Allows determination of protein concentration in solution. (Beer's law) |
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Polar Uncharged Amino acids
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Serine, Threonine, Cysteine
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Cysteine special features
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Side chains S-H oxidize to form disulfide bonds/bridges.
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Oxidation
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Loss of electrons (H+)
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Polar Amino Acids with Basic R chains
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Lysine, Arginine, Histidine
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Polar Amino Acids with Acidic R chains
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Glutamate, Aspartate
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Nonpolar Amino Acids additional
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Asparagine, Glutamine
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Water is a Weak Acid
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just know that
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% of Other ions, metabolites in
-Total cell composition -Dry mass composition |
1%
3% |
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Major classes of biomolecules
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LIPIDS
CARBS NUCLEIC ACIDS PROTEINS WATER |
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NUCLEIC ACIDS
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DNA, RNA
Linear polymers of NUCLEOTIDES Function: Information storage, transfer |
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Proteins
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-Linear polymers of 20 different amino acids
-Chemically, structurally, functionally diverse |
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Water
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-Very small
-Highly structured intermolecular Hydrogen bonding |
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Lipids
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Small, water-insoluble molecules
-Phospholipids form extended bilayers -Structures include long chain FATTY ACIDS |
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Carbohydrates
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-Linear or branched chains of SMALL SUGARS
Functions: -Gives cells STRUCTURE -STORES ENERGY |
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ATP SYNTHASE function
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-A molecular machine
-Functions as a ROTARY ENGINE, synthesizing ATP as it spins |
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ATP Synthase Structure
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8 DIFFERENT POLYPEPTIDE CHAINS
22-24 Total Subunits -1 each: a, y(gamma) delta(d) E(epsl) -2: B -3: alpha, beta -10-12 copies of C |
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Amino Acids
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Building Blocks of Proteins.
Residues hooked together to form long polypeptide chains. |
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Dominant Amino acid conformation
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L-alpha amino acid
other is D |
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Polypeptide Backbone
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NCCNCCNCCNCC...
Nitrogen-Carbon-carbon-.... |
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Number of E.Coli bp
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4.5 x 10e6
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Number of Human base pairs
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3 x 10e9
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% water in cell composition (total)
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70%
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% water in dry mass cell composition
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0 obviously, it's dry
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% of Protein in
-Total cell composition -Dry mass cell composition |
Total = 20%
Dry = 66% |
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% of Lipids in
-Total cell composition -Dry mass cell composition |
5%
16% in dry mass |
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% of Carbohydrates in
-total cell composition -dry mass cell composition |
4%
12% |
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% of Nucleic Acids in
-Total Cell composition -Dry mass cell composition |
1%
3% |
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% of Other ions, metabolites in
-Total cell composition -Dry mass composition |
1%
3% |
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+ charged ions migrate to...
- charged ions migrate to... |
Anode - this occurs below the pI
Cathode - occurs above the pI |
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Native Protein Structure
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the particular folded structure of a protein under biological conditions
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2 Examples of Fibrous Proteins
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Collagin and Keratin
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pKr
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the acid dissociation constant of a SIDE chain on an amino acid - the r group
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Myoglobin
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compact, globular protein with 8 helical regions
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alpha Keratin
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-in hair and nails
-has long coiled helices, fibrous protein, no compact folding. -an alpha-helical coiled coil - alpha helices intertwined to form long fiber |
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4 levels of protein structure
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Primary
Secondary Tertiary Quarternary |
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Primary Protein Structure
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sequence of amino acids
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Secondary Protein Structure
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regular, local folding of peptide backbone.
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tertiary protein structure
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compact folding of a single pp chain.
-aka, domain structure. -Pp chain can have multiple domains. |
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Quaternary Protein Structure
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multiple individually folded chains (subunits) are tightly associated.
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Immunoglobulin domain
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Only Beta-barrels. No helices.
Formed of 8 pp strands. |
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Beta clamp
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A subunit of DNA polymerase
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4 Non-covalent Intermolecular Forces that stabilize Protein Structure:
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Hydrogen bonds
Ionic bonds Van der Waals forces Hydrophobic Interactions |
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Hydrogen bond
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-bond that forms between a polarized h-bond donor and H-bond acceptor with unshared electrons.
-Length: Donor-hydrogen: 0.9A Acceptor-Hydrogen: 2.0A Geometry: 180degrees SP |
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H-bond length
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2.0 A
-That's between the H and the acceptor. -Overall = 2.9 -From H-donor is 0.9 |
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Ionic Bonds/Salt bridges
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strong interaction between two oppositely charged ionic groups.
-Energy depends on distance btwn molecules, dielectric constant of the solvent. |
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Van der Waals forces
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weak nonspecific interactions from transient charge fluctuations in electron shells.
-criticaly depends on distance between atoms/groups of atoms. |
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Contact distance
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how close 2 atoms can get to each other before their van der waals forces become repulsive.
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Hydrophobic interactions
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apparent interactions between nonpolar molecules. But not really.
-Really the highly structured H-bonding of water. |
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Oil-drop effect
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To maximize energy of a system of protein and water: water-molecular surface interface is minimized by nonpolar areas aggregating. Reduces entropy, maximizes H2O's freedom to interact.
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Linus Pauling
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-discovered that peptide bond C-N is PLANAR and ALWAYS TRANS.
-has a PARTIAL DOUBLE BOND due to resonance of the pi electrons of the carboxyl group. |
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A.A. that is exception to the Always Trans, Always Planar Peptide Bond rule:
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PROLINE Energy difference is only small between trans/cis; cis has a little more steric hindrance than trans.
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He predicted 3 secondary structures of pp backbones that maximized H-bonding and had correct geometry.
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Who is Linus Pauling, 1990-1994?
That is correct. ..Paved the way for double helix.. |
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3 2ndary structures
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Alpha helix
Parallel Beta sheet Antiparallel beta sheet -All result from Hydrogen bonds |
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Alpha Helix Features
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-Each A.A. is H-bonded to 4th residue in sequence.
-3.6 residues per turn -5.4 Angstrom Pitch -R-groups (sidechains) stick out away from axis. |
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B(A) and B(P) sheets
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B(A)=Antiparallel; 2 pp chains running opposite; H-bonds are straight between corresponding residues; every other.
B(P)=Parallel; much longer than anti; -Both have repeat every 2 residues |
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Phi angle
Psi angle |
between Alpha Carbon and Nitrogen
between Alpha Carbon and Carbonyl C |
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Which is more common:
Right or Left-handed helices? |
RIGHT. Left is very rare.
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Torsional angles determine..
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Backbone conformation.
Phi and Psi |
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Myoglobin
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Structural relative of Hemoglobin
-Stores oxygen in muscles -predominantly alpha helices -1 single chain. |
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Hemoglobin
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Structural relative of Myoglobin
-transports oxygen in blood. -Tetramer - 2 alpha, 2 beta.(4 subunits) Subunits are structurally similar to myoglobin's 1 unit. (predominantly alpha helices) |
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X-ray crystallography
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1. Grow crystals
2. Collect data - send X-ray through crystals, diffract, beams go around different e- densities and film picks up remaining rays. 3. Use Diffraction Pattern 4. Get E- density map, fit molecular structure. |
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What directs tertiary folding?
(into globular proteins) |
Hydrophobic intercations.
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Oildrop Model of Globular Proteins
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Tertiary Folding; Directed by Hydrophobic interactions. Nonpolar molecules pack densely into protein's interior, polar on exterior. Minimizes surface area btwn water and nonpolar.
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Bonding that aids Tertiary folding
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H-bonds
Ionic - strong when protected from water (otherwise it hydrates them). VanderWaals - tight packing interior of protein; atoms rub shoulders. |
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Porins
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membrane proteins that have reversed distribution of polar and nonpolar groups.
-Nonpolar is EXTERIOR - hydrophobic (in contact w/ membrane) -Polar is INTERIOR - hydrophilic -creates H2O channel inside protein. |
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Not only do Myoglobin/Hemoglobin have similar tertiary folding.. also have..
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Similar amino acid sequences.. hmm what does that tell us?
-Specific amino acids can predict secondary structure AND tertiary structure. |
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What types of secondary structures do Glycine/Proline contribute to?
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SHARP TURNS.
-They're alpha helix breakers. |
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ANFINSEN
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-Demonstrated spontaneous folding of native protein globular 3ary structure.
-Used ribonuclease A, Urea, B-mercaptoethanol. |
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Ribonuclease A
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A digestive enzyme, synthesized in the pancreas.
-124 residues -8 Cysteins, with 4 Disulfide bonds. -Predominantly a B-sheet structure. |
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Protein Denaturation Reagents
(in anfinsen experiment) |
-Excess B-Mercaptoethanol.
-Urea |
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B-Mercaptoethanol
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-reduces disulfide bonds in proteins.
-used by anfinsen on ribonuclease A |
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Urea
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Disrupts H-bonding and hydrophobic interactions.
-Great h-bond former itself. -Interrupts Lattice structure of H2O - so it disrupts the hydrophobic effect. |
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Dialysis
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-removes urea from denatured proteins.
-Small molecules (MW<6000) diffuse out of porous tubing. The desired protein stays inside the tubing. |
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transmissable spongiform encephalopathies
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Mad Cow (BSE)
Scrapie (sheep) Kuru (human, New Guinea) variant Cruetzfeld-Jakob Disease (human) -Associated with PRIONS |
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Prions
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-Infectious agents
-Contain no detectable DNA or RNA -Misfolded cellular proteins in alternate conformation -Pathalogical |
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PrPc and PrPsc
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two prion structures.
PrPc = normal; 3 alpha helices PrPsc = pathogenic; 2 alpha helices, one from normal switches to Bparallel sheet that's very stable. |
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Prion Hypothesis
-why pathogenic? |
-Association of PrPsc the pathogenic form with PrPc the normal form converts the normal to pathogenic too.
-Result: neurotoxic filaments grow. -Causes: nerve cell death in CNS. |
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3 ways to seperate proteins by CHARGE
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-Gel Electrophoresis
-Isoelectric Focusing -Ion-exchange chromatography |
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3 ways to seperate protein by SIZE
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SDS-PAGE electrophoresis
Gel-filtration chromatography Sedimentation (centrifugation) |
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2 Ways to seperate proteins by BINDING
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-affinity chromatography
-immunochemical methods |
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Ion exchange chromatography
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-Column with beads (either - or +)
-Proteins bind to beads w/ opsit charge -Proteins with same charge flow through |
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2 Types Ion Exchange Chromatography
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Carboxymethyl:
- charged, binds + proteins. Diethylaminoethyl: + charged, binds - proteins. |
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Gel Electrophoresis (SDS PAGE)
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SDS - sodium dodecyl sulfate
PAGE - polyacrylamide gel electrophor. SDS creates uniform negative charge. Proteins put at top of acrylamide plate. Migrate down, according to SIZE. Smallest go fastest. |
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SDS
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sodium dodecyl sulfate
-in SDSPAGE, completely denatures all noncovalent (hydrogen) bonds in proteins - only primary sequence remains. Mercaptoethanol also reduces disulfide bonds. |
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Reagents of SDS PAGE
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SDS
Betamercaptoethanol PAGE |
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Limitation of SDS PAGE
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Completely denatures all bonds
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Isoelectric Focusing
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seperates proteins on basis of charge.
Mixture of AMPHOLYTES - many pI's. Sets a pH gradient. Add proteins; seperate as each seeks the pH of its pI. Horizontal migration |
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Proteases
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Trypsin and Chymotrypsin
-Key reagents in protein analysis -Specifically cut proteins into fragments. |
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Trypsin
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hydrolizes peptide bonds after ARG LYS
ARG LYS |
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Chymotrypsin
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hydrolyzes peptide bonds after
PHE TYR TRP |
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WHy use chymotrypsin and trypsin?
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Both cleave peptides after different residues; overlapping the cleaved fragments allows identification of similar bonds, to sequence the whole sequence.
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PITC
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edman's reagent
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Edman's Reagent
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PITC
-phenyl isothiocyanate -cleaves individual amino acids from the amino-terminal end. |