Glossary of Part 1b

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Glucose - two forms
B(beta)-form = CELLULOSE
a(alpha)-form = starch

Beta means up position; axial
Alpha means down posit; equatorial
Nucleic acids
Backbone: sugar-phosphate-sugar-phosph..
Differentiation: comes from bases
Small, water-insoluble molecules
-Phospholipids form extended bilayers
-Structures include long chain FATTY ACIDS
Years ago Earth was formed
4.5 Billion
Years ago Microorganisms formed
3.5 billion
Eukaryotes formed
2.25 billion yrs ago
Oxygen atmosphere formed
1.5-2 billion yrs ago
Early steps in Evolution
-Prebiotic Synthesis of Molecules
-Biosynthetic Cycles began
-Energy transformation/collection
---CELLULAR LIFE (the RNA world?)
Urey-Miller Experiment
Illustrated that simple, prebiotic conditions can generate amino acid products.
-Reducing Atmsphere of NH3, H2, CH3, H2O
-Generated Amino Acid products
Hammerhead Ribozyme
-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.
Imino acid
-3 carbon cyclic side chain
-still non-polar
-only amino acid with side chain bonded to amino group.
2 Ways to make a Buffer
Mix an Acid with its salt to get desired pH.

Mix weak acid or base w/ strong base or acid.
Nonpolar amino acids
Glycine, Alanine, valine, leucine, isoleucine, methionine, proline
only non-chiral amino acid
glycine; not L or D
aromatic amino acids
phenylalanine, tyrosine, tryptophan
Special features of Tyrosine/Tryptophan
-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)
Polar Uncharged Amino acids
Serine, Threonine, Cysteine
Cysteine special features
Side chains S-H oxidize to form disulfide bonds/bridges.
Loss of electrons (H+)
Polar Amino Acids with Basic R chains
Lysine, Arginine, Histidine
Polar Amino Acids with Acidic R chains
Glutamate, Aspartate
Nonpolar Amino Acids additional
Asparagine, Glutamine
Water is a Weak Acid
just know that
% of Other ions, metabolites in
-Total cell composition
-Dry mass composition
Major classes of biomolecules
-Linear polymers of 20 different amino acids
-Chemically, structurally, functionally diverse
-Very small
-Highly structured intermolecular Hydrogen bonding
-Linear or branched chains of SMALL SUGARS
-Gives cells STRUCTURE
-A molecular machine
-Functions as a ROTARY ENGINE, synthesizing ATP as it spins
ATP Synthase Structure
22-24 Total Subunits
-1 each: a, y(gamma) delta(d) E(epsl)
-2: B
-3: alpha, beta
-10-12 copies of C
Amino Acids
Building Blocks of Proteins.
Residues hooked together to form long polypeptide chains.
Dominant Amino acid conformation
L-alpha amino acid
other is D
Polypeptide Backbone
Number of E.Coli bp
4.5 x 10e6
Number of Human base pairs
3 x 10e9
% water in cell composition (total)
% water in dry mass cell composition
0 obviously, it's dry
% of Protein in
-Total cell composition
-Dry mass cell composition
Total = 20%
Dry = 66%
% of Lipids in
-Total cell composition
-Dry mass cell composition
16% in dry mass
% of Carbohydrates in
-total cell composition
-dry mass cell composition
% of Nucleic Acids in
-Total Cell composition
-Dry mass cell composition
+ charged ions migrate to...
- charged ions migrate to...
Anode - this occurs below the pI
Cathode - occurs above the pI
Native Protein Structure
the particular folded structure of a protein under biological conditions
2 Examples of Fibrous Proteins
Collagin and Keratin
the acid dissociation constant of a SIDE chain on an amino acid - the r group
Structural relative of Hemoglobin
-Stores oxygen in muscles
-predominantly alpha helices
-1 single chain.
alpha Keratin
-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
4 levels of protein structure
Primary Protein Structure
sequence of amino acids
Secondary Protein Structure
regular, local folding of peptide backbone.
tertiary protein structure
compact folding of a single pp chain.
-aka, domain structure.
-Pp chain can have multiple domains.
Quaternary Protein Structure
multiple individually folded chains (subunits) are tightly associated.
Immunoglobulin domain
Only Beta-barrels. No helices.
Formed of 8 pp strands.
Beta clamp
A subunit of DNA polymerase
4 Non-covalent Intermolecular Forces that stabilize Protein Structure:
Hydrogen bonds
Ionic bonds
Van der Waals forces
Hydrophobic Interactions
Hydrogen bond
-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
H-bond length
2.0 A
-That's between the H and the acceptor.
-Overall = 2.9
-From H-donor is 0.9
Ionic Bonds/Salt bridges
strong interaction between two oppositely charged ionic groups.
-Energy depends on distance btwn molecules, dielectric constant of the solvent.
Van der Waals forces
weak nonspecific interactions from transient charge fluctuations in electron shells.
-criticaly depends on distance between atoms/groups of atoms.
Contact distance
how close 2 atoms can get to each other before their van der waals forces become repulsive.
Hydrophobic interactions
apparent interactions between nonpolar molecules. But not really.
-Really the highly structured H-bonding of water.
Oil-drop effect
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.
Linus Pauling
-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.
A.A. that is exception to the Always Trans, Always Planar Peptide Bond rule:
PROLINE Energy difference is only small between trans/cis; cis has a little more steric hindrance than trans.
He predicted 3 secondary structures of pp backbones that maximized H-bonding and had correct geometry.
Who is Linus Pauling, 1990-1994?
That is correct.

..Paved the way for double helix..
3 2ndary structures
Alpha helix
Parallel Beta sheet
Antiparallel beta sheet

-All result from Hydrogen bonds
Alpha Helix Features
-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.
B(A) and B(P) sheets
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
Phi angle
Psi angle
between Alpha Carbon and Nitrogen
between Alpha Carbon and Carbonyl C
Which is more common:
Right or Left-handed helices?
RIGHT. Left is very rare.
Torsional angles determine..
Backbone conformation.
Phi and Psi
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)
X-ray crystallography
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.
What directs tertiary folding?
(into globular proteins)
Hydrophobic intercations.
Oildrop Model of Globular Proteins
Tertiary Folding; Directed by Hydrophobic interactions. Nonpolar molecules pack densely into protein's interior, polar on exterior. Minimizes surface area btwn water and nonpolar.
Bonding that aids Tertiary folding
Ionic - strong when protected from water (otherwise it hydrates them).
VanderWaals - tight packing interior of protein; atoms rub shoulders.
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.
Not only do Myoglobin/Hemoglobin have similar tertiary folding.. also have..
Similar amino acid sequences.. hmm what does that tell us?
-Specific amino acids can predict secondary structure AND tertiary structure.
What types of secondary structures do Glycine/Proline contribute to?
-They're alpha helix breakers.
-Demonstrated spontaneous folding of native protein globular 3ary structure.
-Used ribonuclease A, Urea, B-mercaptoethanol.
Ribonuclease A
A digestive enzyme, synthesized in the pancreas.
-124 residues
-8 Cysteins, with 4 Disulfide bonds.
-Predominantly a B-sheet structure.
Protein Denaturation Reagents
(in anfinsen experiment)
-Excess B-Mercaptoethanol.
-reduces disulfide bonds in proteins.
-used by anfinsen on ribonuclease A
Disrupts H-bonding and hydrophobic interactions.
-Great h-bond former itself.
-Interrupts Lattice structure of H2O - so it disrupts the hydrophobic effect.
-removes urea from denatured proteins.
-Small molecules (MW<6000) diffuse out of porous tubing. The desired protein stays inside the tubing.
transmissable spongiform encephalopathies
Mad Cow (BSE)
Scrapie (sheep)
Kuru (human, New Guinea)
variant Cruetzfeld-Jakob Disease (human)
-Associated with PRIONS
-Infectious agents
-Contain no detectable DNA or RNA
-Misfolded cellular proteins in alternate conformation
PrPc and PrPsc
two prion structures.
PrPc = normal; 3 alpha helices
PrPsc = pathogenic; 2 alpha helices, one from normal switches to Bparallel sheet that's very stable.
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.
3 ways to seperate proteins by CHARGE
-Gel Electrophoresis
-Isoelectric Focusing
-Ion-exchange chromatography
3 ways to seperate protein by SIZE
SDS-PAGE electrophoresis
Gel-filtration chromatography
Sedimentation (centrifugation)
2 Ways to seperate proteins by BINDING
-affinity chromatography
-immunochemical methods
Ion exchange chromatography
-Column with beads (either - or +)
-Proteins bind to beads w/ opsit charge
-Proteins with same charge flow through
2 Types Ion Exchange Chromatography
- charged, binds + proteins.

+ charged, binds - proteins.
Gel Electrophoresis (SDS PAGE)
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.
sodium dodecyl sulfate
-in SDSPAGE, completely denatures all noncovalent (hydrogen) bonds in proteins - only primary sequence remains. Mercaptoethanol also reduces disulfide bonds.
Reagents of SDS PAGE
Limitation of SDS PAGE
Completely denatures all bonds
Isoelectric Focusing
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
Trypsin and Chymotrypsin
-Key reagents in protein analysis
-Specifically cut proteins into fragments.
hydrolizes peptide bonds after ARG LYS

hydrolyzes peptide bonds after
WHy use chymotrypsin and trypsin?
Both cleave peptides after different residues; overlapping the cleaved fragments allows identification of similar bonds, to sequence the whole sequence.
edman's reagent
Edman's Reagent
-phenyl isothiocyanate
-cleaves individual amino acids from the amino-terminal end.

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