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TA Freyr Petursson
Monday 5PM Section
Office Hours : 2:15 – 3:15 S&E Library (Main Floor)
Week 2 Handout
Weak interactions (Non-Covelent) – 4 types.
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1.) ________________
a. Need Donor + Acceptor
2.) ________________
a. Attraction = between opposite charges
b. Repulsion = same charges.
3.) ___________________
4.) __________________ = two atoms in close proximity.
Individually these forces are much weak, but many hundreds can add up to be as strong as covalent bond.
o Electrostatic + Hydrogen bonds are on the order of _____ Kj/Mol with Van der Walls significantly
weaker >___Kj/Mol
o A covalent bond is aprox. 80Kj/mol
True or false – H- bonds can only form between water molecules?
Water, Hydrogen Bonding, and Hydrophobic Interactions
Water’s _____ and _______ allow it to form __________ bonds which are central to the behavior of
macromolecules dissolved in it.
When lipids are placed in a water solvent the corresponding effect is that water forms a hydration shell
around the lipid. This highly ordered water shell results in decreasing the entropy of the water, which is
highly energetically unfavorable.  The universe favors increased entropy (disorganization).
The number of ordered water molecules, and therefore the magnitude of the entropy decrease, depends
on the surface area of the hydrophobic molecule enclosed with the cage of water. I.e. more lipid surface
area = more organized water = less entropy which is energetically un favorable.
Water is capable of many reactions
o Hydro/dehydration reactions
o Electron transfer reactions
o Proton transfer reactions
o And Origin of Cavities : Creation of water-free microenvironments
___________________- the clustering of lipids and exclusion of water. -> spontaneous, requires no energy.
Substrate – enzyme complexes can be driven by this force.
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Binding of a substrate to an enzyme releases the ordered water shell which is energetically favorable, and
therefore drives this interaction spontaneously.
____________________ – substances that contain polar or charged and non-polar regions.
Protein and Amino acid structure
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The R group the variable part of amino acids.
The central carbon is the alpha carbon and has a chiral center.
All biological amino acids are in the L- form.
Amino acids are always read amino terminus to the carboxyl terminus.
_______________________ – both the amino terminus and the carboxyl terminus is in its charged form.
Predominates a neutral pH in biological systems.
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I.
Main Chain or backbone of proteins are repeating units of peptide bonds. Basic unit = (NH-CαHC=O).
Side chains or R-Groups are what introduce the different chemistries.
AMINO ACID REVIEW – (write three letter, one letter code and charge, and which ones have sulfur.)
a.) Non-polar hydrophobic
1. )
2.)
3.)
4.)
5.)
6.)
(why is proline special)
7.)
8.)
(why is glycine special)
b.) Polar charged
1.)
2.)
3.)
4)
c.) Polar uncharged (which contain a hydroxyl or sulfhydral in their R groups)
1.)
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2.)
3.)
4.)
5.)
6.)
7.)
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Disulfide bridges from Between 2 ________________ Residues
o R-SH + R-SH ->oxidation-> R-S-S-R
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II.
Disulfide bridges require an ________________ environment that is why intracellular
disulfide bonds are rarely found (Cytosol is a reducing environment) and extracellular
disulfide bonds are frequently found.
Disulfide bridges introduce ______________ to the 3-D structure, and can hold different
polypeptide chains together.
Smaller proteins typically have more commonly have more disulfide bonds.
RAMACHANDRAN PLOT
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Shows various allowable L-Ala phi + psi angles of secondary structure.
Expections, ___________ and _________________.
Can be used to double check work when solving protein structure.
What is the main force that restricts the free rotation of phi and psi angles?
Vocabulary and standard units
1 Angstrom equals_______ meters. One Carbon – Carbon bond is about _____Angstroms. Unit of mass used
from proteins is ____________ and one amino acid is average mass is equal to ______ Daltons. Therefore a
60 amino acid long protein would equal ______ daltons
Interactions between AAs are (covalent/non-covalent) interactions, while the interactions between proteins
are (covalent/non-covalent) .
Proteins are written and numbered from the _______ to the _______ terminus.
Important : Function of a protein depends on its 3-D structure and the 3-D structure of a protein is
determined by the __________________________, (which is determined by the DNA sequence) and
__________________
1 °Primary: simple a.a. sequence read and numbered from _____ to________ terminus.
2° Secondary: recurring structural patterns or folding motifs.
Main chain is hydrophilic; interior of protein is hydrophobic. Secondary structure satisfies/optomizes the hydrogen
bonding requirements on the hydrophilic main chain.
Two Types of secondary structures are _ _______ and ____ ____.