BIOL 4350 Study Guide - Comprehensive Midterm Guide: Alpha Helix, C-Terminus, N-Terminus

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7 Feb 2017
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BIOL 4350
MIDTERM EXAM
STUDY GUIDE
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JANUARY 20 Slides 1-28 LECTURE 2
Atoms of life
- H, O, N, C make up 99% by weight
o Smallest atoms that can share 1, 2, 3, 4 electrons respectively
o O, N, C are the only elements that can form strong covalent bonds
Electronegativity
- Tendency of an atom to hog electrons in a covalent bond
- Increases in atoms as you go up and across (to the right)
- O>N>S>C=H
- Determines what kind of bonds will form between the 2+ atoms
o Covalent bonds
Around 0.1nm or 1 angstrom
o Noncovalent bonds
Interactions between two molecules and allows for dynamic movement
Hydrogen bonds-weak noncovalent bond
Bond between 2 atoms
(Between N and O)
attracted to one another
electrostatically
Donor bond: donates the
hydrogen to the bond
Acceptor atom: accepts
the hydrogen from the
donor bond
Around 0.3 nm or 3
angtrom
o The distance between the H and acceptor must be at least 0.5
angstrom shorter than the van der Waals distance
Van der Waals distance= point at which 2 atoms begin
repelling each other defined by the radii of the atoms
Amount of space that an atom takes up
Van der Waals distance of H + vdw of O 0.5angstrom=H-
bond
Van der Waals interactions
Very weak attractive forces that occur when 2 nonpolar atoms approach
each other
Transient dipoles form (weak)
Water
- Unbonded electron pairs push the hydrogens together
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JANUARY 20 Slides 1-28 LECTURE 2
- How many H bonds can water form? 4
o Both the 2 hydrogens and the 2 lone pairs can form hydrogen bonds
- Hydrogen bonds are constantly forming and breaking in H bonds
- In order to change the temperature of water, you need to first break the H-bonds
o High specific heatstabilizes temperatures for the numerous biochemical reactions
- Water
o Forms around 3.4 H-bonds/molecule when in liquid form
- Ice
o Molecules orient so that they can form 4 H-bonds/ molecule
o Takes up more space and is less dense than water
- Water of solvation
o Waters that surround ions and are less fluid than other water
o Remove waters of solvation in order to allow 2 molecules to interact
o Water can act as a pipe to transport protons to another side of a molecule
- Hydrophobic effect
o Nonpolar molecules are shoved together in the presence of water
Minimize size of the cage in order to maximize the space that the water molecules
surrounding the cage can move around more freely
o Works because entropy
Cage of water molecules form around a nonpolar molecule
Cage is forms similar to waters of solvation
- Water Ionization
o Water can have a proton dissociate from it
Forms hydronium ion (H+) and a hydroxide ion (OH-)
o Does not happen a lot
o Water is a weak acid
o pH= -log[H+] which scales acidity from 0 to 14
acid: gives up a proton
base: takes up a proton
every factor of 2 difference in [H+]=03 pH units
o a oe through a proto ire y proto hoppig
extremely quick reaction
- Buffer
o Minimizes the change in pH if you add free acid or free base
o Ex: Acetic Acid
o For the amount of free proton added to the
solution
The pH becomes lower
????
o most buffers are weak acids
o alternately pick up or give up a proton
o pKapH at which something is 50% ionized or dissociated (amount of nondissociated acetic
acid is equal to the amount of acetate)
buffering region: +/- 1 pH unit away from the pKa
anything that is ionizable in water has a pKa for that specific molecule
o pH=pKa + log [A-]/[HA]
Amino Acid
- N-C-C (amino group-alpha carbon (with 1 H and side chain)-carboxyl group)
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