COMPLETED HOMEWORK

July 6, 2011
Focus on Essential Amino Acids
o R-Groups (Categorizations)
Proteins are polymers of amino acids, with each amino acid
residue joined to its neighbor by a specific type of covalent
bond (Peptide Bond)
All 20 of the common Amino acids are Alpha Amino Acids.
They have a carboxyl group and an amino group bonded to the
same carbon atom, which is called the Alpha carbon. The 20
common Amino Acids differ from each other in their side
chains, R-Groups.
The Alpha carbon is a chiral center because it is bonded to 4
distinct groups therefore amino acids can have two possible
stereoisomers(enantiomers because they are non-
superimposable mirror images).
Nonpolar, Aliphatic Amino Acids
Non-polar and Hydrophobic. Tend to cluster together
within proteins, stabilizing protein structure by means
of hydrophobic interactions.
Glycine-Gly-G
Alanine-Ala-A
Proline-Pro-P
Valine-Val-V
Leucine-Leu-L
Isoleucine-Ile-I
Methionine-Met-M
Aromatic Amino Acids
Are relatively Non-Polar and Hydrophobic. All can
participate in Hydrophobic Interactions. The Hydroxl
group of Tyrosine can form Hydrogen Bonds
Phenylalanine-Phe-F
Tyrosine-Tyr-Y
Tryptophan-Trp-W
Polar, Uncharged Amino Acids
The most Hydrophillic R-groups.
The R-groups of these amino acids are more soluble in
water and are more Hydrophillic because they contain
functional groups that can hydrogen bond with water.
Serine-Ser-S
Threonine-Thr-T
Cysteine-Cys-C
Asparagine-Asn-N
Glutamine-Gln-Q
Positively Charged Amino Acids
The Most Hydrophillic R-Groups
Lysine-Lys-K
Histidine-His-H
Arginine-Arg-R
Negatively Charged Amino Acids
Aspartate-Asp-D
Glutamate-Glu-E
o Be able to take any typical amino acid and draw it
o Amino and Carboxyl groups at different pHs( pH-1, pH-3, pH-7, pH-9..)
o pKa that we will typically use for an alpha carboxyl group is 2.3
o pKa that we will typically use for an alpha amino group is 9.7
Carboxyl or Amino Groups on R-Groups will most likely be
higher than pKas of their alpha carbon counterparts. (Know
Why)
o Focus on Henderson-Hasselbach Equation
Purpose and how it relates to amino acids
Important for understanding buffer action and acid-
base balance in the blood and tissues of vertebrates.
Buffers
Are aqueous systems that tend to resist changes in pH
when small amounts of acid or base are added within a
certain range. A buffer system consists of a weak acid
and its conjugate base. Buffering results from two
reversible reaction equilibria occurring in a solution of
nearly equal concentrations of proton donor and its
conjugate proton acceptor. Whenever H+ or OH- is
added to a buffer the result is a small change in the ratio
of the relative concentrations of the weak acid and its
anion and thus a small change in pH. The decrease in
concentration of one component of the system is
balanced exactly by an increase in the other. The sum of
the buffer components does not change, only their ratio.
Each conjugate acid-base pair has a characteristic pH
zone in which it is an effective buffer.
o Focus on the Internal Environment
What do we mean?
The extracellular fluid is also called the Internal
Environment. In the extracellular fluid are the ions and
nutrients needed by the cells to maintain cell life. All
cells live in essentially the same environment.
Extracellular fluid is in constant motion throughout the
body. About one third of human body fluid is
extracellular. Most fluid is intracellular.
Homeostasis
Used by physiologists to mean maintenance of nearly
constant conditions in the internal environment
Draw a Biological Membrane
Extracellular Vs. Intracellular Environments
Extracellular Environment contains 1/3 of bodily fluid
Intracellular Environment contains 2/3 of bodily fluid
Extracellular Environment contains the ions:
o Sodium
o Chloride
o Bicarbonate ions
o Oxygen
o Glucose
o Fatty Acids
Intracellular Environment contains the ions:
o Potassium
o Magnesium
o Phosphate
Extracellular fluid is transported through all parts of the
body in two stages


July 7, 2011
What is the difference between ionic and electrostatic?
o Both Ionic and Electrostatic interactions refer to the interaction
between similarly or oppositely charged molecules. Attractions and
repulsions based on their charges.
What is the Hydrophobic Effect?
o The Hydrophobic Effect is the observed tendancy of nonpolar
molecules to aggregate in aqueous solution.
What are the 4 Levels of Protein Structure
o Primary
The amino acid Sequence of the Polypeptide Chain
o Secondary
The local conformation of some part of the polypeptide
o Tertiary
The arrangement of all of the proteins atoms in space by the
atomic coordinates
o Quaternary
The arrangement of a protein molecules subunits in space
Subunits(multiple folded proteins or coiling proteins)
Ensemble of inter-subunit interactions
What are the 4 Weak Interactive Forces
o Hydrogen Bonds
Attractive force between a Hydrogen atom and an
Electronegative atom such as F,O, or N.
Between Neutral groups or peptide bonds
o Ionic Interactions
Attractions or Repulsions between ions within molecules
o Van Der Waals Interactions
The sum of attractive or repulsive forces between molecules
other than those due to covalent bonds or to electrostatic
interactions. (any two atoms in close proximity)
o Hydrophobic Interactions
The forces causing nonpolar molecules to aggregate within an
aqueous solution
Collagen
o Primary
Repeating Sequence of Gly-X-Y
X: Proline ; Y: Hydroxyproline
o Secondary: Elongated Left Handed Helix