If a plant is grown in soil with very little phosphate, what component of the plant cannot be synthe

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If a plant is grown in soil with very little
phosphate, what component of the plant cannot be
synthesized?

• Carbohydrates (cell walls)
• Nucleic acids (DNA)
• Proteins (enzymes)
• Lipids (steroids)

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Water is important to the cell

• 70 by weight, 99 by molarity. Why?
• Molecules are either soluble in water
  (hydrophilic) or not soluble in water
  (hydrophic).
• Water forms H bonds (shares H) with itself or
  with other electronegative atoms (O, S, N)

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Water is a solvent for polar molecules
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Phospholipids have two ends. The head is soluble
in water, the tail is not. (They are said to be
amphipathic) How do phospholipids behave in
water?

• They dissolve in water
• They do not dissolve in water
• They form water soluble aggregates (micelles)

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Water in and out of the cell
link
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pH -log10 H
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What is the proton concentration of blood
compared to stomach fluid?

• 7 X greater
• 7X less
• 10 million times greater
• 10 million times less

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Water Dissociates H20 OH- H
hydroxyl ion hydrogen ion (proton)
H30
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What is the ratio of H to H2O at pH 7?

• Answer is the molar concentration of H divided
  by the molar concentration of H20.
• Molar concentration of H is 10-7 M.
• Molar concentration of H20 is 1000 g/l /18g/mole
  55.6 M
• 10-7 moles/liter / 55.6 moles/liter 1.8 x 10-9
• Two per billion

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10-8 M HCl has a pH of 8

• True
• False

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Conjugate acid
Conjugate base

• pKa is the log10 of the equilibrium constant
  for the dissociation of HA.
• pKa is that pH at which the ionized and
  unionized forms are in equal concentration. The
  lower the pKa, the stronger the acid

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Derivation of the Henderson-Hasselbach equation
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Buffers are most effective at their pKa
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Which amino acid has an ionizable side chain?

• A
• B

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What is the pKa of the ionizable side chain?

• 1.6
• 6.0
• 9.2
• insufficient data

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The alpha carbon is chiral
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Could proteins have evolved containing only D-
amino acids?

• Yes
• No

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Proteins contain only L-amino acids. Could
proteins have evolved containing both D- and
L-amino acids?

• Yes
• No

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Histidine is an essential amino acid
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Is the (green) side chain

• Hydrophilic?
• Hydrophobic?

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Is the (green) side chain

• Hydrophilic?
• Hydrophobic?

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A PG FILM VW FAMILY VW
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Water is a poor solvent for non-polar molecules
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Additional forces holding the protein together
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Human insulin is cut into two pieces as it
matures in the Golgi apparatus. The two pieces
are held together by 3 disufide bonds. Insulin
has ___ amino termini, ___ carboxy termini, and
___ cysteine residues.

• 2,2,6
• 1,1,3
• 2,2,3
• 1,1,6

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pKa 6

• pH changes can cause proteins to unfold
  (denature).
• The deprotonation of buried histidines at higher
  pH starts the denaturation process.
• The pKa of amino acid residues is not the same as
  free amino acids.
• Protein unfolding is cooperative.

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Like alpha helices. beta-pleated sheets often
have one side facing the surface of the protein
and one side facing the interior, giving rise to
an amphipathic sheet with one hydrophobic surface
and one hydrophilic surface. From the primary
structures below, pick the one that could form an
amphipathic beta sheet.

• A L S C D V E T Y W L I
• D K L V T S I A R E F M
• D S E T K N A V F L I L
• T L N I S F Q M E L D V
• V L E F M D I A S V L D

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Folding motifs
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The structure of hemoglobin (link)
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Christian Anfinsen, Nobel Prize in Chemistry
(1959) The Thermodynamic Hypothesis sequence
determines structure.
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Denature ribonuclease with 8M urea
(high salt) and beta-mercaptoethanol
native ribonuclease denatured
(reduced) ribonuclease (active) ribonuclease
(inactive)
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Renature ribonuclease by removing
urea and beta-mercaptoethanol
denatured (reduced) native ribonuclease
ribonuclease (inactive) ribonuclease (active)
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When an egg is boiled, the proteins denature and
the egg white hardens. This denaturation is
irreversible. The hard egg white can, however, be
dissolved in a solution containing a strong
detergent and a reducing agent (2-mercapoethanol).
What bonds hold the hard egg white together?

• Disulfide bonds
• Hydrophobic bonds
• Hydrogen bonds
• Ionic bonds
• A and B

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Conclusion? Ribonuclease spontaneously folds
into its active conformation. Primary structure
determines secondary and tertiary structure.
Higher orders of protein structure are formed by
self assembly.
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The folding pathway
1. Formation of transient secondary structures
(localized folding) 2. Hydrophobic groups
cluster inside (hydrophilic outside) stabilizing
the secondary structures 3. Formation of ionic
and hydrogen bonds between distant
groups 4. Oxidation of disulfide bridges
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Molecular chaperones (chaperonins)

• foldases catalyze the folding reactions of
  proteins more complex than ribonuclease
• Two major families of these proteins hsp 70 and
  hsp 60
• HSP stands for heat shock proteins.

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Medical significance of protein folding

• Several neurodegenerative diseases are caused by
  protein precipitates in the brain
• Mad Cow disease
• Creutzfeld-Jakob disease (CJD)
• Kuru
• Alzheimers disease (amyloid plaque)
• These insoluble plaques occur when proteins fold
  differently and, as a consequence, aggregate and
  precipitate.

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AP
AP
The main change in AD is the appearance of a
 plaque, a shapeless structure that contains the
protein amyloid, outside nerve cells.  There are
also deposits of amyloid around many blood
vessels.  The amyloid weakens the walls of the
blood vessels and makes them more vulnerable to
rupture hemorrhage into the brain.
http//www.liebermanparkinsonclinic.com/content/
view/145/25/