Semester Exam #1 Chapters 3, 4, 5 and 6 (6.

4)
Amino Acids, Proteins, Protein Structure, Protein Functions, Enzyme & Inhibitor Kinetics

3 Amino Acids, Peptides and Proteins

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Isoelectric points (pI) which is equal to the pH at which the net charge on the
peptide is zero (neutral).
The approximate number of amino acid residues within a protein can be
calculated by dividing the molecular weight by 110.
When two or more subunits are iden3cal the protein is said to be oligomeric.
By definition, multi-subunit proteins have two or more peptides noncovalently associated. Two or more pep6des covalently linked (usually via a
disulfide bond) are labeled as chains and not subunits.
The non-amino acid component of a conjugated protein is referred to as the
prosthe3c group.
The primary structure consists of a sequence of amino acids linked together
by peptide bonds and includes any disulfide bonds. The resulting polypeptide
can be arranged into units of secondary structure, such as an alpha helix,
which is a particularly stable arrangement of amino acid residues giving rising
to recurring structural patterns. The helix is a part of the tertiary structure of
the folded polypeptide, describing all aspects of the three-dimensional folding
of a polypeptide. Its one of the subunits that make up the quaternary
structure of the multisubunit protein.
Function of a protein depends on its amino acid sequence.

4 The Three-Dimensional Structure of Proteins

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Because free rotation is possible around many of these bonds, the protein can
in principle assume a virtually uncountable number of conformations, but due
to each protein having a specific function that cant happen, because it
suggests a unique three-dimensional structure.
Three-dimensional structure of a protein is determined by its amino acid
sequence.
The function of a protein depends on its structure.
Proteins in any of their functional, folded conformations are called native
proteins.
Stability refers to the tendency to maintain a native conformation.
Higher entropy in unfolded molecules and solvation helps maintain the
unfolded conformation, so disulfide bonds, hydrogen bonds, hydrophobic
interactions and ionic interactions are used to counteract these effects and
stabilize the native conformation.
Inside the cell is a highly reducing environment, so disulfide bonds are more
difficult to happen.
The protein conformation with the lowest free energy is the one with the
maximum number of weak interactions.
When water surrounds a hydrophobic molecule, the optimal arrangement of
hydrogen bonds results in a highly structured shell, ou solvation layer, of
water around the molecula. That causes an unfavorable decrease in entropy

due to the ordering of water molecules. However, when non polar groups
cluster together, the extent of solvation layer decreases, because each group
no longer presents its entire surface to the solution resulting in a favorable
increase in entropy.
The release of structured water as intramolecular interactions form provides
an entropic driving force for folding.
One hydrogen bonds seems to contribute little to the stability of a native
structure, but the presence of hydrogen-bonding groups without partners in
the hydrophobic core of a protein can be so destabilizing that conformations
containing these groups are often thermodynamically untenable.
Salt bridges, especially those that are partly or entirely buried, can thus
provide significant stabilization to a protein structure.
Van der waals interactions are dipole-dipole interactions involving the
permanent electric dipoles in groups such as carbonyls, transient dipoles
derived from fluctuations of the electron cloud surrounding any atom, and
dipoles induced by interaction of an atom with another that has a permanent
or transient dipole.
The angles in the structure of the protein can have any values +-180, but
may are prohibited by steric interference between atoms in the polypeptide
backbone and amino acid side chains.
The range of Pro residues is greatly restricted because phi is limited by the
cyclic side chain to the range of -35 to -85.
Each helical turn includes 3.6 amino acid residues. The repeating unit is a
single turn of the helix, which extends about 5.4A along the long axis.
Left-handed helices are much less stable.
Alpha helices are more stable because of optimal use of internal hydrogen
bonding. The most stable form of an alpha helix consisting of D-amino acids
is left handed.
The twist of an alpha helix ensures that critical interactions occur between an
amino acid side chain and the side chain three residues away on either side
of it.
Pro and Gly are the least likely a.a. to form alpha helices. Pro forms a kink
because of the rigid ring. Gly is too flexible, taking up quite different forms.
In beta sheet, hydrogen bonds form between adjacent segments of
polypeptide chain within the sheet.
In beta sheet, peptide bonds involving the imino nitrogen of Pro readily
assumes cis configuration, a form that is particularly amenable to a tight
turn.
Fibrous proteins = typically one group of secondary structure (provide
support, shape and external protection to vertebrates). Globular proteins =
typically several types of secondary structure (enzymes and regulatory
proteins).
A motif or fold is recognizable folding pattern involving two or more elements
of secondary structure and the connections between them.
o Beta-Alpha-Beta loop = two elements of a secondary structure folded
against each other representing a small part of a protein.
o Beta-barrel = elaborated structure involving scores of protein
segments folded together.

Coiled coil = encountered in alpha keratin

Alpha/Beta-barrel = beta-alpha-beta loops arranged so that the beta
strands form a barrel.
o Alpha/Beta = with alpha and beta segments interspersed or
alternating.
o Alpha+Beta = with alpha and beta regions somewhat segregated.
A domain is a part of a polypeptide chain that could undergo movements as a
single entity with respect to the entire protein.
Chaperones help the folding of a protein to its native conformation.
Denaturation is a loss of three-dimensional structure sufficient to cause loss
of function. Most proteins can be denatured by heat, which has complex
effects on many weak interactions. Proteins can also be denatured by
extremes of pH, certain miscible organic solvents such as alcohol or acetone,
by certain solutes such as urea and guanidine hydrochloride, or by
detergents.
Renaturation is the process where certain denatured proteins will regain their
nature structure and their biological activity if returned to conditions in which
the native conformation is stable.
Protein disulfide isomerase (PDI) is a widely distributed enzyme that catalyzes
the interchange, or shuffling, of disulfide bonds until the bonds of the native
conformation are formed.
Peptide prolyl cis-trans isomerase (PPI) catalyzes the interconversion of the
cis and trans isomers of Pro residue peptide bonds.
Protein folding is generally hierarchical, regions of secondary structure may
form first, followed by folding into motifs and domains
o
o

5 Protein Function
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Function of many proteins involve the reversible binding of other molecules.

A molecule bound reversibly by a protein is called ligand.
The binding site is complementary to the ligand in size, shape, charge and
hydrophobic/hydrophilic character (its said to be selective).
Enzymes bind and chemically transform other molecules, catalyzing
reactions.
The molecules acted upon by enzymes are called reaction substrates and the
ligand-binding site is called catalytic site or active site.
Oxygen is poorly soluble in aqueous solutions and cannot be carried to
tissues in sufficient amounts it is simply dissolved in blood serum. However
none of the amino acid side chains in proteins are suited for the reversible
binding of oxygen molecules, so this role is filled by iron Fe2+ (in a less
reactive form) in a prosthetic group called heme. Fe3+ does not bind oxygen.
Some small molecules such as CO and NO coordinate to heme iron with
greater affinity than does O2, so when a molecule of CO is bound to heme,
O2 is excluded, which is why CO is highly toxic.
The function of myoglobin depends on the proteins ability not only to bind
oxygen but also to release it when and where it is needed.

Here, the Ka is the association constant that describe the equilibrium

between the complex and the unbound components of the complex. Also
provides a measure of the affinity of the ligand L for the protein. Bigger the
Ka bigger the affinity.
Equilibrium constants are denoted with a capital K and rate constants with a
lower case k.
Teta is the binding equilibrium. How many of the available ligand-binding
sites are occupied
The lower the Kd, the higher the affinity of a ligand for a protein.
The more tightly a protein binds a ligand, the lower the concentration of
ligand required for half the binding sites to be occupied, and thus the lower
the value of Kd.
Rapid molecular flexing of the amino acid side chains produces transient
cavities in the protein structure, and O2 makes its way in and out by moving
through this cavities.
Myoglobin functions well as an oxygen-storage protein. Hemoglobin is better
suited for transport because of its multiple subunits and O2 binding sites.
Oxygen has a higher affinity for hemoglobin in the R state (relaxed).
An allosteric protein is one in which the binding of a ligand to one site affects
the binding properties of another site on the same protein. Modulators for
allosteric proteins may be either inhibitors or activators.
When the normal ligand and the modulator are identical, the interaction is
termed homotropic. When not, is called heterotropic.
An nh (hill coefficient) of less than 1 indicates negative cooperativity, in which
the binding of one molecule of ligand impedes the binding of others.