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B2 PROTEINS
Intro:
B.2.6  List the major functions of proteins in the body.
[Include structural proteins (for example, collagen) enzymes, hormones (for example, insulin),
immunoproteins (antibodies), transport proteins (for example, hemoglobin) and as an energy source.]
Proteins are macromolecules of central importance to the chemistry of life.
Functions of Proteins:
a) Structural Components of Cells and Tissues – Growth, repair, and maintenance of an organism are all
dependent on an adequate supply of proteins.
b) Enzymes – Some proteins serve as enzymes - biological catalysts that regulate the thousands of
different chemical reactions that take place in a living system.
c) Hormones – e.g. insulin…controls blood glucose levels
d) Antibodies(immunoproteins) – provide immunity to diseases
e) Transport – e.g. hemoglobin…transports O2 to cells and CO2 away from cells to lungs
f) Energy Source – for newborns and in cases of starvation
B.2.1  Draw the general formula of 2-amino acids.
B.2.2  Describe the characteristic properties of 2-amino acids.
[Properties should include isoelectric point, formation of a zwitterion and buffer action.]
*The structure of amino acids in aqueous solution alters at different pH values.
a) Isoelectric Point(pI) – The isoelectric point of an amino acid is the pH at which the positive and negative
charges are exactly balanced, the molecule has no net charge and it shows no net migration in an electric field.
The amino acid exists as a zwitterion (see below) at the isoelectric point. The isoelectric point of each amino
acid is unique.
b) Formation of zwitterion (tsvit-er-ahy-uh n)
= Zwitterion (structure at pI)
*If the amino acid is in an environment having a pH > than its pI; (i.e. its in a basic environment) the amino
acid will have a negative charge (remove a proton from the amino group on the above zwitterion).
[pneumonic  “BEN”….Basic Environment Negative]
*If the amino acid is in an environment having a pH < than its pI, the amino acid will have a positive charge
(add a proton to the carboxyl group on the above zwitterion).
Summary:
pH of environment
Less than pI (i.e. acidic)
Equal to pI
Greater than pI (i.e. basic)
Charge on amino acid
Positive
No net charge (zwitterion structure)
Negative
c) Buffer Action – Zwitterions are amphoteric which makes them good buffers.
That is:
- carboxyl accepts H+…if acid is added
- the H+ (on the amino group) is donated to OH-…if base is added.
B.2.3.  Describe the condensation reaction of 2-amino acids to form polypeptides
[Reactions involving up to three amino acids will be assessed.]
B.2.4  Describe and explain the primary, secondary (alpha-helix and beta-pleated sheets), tertiary and
quaternary structure of proteins.
[Include all bonds and interactions (both intramolecular and intermolecular) responsible for the protein
structure.
1. Primary Structure – the sequence of amino acids in a
polypeptide chain
2. Secondary Structure
a) Alpha Helix - involves the coiling of the
polypeptide chain into a spiral alpha helix
- maintained by hydrogen bonds between amino acids
in successive turns of the same polypeptide chain
- basic structural unit of wool, hair, skin and nails
b) Beta Pleated Sheet – hydrogen bonding takes place
between polypeptide chains.
- Each zigzag is fully extended, and the hydrogen
bonding between them results in a sheet-like structure.
3. Tertiary Structure – the overall shape assumed by each
polypeptide chain. This three-dimensional structure is
determined by four main factors that involve
interactions between R groups.
a) Hydrogen Bonds between R groups of amino acid
subunits in adjacent loops of the same polypeptide
chains.
b) Ionic attractions between R groups with positive
charges and those with negative charges.
c) Hydrophobic interactions resulting from nonpolar
R groups associating in the interior of the globular
structure away from surrounding water.
d) Covalent bonds known as disulfide bonds (-S-S-)
link the sulfur atoms in cysteine(Cys) subunits.
4. Quaternary Structure – Proteins composed of two or more polypeptide chains have a quaternary
structure. (e.g. Hemoglobin contains four polypeptide subunits. Its quaternary structure consists of the
final shape in which the subunits combine.)
B.2.5  Explain how proteins can be analyzed by chromatography and electrophoresis.
Analysis of Proteins
The primary structure of proteins can be determined by electrophoresis or paper chromatography.
A. Electrophoresis (i.e. PAGE  PolyAcrylamide Gel Electrophoresis)
Steps:
1. hydrolyze (i.e. break amide linkages) protein into constituent amino acids
via the addition of hydrochloric
acid
2. place sample in the centre of the gel
3. apply potential difference (i.e. voltage) across it
*4. amino acids separate by varying degrees depending on their isoelectric
points(pI) *see below
5. spray amino acids with a dye (ninhydrin) and compare the distance travelled with standard samples
*Example:
- pH of buffer = 5.7
If the pI of the amino acid is < 5.7, the amino acid is in a basic environment and will be negatively charged
(Remember “BEN”…Basic Environment =Negative). Being negatively charged means that it will migrate
towards the positive electrode. *What changes if the pI of the amino acid is: a) > 5.7 b) equal to 5.7?
*A larger discrepancy between the pI and pH of the buffer = faster rate of amino acid migration towards the
positive or negative electrode.
B. Paper Chromatography
Steps:
1. Again, hydrolysis via HCl has to happen first.
2. Place small spot of amino acid sample on bottom of chromatography paper.
3. Place paper in solvent…which then rises up the paper due to capillary action.
4. Different amino acids move up paper at different rates and therefore separate.
5. Dry paper and spray with dye.
6. Compare distances travelled to those in a known sample or determine Rf
(retention factor) and compare to known values. *If two amino acids have the
same Rf value, turn the paper sideways and put into a different solvent.
Rf =