1. B2: Proteins!
Caroline Good
Anthony Janocko
Esther Lee
Aaron Skipper

2. B.2.1: Draw the general
formula of 2-amino acids
•2-amino acids: compounds containing the an amino
group and a carboxylic acid group.
•Also called alpha-amino acids.

3. B.2.2: Describe the characteristic
properties of 2-amino acids
• Contain both an amine functional group and a carboxylic
acid functional group.
• 20 naturally occurring 2-amino acids
• 2-amino acids are the monomers of polypeptide chains.
• Crystalline solids with high melting points
• -NH2 group basic, -COOH group acidic; creates internal transfer
of a H+ ion from –COOH to -NH2.
• Called zwitterion: a compound with no overall electrical charge
but with separate parts which are positively and negatively
charged.
• Instead of hydrogen bonds or intermolecular forces, 2-amino
acids exhibit stronger ionic attractions, accounting for higher
melting point with small size.

4. B.2.2: Continued
• Amino acids are generally soluble in water and insoluble
in non-polar organic solvents such as hydrocarbons.
• In water, the ionic attractions between the ions in the solid
amino acid are replaced by strong attractions between polar
water molecules and the zwitterions.
• The size and nature of the R group determines extent of
solubility.
• Amino acids act as buffers
• At low pH the -NH2 group accepts a proton, at high pH the –
COOH group loses a proton.
• For each 2-amino acid, there is a unique pH value where the
acid will exist as a zwitterion known as the isoelectric point.

5. B.2.2: Continued
Diagram of Isoelectric Point

6. B.2.3: Describe the condensation reaction
of 2-amino acids to form polypeptides
•Amino acids bond to each other through condensation
reactions.
•Amino acid residues are joined to each other by an
amide link or a peptide bond.
•Results in the formation of water.
•OH- from –COOH group, H+ from -NH2 group
•Hydrolysis is the process by which water is used to
break apart polypeptide chains into the constituent amino
acids.

7. B.2.3: Continued

8. B.2.4 Describe and explain the
primary, secondary, tertiary, and
quaternary structure of proteins.
 General structure of a protein:
 Large macromolecules made of chains of 2-amino
acids
 Amino acids bond to each other through
condensation reactions to form polypeptides!
 Amino acid residues are joined by an amide link aka a
peptide bond
 Let’s take a look!

10. Primary Structure of a Protein
 A protein’s fixed and
unique sequence of
connected amino acids
 Sequence ex. Gly-his-
ala-ala-leu-…
 Use the abbreviations
of the amino acid
names
 Ex. Leucine – Leu
 Glutamine – Glu
 Aspartic Acid - Asp

11. Secondary Structure of a
Protein
 The way in which the chain
of amino acids folds itself
due to intramolecular
hydrogen bonding
 α-helix: spiral twists like a
coiled spring; the N in the
peptide bond is bonded to
the O of the peptide
carbonyl group, four
residues down the chain
 ß-pleated: sheet-like
structure; adjascent
polypeptide chains of the
same protein are
connected side-by-side
with hydrogen bonding

12. Tertiary Structure of a Protein
 Describes the overall folding of
the chains by interactions
between distant amino acids
creating a 3D shape with
pockets and dents!
 Due to: Hydrogen bonds, Van
der Waals’ attraction between
non-polar side groups, ionic
attractions between polar
groups, and disulfide bridges
 Disulfide Bridges: formed by
two cysteine residues when
their sulfur atoms undergo
oxidation
 Fibrous: long molecules forms
fibers – collagen!
 Globular: chain is folded into a
compact shape and is
generally soluble in water

13. Quaternary Structure of a
Protein
 The interaction of
several polypeptide
chains to create a more
complex structure
 Ex. Haemoglobin’s
quaternary structure =
four protein chains (2
alpha and two beta
chains) grouped around
four haem groups.

14. B.2.5 Explain how proteins can be
analyzed by chromatography and
electrophoresis
 The composition and primary structure of proteins
can be determined by paper chromatography or by
electrophoresis (3D structures is confirmed by X-ray
crystallography)
 The protein must be hydrolyzed by hydrochloric acid first to
successively release the amino acids!
 Chromatography: the separation of a mixture by passing it
in solution or suspension or as a vapor (as in gas
chromatography) through a medium in which the
components move at different rates
 Electrophoresis: the movement of charged particles in a
fluid or gel under the influence of an electric field

15. Paper Chromatography
Analysis
1. Place a small spot of the unknown amino acid
sample near the bottom of chromatographic paper.
2. Place spots of known amino acids alongside it.
3. Place the paper in a solvent which will rise up the
paper due to capillary action.
4. Remove the paper from the tank when the solvent
has nearly reached the top.
5. Dry the paper and spray it with an organic dye
(ninhydrin) to develop the chromatogram by
coloring the acids
6. Compare the positions of all of the spots.

17. Electrophoresis Analysis
 The structure of amino acids alter at different pH
values!
 Low pH (acid medium) = amine group is protonated
 High pH (alkaline medium) = carboxylic acid group will lose
a proton
 Amino Acids can act as buffers
 If H+ ions are added they are removed as NH4+ and if OH-
ions are added they are removed as water
 Isoelectronic Point: an amino acid’s unique pH value
where the acid will exist as the zwitterion.
 Zwitterion: a neutral molecule with a positive and a
negative electrical charge (not dipoles) at different
locations within that molecule. Also called inner salts

18. Electrophoresis (cont.)
 The medium is generally a polyacrylamide gel.  process is
known as PAGE: polyacrylamide gel electrophoresis
 Place sample in the centre of the gel and apply a potential
difference across the gel
 The amino acids will move at different rates towards the positive
and negative electrodes depending on the pH of the buffer.
 An amino acid will stop at its isoelectric point because its charge
will be balanced.
 When separation is complete the acids can be sprayed with
ninhydrin and identified by comparing the distance they have
travelled with standard samples or by comparing their isoelectric
points

20. B.2.6 List the major functions
of proteins in the body.
 Biological catalysts for reactions – enzymes!
 Structural Proteins
 parts of muscle tissue, connective tissue, skin, hair, nails, etc.
 Hair and nails are almost completely polypeptides coiled into
alpha-helixes
 Ex. Collagen – connective tissue in skin and tendons
 Act as a source of energy
 Some proteins are hormones
 Ex. FSH (follicle stimulating hormone): triggers the monthly cycle
for females
 Insulin: 51 amino acid residues; regulates blood sugar levels
 Diabetes: low levels or absent insulin levels prevent glucose from
being transferred sufficiently from the bloodstream to the tissues.

21. List of Functions! (cont.)
 Immunoproteins are antibodies!
 Functional/Transport proteins
 Ex. Hemoglobin: carries oxygen from lungs to all respiring
cells
 Storage Proteins
 Ex. Casein: food substance in milk
 Proteins can act as lubrication
 Ex. Mucoproteins: act as mucous secretions to reduce
friction in many parts of the body like the knee joint
 Pore proteins
 Act as channels that transport ions, water, and other
molecules through the cell membrane