B2: Proteins!Caroline Good

Anthony JanockoEsther Lee

Aaron Skipper

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.

• 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.

B.2.2: Describe the characteristic properties of 2-amino acids

• 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.

B.2.2: Continued

B.2.2: Continued

Diagram of Isoelectric Point

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.

B.2.3: Continued

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!

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

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

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

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.

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

Paper Chromatography Analysis1. 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.

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

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

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.

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