7.5 Proteins

Four levels of protein structure

1. Primary Structure = amino acid sequences

   a) These are polypeptide chains (between 50-1000 amino acids in length)

   b) 20 amino acids

   c) R groups of amino acids aid in shaping the protein

Primary Structure

   a) The primary structure forms a –N-C-C-N-C-C-N-C-C- backbone to the molecules

   b) The primary structure is read from the NH2 – terminal to the –COOH terminal

   c) Each amino acids is identified by its specific R group

Secondary Structure

1. Secondary Structure = describes the shape of the protein

   a) There are two main types:

      i) Alpha helix

      ii) Beta pleated sheets

   b) Both stabilized by hydrogen bonding between groups in the main chains

   c) The primary structure of a polypeptide has group projecting from the N-C-C backbone

   d) There are three noted forms of secondary structure

Secondary Structure- Alpha Helix

   a) Formed from hydrogen bonds

   b) This is drawn as a helix that follows the –N-C-C-N-C- backbone of a polymer

   c) Alpha helices are often the basis of fibrous polymers (i.e. collagen)

   d) Right handed helix

   e) The alpha helix was first discovered by Linus Pauling

Secondary Structure- Beta-Pleated Sheet

   a) Beta-pleated sheets are so called because of the ‘pleated’ or folds when viewed from the side

   b) The polypeptide chain is much more stretched out in comparison to the alpha helix

   c) This ‘sheet’ often has twists that increase the strength and rigidity of the structure

   d) This beta-pleated sheet was discovered by Pauling and Corey

Structure- Open Loops

   a) Alpha helices and beta-pleated sheets are often connected together by short chains of amino acids which form neither of the previous structures but simply link other sections together

   b) They are in fact often important regions of proteins including the active sites of enzymes

Tertiary Structure

   a) The overall shape of conformation of a polypeptide.  Basically its just referring to the folds in a polypeptide chain

   b) These folds are formed just after translation

   c) Caused by bonding of the R groups together

   d) Hydrophilic R groups bond to each other

   e) Hydrophobic R groups bond to each other

   f) Types of intramolecular bonds may include covalent, ionic, hydrogen, disulphide bridges, and hydrophobic interactions

Tertiary Structure- Disulphide Bridges

   a) R groups that have sulfer will form covalent bonds between one another (i.e. between two adjacent cysteine amino acids).  This forms a disulphide bridge.

   b) The covalent bond stabilizes the tertiary shape of a protein

 

Quaternary Structure

   a) A number of tertiary polypeptides joined together

   b) Hemoglobin is a quaternary structure

   c) It is composed of 4 different polypeptide chains

   d) Each chain forms a tertiary structure called a hem (haem) group

   e) Prosthetic groups: proteins are often bond to inorganic groups (e.g. Hemoglobin has four polypeptide ‘hem’ groups each associated with Fe2+.)

Fibrous Proteins

   a) Are water insoluble, long and narrow proteins

   b) Are associated with providing strength and support to tissue

   c) Collagen is the basis of the connective tissue and is composed of three left handed helices.  They make up the extracellular matrix and are found in cartilage, ligiments, tendons, etc.

   d) This is the most common protein in animals

   e) Keratin is another common fibrous protein which is composed of seven helices (major protein in hair and nail structure)

Globular Protein

   a) Are near soluble (colloids)

   b) They have more compact and rounded shape

   c) Are associated with functions such as: pigments and transport proteins (hemoglobin, myoglobin, lipoproteins)

   d) Immune system (immunoglobins)

   e) Structural motifs- sophisticated method of describing protein structure

   f) Examples are enzymes, hormones, hemoglobin and immunoglobin (antibodies)

Significance of Polar and Non-Polar amino acids

   a) Polarity of amino acids depends on the R groups

   b) Polar amino acids have hydrophilic R groups

   c) Non-Polar amino acids have hydrophobic R groups

Polar A.A.

   a) Water soluble

   b) In the cell membrane:

      i) They create channels in proteins for hydrophobic substances to pass through

      ii) They cause part on the membrane proteins to protrude from the cell membrane

      iii) Transmembrane proteins have two polar regions (one on surface and one in channel)

   c) Cell membrane proteins:

      i) The sections of the molecule that contain polar amino acids are hydrophilic and can exist in contact with water.

      ii) Polar amino acids allow the positioning proteins on the external and internal surface of a cell membrane.  Both cytoplasm and tissue fluid are water based regions.

Non-Polar A.A.

   a) Water insoluble

   b) They stabilize the entire protein when found in the center of the water soluble amino acids

   c) They cause proteins to remain embedded in the cell membrane

Polar v. Non-Polar

   a) The lining of the channel itself will be of polar amino acids to allow the diffusion of charged molecules and ions

   b) Polar amino acids within the active site of an enzyme allow a chemical interaction between the substrate and the enzyme to form an activated complex

Four Functions of Protein:

1. Hormones (globular)-

   a) Insulin is a hormone that reduces blood sugar

   b) Produced in the beta- cells of the pancreas islets

   c) Main target tissue is muscle cells and liver cells

   d) Function: to bring about the update of glucose across the cell membrane and the storage of glucose as the insoluble polymers glycogen

2. Immunoglobulins (globular):

   a) Known as antibodies

   b) Produced by the plasma cells in an immune response to an infectious antigen

   c) Great variation exists in the heavy chains which allows a response to virtually any possible antigen surface

3. Enzymes (globular):

   a) Enzymes reduce the energy of activation and allows biochemical reaction to reach equilibrium more quickly

   b) Enzymes are large globular proteins often with prosthetic groups

   c) The maximum number of substrate molecules that can be converted into product per second (excess substrate) is called the ‘turn-over rate’

4. Gas Transport (globular):

   a) Hemoglobin molecules aid in binding oxygen to red blood cells then transporting it to respiring tissues

   b) They are contained within the erythrocytes (red cells) of the circulatory system

   c) Composed of 4 hem groups each associated with a prosthetic Fe2+ ion

   d) Each hem group can carry an oxygen atom

Proteins contd.

   a) Collagen (fibrous): provides structure for the skin

   b) Actin and Myosin (fibrous): aids muscle contraction

   c) Fibrin (fibrous): aids in the clotting of blood