Review of Amino Acid + Protein Lecture 2

Protein

Proteins are polymers of amino acids joined together by peptide bonds.

Each of these amino acids has a fundamental design composed of a central carbon (also called the alpha/chiral carbon) bonded to:

• a hydrogen
• a carboxyl group
• an amino group
• a unique side chain or R-group

Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of the next amino acid. Peptide bond formation occurs in a condensation reaction involving loss of a molecule of water. The head-to-tail arrangment of amino acids in a protein means that there is a amino group on one end and a carboxyl group on the other end.

Levels of Protein Structure

Structural features of proteins are usually described at four levels of complexity:

• Primary structure: the linear arrangement of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids. In the primary structure, it tells you what amino acid is present and the sequence of that amino acid.
• Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding.
• Tertiary structure: the final three-dimensional structure of a protein, which results from a large number of non-covalent interactions between amino acids.
• Quaternary structure: non-covalent interactions that bind multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins.

Summary 🙂

1. Primary
Animo acid sequence

2. Secondary
Alfa helix
Beta plates
Hydrogen bonds with the polypeptide backbone

3. Tertiary 
Basic structure of the protein; alpha helixes and beta plates arranged in the protein
Hydrogen bonds, Ionic bonds, Covalent bonds, Sulfide bonds
They are important interacting with the side chains

4. Quaternary
Interactions between tertiary structures/polypeptide chain
Hydrogen bonds, Ionic bonds, Van der Waals interactions, Disulfide bridges
They are important interacting with the side chains

Denaturing Proteins

Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Denaturation disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape.

Denaturation occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted. In tertiary structure there are four types of bonding interactions between “side chains” including: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions. which may be disrupted. Therefore, a variety of reagents and conditions can cause denaturation. The most common observation in the denaturation process is the precipitation or coagulation of the protein.

Heat, Ultraviolet radiation, Strong Acid/bases, Urea, Some organic solvents, agitation are all conditions that can lead to denaturing a protein. 

Review Of Amino Acid + Protein Lecture 1

Important things to remember about amino acids

Amino acids differ because they have different ‘R’ groups attached to the molecule. The 20 amino acids are subdivided into different categories based on the ‘R’ groups:

• Nonpolar, aliphatic R groups

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine. Glycine = Smallest Amino Acid – the ‘R’ group is hydrogen. Proline = Special because the ‘R’ group is attached to the amino group and forms a ring structure.

• Polar, uncharged R groups.

Serine, Threonine, Cysteine, Asparagine, Glutamine. These are polar because there are atom’s present which differ in electronegative thus giving a polar bond being formed. Eg Oxygen in serine, Sulphur in Cysteine.

• Aromatic R groups.

Phenylalanine, tyrosine and tryptophan. Aromatic ring has double bonds in conjugated form.

• Positively charged R groups.

Lysine, Arginine, Histidine.

• Negatively charged R groups

Aspartate, Glytamate which is both acidic.

How Cystine is formed.

Two cysteine undergoes a a oxidation reaction where the sulphur hydroxyl reacts and loses the Hydrogen and forms disulphide linkage to form one cystine molecule. This process can be reversed where you reduce the disulphide linkage and form the two cysteine molecules. See Image below.

Nonionic forms  Zwitterion

To form a zwitterion, the hydrogen (proton) from the carboxylic group is lost as a proton and the amino acid group accepts the proton. Having two charges on a molecule forms a zwitterions (ie – a positive and negative group).

• Test to distinguish Amino acids – Ninhydrin – turns purple = positive conformation of presence of amino acid.

• Test to distinguish Protein – Biuret

Every amino acid has an amino and carboxyl group.  When a bond is formed between an  amino group and a carboxylic group; a peptide bond is formed. This peptide bond is covalent in nature. The reaction is a condensation reaction. 

Reference

Lecture 1 – Amino Acid + Protein

Facts Corner!!!

1. There ESSENTIAL and NON ESSENTIAL amino acids!!!

2. ESSENTIAL MEANS YOU HAVE TO EAT THEM!! :- Our bodies can’t produce essential amino acids, so we have to get them from the foods we eat. There are 10 essential amino acids… 1. Arginine. 2. Histidine. 3. Isoleucine. 4. Leucine. 5. Lysine. 6. Methionine. 7. Phenylalanine. 8. Threonine. 9. Tryptophan. 10. Valine!!!

3. If you are not able to obtain enough of even ONE of the TEN most essential amino acids, then there is certain degradation in your body’s proteins. IT IS VERY IMPORTANT TO GET THE RIGHT AMOUNT OF PROTEIN IN YOUR DIET!!!

4. On average, we need 40 to 60 gm of protein per day. This is necessary in one’s diet to be healthy. The exact amount of protein needed everyday can be calculated, the RDA is 0.8 grams per kilogram of lean bodyweight!

5. Most amino acid supplements sold over the counter have no side effects if they are taken properly and accordance with their daily-recommended allowance!! Its generally safe!!! 🙂

6.There are arguements that excessive protein consumption can cause a variety of body ailments–such as kidney and heart disease, constipation, and osteoporosis. :O :O :O