Proteins

Proteins / Polypeptides The functional molecules of life

What are proteins? Proteins are amino acid polymers folded into specific three dimensional shapes. A protein structure determines its function.

Are proteins of different types? Enzymes → biological catalysts Immunoglobulins → protect against foreign microbes & cancer cells Haemoglobin → oxygen carrier Proteins Keratin → formation of hair & nails Fibrin → essential for blood clotting Collagen → formation of bones, ligaments tendons

What are the building units of proteins? These are called the amino acids. What is a residue? When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called a residue.

The general structural formula of amino acids:

What are the two functional groups that amino acids posses? Amino acids posses both, the acidic (carboxyl) and the basic (amino) functional groups.

Amino acids When dissolved in water the carboxyl group donates an H+ ion to the amino group, so both groups are ionized.

Acidic and basic amino acids Acidic amino acids posses a carboxyl group on their side chain (R), while basic amino acids have an amino group on the side chain (R). Polar (hydrophilic) amino acids may be Nonpolar (hydrophobic) Charged (acidic or basic)

How many are the amino acids? There are 20 important amino acids used in protein synthesis, 8 of which are “essential amino acids”, meaning that the body can’t synthesize.

What is a proline kink? Proline is the only amino acid whose side chain (R) forms a covalent bond with its amino group, and this results in what's called the proline kink.

How do amino acids bond together and what is the name of the bond (linkage)?

What determines the final shape (conformation) of the protein polymer? The final conformation of the protein is determined by the sequence of the amino acids it contains.

What is an amino terminus (A- terminus)? An amino terminus is the free amino group at one end of the polypeptide. What is a carboxyl terminus (C- terminus) A carboxyl terminus is the free carboxyl group at one end of the polypeptide.

Globular Proteins Are composed of one or more polypeptide chains that take on a rounded or spherical shape. Many enzymes and other functional proteins are globular. collagen e.g.: keratin haemoglobin

Globular proteins may be described in terms of four levels of structure: 1) The primary structure of protein 2) The secondary structure of protein 3) The tertiary structure of protein 4) The quaternary structure of protein

What is the primary structure of protein? Is the of amino acids in the polypeptide chain. sequence

STRUCTURE Primary (1º) – Description:The linear sequence of amino acids (AAs) as determined by the genetic code (DNA). – Bonding:Covalent peptide bonds between AAs. H2OH2O H2OH2OH2OH2O H2OH2O

What is the secondary structure of protein? In certain regions, a hydrogen bond forms between the electronegative oxygen of the carboxyl group of one peptide bond and the electropositive hydrogen of an amino group, that is four bonds away. 1) α helix: A type of polypeptide secondary structure characterized by a tight coil that is stabilized by hydrogen bonds. α helix

2) β-pleated sheet: polypeptide secondary structure that form between parallel stretches of a polypeptide, and are (the stretches) stabilized by hydrogen bonds.

STRUCTURE Secondary (2º) – Description:The twisting and folding of the linear primary (1º) structure. – Bonding:Hydrogen bonds between charged AAs. – Forms: triple helix (e.g. keratin)(e.g. fibrin)(e.g. collagen)

What is the tertiary structure of protein? Is the complex folding (super coiling) of the polypeptide that is stabilized by side chain interactions (R-group - R-group interactions) that include all of the following: 1.Ionic bonds between oppositely charged side chains 2.Hydrogen bonds between certain polar side chains 3.Van Der Waals forces between non-polar groups 4.Proline kinks 5.Disulfide bridges: when the sulfur containing R- groups of two cysteine residues are close they form a disulfide bridge (-S-S-) these are strong stabilizers of the tertiary structure

Disulfide bridges:

What is the quaternary structure of protein? Is the clustering (aggregation) of two or more polypeptides of the tertiary structure.

→→ →

What is protein denaturation? Protein denaturation is the change in the three-dimensional shape of a protein. Denaturation could be due to changes in: 1.Temperature (heat denatures the protein in hair allowing to straighten curly hair, barbecuing meat & boiling an egg) 2.pH (gastrin works best at pH 2 and is denatured in the small intestine at pH 10) 3.Ionic concentration 4.Exposing the protein to liquids (water, alcohol)

What are chaperone proteins? Chaperone proteins are special proteins that aid a growing polypeptide to fold into the tertiary structure.

Nucleic Acids The two nucleic acids DNA and RNA are essential for all living things. DNA consists of sugar, phosphate groups linked together through sugar phosphate Bonds, and four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T) [in case of RNA uracil (U) is used instead of thymine (T) and the sugar is also different, ribose instead of deoxyribose].

DNA All living things have chromosomes All living things have chromosomes inside the nuclei of their cells, the Chromosomes are made of DNA. The number and sequence of amino acids in a protein chain, determines the unique characteristics of that particular protein. The number and sequence of amino acids in a protein chain, determines the unique characteristics of that particular protein. The sequence of the nucleotides (or in other words the nucleotides’ bases) of a gene, is the determining factor that codes for the corresponding sequence of amino acids of that particular protein, this one gene is called one protein hypothesis. The sequence of the nucleotides (or in other words the nucleotides’ bases) of a gene, is the determining factor that codes for the corresponding sequence of amino acids of that particular protein, this one gene is called one protein hypothesis.

DNA Structure

What is a nucleotide? A nucleotide includes a sugar molecule, a phosphate group, and a nitrogenous base bonded together.

The Nitrogenous Bases Adenine Cytosine Guanine Thymine Guanine Thymine Uracil UracilPurines (Double rings) Pyrimidines Pyrimidines (Single rings) (Single rings)

The Nitrogenous Bases Are adenine (A), guanine (G), cytosine (C), Are adenine (A), guanine (G), cytosine (C), and thiamine (T) [in case of RNA uracil (U) is used instead of thiamine (T)]. The nitrogenous bases of the adjacent nucleotides are paired as follows: A-T or T-A G-C or C-G Since there are 4 bases and each codon Since there are 4 bases and each codon that codes for an amino acid is made of 3 Bases, then there is a probability of 64 Codes of base triplets (4 3 =64),which are more than enough to code for the 20 more than enough to code for the 20 available amino acids. available amino acids.