Topic 2 Molecular Biology

2.4 Proteins

What do we know about proteins?

There are 20 different types of amino acids with varying R groups.

What do we know about proteins?

i. Amino acids are linked together by condensation to form polypeptides. Long chains of amino acids are called polypeptides Condensation involves amine group and carboxyl group Water is lost Occurs at ribosome Di contains 2 amino acids whereas poly- contains many Amino Group (-NH 2 ) Carboxylic Acid Group (-COOH)

Condensation reactions make bonds. Hydrolysis bonds break these bonds. Watch this animation and make a generalization about the processes: -function, roles of enzymes, roles of water

Skill: Drawing molecular diagrams to show the formation of a peptide bond. is removed is a product

ii. There are 20 different amino acids in polypeptides synthesized on ribosomes. All amino acids the same but differ in their R group which is bonded to the C

Methionine: an amino acid Methionine is an important amino acid as it is coded by the START codon in mRNA (AUG). This means that is is the first amino acid in all polypeptide chains as it is the first produced in transcription in the ribosomes. Although methionine (Met) has quite a large R- group, we can still identify the amino group and carboxylic acid group on the amino acid. Sulphur forms strong bonds (disulphide bridges) with other S-containing amino acids. The simplest amino acid is glycine, with H in the R-group position.

“OMG I HAVE TO LEARN THE NAMES OF ALL 20 !?!?” “Relax, no you don’t, you just need an awareness of the concepts as outlined.”

iii. Amino acids can be linked together in any sequence giving a huge range of possible polypeptides. Amino acids can be linked in any combination and in any number by the ribosomes Number of possible amino acids can be calculated starting with dipeptides 20 2, for tripeptides 20 3, etc. The number of amino acids in a polypeptide ranges from 20 – 10,000s

iv. The amino acid sequence of polypeptides is coded for by genes. The instructions for producing polypeptides are coded for by genes (DNA) 3 bases are needed to code for each amino acid In theory, a polypeptide with 20 amino acids should have a gene with 60 base sequences In practice, there are always extra bases at both ends of the polypeptide & occasionally in the middle, the actual coding region is called the reading frame.

We will learn all about this later!

v. A protein may consist of a single polypeptide or more than one polypeptide linked together # of polypeptides ExampleBackground 1LysozymeEnzyme in secretions (nasal mucus & tears), kills bacteria 2IntegrinMembrane protein, connects structures inside & outside the cell 3CollagenStructural protein in tendons, ligaments, skin & blood vessel walls, gives strength with limited stretching 4HemoglobinTransport protein in red blood cells, binds to oxygen in lungs & releases it in tissues

vi. The amino acid sequence determines the three-dimensional conformation of a protein The sequence of amino acids and its polypeptides determine a proteins conformation or 3D structure Fibrous proteins, like collagen, are elongate with a repeating structure The amino acid sequence prevents the protein from folding up & remains elongated Globular proteins, like hemoglobin, include parts that are helical or sheet-like These proteins begin folding as they are made to stabilize the bonds between the R groups

Proteins are commonly described as either being fibrous or globular Fibrous proteins have structural roles whereas globular proteins are functional (active in a cell’s metabolism).

vii. Living organisms synthesize many different proteins with a wide range of functions. No other carbon compound can compare with the versatility of proteins!! Catalysis –

vii. Living organisms synthesize many different proteins with a wide range of functions. Muscle contraction –

vii. Living organisms synthesize many different proteins with a wide range of functions. Cytoskeleton –

vii. Living organisms synthesize many different proteins with a wide range of functions. Blood clotting –

vii. Living organisms synthesize many different proteins with a wide range of functions. Transport of nutrients and gases –

vii. Living organisms synthesize many different proteins with a wide range of functions. Hormones

viii. Every individual has a unique proteome. Proteome is all of the proteins produced by a cell, a tissue or an organism, while a genome is all the genes Why might the proteome change at different times of the cells life?

viii. Every individual has a unique proteome. Gel electrophoresis is used to determine what proteins are present in an individual

Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein function.

Review Questions for proteins Draw a “generalized” amino acid (this means using “R” to stand for its side chain). Explain how the 20 different amino acids found in living things are separated into 3 groups. Draw and annotate a molecular diagram showing the formation of a peptide bond.