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2.4 Proteins

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Samar Totonchy

on 7 February 2017

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Transcript of 2.4 Proteins

Thank You
Amino acids and polypeptides
- Polypeptides are chains of amino acids linked together by condensation reactions hence held together by peptide bonds.

- Polypeptides are the main component of proteins


- The condensation reaction involves the amine group (-NH2) of one amino acid and the Carboxyl group (-COOH) of another.

- Water is eliminated and a new bond is formed between the two amino acids, called a peptide bond.


Amino acids and polypeptides
Chains of fewer than 20 amino acids are usually referred to as oligopeptides.

Insulin is a small protein that contains two polypeptides, one with 21 amino acids and the other with
Drawing Peptide Bonds

Features of a Peptide Bond:

- Chain of atoms linked by single covalent bonds forming the backbone of the oligopeptide with a repeating sequence of -N-C-C-

- A hydrogen atom is linked by a single bond to each nitrogen atom and an oxygen atom is linked by a double bond to one of the two carbon atoms.

- The amine (-NH2) and carboxyl (-COOH) groups are used in forming the peptide bond and only remain at the ends of the chain. These are called the amino and carboxyl terminals of the chain.

- The R groups of each amino acid remain and project outwards from the backbone.

The Diversity of Amino Acids

There are twenty different amino acids in polypeptides synthesized on ribosomes.

The amino acids that are linked together by ribosomes to make polypeptides all have some identical structural features:
- A carbon atom in the center of the molecule is bonded to an amine group
- A carboxyl group
- A hydrogen atom

The carbon atom is also bonded to an R group, which is different in each amino acid.

Amino acids and polypeptides
2.4 Proteins
Tetrapeptide: The
green
is the amino end and the
blue
is the carboxyl end
.

Tripeptide: The
green
is the amino end and the
blue
is the carboxyl end.

Common amino acids
The amine group and the carboxyl groups are used up in forming the peptide bond, so it is the R groups of the amino acids that give a polypeptide its character.


Some proteins contain amino acids that are not in the basic repertoire of twenty. In most cases this is due to one of the twenty being modified after a polypeptide has been synthesized.









There is an example of modification of amino acids in collagen, a structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls.


Amino Acids and Origins

Patterns, trends and discrepancies: most but not all organisms assemble polypeptides from the same amino acids.


In some cases amino acids are modified after a polypeptide has been synthesized, but the initial process of linking together amino acids on ribosomes with peptide bonds usually involves the same 20 amino acids.


Hypothesis that have been proposed:

These 20 amino acids were the ones produced by chemical processes on Earth before the origin of life.

They are the ideal 20 amino acids for making a wide range of proteins, so natural selection will always favor organisms that use them.

All life has evolved from a single ancestral species, which used these 20 amino acids.

Polypeptide Diversity
Ribosomes link amino acids together one at a time, until a polypeptide is fully formed.

The number of possible amino acid sequence can be calculated starting with dipeptides. Both amino acids in a dipeptide can be any of the twenty so there are twenty times twenty possible (20 x 20). For a tripeptide sequence there a possible of (20 x 20 x 20) amino acids. For a polypeptide of n amino acids there are 20n possible sequences.

The number of amino acids in a polypeptide can be anything from 20 to tens of thousands.

Genes and Polypeptides

The amino acid sequence of polypeptides is coded for by genes.

A typical cell produces polypeptides with thousands of different sequences and must store the information needed to do this.

The amino acid sequence of each polypeptide is stored in a coded form in the base sequence of a gene.

Some genes have other roles, but most genes in a cell store the amino acid sequence of a polypeptide. Three bases of the gene are needed to code for each amino acid in the polypeptide.

The base sequence that actually codes for a polypeptide is known to molecular biologists as the open reading frame.
Proteins and Polypeptides

A protein may consist of a single polypeptide or more than one polypeptide linked together.

Integrin is a membrane protein with two polypeptides, each of which has a hydrophobic portion embedded in the membrane.

Hemoglobin consists of four polypeptides with associated non-polypeptide structure. The four parts of hemoglobin interact to transport oxygen more effectively to tissues that need it than if they were separate.

Collagen consists of three long polypeptides wound together to form a rope-like molecule. This structure has greater tensile strength than the three polypeptides would if they were separate. The winding allows a small amount of stretching, reducing the chance of the molecule breaking.

Proteins and Polypeptides

Protein Conformations

The amino acid sequence determines the three-dimensional conformation of a protein.

The conformation is determined by the amino acid sequence of a protein and its constituent polypeptides.

Fibrous proteins such as collagen are elongated, usually with a repeating structure.

Many proteins are globular, with an intricate shape that often includes parts that are helical or sheet like.
Proteins Conformations

In globular proteins that are soluble in water, there are hydrophilic R groups on the outside of the molecule and there are usually hydrophobic groups on the inside.

In globular membrane proteins there are regions with hydrophobic R groups on the outside of the molecules which are attracted to the hydrophobic center of the membrane.

In fibrous proteins the amino acid sequence prevents folding up and ensures that the chain of amino acids remains in an elongated form.
Denaturation of Proteins

The three-dimensional conformation of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule.

Most of these bonds and interactions are relatively weak and they can be disrupted or broken. This results in a change to the conformation of the protein, which is called denaturation.

A denatured protein does not normally return to its former structure - the denaturation is permanent.

Soluble proteins often become insoluble and form a precipitate. This is due to the hydrophobic R groups in the centre of the molecule becoming exposed to the water around by the change in conformation.

Denaturation Proteins by Heat or pH extremes

Heat can cause denaturation because it causes vibrations within the molecule that can break intermolecular bonds or interaction. Proteins vary in their heat tolerance.

Extremes of pH, both acidic and alkaline, can cause denaturation. This is because charges on R groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form.

As with heat, the three-dimensional structure of the protein is altered and proteins that have been dissolved in water often become insoluble.

Amino acids are added one by one, to form a polypeptide.

They are always added in the same sequence to make a particular polypeptide.

In globular proteins the polypeptides gradually fold up as they are made, to develop the final conformation.

This is stabilized by bonds between the R groups of the amino acids that have been brought together by the folding.
Functions of Proteins
All the Functions listed above are carried out by proteins:
catalysis
Muscle contraction
cytokenisis
Tensile STRENGTHENING
Blood CLOTTING
TRANSPORT OF Nutrients AND GASES
Cell adhesion
membrane Transport
hormones
Receptors
packing of dna
immunity
Biotechnological uses of proteins
Proteomes
Proteome: All the proteins produced by an organism


Rubisco

INSULIN
Tryptophan: Simply an amino acid
Pellagra and Hartnup Disease
Amino acids, Health and Disease
Lysine: simply another amino acid
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