what part of a cell is this?. what the syllabus says you should know: proteins have a variety of...

What part of a cell is this?

What the syllabus says you should know:

Proteins have a variety of functions within all living organisms.

The general structure of an amino acid

Condensation and the formation of peptide bonds linking together amino acids to form polypeptides.

The relationship between primary, secondary, tertiary andquaternary structure, and protein function.

The biuret test for proteins.

By the end of this session you should:

• know the structure of an amino acid

• understand what an R group is

• be able to join amino acids by condensation and hydrolyse dipeptides

• know what a peptide bond is.

The History of Protein Structure

• The word PROTEIN comes from Greek language (prota) which means "of primary importance".

The History of Protein Structure• This name was introduced by

Jons Jakob Berzelius in 1838 for large organic compounds with almost equivalent empirical formulas. This name was used because the studied compounds were primitive but seemed to be very important for animal nutrition.

The History of Protein Structure• The next crucial step

of the protein study was made by James B. Sumner in 1926 by showing that enzymes could be isolated and crystallized.

The History of Protein Structure• In 1955 Sir Frederick

Sanger sequenced or determined the complete amino acid sequence if the first protein - insulin. This is a first prove that all proteins have specific structure.

The History of Protein Structure• In 1958 the three-

dimensional structures of haemoglobin and myoglobin were solved by Max Perutz and Sir John Cowdery Kendrew, respectively. These structures were solved by X-ray diffraction analysis.

But why is understanding the structure of protein

so important?

You need to understand protein structure to understand the

following aspects of the course:

• Enzymes

DNA ligase

• Movement of substances across cell membranes

• How pathogens attack cells

HIV uses its envelope protein complex, gp120 and gp41, in order to selectively bind with high affinity to its cellular receptor protein, CD4, located on the exterior of T cells.

• How antibodies work

• Why muscles can contract

• Haemoglobin

• Hormones

The structure of an amino acid

Key points

• All proteins contain C, H, O, and N.• Some also contain S.• The basic unit is amino acid (you need to

learn the structure)• There are two reactive groups, amino NH2

and carboxylic acid COOH.• The R group varies from one amino acid to

the next.

Try to spot the R group in each case.

Glycine• Glycine is the

smallest of the 20 amino acids commonly found in proteins.

• Most proteins incorporate only small quantities of glycine. A notable exception is collagen.

• Glycine has an important role in the nervous system.

Alanine• Alanine occurs in

bacterial cell walls and in some peptide antibiotics.

• Alanine is a nonessential amino acid, meaning it can be manufactured by the human body, and does not need to be obtained directly through the diet.

• Alanine is found in a wide variety of foods, but is particularly concentrated in meats.

Serine• Serine is another

non- essential amino acid.

• Serine was first obtained from silk protein, a particularly rich source, in 1865.

Leucine• Leucine is an

essential amino acid, which means that humans cannot synthesise it.

• It has been found to slow the degradation of muscle tissue by increasing the synthesis of muscle proteins

Asparagine• Asparagine was first

isolated in 1806 from asparagus juice, -- hence its name.

• It was the first amino acid to be isolated.

• The characteristic smell observed in the urine of individuals after their consumption of asparagus is attributed to various metabolic biproducts of asparagine.

Cysteine• The side chain on

cysteine often participates in enzymatic reactions.

• It serves an important structural role in many proteins.

• Although classified as a non-essential amino acid, in rare cases, cysteine may be essential for infants, the elderly, and individuals with certain metabolic disease.

Amino acids join together by a condensation reaction to form a dipeptide.

• http://www.biotopics.co.uk/as/aminocon.html

Now try forming a dipeptide by condensation of:

• Alanine and glycine

• Serine and cysteine

Hydrolysis of a dipeptide gives it’s constituent amino acids.• http://www.biotopics.co.uk/as/dipeptidehyd

rolysis.html

Can you hydrolyse this dipeptide?

O H

As there are reactive groups at each end of an amino acid, many amino acids can join together to form a polypeptide.

By the end of this session you should:

• know the structure of an amino acid

• understand what an R group is

• be able to join amino acids by condensation and hydrolyse dipeptides

• know what a peptide bond is.

What the syllabus says you should know:

Proteins have a variety of functions within all living organisms.

The general structure of an amino acid

Condensation and the formation of peptide bonds linking together amino acids to form polypeptides.

The relationship between primary, secondary, tertiary andquaternary structure, and protein function.

The biuret test for proteins.

Primary structure

This is the linear sequence of amino acids in the polypeptide chain.

Secondary structure

• Hydrogen bonds form between a C=O on one amino acid and an N-H on another amino acid.

• This causes the polypeptide chain to coil or pleat forming an α – helix or a β – pleated sheet.

Secondary structure

Tertiary structure

• This is further folding or pleating of the chain to give an overall 3D structure caused when either hydrogen bonds, ionic bonds or disulphide bridges form between R groups.

Tertiary structure

Quaternary Structure

• 2 or more polypeptide chains combine together.

Why is it important proteins fold correctly?

• Amongst other things, incorrect protein folding has bee associated with a number of neurodegenerative diseases including

Creutzfeldt-Jakob disease, bovine spongiform encephalopathy (mad cow disease), Alzheimer's disease, Huntington's and Parkinson's disease.

Why is it important proteins fold correctly?

• In unit 1 you are most likely to get questions relating to non-functional enzymes, membrane proteins and immunity – make sure you can relate these to protein structure as you go through the unit.