ProteinsProteins

• Learning objectiveLearning objective• To be able to describe how To be able to describe how

bonds are made between amino bonds are made between amino acids forming polypeptidesacids forming polypeptides

O

NH2

NH

N

OH

O

NH2

CH3

CH3OH

O

NH2

CH3

CH3

OH

O

NH2

NH2OH

O

NH2

SCH3 OH

O

NH2

OH

O

NH2NH

OH

O

NH2

CH3

CH3 OH

HistidineHistidine MethionineMethionine

IsoleucineIsoleucine PhenylalaninePhenylalanine

LeucineLeucineTryptophanTryptophan

LysineLysine ValineValine

• Proteins are the most complex and most diverse Proteins are the most complex and most diverse group of biological compounds. They have an group of biological compounds. They have an astonishing range of different functionsastonishing range of different functions. .

• How many can you think of?How many can you think of?

• Structure e.g. collagen (bone, cartilage, Structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle)tendon), keratin (hair), actin (muscle)

• Enzymes e.g. amylase, pepsin, catalase, etc Enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others)(>10,000 others)

• Transport e.g. haemoglobin (oxygen), Transport e.g. haemoglobin (oxygen), transferrin (iron)transferrin (iron)

• Pumps e.g. Na+K+ pump in cell membranesPumps e.g. Na+K+ pump in cell membranes• Motors e.g. myosin (muscle), kinesin (cilia)Motors e.g. myosin (muscle), kinesin (cilia)• Hormones e.g. insulin, glucagonHormones e.g. insulin, glucagon• Receptors e.g. rhodopsin (light receptor in Receptors e.g. rhodopsin (light receptor in

retina)retina)• Antibodies e.g. immunoglobulinsAntibodies e.g. immunoglobulins• Storage e.g. albumins in eggs and blood, Storage e.g. albumins in eggs and blood,

caesin in milkcaesin in milk• Blood clotting e.g. thrombin, fibrinBlood clotting e.g. thrombin, fibrin• Lubrication e.g. glycoproteins in synovial fluidLubrication e.g. glycoproteins in synovial fluid• Toxins e.g. diphtheria toxinToxins e.g. diphtheria toxin• Antifreeze e.g. glycoproteins in arctic fleaAntifreeze e.g. glycoproteins in arctic flea• and many more!and many more!

ProteinsProteins• Proteins contain the elements C H O N & Proteins contain the elements C H O N &

sometimes Ssometimes S• They are made by condensation reactions between They are made by condensation reactions between

amino acids forming long polypeptide chains.amino acids forming long polypeptide chains.• The properties of each individual protein are The properties of each individual protein are

determined by the aa sequencedetermined by the aa sequence

• There are 20 different R groups, and so 20 different There are 20 different R groups, and so 20 different amino acids e.g.amino acids e.g.

•Glycine R=H Glycine R=H

•Alanine R=CH3Alanine R=CH3

• Since each R group is slightly different, each amino Since each R group is slightly different, each amino acid has different properties, and this in turn means acid has different properties, and this in turn means that proteins can have a wide range of propertiesthat proteins can have a wide range of properties

H

CH

N C

HH

O

O

R

Amino acidsAmino acids

amino carboxyl

Draw the general Draw the general structure of an amino structure of an amino acid molecule acid molecule There is a central carbon There is a central carbon atom (called the "alpha atom (called the "alpha carbon"), with four carbon"), with four different chemical different chemical groups attached to it:groups attached to it:

a hydrogen atoma hydrogen atoma basic amino groupa basic amino groupan acidic carboxyl groupan acidic carboxyl groupa variable "R" group (or a variable "R" group (or side chainside chain))

Amino acids are so-called because they have both amino Amino acids are so-called because they have both amino groups and acid groups, which have opposite charges. groups and acid groups, which have opposite charges.

At neutral pH (found in most living organisms), the At neutral pH (found in most living organisms), the groups are ionised, so there is a positive charge at one groups are ionised, so there is a positive charge at one end of the molecule and a negative charge at the other end of the molecule and a negative charge at the other end.end.

• In a neutral solution and in a solid state In a neutral solution and in a solid state amino acids exist as a dipolar ion.amino acids exist as a dipolar ion.

• HH33NN++ – CH – CH22 – COO – COO--

• The ion is formed as a result of an The ion is formed as a result of an internal acid base reaction the COOH internal acid base reaction the COOH group donates a proton to the NHgroup donates a proton to the NH2 2 groupgroup

• This kind of ion is called a zwitterionThis kind of ion is called a zwitterion• Amino acids can therefore exist in three Amino acids can therefore exist in three

forms depending on the pHforms depending on the pH

The charge on the amino acid changes with pH:

low pH (acid)low pH (acid)

neutral pHneutral pH

high pH (alkali)high pH (alkali)

It is these It is these changes in changes in charge with charge with pH that pH that explain the explain the effect of pH effect of pH on enzymeson enzymes. .

• Proteins are said to be Proteins are said to be amphotericamphoteric and can act as and can act as buffersbuffers

• An amphoteric substance can act An amphoteric substance can act as both an acid an a baseas both an acid an a base

• Buffers resist changes in pH Buffers resist changes in pH

PolypeptidesPolypeptides

• Amino acids are joined together Amino acids are joined together by by peptide bondspeptide bonds. .

• The reaction involves the The reaction involves the formation of a molecule of water formation of a molecule of water in another condensation in another condensation polymerisation reactionpolymerisation reaction

Peptide bonding

HC

HN C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

HC

HN C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

H

CH

N C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

CH

N C

HH

OR

HC

HN C

H

HO

H

O

O

R

water

Peptide bondPeptide bond

A condensation reactionA condensation reaction

Peptide bonding

CH

N C

HH

OR

HC

HN C

H

O

O

R

A dipeptideA dipeptide

When two amino acids join together a When two amino acids join together a dipeptidedipeptide is is formed. Three amino acids form a formed. Three amino acids form a tripeptidetripeptide. .

Many amino acids form a Many amino acids form a polypeptidepolypeptide. e.g.:. e.g.:

+NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp —COO-+NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp —COO-

In a polypeptide there is always one end with a free In a polypeptide there is always one end with a free amino (NHamino (NH33) group, called the ) group, called the N-terminusN-terminus, and one end , and one end

with a free carboxyl (CO2) group, called the with a free carboxyl (CO2) group, called the C-terminusC-terminus..

• In a protein the polypeptide chain In a protein the polypeptide chain may be hundreds of amino acids may be hundreds of amino acids long. long.

• Amino acid polymerisation to form Amino acid polymerisation to form polypeptides is part of polypeptides is part of protein protein synthesissynthesis..

• It takes place in ribosomes, and is It takes place in ribosomes, and is special because it requires an RNA special because it requires an RNA template. template.

• The sequence of amino acids in a The sequence of amino acids in a polypeptide chain is determined by polypeptide chain is determined by the sequence of the genetic code in the sequence of the genetic code in DNA. DNA.

• The diagram shows the structural formulae of two amino acids

• Name one chemical element found in all amino acids, but not in monosaccharides.

• Nitrogen / N (not N2)• (ii) What type of chemical reaction occurs to form a

dipeptide?• Condensation• (iii) Draw around the amine group, the acid group and

the R group for each amino acid and label them• (iv) Draw the structural formula of the dipeptide

formed when these two amino acids combine.

Amine Amine groupgroup

Acid Acid groupgroup

R groupR group