Protein Chemistry 2007

7/28/2019 Protein Chemistry 2007

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PROTEIN

CHEMISTRY


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Protein

Complex biological polymers.

Many are water soluble (eg: antibodies,

enzymes & haemoglobin).

Some are insoluble, tough & resistant

structures (eg: collagen & keratin).

Makes up 18% of the mass of averageperson.


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Protein(s) Function Location

Myosin muscle

contraction

muscle tissue

Actin

Chymotrypsin digestive

enzymes

small intestine

Pepsin stomach

Insulin hormone blood

Ferritin storage bone marrow,

liver, spleen

Immunoglobulins antibodies blood

Collagen structural

proteins

skin, tendon

Keratin hair

Haemoglobin transport blood


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Amino Acids The Building Block of Proteins

20 different amino acids.

19 containsCOOH andNH2 group

attached to the same C atom.

except Proline which is a cyclic contains 2amino group.

H H O

N C C

H R O - H

N terminal C terminal


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20 amino acids differ in the nature of the R

group which vary in their complexity. The physical & chemical properties of the side

chain determine the unique characteistics of an

amino acid.

The R groups are categorized into 3 broadcategories:

i. Non polar group - hydrophobic

ii. Polar group - hydrophiliciii. Electrically charged group acidic & basic

due to negative & positive charges.


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Type of R

group

Example Structure

Non-polar Alanine (ala) H2N-CH(CH3)-COOH

H2N-CH(CH(CH3)2)COOHValine (val)

Polar Serine (ser) H2N-CH(CH2OH)-COOH

Electrically

charged(acidic or

basic)

Aspartic acid

(asp)

H2N-CH(CH2COOH)-COOH

Lysine (lys) H2N-CH(C4H8NH2)-COOH


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The Ionisation of Amino Acids

Shows both properties of an acid & base(amphoteric).

H2NCH(R)COOH H2NCH(R)COO- + H+

(acidic behaviour)

H2NCH(R)COOH + H+

+H3NCH(R)COOH (basic behaviour)

At pH 7 the structure of glycine is+H3NCH2COO

- (dipolar ion known aszwitterions)


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Polypeptide Chains

2 amino acids adjacent to each other canundergo condensation synthesis forming acovalent linkage called a peptide bond.

The chain has a polarity with an N-terminal(for the nitrogen group) and a C-terminal(for the carbon group).

The repeating sequence of atoms alongthe chain (-N-C-C-N-C-C-) is referred to asthe polypeptide backbone.


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monomers form a long chain polymer via

condensation reaction (polypeptide chain).


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Protein conformation

A proteins function depends on its unique

conformation, which is a consequence of

the specific linear sequence of the amino

acids that make up the polypeptide chain.

The function of a protein depends on its

ability to recognize and bind to some other

molecule (eg: enzyme recognize andbinds to its substrate).


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The Primary Structure of Proteins

Linear (no fold/straight) polymer of aminoacids.

Each polypeptide has direction and

sequence of amino acid residues in achain known as primary structure of thepolypeptide.

A polypeptide chain is always synthesizedfrom the N-terminal end to the C-terminalend.


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The precise primary structure of a proteinis genetically controlled and crucial indetermining the other levels of structurethat protein can adopt.

A slight change in the primary structure

can affect a proteins conformation andability to function. (eg: sickle-cell anemia isan inherited blood disorder where oneamino acid is substituted with another in asingle position in the primary structure ofhaemoglobin.)


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Frederick Sanger, determined the

sequence of amino acids for hormoneinsulin.

He used various protein-digesting

enzymes that cleaves the polypeptide atspecific places into fragments and then

searched for overlapping regions.


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Secondary Structure of Protein

The polypeptide chain repeatedly coiled orfolded in patterns that contribute to theproteins overall conformation.

These structures are stabilized byhydrogen bonding between the peptidebond regions of the chains backbone.

One such secondary structure is the alpha

() helix, a delicate coil held together byhydrogen bonds between every fourthpeptide bond.


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Lysozyme is a typical globular (roughly

spherical) protein that has stretches of-helix.

Another type of secondary structure is the

beta () pleated sheet in which thepolypeptide chain folds back and forth or

where the two regions of the chain lie

parallel to each other.

Hydrogen bond between the parallel

regions hold the structure together.


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Tertiary Structure of Proteins

The 3D shape or conformation of a proteinchain is maintained by a series of mainly

non-covalent, intramolecular interactions

between the R groups of the amino acidsmaking the chain.

Some of these interactions are relatively

easily distrupted, others not so andinclude:

i. van der waals forces between non-polar

side chains,


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ii. Hydrogen bonding between polar R

groups,

iii. Ionic bonds (salt bridges) between

ionised R-groups (positive & negative

charged groups) andiv. Strong covalent disulphide bridges

formed between 2 cysteine residues at

different location in the primarysequence.

Protein Chemistry 2007

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