Macromolecules 3: Proteins

Additional Resources (1)

• The Tree of Life, proteins and DNA module

Additional Resources (2)Protein structure and conformation

links• Molecular Workbench DNA and

protein module• Summary of protein confirmation• Protein movie

7.5.4: State 4 functions of proteins, giving a named example of each

1. Structural support (Fibrous proteins)

Silk: cocoons and webs Keratin: hair, horns, skin, nails, wool, beaksCollagen: tendons and ligamentsPDB 101

2.Enzyme Function (Globular soluble)Amylase CatalasePepsinTrypsinDNA helicaseDNA synthaseEtc etc etc…

3. Protein hormonesGlobular soluble• Insulin• ACTH• Vasopressin• Somatostatin• Prolactin• Growth hormone

4. Transport proteins (Globular, soluble)

Haemoglobin, myoglobin: transport of essential substances (oxygen, carbon dioxide)Myoglobin was the first protein to be thoroughly described

5. Energy storage: solubleOvalbumin, Casein (milk protein), storage proteins in plant seeds

6. Movement proteinsActin and myosin form muscle fibresAnimation of actin/myosin

7. Receptor proteins (also pumps, channel proteins)

• Adrenergic receptors

• G-protein receptors• Cannabinoid

receptors• Opioid receptors• Aquaporin

channels• Na/potassium

pump proteins

8. Immune function:Antibodies (Immunoglobulins)

Globular soluble proteins: IgG, gA, IgM,

Proteins• > 50% of the dry mass of a cell is

proteinProteins are used for:• Structural support• Energy storage• Transport of other substances• Signalling from one part of the

organism to another• Movement• Defence against foreign substance• Enzymes• Humans have tens of thousands of

different proteins• Most structurally sophisticated

molecule, due to unique 3D shape or conformation

Protein Functions

Amino Acid (Monomers)Amino acid structure:

NH2 - C - COOH

Amino acids differ due to the R (functional) group

The structure of the R-group determines the chemical properties of the amino acid

Amino Acids link together to form polypeptides

• 2 Amino Acids form a covalent bond, called a PEPTIDE BOND, through a condensation reaction to form a dipeptide

• Multiple amino acids can bond to each other one at a time, forming a long chain called a POLYPEPTIDE

Peptide Bonds – link amino acids

20 Amino Acids are used in cells

7.5.3: Explain the significance of polar and non-

polar amino acids

Hydrophilic Amino Acids Polar (but uncharged) amino acids are

hydrophilic & can form H-bonds• Serine• Threonine• Glutamine• Asparagine• Tyrosine• Cysteine

Hydrophobic Amino Acids • Glycine• Alanine• Valine• Leucine• Isoleucine• Methionine• Phenylalanine• Tryptophan• Proline)

Nonpolar amino acids are hydrophobic and are usually found in the centre of the protein.

They also found in proteins which are associated with cell membranes.

Electrically charged Amino Acids

The electrically charged amino acids have electrical properties that can change depending on the pH.

Aspartic AcidGlutamic AcidLysineArginineHistidine

Special Amino AcidsCysteine can form covalent disulfide bonds

Proline has a unique structure and causes kinks in the protein chain

‘Essential’ Amino AcidsIn humans, not all

amino acids can be manufactured by the body; 10 (8 in adults)

must be taken in through our diet.

These are the ‘essential’ amino

acids

7.5.1: Explain the four levels of protein structure, indicating the significance of

each level

Four Levels of Protein Structure/ Conformation

1. Primary - unique linear sequence in which amino acids are joined, can have dire circumstances if changed (insulin)

2. Secondary - refers to three dimensional shapes that are the result of H bonding at regular intervals, due to interactions between the amino acid backbones• alpha helix is a coiled

shape• beta pleated sheet is

an accordion shape

3. Tertiary Complex 3-D globular

shape due to interactions between R groups of amino acids in it• Globular proteins such

as enzymes are held in position by these interactions

4. Quaternary Consist of more than one

polypeptide chain subunits, associated with interactions between these chains 2719

Protein Shape Determines Function• Proteins with only primary and secondary structures are

called fibrous proteins (claws, beaks, keratin, wool, collagen, ligaments, reptile scales)

• Proteins with only 1,2,3 shapes are called globular proteins

• If a protein is incorrectly folded, it can’t function correctly

• Not understood how proteins fold themselves, seem to have molecules called chaperone proteins or chaperonins that assist others

• A protein is denatured when it loses its shape and therefore its ability to function correctly

2820

Primary Structure• A unique sequence of

amino acids in a long polypeptide chain

• Involves peptide bonds between the carboxyl and amine groups

• Any changes in primary structure will affect a protein’s conformation and its ability to function• Example: Sickle cell anemia

LYS VAL PHE GLY ARG CYS

Sickle cell anaemiaSickling occurs due to a mutation of the Hb gene, associated with replacement of glutamic acid by valine

Secondary StructureMade by hydrogen bonds between the backbone of the amino acids (amino

group and carboxyl groups)

• α-helices: area with a helical or spiral shape. Held together by H bonds between every 4th amino acid

• β-pleated sheets: area where 2 or more regions of the polypeptide chain lie in parallel

αhelix a β-pleated sheet

• The bonds involved are hydrogen bonds• Large proteins will have regions containing both

structures

Tertiary Structure: FOLDINGThe protein folds up since various

regions on the secondary structure are attracted to each other:

1. Disulfide Bridges: strong covalent bonds between cysteine’s sulfhydryl (-SH) groups

2. Ionic Bonds: between positively and negatively charged side chains

3. Hydrogen Bonds: between polar side groups

4. Hydrophobic Interactions: non-polar side chains end up on the inside of a protein, away from water

Quaternary StructureComplex proteins exist as

aggregations of 2 or more polypeptide subunits

QUATERNARY STRUCTUREE.g. immunoglobulins

• The bonds involved are the same as those for tertiary structure

Chain 1

Chain 3 Chain 2

Protein denaturationProtein denaturation refers to loss of 3 – dimensional structure (and usually also biological function) of a protein – die to changing of the bonds that maintain secondary and 3rd degree structure, even though the amino acid sequence remains unaltered

Denaturation can be caused by:• Strong acids and

alkalis – profound pH change

• Heavy metals – may disrupt ionic bonds

• Heat, radiation, UV radiation

• Detergents and solvents

7.5.2: Outline the difference between fibrous and globular proteins, referring to 2 examples of each

• A review from Cornell University

Fibrous proteinsOnly have primary and secondary structures

• Water insoluble• VERY tough, may also be

supple or stretchy• Parallel polypeptide chains

in long sheets or fibres• STRUCTURAL proteins –

collagen, cartilage, tendons, blood vessel walls

• CONTRACTILE proteins – actin and myosin

Globular proteinsHave all four levels of

protein structure• Water soluble• Tertiary structure critical

to function• CATALYTIC (enzymes)• REGULATORY –

hormones (insulin)• TRANSPORT

(haemoglobin)• PROTECTIVE

(immunoglobulins)