protein structure

Protein Structure

Topic 7.5

Proteins- a.k.a.* polypeptides

• Peptide- short chain of amino acids– Dipeptides- 2 amino acids bonded together– Polypeptides- many amino acids bonded together

• Peptide bond between amino acids– Formed by condensation reaction– Broken by hydrolysis

• Have up to 4 levels of organization– All have 3 levels, most have 4 levels

* a.k.a.- also known as

Primary Structure

• sequence of amino acids • precise sequence is determined by

genes– Changing one of the amino acids in a

sequence can change entire protein

• Polypeptide chains can be 50 to 1000 amino acids in length

• R groups of the amino acids aid in shaping the protein

• Example: Lysosyme- has 129 amino acids, all in a very specific order.

Secondary Structure• Describes the shape of the protein

– 2 types: Alpha helices and Beta pleated sheets

• Local folding, short distance interactions• Can have a mixture of both• Determined by the Hydrogen bonds across amino

acids (the R groups)– From the carboxyl (C=O) group of one a.a. and the

amino group (N-H) of another a.a. – H-bonds help to stabilize the helices or pleated sheets

Alpha helix Beta pleated sheet

Protein with a mixture of both helices and sheets

Tertiary Structure

• Overall 3-dimensional shape of proteins

• Shape results from further interactions between R groups across that are ‘distant’– Also influenced by the

aqueous environment- WHY?

Tertiary Structure

• Interactions include:– +charged R groups interacting with -charged R groups– Hydrophobic amino acids orient themselves away from the

water, towards the interior to avoid contact– Hydrophilic amino acids orient themselves towards water

(outward)– Hydrogen bonds between polar R groups– Disulfide bridges between cysteines (both R groups have sulfur

atoms that covalently bond to each other)

• Formed/Maintained by more distant interactions between R groups

• Globular proteins, have a hydrophobic core

Polar and electrically charged amino acids

Non-polar amino acids

With a partner, make a hypothetical chains of at least 25 amino acids (primary structure).

Show how the amino acids could potentially interact to make a tertiary structure for a protein.

Quaternary Structure

• More than 1 chain of polypeptides that fit together.

• Often has a prosthetic group- a non-protein atom or molecule embedded in it.

• Example- hemoglobin has 4 polypeptide chains with 4 iron prosthetic groups.

Lysozyme- an example

Primary Structure

Secondary Structure

Tertiary Structure

2 main categories of protein shapes

• Globular Proteins-– Have hydrophobic amino acids in the interior,

hydrophilic on the outside

– Compact and rounded

– Soluble in water

– Example- Enzymes, hemoglobin, insulin, anti-bodies

• Fibrous Proteins-– Elongated shapes, tough and insoluble

– Example- collagen in skin, keratin in hair

Fibrous protein Globular protein

Structure leads to function

• Biological activity of the molecule is determined by its structure

• If the structure is changed, the function will change.

• Ability to recognize and bind to some other molecule important to many proteins– Ex.- antibodies and enzymes

Non-polar amino acids

-water insoluble

-stabilize the entire protein when found in the center of water soluble amino acids

-cause proteins to remain embedded in the cell membrane

Polar and Non-polar amino acids

Polar Amino Acids:-water soluble (remember water is polar/when considering polarity ‘like attracts like’)-In the cell membrane:

1. create channels in the proteins for hydrophobic substances to pass through2. cause parts of membrane proteins to

protrude from the cell membrane3. Transmembrane proteins have two polar regions (one on surface and one in

channel)

Polar and Non-polar amino acids

Ways to change the structure of a protein

• pH

• High temperature

• If the shape of the protein changes, it will no longer be able to function in the same way.

• Denatured- protein is permanently changed

• sickle cell anemia- shows how primary sequence affects the quaternary structure.