Protein Modeling

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Protein Modeling review

Primary Structure

the arrangement of amino acids in a protein as they appear linearly. Also contains the location of covalent links (i.e. disulfide bonds)

Secondary Structure

The areas where the protein coils or folds such as alpha helices and beta sheets. They are stabilized by hydrogen bonding

Tertiary Structure

three dimensional structure of a protein that comes from a large number of non-covalent interactions that take place between amino acids.

Quaternary Structure

Interactions that are non-covalent and bind multiple polypeptides into a larger single protein.

Peptide bonds

The covalent bond that amino acids are bonded together with. If the chain of amino acids is short (usually less than 30 amino acids) it is referred to as a peptide. If it is longer it is known as a polypeptide.

Peptide bond formation occurs in a condensation reaction that involves the loss of a water molecule

Hydrophobic amino acids

Hydrophobic amino acids are found on the outside of a protein where there is no water.

Hydrophilic amino acids

Hydrophilic amino acids are found inside a protein where there is water.

Why are Zinc Fingers important?

They allow our cells to make smaller stable structures. Bacteria do not take advantage of them, but they are found in all plants and animals. They play a major role in DNA recognition because they curl along the DNA or RNA strands and recognize the specific base pairs.

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