Alpha Helix Protein: Structure & Definition

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  • 0:04 The Alpha Helix & Structures
  • 1:11 Amino Acid Structure
  • 2:02 The Alpha Helix Structure
  • 2:59 Why Alpha Helix?
  • 3:59 Are Alpha Helices Permanent?
  • 4:47 Lesson Summary
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Lesson Transcript
Stephanie Gorski

Steph has a PhD in Entomology and teaches college biology and ecology.

Expert Contributor
Elaine Chan

Dr. Chan has a Ph.D. from the U. of California, Berkeley. She has done research and teaching in mathematics and physical sciences.

Chains of amino acids often fold into spirals called alpha helices. In this lesson, we will discuss the structure and importance of an alpha helix, why we see so many alpha helices, and what happens when alpha helices fold incorrectly.

The Alpha Helix & Structures

The key to understanding alpha helices is the old saw about opposites attracting. If you're a partially-positive hydrogen atom in an amino acid, you'll be on the lookout for a partially-negative oxygen. When you find a partially-negative oxygen, you'll stick to it with a bond known as a hydrogen bond. Given enough amino acids, this will often make a long, twisted, rod-shaped alpha helix in what you might envision as an old-fashioned dance of amino acids. Just like attraction and dancing, there are things that we can easily predict, but there are some things that still remain a mystery.

When we talk about alpha helices, we are talking about secondary structure. The primary structure of a protein is the order of amino acids that make it up. The secondary structure is the way in which these amino acids interact with each other to form regular shapes, usually alpha helices and beta pleated sheets. The many small secondary structures on a protein molecule interact to form a globular structure called a tertiary structure. Several of these molecules may interact together to form a quaternary structure.

Amino Acid Structure

When we talk about our genetic code, what we mean is that genes code for different amino acids. Chains of amino acids then form proteins. The shape and structure of these proteins determine their function in the body.

Remembering amino acid structure will help us understand why an alpha helix forms the way it does. An amino acid always has a carbon in the middle, and as you may know, carbon forms four bonds. One of the carbon's bonds is to a hydrogen atom. Another bonds to an amino (-NH2) group and one to a carboxyl (-COOH) group. The last bond is to a side chain that is unique to each amino acid. Some of these side chains are relatively large, while some are small; some have charges, while others do not. These individual differences affect how amino acids interact to form proteins.

The Alpha Helix Structure

An alpha helix, sometimes called a Pauling-Corey-Branson alpha helix, is a coil of amino acid chain. It almost always coils in the right-handed direction. In an alpha helix, every partially-positive amino group sticks to the partially-negative oxygen in the carboxyl group of the amino acid four residues earlier on the chain. An alpha helix is tightly packed, and the end result of this twisting formation is that the amino acid chain will form a rod.

The amino acids methionine, alanine, leucine, glutamate, and lysine are highly likely to form an alpha helix. The amino acids proline and glycine are unlikely to form an alpha helix. Proline has a very large side chain, and it's believed that prolines get in the way of alpha helix formation. On the other hand, glycine is small and flexible, so it does not tend to constrain itself in an alpha helix formation.

Why Alpha Helix?

The alpha helix is the most common secondary structure, with beta pleated sheets coming in a close second. Why?

Alpha helices make the most efficient use of hydrogen-bonding, which is the stickiness between hydrogen in amino groups and oxygen in carboxyl groups. As discussed earlier, we can predict whether it is likely that an amino acid chain will form an alpha helix based on which amino acids are in the chain. However, scientists aren't able to predict precisely how a given amino acid chain will fold.

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Additional Activities

Alpha Helix Protein Questions

Quaternary Structure

Hemoglobin (more than 70% alpha helix) has four regions where the oxygen binds and releases. The hemoglobin shape changes with the oxygen phases. The shape of protein also changes slightly due to individual differences.

1.The shape of hemoglobin is what kind of structure? (a) primary (b) secondary (c) tertiary (d) quaternary

Tertiary Structure

2.The three dimensional shape of the protein is determined mainly by what?

(a) sequence of amino acids (b) presence of alanine (c) absence of glycine (d) random amino acids

Secondary Structure

3.The main kinds of secondary structure are?

(a) alpha helices and beta sheets (b) random coils (c) denatured proteins (d) beta sheets

4.Amino acids that are not likely to form an alpha helix are?

(a) proline and glycine (b) alanine (c) leucine

5.A helix propensity scale, based on experimental evidence of the frequency of certain amino acids in alpha helices, finds that the three highest amino acids are?

(a) alanine, leucine, arginine

(b) alanine, tyrosine, valine

(c) glycine, alanine, histidine

Primary Structure

6.The COOH from one amino acid and the NHH of another amino acid form what?

(a) peptide bond (b) H bond (c) resonance

In this section of the carbon backbone of the amino acid chain, -N-C-C-N-C-C- , the first C on the left and the second C from the right have residues (side-chains) attached to them.

7.The carbon atom with the residue is called what?

(a) C-alpha (b) C-beta (c) carbon backbone

These residues are twenty different side-chains that distinguish one amino acid from another. These side chains can rotate about the C(alpha)-C bond and have many conformations.

8.The different rotational positions of the residues are called what?

(a) rotamers (b) isotopes (c) variations (d) translations

The bonds between the C(alpha) and N and C(alpha) and C can rotate. These angles are found experimentally to be restricted to certain values for alpha helices and certain values for beta sheets.

9.This is represented graphically as?

(a) Ramachandran Plot (b) Plotkin Plot (c) Ambrose Plot


1. (d) and (c) 2. (a) 3. (a) 4. (a) 5. (a) 6. (a) 7. (a) 8. (a) 9. (a)

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