An alpha helix is a secondary structure in proteins where the polypeptide chain is curved like a spiral. Proteins are an important part of living things. Inside cells, proteins make up enzymes, which catalyze chemical reactions. They also form structures, transport materials and help with cell motility, cell division, and more. Proteins are able to do a diverse array of jobs inside the cell due to their unique three-dimensional structure. The structure of a protein is determined by its amino acid sequence. Proteins are made of long strands of amino acids called polypeptide chains. The way the polypeptide chains folds and allows amino acids to interact with each other creates the three-dimensional structure necessary for their function.
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The primary structure of a protein is the amino acid sequence of the polypeptide chain. The way the polypeptide chain forms hydrogen bonds determines the secondary structure. There are two main types of secondary structures in proteins, alpha helices and beta pleated sheets. The hydrogen bonding pattern of the amino acids in the polypeptide chain determine whether an alpha helix or a beta pleated sheet will form. Polypeptide chains can have alpha helices, beta pleated sheets or both. Alpha helices are formed like a right handed spiral, whereas beta pleated sheets look like accordion folds.
Alpha helices make more efficient use of hydrogen bonding availability compared to beta pleated sheets and thus are more compressed. Alpha helices are also the most common secondary structure in proteins.
To understand how alpha helices are formed, first the structure of amino acids must be understood. Amino acids are made of a central carbon atom bonded to a carbonyl group on one side, an amino group on the opposite side, a hydrogen atom and a side chain that is variable. In alpha helices the carbonyl group hydrogen bonds to the amino group of the amino acid that is four away from it. This creates a tight spiral pattern that forms the alpha helix. The side chains of the amino acids extend outward from the helix, allowing them to interact and help produce further structures in the protein.
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Secondary structure is important. If a protein that is supposed to have alpha helices misfolds into beta pleated sheets, diseases can occur. For example, prion diseases are protein folding disorders where a protein with alpha helices is converted to having beta pleated sheets. This misfolded protein can then turn neighboring proteins into misfolded proteins as well. These proteins are not able to do their job and can cause problems. Prion diseases, like mad cow disease or Creutzfeldt-Jakob disease are caused by misfolded prion proteins where alpha helices have turned into beta pleated sheets.
The alpha helix secondary structure is one of four layers of structure in proteins. The levels of protein structure include:
Primary structure is the amino acid sequence of the polypeptide chain. The secondary structure is the hydrogen bonding pattern of the polypeptide chain as discussed here. Secondary structures include alpha helices and beta pleated sheets. The tertiary structure of proteins is the three-dimensional structure of the protein. Tertiary structure is especially important for enzyme function and can be disrupted during the process of denaturation. During denaturation excess heat or changes in pH can cause the protein to unfold and lose its shape, thus reducing its ability to do its job in the cell. The last level of protein structure is quaternary structure. In quaternary structure different polypeptide chains interact as subunits in a protein. Not all proteins have a quaternary level of structure.
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Certain amino acids are more likely to form alpha helices compared to beta pleated sheets. The amino acids likely to form alpha helices include:
Proline is an amino acid that tends to disrupt alpha helices. Proline has unique side chain that forms a ring structure with the amino group of its amino acid. This prevents the amino group from creating the hydrogen bonding needed to form an alpha helix. Typically proline is found as a break between different forms of secondary structures as its side chain is too large to be accommodated in alpha helices.
Many proteins have alpha helices as motifs in their structure. Some examples of classes of proteins that include alpha helices are soluble proteins and transmembrane proteins. Soluble proteins are those that have a hydrophilic exterior and are soluble in water. About 35% of all residues in water soluble proteins are composed of alpha helices. Some examples of soluble proteins that have alpha helices include myoglobin and hemoglobin.
Transmembrane proteins are proteins that span the plasma membrane. These proteins help with cellular motility, anchoring the cell to the extracellular matrix or other cells, transporting materials across the cell membrane and more. Transmembrane proteins are often made of alpha helix bundles.
The primary structure of proteins is the sequence of amino acids that makes up the polypeptide chain. The hydrogen bonding pattern of amino acids creates the secondary structure. An alpha helix is one type of secondary structure that is shaped like a curved ribbon due to hydrogen bonding between the carbonyl group and the amino group of amino acids that are four residues apart. The alpha helix is the most common secondary structure, but there are also others, including beta pleated sheets. The secondary structure of proteins is important and misfolding at this step can cause disease. For example, mad cow disease occurs when neural proteins change their secondary structure from alpha helices to beta pleated sheets.
The secondary structure informs the tertiary structure, which is the three-dimensional shape of the protein. Some proteins also have quaternary structure, which is the physical shape of subunits made from different polypeptide chains.
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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
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
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
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)
An alpha helix structure is a type of secondary structure in a protein. In an alpha helix the polypeptide chain twists like a spiral via hydrogen bonding between the amino acids.
An alpha helix is held together with hydrogen bonds. These bonds form between the amino group of one amino acid and the carbonyl group of another located about 4 amino acids away. This forms a twisted, helical structure.
The amino acids that have a high probability of being found in an alpha helix are methionine, alanine, leucine, glutamate, and lysine. These amino acids often form an alpha helix due to the structure of their side chains.
An alpha helix is a secondary level of protein structure. Proteins have four possible levels of structure. The primary structure is the amino acid sequence, the secondary structure is created by hydrogen bonding, the tertiary structure is the overall three dimensional shape of the protein and the tertiary structure is any subunits that are part of the protein.
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