primary structure > secondary structure > tertiary structure > quaternary structure
Proteins are responsible for both the function and the appearance of whole organisms. your build – so the protein structure – is crucial to what proteins can do. The protein structure is divided into four levels that build on each other. One of these levels is the secondary structure.
the secondary structure is the second level of protein structure and describes primary structure connections within its backbone. Through the links, the primary structure is arranged into three-dimensional elements.
For a good understanding of secondary structure, you can check out the article on protein structure for an overview of the four levels of structure of proteins and refresh your knowledge of secondary structure.
Formation of the secondary structure of a protein
Secondary structure refers to folds and links that arise when the individual building blocks in the primary structure of the protein accumulate. To be more precise, this creates links between the bonds that hold individual building blocks together in the primary structure.
Primary structure by peptide bonds between amino acids
The individual building blocks of the primary structure of the protein are amino acids. They are attached one after the other in a long chain and thus form one polypeptide chain. To link individual amino acids together, between them peptide bonds educated.
Linkage of amino acids
Each amino acid contains one amino group (-NH2), one carboxy group (-COOH). For the linking of two amino acids A and B, the carboxy group of amino acid A reacts with the amino group of amino acid B – a peptide bond is formed.
When many amino acids join together, a lot of peptide bonds are strung together. This arrangement is also called the backbone of a protein. This backbone forms the basis for the secondary structure of a protein.
Secondary structure by hydrogen bonding between peptide bonds
The secondary structure of proteins consists of three-dimensional arrangements of the polypeptide chains. These arise when there are differences between different peptide bonds within the polypeptide chain hydrogen bonds form.
hydrogen bonds
To understand hydrogen bonds, you have to think down to the atomic level.
Some atoms of a molecule have free ones electron pairs. These arise when not all electrons are used for the bonds within the molecule. The lone pairs of electrons are negatively charged and are mostly on oxygen– (O) and nitrogen atoms (N) to find. Hydrogen atoms (H), on the other hand, tend to be positively charged.
Positive and negative attract each other, so there are interactions between free electron pairs and hydrogen atoms that have an attractive effect. This attraction can become so strong that a kind of bond is formed and a hydrogen bond is formed.
Since a peptide bond contains both free pairs of electrons and hydrogen atoms, hydrogen bonds can form between different sections of the polypeptide chain. The chain is deformed so that certain structures are formed.
Elements of the secondary structure of proteins
Two such structures occur constantly in a protein and are therefore characteristic of the secondary structure: α-helices and β sheets.
Alpha helix structure
the a-helix (alpha helix) describes a structure in which the chain is right-handed in the form of a helix winds.
Because of the twisted structure, amino acids are located directly below the amino acid in the helix that is actually four positions further down the polypeptide chain. A hydrogen bond can now form between these two amino acids and stabilize the structure of the helix.
An oxygen atom forms a hydrogen bond with a hydrogen atom of the amino acid above it. This arrangement means that an average of 3.6 amino acids fit into each turn of the helix.
While a helix is very stable, it is also a structure that can be dynamic under certain conditions, somewhat like a metal spring. For example, a rarer form of helices found in secondary structures are π-helices. These are characterized by 4.4 amino acids per turn.
The amino acid proline has a special structure that does not allow it to form a hydrogen bond. Therefore, it can only be placed at the beginning or end of the helix without significantly disturbing the structure of the helix. This property has earned proline its nickname «structure breaker».
Beta sheet structure
The three-dimensional structure of a β-Folder (Beta leaflet) is reminiscent of a sheet folded like an accordion. The peptide bonds are in the plane of the folded sheet, while the organic residues of the amino acids protrude upwards and downwards from the folded edges.
Don’t be fooled though: unlike accordions, β-sheets are very stable and rigid.
As with the helices, hydrogen bonds form to stabilize the structures, but here in such a way that the folded sheets are arranged lengthwise next to each other. The hydrogen bonds form in groups of two between oxygen and hydrogen atoms.
Multiple leaflets can also be described based on their orientation to each other. parallel leaflets are aligned in exactly the same way, the residues point in the same directions. antiparallel leaflets on the other hand, are arranged exactly opposite to each other. If a remnant of a leaflet faces up, the rest of the neighboring leaflet faces down at the same point.
The organic residues protruding from the sheet structure are very close to each other. Therefore, if these residues are too large, they can get in each other’s way, disrupting or disrupting the structure. To prevent this, β-sheets mostly contain amino acids that have rather small residues.
Other Structures
Will in the protein structure a turn initiated is often one Ribbon in action. Hydrogen bonds are formed in such a way that the peptide chain can complete a loop and thus undergo a complete change of direction.
β-loops are often used, for example, when there is a need to move from one β-sheet to the next sheet that is positioned lengthways next to the first.
Portions of the peptide chain that do not assemble into sheets or helices appear random. They do not have a specific repeating structure, which is why these parts are also called random coils (dt.: any windings) are called.
When a protein is heated denatured it. This means that all existing structures dissolve and the chain becomes one random coil rearranged. Such a denaturation can e.g. B. be observed when an egg is fried. The heat denatures the proteins in the egg and turns white/yellow. In addition, the egg will harden.
Secondary Structures in Nucleic Acids
nucleic acids are an umbrella term for molecules like that DNA or the RNA. You may have heard that DNA has a double helix structure. This form of DNA can be explained by secondary structures and hydrogen bonds.
A detailed insight into the structure of the DNA can be found in the articles on the structure of the DNA and the structure of RNA.
Double helix structure of DNA
The DNA consists of two opposite strands in which the four bases adenine, cytosine, guanine and thymine alternate. When unfolded, its structure resembles a ladder and the rungs are each formed by two bases located opposite each other in the strands. It must be noted that two bases that form a rung face each other complementary are.
Complementary base pairs are adenine-thymine and cytosine-guanine. They can each form hydrogen bonds between themselves and thus hold the two single strands together in each rung to form a double strand. However, the DNA in a cell is not flat like a ladder, but is twisted. The two strands wind around each other, forming a double helix.
Why exactly is the DNA twisted into a helix and not just a flat ladder?
All bases in DNA contain nitrogen atoms with which they can form hydrogen bonds with one another. However, these nitrogen atoms lead to a problem: due to their incorporation, the bases of the DNA do not like water and try to get as far away from water as possible. Since the DNA is in a water-rich environment, the bases desperately want to be shielded from it – and this is where the double helix structure comes into play.
When the double strand of DNA forms a double helix, the bases inside the helix disappear and are therefore a little more protected. But the deformation has a second effect: when the ladder is twisted, the distance between the two rungs decreases. As a result, the bases are better shielded on the one hand and the DNA takes up less space on the other. Structuring the DNA as a double helix therefore leads to a win-win situation for everyone involved.
Secondary Structures in RNA
RNA has a structure that is very similar to DNA. However, an RNA strand is usually as single strand before and not as a double strand. Further elements of the secondary structure can form in this single strand.
stems as elements of the secondary structure
Some parts of an RNA strand can be complementary to each other and cause the single strand to combine in places to form a double strand. These structures are comparable to the DNA double helix described so far.
loop as elements of the secondary structure
Between the complementary stem-Areas of RNA, however, often still contain a few bases that are not complementary to each other and therefore do not pair. This can lead to so-called loop-Structures (loops) coming.
However, the secondary structure of RNA not only has the purpose of keeping the RNA stable and compact, but also fulfills other important tasks.
Some strands of RNA are created by copying DNA. This process will transcription called. However, the RNA should only reproduce a certain sequence of the DNA. To make sure that only the desired part is copied, a forms hairpin loop in the RNA once the sequence has been fully assembled. This causes the proteins responsible for transcription to fall off the DNA. The transcription can thus be terminated punctually and the RNA strand has the desired length.
Secondary structure – the most important
- The spatial arrangement of the primary structure through hydrogen bonds is referred to as the secondary structure.
- A secondary structure can be formed by proteins, but also by nucleic acids such as DNA or RNA…