Imagine you are supposed to write a book. You only have the title in mind, everything else is still up to you. But how do you start now? How is the book supposed to go? At first, it seems like an overwhelming and almost impossible task. But if you break the book down into elementary parts, it becomes easier. Instead of writing a whole book at once, you start with just one chapter. Because a chapter is still relatively difficult to understand, one first devotes oneself to a paragraph, such as the introduction. And if you don’t yet know exactly how, you simply start with the first sentence.
In a similar way, macromolecules, such as nucleic acids, but also proteins, which take on universal tasks in living beings, have a hierarchical structure. After the sentences and paragraphs we now come analogous to the chapters, the tertiary structure.
primary structure > secondary structure > tertiary structure > quaternary structure
For more information on the other structural hierarchies, please refer to the corresponding explanations!
Building blocks of the tertiary structure
Spatially arranged, complex secondary structures of the polymers are already available as possible “building blocks” of the tertiary structure. These combined result in spatially even more complicated, tertiary structures. A selection of the most significant forms are listed below.
For more in-depth information, please have a look at the explanation of the secondary structure!
building blocks nucleic acids
In the case of nucleic acids, one must distinguish between deoxyribonucleic acid (DNA or DNA from English) and ribonucleic acid (RNA or RNA from English).
double helix of DNA
Viewed in a two-dimensional way, DNA appears like a rope ladder. Here are means hydrogen bonds two complementary base pairs are connected to each other and thus stabilize the two opposite strands.
A single hydrogen bond may be comparatively weak, but thousands can exert enormous structural forces. You can learn more about hydrogen bonding in the «Tertiary Structure Bond Forms» section below.
Now this “ladder” is twisted spatially, as this is more efficient. This results in a double helix and thus the typical structure of DNA.
Structural forms of RNA
Since RNA is usually present as a single strand, complementary sections on the same strand can bind and thus build up certain secondary structures:
- stems: These are deposits that – similar to DNA – combine to form a double strand.
- Loop: Between stem-areas often contain non-complementary sections called loops («loops«) appear.
building blocks proteins
In theory, an almost infinite number of combinations of amino acid chains and thus spatial arrangements in secondary structures can occur. However, there are two typical patterns in particular that occur:
There are many other secondary structures of proteins that occur less frequently.
α helices
at α helices are frequently occurring secondary structures, which are characterized by a right-hand twisted spiral.
β sheets
β sheets are also frequently occurring secondary structures of the proteins, which arrange themselves in strands corrugated to each other. A further distinction is made between parallel and antiparallel arrangements and intermediate forms.
Bonding forms of tertiary structure
The tertiary structure is stabilized by a variety of forces.
In the following, these binding forms are presented in abbreviated form. For more details, please have a look at the corresponding explanation.
hydrogen bonds
One hydrogen bonding (Hydrogen bridge or H-bridge for short) is an electrostatic attraction that can be formed between molecules with covalently bonded H-atoms.
The hydrogen atom must be bound to an atom with high electron negativity, such as B. nitrogen (N), oxygen (O) or fluorine (F). However, the interacting partner must in turn have a free pair of electrons.
disulfide bridges
For the disulfide bridge (or disulfide bond), a covalent bond is formed between two sulfur atoms. The only amino acid that can do this is cysteine.
cysteine is an amino acid that has (-SH) as an organic residue.
Disulfide bonds significantly determine the spatial folding of proteins. This connection is often compared to snaps because of its strength.
hydrophobic interactions
hydrophobic interactions occur with hydrophobic residues of amino acids or generally hydrophobic substances in an aqueous solution.
Since, for physical reasons, molecules try to reach the lowest level of entropy, ie the most stable and therefore lowest level of energy, the hydrophobic residues accumulate together. This effect can be exploited structurally, for example, in proteins with hydrophobic residues of the amino acids. The inner components of proteins are often hydrophobic, while the outer ones tend to be hydrophilic, since these have to interact more with water and other hydrophilic substances.
ionic bonds
One ionic bond describes an electrostatic bond between a positively ionized and negatively charged partner (cation and anion).
There are three positively (arginine, histidine and lysine) and two negatively (aspartic and glutamic acid) charged amino acids. As a molecule as a whole, they carry their respective charge and can therefore enter into an ionic bond within the molecule with a corresponding oppositely charged partner or on the molecule surface with other molecules.
Van der Waals forces
Van der Waals forces are weak omnidirectional forces of attraction between molecules that are not charged and do not have a permanent dipole.
Both van der Waals forces are attractive forces that occur due to spontaneous polarization of the atoms. They are counted among the weak chemical bonds, although they are not an actual bond but an interaction. They occur in particular between uncharged molecules that do not have permanent ones dipole (i.e. a charge asymmetry) own.
The terms «London forces», «Debye» and «Keesom» interactions are different expressions of the Van der Waals forces. However, these topics are so extensive that they require a separate article.
Definition of tertiary structure
the tertiary structure of a polymer describes its spatial arrangement, its conformation.
Tertiary structure of nucleic acids
the Tertiary structure of nucleic acids is mainly characterized by different sized furrows and directions of whorl.
The structure of the furrows is of great importance because many proteins bind to the DNA and processes are regulated by them. However, if the width and depth of the cleavage do not allow this binding, the protein cannot develop its effect.
The cell can presumably also control reactions in the DNA via the cleavages. In this way, many cells can convert sections of DNA from the B to the Z form.
Tertiary Structures of DNA
Depending on the conformation, i.e. the spatial arrangement of the DNA, a distinction is made between different forms of DNA. The respective form of the DNA plays a role, among other things, in the regulation of the reading of the information and thus in the regulation of the cell, of tissue and of entire organisms.
A form of DNA
This form is also called the “crystalline” or called anhydrous to anhydrous structure of DNA. It is larger in diameter than the most common shape: the B shape. The distance between the bases is also smaller and the grooves deviate.
B form of DNA
The most common form of DNA is the B form. It is characterized by a small and large furrow. It has a helix diameter of 2 nm and a complete turn is completed approximately every 10 base pairs (bp).
This form of DNA structure was also proposed by Watson and Crick in 1953.
Z-shape of DNA (zigzag shape)
The diameter of the Z form of DNA is smaller than that of the B form. The furrows are also less pronounced and, what is significant: it is left-handed.
There are numerous other forms of DNA, but these have been synthesized artificially. The above forms represent the predominant forms of DNA in living things.
Tertiary structures of RNA
Even RNA, despite being single-stranded, can, and often does, adopt complex conformations. In the following, only a few conformational peculiarities will be discussed, since there is simply a gigantic variety.
Helical double strands
Like DNA, RNA can also arrange itself in a double helix and adopt corresponding conformations.
Three strand structures
A common RNA conformational feature is a triplex at the minor groove of a duplex. If you look at the strand of a double helix, you can see that the distance between the «turns» is not always the same, and thus has a small and a deep furrow.
Certain RNA molecules can adhere to both the minor and deep grooves by means of hydrogen bonds and thus form triplex structures.
quadruplexes
Just as triplexes are formed, quadruplexes can also be formed. They exist in four ways by means of hydrogen bonds to one another.
Coaxial Stacking
Comparable to hydrophobic effects that can stabilize the interior of proteins, coaxial stacks also stabilize three-dimensional RNA structures. They are also sometimes referred to as helical stacks. The stabilization is due to the juxtaposition of the bases in the helices creating a common pi system.
This may sound complicated, but it is just a chemical phenomenon that increases the stability of the molecule. Such a coaxial stacking can be observed, for example, in t-RNA.
Tertiary structure of proteins
the Tertiary structure of proteins is an asymmetric three-dimensional assembly partially involving α-helix and β-sheet structures. They are stabilized by a variety of forces.
Tertiary structure – the most important thing
- Possible significant secondary structures used in tertiary structure are:
- double helices in DNA; stems and loop at the RNA
- α-helices and β-sheets in proteins
- Bonding forms of the tertiary structure are:
- hydrogen bonds
- disulfide bridges
- hydrophobic interactions
- ionic bonds
- Van der Waals forces
- the tertiary structure of a polymer describes its spatial arrangement, its conformation.
- the Tertiary structure of nucleic acids is mainly characterized by different sized furrows and directions of whorl.
- There are A, B and Z forms of DNA in living things, with the latter being the most common form.
- There are helical duplexes, triple stranded structures, quadruplexes, coaxial stacking, and numerous other tertiary structures of RNA
- The…