Hydrogen Bonds Explained: What They Are and Why They Are So Important in Biology

Hydrogen bonds are critical non-covalent bonds essential for the structural integrity and function of biological molecules such as DNA and proteins. They facilitate proper protein folding, stability, and specific ligand interactions, such as antigen-antibody binding. Hydrogen bonding involves a hydrogen atom (H) connected to a highly electronegative donor atom (D), which electrostatically interacts with an acceptor atom (A) that usually possesses a lone pair of electrons. Other electronegative entities (such as pi bonds) can be acceptors also.

Written by: Daad Abighanem

last updated: July 24, 2024

Hydrogen bonds are ubiquitous in nature and play a vital role in the structure and function of biological structures. 

More than 80 years ago, Linus Pauling recognized the existence of a strong bond between an atom of hydrogen and two other atoms and the importance of the hydrogen bond in protein structure. 

Hydrogen bonds are indeed essential for protein folding and stability and protein-protein interactions. They also contribute to the unique and complex properties of water and account for the fidelity of base pairing in nucleic acids. 

This article breaks down what hydrogen bonds are, how they form, their basic nomenclature, and their biological significance.

What Is a Hydrogen Bond?

Hydrogen bonds are not “true” bonds like covalent and ionic bonds, but rather directional electrostatic attractions between slightly negative and slightly positive atoms. The standard configuration of a hydrogen bond is of the type D — H···A where:

  • H is a hydrogen atom with a partial positive charge.
  • D is a highly electronegative donor atom covalently attached to the H atom.
  • A is an acceptor atom with a full or partial negative charge, lone pair of electrons, or another electronegative feature (such as an adjacent pi bond) directed towards the H atom.

Hydrogen bonds are usually represented using dashed lines (—) or interpuncts (···).

Figure 1 below demonstrates how the standard hydrogen bond nomenclature applies to a water molecule hydrogen bonded to a hydroxyl group.

Hydrogen Bonds Explained: What They Are and Why They Are So Important in Biology

Figure 1. Hydrogen bond nomenclature is illustrated on a hydrogen bond between water and a hydroxyl group. The hydrogen bond is shown as a red dashed line. Lone electron pairs are shown as twin black dots. The single electron of the “donated” hydrogen is retained in the bond between the hydrogen atom and the donor atom, meaning that it’s technically just a proton that’s donated in any given hydrogen bond. (Image credit: Thomas Warwick.)

How Does a Hydrogen Bond Form?

  1. The D atom (usually O, N, F, or sometimes S) attracts the electron from the H nucleus.
  2. The H atom is thus left with a partial positive charge. 
  3. This charge then attracts a lone pair of electrons on the A atom (usually O, N, or occasionally S, C, or Cl), 
  4. The resulting association is known as a hydrogen bond.

Note that a single hydrogen bond acceptor can interact with multiple D — H groups, giving rise to a bifurcated hydrogen bond. 

Figure 2 below gives an example of a bifurcated hydrogen bond between a single carbonyl oxygen acceptor and two water molecules.

Hydrogen Bonds Explained: What They Are and Why They Are So Important in Biology

Figure 2. An example of a bifurcated hydrogen bond. The hydrogen bonds are shown as red dashed lines. The lone electron pairs on the acceptor (carbonyl) oxygen atom are not shown on this occasion. (Image credit: Thomas Warwick.)

Hydrogen bonds are not particularly strong, with a bond strength of about 4–40 kJmol-1 (kilojoules per mol). However, in systems that contain a lot of hydrogen bonds, their strengths can add up, and they can give out or take up a substantial amount of energy when they form or break, respectively.

This is nicely illustrated by the boiling point of water, which is so relatively high because of the amount of energy required to break all the hydrogen bonds to get the water molecules into the vapor state. See the Hydrogen Bonds in Water section below for more info.

Types of Hydrogen Bonds

  1. Intramolecular hydrogen bonds occur within different groups of a single molecule (e.g., between the two hydroxyl groups of ethylene glycol). The hydrogen donor and acceptor atoms must be located close to each other within the same molecule.
  2. Intermolecular hydrogen bonds occur between two or more separate, similar, or different molecules (e.g., between water and a protein, between multiple water molecules, between multiple ammonia molecules, or between water and ammonia molecules).  

Hydrogen Bonding in Biological Systems

Hydrogen Bonds in Water

In a water molecule, the oxygen atom has two lone pairs of electrons, each of which can act as a hydrogen bond acceptor. The two hydrogen atoms in water can each be “donated” to another acceptor atom (such as the oxygen atom on another water molecule). 

Water molecules are bent at an angle of approximately 104.5 degrees, and neighboring molecules will assume the orientation at which the O—H bond of one molecule points towards one of the electron pairs of the other molecule. 

Due to this molecular structure and geometry of water, each water molecule can then participate in a maximum of four hydrogen bonds with other water molecules. 

The sheer number of hydrogen bonds in pure water accounts for its unique properties, such as its role as a biochemical solvent, high boiling point, high dielectric constant, and high surface tension. 

Hydrogen Bonds in DNA Molecules

DNA strands are held together into a double helical structure by hydrogen bonds between the purine and pyrimidine bases on the two complementary strands. 

This highly specific base pairing of A-T (two hydrogen bonds) and G-C (three hydrogen bonds) was instrumental in the discovery of the structure of DNA. 

The polymerase chain reaction (PCR)—one of the most important molecular biology techniques—is based on the denaturation and annealing of DNA via dissociation and reforming of the hydrogen bonds between the complementary bases.

Hydrogen Bonds in Proteins

Hydrogen bonding is a vital feature of proteins and is necessary for maintaining: [1–4]

  • Structure. 
  • Folding status. 
  • Stability.
  • Selectivity and affinity towards ligands. 

Proteins contain many hydrogen bond donors and acceptors, including amide (-NH) donors and carbonyl (-CO) acceptors along the peptide backbone and the polar functional groups on the side chains of individual amino acids.

Let’s take a look at these properties and the corresponding importance of hydrogen bonds in a bit more detail.

Protein Interactions with Water

Water tends to minimize its contact with hydrophobic residues. 

This is called the hydrophobic effect and explains why nonpolar substances are poorly soluble in water. 

Proteins adopt their native shapes in response to the hydrophobic effect. 

When a protein is folded in a cellular environment, side chains of hydrophobic amino acids will cluster in the core of the protein to avoid contact with water, whereas the hydrophilic side chains are exposed on the surface of the protein and are free to form hydrogen bonds with water molecules or other polar amino acid side chains. 

Protein Folding and Stability

Hydrogen bonds contribute favorably to protein stability. A protein can be destabilized and become non-functional if (mis)folded in a manner that prevents a key hydrogen bond from forming. 

In a protein molecule, repeatedly occurring folding patterns are known collectively as secondary structures. 

The two most widespread and stable protein secondary structures that maximize the hydrogen binding pairing capacity of the peptide backbone are α helices and β pleated sheets. 

An α helix is stabilized by strong hydrogen bonds between the C=O group of each amino acid residue of the main chain and the N–H group of the residue located four residues away in the sequence. 

A β strand, the basic element of a β sheet, interacts with other β strands that are either present distantly on the same polypeptide chain or on a different neighboring polypeptide chain. 

The polypeptide chains can run in either the same direction (parallel β sheet) or opposite directions (antiparallel β sheet) and are stabilized by hydrogen bonds formed between the C=O groups of one strand and the N–H groups of another.

Ligand Binding

Proteins perform their functions by interacting with other molecules in a process called “molecular recognition”, characterized by specificity and affinity. 

This protein-ligand binding is facilitated by the breakage of hydrogen bonds with water molecules and the subsequent formation of new protein-ligand hydrogen bonds. 

An antigen-antibody immune complex is a prime example of protein-ligand interaction. 

With a few exceptions, the formation, strength, and stability of such complexes rely entirely on non-covalent interactions, including van der Waals forces, hydrophobic bonds, and hydrogen bonds.

These interactions are greatly dependent on the precise alignment of antigen and antibody. 

Examples of the Critical Importance of Hydrogen Bonds

SARS-Cov-2

A study on the binding of SARS-CoV-2 spike protein to antibodies showed an improvement in antibody specificity when the reaction occurred above 31 °C. [5]

This higher reaction temperature increased the probability of protein quaternary structure unfolding, exposure of more hydrogen bonding sites for pairing, and subsequent increase in the number of hydrogen bonds between the spike proteins and their antibodies. 

At room temperature, however, only two hydrogen bonds were formed, compared to 19 bonds when the reaction occurred at body temperature. More bonds equal higher specificity. 

Hen Egg-white Lysozyme

Strong hydrogen bonds are formed between a particular glutamine in the hen egg-white lysozyme (HEWL) molecule and an anti-HEWL antibody. [6]

The antibody does not recognize lysozymes from other species where glutamine is replaced with another amino acid. 

In another high-affinity complex of HEWL with a different antibody, a 1000-fold decrease in affinity was observed with lysozymes that lack one of two arginine residues on their surface.

Hydrogen Bonds in Biology Summarized

Hydrogen bonds are abundant in biological systems. They impart indispensable properties to water, nucleic acids, and proteins. Without hydrogen bonds, life on Earth cannot be sustained and might never even have arisen.  

Now you know how and why hydrogen bonds form and how to identify donor and acceptor atoms within a hydrogen bond.

Did you find this article helpful? Let us know in the comments section below. Or check out more articles in our Chemistry for Biologists channel.

References

  1. Baker EN. (2006). Hydrogen bonding in biological macromolecules. International Tables for Crystallography Vol. F, Chapter 22.2, pp. 546–52
  2. Pace CN, et al. (2014). Contribution of hydrogen bonds to protein stability. Protein Science. 23:652–51
  3. Hubbard RE, and Haider MK. (2010). Hydrogen Bonds in Proteins: Role and Strength. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.
  4. Cozzone A. (2002). Proteins: Fundamental Chemical Properties. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.
  5. Wang et al. (2021). Binding Strength and Hydrogen Bond Numbers between COVID-19 RBD and HVR of Antibody. Crystals. 11:997
  6. Pons J, Stratton JR, Kirsch JF. How do two unrelated antibodies, HyHEL-10 and F9.13.7, recognize the same epitope of hen egg-white lysozyme? Protein Sci. 11(10):2308–15

I have a PhD in Poultry Science from Texas A&M University. I have held R&D and leadership positions in academic and corporate sectors. I am experienced in antibody production and characterization, immunoassay development, and in vitro diagnostics. I am passionate about science writing, communicating complex scientific concepts effectively, and mentoring and advocating for cancer patients.

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