This biochemistry review activity features free interactives from the Concord Consortium’s Next-Generation Molecular Workbench. These simulations will not work in older versions of Microsoft Internet Explorer. Use Google Chrome instead.
Click HERE for a biochemistry review on protein folding!
Q1: Describe the relationship between temperature and the movement of the water molecules.
Q2: From what you’ve observed in this simulation, what two conditions must be met in order for hydrogen bonds to form? Hint: it may help to view the animations in slow motion.
Q3: Why don’t the hydrogen bonds hold indefinitely?
Q4: How does the organization of the water molecules change once the temperature is cooled completely?
What are hydrogen bonds?
When hydrogen bonds to an atom with high electronegativity (e.g., oxygen), an un-equal sharing of electrons occurs. This electron disparity creates a region of slight positive charge on the hydrogen atom and a region of slight negative charge on the more electronegative atom in which hydrogen is bonded. This separation of positive and negative charges is called an electric dipole and gives rise to a polar molecule. A hydrogen bond is a term used to describe an attraction that can occur between a polar molecule and the hydrogen atom that is bound to a highly electronegative atom.
Hydrogen bonds give water some amazing properties and influence the structure and function of many biological polymers.
The image above is an illustration of hydrogen bonds between adjacent water molecules.
Q5: Take a look at one of the polar molecules. Why is the word “polar” used to describe this molecule?
Q6: Examine the pair of polar molecules. When paired, how do the molecules arrange themselves?
Q7: Which molecule pair demonstrates the strongest attraction?
How are polar and non-polar molecules different?
Polar molecules have separate regions of electrical charge. This separation of charge results when two covalently bonded atoms share electrons unequally. In the case of water, electrons are drawn closer to the larger oxygen nucleus, creating a region of negative charge as seen in red in the image below. The smaller hydrogen atoms have less of a pull on the electrons, leading to regions of positive charge as seen in blue in the image below.
Above: A polar water molecule. Regions of negative charge are in red. Regions of positive charge are in blue.
In non-polar molecules, electrons are shared equally. This prevents the molecule from forming an electric dipole. The molecule below is methane, a non-polar molecule. The symmetrical arrangement of hydrogens around the single atom of carbon prevents the formation of an electric dipole.
Above: A non-polar molecule of methane. Hydrogen atoms are in white and carbon is in black.