Chemical Bonds: Videos & Practice Problems

Chemical bonds are crucial in cell biology, with covalent bonds formed by sharing electrons, leading to molecular polarity. Non-covalent bonds, including ionic bonds, hydrogen bonds, and van der Waals interactions, play significant roles in molecular interactions. The hydrophobic effect explains the aggregation of hydrophobic molecules in water, essential for cellular structures. Understanding these bonds and interactions, including concepts like molecular complementarity and affinity, is vital for grasping biological processes and structures, such as DNA stability and protein interactions.

Properties of Atoms

Hi. In this video, we're going to be talking about important chemical bonds and attractions. So before we can talk about chemical bonds, we really need to understand the property of atoms. Now I know that you've already gone over this in some of your intro chemistry classes, but I'm going to take a minute to just review these concepts and try to connect them to cell biology so that we understand why they're going to be important moving forward.

So the first thing is that the properties and structure of atoms allow for the formation of chemical bonds. We know this, atoms form chemical bonds and that's important. But how they form chemical bonds and what type of bonds form in cells is particularly important for this class. First, atoms have a core of neutrons and protons, which is surrounded by this negatively charged electron cloud. This electron cloud is made up of electron shells, which contain the orbiting electrons. If we look down here at this image, you can see, here's the core of this carbon atom and that's where the protons and neutrons are, and then surrounding here are these electrons, and they are in these shells, orbiting the atom's core.

The formation of chemical bonds happens because each of these electron shells wants a certain number of electrons. When they don't have that number, they are less stable and desire that number. So they seek out that number by forming bonds with other atoms. In this case, we have two carbon atoms here forming a bond, actually sharing those electrons.

Now, for cell biology, in chemistry, there's a ton of atoms that we can deal with and form bonds with. But in cell biology, we really limit this. In cells, the ones we most commonly deal with are carbon, hydrogen, nitrogen, and oxygen, which make up 95% of the chemical bonds in cells. Another unique thing is in chemistry, we deal a lot with individual atoms by themselves, considering how they interact with other individual atoms. But in cells, that doesn't really happen. We don't have the single carbon atom that's floating around doing something, and the same with oxygen. Instead, they form these complex structures that then go on to have particular functions.

When we're talking about cell biology, we're going to be talking about the important bonds that help form these complex structures. For carbon, for instance, which is a hugely important atom in cell biology, it can form four bonds and really serves as this foundational element of biological chemistry. Carbon is going to be really important moving forward. So now let's move on.

Covalent Bonds

Okay. So there are atoms in cells and they form bonds. So now let's talk about some of the bonds that they form. One of the really important bonds atoms form in cells is called a covalent bond, and this is formed through the sharing of electrons. This occurs when the outer electron shells of 2 molecules want to be complete. So, in order to do that, to make themselves complete, they share electrons. Now, they can share 2 electrons and that forms a single covalent bond. They can share 4 electrons that forms a double covalent bond, and they can share 6 electrons, which is referred to as a triple bond. You may remember some of this from your intro chemistry class.

Now, molecular or molecule polarity, which remember is due to the unequal sharing of electrons. So, molecules that are polar, unequally share electrons, and molecules that are non-polar, share electrons equally. So, polarity results in sort of a concentration of these negative or positive charges on different atoms in a molecule. And so if we just scroll down here for one second, I'm going to scroll back up. But if we look at this covalent bond of a water molecule, you can see that they're sharing electrons here. But, in the process of sharing the electrons, the oxygen atom actually, sort of unequally takes all of those electrons. It doesn't share them as equally. So it ends up with this negative charge. Whereas, these hydrogen atoms down here are still sharing the electrons, but they actually end up positive. And this results in a polar water molecule.

So now that, so polarity. So there's a term that we use and it's called electronegativity, and this describes atoms with the ability to attract electrons. So in the case of the water molecule, the oxygen atom is electronegative because it can attract those electrons stronger than the hydrogens it is bonded to.

Now covalent bonds are really strong. And so they have a high bond strength, which is defined as the amount of energy needed to break the bond, which makes sense because if it's a strong bond, then how you measure it through bond strength is going to have to measure how much energy is needed to break it. So more energy to break it, means it's a stronger bond. And so you don't need to know this number, but I just sort of as a comparison moving forward and talking about some other bonds. The bond strength required to break a single carbon-oxygen bond, which is covalent, is going to be 84kilocaloriespermole. So that's just a bond strength that's how it's measured. In chemistry you may see this as kilojoules per mole, instead of kilocalories, but in cell biology, we really do focus on the calories instead of the joules. So now we've talked about covalent bonds. So let's move on to some other type of bonds.

Noncovalent Bonds

Okay. So now let's talk about non-covalent bonds. Non-covalent bonds can also be called intermolecular forces, and they are bonds that do not, this is important, do not involve the sharing of electrons. One type right here that we're going to talk about is ionic bonds, which can be referred to as salt bridges, and they are formed by donating or accepting electrons, so giving or taking away electrons, not sharing. This occurs when the outer shell of electrons donate or take in electrons in order to be complete. So let's look at this image while we talk about how this happens. This is looking at sodium chloride or table salt. This is salt. And you can see that the sodium has an extra electron that is making its shell have too many electrons, and the chloride actually has only 7 and is missing an electron. Both of these atoms want their shells to be complete. So what happens is that sodium then donates its electron to chloride, which then accepts it, and this forms an ionic bond. Now, you may ask, "Well, okay, if it's giving away an electron, then how is that forming a bond?" Well, it's not just the giving away of the electron that allows the formation of the bond. But when the electron is given away, sodium becomes positively charged and chloride becomes negatively charged. And as positively and negatively charged things attract each other, this ionic bond is formed. So, we actually give these ions different names. Sodium is going to be called a cation, and that's because it's positively charged, whereas chloride will be named anion, which is negatively charged. Like I said, they're attracted to each other by their charges after they either donate or accept an electron. Now ionic bonds are weak, so they're around 1 to 5 kilocalories per mol. Remember in cell biology we use kilocalories, not kilojoules, which you'll see more often in chemistry. And they are easily dissolved in water. So that's ionic bonds. So let's talk about another type of non-covalent bond.

A second one is a hydrogen bond. Now these are formed through attractions between a hydrogen atom and an electronegative atom. If you remember back, we talked about what electronegative atoms are, but just as a reminder, they are atoms that sort of unequally share electrons. They are more negative because they take in more of the electrons' negative charge. In hydrogen bonds, the partial positive charge of the hydrogen attracts the electronegative atom, and they are extremely important in providing water its properties. I'll scroll down, and we can look at this water molecule here. One of the properties that hydrogen bonding allows water to do is actually dissolving different molecules in water depends on its ability to create hydrogen bonds. And the second property is that it actually results in attraction between water molecules, which you'll remember, we've referred to before as cohesion. Hydrogen bonds are also weak, 1 to 2 kilocalories per mol. In this image, you can see that it has hydrogens and oxygens. The hydrogen has this partial positive charge, and the oxygen, which is electronegative, has this negative charge. And so the hydrogen bonds in this image, you can see here, are because these positive and negative charges are interacting. So these are hydrogen bonds, which are non-covalent.

So now let's move on to a third type of non-covalent bond, and that's van der Waals attractions. Now van der Waals attractions, the best way to describe them is these sort of nonspecific attractive forces that happen when two atoms approach each other. As things move towards each other, they become slightly more attracted and will continue to move towards each other. Van der Waals is interesting because it can occur in polar molecules, which is what we've dealt with before with water, and these charged molecules like salts. But it also can happen in nonpolar molecules or in molecules which share their electrons equally. And the strength of the bond actually decreases with the distance of the atoms. And so, they're very weak as well, 1 kilocalorie per mol, the weakest bond that we've talked about so far. You can imagine two molecules moving towards each other, the strength of the bond increases. But then as molecules move away from each other, then the strength decreases. Now there's not really, so far, I've been showing you these very chemical description, the chemical images of these bonds happening. But for van der Waals, because it's this sort of nonspecific attractive force that occurs when molecules are moving towards each other, I can't really show you a stationary image that can really demonstrate van der Waals forces that happen when things are moving. So, I just want to give you a real-life example of Van der Waals forces, and that is actually related to the sticky nature of gecko toes. Geckos are able to sort of attach to things because their feet are kind of sticky, and they can crawl up surfaces or actually hang upside down because their little paws or feet actually can have van der Waals attractions to whatever substance they're binding to. And that actually gives them this sticky nature. So we talked about these three non-covalent bonds, ionic binding, hydrogen bonding, and van der Waals forces. So now let's move on.

Attractive Forces

Okay. So now we're going to talk about some attractive forces and just some overarching concepts that have to do with bonding and cell biology. So, one really important attractive force in cell biology is the hydrophobic effect. And this explains attraction between, you guessed it, hydrophobic molecules. And so hydrophobic, if you remember, are molecules that do not dissolve in water while hydrophilic molecules do. We're dealing with hydrophobic molecules and a hydrophobic effect. And so we know that when we put oil in water that it doesn't really dissolve. Oil is hydrophobic, but it not only doesn't dissolve, it actually aggregates. And it'll separate to form water on the bottom and oil on the top. And this aggregation is due to the hydrophobic effect. So, how does this happen? Well, first, hydrophobic molecules have a neutral charge, and therefore, cannot form hydrogen bonds in water and therefore do not dissolve in water. And so but when hydrophobic molecules are put into water, they're surrounded by water molecules which are participating in hydrogen bonding with each other. So there's all these hydrogen bonds going on around them, but they can't participate. And so because they can't participate, they actually, group together in these, sort of these oil droplets, if you will, these hydrophobic droplets, attracting to each other because they can't interact with the hydrogen bonds that are going on around them. So one example of this in biology in cell biology are hydrocarbons, which are nonpolar. These are, molecules. And there are hydrophobic molecules made up of hydrogen and carbon. And we're going to talk about hydrocarbons a lot moving forward. And so because they are nonpolar and hydrophobic, when they are in water, they actually form these really important cellular structures. So we're going to talk about these a lot. I just wanted to introduce them. But let's take a look at what the hydrophobic effect looks like. So, these blue molecules here are water, H₂O, whereas this big fat, brown looking thing is a hydrophobic molecule. Now when these are dropped into water, it doesn't make sense for all of these water molecules to take up so much of their energy forming these structures around these hydrophobic molecules. So instead, what happens and what is the best, way to form, the hydrophobic attraction with using the least the hydrogen bonds can do so easily and, actually with less, energy. And so this is an example of the hydrophobic effect. Now we talked about different hydrophobic effect. Now, we talked about different types of, bonds, and the reason that we did this isn't just because I think you should know them even though you should, but you would have learned these in chemistry. But the reason that we've talked about these bonds is because they're important for the formation of biological structures that we're going to talk about a lot in this course. Now one property of some of these bonds are, for instance, is non-covalent bonds are weak individually. We know this. By themselves, they're very weak. But in cell biology, they can be added together to form these really strong forces that can even be stronger than covalent interactions, whereas, individually, they're weak, but together they're strong. So for instance, DNA molecules are actually held together by non-covalent bonds, but DNA is really stable. I mean, we know we can extract DNA from dinosaur bones from forever ago, that has withstood this, length of time until now. And the reason it can is because it has a combination of non-covalent interactions that make these bonds really strong. Now some molecules, we're talking about bonding, actually can fit together like a lock and key. So this is, can be termed molecular complementarity, which I've, italicized here because some of you may need to know it, some of you may see it in your textbook, and some of you may never see this in your book at all. But really it describes the lock and key model, which all of you will hear about eventually, and that is really just a perfect fit between the properties of 2 molecules. Now we don't typically talk about this in terms of, you know, a carbon atom binding to a hydrogen atom. But instead, we talk about 1 protein or 1 molecule binding to another one. And these are usually larger structures, and they have, the ability to form all different types of bonds. And when they can form these bonds perfectly with each other, they have molecular complementarity, and they fit together like a lock and key. So you can see here this molecule here is shaped perfectly for the binding site of this molecule. So when they come together, they fit together like a lock and key and they show molecular complementarity. And another term that we're going to be talking about a lot, in the future that has to do with this is actually affinity. And affinity is determined by how well these two molecules or more molecules fit together. So the higher the fit, the higher the affinity. So the more they fit together, the more bonds they form. The stronger that connection is, the higher the affinity. So now let's move on.

Which of the following bonds form through the sharing of electrons

• A. Ionic bonds
• B. Hydrophobic effect
• C. Van der Waals attractions
• D. Covalent bonds

Answer: (D)

Which of the following bonds form through the donating and receiving of electrons?

• A. Ionic bonds
• B. Hydrophobic effect
• C. Van der Waals attractions
• D. Covalent bonds

Answer: (A)

Which of the following bonds form through nonspecific attractive forces that arise when two molecules approach each other?

• A. Ionic bonds
• B. Hydrophobic effect
• C. Van der Waals attractions
• D. Covalent bonds

Answer: (C)

Here’s what students ask on this topic:

What are the main types of chemical bonds found in cells?

The main types of chemical bonds found in cells are covalent bonds and non-covalent bonds. Covalent bonds involve the sharing of electrons between atoms, leading to strong and stable connections. They can be single, double, or triple bonds, depending on the number of shared electrons. Non-covalent bonds include ionic bonds, hydrogen bonds, and van der Waals interactions. Ionic bonds form through the transfer of electrons, resulting in attraction between positively and negatively charged ions. Hydrogen bonds occur between a hydrogen atom and an electronegative atom, such as oxygen or nitrogen. Van der Waals interactions are weak, nonspecific attractive forces that occur when atoms are in close proximity. These bonds and interactions are crucial for the structure and function of biological molecules.

How do covalent bonds differ from ionic bonds?

Covalent bonds and ionic bonds differ primarily in how they handle electrons. Covalent bonds involve the sharing of electrons between atoms, resulting in a strong and stable bond. These bonds can be single, double, or triple, depending on the number of shared electrons. In contrast, ionic bonds form through the transfer of electrons from one atom to another, creating positively and negatively charged ions. These oppositely charged ions attract each other, forming the ionic bond. Covalent bonds are generally stronger than ionic bonds and are crucial for the structure of organic molecules, while ionic bonds are important for interactions like those in salts.

What is the hydrophobic effect and why is it important in cell biology?

The hydrophobic effect refers to the tendency of hydrophobic (water-fearing) molecules to aggregate in aqueous environments. Hydrophobic molecules, such as hydrocarbons, have neutral charges and cannot form hydrogen bonds with water. When placed in water, they cluster together to minimize their disruptive effect on the hydrogen-bonded network of water molecules. This aggregation reduces the system's overall energy. The hydrophobic effect is crucial in cell biology because it drives the formation of cellular structures like lipid bilayers, which make up cell membranes, and helps in protein folding, ensuring proper function and stability of biological molecules.

What role do hydrogen bonds play in the properties of water?

Hydrogen bonds play a critical role in determining the properties of water. These bonds form between the partial positive charge of hydrogen atoms and the partial negative charge of oxygen atoms in adjacent water molecules. Hydrogen bonding gives water its high cohesion, leading to surface tension and the ability to form droplets. It also contributes to water's high specific heat capacity, allowing it to absorb and release heat with minimal temperature change. Additionally, hydrogen bonds enable water to dissolve many substances, making it an excellent solvent. These properties are essential for various biological processes, including temperature regulation and nutrient transport.

What is molecular complementarity and how does it relate to biological functions?

Molecular complementarity refers to the precise fit between the shapes and chemical properties of two molecules, allowing them to bind together like a lock and key. This concept is crucial for many biological functions, such as enzyme-substrate interactions, where the enzyme's active site perfectly matches the substrate's shape. It also plays a role in antibody-antigen binding, where the antibody's binding site is complementary to the antigen's structure. High molecular complementarity results in strong binding affinity, ensuring that biological processes occur efficiently and accurately. This principle underlies the specificity and regulation of many cellular interactions and pathways.