Key Concept: Polar and Charged Molecules

The similarites and differences between non-polar, polar and charged molecules (or parts of molecules) are really important. You must understand the difference between polar and charged molecules if you are going to make sense of molecular structure, and of the ways in which molecules interact.

If you’re unsure if water is a polar molecule or are wondering whether ions are polar, this article is for you.

This molecule is polar, but not charged. All is explained below.

Getting this topic straight in your mind will make it much, much easier to grasp key concepts like why glucose dissolves in water, why other things don’t, and how neurons and mitrochondria use membranes to create ion gradients for their function. And you’ll need to understand hydrogen bonding of polar groups to understand how DNA and proteins adopt defined structures.

The fact the molecules are called ‘polar’ and ‘charged’ is part of the problem - this can be pretty confusing! So don’t rely on their names to understand what’s going on.

Let’s start from scratch:

How are Polar and Charged Molecules different from Non-Polar, Uncharged Molecules?

All molecules contain atoms. And all atoms contain positively-charged nuclei and negatively-charged electrons.

In a non-polar, non-charged molecule, these positive and negative charges all neatly cancel each other out. As far as other nearby molecules are concerned, a non-polar molecule behaves as though it has no charges at all.

In both polar and charged molecules, the molecule has regions of positive and/or negative charges that can affect nearby molecules (or even other parts of the same molecule - as happens in proteins and DNA).

What’s the difference between Polar and Charged Molecules?

Polar molecules are charged-balanced overall but have unevenly distributed electrons. This gives them a little bit of a charge in certain places.

Charged molecules do have an overall charge. They have at leat one full unit of charge on at least one atom. (A unit of charge being equal to the magnitude of one electron).

You will also hear about polar and charged groups, which are a part of a larger molecule, where that part (group of atoms) has these properties.

Now, you might read that and think yes! I’ve got it! But to really understand it - and more importantly to remember it - you are going to need to linger a while and spend a bit of time thinking about this. It’s worth going through it all carefully step by step - this will also check your understanding. Have a good think about where those electrons are. Too many students trip up on this topic.

So let’s look at what it means to be non-polar, polar or charged. And then how that affects the behaviour of these molecules.

First step: What’s the difference between Unpolar and Polar Molecules

Atom

The atoms that make up molecules each have a postively-charged nucleus and a cloud of negatively-charged electrons.

Different types of atoms have different numbers of charges.

This means that even non-charged, non-polar molecules contain charges! They just cancel each other out so you don’t notice them.

Non-polar

When you make a molecule out of atoms, electrons are shared between neighbouring atoms. The electrons become one big shared cloud. This makes a covalent bond.

The diagram shows a non-polar molecule with two atoms. In a non-polar molecule, all the charges are balanced, cancelling each other out.

Because the charges are distributed evenly, and cancel out overall, the molecule behaves as though there are no charges (in terms of its electrostatic interactions with other nearby molecules).

So why are they called “non-polar”? To understand that, you need to understand what polar means.

Polar

It turns out that some types of atomic nuclei just LOVE electrons. Like, they are particularly greedy for them. Oxygen, for example.

These greedy atoms yank the electron cloud over towards their nucleus, away from the nucleus of the other atom.

The other atom no longer has enough negative charge to cancel out its positively-charged nucleus. While the greedy one has more negatively charged electrons than it needs.

The charges no longer cancel each other out. The other atom now has just a little bit of a positive charge, and the greedy one has just a little bit of a negative charge.

This is a polar molecule. Its atoms still share one electron cloud, so they are still covalently bonded. But the small charge in charge distribution mean it will now interact differently with its environment.

Overall, the charges still cancel out. They are just unbalanced so that there are places with just a little bit of charge.

Saying "just a little bit” of charge is a pain, so instead the delta symbol is used to show this.

δ+ = just a little bit of positive charge
δ- = just a little bit of negative charge

This can also happen to just one part of a molecule. A good example is a hydroxyl group (OH). The oxygen pulls the electrons toward it, so that there is just a little bit (δ) of charge on the oxygen and hydrogen atoms.

Molecules with hydroxyl groups are polar. Look at glucose - it has loads of hydroxyl groups; this is what makes it a polar molecule. This is important for how it behaves in water, but before we get to that, let’s look at how charged atoms/molecules are different:

Second step: What’s the Difference between Polar and Charged Molecules?

Polar

A polar molecule has no overall charge. The charge of its positive nuclei exactly cancel out the charge of its negative electrons.

The charges are just unevenly distributed, giving a little bit (δ) of positive charge to one atom, and slight negative charge to another atom.

In biology, you’ll normally find it’s a hydrogen atom that has had its electrons yanked away and is now carrying a little bit of positive charge.

Charged

Now look at this. These atoms are not sharing a cloud of electrons - the big one has gone all-in and taken the whole lot for itself.

No shared electron cloud means there is no covalent bond.

No covalent bond means they are no longer a single molecule, but rather two separate atoms … well, except that they’re not even atoms any more …

The atoms no longer just have just a little bit (δ) of charge. The one on the left has lost an entire electron’s worth of charge. Losing negative charge means that overall it is now (properly, not just a little bit) positively charged.

The one on the right has a whole electron’s worth of negative charge more than it needs to cancel out its positive nuclues. It is now (properly) negatively charged.

Because they are (properly!) charged, we no longer call them atoms. Instead they are ions.

Water experiences this sort of electron-theft.

Sometimes it exists as the polar H20 molecule, but sometimes its oxygen gets even more greedy and the molecule dissociates into H+ (a hydrogen ion, aka proton), and OH- (a hydroxyl ion).

This dissociation, and the reforming of H20, is happening all the time in normal liquid water.

Note that the ions each have an overall charge, unlike the polar water molecule where the small charges cancel out.

Bigger Molecules

Atoms that are negatively charged due to having extra electrons, or that are positively charged because they lack electrons, often occur in large molecules too.

Where positive charges are found, it helps to think about this as a positively-charged H+ having been added to the molcule.

Here’s an amine group. It’s just part of a larger molecule, which goes off the edge of the image.

It can exist either as —NH2, or it can add on a proton (H+) to become —NH3+.

In living organisms, there are plenty of available protons (remember how water dissociates?). So amine groups like this usually exist as the charged version.

This is not a polar group, it is charged. (Ignore the shape of the electron cloud for this one, the important thing is that there is an overall charge of +1 because of that extra proton).

Electrostatic Interactions

So. Polar molecules are uncharged overall but have just a little bit (δ) of charge in various places. While charged molecules have a big whack of charge due to having lost an electron or having gained a proton. Why is this difference so important?

It’s to do with how polar and charged molecules interact with their environments. It’s not the same.

Hydrogen bonds

Some polar molecules, like DNA, proteins and water, can form hydrogen bonds between the atoms that have the unevenly distributed charges. These are a special type of weak bond.

Water LOVES making hydrogen bonds - this is why it can hold itself together into a droplet.

Notice in the picture that the water molecules remain separate and can still move around. It doesn’t take much to pull a single hydrogen bond apart. Which is why water can still be poured and stirred around with no trouble.

Water is a polar, hydrogen-bonding molecule, and this explains its properties as a solvent. Molecules like glucose can dissolve in water because they are similarly polar and able to make hydrogen bonds.

Hydrogen bonds are also really important in understanding DNA and protein structures.

These molecules hydrogen-bond to themselves. Each individual bond is weak, but multiple repeating bonds work together to hold the structure into shape.

Protein secondary structures are held together by hydrogen bonds.

The image here shows hydrogen bonds between Guanine (G) and Cytosine (C) in DNA. The hydrogen bonds are shown as dotted lines.

To get a feeling for the strength of hydrogen bonds, think about what happens if you spill water on a book, close it, and let it dry. You know how the pages stick together? This is because hydrogen bonds have formed between the pressed-together pages. When you peel them apart, you are pulling these hydrogen bonds apart.

Dissolving ions

Charged ions like Cl-, Na+ and K+ can’t form hydrogen bonds, but they can still dissolve in water because they can form favourable electrostatic interactions with the water molecules.

This diagram shows salt (NaCl) dissolved in water.

Hydrogen bonds are in yellow. And electrostatic interactions between the charged ions and the polar water molecules are shown in green.

See how the water molecules organise around the ions to provide the opposite charge to that presented by the ion.

Non-polar molecules like lipids cannot form electrostatic interactions with water molecules. And so for this reason, non-polar molecules do not dissolve in water. If you could somehow spread a bunch of non-polar molecule through a glass of water, this would cause all sorts of problems because the water molecules next to the non-polar molecules would be unable to satisfy their charges. Water prefers to hydrogen bond to itself, and it would do so, squeezing the the non-polar molecules out to cluster together in undissolved lumps.

Whisk up a teaspoon of oil in a glass of water and watch - you can see this happening. The oil ends up as a separate layer on the surface. Or get a small glass of oil and carefully put a drop of water on top; the water will ball itself up, hydrogen-bonding to itself and minimising the amount of contact it needs to make with the oil.

This is why membranes don’t dissolve in the cytoplasm. The water molecules would much rather hang out with other water molecules where they can make all those lovely hydrogen bonds. Non-polar molecules are called hydrophobic, or “water-hating”, but to be honest that’s a bit unfair because really it’s the water is excluding them, rather than the other way around.

This also means that non-polar molecules can’t act as solvents for polar molecules or charged ions. The reason being the same: they can’t offer any way to satisfy the polar/charged molecules’ hankering for favourable electrostatic interactions. This is why ions (Na+, K+, H+ etc) cannot dissolve into, and move through, membranes. Which is absolutely vital to understand if you want to make sense of how neurons, mitochondria, and chloroplasts function (and many other things in biology besides).

Ionic bonds

Charged molecules have ‘proper’ charges. They interact more strongly through electrostatic interactions to form ionic bonds.

Here is a positively charged amine group (NH3+) forming an ionic bond with a negatively charged hydroxyl group (OH-).

They are not sharing an electron cloud, so this is not a covalent bond.

Maybe these charged groups are both parts of the same protein (ie from different R groups). If so, this interaction may be important in defining the protein’s tertiary structure.

Or maybe it’s an interaction between an enzyme and its substrate?

Ionic bonds are really important for controlling what binds with what - and what doesn’t. Negatively charged groups will repel other negative charges. And positive will repel positive. This prevents incorrect structures forming.

In summary:

Polar molecules are charge-balanced overall but have unevenly distributed electrons. This gives them a little bit ( δ ) of a negative charge on one atom, and a little bit ( δ ) of positive charge on another. In biology, these weak charges often form hydrogen bonds, or favourable electrostatic interactions with ions.

Charged molecules have an overall charge. They have at leat one full unit of charge on at least one atom. (A unit of charge being equal to the magnitude of one electron). These stronger charges can form ionic bonds with each other.

This article was written by Dr Jenny Shipway

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How to Revise A Level Biology: Keep Forgetting Things? Don't Despair!

A guest blog from Dr Jenny Shipway, who studied biochemistry at university and now works in science communication and education training.

The Art of Forgetting

Your brain is amazing

It’s frustrating when we forget things we want to remember, but this isn’t a failure of our brains - it’s an important feature. Remembering everything would cause all sorts of problems, so our brain spends a lot of time forgetting things. What colour coat was the first person to pass you on the street today wearing? How many bites did you take during lunch? What is the first thing your Year 5 teacher said to you on your third day?

Unfortunately perhaps, we can’t consciously tell our brains what to remember. So sometimes it forgets things we want to recall, like the internal structure of the kidney, or how oxygen dissociation curves work. We can’t tell it to remember these things, but we can encourage it to remember by giving it sigals that this stuff is important.

So how does the brain choose what to remember? There are a variety of signals that can flag things up as worth remembering, including:

1. Information that links nicely to prior knowledge
2. Information that connects to things the brain has already decided are important

Pay attention to the links between a new topic and things you’ve learned before. And make sure they agree - if there is a conflict your brain is more likely to forget (also it means there is something you don’t understand which needs re-studying!). If you previously learned that every human cell has a nucleus, but then read that red blood cells do not have a nucleus, take the time to work out how that can be, or you’re likely to forget the new information.

Information that connects to yourself - like a topic you had to present to the class, a question you answered during a lesson, or something that you can relate to your own body - is particularly likely to be remembered.

3. Information that has proven itself to be useful

Test your recall - if you remember the information successfully and this feels like an achievement, your brain will take note. Brains love feelings of success and are always eager for more. Even better, use the information to successfully solve a problem. Brains LOVE that.

In biology you have the added benefit of having stories about health. The brain is always keen to remember information from stories that could help you avoid future harm. Emotional/personal stories of people with medical problems that were (or could have been) overcome with a little biological knowledge are high priority for the brain.

Putting on your auntie’s hat and trying to ride your next door neighbour’s unicycle is a valid study strategy

4. Information gained during/after novel experiences

In a study, children remembered a lesson better if they had an unexpected music lesson just beforehand. (If the music lesson was expected, they did not remember so much.) How much novelty is required to get this memory boost is sadly unknown, but you could try studying in different places, or wearing something unusual, or trying a new activity beforehand? At least it gives you the excuse to take a break from your desk.

5. Information that satisfies your curiosity

In a study using Trivial Pursuit questions, people better remembered the facts they’d been more curious to know the answers to. Ask yourself questions as you go through a topic, get a step ahead of your learning and try to develop a curiosity for what comes next. If you don’t care, it’s going to be harder to remember. (If you lose all interest, take a break and try to ride a unicycle.)

6. Information that it receives on multiple occasions over a period of time

This one is really important. We generally forget things - even important things - bit by bit unless we think about them again. My memory of childhood holidays is largely centred around photographs, as they have reminded me of specific events over the years.

It’s totally normal to forget things the first time you learn them. And the second time. It can be frustrating to relearn things that you thought you knew, but this is just how learning works. You might feel you have made no progress after re-learning something for the third time, but that’s not true - every time you re-learn it, you will slow the rate of forgetting. Until, with enough recapping, you will fix the information in your long-term memory.

So, when you learn something, try to come back and recap it after about a week. And then again after maybe another couple of weeks. Then again after another month or so. This is called ‘spaced learning’ and it’s one of the most powerful and efficient techniques for getting stuff into your long-term memory.

Luckily for biology students, the topics are really interconnected. This means you will naturally get the chance to recall past topics when new ones relate to them, while you are thinking about all the connections.

Her brain’s still doing good stuff, so I reckon this counts as studying

Be kind to your brain

All of this learning is pretty hard work, and your brain will need some downtime to process everything behind the scenes.

Having a nap can be great for learning, but at the very least make sure you get a decent night’s sleep.

This is why last minute studying, staying up all night studying before an exam, is not recommended. Spreading your learning out over a longer period is much more efficient.

In a nutshell:

• Don’t despair when you forget something you did previously, you’ve still made progress. Trust the process!

• Every time you re-learn something, celebrate that you have moved the information one step closer to long term memory

• Taking a break to do fun, novel activities - or to have a nap - can be good for your studying

Dr Jenny Shipway
www.jennyshipway.com

How to Revise A Level Biology: Making Connections

A guest blog from Dr Jenny Shipway, who studied biochemistry at university and now works in science communication and education training.

Everything’s Connected

Memory Palaces

Some people specialise in memorising long strings of boring information. One trick they use is to imagine the information located along a walking route. Imagine if you had to remember a list of household appliances. You might imagine a kettle outside your front door, and a dishwasher at the end of your garden path. There could be a toaster on the road outside, and a microwave on the corner down the road. As you mentally rewalked the route, you would ‘look’ in each location and see the objects, which would be remembered in the right order.

The reason why such tricks are necessary is that your brain can’t remember unrelated information. Every new tidbit must be linked to something that you already know. Linking it to something you know well, like the route from your house, helps pin it in place.

One of the great challenges of A level biology is that you need to really understand things, rather than just memorising facts and figures. It’s about deeper concepts rather than surface facts. But the good news is that this actually makes it easier to remember the associated facts - each piece of information is related to others, and the more interlinked it is, the easier it will be to recall.

Toto I don’t think we’re in GCSE any more

Synoptic Thinking

Some of the most challenging exam questions are those that require you to think between topics. Rather than drawing on your memory of one specific part of the course, they demand you reach into your understanding of multiple areas to solve a single problem. This is similar to the type of thinking you would need as a researcher, where bringing in knowledge from other disciplines can help solve problems in novel ways.

Although the A-level specification is split into sections, biology itself is a intricately interlinked tangle of concepts with uncountable interdependencies. Pity the teacher who has to decide in which order to tackle the topics given how everything seems to underpin everything else in some way or another.

How to Revise

Don’t avoid the complexities of how the topics interrelate. By noticing and thinking about these, you can make it easier to both understand and remember concepts. And make it easier for you to jump between different areas for those synoptic questions.

To really understand a complex concept, it’s necessary to look at it from different angles, on different days, considering multiple different examples. Brains are incredible things: when they are fed enough examples and surface facts, and allowed to really think, they can magic up a deep understanding beyond anything that is easily written down. It’s not possible to simply read this type of deep understanding in (brains are nothing like computers); the understanding has to be created in the context of your own mind. Looking at topics from the angle of intersecting topics is a great way to feed your brain with new information to help it build understanding.

When you spot a link to a previous topic, give yourself a bit of time to recall what you previously learned, to think about the new topic from that angle and consider how they intersect. As well as helping your brain build understanding, making these links will make it easier to recall information. The more interlinked information is, the easier it is to recall.

What did your kettle look like?

Use Your Self

Every brain is different. Everyone who imagines walking past a kettle on their front step has a different image in mind. Do they imagine tripping over it if the step is narrow? Or is it sat on a plant pot? What colour is the kettle? Everything will be drawn from prior experience, and this is one of the reasons it works well as a memory trick - it’s linking to things your brain already know about.

If you can link anything in your course to strong memories, or especially to yourself, this will help you recall it later. When you learn about parts of the body, link it in your mind to your own experience of having a body. If you learn about a disease, think about someone you know with that disease while you study. Or imagine what it’d be like if you were a doctor treating it, or if you had it yourself - how you would feel, what you would do? Linking new information to our sense of self is possibly the strongest way to flag up information for later recall.

In a nutshell:

• Identify and explore connections / interdependencies between biology topics

• Think about concepts in the context of your own life

• If you find something hard to remember, try finding more links between it and things you already know well

Dr Jenny Shipway
www.jennyshipway.com

How to Revise A Level Biology: Familiarity

A guest blog from Dr Jenny Shipway, who studied biochemistry at university and now works in science communication and education training.

Tricks of the Mind

The lazy brain

There's a dangerous trick your brain can play, which can fool you into using ineffective study techniques and lead to to exam-day confusion and disappointment. But you can overcome it if you know how.

You are sitting in the exam hall. The bell sounds to start the exam. You turn over the paper, read the question and smile. You confidently pick up your pen but … somehow you can’t pull up the knowledge you need. What was that word? You know you learned it, but your mind is blank.

After the exam, you talk to a friend. They tell you the word. “Aaah I knew that!!” you say. But no you didn’t; not when it mattered.

Did it really go in?

Your brain tricked you. Going through your notes before the exam, your brain seemed to be telling you that you knew all the content. However, really it was just telling you that your notes were familiar. You never asked if it could actually recall the information.

Human brains by nature like to minimise mental effort and to feel successful (it should be noted that these are features, not bugs). As a study technique, re-reading notes doesn’t strain your brain or make you feel like you’re failing in any way. You feel like you’re learning. But are you really? Is it possible to learn without making mental effort?

How to revise

In 2006, a study [1] was published comparing two groups of students, who studied some new information in two different ways. First they all had a look through the materials. Next, one set of students were asked to re-read everything, while the other set were asked to put the materials aside and write down everything they could remember. Some time later, both sets of students took an exam to see how much had stuck.

Going into the exam, the students who had had more time studying the information were more confident. They had been able to go through it a few times, so were more familiar with it. In contast, the students who had spent the second part of their time writing down what they had recalled were not so confident. They were aware that there were parts they had forgotten, and that they had been unable to recall it perfectly.

You can probably guess the exam results. Familiarity is not the same as learning, and the first set of students’ confidence was misplaced. The students who had practiced retriving the information from their memory during study time were better able to recall the same information in the exam.

Since then, many other studies have confirmed that practicing retrieval is a particularly effective way to study. It’s called the “Test Effect”. Recalling information flags it up in your brain as being worthwhile remembering for future use. Testing what you can recall even out-performs open-book mind-mapping; in a 2021 study [2] of biology studying techniques, mind-mapping wasn’t found to add anything to the boost students got from retrieval practice.

Keep the faith

Gravity will draw the knowledge down into the brain. Maybe.

Retrieval is hard work and it can be frustrating or demoralising if you can’t remember everything you expected to. But it’s a fantastic way to learn content properly. Be reassured that the brain-ache you experience during retrieval is the feeling of effective learning. And if you can’t remember as much as you expected? You’ve been tricked by familiarity. But it’s great that you discovered this now, rather than in the exam.

So give it a try: after you revise a topic, put your books aside and just write down everything you can remember. See if your expectation matches reality. And when you can’t remember everything, you can still reassure your uncomfortable brain that it’s done a great job.

In a nutshell:

• Practicing recall helps you know for sure what you don’t know

• Practicing recall makes the information more easily remembered again in future

• When you can’t remember something, that’s not failure - you have successfully identified something for re-study

Dr Jenny Shipway
www.jennyshipway.com

References:

[1] Henry L Roediger & Jeffrey D Karpicke, Test-Enhanced Learning: Taking Memory Tests Improves Retention, Psychological Science 2006, 17(3) 249-255.

[2] Garrett M. O’Day and Jeffrey D. Karpicke, Comparing and Combining Retrieval Practice and Concept Mapping, Journal of Educational Psychology 2021, Vol. 113, No. 5, 986–997.