In this explainer, we will learn how to describe the structure of DNA and explain how DNA can be extracted from organic material.
DNA is an incredibly important molecule. It contains the information that makes us, us! All of the DNA and the information it encodes in your body is called your genome. Your genome will be a combination of your biological mother’s and your biological father’s DNA, and this genetic material is passed on to you in a process called inheritance.
Fact: GFP and Transgenesis
The green fluorescent protein (GFP) is a protein that produces a bright green fluorescence when exposed to light. It is commonly isolated from jellyfish and is commonly used in DNA experiments.
For example, scientists can insert the gene that codes for the green fluorescent protein (GFP) into the DNA of a mouse. The mouse may then be able to fluoresce! If this mouse has offspring, these offspring can inherit this gene and also express the green fluorescent protein!
The process of transferring genes between organisms is called transgenesis, and the ability of the offspring to display this trait demonstrates how DNA is inherited from the parent to the offspring.
Now we know that DNA is the unit of inheritance in living organisms; let’s learn more about the structure of DNA.
To visualize what a molecule of DNA looks like, first picture a ladder. The ladder has two long, parallel spines, with rungs at regular intervals. Now, imagine that this ladder is twisted, as shown in Figure 1. This is the shape of a DNA molecule: two strands twisted around one another. This shape is called a double helix.
Key Term: Double Helix
A double helix is a twisted-ladder shape; specifically, it is the shape of a molecule of DNA.
A molecule of DNA is made up of many repeating units. Because it is a molecule with many repeating, similar units, DNA is called a polymer and the individual units monomers. The monomers of DNA are also known as nucleotides. Figure 2 shows where an individual nucleotide sits in a strand of DNA.
Key Term: Nucleotide
A nucleotide is the subunit of a DNA molecule. Nucleotides consist of a pentose sugar, a phosphate group, and a nitrogen-containing base.
Example 1: Explaining Why DNA is Considered a Polymer
Which of the following statements best explains why DNA can be described as a polymer?
- DNA is formed of many similar units (nucleotides) that are joined in a chain.
- DNA is formed of many different units (nucleotides) that are joined in a chain.
- DNA is formed of a few repeating units.
- DNA is formed of many unconnected units.
- DNA forms a double helix shape.
DNA is an incredibly important molecule. Within DNA is our “code for life,” and it is what makes us, us!
A typical molecule of DNA is made up of two strands that twist around each other to form a distinct double helix shape. Each strand is made up of many repeating units, and these units are called nucleotides. These nucleotides bind together to form these strands.
But to understand why DNA is described as a polymer, we need to understand what a polymer is. A polymer is a molecule that is made up of many, similar subunits. These subunits (also called monomers) will typically repeat themselves throughout the polymer.
Using this information, we now know that DNA is a polymer made up of many repeating monomers called nucleotides.
So, our correct answer must be A: we describe DNA as a polymer because DNA is formed of many similar units (nucleotides) that are joined in a chain.
Each nucleotide has three components: a pentose sugar molecule, a phosphate group, and a nitrogen-containing base, as shown in Figure 3.
Pentose sugar is a sugar molecule made of five carbon atoms. Each of these carbon atoms in a pentose sugar will be numbered, and we write these as , , , , and ; you can see this in Figure 4 below. In DNA, the pentose sugar is called deoxyribose.
Key Term: Pentose Sugar
A pentose sugar is a sugar molecule that contains five atoms of carbon. The pentose sugar in DNA is deoxyribose sugar.
There are four different nitrogenous bases in DNA: adenine (A), guanine (G), thymine (T), and cytosine (C). Of these, adenine and guanine are called purines, and they have two-ring structures. Thymine and cytosine, on the other hand, have single-ring structures and are called pyrimidines.
The final component of a nucleotide is the phosphate group. In the pentose sugar molecule, every carbon atom is covalently bound to a phosphate group.
Between each nucleotide and its neighbor, there is a bond called a phosphodiester bond. These phosphodiester bonds help create a strand of DNA nucleotides.
Definition: Phosphodiester Bond
A phosphodiester bond is the chemical bond that forms between a phosphate group and two sugar molecules.
Example 2: Describing the Structure of a Nucleotide
Which of the following best describes the structure of a nucleotide?
- A nucleotide is a small unit made up of a glucose sugar, a phosphate group, and a base pair.
- A nucleotide is a large subunit made up of a phosphate-sugar group.
- A nucleotide is a small unit made up of the four base pairs joined together by hydrogen bonds.
- A nucleotide is a small unit that joins with other nucleotides to form a long chain.
- A nucleotide is a small unit made up of a deoxyribose sugar, a phosphate group, and a base (either A, T, G, or C).
DNA, or deoxyribonucleic acid, is a biological polymer found in every cell of your body! It is our genetic material and encodes all of our genetic information. As a polymer, DNA is made up of many repeating monomers, and these monomers are called nucleotides.
A nucleotide is made up of three main components: a pentose sugar, a phosphate group, and a nitrogenous base. The structure of a single nucleotide is shown in the diagram below.
You can see from the diagram that the pentose sugar (more specifically called deoxyribose in DNA) forms bonds with both the phosphate group and the nitrogenous base.
There are four possible nitrogenous bases that can be found in a nucleotide: adenine (A), cytosine (C), thymine (T) and guanine (G).
Using this information and the diagram provided, we can conclude that our correct answer is E: a nucleotide is a small unit made up of a deoxyribose sugar, a phosphate group, and a base (either A, T, G, or C).
A strand of DNA is a double helix, which means that it has two chains, twisted around one another. How does one strand of DNA connect to the other to form this shape?
This is accomplished through the nitrogenous bases we learned about earlier. Every nitrogenous base on one strand of DNA binds to a nitrogenous base on the opposite strand. This is how the “rungs” in our twisted-ladder shape are formed!
When these nitrogenous bases bind, they do so in a special way. In DNA, adenine can only bind to thymine on the opposite strand, and guanine can only bind to cytosine. This rule is called complementary base pairing and is one of the defining features of DNA. Adenine binds to thymine through two hydrogen bonds, while guanine binds to cytosine through three hydrogen bonds, as shown in Figure 5.
Key Term: Complementary Base Pairing
DNA bases can pair according to specific rules, where adenine (A) binds to thymine (T), while guanine (G) binds to cytosine (C). In RNA, uracil (U) is substituted for thymine (T).
In a double-stranded molecule of DNA, since adenine on one strand can only bind to thymine on the opposite strand, this means that the number of adenine bases in this DNA molecule must be equal to the number of thymine bases. In the same way, since guanine can only bind to cytosine, this means that the number of guanine bases must be equal to the number of cytosine bases. For example, if a DNA molecule has 20 adenine bases, it will also have 20 thymine bases. This is called Chargaff’s rules, and they are useful for the calculation of the percentages of certain bases in a molecule of DNA.
How To: Calculating Percent Composition Using Chargaff’s Rules
When two strands of DNA bind to one another, hydrogen bonds are formed between their nitrogenous bases. In DNA, adenine always pairs with thymine on the opposite strand, and guanine always binds with cytosine on the opposite strand. This is called complementary base pairing. This is illustrated in the diagram below.
Because of complementary base pairing, the number of adenine bases in a molecule of DNA must always be equal to the number of thymine bases. Similarly, the number of guanine bases must always be equal to the number of cytosine bases. This is called Chargaff’s rule.
Using Chargaff’s rules, we can calculate the percentages of the different bases found in a molecule of DNA. Let’s understand how to do this.
Let’s call the total number of bases Btotal and the number of bases for each type of nucleotide BA, BT, BC, and BG for the bases adenine, thymine, cytosine, and guanine.
Using Chargaff’s rule, we know that
Let’s apply this knowledge to an example.
In the diagram above, the expanded segment possesses 12 base pairs.
Since there are 12 pairs, there are 24 total bases.
Let’s say that we are told that 4 of these bases are cytosine; hence, .
Since BC BG, then .
Next, we can figure out the number of bases remaining after we have excluded those that are cytosine and guanine: or
This set of calculations tells us that the number of bases remaining after we have excluded those that are cytosine and guanine is 16.
Since, according to Chargaff’s rule, , we can conclude that half of the remaining 16 bases are adenine and half are thymine:
And, since BA = BT, therefore .
We can check these values by comparing them to what we see in the diagram. Count the number of A, T, C, and G to check our work.
To calculate the percent, we will divide the number of a particular base by the total number of bases and multiply that value by :
If we complete this calculation for each of the bases, we get the information in the table below:
We may be given a sequence of nucleotides on a single strand of DNA and get asked to determine the complementary sequence. So, how would we go about doing this?
It is important to note that when we read a sequence of DNA bases, we read them in a certain direction. The direction we read DNA is from the end to the end. You can see this in Figure 6 below.
One defining feature of DNA is that the two strands of DNA are antiparallel to one another, meaning that they run in opposite directions. The information on the strand we have been given runs in the – direction. This means that the other strand must run from to .
Key Term: Antiparallel
In DNA, the two strands are considered antiparallel because they run parallel to each other but in opposite directions.
Now, let’s think about the sequence of bases on the complementary strand. Another defining feature of DNA is complementary base pairing: adenine pairs with thymine, and guanine pairs with cytosine. Using this information, we can fill in the sequence of bases on the complementary strand to figure out the complementary sequence, as shown in Figure 7.
The opposite strand of DNA, therefore, carries a complementary version of the code carried in the first strand. This essentially means that a single DNA molecule carries two complementary copies of the same information!
Example 3: Determining a Complementary Sequence of Bases
A section of DNA contains the order of bases ATGCTTAA. What would the complementary sequence of bases be?
Within our cells, DNA takes the form of a double helix. This term describes the way that two, complementary strands of DNA pair up and twist around each other. But what does complementary actually mean?
Complementary base pairing in DNA refers to the specific rules that allow some bases to form bonds with certain bases but not with others. In DNA, the base adenine can form hydrogen bonds with thymine. The base cytosine can form hydrogen bonds with guanine. These pairings are the only ones found in DNA; for example, it is not possible for adenine to bind to guanine.
If we want to determine a complementary sequence of base pairs, we need to use these rules to determine what bases would bind to the ones provided on the complementary strand of DNA.
So, for each A, we replace it with T. For each T, we replace it with A. For each C, we replace it with G. For each G, we replace it with C.
Let’s do this for the sequence given in the question.
ATGCTTAA now becomes TACGAATT.
So, the complementary sequence of bases will be TACGAATT.
Now that we have been over the structure of DNA, you might be wondering how this complex molecule stores genetic information! The nitrogenous bases we have learned about play a crucial role here.
The information that a cell needs to perform its functions is coded into a strand of DNA. In a section of DNA, the sequence of nitrogenous bases can be “read” from the end of the strand to the end. The order of the bases forms a genetic code that a cell can interpret.
The cell takes a sequence of DNA bases (called a gene) and converts this code into a specific protein. This protein will perform a specific function. For example, a sequence of nitrogenous bases in DNA might form the code for a protein that controls the color of your eyes or whether your hair is curly or straight!
A gene is a section of DNA that contains the information needed to produce a functional unit (e.g., a protein). It is the functional unit of heredity.
We have learned a lot about DNA, but did you know you can extract DNA and see it with your own eyes using some simple laboratory equipment?
How To: Extracting DNA from Organic Material
Here, we can learn how to use a sample of fruit or vegetables (for instance, strawberries or peas) to extract and visualize the DNA:
- Take a sample of frozen peas, defrost them, and grind them up using a pestle and mortar.
- Mix 10 cm3 of dishwashing liquid with 100 cm3 of water. Add half a teaspoon of salt. This is your extraction buffer!
- Mix the ground-up peas with your extraction buffer in a large beaker. Stir for 1 minute, and if you can, leave it in a warm water bath for 10 minutes.
- Place a piece of filter paper over another beaker.
- Filter the mixture through the filter paper and into the second beaker.
- Carefully pour 10 cm3 of the filtrate (the liquid you have just collected) into a test tube.
- Tilt the test tube, and carefully add an equal amount of cold ethanol.
- Leave for 5 minutes.
- You should see a white precipitate form; this is the DNA!
Let’s summarize what we have learned about DNA.
- DNA is a polymer, made up of monomers called nucleotides.
- Nucleotides are made up of a deoxyribose sugar, a phosphate group, and a nitrogenous base.
- DNA forms a double helix, maintained by complementary base pairings (A to T, C to G).
- DNA is read in the direction, and a particular sequence of DNA bases that produces a functional unit is known as a gene.
- DNA can be extracted from organic material, such as fruit or vegetables, using an extraction buffer and ethanol.