Click the following link for a DNA Structure and Replication Student Learning Guide

1. Introduction

In the last tutorial, we saw how DNA is

  1. the molecule of heredity
  2. able to control the cell through sending RNA messages to the cytoplasm, where those messages get converted into protein.

Now, let’s see how DNA’s structure makes that possible.

2. Nucleotides are the monomers of DNA

01_nucleotide, numbered
A nucleotide, one of the monomers of DNA (modified from Wikimedia commons)

DNA is a nucleic acid. Nucleic acids, along with other macromolecules like proteins and carbohydrates, are polymers. The monomers of nucleic acids are nucleotides.

There are two key nucleic acids: DNA and RNA.

A DNA nucleotide is shown at left (RNA nucleotides are slightly different). Despite the fact that this DNA nucleotide is a monomer, it can be further broken down into three parts.

  • A 5-carbon sugar called deoxyribose (part 1). To 02b_deoxyriboseremember that it’s a sugar, just focus on its pentagonal shape. If the 5-carbon sugar designation is confusing, just look to the right. There, you can see deoxyribose with all of its carbons, oxygens, and hydrogens drawn in.
  • A phosphate group (part 2). Just look for the phosphorus atom in the middle, and you can find the phosphate group.
  • A nitrogenous base (part 3). These bases, as you can tell by their name, have several nitrogen atoms, which together with carbon, oxygen, and hydrogen form one or two rings. In some courses, you might have to distinguish between the bases with two rings (purine bases), and those with one (pyrimidine bases). I’ve always remembered the difference by thinking “two syllables, two rings” for purines.

The four DNA nucleotides

 Purines (bases with two nitrogen rings)  Pyrimidines (bases with one nitrogen ring)

04a_adenine, structural
Adenine

04d_thymine, structural
Thymine

04b_guanine, structural
Guanine

Cytosine
Cytosine

Now that we’ve seen the structural formula for each nucleotide, we can switch to a simpler representation. In what’s below, the circle with “P” stands for the phosphate group; the pentagon with “D” stands for deoxyribose; and the various shapes with letters “A,” “G,” “C,” and “T” for adenine, guanine, cytosine, and thymine, respectively.

Four DNA nucleotides

05b_adenine, no bonds
Adenine

05d_thymine, no bonds
Thymine

05a_guanine, no bonds
Guanine

05c_cytosine, no bonds
Cytosine

3. Checking Understanding: Nucleotides

[qwiz random = “true” qrecord_id=”sciencemusicvideosMeister1961-Nucleotides_Checking Understanding (M13)”]

[h]Quiz: The Monomers of DNA

[i] 

[q]The monomers of DNA are deoxyribo-____________
[hangman]

[c]nucleotides

[f]Yes. The monomers of DNA are deoxyribonucleotides.

[q]In this diagram, the deoxyribose sugar is at 

[textentry single_char=”true”]

[c*]1

[f]Yes. The deoxyribose sugar is at 1

[c]*

[f]No. Look for the part that has a pentagonal (5 sided) shape.

[q]In this diagram, the phosphate is at 

[textentry single_char=”true”]

[c*]2

[f]Yes. The phosphate is at 2.

[c]*

[f]No. Look for the part that has a phosphorus atom in the middle.

[q]In this diagram, the nitrogenous base is at 

[textentry single_char=”true”]

[c*]3

[f]Yes. The nitrogenous base is at 3

[c]*

[f]No. Look for the part that has a nitrogen atom in it. Also, the NH2 part makes it a base.

[q]Part 3 is a ___________ base

[hangman]

[c]nitrogenous

[f]Yes. Part 3 is a nitrogenous base.

[q]Part 2 is a ___________ group

[hangman]

[c]phosphate

[f]Yes. Part 2 is a phosphate group.

[q labels = “top”]

[l]sugar

[fx] No, that’s not correct. Please try again.

[f*] Excellent!

[l]phosphate

[fx] No. Please try again.

[f*] Excellent!

[l]nitrogenous base

[fx] No. Please try again.

[f*] Great!

[q labels = “top”]

[l]sugar

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l]phosphate

[fx] No, that’s not correct. Please try again.

[f*] Great!

[l]nitrogenous base

[fx] No, that’s not correct. Please try again.

[f*] Good!

[/qwiz]

4. Sugar-phosphate bonds form the backbone of a DNA strand.

DNA is composed of two intertwined strands of nucleotides. Let’s look at how each single strand forms.

06_sugar-phosphate bond1. The nucleotides connect through sugar-phosphate bonds: a covalent bond between the phosphate group of one nucleotide and the deoxyribose of the next nucleotide.

2. Through connecting one nucleotide to the next, a cell (or a chemist) can create a single strand of any length. The diagram below shows ten nucleotides chained together. In your chromosomes, tens or hundreds of millions of nucleotides are chained together(wikipedia).

07a_single strand, of DNA, ten nucleotides (labeled)
A single strand of DNA

3. The sequence of nucleotides can be in any order. Whereas the strand above runs G-T-C-A-G-T-C-A-G-T, any sequence is possible. In fact, in a chain of nucleotides that’s 10 nucleotides long, you could make 410 possible combinations, which amounts to 1,048,576 distinct sequences. The flexibility of this system gives DNA the power to be the language of life.

4. The sequence of bases enables DNA to specify the order of amino acids in proteins, giving DNA the power to determine a cell’s (and an organism’s) genetic traits. The chain of deoxyribose sugars and phosphates is known as the sugar-phosphate backbone. The function of the sugar-phosphate backbone is completely structural (whereas the function of the bases is to store and provide information).

5. The two strands of DNA are held together by hydrogen bonds between complementary nitrogenous bases

To understand DNA’s structure as a double stranded molecule, we need to take another look at the nucleotide monomers that make up DNA.

5.a. DNA’s structure is based on the fact that each nucleotide has a shape that complements one (and only one) other nucleotide.

Let’s make sure we understand the terms complement and complementary before proceeding.

  • As a verb, to complement means “to complete, to fit, or to go together with.” When I’m dressing well, my shirt complements my pants. 
  • As an adjective, complementary means “fitting together,” as in complementary colors. 

To use a biological example, think about how enzymes complement their substrates. The reason why enzymes are specific is because of this complementarity. Or how the beak of hummingbird complements the tubular shape of the flowers that the hummingbird pollinates and gets nectar from.

5b. DNA’s base-pairing rules: Adenine and Thymine are complementary; Guanine and Cytosine are complementary

Complementarity (the state of being complementary) among DNA bases is based on both size and shape. Additionally, though many diagrams don’t represent this, the nucleotide pairs are only complementary when the nucleotides are oriented upside down relative to one another.

Adenine and Thymine

Guanine and Cytosine

08-adenine and thymine are complementary 09_cytosine and guanine are complementary

Note that each pairing consists of a purine (where the nitrogenous base has two nitrogen rings) paired with a pyrimidine (where the nitrogenous base has one nitrogen ring). As a result, the width of DNA is constant: 2 nanometers for the entire length of the molecules.

Here’s a flattened-out (non-spiral) depiction of DNA that shows its double stranded structure:

10_DNA, two strands

5c. Hydrogen bonding

12_hydrogen bond, two water molecules, LABELED
Hydrogen bonding between two molecules of water

The paired nitrogenous bases don’t only fit together: they also hold onto each other. The bond that connects adenine to thymine or cytosine to guanine is a hydrogen bond. 

Hydrogen bonds are often between molecules.In DNA, the hydrogen bonds are within the molecule. In the nitrogenous bases, exposed hydrogen atoms have partial positive charges. Exposed nitrogen or oxygen atoms have partial negative charges. As you can see below, hydrogen bonds form between oxygen and hydrogen, or nitrogen and hydrogen.

Hydrogen bonds between complementary bases in DNA
The dotted lines between complementary bases indicate hydrogen bonds
Guanine-Cytosine Adenine-Thymine
11-b_500px-GC_DNA_base_pair.svg 12b_671px-AT_DNA_base_pair.svg

These hydrogen bonds play a key role in both DNA’s structure and function. Structurally, they hold the two strands together. Functionally, they make the molecule easy to replicate. These hydrogen bonds can be easily broken by enzymes. With the two strands separated, each strand can serve as a template for synthesis of a new strand. Replication is a topic we’ll take on in the next tutorial.

6. Base Pair, Hydrogen Bond Practice

[qwiz style=”width: 648px; border: 2px solid black; ” qrecord_id=”sciencemusicvideosMeister1961-Hydrogen Bond Practice”]

[h]Base Pair, Hydrogen Bond Practice

[q labels = “top”]

matching nucleotide

___

___

___

___

___

___

___

___

___

1st nucleotide

A

T

A

G

C

C

G

T

A

[l]A

[fx] No, that’s not correct.  Please try again.

[f*] Great!

[l]C

[fx] No, that’s not correct.  Please try again.

[f*] Correct!

[l]G

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[l]T

[fx] No, that’s not correct.  Please try again.

[f*] Great!

[q labels = “top”]

 

[l]hydrogen bond

[fx] No.  Please try again.

[f*] Good!

[l]covalent bond

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[x]

[restart]

[/qwiz]

7. The Double Helix: Final Points

DNA, the molecule of heredity. At this point, you should have a good understanding of the structure of DNA. Here are a few final points.

1. DNA is called a double helix because of its shape. A helix is like a corkscrew. DNA is like two, intertwined corkscrews. Hence, a double helix.

2. The two strands of the double helix are anti-parallel to one another. What that means is that the two strands will match up through complementary shape and hydrogen bonding only if each strand, (along with its nucleotides) is oriented upside down relative to the other.

3. You already know that DNA is an acronym for deoxyribonucleic acid.

  • The deoxyribo- part refers to the sugar, deoxyribose, that’s a key part of DNA’s structure.
  • The nucleic part refers to the fact that DNA is found in the nucleus of eukaryotic cells.
  • The acid part refers to DNA’s chemistry: DNA is acidic.

4. The Nobel Prize for discovery of DNA’s structure went to James Watson, Francis Crick, and Maurice Wilkins, who received their prize in 1962. A fourth contributor to their efforts was Rosalind Franklin, who died in 1958 (and thus could not share in the prize). Franklin’s work was essential in helping Watson and Crick understand the geometry of the double helix, enabling them to create an accurate model. These key dimensions are as follows:

  • The width of the double helix is two nanometers (two billionths of a meter). This is represented by letter “o” in the diagram to the right.
  • The distance between two adjacent nucleotides is 0.34 nanometer, represented by “n” at right.
  • It takes 10 nucleotides in a row for the helix to make one complete turn (which you can also think of as the wavelength of the helix). One turn, in other words, is 3.4 nanometers long, a distance represented by “m” in the diagram at right.

5. DNA is the substrate for many enzymatic reactions. During replication and transcription, for example, enzymes ride along an exposed strand of DNA, and synthesize new DNA (during replication) or RNA (during transcription) by adding new nucleotides to the growing daughter strand. In both cases, the enzymes can only add new nucleotides in one direction: the 3′ end.

What does that mean? Take a look at the structural formula of the two DNA nucleotides that are connected by a sugar-phosphate bond to your left. A convention used by biochemists is to number the carbons in a sugar. Take a good look at the upper nucleotide, and find the # 1 carbon in the sugar deoxyribose. The # 1 carbon is the one that binds to the nitrogenous base. Now find the # 5 carbon: that’s the one that binds to a phosphate group. The # 3 carbon is the one that forms a sugar-phosphate bond with the next nucleotide.

The key thing to remember here is that during synthesis of DNA or RNA, enzymes move in a 5′ to 3′ direction, always adding new nucleotides at the 3′ end. 

8. Quiz: DNA Structure

Note: You can expect to see questions not only from this tutorial, but from the previous one, too. It’s more difficult, but also more effective. Also, I’m going to quiz you on diagrams of DNA that you haven’t yet seen. Your ability to transfer what you know to these new diagrams will help you consolidate your learning.

[qwiz style=”border:3px solid black; ” random = “true” qrecord_id=”sciencemusicvideosMeister1961-DNA Structure (M13)”][h] Quiz: DNA Structure
[i] Here’s how the quiz works:

  • Each question is multiple choice or fill-in-the-blanks, but the entire quiz is like a series of flashcards.
  • If you get the question right, it comes off the deck.
  • If you get the question wrong, it goes to the bottom of the deck, so you can try it again.

[!]Card 1++++++++++++++++++[/!]

[q]The monomers of nucleic acids are _________

[hangman]

[c]nucleotides

[f]Yes. The monomers of nucleic acids are nucleotides.

[!]Card 2++++++++++++++++++[/!]

[q]In DNA, cytosine always bonds with

[hangman]

[c]guanine

[f]Yes.In DNA, cytosine always bonds with guanine.

[!]Card 3++++++++++++++++++[/!]

[q]In a DNA nucleotide, the sugar is

[hangman]

[c]deoxyribose

[f]In a DNA nucleotide, the sugar is deoxyribose.

[!]Card 4++++++++++++++++++[/!]

 

[!]Card 5++++++++++++++++++[/!]

 

[!]Card 6++++++++++++++++++[/!]

[q]A common name to describe DNA’s shape is double _____________.

[hangman]

[c]helix

[a]A common name to describe DNA’s shape is double helix.

[!]Card 7++++++++++++++++++[/!]

[q]In DNA, guanine always bonds with

[hangman]

[c]cytosine

[f]In DNA, guanine always bonds with cytosine.

[!]Card 8++++++++++++++++++[/!]

[!]Card 8a++++++++++++++++++[/!]

[q]Adenine is ________ to thymine.

[hangman]

[c]complementary

[a]Adenine is complementary to thymine.

[!]Card 9++++++++++++++++++[/!]

[q]The nitrogenous bases with one ring are

[hangman]

[c]pyrimidines

[f]Right. The bases with one ring are pyrimidines

[!]Card 10++++++++++++++++++[/!]

[q]In DNA, thymine always bonds with

[hangman]

[c]adenine

[f]In DNA, thymine always bonds with adenine.

[!]Card 11++++++++++++++++++[/!]

[q]The nitrogenous bases with two rings are

[hangman]

[c]purines

[f]Nice! The nitrogenous bases with two rings are purines

[!]Card 12++++++++++++++++++[/!]

[q]The bonds connecting complementary base pairs are ________ bonds.

[hangman]

[c]hydrogen

[f]The bonds connecting complementary base pairs are hydrogen bonds.

[!]Card 13++++++++++++++++++[/!]

[q]In DNA, the orientation of the two complementary strands is anti-__________

[hangman]

[c]parallel

[f]In DNA,the orientation of the two complementary strands is anti-parallel.

[!]Card 14++++++++++++++++++[/!]

 

[!]Card 15++++++++++++++++++[/!]

[q]In DNA, adenine always bonds with

[hangman]

[c]thymine

[f]Yes. In DNA, adenine always bonds with thymine

[!]Card 16++++++++++++++++++[/!]

[!]Card 16a++++++++++++++++++[/!]

[q]The central dogma of molecular genetics is DNA makes _____ makes protein

[hangman]

[c]RNA

[f]The central dogma of molecular genetics is DNA makes RNA makes protein.

[!]Card 16b++++++++++++++++++[/!]

 

[!]Card 17++++++++++++++++++[/!]

 

[!]Card 18++++++++++++++++++[/!]

[q]DNA stores genetic ____________.

[hangman]

[c]information

[f]Yes. DNA stores genetic information.

[!]Card 19++++++++++++++++++[/!]

 

[!]Card 20++++++++++++++++++[/!]

[q]The molecule that brings DNA information from the nucleus to the cytoplasm is

[hangman]

[c]RNA

[f]Yes. The molecule that brings DNA information from the nucleus to the cytoplasm is RNA.

[!]Card 21++++++++++++++++++[/!]

[q]The photosynthesizing organelle outside of the nucleus with its own DNA is the

[hangman]

[c]chloroplast

[f]The photosynthesizing organelle outside of the nucleus with its own DNA is the chloroplast.

[!]Card 22++++++++++++++++++[/!]

[q]In eukaryotic cells, the DNA in the nucleus is organized into

[hangman]

[c]chromosomes

[f]Yes. In eukaryotic cells, the DNA in the nucleus is organized into chromosomes.

[!]Card 23++++++++++++++++++[/!]

[q]A unit of heredity is a

[hangman]

[c]gene

[f]Correct. A unit of heredity is a gene.

[!]Card 25++++++++++++++++++[/!]

[!] Question 1++++++++++++++[/!]

[q] In the diagram of a DNA molecule below, which number is pointing to a phosphate group?

[c] 1

[c] 2

[c*] 3

[c] 4

[c] 5

[c] 6

[c] 7

[c] 8

[c] 9

[f]No. Number 1 indicates the sugar phosphate backbone.
[f]No. Number 2 indicates a sugar-phosphate bond.
[f]Yes. Number 3 indicates a phosphate group.
[f]No. Number 4 indicates deoxyribose.

[f]No. Number 5 indicates the nitrogenous bases adenine.
[f]No. Number 6 indicates the nitrogenous bases thymine.
[f]No. Number 7 indicates hydrogen bonds.
[f]No. Number 8 indicates the nitrogenous base cytosine.

[f]No. Number 9 indicates the nitrogenous base guanine.

[!] Question 2++++++++++++++[/!]

[q labels = “top”]

 

 

[l]deoxyribose

[fx] No, that’s not correct.  Please try again.

[f*] Good!

[l]hydrogen bonds

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[l]nitrogenous base

[fx] No.  Please try again.

[f*] Great!

[l]nucleotide

[fx] No.  Please try again.

[f*] Correct!

[l]phosphate group

[fx] No.  Please try again.

[f*] Good!

[l]sugar-phosphate backbone

[fx] No.  Please try again.

[f*] Great!

[l]sugar-phosphate bond

[fx] No, that’s not correct.  Please try again.

[f*] Good!

[!] Question X++++++++++++++[/!]

[!] Question 3 ++++++++++++++[/!]

[q labels = “top”]

 

[l]phosphate group

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[l]nitrogenous base

[fx] No, that’s not correct.  Please try again.

[f*] Correct!

[l]deoxyribose sugar

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[!] Question 4++++++++++++++[/!]

[q] In the diagram of a DNA molecule below, which number is pointing to the sugar-phosphate backbone?

[c*] 1

[c] 2

[c] 3

[c] 4

[c] 5

[c] 6

[c] 7

[c] 8

[c] 9

[f]Yes. Number 1 indicates the sugar phosphate backbone.
[f]No. Number 2 indicates a sugar-phosphate bond.
[f]No. Number 3 indicates a phosphate group.
[f]No. Number 4 indicates deoxyribose.

[f]No. Number 5 indicates the nitrogenous bases adenine.
[f]No. Number 6 indicates the nitrogenous bases thymine.
[f]No. Number 7 indicates hydrogen bonds.
[f]No. Number 8 indicates the nitrogenous base cytosine.

[f]No. Number 9 indicates the nitrogenous base guanine.

[!] Question 5+++++DNA makes RNA makes protein interactive diagram+++++++++[/!]

[q labels = “top”]

 

[l]RNA

[fx] No, that’s not correct.  Please try again.

[f*] Great!

[l]translation of RNA to protein

[fx] No, that’s not correct.  Please try again.

[f*] Correct!

[l]DNA

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[l]cell membrane

[fx] No.  Please try again.

[f*] Excellent!

[l]cytoplasm

[fx] No, that’s not correct.  Please try again.

[f*] Good!

[l]protein

[fx] No, that’s not correct.  Please try again.

[f*] Good!

[l]transcription of DNA to RNA

[fx] No, that’s not correct.  Please try again.

[f*] Great!

[l]nuclear membrane

[fx] No, that’s not correct.  Please try again.

[f*] Excellent!

[!] Question 6++++++++++++++[/!]

[q] In the diagram of a DNA molecule below, which number represents hydrogen bonds?

[c] 1

[c] 2

[c] 3

[c] 4

[c] 5

[c] 6

[c*] 7

[c] 8

[c] 9

[f]No. Number 1 indicates the sugar phosphate backbone.
[f]No. Number 2 indicates a sugar-phosphate bond.
[f]Yes. Number 3 indicates a phosphate group.
[f]No. Number 4 indicates deoxyribose.

[f]No. Number 5 indicates the nitrogenous bases adenine.
[f]No. Number 6 indicates the nitrogenous bases thymine.
[f]Yes. Number 7 indicates hydrogen bonds.
[f]No. Number 8 indicates the nitrogenous base cytosine.

[f]No. Number 9 indicates the nitrogenous base guanine.

[!]++++Question 1+++[/!!!]

[q]Which letter in the diagram below corresponds to a distance of 2 nanometers?

[textentry single_char=”true”]

[c*] o

[f] Yes. “o” is the width of DNA, which is two nanometers.

[c]*

[f]No. If you look at the top, you can see that the radius of DNA is 1 nm. If the radius 1, then what’s the diameter?

[!]++++Question 2+++[/!!!][q]Which letter in the diagram below corresponds to a distance of 3.4 nanometers?

[textentry single_char=”true”]

[c*]m

[f] Yes. “m” is the distance required for the helix to make one turn, which corresponds to 10 stacked nucleotides, which corresponds to 3.4 nanometers

[c]*

[f]No. But here’s a hint. Find “n.” The distance between two adjacent nucleotides is 0.34 nanometers. Count how many nucleotides it takes for the helix to make one turn, and you’ll have your answer.

[!]++++Question 3+++[/!!!][q]Which letter in the diagram below corresponds to a distance of 0.34 nanometers?

[textentry single_char=”true”]

[c*]n

[f] Yes. “n” is the distance between two adjacent nucleotides, which is 0.34 nanometers.

[c]*

[f]No. But here’s a hint. It’s the smallest measured dimension on this diagram (and the distance between two adjacent nucleotides).

[!]++++Question 1 for new DNA diagram+++[/!!!]

[q]Which number is the deoxyribose sugar?

[textentry single_char=”true”]

[c*] 1

[f] Yes. “1” is deoxyribose

[c]*

[f]No. Here’s a hint. Deoxyribose is a five carbon sugar. It’s structural formula is a pentagon.

[!]++++Question 1 for new DNA diagram+++[/!!!]

[q]Which number indicates hydrogen bonds?

[textentry single_char=”true”]

[c*] 3

[f] Yes. “3” represents hydrogen bonds.

[c]*

[f]No. Here’s a hint. Hydrogen bonds are between the bases in complementary nucleotides.

[!]++++Question 1 for new DNA diagram+++[/!!!]

[q]Which number is the sugar phosphate backbone?

[textentry single_char=”true”]

[c*] 4

[f] Yes. “4” is the sugar phosphate backbone.

[c]*

[f]No. Here’s a hint. A backbone is pretty long…What’s the longest structure on this diagram?

[!]++++Question 4 for new DNA diagram+++[/!!!]

[q]Which number is an entire nucleotide?

[textentry single_char=”true”]

[c*]5

[f] Yes. “5” is an entire nucleotide

[c]*

[f]No. Here’s a hint. The nucleotide has three subparts: a sugar, a phosphate group, and a nitrogenous base. Where do you see all three of these as one labeled part of the diagram?

[!]++++Question 5 for new DNA diagram+++[/!!!]

[q]Which number indicates a sugar-phosphate bond.

[textentry single_char=”true”]

[c*]7

[f] Yes. “7” represents a sugar phosphate bond.

[c]*

[f]No. Here’s a hint. Look for a covalent bond connecting a sugar and a phosphate group.

[x]
If you want to take this quiz again, click the button below

[restart]

[/qwiz]

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