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RNA Transcription Simulation

Molecular Biology

Molecule Shapes

Chemistry is the branch of science that deals with the study of matter! Did you know that chemistry is also called “the central science,” because of its role in bridging physics with other natural sciences? Let's dive into learning more on the composition and the physical and chemical properties of various forms of matter!  

RNA Translation Simulation

We all know of DNA as the genetic material of our cells and the process of DNA replication is SO important. Let's find out why!

DNA Replication Simulation Image

DNA Replication Simulation 

DNA Thumbnail

Biochemistry

Genetics

Explore the structure, function, and behavior of cells in cell biology. Our interactive 3D models and detailed study guides will help you ace the exams!

Get familiar with the structure and function of different cell organelles by using our interactive 3D models and study guides.

Explore how biology and chemistry intersect all the way down at the molecular level using our extensive library of 3D, interactive content!

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tRNA

Enter the fascinating world of genetics, the study of inheritance with our popular 3D models. Our easy-to-read study guides explain complex concepts in a super simple way!

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Primase

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Helicase

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Release Factor

nucleotide

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# Youtube Guide: 

<iframe width="560" height="315" src="https://www.youtube.com/embed/PmF4spLabbo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

---

### Lesson Objectives

- Understand the importance and structure of an RNA molecule.
- Understand the functions of the three different types of RNA in a cell.

---

## Ribonucleic Acid (RNA) 

Let’s start with the basics. You’ve probably heard of __DNA__ before (<span id="q3"></span> acid). It carries our genetic code–the textbook from which all the information we need to grow, survive, and reproduce originates. DNA is found in the nucleus in the form of either chromatin or chromosomes. It’s composed of a sequence of <span id="q1"></span> that link together into one long <span id="q2"></span>. The order of these nucleotide bases determines our genetic blueprint, kind of like how the order we put the letters of the alphabet in determines our words. 

Thinking about DNA in terms of language is actually pretty useful. It has all of our genetic information written down in its own language, but unfortunately, the rest of the cell doesn’t speak it. Seems like a pretty big oversight in terms of communication (who even designed this thing?), but luckily, there’s another molecule in the mix who can help translate: ribonucleic acid, also known as __RNA__. 

RNA and DNA are two of the three most important macromolecules necessary for life. The third one is proteins, which DNA and RNA work together to produce. In the simplest terms possible, DNA makes RNA, and RNA makes proteins. There are three types of RNA involved in protein synthesis: *<span id="q4"></span>*, *transfer RNA*, and *ribosomal RNA*. We’ll talk about what they do in a minute after we briefly touch on what makes DNA and RNA different, besides the first letter of their name (LOL) (so funny!) (aren’t we funny?) (tell us we’re funny).

<div class="sketchfab-embed-wrapper"> <iframe title="RNA" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" allow="autoplay; fullscreen; xr-spatial-tracking" xr-spatial-tracking execution-while-out-of-viewport execution-while-not-rendered web-share width="640" height="480" src="https://sketchfab.com/models/362542f787ae428bbe2b1085bfde7a9d/embed?autostart=1&ui_animations=0&ui_infos=0&ui_stop=0&ui_inspector=0&ui_watermark_link=0&ui_watermark=0&ui_ar=0&ui_help=0&ui_settings=0&ui_vr=0&ui_fullscreen=0&ui_annotations=0"> </iframe> </div>

---

### How is DNA Different from RNA?

DNA and RNA are actually pretty similar in terms of both structure and function. They’re both nucleic acids made of nucleotides, and those nucleotides are *almost* the same, but not quite. DNA uses the bases __Adenine (A)__, __Cytosine (C)__, __Guanine (G)__, and __Thymine (T)__. RNA uses the first three, but instead of thymine it has __Uracil (U)__. 

Another distinction is that DNA is made of two strands, while RNA is only made of one. The main difference between them though is that the nucleotides that make up RNA are composed of a nucleobase, a ribose sugar, and a phosphate group, while DNA’s nucleotides are made of a nucleobase, a *deoxy*ribose sugar, and a phosphate group. Other than that, they’re pretty similar, so let’s move on to the different types of RNA.

<div class="sketchfab-embed-wrapper"> <iframe title="ConCu3D_DifferenceBetweenDNAandRNA" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" allow="autoplay; fullscreen; xr-spatial-tracking" xr-spatial-tracking execution-while-out-of-viewport execution-while-not-rendered web-share width="640" height="480" src="https://sketchfab.com/models/7f33460f9f864aa1a20cd9ba5f570ad8/embed?autostart=1&ui_animations=0&ui_infos=0&ui_stop=0&ui_inspector=0&ui_watermark_link=0&ui_watermark=0&ui_ar=0&ui_help=0&ui_settings=0&ui_vr=0&ui_fullscreen=0&ui_annotations=0"> </iframe> </div>

---

### The Three Types of RNA

Before we got distracted by the last section, we were talking about how RNA has three different forms– *messenger RNA*, *transfer RNA*, *ribosomal RNA*. They each have a special function to help out with the process of protein synthesis, which we’ll briefly go over below.

- The first step of making proteins is to translate DNA into a message that the rest of the cell can read. This message comes in the form of __Messenger RNA (mRNA)__, which is then transferred from the nucleus to the cytoplasm.

- Once in the cytoplasm, the small subunit of a ribosome attaches to the mRNA and translates it for the large subunit, which synthesizes a <span id="q5"></span> chain of amino acids–the base form of a protein. __Transfer RNA (tRNA)__ delivers the amino acids to the ribosomes as they synthesize these chains.

- Ribosomes are composed of proteins and __Ribosomal RNA (rRNA)__, our final type of RNA. Once the polypeptide chain has been assembled, the ribosome transports it to the rough endoplasmic reticulum, embeds itself into its membrane, and releases the chain so that it can be folded into its final, functional protein form.

![trna mrna rrna](//images.ctfassets.net/4yflszkpcwkt/2MtJytM6qnPouTgkGVBumc/ce056142b48560a6d59c5083db4f5bfc/slide-47.jpg)

[Source](https://ppt-online.org/275669)

---

## 💡 Summary

- __DNA__ is the carrier of our genetic information.

- __RNA__ translates DNA so that it can be used to create proteins.

- DNA and RNA are mostly similar, with a few __key differences__. DNA is double-stranded, while RNA is single-stranded. DNA is composed of the nucleotides A, C, G, and T, while RNA is composed of the nucleotides A, C, G, and U. Lastly, the sugar used in the backbone of RNA is ribose, while the sugar in DNA is deoxyribose.

- There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

- __Messenger RNA__ translates DNA and transfers it from the nucleus to the cytoplasm.
- Once in the cytoplasm, ribosomes use the mRNA to synthesize a string of amino acids called a polypeptide chain. __Transfer RNA__ delivers the amino acids to the ribosome.
- Ribosomes are composed partially of __ribosomal RNA__.

---

### FAQs

__1. What is the purpose of tRNA?__

Transfer RNA is responsible for delivering amino acids to the ribosome as it synthesizes a polypeptide chain. 

__2. What is the difference between DNA and RNA?__

- RNA is made of a sugar called ribose. DNA contains a slightly varied sugar called deoxyribose.

- RNA has the nucleobase named uracil, while DNA contains the nucleobase thymine.

- DNA is double-stranded, while RNA is composed of a single strand.

__3. What is the purpose of rRNA?__

Ribosomal RNA, along with proteins, make up the composition of ribosomes, the organelle respomsible for protein synthesis. 

__4. What is the purpose of mRNA?__

DNA is translated into Messenger RNA, which is then transported from the nucleus to the cytoplasm where it delivers instructions to ribosomes for protein synthesis. 

__5. What do the two subunits of a ribosome do?__

The small subunit uses mRNA to provide instructions to the large subunit, which is responsible for building polypeptide chains to synthesize proteins. 

__6. Why is DNA better genetic material as compared to RNA?__

The deoxyribose sugar of the DNA is composed of one less oxygen-containing hydroxyl group. DNA is thus a more stable nucleic acid. RNA contains a ribose sugar, which  is more reactive than DNA. Thus DNA is a better genetic material as compared to RNA.

---

*We hope you enjoyed studying this lesson and learned something cool about __RNA__! Join our Discord community to get any questions you may have answered and to engage with other students just like you! Don't forget to download our App and check out our awesome VR room for this guide - we promise, it makes studying much more fun* 😎

## Sources

1. Wan, Yao, and Kunal Chatterjee. “RNA | Definition, Structure, Types, & Functions.” *Encyclopædia Britannica*, 13 July 2018, [https://www.britannica.com/science/RNA](https://www.britannica.com/science/RNA) .Accessed 11 Nov. 2021.

2.  “RNA ( Read ) | Biology.” *Www.ck12.org*, [htps://www.ck12.org/biology/rna/lesson/RNA-BIO/?referrer=concept_details](https://www.ck12.org/biology/rna/lesson/RNA-BIO/?referrer=concept_details). Accessed 11 Nov. 2021.


RNA Study Guide

# Interactive Simulation
[Launch Simulation!](http://rnatranscriptions.com)

## Youtube Guide

<iframe width="560" height="315" src="https://www.youtube.com/embed/PmF4spLabbo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## Introduction

What’s RNA polymerase? Since you asked, __RNA polymerase__ is a special enzyme that’s responsible for translating DNA into RNA in a process <span id="app-select-1"></span> *transcription*. Well, what’s transcription? Is it important? Yes, it *is* important! But why is it important? How does it work? Read on to find out! 

---

### Lesson Objectives

- Understand the process of RNA transcription in biology
- Understand the post-transcriptional modification of mRNA
- Understand the differences between transcription and translation

---

### Transcription

__Transcription__ is a key player in the creation of proteins, macromolecules that perform a variety of functions in a cell to keep it running. Some proteins serve as antibodies and enzymes, some provide structural support, and others are used to transport and store atoms or other small molecules around a cell. They’re involved in virtually every single cell function that exists (which is super cool, but we’re here to talk about transcription today, so let’s get back to that).

Transcription is basically the first step to create a protein. During the process, RNA polymerase uses DNA as a template to translate <span id="app-select-2"></span> into a format that the rest of the cell can read through base pairing. The format in question is that of messenger RNA (mRNA for short). The mRNA is transported to the <span id="app-select-3"></span>, where it’s picked up by a ribosome, which translates it again, and blah blah blah a bunch of other steps, and we finally end up with our protein (we don’t think the part in the middle is actually blah, but it’s not important for us to know right now). Now that we’ve got the gist, let’s move on to learn about the actual process of transcription.

---

### Stages of Transcription

Transcription occurs in three stages: Initiation, Elongation, and Termination. Let’s jump right in with initiation.

![rna transcription](//images.ctfassets.net/4yflszkpcwkt/Rbpl5ScAUho86vpk1dEll/50a12e8712900adc7c52fd5c220f5f83/Eukaryotic_Transcription-removebg.png)

[Source](https://en.wikipedia.org/wiki/Eukaryotic_transcription)

---

### Initiation

__Initiation__ is the first step of transcription. It starts when RNA polymerase binds to a region on the DNA strand called a __Promoter__ (which basically tells the RNA polymerase where to start transcribing). When the RNA polymerase attaches to the promoter, it unwinds a portion of the double-helix to create a sort of bubble between its strands as can be seen in the image above.

---

### Elongation

After RNA polymerase binds to the promoter, __Elongation__, the second stage of transcription, can begin. During elongation, RNA polymerase attaches to one of the strands of the DNA (known as the __Template Strand__) and moves along it in the 3’ to 5’ direction, adding nucleotides along the way. 

![Elongation rna transcription](//images.ctfassets.net/4yflszkpcwkt/7LI7OFmXEDtEZqNB0dUsXq/b27584d7bd62ae0086cedb5fe734f312/OSC_Microbio_11_03_TxnElong.jpg)

[Source](https://courses.lumenlearning.com/microbiology/chapter/rna-transcription/)

RNA nucleotides are mostly the same as the DNA nucleotides, but they have one major difference. Adenine (A), thymine (T), cytosine (C), and guanine (G) are the four different DNA nucleotides. RNA nucleotides are the same, except instead of thymine, they have uracil (U). As always, nucleotide base pairs are complementary. C always pairs with G, and A always pairs with T, except in the case of RNA, where A matches with U instead. 

As it moves along the template strand, RNA polymerase adds the appropriate complementary nucleotides in a sequence almost identical to the other strand of DNA (known as the __Coding Strand__). The only difference is that uracil is substituted for thymine, as you can see in the A-U pairing in the diagram below. As new nucleotides are added, the RNA strand becomes longer, which is where this particular stage of transcription gets its name  (*long*-er, e-*long*-ation, get it?). 

---

### Termination

Elongation continues until the RNA polymerase encounters a “stop sequence" called a __Terminator__ on the DNA strand. A terminator is a chunk of nucleotides in a specific order that indicates the replication process is over. __Termination__ begins once the terminator has been reached, and as quickly as it starts, it ends. Because once the new RNA strand is complete and RNA polymerase detaches from the DNA, the process of transcription is over.

---

### Pre-translational mRNA Processing

Remember before when we were talking about mRNA? Well, that brand new strand of RNA that we just spent all this time making isn’t actually messenger RNA yet. We call it __Pre-mRNA__, and during __Pre-mRNA Processing__, we apply the finishing touches by adding a *5’ cap* and a *poly-A tail* and removing “junk” sequences through a process called *splicing*.

![5' cap and poly a tail](//images.ctfassets.net/4yflszkpcwkt/6lJHEic3jV6It5zRBUtxzm/86919da610a9060e62e9ee71baaa9f0a/Post-transcriptional_modification_of_pre-mRNA.png)

[Source](https://commons.wikimedia.org/wiki/File:Post-transcriptional_modification_of_pre-mRNA.png)

---

### 5’ Cap and Poly-A Tail 

Think of our strand of RNA as a shoelace that’s fraying at the ends. If we leave the ends loose, our entire shoelace may end up unraveling, which is why we seal the tip with an aglet (a fun new little vocab word for you). The 5’ cap that we add to the RNA strand works in a similar way.

The __5’ Cap__ is made of methylated guanine and is attached to the first nucleotide of the strand at the 5’ end to protect it from being broken down. It’s also the point where ribosomes in the cytoplasm can attach to it to begin protein synthesis. The __Poly-<span id="app-select-4"></span> Tail__ is made of hundreds of adenine nucleotides and is attached to the 3’ end of the strand to stabilize the RNA molecule and help it move from the nucleus to the cytoplasm.

---

### Splicing

Now that we’ve tied up all of our loose ends (hah), the final RNA processing event, __RNA splicing__, can begin. In our strand of RNA, we have a bunch of good parts that we call __Exons__ and a few bad ones that we call __Introns__. Introns aren’t inherently bad, they’re just sort of useless, and they prevent the mRNA from coding a new protein with all of the good parts of the sequence. Introns are removed with a protein-RNA complex called a spliceosome. Once they’re gone, the spliceosome seals together the rest of the exons to create the final, complete strand of mRNA that is then shipped out of the nucleus to the cytoplasm.

---

### Translation vs Transcription

In *__Transcription__*, RNA polymerase creates a strand of RNA by using DNA as a template. We’ve already gone through that process, so let’s skip ahead to when the finished strand is shipped out from the nucleus. 

*__Translation__* begins when a ribosome in the cytoplasm attaches to the new mRNA strand. The small subunit of the ribosome translates the mRNA for the large subunit of the ribosome, which then creates a polypeptide chain (an incomplete protein) based on what it says. 

Basically, transcription uses DNA to make mRNA in the nucleus, and translation uses mRNA to synthesize proteins in the cytoplasm. 

![translation transcription ](//images.ctfassets.net/4yflszkpcwkt/7Jscw1lyOIgrj6EwQ6PBdP/d49bcb8a7f2324a96e83bfbee9549210/dna-replication-protein-synthesis-transcription-vector-21211393.jpeg)

[Source](https://www.vectorstock.com/royalty-free-vector/dna-replication-protein-synthesis-transcription-vector-21211393)

---

### FAQs

__1. What is transcription?__

The process through which DNA is copied to RNA is called transcription. 

__2. What are the 3 stages of transcription?__

Initiation, elongation, and termination are the three stages of transcription.

__3. What is the difference between transcription and translation?__

During transcription, DNA polymerase makes mRNA from a DNA template in the nucleus, while in translation, ribosomes synthesize proteins from the mRNA instructions in the cytoplasm. 

__4. What is an intron?__ 

An intron is a “junk” sequence in an RNA strand that is removed during the splicing stage of pre-translational mRNA processing. 

__5. What occurs during initiation?__

During initiation, RNA polymerase binds to the promoter on the DNA strand. 

__6. How does DNA polymerase know when to stop transcribing RNA from DNA?__

DNA polymerase stops transcription when it meets a specific sequence of nucleotides on the DNA strand called a terminator. 

__7. Does DNA polymerase add nucleotides to the template strand or the coding strand?__ 

The template strand. 

---

*We hope you enjoyed studying this lesson and learned something cool about __Transcription__! Join our Discord community to get any questions you may have answered and to engage with other students just like you! Don't forget to download our App and check out our awesome VR room for this guide - we promise, it makes studying much more fun* 😎

## Sources

1. “Transcription | Definition, Steps, & Biology | Britannica.” Encyclopædia Britannica, 2019, [www.britannica.com/science/transcription-genetics](http://www.britannica.com/science/transcription-genetics). Accessed 15 Nov. 2021.

2. Khan Academy. “Stages of Transcription.” Khan Academy, 2018, [www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/stages-of-transcription](http://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/stages-of-transcription). Accessed 15 Nov. 2021.

3. Wikipedia Contributors. “Transcription (Biology).” Wikipedia, Wikimedia Foundation, 14 June 2019, [en.wikipedia.org/wiki/Transcription_(biology)](http://en.wikipedia.org/wiki/Transcription_(biology)). Accessed 15 Nov. 2021.

rna-transcription-screenshot

RNA Transcription Study Guide

## Interactive Simulation
[Launch Simulation!](https://www.dnareplicationsimulation.com)

---

## Introduction

You've probably heard of DNA as the genetic blueprint of our cells, but ahe genetic template. Wh better term might be ty? You create a blueprint from scratch to make something once, but you use a template over and over again to create identical copies of the same item. That's how DNA replication works, and it may seem intimidating, but it really isn’t as complicated as you might think. Let's get into it.

### Lesson Objectives

- Understand the semi-conservative mechanism of replication.
- Understand the functions of the enzymes that play a role in this process.

---

### What is DNA?

<div class="sketchfab-embed-wrapper"> <iframe title="DNA" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" allow="autoplay; fullscreen; xr-spatial-tracking" xr-spatial-tracking execution-while-out-of-viewport execution-while-not-rendered web-share width="640" height="480" src="https://sketchfab.com/models/fa9165bf23d742cf9ba584fff18be1a9/embed?autostart=1&ui_animations=0&ui_infos=0&ui_stop=0&ui_inspector=0&ui_watermark_link=0&ui_watermark=0&ui_ar=0&ui_help=0&ui_settings=0&ui_vr=0&ui_fullscreen=0&ui_annotations=0"> </iframe> </div>

__[Deoxyribonucleic acid](https://www.inspiritvr.com/general-bio/introduction-to-biology/nucleic-acids-study-guide "Deoxyribonucleic acid")__, or __DNA__, is the molecule that contains the unique genetic material of nearly every organism on earth. In other words, DNA is what makes you, “you”. 

- DNA was first identified in the 1860s by Swiss chemist Friedrich Miescher. However, it wasn’t until the 1950s that we knew what it actually looked like. 

- In 1953, James Watson and Francis Crick used images of DNA obtained by Rosalind Franklin to create their unique, double-helical model of DNA that resembles a twisted ladder.

- DNA is made up of two long matching strands of __nucleotide bases__ ─molecules that are essentially the building blocks of our genetic material. 

- There are four types of bases: adenine (A), thymine (T), guanine (G), and cytosine (C). The bases of each strand of DNA are bound together by hydrogen bonds to create the unique structure of the twisted double helix.

<aside>
☝️ Nucleotide bases are complementary, meaning that A will always pair with T, and G will always pair with C. 

</aside>

![LxAofVs](//images.contentful.com/4yflszkpcwkt/5lEoEhPkeyaaidn0KUNZxO/f6c2a8fc4e5df39fc0ea4f34afd00b80/LxAofVs.jpg)
                  [Source](https://img.brainkart.com/imagebk28/LxAofVs.jpg)

---
### When does DNA replication occur?

- DNA replication is an important phase of the __cell cycle__ ─an ordered series of events that take place as a cell grows and divides. It’s split into 4 phases: gap 1 (G1), synthesis (S), gap 2 (G2) and mitosis (M). 

- DNA replication occurs in the synthesis, or __S phase__, of the cell cycle. During this phase, the entire parent cell’s DNA is copied into two new strands that will be used to create a pair of identical daughter cells.

<aside>
🧬 Making a copy requires a template. The double-stranded nature of DNA ensures that each strand has the same genetic information so that both the strands in the helix are available as templates.

</aside>

---

### The Semi-Conservative Model

As discussed before, DNA’s unique double-helical shape was discovered by James Watson and Francis Crick in 1953. It wasn’t until four years later, however, that we gained a clear idea of how it actually replicates. 

- Before we discovered the actual series of steps of DNA replication, three hypotheses existed to explain how it might occur. These hypotheses were categorized as the conservative, semi-conservative, and dispersive models.

- Today, we know conclusively that DNA replication follows the __semi-conservative model__, in which each strand of the original DNA’s double helix acts as a template for a new, complementary strand, as proven by the Meselson-Stahl Experiment in 1957. 

![Untitled (1)](//images.contentful.com/4yflszkpcwkt/6YjQsahrid8PUzM1nj581K/7ddbfcdfd7f7ad9f77b06afe1614705e/Untitled__1_.png)
[Source](https://images.app.goo.gl/oHKAVbXvWaRPhBN19)

---

### What are the steps of DNA replication?

<div class="sketchfab-embed-wrapper"> <iframe title="DNA Replication" frameborder="0" allowfullscreen mozallowfullscreen="true" webkitallowfullscreen="true" allow="autoplay; fullscreen; xr-spatial-tracking" xr-spatial-tracking execution-while-out-of-viewport execution-while-not-rendered web-share width="640" height="480" src="https://sketchfab.com/models/35b5f49c792743d4aa7c23243d20bca1/embed?autostart=1&ui_animations=0&ui_infos=0&ui_stop=0&ui_inspector=0&ui_watermark_link=0&ui_watermark=0&ui_ar=0&ui_help=0&ui_settings=0&ui_vr=0&ui_fullscreen=0&ui_annotations=0"> </iframe> </div>

Before a cell can divide, it needs to make two copies of its DNA to allocate into each of its new daughter cells. This process, called DNA replication, occurs in the S phase of the cell cycle in three stages: __Initiation__, __Elongation__, and __Termination__. 

Seven important enzymes and proteins catalyze DNA replication: *DNA helicase*, the *SSB protein*, *DNA tospieromase*, *DNA primase*, *DNA polymerase*, *DNA exonuclease*, and *DNA ligase*. Here’s how the process is done. 

(*If you’re a visual learner, check out our interactive simulation at the top of the page to see what replication looks like and to go through the steps yourself!*) 

### __Stage 1: Initiation__

- Initiation begins when the enzyme __DNA helicase__ causes the DNA strand to uncoil into what looks like a normal ladder instead of a twisted one. It then cuts down the middle of the double DNA strand and separates each half, creating what is known as the __replication fork__. 

<aside>
💡 Think of helicase as the zipper slider of a DNA molecule, and the DNA as the zipper. Now imagine you’re unzipping a jacket. Before you begin, the zipper is still connected as one single strand. Now imagine pulling the zipper slider halfway down the jacket. The upper half of the zipper is now separated into two strands, while the lower half of the zipper is still connected as one. The point at which the zipper slider sits is what we can envision as the replication fork of the jacket. 

</aside>

- After the double-helix has been “unzipped”, the single stranded binding protein, or __SSB protein__, binds to the newly separated DNA strands to hold them in place. If the SSB protein is not present, the individual strands of DNA would bind back together and the process of replication could not occur. 

- As helicase further unwinds the DNA, the still zipped portion of the DNA behind the replication fork winds tighter and tighter. This is known as __supercoiling__. 

- If the coil gets too tight, it will physically prevent helicase from moving further down the strand. __DNA topoisomerase__ relieves this strain so that the process of replication can continue.

- With the SSB protein in place and supercoiling relieved, __DNA primase__ creates a strand of RNA bases called a __primer__. Primers are bound to each unzipped half of the DNA, and serve as the starting point for the assembly of new DNA strands in the next step of replication, elongation.

### Stage 2: Elongation

*Before you read this section, it is HIGHLY recommended that you complete the interactive simulation, as elongation is the most complex portion of the DNA replication process.*

- During elongation, the enzyme <span id="app-select-2"></span> binds to the primer and moves along each strand, adding complementary nucleotide bases to each half of the original DNA as visualized in the image above. (*Remember─A always pairs with T, and C always pairs with G*). 

- This process occurs continuously and in one direction on the upper, or <span id="app-select-3"></span> of DNA. 

- For the lower, or <span id="app-select-4"></span>, however, this process is not continuous and has a slightly different process than that of the leading strand. Here’s the rundown for both.

Let’s start by taking a look at DNA as it replicates in the image below and establish a few basic facts:

- Each strand of DNA has a __5’__ (pronounced 5 prime) and a __3’__ end.
- DNA polymerase can only add nucleotides from the 5’ end to the 3’ end.
- DNA synthesis always moves in the direction toward the replication fork.

![DNA Replication](//images.contentful.com/4yflszkpcwkt/7BeJshl8uydLVSB03Oo6kb/5953ebd22596d6e020dcdde249124bea/DNA-Replication.jpg)

[Source](https://www.microblife.in/what-is-dna-replication/)

Okay, now that we’ve got that down, let’s unpack the diagram.

- The upper parental strand runs 5’ to 3’ from left to right. The leading strand is oriented inversely to its parent strand, running 5’ to 3’ from right to left toward the replication fork. 

- The lower parental strand runs 3’ to 5’ from left to right. Its complementary lagging strand runs 5’ to 3’ away from the replication fork.

- We already know that DNA synthesis always moves toward the replication fork and that DNA polymerase can only synthesize DNA in the 5’ to 3’ direction. This makes things easy for the leading strand, as DNA polymerase can easily and continuously add nucleotides from 5’ to 3’ in the direction of the replication fork’s movement. 

- Because of its orientation, the leading strand only requires one primer from which to bind and attach nucleotides in DNA synthesis. 

- The lagging strand runs from 5’ to 3’ away from the replication fork. Because DNA synthesis always moves toward the replication fork, and DNA polymerase can only add nucleotides in the 5’ to 3’ direction, DNA cannot be synthesized continuously toward the fork in the lagging strand. Instead, it must be added in a series of chunks, known as __Okazaki fragments__.

- Each Okazaki fragment requires its own individual RNA primer from which to attach its nucleotide bases. As DNA synthesis occurs, DNA primase attaches a new primer further up the lagging strand toward the replication fork. 

- DNA polymerase then attaches a new Okazaki fragment to this primer in the 5’ to 3’ direction, moving in the direction opposite to the replication fork. As the fork continues to open, a new primer is added further up the lagging strand, and a new Okazaki fragment is synthesized. This process is repeated until the new DNA has been completed.

### Stage 3: Termination
Okay, so we finished making the DNA. We’re done now, right? Nope! After elongation comes the final stage of the DNA replication process: termination. During termination, the enzymes *DNA exonuclease* and *DNA ligase* serve as a cleanup crew for all of the other enzymes and proteins utilized during replication.

- __DNA exonuclase’s__ job is to remove all of the residual primers from both the leading and lagging strands of DNA. Once this is done, DNA polymerase makes another appearance, filling in all of the gaps with their appropriate base pairs. 

- Now it’s __DNA ligase’s__ turn to seal together both strands, serving as the glue that binds each new strand of DNA together. Finally, the strands re-coil into their original twisted ladder shape, and the process of DNA replication is complete. 

- We should now have two new complete strands of DNA, both identical to the original strand. Each double-strand is formed with one old, conserved strand of DNA, and one newly synthesized one. 

<aside>
💡 Only half of the original DNA has been conserved, which is where we get the name semi-conservative model!

</aside>

---

### 💡 Summary 

- __DNA__ is the carrier of genetic information. 

- DNA is a molecule composed of two identical strands of __nucleotide bases__.

- Each original strand of DNA serves as a template from which to synthesize new strands.

- DNA was first identified by Friedrich Miescher in the 1860s. James Watson and Francis Crick used images of DNA obtained by Rosalind Franklin to create their double-helical model in 1953.

- DNA replication occurs during the S phase__ of the cell cycle.

- DNA replication follows the __semi-conservative model__, because each new daughter strand contains both one one newly synthesized and one original, or conserved, strand of DNA.

- DNA replication occurs over 3 stages: __Initiation__, __Elongation__, and __Termination__.

- During initiation, __DNA helicase__ uncoils and separates the two original strands of DNA. The __SSB protein__ keeps these strands from binding together, and __DNA topoisomerase__ keeps the DNA from __supercoiling__. DNA primase then creates __primers__ which bind to each newly separated half of the original double-stranded DNA. 

- During elongation, __DNA polymerase__ adds complementary nucleotide bases to each strand.

- The __leading strand__ of DNA produces DNA continuously, while the __lagging strand__ must produce DNA in chunks called <span id="app-select-1"></span>.

- During __termination__, __DNA exonuclease__ removes all residual RNA primers from the leading and lagging strands, which are replaced with the appropriate nucleotide bases by DNA polymerase. __DNA ligase__ seals together each new strand of DNA.

## ✅ Conclusion
You made it to the end! Congratulations, we’re so proud of you! 🎉 🧑‍🎓🎊 Hopefully you now know all about DNA replication–where it occurs, how it happens, and all of the important enzymes and proteins that play a part in the process. To check your understanding, take a look at some of common FAQs about DNA replication below. 

---

### 🧐 FAQs

<aside>

__1. What are the four nucleotide bases, and how do they pair together?__
*Adenine (A), thymine (T), guanine (G), and cytosine (C). A always pairs with T, and G always pairs with C.*

__2. In what phase of the cell cycle does DNA replication occur?__
*The S phase.*

__3. What model does DNA replication follow? What does it mean?__
*The semi-conservative model, in which each strand of the original DNA’s double helix serves as a template for a new, complementary strand.*

__4. What are the three stages of replication?__
*Initiation, elongation, and termination.*

__5. What enzyme relieves supercoiling?__
*DNA topoisomerase.*

__6. What enzymes are involved in termination, and what do they do?__
*DNA exonuclease, DNA ligase, and DNA polymerase are all involved in termination. DNA exonuclease removes all residual primers from the leading and lagging strands of DNA, and DNA polymerase fills the gaps left behind. DNA ligase seals the new strands of DNA together.*

__7. Why can’t DNA polymerase synthesize DNA continuously on the lagging strand?__
*DNA polymerase can only add nucleotides from the 5’ to 3’ end of a strand of DNA, and DNA synthesis always moves toward the replication fork. The lagging strand runs 5’ to 3’ away from the replication fork, so new DNA must be added in chunks called Okazaki fragments.*

</aside>

*We hope you enjoyed studying this lesson and learned something cool about __DNA Replication__! Join our Discord community to get any questions you may have answered and to engage with other students just like you! Don't forget to download our App and check out our awesome VR room for this guide - we promise, it makes studying much more fun* 😎

## Sources

1. “Nucleic Acid - Nucleic Acid Metabolism | Britannica.” Www.britannica.com, [www.britannica.com/science/nucleic-acid/Nucleic-acid-metabolism#ref900898](https://www.britannica.com/science/nucleic-acid/Nucleic-acid-metabolism#ref900898). Accessed 15 Nov. 2021.
2. What Is DNA Replication And Its Steps?[https://www.microblife.in/what-is-dna-replication/](https://www.microblife.in/what-is-dna-replication/). Accessed Nov 17, 2021.
3. 7.3B: DNA Replication in Eukaryotes. (2021, January 3). Biology LibreTexts. [https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/7%3A_Microbial_Genetics/7.03%3A_DNA_Replication/7.3B%3A_DNA_Replication_in_Eukaryotes](https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/7%3A_Microbial_Genetics/7.03%3A_DNA_Replication/7.3B%3A_DNA_Replication_in_Eukaryotes) 
4. Bailey, R. (2018). Steps of DNA Replication. ThoughtCo. [https://www.thoughtco.com/dna-replication-3981005](https://www.thoughtco.com/dna-replication-3981005) 
5. Introduction: What is DNA? | Learn Science at Scitable. (2014). Nature.com. [https://www.nature.com/scitable/topicpage/introduction-what-is-dna-6579978/](https://www.nature.com/scitable/topicpage/introduction-what-is-dna-6579978/) 
6. Sabay, P. (2019, August 11). Okazaki Fragments in the Lagging Strand. Www.youtube.com. [https://www.youtube.com/watch?v=gS7Pdghv9js](https://www.youtube.com/watch?v=gS7Pdghv9js) 
7. yourgenome. (2015). DNA replication - 3D. In YouTube. https://www.youtube.com/watch?v=TNKWgcFPHqw 


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