AP Biology

## Learning Outcomes

- Describe the role of RNA polymerase in transcription.
- Explain how promoters help determine where transcription begins.
- Distinguish the template strand from the coding strand of DNA.
- Predict an RNA sequence from a DNA template strand using base-pairing rules.
- Explain why promoter mutations can reduce RNA and protein production.
- Compare promoter use in prokaryotic operons and eukaryotic genes.
- Connect transcription initiation to gene regulation and RNA processing.

## AP Biology Syllabus

For AP Biology Unit 6, you should understand transcription as the process by which genetic information in DNA is copied into RNA. This subtopic focuses on how RNA polymerase identifies the correct starting region of a gene, binds near a promoter, reads one DNA strand, and builds an RNA transcript in the correct direction. Questions often ask you to interpret a DNA sequence, identify the effect of a promoter mutation, or explain how altered transcription changes protein levels and phenotype.

- RNA polymerase is the enzyme that synthesizes RNA during transcription.
- A promoter is a noncoding DNA sequence that helps RNA polymerase bind and begin transcription.
- RNA polymerase reads the DNA template strand in the 3′ to 5′ direction.
- RNA polymerase builds RNA in the 5′ to 3′ direction.
- The RNA transcript is complementary to the template strand and nearly identical to the coding strand, except RNA has uracil instead of thymine.
- In eukaryotes, transcription factors help RNA polymerase bind to promoters.
- Many eukaryotic promoters include a TATA box, a DNA region rich in thymine and adenine.
- Promoter changes can reduce transcription, lowering mRNA and protein levels.

## Test Your Knowledge

Attempt these questions before reading this article. If you find some difficult or cannot remember the answers, look more closely at that area during your revision.

1. What enzyme synthesizes RNA from a DNA template during transcription?
2. If the DNA template strand is 3′-ACGTAC-5′, what RNA sequence will be produced?
3. Why would deleting a TATA box from a eukaryotic promoter usually decrease protein production?
4. What is the difference between the template strand and the coding strand of DNA?
5. How do promoters help regulate which genes are expressed in a cell?

## Introduction

Transcription is the first major step in gene expression. During transcription, a cell copies the information in a specific DNA sequence into RNA. This does not mean the entire genome is copied at once. Instead, cells transcribe particular genes when their products are needed. For a protein-coding gene, the RNA product will eventually help direct the production of a polypeptide during translation.

RNA polymerase is the enzyme that carries out transcription, but it does not begin randomly on DNA. It must recognize a nearby DNA region called a promoter. Promoters are central to gene expression because they help determine where transcription starts, which strand is used as the template, and how often a gene is transcribed.

> **Key Term: transcription**
> The process in which genetic information in a DNA sequence is copied into a newly synthesized RNA molecule.

### RNA Polymerase Builds RNA from a DNA Template

RNA polymerase is the enzyme responsible for making RNA. Like DNA polymerase, it adds nucleotides to the 3′ end of a growing nucleic acid strand, so the new RNA molecule is built in the 5′ to 3′ direction. However, RNA polymerase differs from DNA polymerase in a key way: RNA polymerase does not require a primer to begin synthesis.

During transcription, RNA polymerase uses only one of the two DNA strands as a template. The DNA double helix opens locally around the gene being transcribed, allowing RNA polymerase to read the template strand and match RNA nucleotides by complementary base pairing.

The base-pairing rules for transcription are:

- DNA A pairs with RNA U.
- DNA T pairs with RNA A.
- DNA C pairs with RNA G.
- DNA G pairs with RNA C.

For example, if the DNA template strand is:

3′-ACG TAC GTA-5′

RNA polymerase produces:

5′-UGC AUG CAU-3′

The direction matters. RNA polymerase reads the DNA template strand in the 3′ to 5′ direction while synthesizing the RNA strand in the 5′ to 3′ direction. The strands are antiparallel.

> **Key Term: RNA polymerase**
> The enzyme that carries out transcription by linking RNA nucleotides into a growing RNA strand using a DNA template.
>
> **Test Tip:**
> If an AP question gives you a DNA template strand, write the RNA as the complementary sequence and replace thymine with uracil. Also check strand direction: RNA is written 5′ to 3′ unless the question states otherwise.

RNA polymerase can produce different types of RNA. Messenger RNA, or mRNA, carries information used to build proteins. Transfer RNA, or tRNA, helps bring amino acids to the ribosome during translation. Ribosomal RNA, or rRNA, forms part of ribosomes and helps catalyze peptide bond formation. Not all RNA molecules become proteins; many RNAs function as RNA.

> **Key Term: mRNA**
> Messenger RNA; an RNA molecule that carries genetic information from DNA to ribosomes as codons.
>
> **Key Term: tRNA**
> Transfer RNA; an RNA molecule that carries amino acids and uses an anticodon to pair with mRNA codons during translation.
>
> **Key Term: rRNA**
> Ribosomal RNA; an RNA molecule that forms part of ribosomes and helps catalyze reactions during translation.

### Promoters Mark Where Transcription Begins

A promoter is a noncoding DNA sequence located near a gene. Its main role is to serve as a binding region for RNA polymerase and associated proteins. Because the promoter is not part of the protein-coding sequence, it does not directly code for amino acids. Instead, it helps control transcription.

Promoters are often described as being upstream of the coding region of a gene. “Upstream” means before the gene’s transcribed or coding region, relative to the direction of transcription. This position allows RNA polymerase to bind and prepare to begin RNA synthesis at the transcription start site.

> **Key Term: promoter**
> A noncoding DNA sequence that serves as a binding site for RNA polymerase and helps initiate transcription.
>
> **Key Term: upstream**
> A position before the coding or transcribed region of a gene, relative to the direction of transcription.

In eukaryotes, RNA polymerase usually needs help binding to the promoter. Proteins called transcription factors bind to DNA and assist RNA polymerase in forming the transcription initiation complex. Some transcription factors make transcription more likely, while others can reduce transcription by making it harder for RNA polymerase to bind or start.

Many eukaryotic promoters contain a TATA box, a region rich in thymine and adenine nucleotides. The TATA box is not a universal feature of every promoter, but it is a common AP Biology example. If a mutation deletes or damages the TATA box, RNA polymerase and transcription factors may have more difficulty recognizing the promoter. As a result, transcription often decreases, less mRNA is made, and less protein may be produced.

> **Key Term: transcription factor**
> A protein that helps regulate transcription, often by helping RNA polymerase bind to a promoter or begin transcription.
>
> **Key Term: TATA box**
> A promoter region found in many eukaryotic genes that is rich in thymine and adenine nucleotides and helps transcription machinery bind.
>
> **Exam Warning:**
> Do not say that a promoter codes for a protein. A promoter is a regulatory DNA sequence. It affects transcription, but it is not translated into amino acids.

Promoter sequences tend to be conserved because RNA polymerase and transcription-associated proteins must recognize them. If promoter sequences changed too much, transcription might fail or occur at the wrong level. This is why AP questions may ask you to explain why similar promoter sequences are found across organisms or why mutations in promoters can have strong effects.

### Template Strand, Coding Strand, and Directionality

In a DNA double helix, either strand can serve as the template for a particular gene, but only one strand is used for a given transcription event. The strand read by RNA polymerase is called the template strand. It is also called the antisense strand, noncoding strand, or minus strand.

The other DNA strand is called the coding strand, sense strand, or plus strand. The coding strand is not read by RNA polymerase for that gene, but its sequence matches the RNA transcript except that DNA has thymine and RNA has uracil.

> **Key Term: template strand**
> The DNA strand read by RNA polymerase during transcription; the RNA transcript is complementary to this strand.
>
> **Key Term: coding strand**
> The DNA strand with nearly the same sequence as the RNA transcript, except DNA contains thymine where RNA contains uracil.

Example:

Template strand: 3′-TAC GGA CTT-5′
RNA transcript: 5′-AUG CCU GAA-3′
Coding strand: 5′-ATG CCT GAA-3′

Notice that the RNA transcript and coding strand have the same sequence pattern, except RNA uses U instead of T. This is a common source of mistakes. If the question gives the coding strand, you usually only need to replace T with U to get the RNA sequence. If the question gives the template strand, you must make the complementary RNA sequence.

> **Test Tip:**
> Before converting a DNA sequence to RNA, identify whether the question gives the template strand or coding strand. Many incorrect answers come from treating the template strand as if it were the coding strand.

AP Biology questions may also ask about the effect of changing the template or promoter. A mutation in the coding region may alter the RNA codons and possibly the amino acid sequence. A mutation in a promoter may leave the protein-coding sequence unchanged but reduce or increase how much RNA is made. Both types of mutation can affect phenotype, but they do so in different ways.

### Promoters as Gene Regulation Sites in Prokaryotes and Eukaryotes

Promoters are not just start signals; they are also major control points for gene expression. A gene can only be transcribed efficiently if RNA polymerase can bind and initiate transcription. Therefore, anything that changes promoter access can change gene expression.

In prokaryotes, genes with related functions are often organized in operons. An operon is a cluster of genes controlled by a common promoter. This arrangement allows a bacterium to transcribe several genes together in one RNA transcript. For example, if several enzymes are needed to break down a sugar, a bacterium can turn the whole group on when that sugar is available.

> **Key Term: operon**
> A cluster of functionally related genes in prokaryotes that is controlled by a common promoter and regulated as a unit.

In an operon, the promoter binds RNA polymerase, while another regulatory sequence called the operator can bind a repressor protein. These two sequences have different roles. The promoter is for RNA polymerase binding. The operator is for repressor binding. If a repressor blocks RNA polymerase from transcribing the genes, the operon is turned off or reduced.

> **Exam Warning:**
> Do not confuse promoters and operators. Promoters bind RNA polymerase. Operators bind repressors in many prokaryotic operons.

In eukaryotes, most protein-coding genes are regulated individually rather than in operons. Eukaryotic gene regulation often involves promoters, transcription factors, enhancers, silencers, mediators, and chromatin structure. Enhancers can bind activator proteins that increase transcription, while silencers can bind repressor proteins that reduce transcription. These regulatory sequences may be located far from the gene, but DNA folding can bring them near the promoter region.

Chromatin structure also affects whether RNA polymerase can access promoters. DNA wrapped tightly around histone proteins is less accessible and is usually transcribed less often. DNA that is more loosely packed is more accessible to RNA polymerase and transcription factors, so genes in those regions are more likely to be expressed.

> **Key Term: pre-mRNA**
> The initial eukaryotic RNA transcript before processing, including intron removal, exon joining, addition of a 5′ cap, and addition of a poly-A tail.

Although this article focuses on RNA polymerase and promoters, remember that eukaryotic mRNA must be processed after transcription. A newly made eukaryotic pre-mRNA is modified before it leaves the nucleus. Introns are removed, exons are joined, a 5′ GTP cap is added, and a poly-A tail is added to the 3′ end. These processing steps help protect the RNA, support nuclear export, and prepare the mRNA for translation.

Promoter strength and RNA processing can both affect final protein output. For example, if a promoter mutation reduces transcription, fewer pre-mRNA molecules are made. If splicing is altered, the mature mRNA may code for a different or shorter protein. AP free-response questions often expect you to connect changes at the DNA or RNA level to changes in protein production.

> **Test Tip:**
> When explaining a promoter mutation, use a cause-and-effect chain: altered promoter recognition → reduced RNA polymerase binding or initiation → less transcription → less mRNA → less protein.

## Key Point Checklist

This article has covered the following key knowledge points:

- Transcription copies genetic information from DNA into RNA.
- RNA polymerase is the enzyme that synthesizes RNA during transcription.
- RNA polymerase does not require a primer to begin RNA synthesis.
- RNA is synthesized in the 5′ to 3′ direction.
- RNA polymerase reads the DNA template strand in the 3′ to 5′ direction.
- The RNA transcript is complementary to the template strand.
- The RNA transcript matches the coding strand except that RNA contains uracil instead of thymine.
- Promoters are noncoding DNA sequences that help RNA polymerase bind and begin transcription.
- Many eukaryotic promoters contain a TATA box that helps transcription machinery recognize the promoter.
- Transcription factors help RNA polymerase bind to promoters and regulate transcription.
- In prokaryotic operons, a common promoter can control multiple related genes.
- Promoter mutations can change mRNA and protein levels without changing the protein-coding sequence.

## Key Terms and Concepts

- transcription
- RNA polymerase
- mRNA
- tRNA
- rRNA
- promoter
- upstream
- transcription factor
- TATA box
- template strand
- coding strand
- operon
- pre-mRNA


Transcription and RNA processing - RNA polymerase and promoters