C7: From Genes to Protein

Introduction

Welcome to the pre-lab reading for Lab C7: From Genes to Protein. Last time, we might have discussed the structure of DNA and its role as the blueprint of life. But how does that blueprint actually get used to build the molecules that do the work in our cells – primarily proteins? This week, we’ll explore the fundamental processes of transcription and translation, collectively known as gene expression. This journey from DNA sequence to functional protein is often called the Central Dogma of molecular biology. Understanding this process is key to comprehending almost everything else in biology, from how organisms develop to how diseases occur.

Learning Objectives:

• Understand the Central Dogma (DNA → RNA → Protein).
• Describe the process of transcription, including initiation, elongation, and termination.
• Explain the role of RNA polymerase, template strand, and coding strand.
• (Briefly) Describe RNA processing in eukaryotes (splicing, capping, polyadenylation).
• Describe the process of translation, including initiation, elongation, and termination.
• Explain the roles of mRNA, tRNA, ribosomes, codons, and anticodons.
• Understand the genetic code and how it relates nucleotide sequences to amino acid sequences.

1. The Central Dogma: An Overview

The Central Dogma, first proposed by Francis Crick, describes the flow of genetic information within a biological system. In its simplest form, it states that information flows from:

DNA → RNA → Protein

1. Transcription: The information encoded in a specific segment of DNA (a gene) is copied into a messenger RNA (mRNA) molecule. Think of it like making a working copy of a specific recipe from a large cookbook.
2. Translation: The information carried by the mRNA molecule is used to assemble a specific sequence of amino acids, forming a polypeptide chain, which then folds into a functional protein. This is like using the recipe copy to actually bake the cake.

 Figure 1: A simplified representation of the Central Dogma, showing the flow of genetic information from DNA replication, to transcription into RNA, and finally translation into protein. (Source: Wikimedia Commons, User: Dhorspool, CC BY-SA 4.0)

The Central Dogma states that information flows from Protein to RNA to DNA.

True False

2. Transcription: From DNA to mRNA

Transcription is the process of synthesizing an RNA molecule from a DNA template. It occurs in the nucleus in eukaryotes and in the cytoplasm in prokaryotes.

Key Players:

• DNA Template Strand: The strand of the DNA double helix that is read by the enzyme.
• RNA Polymerase: The enzyme responsible for synthesizing the RNA molecule. It binds to the DNA, unwinds it, and links RNA nucleotides together using the DNA template as a guide.
• Promoter: A specific DNA sequence located near the start of a gene that signals where RNA polymerase should bind and begin transcription.
• Terminator: A specific DNA sequence that signals the end of transcription.

The Process:

Transcription proceeds in three main stages:

1. Initiation: RNA polymerase binds to the promoter region of the gene on the DNA. The DNA double helix unwinds near the promoter, exposing the template strand.
2. Elongation: RNA polymerase moves along the DNA template strand, reading the DNA sequence (from 3’ to 5’ direction on the template strand). For each DNA nucleotide it reads, it adds a complementary RNA nucleotide (A pairs with U, G pairs with C) to the growing mRNA chain (synthesized in the 5’ to 3’ direction).
3. Termination: When RNA polymerase reaches the terminator sequence on the DNA, it detaches from the DNA, and the newly synthesized RNA molecule (called a pre-mRNA in eukaryotes, or mRNA in prokaryotes) is released.

Figure 2: Overview of Transcription. RNA Polymerase binds to DNA, unwinds it, and synthesizes an RNA strand complementary to the template DNA strand. (Source: Wikimedia Commons, User: Sponk, CC BY-SA 3.0)

Watch this animation for a visual overview of Transcription: Transcription Animation (YouTube) (Note: Video length ~2 min)

Place the steps of Transcription in the correct order:

Click the items below in the order you think is correct.

• RNA polymerase adds complementary RNA nucleotides to the template strand.
• RNA polymerase detaches from the DNA and releases the RNA molecule.
• RNA polymerase binds to the promoter region on the DNA.

Reset Check Order

2.1 RNA Processing in Eukaryotes (A Brief Look)

In eukaryotes, the initial RNA transcript (pre-mRNA) undergoes processing before it can leave the nucleus and be translated. This involves:

• Splicing: Non-coding regions called introns are removed, and the coding regions called exons are joined together.
• 5’ Capping: A modified guanine nucleotide is added to the 5’ end of the mRNA. This helps protect the mRNA from degradation and aids in ribosome binding during translation.
• 3’ Polyadenylation: A tail of adenine nucleotides (poly-A tail) is added to the 3’ end. This also protects the mRNA and helps in its export from the nucleus.

Figure 3: Animation showing RNA splicing where introns are removed and exons are joined together. (Source: Wikimedia Commons, User: Boumphreyfr, CC BY-SA 3.0)

Click to flip

What is removed during RNA splicing in eukaryotes?

Back

Introns (non-coding intervening sequences) are removed, and exons (expressed sequences) are joined together.

Click or tap the card to reveal the back.

3. Translation: From mRNA to Protein

Translation is the process where the genetic information carried by mRNA is decoded to synthesize a specific sequence of amino acids, forming a polypeptide. This occurs in the cytoplasm on molecular machines called ribosomes.

Key Players:

• mRNA (Messenger RNA): Carries the genetic code from the DNA (in the form of codons) to the ribosome.
• Ribosomes: Composed of ribosomal RNA (rRNA) and proteins. They provide the site for translation, binding the mRNA and facilitating the interaction with tRNA. They have two subunits (large and small).
• tRNA (Transfer RNA): Acts as an adapter molecule. Each tRNA molecule has an anticodon region that is complementary to a specific mRNA codon, and it carries the corresponding amino acid specified by that codon.
• Codons: Three-nucleotide sequences on the mRNA (e.g., AUG, GGC, UAA) that specify a particular amino acid or a stop signal.
• Anticodon: A three-nucleotide sequence on a tRNA molecule that base-pairs with a complementary codon on the mRNA.
• Amino Acids: The building blocks of proteins.

The Genetic Code:

The relationship between mRNA codons and the amino acids they specify is known as the genetic code. It’s nearly universal across all life. There are 64 possible codons (4 bases taken 3 at a time), but only 20 common amino acids. This means the code is redundant (multiple codons can specify the same amino acid) but not ambiguous (one codon never specifies more than one amino acid).

• Start Codon: AUG typically signals the start of translation and also codes for the amino acid Methionine.
• Stop Codons: UAA, UAG, and UGA signal the termination of translation.

Figure 4: The Genetic Code table showing which amino acid corresponds to each mRNA codon. To read it, find the first base on the left, the second base across the top, and the third base on the right. (Source: Wikimedia Commons, User: NIH, Public Domain)

The Process:

Translation also occurs in three stages:

1. Initiation: The small ribosomal subunit binds to the mRNA near the 5’ end (often at the start codon AUG). The initiator tRNA carrying Methionine binds to the start codon. The large ribosomal subunit then joins, forming the complete initiation complex.
2. Elongation: The ribosome moves along the mRNA one codon at a time (5’ to 3’ direction).
   • A tRNA with an anticodon complementary to the next codon enters the ribosome’s A-site (aminoacyl site).
   • A peptide bond is formed between the amino acid carried by the new tRNA and the growing polypeptide chain held by the tRNA in the P-site (peptidyl site).
   • The ribosome translocates (moves) one codon down the mRNA. The tRNA that was in the P-site moves to the E-site (exit site) and is released, while the tRNA carrying the growing chain moves from the A-site to the P-site. This cycle repeats, adding amino acids one by one.
3. Termination: When the ribosome encounters a stop codon (UAA, UAG, or UGA) in the mRNA sequence, no tRNA matches. Instead, a release factor protein binds to the stop codon in the A-site. This triggers the release of the completed polypeptide chain from the tRNA in the P-site, and the ribosomal subunits dissociate from the mRNA.

Figure 5: Animation overview of Translation. The ribosome moves along the mRNA, matching tRNA anticodons to mRNA codons and linking amino acids into a polypeptide chain. (Source: Wikimedia Commons, User: Darryl Leja, NHGRI, Public Domain)

Watch this animation for a visual overview of Translation: Translation Animation (YouTube) (Note: Video length ~3 min)

Which molecule carries the amino acid to the ribosome and matches it with the correct codon on the mRNA?

• rRNA
• DNA Polymerase
• tRNA
• mRNA

Complete the sentence summarizing the core processes:

The process of copying genetic information from DNA into mRNA is called . The process of synthesizing a polypeptide chain from the mRNA sequence is called . These two processes form the core of the Dogma.

Check Answers

4. From Polypeptide to Functional Protein

The polypeptide chain synthesized during translation is often not yet a functional protein. It needs to fold into a specific three-dimensional shape. This folding is critical for its function. Sometimes, proteins also undergo further chemical modifications (post-translational modifications) like adding sugars or lipids, or being cleaved into smaller pieces, before they become fully active.

5. Relevance to the Lab

In this week’s lab, we will likely be simulating or analyzing aspects of transcription and translation. This might involve:

• Working with DNA and RNA sequences on paper or using bioinformatics tools.
• Simulating the processes using models or kits.
• Analyzing the effects of mutations (changes in DNA sequence) on the resulting protein.

Having a solid grasp of the mechanisms of transcription and translation, the roles of the different molecules involved, and how to use the genetic code will be essential for understanding the lab activities and interpreting your results.

Conclusion

The journey from gene to protein is a tightly regulated and fundamental process essential for all life. Transcription faithfully copies the genetic blueprint from DNA into mRNA, and translation decodes this message to build functional proteins. Understanding these steps provides insight into how genetic information dictates cellular structure and function. Prepare any questions you have for the lab session!