Welcome to the DNA to Protein Simulation!

This simulation will guide you through three essential steps of molecular biology: transcription (from DNA to mRNA) and translation (from mRNA to protein). Along the way, you will interact with complementary DNA strands, mRNA codons, and amino acid sequences. Follow the steps below to complete the simulation!

Step 1: Generate a Random DNA Sequence

In this step, you will first see a random DNA sequence. Your task is to generate the complementary DNA strand based on the base-pairing rules.

How to Proceed:

1. Look at the DNA sequence on the screen. You will see a series of DNA codons (three nucleotide bases per codon).

2. Use the DNA base-pairing rules to fill in the complementary strand.

   • A (Adenine) always pairs with T (Thymine).

   • T (Thymine) always pairs with A (Adenine).

   • C (Cytosine) always pairs with G (Guanine).

   • G (Guanine) always pairs with C (Cytosine).

3. Example:
   If you see the codon ATG, you should type TAC in the input box as the complementary strand.

4. Input the complementary DNA sequence in the boxes provided.

   • As you type, the input box will turn blue if your answer is correct and red if it's incorrect.

5. Once you've correctly filled in all the boxes for the complementary DNA sequence, you will be able to proceed to Step 2.

Step 2: Transcribe DNA to mRNA

Now that you have the complementary DNA strand, it's time to transcribe it into mRNA. This is the process where the DNA sequence is copied into RNA, which can then be translated into proteins.

How to Proceed:

1. Look at the complementary DNA sequence you just created.

   • In this step, you will convert the DNA sequence into mRNA.

2. Use the RNA base-pairing rules to complete the mRNA sequence:

   • A (Adenine) in DNA pairs with U (Uracil) in RNA (not Thymine, since RNA uses Uracil instead).

   • T (Thymine) in DNA pairs with A (Adenine) in RNA.

   • C (Cytosine) in DNA pairs with G (Guanine) in RNA.

   • G (Guanine) in DNA pairs with C (Cytosine) in RNA.

3. Example:
   If your complementary DNA sequence is TAC, the mRNA sequence will be AUG.

4. Type the mRNA codons in the boxes on the screen. Just like in Step 1, the input box will turn blue when the correct mRNA codon is entered.

5. Once you've completed the mRNA sequence, you can move on to Step 3.

Step 3: Translation - From mRNA to Protein

In this final step, you will translate the mRNA sequence into a chain of amino acids, which will form a protein.

How to Proceed:

1. Look at the validated mRNA sequence that you generated in Step 2.

2. Use the mRNA codon chart to identify the corresponding amino acid for each mRNA codon:

   • Every set of three mRNA bases (codon) codes for a specific amino acid.

   • Directions for Decoding mRNA Codons Using a Circle Codon Chart

   • Identify the Codon: Look at the mRNA sequence and select the first three nucleotide bases (codon) you want to decode. Each codon consists of three bases (A, U, C, or G).

   • Locate the First Base: Starting from the center of the circle, find the first base of your codon (e.g., A, U, C, or G). This will be in the innermost ring of the chart.

   • Move to the Second Base: From the first base, move outward to the next ring where you’ll find the options for the second base of the codon.

   • Find the Third Base: Continue outward to the third ring, where the third base of the codon is located. This leads you to a specific section of the chart where a three-letter abbreviation for an amino acid is shown.

   • Read the Amino Acid: The name or abbreviation of the amino acid corresponding to the codon will be found at the outermost part of the chart. This is the amino acid that the codon codes for.

   • Repeat for Each Codon: Continue these steps for each three-base codon in the mRNA sequene

Example

2. • For the mRNA codon AUG:

   • First Base (A): Start at the center and find “A.”

   • Second Base (U): Move to the next ring and find “U.”

   • Third Base (G): Move to the outermost ring and find “G.”

   • This takes you to Methionine (Met), the amino acid coded by AUG.

   • Use these steps to decode each codon in an mRNA sequence!

   • Alternatively, you can use the square mRNA codon chart which has all the codons laid out in a grid format. Find your mRNA codon on the chart to determine the corresponding amino acid.

3. Input the amino acid (or ‘stop’) for each codon:

   • Type in the corresponding amino acid abbreviation (e.g., PHE for Phenylalanine, LEU for Leucine, etc.) for each mRNA codon.

   • If the codon is a stop codon (UAA, UAG, or UGA), enter STOP.

4. Check your work:

   • The input box will turn blue if your answer is correct and red if your answer is incorrect.

   • Keep entering the correct amino acids until you have completed the entire translation.

Hints and Tips

DNA Base-Pairing Hints:

• Remember: A-T and C-G. This is crucial for understanding how DNA strands pair with each other.

• If you're unsure, always double-check your pairings. Mistakes in the complementary DNA sequence will affect the mRNA and amino acid sequence.

DNA to RNA Base-Pairing Rules:

• A-T pairs in DNA, but when making RNA, A pairs with U (Uracil) instead of T.

• Be careful when switching from DNA to RNA—this is one of the most common mistakes!

Base Pairing Recap:

• DNA to DNA: A pairs with T, C pairs with G

• DNA to RNA: A pairs with U, T pairs with A, C pairs with G, G pairs with C

• mRNA Codons to Amino Acids: Use the codon chart to translate mRNA into the corresponding amino acids.