Protein Biosynthesis Simulation Playbook
Before Starting the Simulation:
- Ensure all VR headsets are charged and properly calibrated
- Review safety guidelines for VR equipment use
- Show students the essential VR gestures and controls
- Plan your time: allocate 20 minutes for interaction and 10–15 minutes for reflection
During the Simulation:
- Designate student helpers to assist their peers
- Circulate throughout the classroom to support struggling students
- Guide students to observe and document cellular changes
- Prompt students to share their observations verbally
Group Organization:
- For classes with limited devices, form triads: one in VR, two observing/discussing
- Rotate roles every 5–7 minutes
- Provide printed diagrams of cellular structures for note-taking during observation
Troubleshooting Technical Issues:
- Preload simulation and test each headset prior to class
- Keep a backup tablet with 2D version of the lab in case of headset malfunction
- Maintain clear VR boundaries and warn students about physical obstacles
Recommendations for Teachers
Before simulation:
- Start with a quick quiz:
– “What is transcription?”
– “Which organelle performs it?”
– “What’s the difference between DNA and RNA?” - Distribute flashcards with key molecules (RNA polymerase, nucleotides, transcription factors) and ask students to guess their functions.
During simulation:
- Pause after the component tablet appears and ask students to predict where each object should be placed.
- During nucleus resizing, discuss why scaling matters in cellular models.
- Assign one student to act as a “narrator” describing aloud what they’re doing and why.
After simulation:
- Have students redraw the full transcription process with labels and steps.
- Ask: “What errors could stop mRNA from being produced?” (for example: no polymerase).
- Short writing prompt: “If I were an mRNA molecule, my journey would begin like this…”
1. Simulation Overview
Simulation title: Protein Synthesis VR Simulation
Description: The student assembles the three key stages of protein synthesis: transcription in the nucleus, translation on the rough ER, and protein packaging in the Golgi apparatus. They explore the spatial logic of cellular function through interaction.
Simulation type: VR
Subject and age: Biology, Grades 8–10
Key topics:
- Transcription and translation
- DNA → mRNA → polypeptide
- Organelle roles in protein synthesis
- Visualization of synthesis in 3D space
2. Key Simulation Milestones
| Time | Simulation stage | What happens before the action? | What should be done? | What happens after the action? |
|---|---|---|---|---|
| 00:00 | The cell 1. Nucleus placement | The student sees a cell with some organelles. In front of them is a tablet with some organelles. |
1. Trigger nucleus from tablet 2. Grab and stretch to enlarge |
1. Nucleus appears (small size) 2. Nucleus resizes and activates |
| 00:48 | Transcription setup | The student stands on a platform in the nucleus. A semi-transparent DNA model is in front. A tablet opens with transcription components. |
1. Pull transcription components (factors) 2. Place all components using hint 3. Watch animation; press “Next” |
1. DNA, ATP, polymerase etc. appear 2. DNA enlarges and moves into position; all factors settle 3. mRNA synthesis is visualized |
| 02:59 | The cell 2. Rough ER placement | The student sees a cell with several organelles, including the nucleus already placed earlier. The same organelles appear on the tablet again. |
1. Trigger ER from tablet 2. Grab and stretch to enlarge |
1. ER appears (small size) 2. ER resizes and activates |
| 03:44 | Translation setup | The student stands on a platform on the rough ER. In front is an mRNA with a cap on its 5′ end. A tablet with translation components appears. |
1. Activate the cap at the left end of the mRNA 2. Trigger ribosome, amino acids 3. Place ribosome (5′ cap), tRNA, RF 4. Watch animation; press “Next” |
1. mRNA activates; components become placeable 2. Components appear 3. All translation components settle in place 4. Polypeptide chain synthesis visualized |
| 05:56 | The cell 3. Golgi placement | The student sees a cell with several organelles, including the nucleus and rough ER placed earlier. The tablet again displays the same organelles. |
1. Trigger Golgi from tablet 2. Grab and stretch to enlarge 3. Observe vesicle formation |
1. Golgi appears (small size) 2. Golgi resizes and activates 3. Simulation ends |
3. Theoretical Anchors (from the scene)
- Central Dogma: The central dogma of molecular biology describes the flow of genetic information in cells. DNA is transcribed into RNA, which is then translated into proteins. This sequence is the foundation of cellular biology and explains how cells produce what they need to function.
- Transcription: In the nucleus, a section of DNA serves as a template to build messenger RNA (mRNA). Transcription factors help RNA polymerase locate and bind to the promoter—the “start” region on DNA. RNA polymerase then copies the genetic code from DNA into mRNA.
- mRNA: Messenger RNA carries genetic instructions from the nucleus to the ribosome, where proteins are built.
- Translation: On the rough endoplasmic reticulum (ER), the ribosome reads the mRNA sequence in three-nucleotide units called codons. With help from translation factors, the ribosome links amino acids together in order to form a polypeptide chain—the beginning of a functional protein.
- Ribosome: The ribosome is a molecular machine with two subunits that assemble during translation. It moves along the mRNA, matching each codon with the correct amino acid to build the protein chain.
- tRNA: Transfer RNA brings amino acids to the ribosome. Each tRNA has an anticodon that matches a specific mRNA codon, ensuring the correct amino acid is added to the protein.
- Start and Stop Signals: Translation begins at the start codon (usually AUG, coding for methionine) and ends at a stop codon (UAA, UAG, or UGA). These signals ensure protein synthesis begins and ends at the right points.
- Release Factor: When the ribosome reaches a stop codon, the release factor binds to it. This releases the finished polypeptide chain from the ribosome and tRNA, ending translation.
- Golgi Apparatus: After synthesis, the protein travels through the ER to the Golgi apparatus—the cell’s processing center. Here, the protein is folded, modified (such as adding sugar groups), sorted, and packaged into vesicles for delivery.
- Vesicles: Vesicles are membrane-enclosed structures that transport proteins from the Golgi to their destinations—other organelles, the cell membrane, or outside the cell.
4. Reflection Questions
- Why do you think transcription and translation are separated in space (nucleus vs ER)?
- What might happen if the release factor wasn’t added?
- Which part of the process felt most complex to organize?
- Why is the Golgi apparatus needed after the protein is built?
5. Hard Skill Questions
- What is the full pathway from DNA to finished protein?
- What enzymes and molecules are required for transcription?
- What are the roles of tRNA and ribosomes in translation?
- What is the function of the 5′ cap and 3′ end of mRNA?
- Why are vesicles important in protein delivery?
6. Attachments
-
Video walkthrough
- QR code to simulation
- Printable summary chart (DNA → mRNA → Protein)
- Organelle flashcards
- Google Form quiz
- Animation worksheet