Protein Synthesis (IB Topic D1.2)

Essential Idea(s): Proteins are the final product of the central dogma of DNA, in which Information transferred from DNA to mRNA is translated into an amino acid sequence. These proteins then carry out most essential functions of life.

Unit Length: 5 Lessons (+4 AHL)

  Guiding Questions

◊ How does a cell produce a sequence of amino acids from a sequence of DNA bases?

◊ How is the reliability of protein synthesis ensured?

Materials:

Self-Teaching Slides (SL) / Self-Teaching Slides (AHL) Quizlet Vocab Set (Transcription – SL / AHL) / Quizlet Vocab Set (Translation – SL / AHL)
Teaching Slides (SL) Notes Template (SL) / Notes Template (AHL)

 

IB Statement(s) and Objective(s)

 

D1.2.1: Transcription as the synthesis of RNA using a DNA template

  • Define transcription
  • Outline the process of transcription, including the role of RNA polymerase and complementary base pairing

 

D1.2.2: Role of hydrogen bonding and complementary base pairing in transcription

  • State the complementary base pairing utilized in transcription
  • Identify the sense and antisense strands of DNA given a diagram of translation

 

D1.2.3: Stability of DNA templates

  • Outline how stability of the information stored in DNA is maintained

 

D1.2.4: Transcription as a process required for the expression of genes

  • Define gene expression
  • Outline the role of transcription in regulating gene expression

 

D1.2.5: Translation as the synthesis of polypeptides from mRNA

  • Define translation
  • State the location of translation in the cell
  • Give an overview of translation

 

D1.2.6: Roles of mRNA, ribosomes and tRNA in translation

  • Outline the roles of mRNA, ribosomes and tRNA in translation
  • Describe the structure of the ribosomes, including the small and large subunits and the names and roles of the tRNA binding sites

 

D1.2.7: Complementary base pairing between tRNA and mRNA

  • Define codon and anticodon
  • State the type of bond found between mRNA and tRNA nucleotides.

 

D1.2.8: Features of the genetic code

  • Use a genetic code table to deduce the mRNA codon(s) given the name of an amino acid
  • Explain the reason that a sequence of three nucleotides is required to code for the 20 amino acids commonly utilized by organisms

 

D1.2.9: Using the genetic code expressed as a table of mRNA codons

  • Define degenerate as related to the genetic code
  • Define universal as related to the genetic code

 

D1.2.10: Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain

  • Outline the process of translation, including codon recognition, bond formation and translocation
  • Define elongation as related to translation
  • Define translocation as related to translation
  • Outline the process of translation elongation

 

D1.2.11: Mutations that change protein structure

  • Define gene mutation
  • Describe an example of a point mutation affecting protein structure
  • Outline the consequences of the Hb mutation on the impacted individual

Additional Higher Level Topics

D1.2.12: Directionality of transcription and translation

  • Identify the 5’ ends and 3’ ends of a strand of RNA
  • Describe the formation of the covalent bond between adjacent nucleotides during transcription
  • State that RNA polymerases can only add the 5’ phosphate of a free nucleotide to the 3’ deoxyribose of the elongating strand
  • State the direction of movement of the ribosome along the mRNA molecule

 

D1.2.13: Initiation of transcription at the promoter

  • Outline the structure and function of promoter regions of DNA
  • Describe the initiation of transcription, including the role of the promoter sequence, transcription factors and RNA polymerase
  • Define “transcription factor” and outline their function in regulating transcription
  • State the role of regulatory proteins 
  • Give an example of a transcription factor at work

 

D1.2.14: Non-coding sequences in DNA do not code for polypeptides

  • Define “coding” and “non-coding” sequences of DNA
  • Outline five functions of non-coding DNA sequences found in genomes 

 

D1.2.15: Post-transcriptional modification in eukaryotic cells

  • Outline the location and timing of post-transcriptional modification of RNA
  • Compare intron and exon sequences of genes

 

D1.2.16: Alternative splicing of exons to produce variants of a protein from a single gene

  • Outline the process of RNA splicing
  • Give an example of alternative splicing resulting in different protein products

 

D1.2.17: Initiation of translation

  • Outline the process of translation initiation, including the steps of: initiation, elongation, translocation and termination

 

D1.2.18: Modification of polypeptides into their functional state

  • List types of modifications of polypeptides that may be required to form a functional protein
  • Outline the two stages of modification of preproinsulin to form functional insulin

 

D1.2.19: Recycling of amino acids by proteasomes

  • Define proteasome
  • List reasons when proteins typically exist for a relatively short time within a cell

Activities: ⓟ = podcast / ⍰ = inquiry 5 / ⓦ = Write it /  Ӕ = The academy  / Ⓡ = Read it

Ⓛ +Ӕ (recommended): An Interactive Journey through the Central Dogma  (💁)

Work your way through this interactive lesson on transcription and translation. Then do it a 2nd time, only this time, screencast a recording of you teaching the content as you work your way through the app. Your final product should be a recording of your screen as you work through the app, with your voice explaining what you’re doing at each step. 

 

ⓟ/ⓦ (recommended): The 2024 Nobel Prize in Chemistry Goes to… Protein- Predicting AI! (and the scientists who built it)

(💁 [writeup] / 👭 [podcast – max 3])

Imagine solving one of biology’s most elusive mysteries — called “the protein-folding problem” — with the click of a button, or designing entirely new proteins to combat diseases, or new proteins to clean up the environment. This is the legacy of the Nobel-winning breakthroughs in AI in 2024. Demis Hassabis, John Jumper, and David Baker brought together biology and artificial intelligence to transform how we study proteins. Read through this summary article, do whatever further research you feel necessary then discuss:

  1. What makes proteins essential for life, and how does their structure influence their function?
  2. Why was predicting protein structure such a difficult problem, and how does AlphaFold solve it?
  3. How are AlphaFold and protein design changing real-world research and applications? What kind of work will scientists be doing (around the same time you are pursuing a career? 😉)
  4. What ethical, scientific, or societal questions arise from these technologies? 

(Side note: It’s super interesting to align this task to David Baker’s 2019 TED Talk to see how far we’ve progressed in 5 years. 

 

ⓟ (recommended): The DNA Revolution (👭 max 3)

Note: this can also be done in the next unit: Mutations and Gene Editing (D1.3)

The discovery of DNA was just the beginning. In 2012, CRISPR finally unlocked the ability that was previously science fiction: the ability to freely edit DNA. Discuss the implications of the history of DNA: Choose either a historical moment in DNA’s history (e.g. Franklin and Wilkins), OR the outlook for the future of DNA technology – and make your finest podcast to date. Follow the directions on this assignment sheet. 

 

Old school worksheet (Recommended): Central Dogma, Disease, and Genetic  Medicine (💁 / 👭 max 3)

In groups of 2-3, go through this interactive presentation on genetic medicine. Once you finish, complete questions 1-2 on this worksheet. Your group will then be assigned one of the genetic medicines being developed in hopes of treating this disease. With your group, complete question 3 – and be ready to teach about your disease to the rest of the group. 

 

📄: (Old-School Worksheet): Breaking the Genetic Code  (💁)

This worksheet will help you get familiar with a lot of the terms from levels 15-17 (think: codon, mRNA, transcription, translation, genetic code). Use it for practice!

 

ⓦ: “Inquiry 5″: Q&A on Central Dogma (💁/ 👭max 2)

Create a list of 5 inquiry questions related to the central dogma of biology. Remember that good inquiry questions are conceptual / open-ended…

Such as:   “How can the change in a single nucleotide result in 

                    a genetic disorder that affects the whole body? 

NOT:         “What is the function of mRNA?” 

If working solo, write out answers to your own questions; if working in pairs, record yourselves asking each other your 5 questions.

 

Ⓛ: Make a model: DNA and Translation (💁/ 👭max 3) 

Grab some paper or play-doh or some candy, and follow the guidelines on this worksheet to build an actual model of DNA. Make sure you can easily remove the pieces – you’ll need to be able to identify clear A/T/C/G nucleotides, so that you can show what happens during translation. 

 

(Recommended): Label a Drawing of Translation (💁) 

Label this diagram of translation in this drawing. Include ALL of the required labels listed on the first page. Submit to G. Classroom once you’re done. 

 

ⓟ/ⓦ: 1 mutation in 6 billion = A Life-Debilitating Disease (The Story of Sickle Cell Anemia) (💁/ 👭 max 2)

Sickle Cell Anemia starts with a single mutation of a single nucleotide on a single gene. It results in an extensive list of symptoms, often which end in an early death. Learn about the cause of sickle-cell anemia, and discuss: 1) What is a mutation?;  2) What causes sickle cell?; and 3) How can a single mutation result in so many symptoms?  

 

ⓟ/ⓦ: Proteins: Our Ticket to a COVID-free World 

(💁 [writeup] / 👭 [podcast – max 3])

The COVID vaccine currently being rolled out is unique: it introduces mRNA into the body, which the body reads to make the spike proteins found on the outside of the virus (see the spike proteins in this image). Then, the body makes immunoglobulin proteins (antibodies) to attack these spike proteins. Should the real coronavirus ever show up…those antibodies will be ready for the fight, and will keep you from getting sick. Read the article and discuss: 1) How the coronavirus spike proteins are “coded for” from RNA;  2) How the variety of proteins in nature gives us everything from spike proteins to antibodies; and 3)  How you could clearly ease the mind of someone nervous that the COVID vaccine might accidentally give them the disease (see me if you need any clarification…I’m happy to discuss!). 

 

ⓟ/ⓦ: The Most Amazing Machines in the World  

(💁 [writeup] / 👭 [podcast – max 3])

From TED.com: “Proteins are remarkable molecular machines: they digest your food, fire your neurons, power your immune system and so much more. What if we could design new ones, with functions never before seen in nature?” Watch this 10-minute TED Talk about a potentially huge future realm of science: custom proteins. Then, write/discuss some inquiry prompts related to the talk. Here are a few to get you started: 

  • What exactly is it that proteins DO in the world of biology? 
  • How are proteins manufactured in the body (hint: DNA translation)
  • What do you think about the idea of customizing proteins? Would this be a good thing, or a bad thing, and why?

 

ⓡ: Protein Misfolding and the Seeds of Dementia (💁)

It’s hard to fathom, but something as seemingly unharmful as a misfolded protein might be responsible for several forms of dementia; including Alzheimer’s to Parksinson’s disease. Read this article and/or this article, and discuss: 1) What protein folding actually is (refer specifically to tertiary/quaternary structure);  2) How misfolding can lead to terrible consequences, such as disease; and  3) If there is any hope to overcome the diseases caused by misfolding proteins.

—————————————–

Activities for Gene Expression: 

 

ⓟ/ⓦ: Biotech and the Discovery of DNA Expression 

(💁/ 👭 max 2)

Watch this video on transcription and the biotech behind the study of gene expression. Discuss/write a response, answering: 1) What is gene expression?;  2) What is happening in the clips where glowing green/red spots can be seen?  3) What are transcription factors, and how are genes turned “on” or “off”?

 

📄(old school worksheet): Alternative Splicing Activity (💁)

Grab some colored pencils — in this activity, you will use them to color-code different players in gene expression. You’ll label exons and see the different possible gene expressions from a single DNA sequence.

 

 

Extra Resources: