Translation/Protein synthesis

Topic: Translation of mRNA to protein

Abstract

In this lab exercise the processes of information storage and transfer will be simulated by using marshmallows of various colors. Students will translate a strand of DNA, to mRNA, and this mRNA will be used in a simulated ribosome to create a specific polypeptide chain. Discussion will be led using engaging examples and a YouTube video during the presentation of the material prior to the lab exercise. Students will be able to grasp concepts of translation and how this process fits into the core idea of DNA as a blueprint for living organisms.

Part II: Clarifying Your Goals for the Topic

Big Ideas

In molecular biology and genetics, translation is the third stage of protein biosynthesis (part of the overall process of gene expression). In translation, messenger RNA (mRNA) produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In Bacteria, translation occurs in the cell’s cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In Eukaryotes, translation occurs across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. The ribosome facilitates decoding by inducing the binding of tRNAs with complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is “read” by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.
In many instances, the entire ribosome/mRNA complex will bind to the outer membrane of the rough endoplasmic reticulum and release the nascent protein polypeptide inside for later vesicle transport and secretion outside of the cell. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA, do not undergo translation into proteins.
Translation proceeds in four phases: activation, initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation). Amino acids are brought to ribosomes and assembled into proteins.

- In activation, the correct amino acid is covalently bonded to the correct transfer RNA (tRNA). The amino acid is joined by its carboxyl group to the 3′ OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to it, it is termed “charged”.

- Initiation involves the small subunit of the ribosome binding to the 5′ end of mRNA with the help of initiation factors (IF).

- Elongation involves the building of the polypeptide from tRNAs with anticodons that bring the amino acids that correspond with the codon. In the ribosome there are three sites, the Aminoacyl site, the peptiyl site, and the exit site. Aminoacyl site is where the tRNA brings the amino acid and the peptide bond is formed with the amino acid before it. The peptidyl site is where the tRNA indicates what the next condon in the sequence is. The exit site is where the tRNA leaves the ribosome.

- Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). No tRNA can recognize or bind to this codon. Instead, the stop codon induces the binding of a release factor protein that prompts the disassembly of the entire ribosome/mRNA complex.
- wikipedia.org

- mRNA to protein
- codons are along an mRNA strand
- tRNA is the interpreter of the codons
- all 20 amino acids are in the cells cytoplasm floating around
- tRNA transfers these amino acids to the ribosome when needed
- tRNA’s are unique according to the amino acid they code for
- each type of tRNA translates a particular mRNA codon into a particular amino acid
- the tRNA is a translator because it can read a nucleic acid word (the mRNA codon) and interpret it as a protein word (the amino acid)
Key Points/Terms
- Translation: mRNA is used to determine the sequence of amino acids within a polypeptide.
- Proteins: biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function.
- A polypeptide is a single linear polymer chain of amino acids bonded together
- The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code.
- Codon: groups of 3 nucleotides
- Sense Codon: sequence of 3 nucleotides that specify for a particular amino acid
- Start Codon: first codon that begins a polypeptide sequence
- Stop Codons: end translation
- Codons in mRNA are recognized by the anticodons in tRNA
- Anticodons: 3-nucleotide sequences that are complementary to codons in mRNA
- tRNA carries the amino acid that corresponds to the codon in mRNA
- More than one codon can specify the same amino acid.
- Reading Frame: a series of codons beginning with the start codon as a frame of reference. ex) if we remove one base, the reading frame shifts to make different amino acids. If we remove 3 bases in sequence, it will have the same reading frame but an amino acid will have been deleted.
- Adaptor Hypothesis: the position of an amino acid within a polypeptide is determined by the binding between the mRNA and an adaptor molecule carrying a specific amino acid.
- Anticodon in the tRNA binds to a codon in mRNA due to complementary sequences
- Synthesized from 5’ -> 3’
(Concepts of Genetics – Robert J. Brooker)

Objectives for Student Learning

 

Objective

Type

Michigan Objective(s)

1.B4.2x DNA, RNA, and Protein Synthesis Choose one:

Identifying SP

2.B4.2f Demonstrate how the genetic information in DNA molecules provides instructions for assembling protein molecules and that this is virtually the same mechanism for all life forms.

B4.2g Describe the processes of replication, transcription, and translation and how they relate to each other in molecular biology.

Using SP

 

Identifying SP

Specific Lesson Objective(s)

1. Students will model translation of nucleotides into amino acids Using SP
2. Students will model how transcription and translation relate Using SP

 

Part III: Classroom Activities

Materials

Each student will need:

  • Marshmallows (15 per bag)
  • Toothpicks (7 per bag)
  • Marshmallows and toothpicks will be organized into plastic bags to be given to a pair of studetns, to save time and to make for easy clean up. (what are the components necessary to do the activity? You need to think of this as an instruction guide for someone who wants to duplicate your lesson without having any background information, or any idea how you will organize the bags).
  • Worksheet containing the tRNA codon sheet (15 total)

tRNA Anticodon Sheet

Activities

Introduction (30 minutes)

We are going to discuss the mechanics behind translation for the first 30 minutes or so of the class. We will be using a dry erase board to draw the necessary molecules and pieces of translation to illustrate our points visually. We will cover the following topics during our lecture portion of the lesson:
- Begin lecture by asking students what they remember about transcription (they went over it the previous week)
- Draw a DNA sequence and ask the students what is the template strand and what changes are made during transcription.
- Once we have drawn a sample mRNA on the board, we will define translation:mRNA is used to determine the sequence of amino acids within a polypeptide. Write these definitions on the board
- Ask if they know what an amino acid is? If not describe that it is a single unit of a protein
- Will also define what a codon is: set of 3 nucleotides
- We will define what start, stop, and sense codons are: where translation starts, ends, and a codon that codes for a single amino acid
- We then will describe that the ribsomes facilitate translation and attach ahead of the start codon
- Bring up the codon sheet on the overhead projector and explain that each codon translates into a specific animo acid.
- Ask them what amino acids the codons translate in the mRNA written on the board.
- We will also be showing a short YouTube video clip in order to illustrate our points further.
http://www.youtube.com/watch?v=5bLEDd-PSTQ&feature=related
- Relay to them that it is mRNA being translated not DNA
- Ask them what the blue thing is? (ribosome)

Main Teaching Activities (25 minutes)

Procedure
After completing our lecture on Translation, we’ll proceed to an activity where the students will synthesize a polypeptide from a specific genetic sequence provided to them.
- Students will be broken into pairs and given a worksheet and a plastic bag containing the marshmallows and toothpicks.

  1. Students will be given a DNA template strand which they will write the mRNA strand. This starts the relationship of transcription to translation.
  2. Students will then write the anticodon sequence that would be on the tRNA molecules.
  3. Next, they will use the tRNA codon sheet in order to translate each codon into its amino acid equivalent.
  4. The students will then assemble polypeptide by matching their amino acids to the corresponding type of marshmallow. They will connect the marshmallows using the toothpicks however they think resembles a peptide bond most accurately.
  5. The following list of marshmallow type will be written on the board so that the students know how to build their polypeptide once they have determined what amino acids the DNA sequence is transcribed and translated to.

- Long Red Marshmallow = Pro
- Long Yellow Marshmallow = Tyr
- Long Green Marshmallow = Leu
- Long Orange Marshmallow = Met
- Short Yellow = Thr
- Short Green = Val
- Short Red = Asp

The students will be working in groups of two.
- We will be walking around the room going from group to group, checking on their progress as they go through the lab.
- We will answer any questions students might have while conducting this assessment

Conclusion (5 minutes)

The students will have made a polypeptide chain at the end of their lab and that will be used as an exit ticket item. We will determine whether or not the sequence they came up with was correct, and if it isn’t, we will ask them to look at it further to see if they can identify where they went wrong.

Part IV: Assessment of Focus Students

Focus Objective

Monitor the student’s comprehension of translation by observing the polypeptide they made out of marshmallows to see if they have developed an understanding of the process and its end products.

Developing Assessment Tasks

-          Did the students end up with the correct sequence of amino acids from their lab? If no, question them where they think they went wrong.

-          Exit ticket: What is the central dogma?

What are unique about the first and last codons coding for protein?

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