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Protein synthesis

 

Welcome to the Genetic information Unit!

This unit has 5 sections, but this is just one part based on "Protein synthesis". This lesson is divided into two stages. In stage 1, you are going to learn the phases of protein synthesis through an online resource called BBC bitesize and you can support the new contents watching/listening to the video called "Protein synthesis". Several activities will be proposed in order to work its content. And in stage 2, you are going to deepen in the central dogma of molecular biology through another online resource called Khan Academy and you will have to decode a secret DNA message following the same steps that cells. Finally, you can check the new contents learnt through the consolidation suggested activities.

In this unit, the teacher will evaluate all the proposed tasks. In addition, he/she will take into account the language knowledge and student´s behaviour. You can consult the evaluation criteria in the lesson plan of the unit.

After this presentation of the unit is time to work so pay attention to the instructions to follow the correct development of the activities.

Stage 1

Brainstorming activity

The first step is to gather some information about your previous knowledge so, it is time to think!. For this purpose, click on the button "First activity" and think about the suggested questions in Brainstorming activity. After a few minutes thinking, share your answers with the whole class by the guidance of the teacher.

In order to help you with the speaking, you can click on the button "Language support" where you can find useful expressions that will support your speaking.

Glossary activity

Now you have to focus on the Glossary, that you can find clicking the same button, where you are going to find a list with the specific vocabulary in English that you need to know to follow and understand the explanations and the proposed activities. With the guidance of the teacher, some student has to read a word out loud and explain its meaning. Then the rest of the group have to repeat the word loud, all together, focusing on the pronunciation. In addition, each student has to write each word in his/her notebook focusing on the grammar.

The next step consists in reading carefully the following content obtained from the online resource called BBC bitesize where explains the phases of protein synthesis: transcription and translation.

Transcription from BBC bitesize

Transcription is the first part of the process of making a protein. It takes place inside the cell nucleus. Transcription involves copying the DNA and the stages are:

  1. The DNA in a gene unzips so that both strands are separate – one strand is used as a template.
  2. Complementary bases attach to the strand being copied – C joins to G and so on.
  3. Thymine (Base T) is not present and a different base, U, joins with A in the way that T would have done.
  4. This forms a strand of messenger RNA (mRNA)
DNA helix unzipping and being copied

DNA helix unzipping and being copied

Messenger RNA is small enough to move out of the nucleus and so it travels to the ribosomes in the cytoplasm.

Translation from BBC bitesize

Translation takes place in the ribosomes that are found in the cytoplasm. This is where the messenger RNA is 'interpreted' and the new protein formed. The stages are:

  1. The mRNA attaches to a ribosome. The ribosome "reads" the mRNA.
  2. The ribosome decodes the mRNA in groups of three – base triplets or codons – which are complementary to bases in transfer RNA (tRNA).
  3. The tRNA is specific to an amino acid that it collects and returns to the mRNA.
  4. The amino acids are now lined up in order of the instructions on the mRNA.
  5. Bonds form between the amino acids and a polypeptide chain is formed.
  6. The polypeptide chain folds and becomes a specific shape forming a protein.
Diagram of a translation

Diagram showing a translation taking place.

Video (listening activity)

Now it is the time to support the new contents watching/listening to the video called "Protein synthesis" presented below. First of all, you have to watch/listen to the video without transcription and without taking notes, only listening to understand its content and focusing on the specific words that you have previously seen with the teacher. Once the first listening is done, the teacher will take the next few minutes to resolve doubts. Then you can watch and listen to the video a second time. This time you can support your listening with the transcription presented below the video in order to facilitate its meaning with the support of Wordlink tool. While you are watching and listening to the video you have to complete the activity 1 that you can find clicking the button "Video activity" with the information of the video.  This activity has been designed to help you to get focused while you are watching/listening to the video. Clicking this button you will find two activities more. You will work them in pairs (the teacher will make the pairs taken into account different aspects).

 

 Transcription of video

DNA is very long and cumbersome.
0:16
The strands of DNA also code for many different proteins.
0:19
To get the code for the desired protein from the nucleus to the ribosomes in the cytoplasm,
0:23
a copy of the small necessary section of DNA will be made.
0:28
The copying process is called transcription and it occurs in the nucleus.
0:32
It's the first step in protein synthesis--the process of making protein.
0:36
The second step is called translation.
0:39
A portion of the DNA is unzipped so that the mRNA can be made from the DNA like a template--that's
0:44
transcription.
0:46
Nucleotides of RNA match with one strand of DNA and make mRNA.
0:51
RNA polymerase unzips the DNA and puts RNA nucleotides into the right place.
0:57
C and G nucleotides match up.
0:59
A and T nucleotides match up, but any time the mRNA places a compliment to an A on the
1:05
DNA it places a U instead of a T on the RNA.
1:09
Remember, RNA uses Uracil instead of Thymine.
1:13
So, if the DNA strand looked like this, the complimentary mRNA strand would be the compliment
1:19
but each time there would normally be a Thymine there's a Uracil in its place.
1:24
The mRNA also doesn't copy the entire strand of DNA.
1:27
It only copies the portion of DNA that codes for the protein it wants at the time.
1:31
In fact, most of DNA doesn't code for anything.
1:35
Only about two percent of it codes for protein.
1:38
So this small section of coding DNA has the start and stop signal.
1:42
After the mRNA is formed, it moves out of the nucleus through a nuclear pore and goes
1:46
into the cytoplasm.
1:48
Remember, there are three different types of RNA.
1:51
The purpose of the mRNA is to get the protein code out of the nucleus without pulling the
1:55
DNA out of the nucleus.
1:56
Then the mRNA will need to find a ribosome in the cytoplasm.
2:01
Ribosomes can be found on the rough ER or floating in the cytosol.
2:04
mRNA is read three bases at a time and these three bases are called codons.
2:10
Now, the ribosomes are made of protein and RNA.
2:15
And the ribosomes are the protein making machines that read the mRNA code and add the correct
2:20
amino acid using tRNA.
2:21
Remember, tRNA stands for: transfer RNA and that's because its purpose is to transfer
2:28
the right amino acid to the ribosome to build the protein.
2:32
The tRNA has an anti-codon on one end which will match a specific codon on the mRNA and
2:38
has a specific amino acid on the other end.
2:41
Together these three parts will make translation happen.
2:47
Translation occurs in the cytoplasm of the cell wherever there is a ribosome.
2:51
To get translation started, mRNA attaches to a ribosome and a start codon must be read.
2:56
It's usually AUG and I remember that school usually starts in August and that helps me
3:01
remember AUG.
3:03
The first amino acid is brought in by tRNA.
3:06
The anti-codon on tRNA matches up to the codon on mRNA then the next the next tRNA molecule
3:12
moves in and matches up with the mRNA codon.
3:17
This time the amino acids form a peptide bond and link together, then the first tRNA can
3:23
detach and the mRNA shifts through like ticker tape and the next tRNA molecule can come in.
3:30
The protein grows until a stop codon is reached.
3:37
Once the stop codon is read, the protein is formed and ready to finish folding to become
3:42
functional.
3:44
And that's the end of protein synthesis.
3:47
Now we can figure out the sequence of amino acids using the mRNA and amino acid chart
3:52
like this one.
3:53
Let's use an example.
3:55
Starting with the first three letters "AUG" we can find the amino acids.
3:59
The first letter is A which narrows it down to this row.
4:02
The second letter is U which narrows it down to this column and the third letter is G which
4:07
means that this is methionine which is the starting amino acid.
4:13
Next is "CCC" which is the second row, second column and second row on the right.
4:19
But we don't even have to look at the third letter in this case because every third letter
4:23
will bring the same amino acid: proline.
4:27
Next is "GGC".
4:29
Fourth row, fourth column, second row on the right.
4:32
That gives us glycine.
4:35
And lastly is "UAA".
4:37
Row one, column three, row three and that gives us STOP.
4:42
There's no amino acid here.
4:43
It just means the protein will detach and it marks the end of protein synthesis.
4:49
Thanks for watching this episode of Teacher's Pet!

Once the activities are completed, the teacher will guide a brief discussion with the whole class. Firstly to correct the activities and secondly, to focus on determining the main aspects related to the phases of protein synthesis such as their cellular importance, where does each phase take place and which molecule is formed.

Before ending this session, it is advisable that you self-assess your knowledge clicking on the BBC activities stage 1.

Finally, at the end of the session, you will have to hand over your glossary to the teacher and send by Classroom tool the video activities in order to be assessed by the teacher.

Stage 2

First of all, think about the following questions:

  • Have you ever thought how does the sequence of nucleotides in your DNA determine, for example, the color of your eyes? You can find the answer in the central dogma of molecular biology.
  • Have you ever received a secret message? If so, you will have used a code to deciphering the message hidden.

Decoding messages is a key step in gene expression, in which information from a gene is used by cells to build a certain protein. For this reason and although this may perhaps surprise you, in this stage, your new task consists of decoding a secret message.

In order to work successfully this activity firstly, you will have to read carefully the following article called "The genetic code" from the online resource called Khan Academy.

The genetic code from Khan Academy

Background: Making a protein

Genes that provide instructions for proteins are expressed in a two-step process.
  • In transcription, the DNA sequence of a gene is "rewritten" in RNA. In eukaryotes, the RNA must go through additional processing steps to become a messenger RNA, or mRNA.
  • In translation, the sequence of nucleotides in the mRNA is "translated" into a sequence of amino acids in a polypeptide (protein chain).

Codons

Cells decode mRNAs by reading their nucleotides in groups of three, called codons. Here are some features of codons:
  • Most codons specify an amino acid
  • Three "stop" codons mark the end of a protein: UAA, UAG, and UGA. Unlike start codons, stop codons don't correspond to an amino acid.
  • One "start" codon, AUG, marks the beginning of a protein and also encodes the amino acid methionine so, every polypeptide typically starts with methionine, although the initial methionine may be snipped off in later processing steps.
Codons in an mRNA are read during translation, beginning with a start codon and continuing until a stop codon is reached. mRNA codons are read from 5' to 3', and they specify the order of amino acids in a protein from N-terminus (methionine) to C-terminus.

The genetic code table

The full set of relationships between codons and amino acids (or stop signals) is called the genetic code. The genetic code is often summarized in a table.
 
 
 
Notice that many amino acids are represented in the table by more than one codon. For instance, there are six different ways to "write" leucine in the language of mRNA (see if you can find all six).
An important point about the genetic code is that it's universal. That is, with minor exceptions, virtually all species (from bacteria to you!) use the genetic code shown above for protein synthesis.

Reading frame

To reliably get from an mRNA to a protein, we need one more concept: that of reading frame. Reading frame determines how the mRNA sequence is divided up into codons during translation.
That's a pretty abstract concept, so let's look at an example to understand it better. The mRNA below can encode three totally different proteins, depending on the frame in which it's read:
 
 
So, how does a cell know which of these proteins to make? The start codon is the key signal. Because translation begins at the start codon and continues in successive groups of three, the position of the start codon ensures that the mRNA is read in the correct frame (in the example above, in Frame 3).
 
Interactive activity from Learn. Genetics link

Before working the following task, you are going to become familiar with the genetic expression in a funny way because it is time to play. With your partner, you are going to review the new contents explained by Khan academy resources with an interactive activity called “Transcribe and translate a gene".

You can start to play clicking the button "Interactive activity"

Even though it is a game, you should pay attention to the activity because it will help you to consolidate the new contents explained.

The teacher will go around the class evaluating this activity.

 
Activity "Decoding a secret message"

At this point, you are already able to decipher a DNA message following the same steps that your cells. Click on the button "Decipher DNA" and work the suggested task. This activity has been designed to work with the same pair.
 
Once the activity is completed, the teacher will guide a brief discussion with the whole class in order to correct the activity and to focus on the central dogma of molecular biology. The activity will be sent to the teacher by Classroom tool in order to be evaluated.
 
Again, it is advisable that you self-assess your knowledge clicking on the BBC activities stage 2.
 
Closure activities

In order to finalize the lesson, you will have to work two activities to consolidate the new concepts learnt. Again, you will work with your pair. Clicking on the button "Consolidation activities" you will find a worksheet with three tasks. Activity 1 and activity 2 have been designed to compare concepts using tables. In this way, you will have to organize the new concepts learnt in an easy way and very visual way. The activity 3 has been designed to practice your writing skills so you will work it alone. In order to help you with the writing, you can click on the button "Language support" where you can find useful expressions that will support your task.

These activities are suggested in order to help you retain and reinforce the new content. Remember that consolidation is a good opportunity to clarify and address any doubts.

By the end of the session, you will have to send the worksheet to the teacher in order to be evaluated.
 
At that point, you have reached the end of the unit. I hope you have got the proposed goals in a funny and effective way.
 

 

Clilstore BBC activities stage 2First activityVideo activityBBC activities stage 1Language supportDecipher DNAInteractive activityConsolidation activities

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