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Merged
merged 9 commits into from
Nov 18, 2024
Merged

Rename "proteins"->"amino acids" in protein-translation description table #2478

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6aac39c
Rename proteins->polypeptide in protein-translation canonical-data.json
0xNeshi Sep 22, 2024
b70c903
Update description.md
0xNeshi Sep 22, 2024
271d870
Revert polypeptide to protein
0xNeshi Sep 22, 2024
a82e2a5
Update canonical-data.json: "protein"->"proteins"
0xNeshi Sep 23, 2024
0935dde
Revert canonical-data.json
0xNeshi Sep 24, 2024
7ea760c
Update description.md
0xNeshi Sep 24, 2024
e335c63
Switch all "polypeptide" mentions to "protein"
0xNeshi Sep 30, 2024
c317ea0
hyphenate "three nucleotide"
0xNeshi Sep 30, 2024
44beea8
Update exercises/protein-translation/description.md
Cool-Katt Sep 30, 2024
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64 changes: 32 additions & 32 deletions exercises/protein-translation/canonical-data.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,12 @@
"cases": [
{
"uuid": "2c44f7bf-ba20-43f7-a3bf-f2219c0c3f98",
"description": "Empty RNA sequence results in no proteins",
"description": "Empty RNA sequence results in no amino acids",
"comments": [
"Tracks may choose to expect an error when an empty RNA sequence ",
"is given, or use this test to expect an empty result. "
],
"property": "proteins",
"property": "protein",
"input": {
"strand": ""
},
Expand All @@ -17,7 +17,7 @@
{
"uuid": "96d3d44f-34a2-4db4-84cd-fff523e069be",
"description": "Methionine RNA sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "AUG"
},
Expand All @@ -26,7 +26,7 @@
{
"uuid": "1b4c56d8-d69f-44eb-be0e-7b17546143d9",
"description": "Phenylalanine RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUU"
},
Expand All @@ -35,7 +35,7 @@
{
"uuid": "81b53646-bd57-4732-b2cb-6b1880e36d11",
"description": "Phenylalanine RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUC"
},
Expand All @@ -44,7 +44,7 @@
{
"uuid": "42f69d4f-19d2-4d2c-a8b0-f0ae9ee1b6b4",
"description": "Leucine RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUA"
},
Expand All @@ -53,7 +53,7 @@
{
"uuid": "ac5edadd-08ed-40a3-b2b9-d82bb50424c4",
"description": "Leucine RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUG"
},
Expand All @@ -62,7 +62,7 @@
{
"uuid": "8bc36e22-f984-44c3-9f6b-ee5d4e73f120",
"description": "Serine RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UCU"
},
Expand All @@ -71,7 +71,7 @@
{
"uuid": "5c3fa5da-4268-44e5-9f4b-f016ccf90131",
"description": "Serine RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UCC"
},
Expand All @@ -80,7 +80,7 @@
{
"uuid": "00579891-b594-42b4-96dc-7ff8bf519606",
"description": "Serine RNA sequence 3",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UCA"
},
Expand All @@ -89,7 +89,7 @@
{
"uuid": "08c61c3b-fa34-4950-8c4a-133945570ef6",
"description": "Serine RNA sequence 4",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UCG"
},
Expand All @@ -98,7 +98,7 @@
{
"uuid": "54e1e7d8-63c0-456d-91d2-062c72f8eef5",
"description": "Tyrosine RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UAU"
},
Expand All @@ -107,7 +107,7 @@
{
"uuid": "47bcfba2-9d72-46ad-bbce-22f7666b7eb1",
"description": "Tyrosine RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UAC"
},
Expand All @@ -116,7 +116,7 @@
{
"uuid": "3a691829-fe72-43a7-8c8e-1bd083163f72",
"description": "Cysteine RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGU"
},
Expand All @@ -125,7 +125,7 @@
{
"uuid": "1b6f8a26-ca2f-43b8-8262-3ee446021767",
"description": "Cysteine RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGC"
},
Expand All @@ -134,7 +134,7 @@
{
"uuid": "1e91c1eb-02c0-48a0-9e35-168ad0cb5f39",
"description": "Tryptophan RNA sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGG"
},
Expand All @@ -143,7 +143,7 @@
{
"uuid": "e547af0b-aeab-49c7-9f13-801773a73557",
"description": "STOP codon RNA sequence 1",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UAA"
},
Expand All @@ -152,7 +152,7 @@
{
"uuid": "67640947-ff02-4f23-a2ef-816f8a2ba72e",
"description": "STOP codon RNA sequence 2",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UAG"
},
Expand All @@ -161,7 +161,7 @@
{
"uuid": "9c2ad527-ebc9-4ace-808b-2b6447cb54cb",
"description": "STOP codon RNA sequence 3",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGA"
},
Expand All @@ -170,7 +170,7 @@
{
"uuid": "f4d9d8ee-00a8-47bf-a1e3-1641d4428e54",
"description": "Sequence of two protein codons translates into proteins",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUUUUU"
},
Expand All @@ -182,7 +182,7 @@
"comments": [
"The codons are different, the proteins they translate into are not."
],
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUAUUG"
},
Expand All @@ -191,7 +191,7 @@
{
"uuid": "d0f295df-fb70-425c-946c-ec2ec185388e",
"description": "Translate RNA strand into correct protein list",
"property": "proteins",
"property": "protein",
"input": {
"strand": "AUGUUUUGG"
},
Expand All @@ -200,7 +200,7 @@
{
"uuid": "e30e8505-97ec-4e5f-a73e-5726a1faa1f4",
"description": "Translation stops if STOP codon at beginning of sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UAGUGG"
},
Expand All @@ -209,7 +209,7 @@
{
"uuid": "5358a20b-6f4c-4893-bce4-f929001710f3",
"description": "Translation stops if STOP codon at end of two-codon sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGGUAG"
},
Expand All @@ -218,7 +218,7 @@
{
"uuid": "ba16703a-1a55-482f-bb07-b21eef5093a3",
"description": "Translation stops if STOP codon at end of three-codon sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "AUGUUUUAA"
},
Expand All @@ -227,7 +227,7 @@
{
"uuid": "4089bb5a-d5b4-4e71-b79e-b8d1f14a2911",
"description": "Translation stops if STOP codon in middle of three-codon sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGGUAGUGG"
},
Expand All @@ -236,7 +236,7 @@
{
"uuid": "2c2a2a60-401f-4a80-b977-e0715b23b93d",
"description": "Translation stops if STOP codon in middle of six-codon sequence",
"property": "proteins",
"property": "protein",
"input": {
"strand": "UGGUGUUAUUAAUGGUUU"
},
Expand All @@ -245,7 +245,7 @@
{
"uuid": "f6f92714-769f-4187-9524-e353e8a41a80",
"description": "Sequence of two non-STOP codons does not translate to a STOP codon",
"property": "proteins",
"property": "protein",
"input": {
"strand": "AUGAUG"
},
Expand All @@ -260,7 +260,7 @@
"order to remove the requirement for input validation. "
],
"scenarios": ["input-validation"],
"property": "proteins",
"property": "protein",
"input": {
"strand": "AAA"
},
Expand All @@ -279,7 +279,7 @@
"order to remove the requirement for input validation. "
],
"scenarios": ["input-validation"],
"property": "proteins",
"property": "protein",
"input": {
"strand": "XYZ"
},
Expand All @@ -296,7 +296,7 @@
"remove the requirement for input validation. "
],
"scenarios": ["input-validation"],
"property": "proteins",
"property": "protein",
"input": {
"strand": "AUGU"
},
Expand All @@ -314,7 +314,7 @@
"it into proteins. "
],
"scenarios": ["input-validation", "runtime-validation"],
"property": "proteins",
"property": "protein",
"input": {
"strand": "UUCUUCUAAUGGU"
},
Expand Down
10 changes: 6 additions & 4 deletions exercises/protein-translation/description.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,27 +9,29 @@ RNA: `"AUGUUUUCU"` => translates to
Codons: `"AUG", "UUU", "UCU"`
=> which become a polypeptide with the following sequence =>

Protein: `"Methionine", "Phenylalanine", "Serine"`
Polypeptide: `"Methionine", "Phenylalanine", "Serine"`

The polypeptide later folds into an active protein and performs its functions in the cell.

There are 64 codons which in turn correspond to 20 amino acids; however, all of the codon sequences and resulting amino acids are not important in this exercise.
If it works for one codon, the program should work for all of them.
However, feel free to expand the list in the test suite to include them all.

There are also three terminating codons (also known as 'STOP' codons); if any of these codons are encountered (by the ribosome), all translation ends and the protein is terminated.
There are also three terminating codons (also known as 'STOP' codons); if any of these codons are encountered (by the ribosome), all translation ends and the polypeptide is terminated.

All subsequent codons after are ignored, like this:

RNA: `"AUGUUUUCUUAAAUG"` =>

Codons: `"AUG", "UUU", "UCU", "UAA", "AUG"` =>

Protein: `"Methionine", "Phenylalanine", "Serine"`
Polypeptide: `"Methionine", "Phenylalanine", "Serine"`

Note the stop codon `"UAA"` terminates the translation and the final methionine is not translated into the protein sequence.

Below are the codons and resulting Amino Acids needed for the exercise.

| Codon | Protein |
| Codon | Amino Acid |
| :----------------- | :------------ |
| AUG | Methionine |
| UUU, UUC | Phenylalanine |
Expand Down