Which frame has the correct peptide and why? Please explain. 5\'3\' Frame 1 S P

Question

Which frame has the correct peptide and why? Please explain.

5'3' Frame 1
S P P G Q A A S E E A I K Q V C S K G L C V R W A Q D S R V A G P Q A P A L Q Q G G R G W A R E A C G G E P R G P K A G H L A F S L P Q P C L S P R S L S F C H G P V D A P P A P A G A A G P L G T Stop P S R S L C E P T P V R L T P G G S S L P S V R G T R L L L H T Q D P P G G R G P A G Stop A N C P L L P L A A P S H P L L L A L P P S Met G R R G Q E A A T Q Q G V R C T F L K R S S L G H V L K V T S S L W P S Q N L S L R T V L A S A A P R Y I R G W A R S S L H S P L K Q Met P R S P F L H P H L Met T A D S S V L L S K V L G D L G S Q G A P R C L P L G E H P I T P G G G R G C L P E W A R P L S P G L T A A P Stop S G D G E D A G D R P W G E V L G S P V Q A P T V T L P R G G G R R W D Met W A L G P V G P H P V W V T L P L T W V Q P G W R W V G V R P R A G G Q A G T V S P Stop L C P P V S L C L A A V P E P A L R G T S W Q W G R W S W A G A L V Q A A C S P W P W R G P C R S V A L W N N A V P A S A P S T S W R T T A T R R S P Q A A P H P P P P A P R E Met E Stop S P Stop T S

5'3' Frame 2
A L Q D R L H Q K R P S S R S V P R A F A S G G L R I P G W L D P R P Q L C S R E D V A G L V K H V G V S P G A P R Q G T W P S A C L S P A C L P D H C P S A Met A L W Met R L L P L L A L L A L W G P D P A A A F V N Q H L C G S H L V E A L Y L V C G E R G F F Y T P K T R R E A E D L Q G E P T A H C C P W P P P A T P C S W R S H P A W A E G G R R L P P S R G S G A L F Stop K E V L L V T S Stop K Stop P A P C G P V R I S A Stop G R C W L R Q P R D T S E G G H A P P S T R P S N K C P A A H F S T L I Stop Stop P Q I Q V F C Stop V K S W V T W G H R V P H A A C L W A N T P S R P E E G V A A C L S G P D P C R Q A S R Q L H S Q E Met G K Met L G T G P G E K Y W D H L F R L P L Stop R C P G A G E G G G T C G R W G L Stop V H T Q C G Stop P S L Stop P G S S P A G D G W E C D L G L A G R R A L C L P D C V L L C P S A S P L F R N L L C A A R P G S G A G G A G R G P W C R Q P A A L G P G G V P A E A W H C G T Met L Y Q H L L P L P A G E L L Q L D A A R R Q P H T R R L L H R E R W N K A L E P

5'3' Frame 3
P S R T G C I R R G H Q A G L F Q G P L R Q V G S G F Q G G W T P G P S S A A G R T W L G S Stop S Met W G Stop A Q G P Q G R A P G L Q P A S A L P V S Q I T V L L P W P C G C A S C P C W R C W P S G D L T Q P Q P L Stop T N T C A A H T W W K L S T Stop C A G N E A S S T H P R P A G R Q R T C R V S Q L P I A A P G R P Q P P P A P G A P T Q H G Q K G A G G C H P A G G Q V H F F K K K F S W S R P K S D Q L P V A Q S E S Q P E D G V G F G S P E I H Q R V G T L L P P L A P Q T N A P Q P I S P P S F D D R R F K C F V K Stop S P G Stop P G V T G C P T L P A S G R T P H H A R R R A W L P A Stop V G Q T P V A R P H G S S I V R R W G R C W G Q A L G R S T G I T C S G S H C D A A P G R G K E V G H V G V G A C R S T P S V G D P P S N L G P A R L E Met G G S A T Stop G W R A G G H C V S L T V S S C V P L P R R C S G T C S A R H V L A V G Q V E L G G G P G A G S L Q P L A L E G S L Q K R G I V E Q C C T S I C S L Y Q L E N Y C N Stop T Q P A G S P T P A A S C T E R D G I K P L N Q

3'5' Frame 1
A G S R A L F H L S R C R R R R V W G C L R A A S S C S S S P A G R G S R C W Y S I V P Q C H A S A G T P P G P R A A G C L H Q G P R P A P P A P L P G R A A Q S R F R N S G E A E G H R R T Q S G R H S A R L P A S P R S H S H P S P A G L D P G Stop R E G H P H W V W T Y R P Q R P H V P P P S P A P G Q R H S G S L N R Stop S Q Y F S P G P V P S I F P I S Stop L W S C R E A W R Q G S G P L R Q A A T P S S G R D G V F A Q R Q A A W G T L Stop P Q V T Q D F T Stop Q N T Stop I C G H Q Met R V E K W A A G H L F E G R V E G G A C P P S D V S R G C R S Q H R P Q A E I L T G P Q G A G H F Stop D V T K R T S F Stop K S A P D P L L G G S L L P P S A H A G W E R Q E Q G V A G G G Q G Q Q W A V G S P C R S S A S R R V L G V Stop K K P R S P H T R Stop R A S T R C E P H R C W F T K A A A G S G P Q R A S S A S R G R R R I H R A Met A E G Q Stop S G R Q A G L R Q A E G Q V P C L G A P G L T P T C F T S P A T S S L L Q S W G L G S S H P G I L S P P D A K A L G T D L L D G L F Stop C S L S W R A

3'5' Frame 2
L V Q G L Y S I S L G A G G G G C G A A C G L R L V A V V L Q L V E G A D A G T A L F H N A T L L Q G P L Q G Q G L Q A A C T R A P A Q L H L P H C Q D V P R R A G S G T A A R Q R D T G G H S Q G D T V P A C P P A L G R T P T H L Q P G W T Q V R G R V T H T G C G P T G P N A H Met S H L L P P P R G S V T V G A Stop T G D P S T S P Q G L S P A S S P S P D Y G A A V R P G D R G L A H S G R Q P R P P P G V Met G C S P R G R Q R G A P C D P R S P R T L L N K T L E S A V I K Stop G W R N G L R G I C L R G E W R E E R A H P L Met Y L G A A E A N T V L R L R F Stop L G H R E L V T F R T Stop P R E L L F K K V H L T P C W V A A S C P L L P Met L G G S A R S R G W L G A A R G S N G Q L A H P A G P L P P G G S W V C R R S L V P R T L G R E L P P G V S R T G V G S Q R L R L G Q V P R G P A A P A G A G G A S T G P W Q K D S D L G D R Q G Stop G R L K A R C P A L G P L G S P P H A S R A Q P R P P C C R A G A W G P A T L E S Stop A H L T Q R P L E Q T C L Met A S S D A A C P G G

3'5' Frame 3
W F K G F I P S L S V Q E A A G V G L P A G C V Stop L Q Stop F S S W Stop R E Q Met L V Q H C S T Met P R F C R D P S R A K G C R L P A P G P P P S S T C P T A R T C R A E Q V P E Q R R G R G T Q E D T V R E T Q C P P A R Q P Stop V A L P P I S S R A G P R L E G G S P T L G V D L Q A P T P T C P T S F P R P G A A S Q W E P E Q V I P V L L P R A C P Q H L P H L L T Met E L P Stop G L A T G V W P T Q A G S H A L L R A Stop W G V R P E A G S V G H P V T P G H P G L Y L T K H L N L R S S N E G G E Met G C G A F V Stop G A S G G R S V P T L Stop C I S G L P K P T P S S G Stop D S D W A T G S W S L L G R D Q E N F F L K K C T Stop P P A G W Q P P A P F C P C W V G A P G A G G G W G R P G A A Met G S W L T L Q V L C L P A G L G C V E E A S F P A H Stop V E S F H Q V Stop A A Q V L V H K G C G W V R S P E G Q Q R Q Q G Q E A H P Q G H G R R T V I W E T G R A E A G Stop R P G A L P W G P W A H P H Met L H E P S H V L P A A E L G P G V Q P P W N P E P T Stop R K G P W N R P A Stop W P L L Met Q P V L E G

Explanation / Answer

Answer: First we need to know why these frames are given and in response what is the correct order we should be looking after? Any peptide sequence arising from the mRNA codons and the anticodons carries by the tRNA have its certain position in a peptide chain. We are talking about the Open Reading Frame of ORF.

An ORF consists of an initiator condon, this part is applies universally to all organisms, and it is always the Methionine amino acid, while in case of eukaryotes fMethionine. Next we will look for the later sequences as giving rise to any amino acids, here the amino acids short or code names are being in use. Finally the peptide chain has to have one terminator chain or the chain breaker. Universally for mRNA there are 3 stop codons present (UAA, UGA and UAG). Also another important part is to read the sequence in correct order, the 5’ – 3’ or from 3’ – 5’ order.

A true ORF would be having a minimum length, (consider the smallest protein as 20 amino acids long), in between false start codons as Met could be present. Also the sequence always reads from 5’ – 3’ direction. So for the second set of frames we need to read them from the end, stop to start.

Now let’s go to the sequences and see the matching correct orders one by one. In order to look into each of the frame we need to keep it in mind that after a code starts from Met it could get one more Met on the way, but once it is stop, it gets terminated. So, no two stop codons.

S P P G Q A A S E E A I K Q V C S K G L C V R W A Q D S R V A G P Q A P A L Q Q G G R G W A R E A C G G E P R G P K A G H L A F S L P Q P C L S P R S L S F C H G P V D A P P A P A G A A G P L G T Stop P S R S L C E P T P V R L T P G G S S L P S V R G T R L L L H T Q D P P G G R G P A G Stop A N C P L L P L A A P S H P L L L A L P P S Met G R R G Q E A A T Q Q G V R C T F L K R S S L G H V L K V T S S L W P S Q N L S L R T V L A S A A P R Y I R G W A R S S L H S P L K Q Met P R S P F L H P H L Met T A D S S V L L S K V L G D L G S Q G A P R C L P L G E H P I T P G G G R G C L P E W A R P L S P G L T A A P Stop S G D G E D A G D R P W G E V L G S P V Q A P T V T L P R G G G R R W D Met W A L G P V G P H P V W V T L P L T W V Q P G W R W V G V R P R A G G Q A G T V S P Stop L C P P V S L C L A A V P E P A L R G T S W Q W G R W S W A G A L V Q A A C S P W P W R G P C R S V A L W N N A V P A S A P S T S W R T T A T R R S P Q A A P H P P P P A P R E Met E Stop S P Stop T S

2. 5’3’ Frame 2 : Here also the abrupt nature could be seen. Although there are two complete peptide chains are present, rightly arranged as follows:

A L Q D R L H Q K R P S S R S V P R A F A S G G L R I P G W L D P R P Q L C S R E D V A G L V K H V G V S P G A P R Q G T W P S A C L S P A C L P D H C P S A Met A L W Met R L L P L L A L L A L W G P D P A A A F V N Q H L C G S H L V E A L Y L V C G E R G F F Y T P K T R R E A E D L Q G E P T A H C C P W P P P A T P C S W R S H P A W A E G G R R L P P S R G S G A L F Stop K E V L L V T S Stop K Stop P A P C G P V R I S A Stop G R C W L R Q P R D T S E G G H A P P S T R P S N K C P A A H F S T L I Stop Stop P Q I Q V F C Stop V K S W V T W G H R V P H A A C L W A N T P S R P E E G V A A C L S G P D P C R Q A S R Q L H S Q E Met G K Met L G T G P G E K Y W D H L F R L P L Stop R C P G A G E G G G T C G R W G L Stop V H T Q C G Stop P S L Stop P G S S P A G D G W E C D L G L A G R R A L C L P D C V L L C P S A S P L F R N L L C A A R P G S G A G G A G R G P W C R Q P A A L G P G G V P A E A W H C G T Met L Y Q H L L P L P A G E L L Q L D A A R R Q P H T R R L L H R E R W N K A L E P

3. 5’3’ Frame 3: We can see the fallacies in the sequence as there are not enough initiator sequence as Met but there are more stop sequences. It is an incorrect sequence. The peptides sequences are very short, no complete sequence present.

4. 3’5’ Frame 1: Here also the fallacy of not having a complete ORF could be seen except one complete sequence in the middle. Reading from the opposite direction, from stop to start. AS we have the sequence from 3’ to 5’ direction.

A G S R A L F H L S R C R R R R V W G C L R A A S S C S S S P A G R G S R C W Y S I V P Q C H A S A G T P P G P R A A G C L H Q G P R P A P P A P L P G R A A Q S R F R N S G E A E G H R R T Q S G R H S A R L P A S P R S H S H P S P A G L D P G Stop R E G H P H W V W T Y R P Q R P H V P P P S P A P G Q R H S G S L N R Stop S Q Y F S P G P V P S I F P I S Stop L W S C R E A W R Q G S G P L R Q A A T P S S G R D G V F A Q R Q A A W G T L Stop P Q V T Q D F T Stop Q N T Stop I C G H Q Met R V E K W A A G H L F E G R V E G G A C P P S D V S R G C R S Q H R P Q A E I L T G P Q G A G H F Stop D V T K R T S F Stop K S A P D P L L G G S L L P P S A H A G W E R Q E Q G V A G G G Q G Q Q W A V G S P C R S S A S R R V L G V Stop K K P R S P H T R Stop R A S T R C E P H R C W F T K A A A G S G P Q R A S S A S R G R R R I H R A Met A E G Q Stop S G R Q A G L R Q A E G Q V P C L G A P G L T P T C F T S P A T S S L L Q S W G L G S S H P G I L S P P D A K A L G T D L L D G L F Stop C S L S W R A

5. 3’5’ Frame 2: Here the frame has got 3 complete sequences, as given below:

L V Q G L Y S I S L G A G G G G C G A A C G L R L V A V V L Q L V E G A D A G T A L F H N A T L L Q G P L Q G Q G L Q A A C T R A P A Q L H L P H C Q D V P R R A G S G T A A R Q R D T G G H S Q G D T V P A C P P A L G R T P T H L Q P G W T Q V R G R V T H T G C G P T G P N A H Met S H L L P P P R G S V T V G A Stop T G D P S T S P Q G L S P A S S P S P D Y G A A V R P G D R G L A H S G R Q P R P P P G V Met G C S P R G R Q R G A P C D P R S P R T L L N K T L E S A V I K Stop G W R N G L R G I C L R G E W R E E R A H P L Met Y L G A A E A N T V L R L R F Stop L G H R E L V T F R T Stop P R E L L F K K V H L T P C W V A A S C P L L P Met L G G S A R S R G W L G A A R G S N G Q L A H P A G P L P P G G S W V C R R S L V P R T L G R E L P P G V S R T G V G S Q R L R L G Q V P R G P A A P A G A G G A S T G P W Q K D S D L G D R Q G Stop G R L K A R C P A L G P L G S P P H A S R A Q P R P P C C R A G A W G P A T L E S Stop A H L T Q R P L E Q T C L Met A S S D A A C P G G

6. 3’5’ Frame 3: This final frame over here has got

W F K G F I P S L S V Q E A A G V G L P A G C V Stop L Q Stop F S S W Stop R E Q Met L V Q H C S T Met P R F C R D P S R A K G C R L P A P G P P P S S T C P T A R T C R A E Q V P E Q R R G R G T Q E D T V R E T Q C P P A R Q P Stop V A L P P I S S R A G P R L E G G S P T L G V D L Q A P T P T C P T S F P R P G A A S Q W E P E Q V I P V L L P R A C P Q H L P H L L T Met E L P Stop G L A T G V W P T Q A G S H A L L R A Stop W G V R P E A G S V G H P V T P G H P G L Y L T K H L N L R S S N E G G E Met G C G A F V Stop G A S G G R S V P T L Stop C I S G L P K P T P S S G Stop D S D W A T G S W S L L G R D Q E N F F L K K C T Stop P P A G W Q P P A P F C P C W V G A P G A G G G W G R P G A A Met G S W L T L Q V L C L P A G L G C V E E A S F P A H Stop V E S F H Q V Stop A A Q V L V H K G C G W V R S P E G Q Q R Q Q G Q E A H P Q G H G R R T V I W E T G R A E A G Stop R P G A L P W G P W A H P H Met L H E P S H V L P A A E L G P G V Q P P W N P E P T Stop R K G P W N R P A Stop W P L L Met Q P V L E G

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