Genetics: Reading frames/codons Watch

LeaX
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I'm having trouble understanding what my textbook is going on about and its lack of diagrams isn't really helping lol. I was wondering if someone could explain what this means:

"The degeneracy of the genetic code minimises the effect of mutations so any alterations to the base sequence are unlikely to effect the amino acid coded"
I know degeneracy is to do with multiple codons coding for amino acids but not sure how this reduces mutations?


Reading Frames
Initiation codon (AUG) determines the reading from of the RNA sequence. Depending on which base is chosen as the start of a codon, three possible sets of codons may be read from any base sequence.
In practice, during protein synthesis normally only one reading frame contains useful information and the other two reading frames usually contain stop codons which prevent them from being used to direct protein synthesis.
A set of codons that run continuously and is bounded at the start by an initiation codon and at the end by a termination codon is known as an open reading frame. This characteristic is used to identify protein-coding DNA sequences in genome-sequencing projects.


I have no clue what any of this means lol. I thought codons were a long string (?) and so I don't understand what it means that there are three possible sets of codons that may be read?
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loukas2993
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(Original post by LeaX)
I'm having trouble understanding what my textbook is going on about and its lack of diagrams isn't really helping lol. I was wondering if someone could explain what this means:

"The degeneracy of the genetic code minimises the effect of mutations so any alterations to the base sequence are unlikely to effect the amino acid coded"
I know degeneracy is to do with multiple codons coding for amino acids but not sure how this reduces mutations?


Reading Frames
Initiation codon (AUG) determines the reading from of the RNA sequence. Depending on which base is chosen as the start of a codon, three possible sets of codons may be read from any base sequence.
In practice, during protein synthesis normally only one reading frame contains useful information and the other two reading frames usually contain stop codons which prevent them from being used to direct protein synthesis.
A set of codons that run continuously and is bounded at the start by an initiation codon and at the end by a termination codon is known as an open reading frame. This characteristic is used to identify protein-coding DNA sequences in genome-sequencing projects.


I have no clue what any of this means lol. I thought codons were a long string (?) and so I don't understand what it means that there are three possible sets of codons that may be read?
This is a difficult concept to explain on a forum thread, but I'll give it a go.

As you mentioned, you understand what a "degenerate code" means and how that relates to the genetic code. Just to clarify, the fact that the genetic code is considered a degenerate code essentially means that an amino acid can be coded for by more than one codon. This characteristic minimises the effect of mutations by reducing the likelihood that an altered base will produce an altered or nonfunctioning protein. For instance, take this genetic code into consideration:

AUG-CCU-CGU-UAG (this corresponds to=) Initiation codon-Proline-Arginine-Stop codon

If the genetic code was not degenerative, a single base mutation to the Arginine codon (CGU) would theoretically code for a completely different amino acid and could, therefore, produce a completely altered or nonfunctional protein. However, because the genetic code is degenerative, a base mutation that changes the Arginine codon (CGU) to CGC, CGA or CGG will still result in the mutated codon coding for the same amino acid (i.e. Arginine). This idea can be tied together in the Wobble Hypothesis, which states:

...the third base can often vary without changing the resulting amino acid.
As for your second concern, take this genetic code into consideration:

AUG-CCU-CGU-CCU-CGU-CCU-CGU-UAG (this corresponds to=) Initiation codon-Proline-Arginine-Proline-Arginine-Proline-Arginine-Stop codon

If you consider a reading frame that covers the first Proline and Arginine codons (-CCU-CGU-) and induce a hypothetical deletion mutation which removes the Guanine base from the Arginine codon, you are left with -CCU-CU[C]. The Guanine has been deleted from the Arginine codon and so the reading frame shifts 1 base to the right to include the Cytosine base from the next Proline codon. I know this is an extremely difficult concept to explain and understand, but I hope this has helped.
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Joshalos
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(Original post by LeaX)
I'm having trouble understanding what my textbook is going on about and its lack of diagrams isn't really helping lol. I was wondering if someone could explain what this means:

"The degeneracy of the genetic code minimises the effect of mutations so any alterations to the base sequence are unlikely to effect the amino acid coded"
I know degeneracy is to do with multiple codons coding for amino acids but not sure how this reduces mutations?


Reading Frames
Initiation codon (AUG) determines the reading from of the RNA sequence. Depending on which base is chosen as the start of a codon, three possible sets of codons may be read from any base sequence.
In practice, during protein synthesis normally only one reading frame contains useful information and the other two reading frames usually contain stop codons which prevent them from being used to direct protein synthesis.
A set of codons that run continuously and is bounded at the start by an initiation codon and at the end by a termination codon is known as an open reading frame. This characteristic is used to identify protein-coding DNA sequences in genome-sequencing projects.


I have no clue what any of this means lol. I thought codons were a long string (?) and so I don't understand what it means that there are three possible sets of codons that may be read?
With regards to degeneracy reducing mutation, you are correct in saying that multiple codons can code for a single amino acid. This reduces the effect of a mutation in the sense that if a point mutation were to occur in the sequence AUGCUUGCA that then read AUGCCUGCA, it would still code for Methionine-Leucine-Alanine since both CUU and CCU codes for leucine. It just increases the chance that a point mutation would still code for the same amino acid.
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LeaX
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(Original post by loukas2993)
This is a difficult concept to explain on a forum thread, but I'll give it a go.

As you mentioned, you understand what a "degenerate code" means and how that relates to the genetic code. Just to clarify, the fact that the genetic code is considered a degenerate code essentially means that an amino acid can be coded for by more than one codon. This characteristic minimises the effect of mutations by reducing the likelihood that an altered base will produce an altered or nonfunctioning protein. For instance, take this genetic code into consideration:

AUG-CCU-CGU-UAG (this corresponds to=) Initiation codon-Proline-Arginine-Stop codon

If the genetic code was not degenerative, a single base mutation to the Arginine codon (CGU) would theoretically code for a completely different amino acid and could, therefore, produce a completely altered or nonfunctional protein. However, because the genetic code is degenerative, a base mutation that changes the Arginine codon (CGU) to CGC, CGA or CGG will still result in the mutated codon coding for the same amino acid (i.e. Arginine). This idea can be tied together in the Wobble Hypothesis, which states:



As for your second concern, take this genetic code into consideration:

AUG-CCU-CGU-CCU-CGU-CCU-CGU-UAG (this corresponds to=) Initiation codon-Proline-Arginine-Proline-Arginine-Proline-Arginine-Stop codon

If you consider a reading frame that covers the first Proline and Arginine codons (-CCU-CGU-) and induce a hypothetical deletion mutation which removes the Guanine base from the Arginine codon, you are left with -CCU-CU[C]. The Guanine has been deleted from the Arginine codon and so the reading frame shifts 1 base to the right to include the Cytosine base from the next Proline codon. I know this is an extremely difficult concept to explain and understand, but I hope this has helped.

(Original post by Joshalos)
With regards to degeneracy reducing mutation, you are correct in saying that multiple codons can code for a single amino acid. This reduces the effect of a mutation in the sense that if a point mutation were to occur in the sequence AUGCUUGCA that then read AUGCCUGCA, it would still code for Methionine-Leucine-Alanine since both CUU and CCU codes for leucine. It just increases the chance that a point mutation would still code for the same amino acid.
Ahh thank you both so much, I completely understand now!
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kanra
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It makes a little more sense if you actually look at the codons that code for each amino acid (just google "degenerate codons" or something). In many cases, different codons for the same amino acid are quite similar and differ in only the final base. For example, Glycine is GGU, GGC, GGA and GGG - if you mutate the final base into any other base, you still have Glycine.

In terms of reading frames, consider GGACGUAGCGAUGGA.

If you start from the first base, your codons are: GGA CGU AGC GAU GGA

If you start with the second base, your codons are G GAC GUA GCG AUG GA

In other words, the amino acid you get will change depending on the starting position.
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