Biochemistry 2280A Lecture Notes - Lecture 25: Transfer Rna, Silent Mutation, Cistron

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maroongoat576

17 Dec 2015

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The genetic code spells out the amino acid sequence in 3 letter . Have to have 20 because there are 20 amino acids. A one letter code with a g u c would provide: 4 codons. A two letter code would provide: 4 x 4 = 16 codons. A three letter code would provide: 4 x 4 x 4 = 64 codons. As there are 20 amino acids, a 3 letter code (64 codons) is sufficient. Overlap would place significant restrictions on what amino acid resides. Any amino acid can follow any other amino acid could follow each other. Redundancy some codons specify the same amino acid. Redundancy often occurs at the third position of the codon. Generally amino acids found less frequently in proteins have fewer codons: for example: met aug, trp ugg. Asp and glu are both acidic, negatively charged, etc. Glu and gln are similar 2 bases at the end are same, just differ in the first.

Related Questions

EVOLUTIONARY BIOLOGY HELP!!! Please answer all of them.

1. When k_A>k_S, then:

a. Scientists would reject the null hypothesis of neutral evolution because the number of replacement substitutions is greater than expected.

b. Scientists would reject the hypothesis that natural selection took place millions of years ago and is no longer relevant

c. Scientists would accept the hypothesis that neutral evolution took place millions of years ago and is no longer relevant

2. Consider the following protein-coding genetic regions (shown starting with their first codons). How many amino acids would be different between AUGUCAGACGCGAAA and AUGUCAGAGGCGAAC based on the standard universal genetic code?

a. There would be a difference in 1 amino acid when translated

b. There would be a difference in 2 amino acids when translated

c. none of the above

3. Which of the following statements is true?

a. Some fossil remnants have revealed pigmentation of body structures

b. Carbon-14 is an unstable isotope with a half-life of less than 10,000 years

c. Oxygen-18 is an unstable isotope with a half-life of less than 10,000 years

d. all of the above

e. A and B, but not C

4. Based on current fossil evidence:

a. ancestors of whales were artiodactyls

b. evolution of baleen forced ancestors of land mammals to become aquatic

c. whales and walruses are more recently diverged than whales and dolphins

d. A and C are correct

ochremallard624

I need help with Part B. I believe that part A is correct.

a) You also wish to synthesize a degenerate oligonucleotide primer that could be used eventually to clone DNA that encodes your mutant protein. Design this degenerate oligo, keeping in mind the rules we talked about in class. More information about designing degenerate primers and primers in general are located on the following page.

Write out the sequence of this oligo here based on this amino acid sequence (Met Ala Pro Met Val Ala Glu):

My answer (Is it correct?)

I got:

5â AUG - (GCU/C/A/G) - (CCU/C/A/G) - (AUG) - (GUU/C/A/G) - (GCU/C/A/G) - (GAA/G) â3

3â UAC - (CGA/G/U/C) - (GGA/G/U/C) - (UAC) - (CAA/G/U/C) - (CGA/G/U/C) - (CUU/C) 5â

______________________________________________________________________________

(What I actually need help with and have no idea where to begin. Please help me)

b) If you synthesized the above oligonucleotide primer, how many different oligos would be present in the mixture?

Follow these rules Modified from the Thermo Fisher web site:

Designing degenerate primers:

Write out your amino acid sequence, label amino and carboxy termini

For each amino acid, use the genetic code to predict the various nucleic acid codons that can encode this amino acid. For all but Met, you should have redundancy present.

Now you need think about 5â and 3â considerations, and keep in mind that DNA within genes is double-stranded. It is helpful to keep in mind that the 5â end of a gene corresponds to the amino terminus of a protein. Using 5â and 3â labels write out a single strand DNA sequence corresponding to the your amino seq of interest. You may choose to start with only possible codon for each amino acid, or you can do all possibilities using the notation I showed you in class to account for the wobble position of codons.

Now make your DNA double stranded by filling in the opposite DNA strand; label the 5â and 3â ends of this second strand and make sure you have an anti-parallel arrangement of DNA strands.

If you havenât already, now consider the redundancy present on both strands, and make sure you have indicated sequences that account for all possible redundancies.

Realize that when a researched synthesizes a degenerate oligo that the final synthesis contains oligos with every substitution possible. The amount of degeneracy is defined by the number of different primer combinations in the mix. You can determine the degree of degeneracy by multiplying the number of changes present at each position together. If a position has no degeneracy then you multiple by 1 for that position.

Keep in mind that the trade-off between primer specificity and efficiency can be modified by altering the degeneracy of the primer. For example, the more degenerate the primers, the less specific annealing will be; however, decreased degeneracy will allow more potential to identify unknown variants. Anything over 1024 fold degeneracy is at the upper limit of potential usefulness.

DNA and Genes Lab Activity
Complete your answers in the spaces provided. USE YOUR OWN WORDS â Yes even
for definitions! Remember to add your last name and first initial to the file name prior to
saving and submitting your completed assignment through Canvas.
Use your textbook, notes and these websites to answer the pre lab questions.
http://learn.genetics.utah.edu/content/molecules/transcribe/
http://www.vcbio.science.ru.nl/en/virtuallessons/cellcycle/trans/
Pre Lab Questions:
1. What is the product of transcription?
2. What is the region of DNA called where transcription begins?
3. What is the product of translation?
4. In your own words define each of the following:
Silent mutation
Missense mutation
Nonsense mutation
Frame shift mutation
5. Where in the cell does translation take place?
Click on the link below to access the online lab.
http://www.mhhe.com/biosci/genbio/virtual_labs_2K8/pages/DNA_And_Genes.html
Download and print the instructions for reference as you work through the lab. As you work through the lab fill in the table below. Use this information to answer the questions that follow contained in this document.
First read through the mutation guide. Once you close the guide you will see the buttons to begin the simulation. Note, you will be translating the mRNA strand into a protein. As you work through each of the mutations fill in the charts below. You must complete 4 mutations for this lab activity. Itâs good practice working with the codon table .
â Aris labs calls the codon table the âGenetic Code Chartâ. Use the amino acid abbreviation for the protein sequence. For example the amino acid proline is abbreviated as pro.
You have to fill in all the letters AND the resulting amino acid sequence by dragging and dropping before you click the [check] button. Abrieviate STOP as either STP or END.
For each of the three mutations you will complete, fill in the table in this lab document with the original mRNA and amino acid sequence and the mRNA sequence and the resulting amino acid sequence RESULTING FROM the mutation as outlined in the mutation rule.
The various mutations represent missense, nonsense, silent and frame shift mutations. You must complete one of each. The lab will not necessarily present the mutations in this order. You must do the mutation and identify which type it is and make sure you do one of each.
6. Frame Shift Mutation example:
Provide the mutation rule you are following.
Original A. Acids
Original mRNA
Mutated mRNA
Mutated A. Acids
7. Missense Mutation example:
Provide the mutation rule you are following.
Original A. Acids
Original mRNA
Mutated mRNA
Mutated A. Acids
8. Nonsense Mutation example:
Provide the mutation rule you are following.
Original A. Acids
Original mRNA
Mutated mRNA
Mutated A. Acids
9. Silent Mutation example:
Provide the mutation rule you are following.
Original A. Acids
Original mRNA
Mutated mRNA
Mutated A. Acids
Post Lab Questions
10. From the mutations you have explored, which one is the least severe. Explain your answer.
11. From the mutations you have explored, which one is the most severe. Why?
12. Aside from silent mutations which have no effect on amino acid sequence, are all mutations bad? Explain your answer.

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Biochemistry 2280A Lecture Notes - Lecture 25: Transfer Rna, Silent Mutation, Cistron

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