Biochemistry 2280A Lecture Notes - Lecture 20: Aminoacyl-Trna, Missense Mutation, Frameshift Mutation

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silverferret42

12 Dec 2017

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Genetic code, trna, aminoacyl trna synthetases, ribosome, mechanism of translation, initiation, termination, antibiotics. Genetic code spells out the aa sequence in 3 letter words called codons. There are 20 aa, each needs at least one codon. 3 is minimum sufficient for 20 aa (2 would be 16) Non overlapping, read in blocks of 3, no overlap. If it was overlapping would place significant restrictions on what amino acid residues could follow each other. Redundancy some codons specify the same amino acid. Often occurs at the third position of the codon. Generally amino acids found less frequently in proteins have fewer codons. Increases the chance of a functional protein in the case of a single base mutation. Missense mutation single base change, single amino acid change. Frameshift mutation insertion/deletion of base pairs, changes the reading frame of the protein from the point of the mutation onward, will almost always cause a big problem. Insertion of 3 consecutive bases to a gene.

Related Questions

22. There are 20 amino acids and 64 possible codons. Which of the following is closer to the actual number of different tRNA molecules in a cell?

A. 4

B. 16

C. 20

D. 61

E. 64

23. There are 20 amino acids and 64 possible codons. How many different eukaryotic aminoacyltRNA synthetases are there? A. 1

B. 16

C. 20

D. 61

E. 64

24. Which way are the amino acid and tRNA attached in a charged tRNA?

A. Amino acid-5'tRNA3'-AMP B

. Amino acid-AMP-3'tRNA

C. AMP-amino acid-3'tRNA

D. Amino acid-3'tRNA5'-AMP

E. Amino acid-AMP-5'tRNA

25. The anticodon that recognizes the initiation codon in translation is

A. 5' AUG 3'

B. 3' AUG 5'

C. 5' ACU 3'

D. 5' UAC 3'

E. 3' UAC 5'

26. The first amino acid incorporated into a growing polypeptide

A. In bacteria is methionine and it is also methionine in eukaryotes

B. In bacteria is tryptophan, while it is methionine in eukaryotes

C. In bacteria is N-formyl methionine, while it is methionine in eukaryotes

D. In bacteria is N-formyl methionine and it is also N-formyl methionine in eukaryotes

E. In bacteria is methionine, while it is N-formyl methionine in eukaryotes

27. In E. coli the IF3 forces tRNAf Met to bind with

A. The A site of the ribosome

B. The P site of the ribosome

C. The E site of the ribosome

D. IF1

E. IF2

22. What is probably the single most important distinction between bacteria and eukaryotes?

a. transcription

b. the separation of the cell's genetic material from the surrounding cytoplasm

c. the existence of ribosomes

d. RNA processing in bacteria

e. antibiotics

23. Which one does NOT characterize an open reading frame (ORF)

a. Uses six reading frames during translation

b. Contains a start codon

c. Contains a stop codon

d. Its length is in multiples of 3 nucleotides

e. It should have the number of codons for a protein or on average ~250 codons in length.

24. Nested intronic genes lie within the non-coding intronic region of a larger gene, and occur in the human genome.

a. True

b. False

25. How would you characterize this statement: EF-Tu will hydrolyze GTP only if the codon:anticodon & tRNA:amino acid matchings are correct

a. Transcription; initiation steps

b. Transcription; termination steps

c. Translation: initiation steps

d. Tanslation: elongation steps

e. Spliceosome

26. Regarding the transcription unit architecture of the Escherichia coli genome, which one is FALSE?

a. Each of the 4,661 transcription units comprised an average of 1.1 modular units.

b. 3,010 transcription units (~65%) are monocistronic.

c. 1,652 transcription units (35%) contain more than one ORF (polycistronic)

d. The largest transcription unit is equivalent to 16 ORFs with numerous introns.

e. 398 transcription units (~9%) are nested within each other in opposite transcriptional orientation

27. Regarding RNA interference (RNAi), which one is FALSE?

a. It is a common and conserved mechanism in eukaryotic cells.

b. Originally discovered in bacteria and plant viruses.

c. A form of primitive immunity to protect the genome.

d. Pre microRNA (miRNA) genes have been found in introns.

e. Recent research shows that exogenous plant miRNAs in food can regulate the expression of target genes in mammals.

28. Aminoacyl-tRNA synthetases

a. Recognize the 3âUTR

b. The genes for these enzymes fall into the family of inducible genes

c. The enzymes are imported into the nucleus

d. Covalently attaches an amino acid to the appropriate tRNA. This takes place in the cytoplasm.

e. Forms the peptide bond during protein synthesis

29. What is the process by which complementary RNAs are made from a DNA template?

a. translation

b. transcription

c. protein synthesis

d. transduction

e. transliteration

cyanbee225

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.

Biochemistry 2280A Lecture Notes - Lecture 20: Aminoacyl-Trna, Missense Mutation, Frameshift Mutation

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