BIOL 4087 Chapter : Amino Acids On One Page
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Consider the peptide:
NH2-GAPAGPAGTGKTETTKDLAKSMALLCWFNCS-COOH
Table I. pK values of some amino acids
amino acid | pK of side chain or terminal group |
---|---|
Alanine (Ala or A) | uncharged |
Arginine (Arg or R) | 12.5 |
Asparagine (Asn or N) | uncharged |
Aspartic acid (Asp or D) | 3.9 |
Cysteine (Cys or C) | 8.3 |
Glutamic acid (Glu or E) | 4.3 |
Glycine (Gly or G) | uncharged |
Histidine (His or H) | 6.0 |
Leucine (Leu or L) | uncharged |
Lysine (Lys or K) | 10.8 |
Phenylalanine (Phe or F) | uncharged |
Serine (Ser or S) | uncharged |
Tryptophan (Trp or W) | uncharged |
Tyrosine (Tyr or Y) | 10.9 |
Valine (Val or V) | uncharged |
peptide N terminus | 7.8 |
peptide C terminus | 3.6 |
Using Table I above, determine the net charge of the peptide at pH9.
(the answer is not -1 or 1)
For the following strand of DNA, use the table below to provide: bases for the complementary mRNA and the associated amino acids. What do you notice about the genetic code for proline in the peptide? How would the loss of the first G or switching that G to a T affect the structure and function of this protein?
DNA: GGC CTA CAA GCC GGA ACA GTT ACC GCG TAA CGA
RNA: ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ???
Amino Acid:??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ???
(3 Letters)
Genetic Code Table (mRNA)
1st position (5' end) | 2nd position (middle) | 3rd position (3' end) | |||
U | C | A | G | ||
U | Phe F Phe F Leu L Leu L | Ser S Ser S Ser S Ser S | Tyr Y Tyr Y STOP STOP | Cys C Cys C STOP Trp W | U C A G |
C | Leu L Leu L Leu L Leu L | Pro P Pro P Pro P Pro P | His H His H Gln Q Gln Q | Arg R Arg R Arg R Arg R | U C A G |
A | Ile I Ile I Ile I Met M | Thr T Thr T Thr T Thr T | Asn N Asn N Lys K Lys K | Ser S Ser S Arg R Arg R | U C A G |
G | Val V Val V Val V Val V | Ala A Ala A Ala A Ala A | Asp D Asp D Glu E Glu E | Gly G Gly G Gly G Gly G | U C A G |
SEQUANCE:
5'- GCU UGG GCU GCU GAU GCU CUU UAA CAU AGA GCU AAU AUU -3'
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3- Convert your mRNA sequence into a DNA sequence, then make itdouble-stranded by writing the complementary sequence below.
4- Transcribe (write an RNA sequence) and translate (write anamino acid sequence) both the "top" and "bottom" strands startingwith the first nucleotide. You must use the genetic code in yourtextbook or in your lecture notes for this step. DO NOT use thetable above. If you encounter a stop codon, your protein sequenceis done at that point.
Use the single letter designation for amino acids as givenbelow.
Alanine (A) | Aspartic acid (D) | Asparagine (N) | Arginine (R) |
Cysteine (C) | Glycine (G) | Glutamic acid (E) | Glutamine (Q) |
Histidine (H) | Isoleucine (I) | Leucine (L) | Lysine (K) |
Methionine (M) | Proline (P) | Phenylalanine (F) | Serine (S) |
Threonine (T) | Tryptophan (W) | Tyrosine (Y) | Valine (V) |
5- Use your original DNA sequence from #3. Add an A to the 5'end of the "top" strand, then write the complementary sequence onthe bottom. Add a GC to the 5' end of the
"bottom" strand, then write the complementary sequence on the top.Transcribe and translate both the "top" and "bottom" with this newsequence.
What kind of mutation(s) was introduced in the "top" strand?
What kind of mutation(s) was introduced in the "bottom"strand?
6- Use your original DNA sequence from #3. Starting at the 5'end on the "top" strand of your original sequence from part 3,delete the second A, the third G, and the fourth C along with thecomplementary nucleotides on the bottom strand. Transcribe andtranslate both the "top" and "bottom" with this new sequence.
What kind of mutation(s) was introduced in the "top" strand?
What kind of mutation(s) was introduced in the "bottom"strand?
7. Use your original DNA sequence from #3. Starting at the 5'end of the "top" strand, change the third G to an A, then changethe complementary nucleotide in the bottom. Starting at the 5' endof the "bottom" strand, change the third C to a T, then change thecomplementary nucleotide on the top. Transcribe and translate boththe "top" and "bottom" with this new sequence.
a. What kind of mutation(s) was introduced in the "top"strand?
b. Whatkind of mutation(s) was introduced in the "bottom" strand?