Biochemistry 2280A Lecture Notes - Lecture 2: Proline, Alanine, Phenylalanine

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12 Dec 2016

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Biochem Lecture 2 September 11,2013

Topic 1 continued

o Proteins

 Most abundant molecules in living systems

 Made up of amino acids

 There are 20 amino acids – each one has a carboxylic acid group +

amino group + side chain

 Only different aspect between amino acids is the side chain

 Amino acids can have stereoisomers but only the L-form is active in the

body

o MEMORIZE 8 AMINO ACIDs

 Know: properties, 3 letter code, 1 letter code, structure

 Aspartic acid

 Lysine

 Serine

 Alanine

 Glycine

 Proline

 Phenylalanine

 Cysteine

o Amino acid structure

 Properties of the side chain determine protein’s character

 Hydrophobic or hydrophilic (charged or uncharged)

 Physical size

 Ability to form hydrogen bonds

o 4 classes of amino acids

 Polar side chain

 Negative side chain

 Neutral side chain

 Positive side chain

 Nonpolar side chain

o Non-polar side chains: hydrophobic

 Glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan,

methionine, proline, cysteine

 Proline is the only amino acid that rejoins itself (alpha nitrogen is bound

to the side chain)

 Technically is an “imino acid” because nitrogen has 2 bonds, instead

of just one

 Least flexible

 Can be hydroxylated (take on a hydroxyl group)

 All of these groups are maximally protonated

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Document Summary

There are 20 amino acids each one has a carboxylic acid group + amino group + side chain. Only different aspect between amino acids is the side chain. Amino acids can have stereoisomers but only the l-form is active in the body: memorize 8 amino acids. Know: properties, 3 letter code, 1 letter code, structure. Properties of the side chain determine protein"s character. Ability to form hydrogen bonds: 4 classes of amino acids. Nonpolar side chain: non-polar side chains: hydrophobic. Glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, proline, cysteine. Proline is the only amino acid that rejoins itself (alpha nitrogen is bound to the side chain) Technically is an imino acid because nitrogen has 2 bonds, instead of just one. Can be hydroxylated (take on a hydroxyl group) All of these groups are maximally protonated. Whether they"re protonated or not, depends on the ph of the solution that the amino acid is in.

Related Questions

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)

The peptide hormone vasopressin is used in the regulation of Na+ in many vertebrate. Porcine(pig) vasopressin has the sequence Asp-Tyr-Phe-Glu-Asn-Cys-Pro-Lys-Gly.

a) What is the pI of this peptide? Use the pKa values in the table on the last page for your calculations.

b) Could this peptide have an a helical secondary structure? Why or why not.

c) Will this peptide absorb UV light(280nm)? Why?

SEQUANCE:

5'- GCU UGG GCU GCU GAU GCU CUU UAA CAU AGA GCU AAU AUU -3'

=======================================================================================

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?

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Biochemistry 2280A Lecture Notes - Lecture 2: Proline, Alanine, Phenylalanine

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