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13 Jan 2018

Given a mixture of GIVE (AMINO ACIDS, GLYCINE, ISOLEUCINE, VALINE, GLUTAMIC ACID,) and TAKE (ALSO AMINO ACIDS), and buffers at pH 2,7 and 10, which buffer would you use to achieve their electrophoretic separation. Explain the answer based upon the charges on the two molecules.

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Reid Wolff
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14 Jan 2018
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Related questions

Directions: Look at the following amino-acid sequences from two warm-water species and one cold-water species and identify where changes in the sequence occurred.

Line 1: C. punctipinnis: Temperate (cold-adapted)

Line 2: C. caudalis: Tropical (warm-adapted)

Line 3: C. xanthochira: Tropical (warm-adapted)

151

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIVG EHDGSSVPVW

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIVG EHDGSSVPVW

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIIG EHDGSSVPVW

201

SGVNVAGVSL QGLNPQMGTD GDSEKWKEVH KLVVDGAYEV IKLKGYTSWA

SGVNVAGVSL QALNPQMGAE GDSENWKAVH KQVVDGAYEV IKLKGYTSWA

SGVNVAGVSL QGLNPKMGAE GDSENWKEVH KLVVDGAYEV IKLKGYTSWA

251

IGMSVADLVE SIMKNLHKVH PVSTLVQGMH GVKDEVFLSV PCVLGNSGLT

IGMSVADLVE SIMKNLHKVH PVSTLVQGMH GVKDEVFLSV PCVLGNSGLT

IGMSVADLVE SIMKNLHKVH PVSTLVQGMH GVKDEVFLSV PCVLGNSGLT

301

DVIHMTLKPE EEKQLVKSAE TLWGVQKELT

DVIHMTLKPD EEKVLVKSAE TLWGVQKELT

DVIHMTLKPD EEKQLVKSAE TLWGVQKELT

1. Which amino acids changed between the three species? List four of them below, using the number of the amino acid.

Example: Amino acid 189 changed from valine to isoleucine in a warm adapted species.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

2. What were the changes in the chemical properties of the R-groups? Use the amino-acid chart to in the Powerpoint file to answer this question.

Example: Both valine and isoleucine are nonpolar.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

3. How might the changes that you identified affect the protein’s structure?

Example: The change would likely have no effect. Neither valine and isoleucine would promote hydrogen bonding with water, because their R groups are nonpolar and thus hydrophobic.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

4. Assuming that the mutations are adaptive, how should the changes that you identified affect the stability of the protein at low and high temperatures?

1. A polypeptide chain has a large percentage of acidic and basic amino acids in it. The R groups of these amino acids form ionic interactions, which helps the protein to maintain it’s structure. This particular polypeptide works well under an optimum pH of 7. Ignoring effects of strong acids and bases on peptide bonds, what will happen to the tertiary structure of the protein if you move it stomach acid, which has a pH of 1-2. Why? Be specific regarding what influence the pH will have on the bonds maintaining tertiary structure in the molecule. Include the amino acid charges of the acidic and basic amino acids at the acidic pH, as well as the concept of pK in your answer. Assume that acidic amino acids have a pK of approximately 4.7 and basic amino acids have a pK of approximately 10.

2. Ignoring peptide length (or lack thereof) where would this portion of a polypeptide be most likely to be found: On the inside or on the outside surface of a protein floating around in the cytoplasm? Explain

3. A mutation occurs in the SRC kinase such that the tyrosine on the loop over the active site is changed to aspartic acid. This mutation mimics phosphorylation.
a. knowing what you know about the properties of phosphate groups and aspartic acid, why does aspartic acid mimic phosphorylation?
b. What would be the implication of this mutation on the function of the SRC kinase?

Instructions

BACKGROUND

The amino acid sequence for a protein that is associated with the onset of Huntington's Disease in humans is 582 amino acids long and is provided below. This disease is autosomal dominant and results in a prolonged degeneration of nerve cells in the brain.

INSTRUCTIONS

For this assignment, use any method you determine most feasible (i.e. programming in MATlab, R script, Crystal Ball, Witchcraft/Hocus Pocus, etc.) to decipher the amino acid composition of this protein and answer the 15 questions associated with this protein and its associated amino acid structure.

You will be calculating proportions (percentages - %) for this assignment. Calculate all proportions to 1 decimal place and make sure you have rounded up or down correctly. If unsure, use a spreadsheet program such as Excel to display your proportional calculations to 1 decimal place.

Spelling matters (Incorrect spelling will be graded as such - incorrect).

Huntington Disease Associated Protein Amino Acid Sequence

The first amino acid below ('m') represents the amino (NH3) terminus of this protein. The last amino acid in this sequence represents the carboxy (COOH) terminus and is the very last 'c' at the bottom of this protein sequence structure. The amino acids are numbered individually across the rows (left to right) beginning from the amino terminus (#1) to the carboxy terminus (#582).

mvskreniat

hhlyqawdpv

pslspattga

lisheklllq

inperelgsm

syklgqvsih

svwlgnsitp

lreeewdeee

eeeadapaps

spptspvnsr

khragvdihs

csqfllelys

rwilpsssar

rtpailisev

vrsllvvsdl

fternqfelm

yvtltelrrv

hpsedeilaq

ylvpatckaa

avlgmdkava

epvsrllest

lrsshlpsrv

galhgilyvl

ecdllddtak

qlipvisdyl

lsnlkgiahc

vnihsqqhvl

vmcatafyli

enypldvgpe

fsasiiqmcg

vmlsgseest

psiiyhcalr

glerlllseq

lsrldaeslv

klsvdrvnvh

sphramaalg

lmltcmytgk

ekvspgrtsd

pnpaapdses

vivamervsv

lfdrirkgfp

cearvvaril

pqflddffpp

qdimnkvige

flsnqqpypq

fmatvvykvf

qtlhstgqss

mvrdwvmlsl

snftqrapva

matwslscff

vsastspwva

ailphvisrm

gkleqvdvnl

fclvatdfyr

hqieeeldrr

afqsvlevva

apgspyhrll

tclrnvhkvt

tc

CARBOXY TERMINUS

I need these decoded in order to answer the following questions:

a.) What is the name of the least abundant amino acid in this protein and what proportion of the total amino acids in the protein does this individual amino acid represent?

b.) What is the proportion of essential amino acids included in this protein sequence?

c.)How many Tryptophan residues are present in this protein sequence?

d.) The amino acid sequence from residues 73-85 is represented by the amino acids EEEWDEEEEEEAD, how would you generally classify this small region of the protein

e.) Two amino acids are present in the same proportion in this protein, which two are those?

f.) How many positively charged amino acids are present in this protein?

g.)Which class of amino acids is the most abundant in this protein?

h.) What amino acid(s) is/are present at locations 572 and 582 in the Huntington Disease protein (Full Amino Acid Name(s))

i.) What type of structure could form between these amino acids that could help stabilize this protein's structure?

j.) How many valine residues are present in this protein?

k.)Which class of amino acids is least abundant in this protein?

l.) How may negatively charged amino acids are present in the Huntington disease protein?

m.) How many Aspartic Acid residues are present in this protein and what proportion do they represent of the total amino acids in this protein?

n.)Summed together, how many hydrophilic amino acid residues are present in this protein?

o.)What is the sequence of amino acids from positions 487-492 (First letters only)?

p.) How would you classify this area of the Huntington protein based on these amino acids?

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