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23 Feb 2018

Tertiary proteins are determined by the primary amino acid sequence. Should a protein, in which the order of all amino acids is reversed have the same tertiary structure?

a. Yes even though the amino acid sequence is reversed the tertiary folding remains the same

b. yes the protein remains the same

c. yes and no it depends if the amino acid is palindromic

d. no the amino acid sequence is the same but the amino and carboxyl termini are not

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Related questions

What is the percent sequence identity between hemoglobin (2HHB) and myoglobin (1A6M)?

A.

93%
B.

39.46%
C.

25.17%
D.

4.08%

QUESTION 2

Which of the following statements is consistent with the sequence similarity parameter?

A.

The abundance of amino acids with similar properties that are arranged in the same order is equal to the abundance of identical amino acids.
B.

These parameters are not related and cannot be compared.
C.

The abundance of amino acids with similar properties that are arranged in the same order is less than the abundance of identical amino acids.
D.

The abundance of amino acids with similar properties that are arranged in the same order is higher than the abundance of identical amino acids.

QUESTION 3

Which of the following statements is consistent with the similarity parameter and visualization of the aligned structures?

A.

Hemoglobin and myoglobin do not have similar structures.
B.

Hemoglobin and myoglobin have only moderately similar structures, as indicated by the large abundance of gray chains.
C.

Hemoglobin and myoglobin have very similar structures.
D.

Hemoglobin and myoglobin are perfectly aligned at every amino acid.

QUESTION 4

Hemoglobin (2HHB) is ___ amino acids shorter than myoglobin; the sequence alignment considers only ___ amino acids, and alignment results show that hemoglobin is missing a contiguous strand of ___ amino acids.

A.

10; 141; 6
B.

10; 141; 5
C.

10; 147; 6
D.

10; 147; 5

QUESTION 5

Which of the following statements best describes the evolutionary relationship between hemoglobin and myoglobin?

A.

The low sequence identity indicates that hemoglobin and myoglobin are not related, as tertiary structure cannot be used to study protein evolution.
B.

Both the high sequence identity and structural similarity suggest that hemoglobin and myoglobin are related.
C.

The difference in sequence identity and similarity values suggests that hemoglobin and myoglobin are related.
D.

The high structural similarity suggests that hemoglobin and myoglobin are related, while the low sequence identity suggests that the genes for each protein have diverged through mutation and deletion of several amino acids.

QUESTION 6

The comparison of sequences and tertiary structures in this exercise indicates that:

A.

only similar amino acid sequences can provide the same tertiary structure.
B.

different amino acid sequences can provide very similar tertiary structures.

QUESTION 7

The structures of deoxyhemoglobin and oxyhemoglobin are derived from the same source, have the same exact amino acid sequence and length, and differ only in the presence of noncovalently bound oxygen.

A.

True
B.

False

QUESTION 8

When using the Sequencing and Structure Alignment tool, the degree of the structural similarity is shown by the superimposition of the backbones. Accordingly, which of the following statement best describes the comparison of deoxyhemoglobin and oxyhemoglobin?

A.

Only slight differences in the backbone traces occur throughout the aligned proteins.
B.

The only differences in the backbone traces occur near the oxygen-binding sites.
C.

The backbone traces of the proteins are drastically different.
D.

The backbone traces of the proteins are identical.

QUESTION 9

The alignment of 2HHB and 1HHO shows that the binding of oxygen results in _______ in the protein.

A.

minor conformational changes at sites proximal and distal to the oxygen-binding site
B.

no conformational change
C.

drastic conformational changes
D.

minor conformational changes only within the oxygen-binding site

QUESTION 10

The alignment of 2HHB and 1HHO shows that the conformation of the Fe-heme group _____ upon oxygen binding.

A.

changes
B.

does not change

The linear sequence of amino acids is referred to as the primarylevel of protein structure. However, the primary sequence affectsall other aspects of protein structure.

a. Explain how an amino acidchange outside of the active site of a particular enzyme couldaffect the function of that enzyme. (2pts)

b. Explain how that same aminoacid change could have no affect on the function of the enzyme.(2pts)

c. Imagine a protein in which acysteine is converted to a serine. How would this mutation affectthe secondary, tertiary and quaternary structure? (3pts)

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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