BCH 261 Lecture Notes - Lecture 10: Size-Exclusion Chromatography, Diethylethanolamine, Sequence Logo

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6 Mar 2018

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Bioinformatics- process of computationally comparing the primary structure of a protein in order to: Proteins with similar structure and functions can have similar primary structure: Identical amino acids- refers to an amino acid sequence that is identical to an amino acid sequence on another protein. % identity- refers to the percentage of amino acids that are identical between two proteins. Similar amino acids- refers to an amino acid sequence that has similar sequences/similar functions to an amino acid sequence on another protein. 2 or more proteins can be aligned and therefore you can detect the identity and similarity between them. Similar amino acid sequences on a protein can have slight deviations from the protein being compared to: therefore, the two proteins can have a similar shape and function. Computerized method of aligning and comparing two amino acid sequences: blue = identical amino acids on both proteins, green = similar amino acids on both proteins, red = amino acid gaps.

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

1. Enzyme A is an enzyme that catalyzes the reaction of glucose + fructose to sucrose by coupling this +âG reaction with the -âG hydrolysis of ATP. A chemical is discovered that keeps Enzyme A from entering its transition state. What will happen when this enzyme is added to a solution containing ATP and equal parts of glucose, fructose, and sucrose?

A. All of the glucose + fructose will be converted to sucrose.

B. All of the sucrose will be converted to glucose + sucrose.

C. The glucose + fructose will reach their equilibrium constant with sucrose.

D. The ATP will phosphorylate the glucose to produce sucrose while leaving fructose.

2.Which of the following does not contribute to how an individual protein functions?

A. sequence of amino acids.

B. The quaternary structure of that protein.

C. The shape of the binding site.

D. The number and position of charged and polar amino acids.

3. In order to perform functions that proteins alone cannot do, proteins can:

A. Incorporate other molecules into their structure.

B. bind to other proteins to form a complex.

C. signal to non-protein enzymes to perform the function.

D. undergo a conformational change to perform the function.

4. Which of the following is not a function of intrinsically disordered sequences in a protein?

	A. Acting as substrates for chemical interactions.
	B. Increasing variation in a protein by swapping amino acids.
	C. Providing elasticity to tissues.
	D. Flexing to enable interactions between domains.

BCH 261 Lecture Notes - Lecture 10: Size-Exclusion Chromatography, Diethylethanolamine, Sequence Logo

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