BIOL 540 Lecture Notes - Lecture 7: Protein Structure, Conformational Change, Ammonia

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13 Feb 2020

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Metabolism

Lecture 7:

Protein Structure

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7.1 Intro

Proteins provide many functions in the body. Almost all of the body functions depend on the actions of

various types of proteins in the body.

Proteins are classified by function. The structure of a protein and its function are tightly correlated.

Modifications to a protein can have a conformational change which are an important regulatory

function. Conformational Change changes the function of a protein.

7.2 Basics of Protein /Peptide:

A Protein is an amino acid polymer composed of more than 50 amino acids. A Peptide consists of less

than 50 aa. Small peptides tend to be involved in defense or regulation. A domain requires more than

100 amino acids.

Amino acids tend to have all the same general structure:

Amino acids have a positively charged Amino group (NH3+) and a negatively charged carbonyl group

(COO-). All 20 of the amino acids in the human body have the same general structure.

The Amino acids differ in their side chain or ‘R’ group.

Since amino acids have a chiral center, they can exist as enantiomers. Only L- amino acids are found in

mammals however.

7.3 Amino Acid Classification

Amino acids are classified based on the chemical nature of the R group

Three general groups of Amino Acids:

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Document Summary

Almost all of the body functions depend on the actions of various types of proteins in the body. The structure of a protein and its function are tightly correlated. Modifications to a protein can have a conformational change which are an important regulatory function. Conformational change changes the function of a protein. A protein is an amino acid polymer composed of more than 50 amino acids. A peptide consists of less than 50 aa. Small peptides tend to be involved in defense or regulation. Amino acids tend to have all the same general structure: Amino acids have a positively charged amino group (nh3+) and a negatively charged carbonyl group (coo-). All 20 of the amino acids in the human body have the same general structure. The amino acids differ in their side chain or r" group. Since amino acids have a chiral center, they can exist as enantiomers. Only l- amino acids are found in mammals however.

Related Questions

Protein Structure

a.Different function of proteins and examples:

b. Protein building blocks:

1. atomic composition of building block:

2. "parts" or "functional groups" of the building block:

c. Importance of side chain (R group):

d. Hydrophobic amino acids characteristics:

e. Hydrophilic amino acids characteristics:

f. Charged amino acids characteristics

Copy and complete the table below regarding the characteristics and which groups in the polypeptide interact together at each structural level of the protein.

	characteristics	groups interacting
Primary structure
Secondary structure
Tertiary structure
Quartenary structure

Value: 2

Choose the correct statement(s). You may choose more than one answer.

[mark all correct answers]
a. Proteins are the building blocks of amino acids.

b. Enzymes are a type of protein.

c. Quartenary structure consists of two or more polypeptide chains interacting.

d. Amino acids are made of carbon, hydrogen, nitrogen and phosphorus.

e. The primary structure of a protein is formed due to the interaction of side groups.

Value: 3

Put the following statements regarding the structural levels of a protein formation in the correct order.

Below is a sequence of events. Place them in the order they should occur, number 1 being the first item. Select the step number from the drop down next to each item.

Items to order:

1. Individual amino acids are bonded together via peptide bonds.

2. Two or more polypeptide chains interact via bonds.

3. Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets.

4. Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape.

Value:4

Put the following statements regarding the structural levels of a protein formation in the correct order

Individual amino acids are bonded together via peptide bonds.	1 2 3 4
Two or more polypeptide chains interact via bonds.	1 2 3 4
Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets.	1 2 3 4
Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape.	1 2 3 4

Value: 5

Hydrophobic amino acids will be found _______________.

a. In the interior (inner core) of a protein, away from the watery environment.

b. in the interior of a plasma membrane.

c. Both A and B

d. Neither

Value: 6

A protein's function is defined by ____________.

a. enzymatic reactions

b. it's shape.

c. chain of nucleotides.

d. the presence of carbon and hydrogen.

Value: 7

Which of the following is NOT considered a protein function?

a. transport of substances across membrane

b. enzymatic reactions

c. provides structural support

d. carries genetic information

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.

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

BIOL 540 Lecture Notes - Lecture 7: Protein Structure, Conformational Change, Ammonia

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