BIOL 100 Chapter Notes - Chapter 12: Protein Precursor, Dehydration Reaction, Covalent Bond

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18 Feb 2018

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Concept 1: monomers of proteins are amino acids. Proteins are one of the most diverse biological molecules. Large, complex macromolecules that have specific structural function. Can be used as enzymes to speed up chemical reactions within the body and digest foods we eat. Can also form the hemoglobin our blood cells that is responsible for carrying oxygen and hep transmit signals from one cell to another. R group can be any one of 20 different side groups that give each amino acid its own distinctive chemical property. The way that each amino acid affects the shape of a protein depends the chemical/electrical nature of the amino acid"s side group. Exact type, position, and number of different r groups of the amino acids of a protein determine both the structure of the protein and its biological function. Hydrophilic - water loving" amino acids contain atoms (oxygen and nitrogen) that are polar which make the r- groups soluble in water.

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. Amino acid changes in the primary structure of the protein arenot capable of causing changes in the
overall shape of a protein.
a.) True
b.) False

2. An alpha helix:
a.) is destabilized by the amino acid alanine
b.) can only form by hydrogen bonding between different polypeptidechains
c.) can only form when cysteines form disulfide bridges within thisstructure
d.) all of the above
e.) none of the above

3. What will likely happen if two aspartates at pH 5 are next toeach other in a polypeptide chain?
a.) The side chains of these amino acids will be uncharged andthere will be no effect.
b.) The side chains of these amino acids will be charged and theywill attract each other.
c.) The side chains of these amino acids will be charged and theywill repel each other.
d.) Not enough information is given to determine the effect.

4. Consider the amino acid phenylalanine. Which of the followingbest describes where you predict this
amino acid would be found?
a.) This amino acid is hydrophobic and would be on the surface of aprotein that is in the middle
of a membrane.
b.) This amino acid is hydrophilic and would be on the surface of aprotein that is in the middle
of a membrane.
c.) This amino acid is hydrophobic and would be in the interior ofa protein that is in the middle
of a membrane.
d.) This amino acid is hydrophilic and would be in the interior ofa protein that is in the middle of
a membrane.
e.) Not enough information is given to determine.

5. The difference between fetal and adult hemoglobin with regard tooxygen binding occurs because fetal
hemoglobin has an amino acid substitution in one of its chains thatresults in a histidine being replaced by a
serine.
a.) True
b.) False

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 100 Chapter Notes - Chapter 12: Protein Precursor, Dehydration Reaction, Covalent Bond

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