Unit 1 (Chapter 3 Part 4) Proteins

Question 1

What is a functional unit composed of one or more polypeptides? Each polypeptide is composed of a linear sequence of amino acids.

Answer 1

Proteins.

Accounts for 50% of the organic material in a typical animal’s body,

Comes from the Greek word, proteios, meaning first rank.

Question 2

What are the different categories of major proteins? (7)

Answer 2

• Proteins involved in gene expression and regulation
• Motor proteins
• Defense proteins
• Metabolic enzymes
• Cell-signaling proteins
• Structural proteins
• Transporters

Question 3

What elements are proteins composed of?

Answer 3

Carbon, hydrogen, oxygen, nitrogen, and small amounts of sulfur.

Question 4

What are the monomers of proteins?

Answer 4

Amino Acids

Any of the monomers that are linked to form a protein. Amino acids have a common structure in which a carbon atom, called the α-carbon, is linked to an amino group (─NH2) and a carboxyl group (─COOH), as well as to a hydrogen atom and a side chain that distinguishes the particular amino acid.

Question 5

When an amino acid is dissolved in water, what happens to its functional groups?

Answer 5

The amino group, -NH2, accepts a positively charged hydrogen ion or cation.

Whereas the carboxyl group, loses a hydrogen ion, and becomes negatively charged.

THIS is why the name amino acid was given to such molecules because their amino and carboxyl group acts like an acid.

Question 6

All amino acids have isomeric forms except what protein?

Answer 6

Glycine.

Question 7

What are the isomeric forms of proteins?

Answer 7

D and L forms.

They are enantiomers. Remember: enantiomers are mirror images of each other.

Question 8

What amino acid enantiomers are found in proteins?

Answer 8

L-amino acids

Question 9

Where can the enantiomers, D-amino acids, be found in nature?

Answer 9

In the cell walls of bacteria, where they play a protective role against molecules secreted by the host organism in which the bacteria live.

Question 10

How are amino acids distinguished?

Answer 10

By their side chains.

Question 11

How are amino acids categorized?

Answer 11

Whether or not their side chains are nonpolar, polar and uncharged, or polar and charged.

Question 12

What is critical in how side chains of proteins function?

Answer 12

Their structure.

Question 13

How are amino acids joined together in which the carboxyl group of one amino acid to the amino group of another?

Answer 13

Dehydration reaction

Question 14

What do you call the covalent bond between a carboxyl and amino group that links amino acids in a polypeptide?

Answer 14

A peptide bond.

Question 15

What is a molecule consisting of a linear sequence of amino acids; the term denotes structure?

Answer 15

Polypeptide

Question 16

What do you call the amino and carboxyl ends on a polypeptide?

Answer 16

The N-terminus and C-terminus.

The C-terminus has a free carboxyl group while the other end is a free amino group.

Question 17

How many water molecules would be produced during the formation of a polypeptide that is 72 amino acids long?

Answer 17

71; one less than the total number of amino acids in a polypeptide (linear sequence of amino acids).

Question 18

What is a FUNCTIONAL unit composed of one or more polypeptides?

Answer 18

A protein which has folded and twisted into a precise-three dimensional shape.

Each polypeptide is composed of a linear sequence of amino acids.

Question 19

What are proteins called when they have carbohydrates or lipids attached to them changing their function?

Answer 19

Glycoproteins and Lipoproteins.

These modifications impart unique functions to such proteins.

Question 20

What are the different levels of a protein as in hierarchy?

Answer 20

Primary, secondary, tertiary, and quaternary.

Each higher level of structure depends on the preceding level. If the primary structure is changed, it may as well have an affect on the subsequent levels.

Question 21

What is considered the primary structure of a protein?

Answer 21

The linear sequence of amino acids of a polypeptide(s).

Question 22

How are the primary structures of a protein determined?

Answer 22

Genes and their expressions.

Question 23

What does the secondary structure of a protein? (2) basic forms

Answer 23

The bending or twisting of a region of a protein into an (a helix) or (b sheet).

Question 24

How is the polypeptide backbone of the helix structure stabilized? What about the plated sheet?

Answer 24

Hydrogen bonds.

The hydrogen atoms linked to a nitrogen atom forms a bond with oxygen atom that is double bonded to a carbon atom. These occur at regular intervals.

Same with the pleated sheet, but the polypeptide backbone runs parallel with each with hydrogen bonds between them.

Question 25

A helices and B pleated sheets are key determinates of a protein’s characteristics… For example, what type of amino acids are a helices composed of primarily and why is that important?

Answer 25

They are composed of primarily nonpolar amino acids which tend to anchor themselves in a lipid-rich environment, like a cell’s membrane.

This helps retain the protein where their function is required in a specific location.

Question 26

What type of emphasis is placed on the secondary structure?

Answer 26

Its strength like keratin in hair, hooves, and fingernails; the proteins in spiderwebs; and collagen, which is the cartilage in vertebrae animals.

Question 27

What is a region in a polypeptide that do not assume a helix or pleated sheet and do not have a secondary structure?

Answer 27

Random coiled region. A bit misleading because they have very specific and it is important for the protein’s function.

Question 28

Remember: the secondary structure of a polypeptide is established due to the primary structure; how the side chains of amino acids interact with each other.

Answer 28

No Answer

Question 29

What is the tertiary structure?

Answer 29

The three-dimensional shape of a single polypeptide. It folds and refolds upon itself.

Question 30

What is an individual polypeptide within a functional protein; most functional proteins are composed of two or more polypeptides.

Answer 30

Protein subunits

Question 31

What is the association of two or more polypeptides to form a protein?

Answer 31

Quaternary structure. 1 of 4 levels.

Question 32

What is a common example of a oxygen-binding protein with four levels in the body?

Answer 32

Hemoglobin.

This is found in the red blood cells of vertebrae animals. Four protein subunits combine to form one hemoglobin protein.

Each subunit can bind a single molecule of oxygen… therefore, each hemoglobin protein can carry four molecules of oxygen in the blood.

Question 33

What are the five important factors for protein folding and stability?

Answer 33

1. Hydrogen Bonds - protein folding and stability. Important for all levels of structure.
2. Ionic bonds and other polar interactions - polar charged and uncharged polar ends of amino acids create interactions and bonds that are particularly important in tertiary and quaternary structure.
3. Hydrophobic effect - since some amino acid chains have nonpolar regions, they can be found in the center of a protein away from water. Sometimes these stretches of proteins will anchor themselves in the hydrophobic portion of the cell membranes. Key player in tertiary and quaternary structures.
4. van der Waals dispersion forces - these weak attractions and forces are important in tertiary structures.
5. Disulfide bridges - The covalent chemical bond formed between two sulfhydryl groups on cysteine side chains in a protein; important in the tertiary structure of proteins.

Question 34

What is the specific interactions between proteins that occur during many critical cellular processes?

Answer 34

Protein-protein interactions. These provide shape and organization to cells.

Question 35

Where are polypeptides synthezied?

Answer 35

In the ribosomes of the cells.

Question 36

How did Anfinsen prove that the primary structure or level of a protein determined the tertiary shape (3-dimensional)?

Answer 36

He was able to isolate a purified ribonuclease, a protein synthesized by the ribosome of a cell, and break its hydrogen disulfide bonds, allowing the protein to lose it 3 dimensional shape.

Then, by removing the molecules that broke the bonds from the solution, the protein sat for 20 hours where it regain most of its 3 dimensional shape.

This proved that the primary structure of the protein (primary structure does not bond with itself) was necessary for the protein to fold on itself again.

Question 37

What are domains? (2)

Answer 37

1. A defined region of a protein with a distinct structure and function.
2. One of the three major categories of life: Bacteria, Archaea, and Eukarya.

Question 38

What is a example of the irreversible, denaturation of protein?

Answer 38

Cooking an egg and the white turn opaque trapping water molecules inside created a semisolid.