Protein Structure, Folding, & Function

Question 1

What are the four levels of protein organization?

Answer 1

1. Primary
2. Secondary
3. Tertiary
4. Quaternary

Question 2

Summarize the primary structure of a polypeptide.

Answer 2

The primary structure is controlled by the specific linear sequence of amino acids that constitute the chain. Because there are 20 different types of amino acids and polypeptides contain well over 100 amino acids, the variety in protein structure is essentially unlimited.

Question 3

What did the sequencing of insulin reveal about proteins?

Answer 3

It revealed that proteins, which are the most complex molecules in the cell, have a definable substructure that is neither regular nor repeating, unlike polysaccharides.

Question 4

How can the amino acid structure of a protein be determined?

Answer 4

Using DNA and genome sequencing. The nucleotide sequence of the encoding gene determines how a polypeptide chain is formed, so by analyzing it, scientists can determine the substructure of the protein.

Question 5

Summarize the secondary structure of proteins.

Answer 5

Conformation refers to the three-dimensional arrangement of the atoms of a molecule (their spatial organization). Secondary structure describes the conformation of portions of the polypeptide chain.

Question 6

Describe the work of Linus Pauling and Robert Corey.

Answer 6

These two scientists studied the structure of simple peptides consisting of a few amino acids linked together. They found that polypeptide chains exist in preferred conformations that provide the maximum possible number of hydrogen bonds between neighboring amino acids.

Question 7

What are the differences in the two conformations of polypeptide chains? (alpha-helices and beta-sheets)

Answer 7

In an alpha helix, the backbone of the polypeptide assumes the form of a cylindrical, twisting spiral. It is stabilized by hydrogen bonds. Surfaces on opposite sides of an alpha helix often contain contrasting properties.
In a beta sheet, the segments of backbone lie side by side and assume a folded or pleated conformation. Like the alpha helix, the beta sheet is stabilized by hydrogen bonds, but the bonds are perpendicular to the axis of the chain.

Question 8

Describe the portions of a polypeptide chain not organized into alpha helices or beta sheets.

Answer 8

These portions may consist of loops, hinges, turns, or finger-like extensions. These are the most flexible portions of a polypeptide chain and the sites of biological activity. For example, antibody molecules use these sites to bind to antigens.

Question 9

Summarize the tertiary structure of proteins.

Answer 9

While the secondary structure describes the conformation of the atoms of the molecule, the tertiary structure describes the conformation of the entire polypeptide.

Question 10

What type of bonds stabilizes the secondary structure of a protein?

Answer 10

Hydrogen bonds.

Question 11

What type of bonds stabilizes the tertiary structure of a protein?

Answer 11

An array of non-covalent bonds between the diverse side chains of the protein.

Question 12

Define X-ray crystallography. What level of protein structure is it aimed at analyzing?

Answer 12

This technique is used to determine the tertiary structure of a protein. A crystal of a protein is bombarded with a thin beam of X-rays, and the radiation that is diffracted by the electrons is allowed to strike a detector, forming an image. Then, using complex mathematical analysis, a three-dimensional image of the protein can be derived.

Question 13

Define and describe disordered segments of proteins.

Answer 13

Though scientists once believed that all proteins had a fixed three-dimensional structure, there are some that have segments that can vary, meaning they cannot be studied by X-ray crystallography. These segments tend to have a predictable amino acid composition, are enriched in charged and polar residues, and are deficient in hydrophobic residues. These segments are often vital to the processes of the cell.

Question 14

Define fibrous proteins.

Answer 14

These proteins have an elongated shape and are usually found outside living cells acting as a structural material for collagens, keratin, or elastins. These proteins resist pulling or shearing forces to which they are exposed.

Question 15

Define globular proteins.

Answer 15

Globular proteins have a compact shape and are mostly found within the cell.

Question 16

Define myoglobin and describe its functions.

Answer 16

Myoglobin acts as a storage site for oxygen in the muscle tissues. The oxygen molecule is bound to an iron atom in the center of a heme (a portion of the protein not made of amino acids) group.

Question 17

Why was the study on myoglobin important (ie, what did it reveal about proteins?)

Answer 17

The study discovered all the noncovalent bonds present in a protein (hydrogen, ionic, and van der Waals). It also revealed that each protein has a unique tertiary structure that can be correlated with its amino acid sequence and its biological function.

Question 18

Define domain (in the context of protein structure).

Answer 18

Domains are spatially independent modules of proteins that fold independently of one another.

Question 19

What role do differing domains play in a protein?

Answer 19

The different domains often represent parts that function in a semi-independent manner. For example, they might bind different factors or move independently of one another. The functions of a newly identified protein can often be determined by its domains.

Question 20

Why does X-ray crystallography fall short of perfect in its details of protein structure?

Answer 20

This technique falls short because it offers an immovable snapshot in time of the protein structure. Proteins, however, are not static and inflexible. They have moving parts that are influenced by the energy of the environment. The X-ray can be considered a “ground state” of the protein, one from which the protein can still undergo dramatic changes and alternate conformations driven by the amount of energy the protein contains.

Question 21

Define conformational changes and explain how they work.

Answer 21

Conformation changes are nonrandom and predictable movements within a protein that are triggered by the binding of a specific molecule. For example, the movements of the body result from the additive effect of millions of conformational changes taking place within the contractile proteins of the muscles.

Question 22

What links together the subunits of a protein?

Answer 22

Sometimes covalent bonds form to link subunits into a larger protein, but more commonly found are noncovalent bonds, often caused by hydrophobia.

Question 23

Define quaternary structure in reference to a protein.

Answer 23

Quaternary structure means that a protein is composed of subunits.

Question 24

Define homodimer.

Answer 24

A quaternary protein composed of two identical subunits.

Question 25

Define heterodimer.

Answer 25

A quaternary protein composed of two nonidentical subunits.

Question 26

What is a multiprotein complex and why is it important/what role does it play in the cell?

Answer 26

A multiprotein complex is created when different proteins, each with a specific function, become physically associated to form a much larger multiprotein complex. This complex is important because it causes the enzymes to be closely associated. This causes them to be channeled directly to the next enzyme in the sequence without becoming diluted in the aqueous environment of the cell.

Question 27

How do proteins interact with other proteins in the cell?

Answer 27

Proteins interact with each other in highly dynamic ways, associating and dissociating depending on conditions within the cell. Those interacting tend to have complementary surfaces, projecting into the pocket of another protein. Once they are close, the interaction is stabilized by noncovalent bonds. Sometimes phosphate groups or amino acids regulate the interactions of proteins, acting as an on-off switch.

Question 28

Name some examples of protein interactions that are driven by this interaction.

Answer 28

DNA synthesis, ATP formation, and RNA processing.

Question 29

On average, how many protein partners does each individual protein interact with in a eukaryotic organism?

Answer 29

About five. This means that human proteins would engage in roughly 100,000 different protein interactions.

Question 30

What is the difference between hub and non-hub proteins?

Answer 30

Hub proteins are more likely to be critical to the cell’s survival. They are capable of binding to several other proteins at the same time.

Question 31

Define denaturation and describe the ways it can be brought about.

Answer 31

Denaturation is the unfolding or disorganization of a protein. it is brought about by detergents, organic solvents, radiation, heat, and compounds such as urea and guanidine chloride. All of these compounds interfere with the various interactions that stabilize a protein’s tertiary structure.

Question 32

Explain proteins’ ability to self-assemble.

Answer 32

When a protein is denatured, it is broken down and reorganized. However, it can return to the structure of the native molecules because the linear formation of amino acids contained all the information needed to rebuild the protein. The state the tertiary structure assumes after folding uses the least thermodynamic energy possible.

Question 33

Define molecular chaperones and explain their purpose/function.

Answer 33

Proteins can self-assemble, but sometimes they nonselectively interact with other molecules or proteins. Molecular chaperones are “helper proteins” that guide the unfolded or misfolded proteins into their proper three-dimensional conformation.

Question 34

What gives the secondary structure of proteins its stability?

Answer 34

Hydrogen bonds between backbone peptide bonds.

Question 35

Describe the structure of the alpha-helix.

Answer 35

The a-helix is stabilized by H-bonds forming between the N-H of one peptide bond and the carbonyl C=O of another. Side chains are arrayed around the outside of the helix. There is a 3.6 aa/turn and 0.54 nm rise. The a-helix structure remains constant across all proteins.

Question 36

What determines whether a protein will use a-helices or B-sheets?

Answer 36

The amino acids.

Question 37

How are B-sheets stabilized and structured?

Answer 37

They are stabilized by H-bonds between N-H and C=O of peptide bonds in adjacent strands. The side chains of the amino acids alternate above and below the plane of the sheet. 2 aa per 0.7 nm along the strand.

Question 38

What is the difference between parallel and anti-parallel strands in B-sheets?

Answer 38

When the strands are anti-parallel, each strand runs the opposite direction of the strands on either side of it. This generates a sheet shape.
When the strands are parallel, they run in the same direction. The backbone must loop over the top in order to maintain that direction. This generates a shape similar to a flattened barrel.

Question 39

How do weak bonds stabilize the three-dimensional conformation of proteins and protein domains?

Answer 39

1. Ionic bonds between charged amino acid chains.
2. H-bonds between polar amino acid side chains.
3. Hydrophobic interactions: nonpolar side-chains are buried in the interior, causing many proteins to have an oily inside.
4. Van der waals interactions.

Question 40

Describe the only covalent bond within a protein.

Answer 40

Disulfide bonds between cysteine side chains contain a reactive sulfhydryl (-SH). This bond usually only forms outside the protein when it is in distress.

Question 41

Define cofactors.

Answer 41

Cofactors are molecules with which a protein binds in order to enhance its function. Heme in hemoglobin is an example of this. Cofactors can be as critical to determining the function of a protein as the protein structure itself.

Question 42

Define heptad repeats.

Answer 42

A heptad repeat is a pattern of 7 amino acids that repeats over and over again in a protein. It is a repetitive primary structure.

Question 43

How is a coiled coil formed?

Answer 43

A coiled coil is formed when heptad repeats form an a-helix with a hydrophobic stripe winding around the helix. At the primary level, nonpolar hydrophobic amino acids take the same positions over and over. This leads to a coiled coil (which is two a-helices coiled around one another). A coiled coil in turn leads to the formation of protein dimers (a quadernary structure) This illustrates the way in primary structure translates into a change in secondary, tertiary, and quadernary structure.

Question 44

How does an active site of a protein work?

Answer 44

The active site is the “grotto” at which the side chains concentrate on a row of amino acids. The combination of shape and weak intermolecular interactions determines what ligand will fit into the enzyme active site of a protein.

Question 45

Describe the steps of SDS: Polyacrylamide Gel Electrophoresis.

Answer 45

1. Denature proteins by boiling in SDS and 2-Me.
2. Load protein samples to cross-linked polyacrylamide gel.
3. Apply strong electric field.
4. SDS-coated proteins migrate towards positive pole.
5. Stain with protein dye or antibodies.

Question 46

What characteristics of proteins are essential to SDS-Page? (and can be inferred from the technique)

Answer 46

Smaller proteins move faster.
Small proteins can readily pass through solution.
Larger proteins are retarded by cross-linked polymer.

Question 47

Define Western blot.

Answer 47

A labeling technique that uses an antibody to reveal a protein.