SmartWork5 Chapter 2

Amino acids with side chains that contain -COOH groups, like those shown, would be ___________ in the aqueous environment of a cell.

Acidic

Which type of noncovalent interaction can involve either the polypeptide backbone or amino acid side chains?

Hydrogen bonds- The backbone of the polypeptide consists of uncharged polar covalent bonds. Because the bonds in the backbone are neither charger nor hydrophobic (i.e. nonpolar), hydrophobic forces and electrostatic interactions do not involve the backbone. Hydrogen bonds, however, are formed between atoms in the polar covalent bonds found in both amino acid side chains and in the carboxyl group and amino groups of the polypeptide backbone.

Noncovalent bonds in macromolecules are primarily important for

forming the three-dimensional folded conformation and interactions with other macromolecules

Hydrogen bonds between which types of atoms have been found to stabilize a polypeptide's folded shape?

side-chain atoms, backbone atoms

Hydrolysis reaction

uses water to split the bond that joins two subunits of a polymer

Both alpha helix and beta sheet

Can be formed by many sequences, formed by hydrogen-bonding between backbone atoms

How many different polypeptide chains are possible from a sequence that is 10 amino acids long?

20^10

What is a protein family?

A protein family is a set of proteins that have similar primary structures (amino acid sequences) and thus have related three-dimensional structures. If the structure of one member of a protein family is determined, it can be used to make predictions about the structure of other members of the protein family.

Generally speaking, what determines the biological activity of a protein?

Amino acid sequence

What provides the information necessary to specify the three-dimensional shape of a protein?

Amino acid sequence- The ordering of amino acids is what allows some amino acids to interact noncovalently with other amino acids when the protein begins to fold. Each type of protein has a particular three-dimensional structure, which is determined by the order of amino acids in its polypeptide chain. The final folded structure, or conformation, adopted by any polypeptide chain is determined by energetic considerations: a protein generally folds into the shape in which its free energy (G) is minimized. The folding process is thus energetically favorable, as it releases heat and increases the disorder of the universe. Peptide bonds are important in keeping amino acids bonded together and the protein intact, but the peptide bond does not provide the information necessary to specify the protein's three-dimensional shape. Though interactions with other polypeptides and chaperones can be important for protein function, these interactions also do not specifically provide the information for a protein's three-dimensional shape. Urea destabilizes protein structure. A protein can be unfolded, or denatured, by treatment with solvents like urea that disrupt the noncovalent interactions holding the folded chain together.

Which chemical groups are found on all amino acids?

Amino group and carboxyl group

In a globular protein, where will the amino acid that occurs at the N-terminus generally be found?

At the protein's surface- Regardless of its identity, the N-terminal amino acid will have a positive charge on its amino group. Thus, this amino acid will tend to be exposed at the protein's surface. The N-terminus describes the amino acid positioned at the first location of the protein. Thus, it would be impossible for this amino acid to be in the middle of a β sheet or an α helix.

In a globular protein, where would the amino acid tryptophan most likely be found?

Buried in the protein's interior- Nonpolar, hydrophobic amino acids, such as tryptophan, tend to cluster in the interior of the folded protein to avoid contact with the aqueous cytosol. Hydrophobic forces help proteins fold into compact conformations. In a folded protein, polar amino acid side chains tend to be displayed on the surface, where they can interact with water; nonpolar amino acid side chains are buried inside the protein to form a tightly packed hydrophobic core of atoms that are hidden from water.

Beta sheet

Consists of antiparallel/parallel sheets, side chains alternating above/below the structure

Disulfide bonds stabilize protein shape outside the cell by

Covalent bonds bw cysteines

Alpha helix

Cylindical structure, 1 full turn every 3.6 amino acids

A stretch of amino acids in a polypeptide chain that is capable of independently folding into a defined structure is called a

Domain- A domain is a sequence of amino acids in a polypeptide chain that adopts a defined folding pattern based on the interactions of the side chains, as well as contributions from the polypeptide backbone molecules. This is distinct from a subunit, which is a term used for a single, complete polypeptide chain that can interact with other subunits to form a larger complex.

In an α helix, hydrogen bonds form between which of the following?

Every fourth amino acid An α helix is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder. A hydrogen bond is made between every fourth amino acid, linking the C=O of one peptide bond to the N-H of another. This pattern gives rise to a regular right-handed helix with a complete turn every 3.6 amino acids.

A binding site on the surface of a protein interacts specifically with another protein through

Many weak noncovalent interactions

A protein domain is another phrase describing what type of structure of a protein?

None of these- The protein domain is an organizational unit that is distinct from the primary, secondary, tertiary, and quaternary levels of organization. Studies of the conformation, function, and evolution of proteins have also revealed the importance of a level of organization distinct from these four levels of protein structure.

In a globular protein, where will the amino acid that occurs at the C-terminus generally be found?

Protein's surface- Regardless of its identity, the C-terminal amino acid will have a negative charge on its carboxyl group. Thus, this amino acid will tend to be exposed at the protein's surface.

Best model for visualizing secondary structure of a protein

Ribbon

The majority of proteins belong to "protein families" that share which attribute?

Similar sequence patterns and therefore structural domains

Best model for visualizing the surface of a protein

Space-filling

For which reason are α helices and β sheets common folding patterns in polypeptides?

The amino acid side chains are not directly involved in their formation. Both of these folding patterns result from hydrogen bonds that form between N-H groups and C=O groups along the polypeptide backbone. The hydrogen of the amino hydrogen is partially positively charged and the oxygen of the carbonyl is partially negatively charged. Because amino acid side chains are not directly involved in forming these hydrogen bonds, α helices and β sheets can be formed by many different amino acid sequences.

In their search for the molecular basis of cystic fibrosis, researchers identified a chlorine ion channel in which a variety of inherited mutations can precipitate the disease. These studies also showed that people who do not have cystic fibrosis can harbor amino acid substitutions in this protein—even in a critical stretch of amino acids that forms a membrane-spanning α helix. How is it possible for such amino acid substitutions to exist within the population without disrupting the α helical structure of that region of the channel?

The formation of an α helix is governed by hydrogen bonding between atoms that are not in the side chains (R groups) of the amino acids in this region. The most common stabilizing force responsible for the helical arrangement of amino acids in an α helix conformation is hydrogen bonding between the backbone atoms in that region. Since this hydrogen bonding does not involve atoms from the amino acid side chains, a variety of different amino acids can be compatible with the protein's normal function.

In a cytosolic folded protein, what orientation and/or interaction do the hydrophobic amino acids tend to have?

Tucked away inside the protein and interacting with other nonpolar amino acids

In a β sheet, hydrogen bonds form between which of the following?

adjacent spans- The amino acid side chains in each strand project alternately above and below the plane of the sheet. Side chains are not involved in the hydrogen bonds that stabilize a β sheet. Rather, the C=O of one peptide bond noncovalently interacts with the N-H of another.

What is the definition of a protein-binding site?

any region on a protein's surface that interacts with another molecule through noncovalent bonding

For a given protein, hydrogen bonds can form between...

atoms in the polypeptide backbone, between atoms of two peptide bonds, between atoms in two side chains, and also between a side chain and water.

What are protein families?

evolutionarily related proteins that are similar in amino acid sequence and three-dimensional conformation

In a globular protein, where would the amino acid arginine most likely be found?

exposed at the protein's surface- Polar, charged amino acids, such as arginine, tend to be found near a protein's surface, where they can form hydrogen bonds with water and other polar molecules. Nonpolar amino acid side chains are buried inside the protein to form a tightly packed hydrophobic core of atoms that are hidden from water.

Condensation reaction

joins two monomers together, releasing water

Covalent bonds in macromolecules are primarily important for

linking together monomers

A coiled-coil can be formed from α helices that have which of the following attributes?

many nonpolar, hydrophobic side chains along one side of the helix This particularly stable structure forms when the α helices have most of their nonpolar (hydrophobic) side chains along one side, so they can twist around each other with their hydrophobic side chains facing inward, minimizing contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins, including the α-keratin found in hair and the outer layer of the skin, as well as myosin, the motor protein responsible for muscle contraction. The helices wrap around each other to minimize exposure of hydrophobic amino acid side chains to an aqueous environment.

Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?

methionine to arginine- Arginine and methionine have different chemical properties. Methionine has a nonpolar side chain that would likely be buried in the protein's interior; arginine, on the other hand, is a positively charged amino acid that would likely be facing the protein's exterior. Replacing methionine with arginine would likely disrupt a protein's structure. Alanine and glycine, leucine and isoleucine, asparagine and threonine, and tryptophan and phenylalanine all have similar chemical properties compared to each other, so these substitutions would probably not greatly perturb the structure of a protein.

What are the two types of beta sheets?

parallel and antiparallel- In a β sheet, several segments (strands) of an individual polypeptide chain are held together by hydrogen bonding between peptide bonds in adjacent strands. The amino acid side chains in each strand project alternately above and below the plane of the sheet.