Chapter 3

Why are proteins not considered to be a good candidate for the first living molecule? A. Their catalytic capability is not sufficient for most biological reactions. B. Their amino acid monomers were not likely present in the prebiotic soup. C. They cannot serve as a template for replication D. They could not have polymerized from amino acid monomers under early Earth conditions.

C.

If proteins could fold only into rigid, inflexible structures, how might this affect the cell's ability to regulate their function?

A protein's activity is regulated by controlling when or where it is folded into its active form. Many proteins are in a flexible, inactive form until bound to molecules or ions. If proteins had only a single, inflexible folded conformation, this type of control could not occur.

Which of the following is true of protein folding? Once proteins fold, their structure doesn't change. Correct folding is aided by high temperatures. Misfolded proteins can still function correctly. Some proteins can fold spontaneously.

Some proteins can fold spontaneously.

The location in an enzyme molecule where substrates (reactant molecules) bind and react.

Active Site

A small organic molecule with a central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH), a hydrogen atom, and a side chain. When amino acids are linked together to form proteins, they are referred to as residues.

Amino acid

In proteins, secondary, tertiary, and quaternary levels of structure depend on primary structure. Which of the following most accurately lists elements of any protein's primary, secondary, tertiary, and quaternary structure, in that order? Amino acid sequence, hydrogen bonding between backbone groups, overall shape of a single polypeptide, and combinations of tertiary structures One polypeptide chain, two polypeptide chains, three polypeptide chains, and more than three polypeptide chains Amino acid sequence, hydrogen bonding between R-groups, overall shape of a single polypeptide, and multiple polypeptide subunits Covalent bonding, van der Waals interactions, hydrogen bonding, and hydrophobic interactions,

Amino acid sequence, hydrogen bonding between backbone groups, overall shape of a single polypeptide, and combinations of tertiary structures

A secondary structure in proteins formed when the polypeptide backbone folds into a sheetlike shape stabilized by hydrogen bonding.

B-pleated sheet

A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers into polymers. Also called a dehydration reaction.

Condensation reactions

For a macromolecule, loss of its three-dimensional structure due to breakage of chemical bonds and interactions, usually caused by exposure to heat, certain chemicals, or extreme pH conditions.

Denatured

A covalent bond between two sulfur atoms, typically in the side chains of certain amino acids. Often contributes to tertiary and quaternary levels of protein structure.

Disulfide bond

A protein catalyst used by living organisms to increase the rate of biological reactions.

Enzyme

A chemical reaction in which a molecule is split into smaller molecules by reacting with water. In Biology, most hydrolysis reactions involve the splitting of polymers into monomers.

Hydrolysis

Interact readily with water typically polar compounds containing partially or fully charged atoms

Hydrophilic

do not readily interact with water typically nonpolar molecules.

Hydrophobic

Nonpolar amino acid residues are typically found in the interior of globular proteins like chymotrypsin (Fig. 3.8d). Which chemical force is most directly responsible? Ionic bonding Covalent bonding Hydrophobic interactions Tertiary structure

Hydrophobic interactions

A chain composed of fewer than 50 amino acid residues linked together by peptide bonds. Often referred to simply as peptide.

Oligopeptide

A group of proteins, and possibly other macromolecules, that assemble to carry out a specific function.

Macromolecular Machine

Generally, any large organic molecules made up of smaller molecules (monomers) joined together into a polymer. The main biological macromolecules are proteins, nucleic acids, and polysaccharides

Macromolecules

A protein that facilitates the folding or refolding of a protein into its correct three-dimensional shape.

Molecular chaperone

Explain how molecular chaperones facilitate protein folding in many different polypeptides, each with their own specific shape.

Molecular chaperones facilitate folding by preventing unfolded proteins from clumping together so that they can fold into the shapes that are determined by the information in their primary structures.

A small molecule that can covalently bind to other similar molecules to form a larger macromolecule.

Monomer

The covalent bond formed by a condensation reaction between two amino acids.

Peptide bond

Any large molecule composed of small repeating units (monomers) bonded together. The main biological polymers are proteins, nucleic acids, and polysaccharides.

Polymer

The process by which many identical or similar small molecules (monomers) are covalently bonded to form a large molecule (polymer).

Polymerization

A chain typically consisting of 50 or more amino acids linked together by peptide bonds.

Polypeptides

The sequence of amino acid residues in a protein; also the sequence of nucleotides in a nucleic acid.

Primary Structure

An infectious particle that consists entirely of protein. Prion proteins adopt two differently folded shapes: a normally folded shape and an infectious, often disease causing shape. The infectious version can bind normally folded prion proteins and cause them to adopt the infectious shape. Also called proteinaceous infectious particles.

Prions

A macromolecule consisting of one or more polypeptide chains composed of 50 or more amino acids linked together. Each protein has unique sequence of amino acids and generally possesses a characteristic three-dimensional shape.

Protein

In proteins, the overall three-dimensional shape formed from the combination of two or more polypeptide chains; determined by the number, relative positions, and interactions of the subunits. In single-stranded nucleic acids, the hydrogen bonding between two or more distinct strands will form this level of structure through hydrophobic interactions between complementary bases.

Quaternary Structure

Part of an amino acid's core structure that varies from a single hydrogen atom to large structures containing carbon rings. R-group variability is responsible for the variability in amino acid structure and function. Also called side chains.

R-Group

In proteins, localized folding of a polypeptide chain into regular structures (i.e. alpha-helix and beta-pleated sheet) stabilized by hydrogen bonding between atoms of the peptide backbone. In nucleic acids, elements of structure (e.g. helices and hairpins) stabilized by hydrogen bonding and hydrophobic interactions between complementary bases.

Secondary Structure

A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction.

Substrate

The overall three-dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and the peptide backbone. In single-stranded nucleic acids, the three-dimensional shape is formed by hydrogen bonding and hydrophobic interactions between complementary bases.

Tertiary Structure

Based on what you know of the peptide bonds that link together amino acid residues, why would proline's side chain reduce the flexibility of the backbone?

The side chain of proline is covalently bonded to the nitrogen in the core amino group as well as to the central carbon. This would restrict the movement of the side chain relative to the core nitrogen and would further restrict the backbone when the nitrogen participated in a peptide bond with a neighboring amino acid.

Which of the following correctly orders amino acids Asp, Tyr, and Val from most hydrophobic (on the left) to most hydrophilic (on the right)? Val, Tyr, and Asp Asp, Val, and Tyr Tyr, Val, and Asp Val, Asp, and Tyr

Val, Tyr, and Asp

A secondary structure in proteins formed when the polypeptide backbone coils into a spiral shape stabilized by hydrogen bonding.

a-helix

Proteins are polymers of _____. nucleotides hydrocarbons amino acids CH2O units glycerol

amino acids

Explain how molecular chaperones facilitate protein folding in many different polypeptides, each with their own specific shape. by changing the primary structure of improperly folded proteins by binding substrates at their active site, where catalysis takes place by treating it with compounds that break hydrogen bonds and disulfide bonds by preventing unfolded proteins from clumping together

by preventing unfolded proteins from clumping together

Acceleration of the rate of a chemical reaction due to a decrease in the free energy of the transition state, called the activation energy.

catalyze

What is another name for a condensation reaction? hydrolysis water formation monomerization dehydration catabolism

dehydration

The secondary structure of a protein results from _____. hydrophobic interactions hydrogen bonds peptide bonds bonds between sulfur atoms ionic bonds

hydrogen bonds

What is the name of the process during which a bond between two monomers is broken? dehydration combustion condensation hydrolysis

hydrolysis

Defensive proteins are manufactured by the _____ system. cardiovascular immune integumentary nervous digestive

immune

Which of these does NOT contain a structural protein? muscles ovalbumin tendons spider silk ligaments

ovalbumin

What type of bond joins the monomers in a protein's primary structure? hydrophobic S - S peptide ionic hydrogen

peptide

Tertiary structure is NOT directly dependent on _____. hydrophobic interactions bonds between sulfur atoms hydrogen bonds ionic bonds peptide bonds

peptide bonds

The main reason that proteins outperform other macromolecules in terms of catalytic ability is because ____. proteins are soluble in water proteins can contain a variety of R groups peptide bonds are covalent proteins are polymers

proteins can contain a variety of R groups

What type of information is used to direct different polypeptides to fold into different shapes? Select all that apply. type of amino acids that make up the polypeptide the molecular mass of the polypeptide the temperature of denaturation of the polypeptide order of amino acids that make up the polypeptide

type of amino acids that make up the polypeptide, order of amino acids that make up the polypeptide

A weak electrical attraction between two nonpolar molecules that have been brought together through hydrophobic interactions. Often contributes to tertiary and quaternary structures in proteins.

van der waals Interactions