Bio 1107: Chapter 3- Protein Structure and Function

Five types of interactions involving R-groups: Van Der Waals Interactions

Once hydrophobic side chains are close to one another, their association is further stabilized by electrical attractions known as van der waals interactions. If nonpolar molecules get extremely close to each other, the minute partial charge on one molecule induces an opposite partial charge in the nearby molecule induces an opposite partial charge in the nearby molecule and causes an attraction. Although the interaction is very weak relative to covalent bonds, a large number of van der waals interactions can significantly increase the stability of the structure.

Why are peptide bonds unstable?

Peptide bonds are usually unstable because a pair of valence electrons on the nitrogen is partially shared in the C-N bond.

Define Polypeptides

Polymers that contain 50 or more amino acids are called polypeptides.

Primary function is fundamental to...

Primary function is also fundamental to the higher levels of protein structure: secondary, tertiary, and quarentary.

Define Dimers

Proteins With two polypeptide subunits are called dimers.

Define macromolecules

Proteins are macromolecules-- large molecules made up of smaller molecular subunits joined together.

How can proteins form the tertiary structure?

Proteins can spontaneously fold into the shape of the tertiary structure. Because an unfolded protein has many more ways to move about, it has much higher entropy than the older version Folding is crucial to the function of a completed protein.

What do several of the side chains contain and what are their purpose?

Several side chains contain carbonyl, sulfhydryl, hydroxyl or amino functional groups. Under the right conditions, these functional groups can participate in chemical reactions. Ex. Amino acids with sulfhydryl group in their side chain can form disulfide bonds that help link different parts of large proteins. Some amino acids also contain side chains that are devoid of functional groups-- consisting solely of carbon and hydrogen atoms. These groups rarely participate in chemical reactions. As a result, these merely influence amino acids depending on their size and shape rather than reactivity.

How is protein activity regulated?

Since the function of a protein is dependent on its shape, controlling when or where it is folded into its active shape will regulate the proteins activity. Many of these proteins are disordered and do not complete their folding until after binding to ions or other molecules that are present only during a signaling event. This induces the protein to fold into an ordered, active conformation

The order and type of amino acids in the primary structure is responsible for?

The order and type of amino acids in the primary structure is responsible for the secondary structure, which then fold up to form tertiary structure

Define Polymerization

The process of linking monomers together is called polymerization. The polymerization reaction organizes multiple simpler monomers into a single more complex and ordered structure. Polymerization decreases the disorder, or entropy, of the molecules involved.

Define hydrolysis

The reverse reactions, called hydrolysis, breaks polymers apart by adding a water molecule. The water molecule reacts with the bond linking the monomers, separating one monomer from the polymer chain. Hydrolysis both increases entropy and is favorable energetically.

Define Protein

The term protein is used to describe any chain of amino acid residues. In formal use, proteins refers to the complete, often functional form of the molecule.

What is responsible for the structure of a protein?

The variability in size and shape, as as in the chemical properties of their amino acid residues, is responsible for the diverse function that proteins perform in cells.

In the secondary structure, functional groups...

They are distinctively shaped sections that are stabilized largely by hydrogen bonding that occur between the oxygen on the C--O group of one amino acid residue and the hydrogen on the N--H groups of another.

Quaternary structures may include...

This structure may include polypeptides that are distinct in primary, secondary, and tertiary structures.

True or false: A proteins primary structure is fundamental to its function

True

True or false: An input of energy is required for monomer to link together and form macromolecules as an offset of the reduction in entropy and to allow the reaction to become spontaneous.

True

Is folding spontaneous?

Unlike polymerization, however, folding does tend to be spontaneous because the chemical bonds and interactions that occur release enough energy to overcome this decrease in entropy and will also increase entropy in the surrounding environment. As a result, the folded molecule has less PE and is thus more stable than the unfolded molecule.

Define Polymer

When a large number of monomers are bonded together, the resulting structure is called a polymer.

Define residues

When amino acids are linked by peptide bonds into a chain, they are referred to as residues to distinguish them from free amino acid monomers.

How do we know primary structures hold all the information?

When chemical denaturing agents were remove, ribonuclease refolding spontaneously and began to function normally again. This proved that the primary sequences contains all the info for folding and that folding is essential for protein function.

Define oligopeptide

When fewer than 50 amino acids are linked together in this way, the resulting polymer is called an oligopeptide, or peptide.

Which type of secondary structure forms depends on...

Which secondary structures form depend on the molecules primary structure, specifically the geometry and properties of amino acids in the sequence.

Define Molecular chaperones

Work has shown that cells contain special proteins called molecular chaperones that can facilitate protein folding. These belong to a family of molecules called the heat-shock proteins, because they are produced in large quantities after cells experience the denaturing effects of high temperatures. Chaperones recognize unfolded proteins by binding to hydrophobic patches that are not normally exposed when the proteins are folded properly. This interaction prevent the unfolded proteins from clumping together, allowing them to fold into the shape specific by their primary sequence. In this way, chaperones help fold new proteins, and in some cases denatured proteins, before these unfolded aggregates can form.

Quaternary structure (if present) is based on?

interactions between the tertiary structures of the polypeptide subunits.

Define Monomers

A molecular subunit used to build a macromolecule is called a monomer.

Describe the tertiary structures

A proteins distinctive three-dimensional shape results from interactions between residues that are brought together as the chain bends and folds in space. The residues that interact with one another are often far apart in the linear sequence. Tertiary structures form using a variety of bonds and interactions between R-groups or between R-groups and the backbone. (secondary structures involve only hydrogen bonds between backbone components)

Are proteins flexible?

Although each protein has a characteristic folded shape, most proteins maintain a flexible and dynamic shape when they are not actively performing that function. Many proteins that have been analyzed have disordered regions lacking any apparent structure when they are in an inactive estate. Each of these proteins will exist in this disorder until they are prompted to adopt a single folded and functional form which is accomplished when the proteins interact with particular ions or molecules or when they are chemically modified.

Amino Acid R-groups are either...

Amino acid R-groups are either charged, which includes acidic and basic; uncharged polar; and nonpolar.

Define Amino Acids

Amino acids are the building blocks of proteins, and proteins are vital, as they are tremendously versatile components of today's cells. Proteins are composed of 20 different building blocks, known as the amino acids.

Amino acids are the....

Amino acids are the monomers that polymerize to form proteins.

Amino acids polymerize when...

Amino acids polymerize when a bond forms between the carboxyl group of one amino acid and the amino acid group of another.

Describe the term denatured

Anfinsen found that ribonuclease could be unfolded, or denatured, by treating it with compounds that break hydrogen bonds and disulfide bonds. The denatured ribonuclease was unable to function normally--- it could not longer break apart nucleic acids.

Define Primary Structure

Biochemists refer to the unique sequence of amino acids in a proteins as its primary structure.

Are polar R-groups hydrophilic or hydrophobic?

Both polar and electrically charged R Groups interact readily with water and are hydrophilic. Hydrophilic R- Groups dissolve easily in water.

Proteins are crucial to most tasks required for cells to exist:

Catalysis: Many proteins are specialized to catalyse, or speed up, chemical reactions. A protein that functions as this is an enzyme. Defense: Proteins called antibodies attack and destroy viruses and bacteria that cause disease. Movement: Motor proteins and contractile proteins are responsible for moving the cell itself or for moving large molecules and other types of cargo inside the cell. Signaling: Proteins are involved in carrying and receiving signals from cell to cell inside the body. Structure: Structural proteins make up body components such as fingernails and hair and form the internal "skeleton" of individual cells. Transport: Proteins allow particular molecules to enter and exit cells or carry them throughout the body.

When is hydrogen bonding possible between sections of the same backbone?

Hydrogen bonding between sections of the same backbone is only possible when a polypeptide bends in a way that puts C--O and N--H groups close together. In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form one o the two possible structures: 1. An alpha helix, in which the polypeptides bone is coiled 2. A beta-pleated sheet, in which segments of a peptide chain bend 180 degrees and then fold in the same place. Alpha helices are ribbon shaped and Beta pleated sheets with arrows in a plane.

Five types of interactions involving R-groups: hydrogen Bonding

Hydrogen bonds form between polar side chains and opposite partial charges either in the peptide backbone or other R-groups.

Does the R-group have a negative charge?

If so, it is acidic and will lose a proton, like aspartate.

Does the R-group have a positive charge?

If so, it is basic and will pick up a proton, like lysine.

If the R-group is uncharged, does it have an oxygen atom?

If so, then the highly electronegative oxygen will form a polar covalent bond in the R-group, thus making it uncharged polar like serine.

Five types of interactions involving R-groups: Hydrophobic Interactions

In an aqueous solution, water molecules interact with the hydrophilic polar side chains of a polypeptide, forcing the hydrophobic nonpolar side chains to coalesce into globular masses. When these nonpolar R Groups come together, the surrounding water molecules form more hydrogen bonds with each other and the polar residues on the surface of the protein, increasing the stability of their own interactions and the disorder of the sequoias solution.

In water, amino acids do what?

In water, amino acids Ionize. The concentration of protons at this ph causes the amino acid group to act as a base and it attracts a protons to form NH3+.

Five types of interactions involving R-groups: Ionic Bonding

Ionic bonds may form between groups that have full and opposing charges.

Define Condensation Reactions

Monomers polymerize through condensation reactions, also known as dehydration reactions.

Are nonpolar R groups hydrophobic or hydrophilic?

Nonpolar R Groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These groups are hydrophobic, meaning that they do not interact with water. INstead, they tend to coalesce in aqueous solution.

Why are enzymes good catalysts?

Catalyzed reactions involve one or more reactants, called substrates. Enzymes and substrates in a precise orientation so they can react. Lock And keys: Enzymes are the lock and substrates are the key that fit into the lock and then react. The location where substrates bind and react became known as the enzyme's active site. The active site is where catalysis actually occurs

Define Macromolecular Machines

Cells contain macromolecular machines: groups of multiple proteins that assemble to carry out a particular function.

Define Prisons

Certain normal proteins can be induced to dlf into infectious, disease causing agents These proteins are called prisons, or proteinaceous infectious particles. These are alternatively folded forms of normal proteins that are present in healthy individuals. They do not differ in their primary structure, but their shapes are dramatically different. These proteins propagate by binding to normal pistons and including conformational changes that cause them to adopt the alternate, infectious shape.

Five types of interactions involving R-groups: Covalent Bonding

Covalent bonds can form between the side chains of two cysteines through a reactions between the sulfhydryl groups. These disulfide bonds are known as bridges becasse they create strong links between distinct regions of the same polypeptide or two separate polypeptides.

Are secondary structures stable?

The large number of hydrogen bonds in these structures make them highly stable. As a result, they increase the stability of the molecule as a whole and help define its shape.

In all 20 amino acids, a central carbon atom bonds covalently to the four different atoms or groups of atoms...

H - a hydrogen atom NH2 - An amino functional group COOH- A carboxyl functional group A distinctive "R-group" (often referred to as a side chain)

Proteins that provide structural support for cells...

Proteins that provide structural support for cells or tissues are often long and cable-like fibers. The TATA box protein has a groove where a molecule of DNA fits; proin has a hole that forms a pore. THe groove of the TATA box interacts with specific region of a DNA molecule to regulate gene activity while proin fits in cell membranes and allows certain hydrophilic molecules to pass through.

Ways polymers could have become about in early earth

Researchers have generated stable polymers by mixing free amino acids with a source of chemical energy and tiny mineral articles. Monomers are protected from hydrolysis if they cling to a mineral surface. In conditions that stimulate the hot, metal rich environments of undersea volcanoes, researchers have observed the amino acids being formed and even polymerized. In lab experiments, amino acids have joined into polymers in cooler water if an energy rich carbon and sulfur containing gas (one commonly ejected from undersea volcanoes) is present.

How is the secondary structure created?

Secondary structure is created in part by interactions between functional groups in the peptide-bonded backbone.

Describe the Quaternary Structure

Some proteins contain multiple polypeptides that interact to form a single functional structure. The combination of polypeptides, referred to as subunits, gives some proteins quaternary structure. The individual polypeptides are held together by the same types of bonds in the tertiary level.

Structures give rise to...

Structures give rise to functions

Define peptide bond

The C-N covalent bond that results from this condensation reaction is called a peptide bond. When a water molecule is removed in the condensation reaction, the carboxyl group is converted to a carbonyl functional group and the amino group becomes simply N-H in the resulting polymer

Describe the peptide bond backbone

The Peptide-bonded backbone: R-group orientation: The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water. Directionality: There is an amino group (-NH3+) on one end of the backbone and a carboxyl group (-COO-) on the other. The end of the residue sequence that has the free amino group is called the N-terminus or amino terminus and the end with the free carboxyl group is called the C-terminus or carboxy-terminus. Always write amino acids from the N-terminus to the C-terminus. N-terminus is that start where proteins are synthesized in cells. Flexibility: ALthough the peptide bond itself cannot rotate because of its double bond nature, the single bonds on either side of the peptide bond can rotate.

Define R-group

The R-group, or side chain, represents the part of the amino acid core structure that makes each of the 20 different amino acids unique. The properties of amino acids vary because their R-groups vary.

Why is the order and type of residues in the primary structure of a protein important?

The R-groups present on each amino acid affect its chemical reactivity and solubility. Is therefore reasonable to predict that the order of the R-groups present in a polypeptide will affect that molecule's properties and function. Even a single change in the sequence of amino acids can cause striking changes in the way the protein as a whole behaves.

How does the carboxyl group act

The carboxyl group acts as an acid. The two highly electronegative oxygen atoms in this group pull the electron away from its hydrogen atom, which means that it is relatively easy for this group to lose a proton to form COO-

Why are the charges of the amino acids and carboxyl groups important?

The charges of these groups are important for two reason: They help amino acids stay in solution where they can interact with one another and with other solutes They affect the amino acid's chemical reactivity.

Three important messages about the above!

The combination of primary, secondary, tertiary and quaternary levels of structure is responsible for the fantastic diversity of sizes and shapes observed in proteins. Protein folding is directed by the sequence of amino acids present in the primary structure Most elements of protein structure are the result of folding polypeptide chains