Exam 1 Chapter 4 Protein Structure and Function

Retinal (non protein portion essential for the protein's function)

Retinal is covalently attached to rhodopsin protein in rods of the eye to aid its function.

Protein phosphorylation

Reversible. Controls the activity of many types of proteins in eukaryotic cells. Involves the enzyme catalyzed transfer of the terminal P group of ATP to the OH group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. The reverse reaction, removal of the phosphate group, or dephospho rylation, is catalyzed by a protein phosphatase.

Aggregates

When proteins fold incorrectly they can form aggregates that can damage cells and even whole tissues.

Feedback Inhibition

A common type of control required to regulate when and how rapidly each reaction occurs. In this process, an enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. Thus, whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway. This is a negative regulation.

Serine proteases

A family of protein cleaving (proteolytic) enzymes that include the digestive enzymes.

Hemoglobin (non protein portion essential for its function)

A molecule of hemoglobin carries four non covalently bound heme groups, ring shaped molecules. Heme enables hemoglobin to pick up oxygen in the lungs and release it in tissue that needs it.

Renature

A protein refolds spontaneously when denaturing solvent is removed.

Helix

A regular structure that resembles a spiral staircase. Is said to be either right or left handed.

Hydrophobic interaction

A weak force which also has a central role in determining the shape of a protein. In an aqueous environment, hydrophobic molecules are forced together on the interior of the protein.

Lysozyme

An enzyme that acts as a natural antibiotic in egg white, saliva, tears, and other secretions. Lysozyme severs the polysaccharide chains that form the cell walls of of bacteria. Causes bacteria cell to burst, or lyse.

GTP binding proteins

Another way that cells regulate protein activity using phosphate addition and removal. In this case, the phosphate is part of GTP that is bound tightly to various types of GTP binding proteins. These proteins act as molecular switches. They are in their active conformation when GTP is bound, but they can hydrolyze this GTP to GDP, which releases a phosphate and flips the protein to an inactive conformation. This process is reversible.

Binding site

Any region on a nonequivalent bond is termed a binding site, where two proteins can bind to each other with weak nonequivalent bonds. A protein can contain binding sites for a variety of molecules, large and small. Each polypeptide chain is called a subunit and each subunit may contain more than one domain.

Protein domain

Any segment of a polypeptide chain that can fold independently into a compact stable structure. The different domains of a protein are often associated with different functions.

Ligand

Any substance that is bound by a protein is referred to as a ligand for that protein.

Phosphorylation

Can control protein activity by causing a conformational change. Requires attaching a phosphate group covalently to one or more of the protein's amino acid side chains. This addition can cause a major conformational change in a protein. This conformational change can in turn affect the binding of ligands elsewhere not he protein surface, thereby altering the protein's activity.

Covalent cross linkages

Help to keep the shape of proteins stabilized when proteins go outside of the cell.

Peptide Bonds

Covalent bonds that hold together amino acids.

Amyloid Fibers

Insoluble protein aggregates that include those associated with neurodegenerative disorders and pride diseases. Formation of amyloid is permitted by beta sheets. Associated with disease, but some organisms use them to perform novel tasks.

Protein families

Each family member has an amino acid sequence and a 3D conformation that closely resemble those of the other family members.

Conformation

Each type of protein has a particular three d structure, determined by the other of the amino acids in the chain. The final conformation is determined by energetic considerations so that G is minimized, thus the folding process is energetically favorable, releasing heating and increasing disorder.

Elastin

Elastin molecules are formed from relatively loose and unstructured polypeptide chains that are covalently cross linked into a rubberlike elastic meshwork.

Positive Regulation

Enzyme's activity is stimulated by a regulatory molecule rather than being suppressed. This occurs when a product in one branch o the metabolic maze stimulates the activity of an enzyme in another pathway.

Substrates

Enzymes bind to one or more ligands called substrates.

Enzymes encourage catalysis

Enzymes use mechanisms to lower the activation energies and speed up the reactions they catalyze. (A) In reactions involving two or more substrates, the active side also acts like at template or mold that brings the reactants together in the proper orientation for the reaction to occur. (B) Binding of substrate to enzyme rearranges electrons n the substrate, creating partial negative and positive charges that favor a reaction. (C) Enzyme strains the bound substrate molecule, forcing it toward a transitions state to favor a reaction.

Fibrous proteins

Especially abundant outside the cell, where they form the gel like extracellular matrix.

A-helix

Generated when a single polypeptide chain turns around itself to form as 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 gives rise to a regular right handed helix. Especially abundant in proteins that are embedded in cell membranes. They cross the lipid bilayer and usually form an a helix that is composed of amino acids with non polar side chains. The polypeptide backbone is H bonded to itself in the a helix and is shielded from the hydrophobic lipid environment of the membrane by its protruding non polar side chains.

Fibrous proteins vs. Globular proteins

Globular proteins have polypeptide chain folds up into compact shape like a ball with an irregular surface. Fibrous proteins have roles in the cell that require them to span a large distance. These proteins generally have a relatively simple elongated 3D structure and are commonly referred to as fibrous proteins.

Allosteric Enzymes

Have two or more binding sites that influence one another. The regulatory molecule often has a shape that is totally different from the shape of the enzyme's preferred substrate. Many enzymes must have at least two different binding sites on their surface: the active site that recognizes the substrates and one or more sites that recognize regulatory molecules. These sites must somehow communicate to allow the catalytic events at the active site to be influenced by the ending of the regulatory molecule at its separate its. This triggers a conformational change in the protein.

Protein machines

Highly coordinated, linked set of many proteins.

Allosteric

Many if not most protein molecules are allosteric, they can adopt two or more slightly different conformations another activity can be regulated by a shift from one to another.

Prions

Misfolded proteins. Are the cause of certain neurodegenerative disorders. Prions can convert the properly folded version of the protein in an infected brain into the abnormal conformation. Prions are considered infectious because they can also spread from an affected individual to a normal individual via contaminated food, blood, or surgical instruments.

Disulfide Bond

Most common covalent cross link in proteins is a sulfur-sulfur bond. They are formed before a protein is secreted by an enzyme in the ER. These bonds do not change a protein's conformation, but act as a "atomic staple" to reinforce the protein's most favored confirmation.

Conformational changes purpose

Plays a central part in enzyme regulation and cell signaling. But also enables certain specialized proteins to drive directed movements of cells and their components. These motor proteins generate the forces responsible for muscle contraction and most other cell moments. They also power the intracellular movements of organelles and macromolecules.

Negative Regulation

Prevents an enzyme from acting.

Chaperone proteins

Protein folding in a living cell is generally assisted by chaperone proteins, which bind to partly folded chains and help them to fold along the most energetically favorable pathway.

Denature

Protein unfolds y treatment with solvents that disrupt the non covalent interactions holding the folded chain together.

Polypeptide Backbone

Repeated sequence of the core atoms (-N-C-C-) found in every amino acid. It is hydrophilic.

Isolation chambers

Single polypeptide chains can fold without the risk of forming aggregates in the crowded conditions of the cytoplasm.

Coiled-coil

Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This forms when the alpha helices have most of their non polar side chains on one side, so that they can twist around each other with these side chains facing inward.

Antigen

Target molecule that an antibody recognizes with remarkable specificity, and because there are potentially billions of different antigens that a person might encounter, we have to be able to produce billions of different antibodies. Antibodies are Y shaped, with two identical antigen binding sites, each of which is complementary to a small portion of the surface of the antigen molecule.

Specificity

The binding of a protein to other biological molecules always shows great specificity: each protein molecule can bind to just one or a few molecules out of the many thousands of different molecules it encounters.

N terminus

The end carrying the amino group (aka amino terminus).

C-terminus

The end carrying the carboxyl group (aka carboxyl terminus.

Proteins

The main building blocks from which cells are assembled, and they constitute most of the cell's dry mass.

Collagen

The most abundant fibrous extracellular protein in animal tissue. Consists of three long polypeptide chains, forming a triple helical structure with glycine at its core.

Binding site

The region of a protein that associates with a ligand

Bonds within proteins

The shape of a folded chain is constrained by many sets of weak noncovalent bonds (hydrogen bonds, electrostatic attractions, van der Waals) that form within proteins. These bonds involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains. It takes many noncovalent bonds to hold two regions of a polypeptide chain tightly.

Side chains

The side chains (R group) of each amino acid give it its unique properties; some are polar and hydrophilic and some are non polar and hydrophobic. Some are positively or negatively charged.

Motor proteins

To make the conformational changes unidirectional and force the entire cycle of movement to proceed in one direction it is enough to make any one of the steps irreversible. By coupling one of the conformational changes to hydrolysis of an ATP molecule bound to the protein.

A-helix, B pleated sheets

Two common folding patterns present in many different proteins. They result from H bonds that form between the N-H and C=O groups in the backbone.

Dimer

Two identical folded polypeptide chains form a symmetrical complex of two protein subunits.

Antibodies

immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism. Each antibody binds to a particular target molecule extremely tightly, either inactivating the target directly or marking it for destruction.

B pleated sheets

made when hydrogen bonds form between segments of a polypeptide chains hat lie side by side. When the neighboring segments run in the same orientation the structure is a parallel B sheet, when they run in opposite directions, it is antiparallel. Both types produce a very rigid, pleated structure, and they form the core of many proteins.