Chapter 3 - Protein Structure and Function

polypeptide chain

A(n) ________ is synthesized by a complex process called translation.

catalytic core of protein

The ________ kinase A exists in an "open "and "closed "conformation.

DNA

________ encoding a protein can be subjected to mutagenesis so that segments of the proteins backbone are removed or changed.

Proteins

________ and peptides have been considered natural products of a cell.

Domains

________ are sometimes defined in functional terms on the basis of observations that an activity of a protein is localized to a small region along its length.

Long chains

________ are referred to as polypeptides.

Chemicals

________ such as urea or guanidine hydrochloride at concentrations of 6- 8 M can disrupt the weak noncovalent interactions that stabilize the native conformation of a protein.

carboxypeptidases

To protect a cell from degrading itself, endoproteases and ________ are synthesized and secreted as inactive forms (zymogens): pepsin by chief cells in the lining of the stomach; the others by pancreatic cells Alternatively Folded Proteins Are Implicated in Slowly Developing Diseases.

capsid

Include the ________ that encases the viral genome and bundles of cytoskeletal filaments that support and give shape to the plasma membrane.

maximal velocity

The catalytic action of an enzyme on a given substrate can be described by two parameters: Vmax, the ________ of the reaction at saturating substrate concentrations, and Km (the Michaelis constant), a measure of the affinity of an enzyme for its substrate.

Cells

________ have systems that reduce the chances for misfolded proteins to form.

immune system

The ________ also makes use of the ubiquitin- mediated pathway in the response to altered self- cells, particularly virus- infected cells.

DNA site

The ________ determines where transcription of a specific gene begins Members of Protein Families Have a Common Evolutionary Ancestor.

Thermal energy

________ from heat, extremes of pH that alter the charges on amino acid side chains.

size of a protein

The ________ (polypeptide) is represented by daltons.

major extracellular pathway

The ________ for protein degradation is the system of digestive proteases that breaks down ingested proteins into peptides and amino acids in the intestinal tract.

Protein folding

________ occurs in vitro, only a minority of unfolded molecules undergo complete folding into the native confirmation within a few minutes.

different amino acids

There are 20 ________ construed by polymerization into linear chains.

epidermal growth factor

The ________ (EGF) domain is one example of a module that is present in several proteins.

Eukaryotic cells

________ have several intracellular proteolytic pathways for degrading misfolded or denatured proteins.

Adjacent B strands

________ can be oriented in the same (parallel) or opposite (antiparallel) directions with respect to each other.

Molecular chaperones

________ consist of Hsp70 and its homologs: Hsp70 in the cytosol and mitochondrial matrix, BiP in the endoplasmic reticulum, and DnaK in bacteria.

torque

The ________ generated by the stator rotates an inner ring of proteins and the attached flagellum.

Any polypeptide chain

________ containing n residues could, in principle, fold into 8n conformations.

B

Interactions between the subunit and the ________ subunits directs the synthesis of ATP.

EGF

________ is a small, soluble peptide hormone that binds to cells in the embryo and in the skin and connective tissue in adults, causing them to divide.

Proteolytic processing

________, protein self- splicing is an autocatalytic process, which proceeds by itself without the participation of enzymes Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes.

Tertiary Structure

________ refers to the overall conformation of a polypeptide chain- that is, the three- dimensional arrangement of all its amino acid residues.

ability of proteins

The ________ to distinguish different molecules is perhaps most highly developed in the blood proteins called antibodies.

three-dimensional structure

A protein is only able to function correctly when it is in its ________ or conformation.

Protein misfolding

________ is suppressed by two distinct mechanisms.

Phosphoryl Transfer

________ by Protein Kinases; after substrates have bound and the catalytic core of protein kinase A has assumed the closed conformation, the phosphorylation of a serine or threonine residue on the target peptide can take place Vmax and Km Characterize and Enzymatic Reaction.

major intracellular pathway

The ________ is degradation by enzymes within lysosomes, membrane- limited organelles whose acidic interior is filled with hydrolytic enzymes.

secondary structure

A single polypeptide may exhibit multiple types of ________ depending on its sequence.

Functional Domains

The overall helical structure is amphipathic Structural and ________ are Modules of Tertiary Structure.

Large proteins

________, domains can be recognized in structures determined by x- ray crystallography or in images captured by electron microscopy.

EGF modules

________ are also present in other proteins and are liberated by proteolysis.

Specificity

________ refers to the ability of a protein to bind one molecule in preference to other molecules.

nanoscale of cells

At the ________ and molecules, movement is affected by many different forces from those in the macroscopic world.

DNA

________ and RNA polymerases also are linear motor proteins because they translocate along with ________ during replication and transcription.

Proteins

________ (working molecules of a cell) carry out a program of activities encoded by genes.

Molecular chaperones

________ are thought to bind all nascent polypeptide chains as they are being synthesized on ribosomes.

Polypeptide Chain

Turns are composed of three or four residues, turns are located on the surface of a protein, forming sharp bends that redirect the polypeptide backbone back toward the interior Overall Folding of a(n) ________ Yields Its Tertiary Structure.

Tertiary structure

________ is primarily stabilized by hydrophobic interactions between the nonpolar side chains, hydrogen bonds between polar side chains, and peptide bonds.

Proteins

________ that have a common ancestor are referred to as homologs.