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.

Long chains

________ are referred to as polypeptides.

DNA

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

Any polypeptide chain

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

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.

cellular protein

The activity of a(n) ________ depends on the amount present, which reflects the balance between its rate of synthesis and the rate of degradation in the cell.

Proteins

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

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.

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.

EF hand

Motif, also called** the ________**, has been found in more than 100 calcium- binding proteins.

asparagine

The side chains of ________, serine, and threonine are sites for glycosylation, the attachment of linear and branched carbohydrate chains.

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.

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.

inactive forms

To protect a cell from degrading itself, endoproteases and carboxypeptidases are synthesized and secreted as ________ (zymogens): pepsin by chief cells in the lining of the stomach; the others by** pancreatic cells**

same cellular compartment

Enzymes taking part in a common** metabolic process** are generally located in the ________.

Eukaryotic cells

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

different amino acids

There are 20 ________ construed by** polymerization** into linear chains.

cellular processes

The** catalytic activity** of some enzymes is critical to ________ other than the synthesis or degradation of molecules.

epidermal growth factor

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

Adjacent B strands

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

torque

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

Molecular chaperones

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

B

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

hydrophobic

The ________ or hydrophilic quality of the helix is determined entirely by the side chains.

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.

Specificity

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

ability of proteins

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

nanoscale of cells

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

Tertiary Structure

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

program of activities

Proteins** (working molecules of a cell) carry out a(n) ________ encoded by genes.

Proteolytic processing

________, protein self- splicing is an autocatalytic process, which proceeds by itself without the participation of enzymes.

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.

major intracellular pathway

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

multiple types of secondary structure

A single polypeptide may exhibit ________ depending on its sequence.

Viral proteins

________ within the cytosol of infected cells are ubiquitinated and then degraded in proteasomes specially designed for this role.

EGF modules

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

Large proteins

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

DNA

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

Molecular chaperones

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

Tertiary structure

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