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noncovalent interactions are

weak but collectively strong enough to define the folded structure of a protein

in a folded polypeptide, nonpolar side chains

tend to cluster at the core of the protein and away from the aqueous surrounding, leaving the polar and charged side chains at the surface

nonpolar amino acids form the

transmembrane domains of membrane proteins

polar and charged amino acids tend to be at the

regions of proteins that are exposed to the aqueous surrounding

hydrophobic core regions of polypeptides contain

nonpolar side chains

hydrogen bonds in polypeptides

can be formed to the polar side chains on the outside of the molecule

secondary structures are

alpha helixes and beta sheets

proteisn are synthesized as


maturation of proteins involves

correct folding, proteolytic cleavage, chemical modifications, formation of quaternary structures, association with co-factors

each step in protein synthesis and maturation can be a target for

control (gene expression)

protein degradation is

under tight control

chaperones bind to

nascent polypeptides andmaintina a stable unfolded state

when synthesis is complete

the chaperons release the polypeptides and allow them to fold correctly

chaperones stabilize the

newly synthesized polypeptide


transport polypeptides

chaperons on the other side maintain

the unfolded state until translocation is complete

polypepties are allowed to fold when

they reach their final destination

what kind of bonds form between adjacent cysteine residues?


disulfide bonds can link what?

two domains of the same polypeptide or different polypeptide chains

elastin fibers

a rubberlike elastic meshwork present in the extracellular matrix of some cell types

elastin fibers allow tissues such as skin, arteries and lungs to

stretch and recoil without tearings

examples of denaturants

urea or heat

denaturants can

unfold a polypeptide by breaking non-covalent interactions between amino acids

reducing agents ex.


reducing agents are necessary to

break disulfide bonds

urea is produced in

the liver of mammals

urea helps

excrete ammonia (a toxic metabolic waste product)

urea can break

noncovalent interactions between amino acids

fibrillar collagens are

the major structural proteins of connective tissues

fribrillar collagens are built of

triple helices of procollagen polypeptides


transmissible spongiform encephalopatheies

TSEs are a family of

fatal brain diseases characterized by lesions that appear as small cavities (spongy appearance)

Ex. of TSEs

scrapie (sheep), mad-cow disease (cattle), and Creutzfeldt-Jakod disease (CJD), or kuru ("to tremble with fear") (humans)

infectious agent in TSEs

prions (proteinaceous infectious particle)

TSEs protein only hypothesis

diseases are caused by incorrectly folded versions of the prion protein

prions (PrP^sc) are variations of

normal brain protein (PrP^c)

a PrP^sc can direct a PrP^sc

to unfold and re-fold into an identical PrP^sc prion

new prions can

continue propagation of PrP^sc

several strains of prions exist

variations of the prion protein tertiary structure that are also infectious

insulin protein

pancreatic hormone that regulates blood glucose levels

insulin protein is two chains linked by

disulfide bonds (between closely places cysteines)

the insulin protein is originally synthesized as a

single polypeptide preproinsulin

insulin protein: connecting polypeptide is removed after

disulfide bonds are made, result = mature insulin

regulation of protein activity may occur

at two levels

two levels of protein regulation:

regulation of gene expression (determines the amount of protein produced by the cell by limiting transcription and or translation), control of protein function (the protein is synthesized by its activity is restricted according to the needs of the cell

the folding of a polypeptide may create a specific ligand...

binding site


promotes glycogen metabolism

inactive PKA is a

tetramer: two regulatory subunits bound to two catalytic subunites

what activates PKA by binding to the regulatory subunits, causing the release of the catalytic subunits?


the kinase activity of the released catalytic subunits (in PKA) do what?

phosphorylate multiple effector proteins

feedback inhibition: allosteric regulation:

a change in the conformation of a protein that affects its activity due to the binding of regulatory molecule

feedback inhibition: the end product of a biosynthetic pathway does what?

inhibits the enzyme that catalyzes the first step of its synthesis, causing the entire pathway to shut down

ex. of GTP regulated enzyme activity

the activation of Ran

phosphorylation is necessary for what?

the activation or inactivation of many proteins

protein kinase enzymes:

transfer a phosphate group from ATP to proteins

two types of kinases (depending on target amino acids_

serine/threonine, tyrosine


enzymes that remove phosphate groups from phosphorylated proteins


a small protein that is attached to a target protein and is a label for regulation or destruction

the central cylinder of the proteasome contains

the active protease domain

ubiquitylation and proteasomal degradation: a ubiquitin ligase enzyme attaches several

ubiquitins to the target protein

ubiquitylation and proteasomal degradation: a cap domain of the proteasome (a protease complex)

recognizes the polyubiquitylated target protein

ubiquitylation and proteasomal degradation: the ubiquitins are

removed and recycled

ubiquitylation and proteasomal degradation: the proteasome degrades the target protein by

sequential ATP-dependent steps

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