2. (a) The linear sequence of
amino acids (10 structure)
folds into helices or sheets
(20 structure) which pack
into a globular or fibrous
domain (30 structure).
Some individual
proteins self-associate into
complexes (40 structure).
(b) Proteins display
functions that arise from
specific binding
interactions and
conformational
changes in the structure of
a properly folded protein.

3.  Sometimes the primary sequence of amino acids is sufficient
to spontaneously direct the folding of proteins into their
proper shape.
 However, often newly-made proteins require the help of
molecular chaperones to attain their final shape.
 Members of the heatshock protein family (Hsp70 and Hsp60)
briefly bind to and stabilize hydrophobic regions of proteins
(especially rich in Trp, Phe, Leu) allowing proper folding
instead of aggregation with other immature proteins.
 Heat-denatured proteins can be renatured through the activity
of molecular chaperones and heatshock proteins are made
during times of stress.
 A number of diseases, including Alzheimer's disease, may be
considered to be protein-folding diseases.
 Prion diseases, such as "mad cow" disease, may "self-
propagate" based upon a misfolded protein that can, in turn,
misfold other versions of the same protein.

4. Amyloid Fibers-involved in Alzheimer’s
Protein amyloid fibers are often found to have a β-
pleated sheet structure regardless of their
sequence, leading some to believe that it is the
molecule's misfolding that leads to aggregation.
Enzymes act on the APP (Amyloid Precursor Protein)
and cut it into fragments of protein, one of which is
called beta-amyloid and is crucial in the formation of
senile plaques in Alzheimer.

5. (a) Many proteins fold into their
proper 3-D structures with the assistance of Hsp70-like proteins (top). These chaperones
transiently bind to a nascent polypeptide as it emerges from a ribosome. Proper folding of
other proteins (bottom) depends on chaperonins such as the prokaryotic GroEL, a
hollow, barrel-shaped complex of 14 identical 60,000-MW subunits arranged in two stacked
rings. One end of GroEL is transiently blocked by the co-chaperonin GroES, an assembly of
10,000-MW subunits. (b) In the absence of ATP or presence of ADP, GroEL exists in a “tight”
conformational state that binds partly folded or misfolded proteins. Binding of ATP shifts
GroEL to a more open, “relaxed” state, which releases the folded protein.

6. The ER membrane-bound chaperone protein calnexin, or a
resident chaperone calreticulin binds to incompletely folded
proteins, trapping the protein in the ER. Glucosyl transferase
determines whether the protein is folded properly or not: if the
protein is still incompletely folded, the enzyme renews the
protein's affinity for calnexin & retains it in the ER. The cycle
repeats until the protein has folded completely.

7. Misfolded soluble proteins in the ER lumen or membrane
proteins are translocated back into the cytosol, where they are
deglycosylated, ubiquitylated, and degraded in proteasomes.
Misfolded proteins are exported through the same type of
translocator that mediated their import; accessory proteins
allow it to operate in the export direction.

8. (a) Enzyme E1 is activated by
attachment of an ubiquitin (Ub)
molecule (1) and then transfers
this Ub molecule to E2 (2).
Ubiquitin ligase (E3) transfers
the bound Ub molecule on E2 to
the side-chain-NH2 of a lysine
residue in a target protein (3).Ub
molecules are added to the
target protein by repeating steps
1–3 , forming a polyubiquitin
chain that directs the tagged
protein to a proteasome (4).
Within this complex, the protein
is cleaved into small peptide
fragments (5).
(b) Computer-generated image
reveals that a proteasome has a
cylindrical structure with a cap
at each end of a core region.
Proteolysis of ubiquitin-tagged
proteins occurs along the inner
wall of the core.

9. After the amino chain is made, many
proteins undergo posttranslational
processing (including removal of
stretches of amino acids).
1. In prokaryotes, the N-formyl
group is always removed in the
mature protein and often the
methionine and, sometimes, a
number of N-terminal amino acids
are cleaved away from the final
protein product.
 Example: Proinsulin is converted
to the active hormone by the
enzymatic removal of a long
internal section of polypeptide.
 The two remaining chains
continue to be covalently
connected by disulfide bonds
connecting cysteine residues in
insulin.
2. Recently discovered, the process
of protein splicing (analagous to
RNA splicing) removes inteins
and splices the exteins together
to make a mature protein.

10. PROTEIN TARGETING AND SORTING
 Free and bound populations of ribosomes are active
participants in protein synthesis.
 Free ribosomes are suspended in the cytosol and
synthesize proteins that reside in the cytosol.
 Bound ribosomes are attached to the cytosolic side
of the endoplasmic reticulum.
 They synthesize proteins of the endomembrane
system as well as proteins secreted from the cell.
 Secretory proteins are released entirely into the
cisternal space, but membrane proteins remain
partially embedded in the ER membrane.
 While bound and free ribosomes are identical in
structure, their location depends on the signal
peptidase of proteins that they are synthesizing.

11. Overview of major protein-sorting
pathways in eukaryotic cells.

13.  In cotranslational import, proteins to be targeted to the ER initially have an N-terminal
peptide, the ER signal sequence, translated by a cytosolic ribosome.
 The ER signal sequence is bound by a signal-recognition particle (SRP), a
ribonucleoprotein complex composed of 6 peptides and a 300 nucleotide RNA molecule.
 The SRP binds to the SRP receptor to dock the ribosome on the ER membrane.
 When the SRP receptor binds GTP, the nascent polypeptide enters the pore.

14.  The SRP is released with hydrolysis of the GTP.
 The growing polypeptide translocates through a hydrophilic pore created by one or more
membrane proteins called the translocon.
 The ribosome fits tightly across the cytoplasmic side of the pore and the ER-lumen side is
somehow closed off until the polypeptide is about 70 amino acids long.
 When the polypepide is complete, the signal peptidase cleave the signal to release the
protein into the ER lumen while retaining the signal peptide, for a time, in the membrane.
 Afterwards the ribosome is released and the pore closes completely.

15. Integral membrane proteins are inserted into the ER
membrane as they are made, rather than into the lumen.

16. Major topological classes of integral membrane proteins synthesized on
the rough ER. The hydrophobic segments of the protein chain form helices
embedded in the membrane bilayer; the regions outside the membrane are
hydrophilic and fold into various conformations. All type IV proteins have
multiple transmembrane helices. The type IV topology depicted here
corresponds to that of G protein–coupled receptors: seven helices, the N-
terminus on the exoplasmic side of the membrane, and the C-terminus on the
cytosolic side. Other type IV proteins may have a different number of helices
and various orientations of the N-terminus and C-terminus.

17.  Other kinds of signal peptides are used to target polypeptides to
mitochondria, chloroplasts, the nucleus, and other organelles that
are not part of the endomembrane system.
 In these cases, translation is completed in the cytosol before the
polypeptide is imported into the organelle.
 Each of these polypeptides has a “postal” code that ensures its
delivery to the correct cellular location.
 In principle, a signal could be required for either retention in, or
exit from a compartment.

18. Posttranslational import allows some polypeptides to enter
organelles after protein synthesis. Like cotranslational import
into the ER, posttranslational import into a mitochondrion (and
chloroplast) involves a signal sequence (called a transit
sequence), a membrane receptor, pore-forming membrane
proteins, and a peptidase.

19.  In the mitochondrion, the membrane receptor
recognizes the signal sequence directly without
the intervention of a cytosolic SRP.
 Furthermore, chaperone proteins play several
crucial roles in the mitochondrial process:
o Chaperones keep the polypeptide partially
unfolded after synthesis in the cytosol so that
binding of the transit sequence and
translocation can occur.
o Chaperones drive the translocation itself by
binding to and releasing from the polypeptide
within the matrix, an ATP-requiring process
o Chaperones often help the polypeptide fold
into its final conformation.

20. Protein import into the mitochondrial
matrix. Precursor proteins
synthesized on cytosolic ribosomes are
maintained in an unfolded or partially
folded state by bound chaperones,
such as Hsc70 (1). After a precursor
protein binds to an import receptor
near a site of contact with the inner
membrane (2), it is transferred into the
general import pore (3). The
translocating protein then moves
through this channel and an adjacent
channel in the inner membrane (4-5).
Note that translocation occurs at rare
“contact sites” at which the inner and
outer membranes appear to touch.
Binding of the translocating protein by
the matrix chaperone Hsc70 and
subsequent ATP hydrolysis by Hsc70
helps drive import into the matrix.
Once the uptake-targeting sequence is
removed by a matrix protease and
Hsc70 is released from the newly
imported protein (6), it folds into the
mature, active conformation within the
matrix (7). Folding of some proteins
depends on matrix chaperonins.

21. Pathways for transporting proteins from the cytosol to the
inner mitochondrial membrane.

22.  In all three pathways, proteins cross the outer membrane via
the Tom40 general import pore.
 Proteins delivered by pathways A and B contain an N-
terminal matrix-targeting sequence that is recognized by the
Tom20/22 import receptor in the outer membrane.
 Although both these pathways use the Tim23/17 inner-
membrane channel, they differ in that the entire precursor
protein enters the matrix and then is redirected to the inner
membrane in pathway B. Matrix Hsc70 plays a role similar its
role in the import of soluble matrix proteins.
 Proteins delivered by pathway C contain internal sequences
that are recognized by the Tom70 import receptor.
 A different inner-membrane translocation channel (Tim22/54)
is used in this pathway.
 Two intermembrane proteins (Tim9 and Tim10) facilitate
transfer between the outer and inner channels.

23. The major difference is that the Two pathways for transporting
internal targeting sequence in proteins proteins from the cytosol to the
such as cytochrome b2 destined for mitochondrial intermembrane
the intermembrane space is space. Pathway A, the major one
recognized by an innermembrane for delivery to the inter-membrane
protease, which cleaves the protein on space, is similar to pathway A for
the inter-membrane-space delivery to the inner membrane.
side of the membrane. The
released protein then folds
and binds to its heme
cofactor within the
intermembrane
space. Pathway B
involves direct
delivery to the
intermembrane
space through the
Tom40 general
import pore in the
outer membrane.

24. Two of the four pathways for transporting
proteins from the cytosol to the thylakoid
lumen. In these pathways, unfolded
precursors are delivered to the stroma via the
same outer-membrane proteins that import
stromal-localized proteins. Cleavage of the N-
terminal stromal-import sequence by a
stromal protease then reveals the thylakoid-
targeting sequence. At this point the two
pathways diverge. In the SRP dependent
pathway (left), plastocyanin and similar
proteins are kept unfolded in the stromal
space by a set of chaperones and, directed by
the thylakoid targeting sequence, bind to
proteins that are closely related to the
bacterial SRP, SRP receptor, and SecY
translocon, which mediate movement into the
lumen. After the thylakoid-targeting sequence
is removed in the thylakoid lumen by a
separate endoprotease, the protein folds
into its mature conformation. In the pH
dependent pathway (right), metal-binding
proteins fold in the stroma, and complex
redox cofactors are added. Two arginine
residues (RR) at the N-terminus of the
thylakoid-targeting sequence and a pH
gradient across the inner membrane are
required for transport of the folded protein
into the thylakoid lumen. The translocon in
the thylakoid membrane is composed of
at least four proteins related to proteins in
the bacterial inner membrane.

25. (1) Catalase and most other peroxisomal
matrix proteins contain a C-terminal
Import of PTS1 uptake-targeting sequence (red)
peroxisomal that binds to the cytosolic receptor Pex5.
(2) Pex5 with the bound matrix protein
matrix interacts with the Pex14 receptor located
proteins on the peroxisome membrane. (3) The
directed by matrix protein–Pex5 complex is then
PTS1 transferred to a set of membrane
targeting proteins (Pex10, Pex12, and Pex2) that
sequence. are necessary for translocation into the
peroxisomal matrix by an unknown
mechanism. (4) At some point, either
during translocation or in the lumen,
Pex5 dissociates from the matrix
protein and returns to the
cytosol, a process that involves
the Pex2/10/12 complex and
additional membrane and
cytosolic proteins. Note that
folded proteins can be imported
into peroxisomes and that the
targeting sequence is not
removed in the matrix.

26.  Mutations are changes in the genetic material
of a cell or virus. MUTATION AND DNA REPAIR MECHANISMS.pptx
 These include large-scale mutations in which
long segments of DNA are affected (for
example, translocations, duplications, and
inversions).
 A chemical change in just one base pair of a
gene causes a spontaneous or point mutation.
 If these occur in gametes or cells producing
gametes, they may be transmitted to future
generations.

27.  For example, sickle-cell disease is caused by a
mutation of a single base pair in the gene that codes
for one of the polypeptides of hemoglobin.
 A change in a single nucleotide from T to A in the
DNA template leads to an abnormal protein.

29. http://highered.mcgraw-
hill.com/olc/dl/120077/bio25.swf
http://highered.mcgraw-
hill.com/olc/dl/120077/micro06.swf
http://highered.mcgraw-
hill.com/olc/dl/120077/bio30.swf
http://www.wiley.com/college/boyer/0470003790/ani
mations/translation/translation.htm