Download Structure - chula ise

2. Cell structure and organelle function
• eukaryotes
• membrane enclosed organelles: nucleus, ER,
mitochondria, Golgi apparatus
• hitchhiker: virus
The minimal requirements for a cell appear to be
• Molecules to store information and a mechanism to copy it
• A way to find and extract energy
• A way to enclose the space where these process happen
Figure 1-18
Molecular Biology
of the Cell, 4th
edition
Bacterium---the very basic cell structure
The bacterium Vibrio cholerae, showing its simple internal organization.
Like many other species, Vibrio has a helical appendage at one end—a
flagellum—that rotates as a propeller to drive the cell forward.
The minimal requirements for a cell appear to be
• Molecules to store information and a mechanism to copy it
• A way to find and extract energy
• A way to enclose the space where these process happen
As things get more complex additional machinery is needed
• To move when diffusion (thermal energy) is too slow or random
cell motility, division (cytokineses), intracellular transport
• To bind and communicate with other cells
• To invade or prevent invasion by other cells
The types of unique intracellular organelles appear to be
limited and well conserved even in very different cell types
Eukaryotic cell structure
Animal
cell
Figure 1-31 Molecular Biology of the Cell, 4th edition
Plant cell
The three major domains of the living world
• Originally living organisms are classified as procaryotes
and eucaryotes.
• Due to divergence in evolution, the two groups of
procaryotes are further divided into eubacteria and archaea.
•The living organisms are classified into 3 major domains.
procaryotes
Figure 1-21 Molecular Biology of the Cell, 4th edition
Basic terminology for part of (eukaryotic) cells
Nucleus
Cytoplasm
Cytosol
Endoplasmic reticulum (ER)
Ribosomes
Golgi apparatus
Mitocondria; (chloroplasts in plants)
Lysosomes
Figure 12-1
Endosomes
Structure of a highly specialized eukaryotic
Peroxisomes
cell: the epithelial lining e.g. the gut or lung
Centrosome
Cytoskeleton
red = membrane bounded
Table 12.1 Relative volumes occupied by the major intracellular
compartments in a liver cell (hepatocyte)
Intracellular compartment
% of total cell volume
cytosol
54
mitocondria
22
rough ER cisternae
9
smooth ER cisternae + Golgi cisternae
6
nucleus
6
peroxisomes
1
lysosomes
1
endosomes
1
Internal membrane helps organelles to perform
their specialized functions
Hypothetical model for the evolution of eukaryotic cells
1. nucleus
Figure 12-4 Molecular Biology of the Cell, 4th edition
Internal membrane helps organelles to perform
their specialized functions
2. mitocondria
Figure 12-4 Molecular Biology of the Cell, 4th edition
Mitocondria have their own genomes independently from the
nucleus. Their genomes share resemblance with those in bacteria.
Nucleus
Figure 4-9
Molecular Biology of
the Cell, 4th edition
Structure: double-membrane nuclear envelope, nuclear pores,
nuclear lamina, contains DNA, DNA-associated proteins
Functions: store and regulate genetic information. Also regulate all
other cellular activities
Nucleus: nuclear pores
Specialized proteins,
nucleoporins, form
octagonal-shape channels
through the nuclear
envelope that regulate
passage of molecules.
Figure 12-10 Molecular Biology of the Cell, 4th edition
Open aqueous
channels
 5 kDa freely
diffuse
Figure 12-10 Molecular Biology of the Cell, 4th edition
How nucleus regulates cellular activities?
Figure 12-19 Molecular Biology of the Cell, 4th edition
Key: nuclear import receptor
Nucleus: nuclear membrane
Figure 12-20 Molecular Biology of the Cell,
4th edition
Figure 12-9 Molecular Biology
of the Cell, 4th edition
The nuclear lamina gives shape and stability to the
nuclear envelope.
Nucleus: how DNA is packed inside the nucleus?
DNA
nucleosome
chromosome
nucleus
Figure 4-24 Molecular Biology of
the Cell, 4th edition
2m
6 m
• human genome—approximately 3.2 × 109 nucleotides
• Specialized proteins bind to and fold the DNA, generating a
series of coils and loops that prevens DNA from becoming an
unmanageable tangle.
• Those 3.2 × 109 nucleotides are now packed and
distributed over 24 different chromosome.
Endoplasmic recticulum (ER)
Structure: labyrinth (network) of
continuous sheet enclosing a
single internal space  ER lumen
or ER cisternal space. ER
membrane is selective for
molecular transport between the
ER lumen and the cytosol.
http://media-2.web.britannica.com/ebmedia/79/117279-004-4B7393C9.jpg
Function: synthesize proteins (RER) and lipids (SER). ER also
sequester Ca ++ in the cytoplasm (Ca++ storage) necessary for the
rapid response to extracellular signals such as the contraction and
relaxation of muscle.
Two types of ER
RER
Ribosomes attach to
the ER membrane
Note: a few free
ribosomes
synthesize proteins
in the cytosol
SER
SER is abundant in
cells that specialize
in lipid metabolism
such as hormonesecreting cells and
hepatocytes.
Figure 12-38 Molecular Biology of the Cell, 4th edition
Ribosomes synthesize proteins
Figure 12-37 Molecular Biology of the Cell, 4th edition
Addition of sugars to the newly synthesized and
folded proteins in ER
Most proteins synthesized in RER
are glycosylated by N-linked
oligosaccharides.
Panel 3-1 Molecular Biology
of the Cell, 4th edition
The added sugars can be further trimmed
or processed in the Golgi apparatus.
Proteins are synthesized and
completely folded in the ER.
Figure 12-51 Molecular Biology of the Cell, 4th edition
Golgi apparatus
Figure 13-22
Molecular Biology of
the Cell, 4th edition
Structure: stack of membrane-enclosed cisternae (about 4-6 per
stack). Each stack has two distinct faces: cis face (entry face) and
trans face (exist face). Located close to the nucleus.
Function: major site for carbohydrate synthesis as well as
modification of proteins and lipids.
Oligosaccharide chains are processed in the
Golgi apparatus
N-linked oligosaccharides can be processed into complex
oligosaccharides and high-mannose oligosaccharides.
Figure 13-25 Molecular Biology of the Cell, 4th edition
Transport from ER to the Golgi apparatus is
mediated by vesicular tubular clusters
Figure 13-20 Molecular Biology of the Cell, 4th edition
Figure 13-41 Molecular Biology of the Cell, 4th edition
Movie 13.2 intracellular protein traffic
Mitocondria
Structure: stiff, elongated cylinders with
diameter of 0.5-1 um. They are very
mobile and plastic. Unique orientation
and location in different cell types.
One of the first organelles imaged by
light microscope
Figure 1-34 Molecular Biology of the Cell, 4th edition
Function: generate energy in the form of ATP in eucaryotes. Most of
a eukaryotic cell’s ATP is generated from oxidation reactions (fatty
acid breakdown, Kreb’s cycle) in the mitocondrion using a proton
gradient set up in the space between the two membranes (chemiosmotic coupling).
The highly convoluted structure
Matrix: large internal space
containing a mixture of enzymes
for oxidation reaction,
mitocondrial genome
Inner membrane: folds into many infoldings
(cristae) to carry out electron transport and
ATP production
Outer membrane: contain a permeable
membrane (molecules < 5 kDa) and enzymes
for mitocondrial lipid synthesis
Intermembrane space: contain enzymes
that aid the outflow of ATP
Figure 14-8 Molecular Biology of
the Cell, 4th edition
Energy generation in mitochondria
Electron transfer release energy to drive
proton gradient across the membrane.
Proton is used to drive the
conversion of ADP  ATP
Oxidative phosphorylation
NADH (nicotine adenine
dinucleotide) carries
electrons
to a series
of
NADH (nicotine
adenine
Conversion
C atoms
three
H+ pump of
the
inner in
dinucleotide)
carries
acetyl CoA
to CO
mitocondrial
2
electrons
tomembrane
the
inner
generate high
energy
mitocondrial
membrane
electron
Oxidation of pyruvate
and fatty acids produce
acetyl CoA
Figure 14-10 Molecular Biology of the Cell, 4th edition
~ 30 ATP is produced,
15 times higher than
glycolysis
Viruses---the hitchhikers
T4
Bacteriophage (bacterial virus)
http://en.wikipedia.org/wiki/Bacteriophage
Figure 1-27 Molecular Biology of the
Cell, 4th edition
Genes Can Be Transferred Between Organisms
Inside the host cell, the virus may remain as separate
fragments of DNA (plasmids) and replicate independently from
the host genes OR insert their plasmids into the DNA of the
host cell.
T4 infects host bacterium
Figure 1-27 Molecular Biology of the Cell, 4th edition
3. Protein Structure and Function
'Glowing' jellyfish grabs Nobel
Jellyfish will glow under blue and ultraviolet light because of a
protein in their tissues. Scientists refer to it as green fluorescent
protein, or GFP.
Fluorescence protein is
part of the gene---cells
constantly emits green
fluorescence
Fluorescence protein has been
bounded to protein inside the cells--fade within weeks in the absence of
antifading mounting media
Brainbow
Glowing
mouse
http://news.bbc.co.uk/2/hi/science/natu
re/7658945.stm
'Glowing' jellyfish grabs Nobel
Jellyfish will glow under blue and ultraviolet light because of a
protein in their tissues. Scientists refer to it as green fluorescent
protein, or GFP.
Fluorescence protein is
part of the gene---cells
constantly emits green
fluorescence
Fluorescence protein has been
bounded to protein inside the cells--fade within weeks in the absence of
antifading mounting media
Brainbow
Glowing
mouse
http://news.bbc.co.uk/2/hi/science/nature/7658945.stm
There are 20 amino acids
It is useful to remember their most important structural features.
At a minimum, memorize their names and one letter codes.
Know which one is acidic, basic, hydrophobic, polar, big, small,
reactive, inert
There are a few modifications done to amino acids as or immediately
after the protein is made:
e.g. phosphorylation, acetylation, acylation, glycosylation
Essential amino acids
Figure 3-3. Cell and Molecular Biology, 4th edition
The side chains
Panel 3-1 Cell and Molecular Biology, 4th edition
Panel 3-1 Cell and Molecular Biology, 4th edition
Peptide sequence
Figure 3-2. Cell and Molecular Biology, 4th edition
Non-covalent bonds in protein folding
Figure 3-5. Cell and Molecular Biology, 4th edition
Three types of noncovalent bonds that help proteins fold. Although a
single one of these bonds is quite weak, many of them often form
together to create a strong bonding arrangement. The final folded
structure, or conformation, adopted by any polypeptide chains is the
one with the lowest free energy.
Formation of hydrogen bonds
Figure 3-7. Cell and Molecular Biology, 4th edition
Large numbers of hydrogen
bonds form between adjacent
regions of the folded
polypeptide chain and help
stabilize its three-dimensional
shape. The protein depicted is a
portion of the enzyme
lysozyme, and the hydrogen
bonds between the three
possible pairs of partners have
been differently colored, as
indicated.
Proteins have hydrophobic cores
Figure 3-6. Cell and Molecular Biology, 4th edition
The polar amino acid side chains tend to gather on the outside of the
protein, where they can interact with water; the nonpolar amino acid
side chains are buried on the inside to form a tightly packed
hydrophobic core of atoms that are hidden from water. In this
schematic drawing, the protein contains only about 30 amino acids.
Changes in protein conformation
Figure 3-8. Cell and Molecular Biology,
4th edition
A protein can be unfolded, or denatured, by treatment with certain
solvents to disrupt the non-covalent bonds or heat (heat denaturation)
and cold (< 20C for certain antibodies)
Some proteins, often small ones, reach their proper folded state spontaneously.
Once unfolded, kT allows them to find their equilibrium structure when
returned to physiological conditions. Other proteins are metastable: they are
helped to fold to structures they would practically never find at random. Protein
folding in a living cell is often assisted by special proteins call molecular
chaperones.
Disulfide bonds stabilize protein structure
Figure 3-29. Cell and Molecular
Biology, 4th edition
Figure 3-42. Cell and Molecular
Biology, 4th edition
Disulfide bond covalently link polypeptide chains together, providing
a major stabilizing effect on a protein.
Recap: Protein structure and protein function
Hierarchy of protein structure
Primary structure
amino acids joined
together in a linear
polypeptide chain
Secondary structure
local folding through
H-bonds into -helix
or -pleated sheet
Tertiary structure
full 3-D organization of
a polypeptide chain
Quaternary structure
multi-subunit complex
consisting of multiple
polypeptide chains
Secondary structure: alpha helix
Figure 3-9. Cell and Molecular Biology, 4th edition
The regular conformation of the polypeptide backbone observed in the α
helix and the β sheet. (A, B, and C) The α helix. The N–H of every
peptide bond is hydrogen-bonded to the C=O of a neighboring peptide
bond located four peptide bonds away in the same chain.
Secondary structure: beta sheet
Figure 3-9. Cell and Molecular Biology,
4th edition
(D, E, and F) The β sheet. In this example, adjacent peptide chains
run in opposite (antiparallel) directions. The individual polypeptide
chains (strands) in a β sheet are held together by hydrogen-bonding
between peptide bonds in different strands, and the amino acid side
chains in each strand alternately project above and below the plane
of the sheet
Beta sheets can have parallel or
antiparallel strands
Figure 3-10. Cell and Molecular Biology, 4th edition
Protein domains, e.g. Src protein
Protein domains have a unit of organization distinct from the four
levels of protein structure. Any part of the polypeptide chain can
fold independently into a compact, stable structure (folded
domains).
In Src protein, SH2 and SH3 domains perform regulatory functions and
the other two domains from a protein kinase enzyme—notice the ATP
binding cleft within the unit.
Only a very small fraction of random sequences of amino acids
make polymers with a unique or stable structure. Nature has
selected those sequences with specific folded shapes. The shapes
and therefore functions can be very fragile to even tiny changes in
atomic structure (mutation). A single protein can have separate
sections each with its own folded domain, and linked by spacers.
Figure 19-53. Cell and Molecular Biology, 4th edition
http://www.ks.uiuc.edu/Research/fibronectin/
Large protein molecules contain more than one
polypeptide chain
Weak noncovalent bond allows protein chain to fold into a
specific conformation and bind to each other to produce a
larger structure.
protein
subunit
binding site
Two identical subunits bind
head-to-head, held together
by a combination of
hydrophobic forces (blue)
and a set of hydrogen bonds
(yellow region).
Protein: classified by functions
Enzymes  catalytic activity and function (-ase)
Structural  collagen of tendons and cartilage, keratin
of hair and nails
Transport proteins  bind and carry ligand
Motor proteins  can contract and change the shape of
cytoskeleton
Defensive  antibodies, thrombin
Regulatory  growth factors, hormones, transcription factors
Receptor  cell surface receptors
Protein Function: How shape determines function?
The specific binding of protein molecules determines their
activity and function--- 3-D shape/conformation matters.
Binding always shows great specificity.
enzyme
receptor
transport protein
Figure 3-37. Cell and Molecular Biology, 4th edition
A protein to bind tightly to a second molecule, which is called a
ligand for that protein, through many weak non-covalent
bonds. A ligand must fit precisely into a protein's binding site.
Allosteric enzymes: feedback mechanism
Many enzyme has at least two different binding sites:
active site--- recognizes the substrate
regulatory site--- recognizes regulartory molecule
Interaction depends on a conformational change in the
protein: binding at one of the sites causes a shift from one
folded shape to a slightly different folded shape.
positive regulation
Figure 3-57. Cell and Molecular Biology, 4th edition
negative regulation
Figure 3-58. Cell and Molecular Biology, 4th edition
Many protein functions are driven by phosphorylation
Phosphorylation regulates thousands of protein functions in a
typical eukaryotic cells. Phosphorylation occus by the addition of a
phosphate group to amino acid side chains, usually the OHterminal of serine, threonine and tyrosine.
Figure 3-63. Cell and Molecular Biology, 4th edition
Protein kinases: catalyze phosphorylation (addition of phosphate)
Proten phosphatases: catalyze dephosphorylation (removal of phosphate)
Individual protein kinases serve
as microchips.
Cyclin-dependent protein kinase
(Cdk) regulates the cell cycle.
Figure 3-66. Cell and Molecular Biology, 4th edition
Cdk becomes active when:
1. Cyclin is present
2. Pi added to specific threonine
side chain
3. Pi removed from tyrosine side
chain
When all 3 requirements are met,
Cdk is turned on.
GTP binding proteins as molecular switches
• The activity of a GTP-binding protein (also called a
GTPase) generally requires the presence of a tightly bound
GTP molecule (switch “on”).
• Hydrolysis of this GTP molecule produces GDP and inorganic
phosphate (Pi), and it causes the protein to convert to a different,
usually inactive, conformation (switch “off”).
• Resetting the switch requires the tightly bound GDP to
dissociate, a slow step that is greatly accelerated by specific
signals; once the GDP has dissociated, a molecule of GTP is
quickly rebound.
th
Figure 3-70. Cell and Molecular Biology, 4 edition
Phosphorylation in cell signaling
Many signaling pathways important for the cell survival involve
GTP-binding proteins (GTPases). The phosphate group is part
of GTP that binds very tightly to the protein it regulates. When
the tightly bound GTP is hydrolyzed to GDP, this domain
undergoes a conformational change that inactivate it.
GTP = molecular
switch
Figure 3-72. Cell and Molecular Biology, 4th edition