Download Proteins

Cells and Their
Housekeeping
Functions – Nucleus and
Other Organelles
Shu-Ping Lin, Ph.D.
Institute of Biomedical Engineering
E-mail: [email protected]
Website: http://web.nchu.edu.tw/pweb/users/splin/
Chloroplasts, Cell Wall, and Vacuole
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Chloroplasts: green organelles that make food, found only in green
plant cells  Convert energy of light into chemical energy
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Chlorophyl: green pigment that gives leaves & stems their color  Captures
sunlight energy that is used to produce food called glucose (Glucose is a type of
sugar)
Cell wall: restrict shape change and mobility
Vacuole: collect and store nutrient molecules and waste products
Chloroplasts
Cell wall
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From Cell to Organism
Cell
The basic unit of life
Tissue
Group of cells working together
Organ
Group of tissues working together
Organ System
Group of organs working together
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Organism
Any living thing made of 1 or more cells
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1- Nucleus
2- Chromosomes
3- Mitochondria
4- Ribosomes
5- Chloroplasts
6- Vacuoles
7- ER
8- Cell Membrane
Nucleus
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Largest organelle within the cell, containing DNA
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DNA replication: necessary for cell division (so that both daughter cells
have identical copies of DNA)
Transcription: formation of an RNA template of a gene, essential for
protein synthesis
Library of genetic information
Bounded by nuclear membrane, 2 lipid bilayers of double
membrane are separated by a gap (20~ 40nm) with many
openings or pores for trafficking small molecules and proteins
Chromosome
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Identical sets of chromosomes
(long and thin DNA molecules,
store genetic information) in each
eukaryote
Histone: beadlike protein
structure, Ex: each human cell
has about 1.8 meters of DNA, but
wound on the histones it has
about 90 millimeters of chromatin
Before cell division, DNA is
replicated and tightly coiled and
bound in identical pairs called
chromatids  Chromosomes
can be seen by light microscopy.
Chromatin
DNA molecules are packed around and attached to beadlike protein structure (histon)
 Nucleosomes
http://en.wikipedia.org/wiki/Chromosome
Chromatin  Chromosome
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Different levels of DNA condensation. (1) Single DNA strand. (2) Chromatin strand
(DNA with histones). (3) Chromatin during interphase with centromere. (4)
Condensed chromatin during prophase. (Two copies of the DNA molecule are now
present) (5) Chromosome during metaphase.
http://zh.wikipedia.org/zh-tw/File:Chromatin_chromosome.png
Protein Synthesis-1
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RNA polymerase: transcribe RNA
from DNA template at average rate
30 nucleotides/sec, an enzyme
consisting of 12 different
polypeptides with mass of 500kDa,
arrange in 10 subunits
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RNA polymerase II (pol II): central
machine for synthesis protein of mRNA
in eukaryotes
Polymerase I: ribosomal RNA,
polymerase III: transfer RNA
9 out of 10 subunits are identical in
these 3 enzymes
Begin in nucleus with binding of
transcription factors to regulatory
sequence (protein-coding gene)
Transcription: energyconsuming process and driven
by energy-released by ATP
hydrolysis
Protein Synthesis-2
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Binding of transcription factors to
regulatory sequence (protein-coding
gene) on DNA ––Activate Pol II unwind
DNA double helix  Polymerize mRNA
and proofread the resulting transcript
Pol II recognize promoter region of genes
if DNA interact with transcription factors
Subunits 1, 5, and 9 of pol II grip DNA
downstream of active center
Subunits 1, 2, and 6 clamp on DNA near
active center  Growing mRNA strand
locks this clamp, thus stabilizing
transcribing complexes
Complete RNA molecule (primary
RNA transcript, pre mRNA): 20,000
nucleotides because of noncoding introns
 RNA splicing  mRNA  Transport out
of nucleus and interact with ribosomes in
cytoplasm to begin translation
Spliceosome: recognize exon/intron
 Excised intron transcripts rapidly
interface , mediate excision, and anneal degrade in nucleus to provide raw material
ends of exons
for new transcripts
Ribosomes
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Small and darkly staining spherical
structures: ~20 nm in diameter that are
made of 50 proteins and several long RNAs
intricately bound together
Ribosomes are made in the nucleolus,
compartment in nucleus.  Once
constructed, ribosomes leave nucleus
through nuclear pores.
Float freely in the cytoplasm to synthesize cytoplasmic proteins without any
further modification or attach to the endoplasmic reticulum (ER) to
manufacture membrane proteins
Make proteins  Translate sequence information on mRNA into
polypeptides
No membrane and disassemble into 2 subunits when not actively
synthesizing protein
Protein synthesis is extremely important, so eukaryotic cells contain million
of ribosomes.
Take 30 sec to synthesize a protein containing 400 amino acids, and human
cell synthesize 1010 proteins in 24 hr
Translation
of mRNA by
Ribosomes
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1. Attachment of
mRNA to a
ribosome
2. Begin knitting
together amino
acids, according
to template
encoded mRNA
3. Translation is initiated by tRNA, acting as adapter
and matching each codon on mRNA with amino acid
the codon prescribes.
tRNAs: amino-acid-specific adapter molecules
Ribosome has binding sites for 2 different tRNA
molecules so that 2 amino acids joined to the growing
polypeptide chain at one time.
Endoplasmic Reticulum
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A series of folded membranes that move materials (proteins) around in a
cell – like a conveyer belt
Large surface area provides template for enzyme-mediated chemical
reactions
Ribosomes manufacture membrane proteins or proteins  Will be secreted
or transported to other membranous organelles – ER
Smooth ER – ribosomes not attached to ER; lipid synthesis in the cell
(cell’s membranes); houses detoxifying enzymes (particular in liver); early
stages of synthesis of steroid hormones – testosterone (contain large
amounts of SER in testes, ovaries, and adrenal glands; SER a storage site
for calcium in skeletal cells
Rough ER – ribosomes attached to ER; protein synthesis, folding, and
some posttranslational modifications – addition of carbohydrates
(glycosylation), membranebound polypeptides
threaded through
membrane of RER have 3D
shapes
ER
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Information dictates polypeptide is synthesized on free or ER-bound
ribosomes  mRNA contain primary sequence of gene and
does not depend on protein-synthesizing apparatus (ribosome or ER)
Proteins are targeted to their specific cellular destinations by
address labels.
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Targeting to RER – Signal sequence consists of about 20 hydrophobic amino
acids at the N terminal end of the protein
Nuclear proteins synthesized on free
ribosomes, tag that directs them to
nucleus including stretch or patch of
basic amino acids, Ex: transmembrane
proteins have multiple signal
sequences.
Ribosome attached mRNA with a
signal-sequence coding sequence is
directed to outer surface of RER 
Protein is processed by enzymes
and folded into its correct 3D
conformation.
Proteins Processed in ER
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Protein are inserted into lumen of ER as they are being synthesized rather than as
fully made polypeptides  Protein to be passed into lumen of ER, the end of
polypeptide must be identified by a signal-recognition particle (a receptor) and
machinery must exist to pull the thread into the lumen (ATP and GTP-driven
motors)
Protein translocation across ER membrane, pore in hydrophobic lipid membrane
presents a hydrophilic interior to accommodate newly synthesized protein.
Proteins on the outside of pore recognize polypeptide and ribosome.
Ratchet-like mechanism: ER simultaneously bind and pull polypeptide into lumen by
utilizing energy driving from the hydrolysis of GTP and ATP
Translocated protein enters ER lumen, signal peptide is cleaved by enzyme called
signal peptidase.  Emerging protein is sequestered by heat shock protein hsp70
and assisted with proper folding, this chaperone can prevent aggregation in ER
lumen.
Disulfide bonds are rate-limiting step in protein
folding in ER.
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Extensive post-translation modification in
secretory proteins is glycosylation: carbohydrate
motifs; starts in ER with further processing in Golgi
apparatus
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Golgi Apparatus
Following synthesis, small vesicles transport
concentrated proteins from ER to another
membranous compartment – Golgi apparatus:
stacked flattened membranes
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Lumenal and transmembrane proteins are
concentrated in lipid vesicles
Golgi complex modifies proteins by adding to
and modifying their carbohydrate chains to form
mature glycoproteins
Golgi vesicles pinch off from edges of flattened
sacks to transport the modified proteins their
destinations in cell and to its exterior
Mechanism of concentration, vesicle formation, and
subsequent fusion with Golgi (Process proteins)
– Sort and package proteins
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Pinch off coated vesicles (coatomer proteins or COPs
coat vesicle) binding GTP to form G-protein (once release
from ER, vesicle is protected and allow to fuse with Golgi)
COPs cover naked lipid membrane and some selected
proteins target vesicle to correct Golgi stack; others
catalyze fusion of vesicle and Golgi membranes
(simultaneous uncoating and fusion of vesicle requires
hydrolysis of GTP and ATP)
Protein Transport in Golgi Apparatus
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Similar process mediates vesicular transport between different Golgi
stacks and between Golgi and plasma membrane.
Proteins reside in ER or Golgi selectively retained during vesicle
formation or retrieved from distal compartments.
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ER proteins possess short amino-acid sequence marking them for retention in ER
Membrane vesicle involved in retrieval of ER proteins from Golgi apparatus
Cisternal maturation model: intra-Golgi transport
Cisternal Maturation Model
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Hypothesis: Vesicles are used only in retrograde transport, to retrieve ER
components that pass into Golgi.
Cisternal maturation models (changing their molecular makeup) are
correct, but the rate is too slow to account for the speed at which many
proteins pass through the Golgi stack
Large aggregates of extracellular matrix proteins, ex: pro-collagen,
requires a lot posttranslational modification and passes through Golgi
without entering vesicles and the rate of passage coincides with its in
cisternal maturation.
Other proteins are concentrated in vesicles and pass rapidly from
one stack to another.
Final cis-trans directionally of cargo transport being dependent on a sort of
iterative progression
Small vesicles only contain ER proteins with ER-retrieval label are passing
from the Golgi to the ER.
Rapid vesicular transport system is superimposed on a more slowly maturing
cisternal system.
Lysosomes
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The word "lysosome" is Latin for "kill body".
The purpose of the lysosome is to digest things. They might be
used to digest food or break down the cell when it dies.
Break down food molecules, cell wastes & worn out cell parts
They are found in animal cells, while in yeast and plants the
same roles are performed by lytic vacuole
Cytoskeleton
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Organelles of eukaryotic cells are not freely suspended in cell
cytoplasm, but are anchored to cytoskeleton.
Cytoplasm: an aqueous medium containing many enzymes and
other compounds needed by cell, also contains dynamic
cytoskeletal network including microfilaments, intermediate
filaments, and microtubules
Cytoskeleton
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Give cell physical strength and rigidity and hold intracellular
structures in place
Facilitate and control movement within cell and locomotion of cell
Actin Microfilaments
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Actin cytoskeleton: for cell motility (actin interact with molecular
motor myosin leads to contraction of actin cytoskeleton and enables
cells to move and change shape) and phagocytosis (macrophages eat
microbes), adhesion of cells to other cells and to
extracellular matrix (signaling receptors on cell
surfaces anchor to actin either directly or
through adapter proteins), conserved ancient
protein of eukaryotes, and (~20%) the most
abundant protein in cytoplasm of mammals
Actin microfilaments: 5nm in diameter,
including G-actin (globular monomer) and
F-actin (filament, formed by head-to-tail
polymerization of asymmetric G-actin)
Create dynamic (continuously remodeling)
and intricate cytoskeletal network and
contractile (F-actin associate with
myosin(motility engine))
TEM of crosslinked actin
cytoskeleton of macrophage
Formation of Actin Filament
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3 actin monomers  Unstable trimeric
nucleus: dissociate back into monomers
rapidly or survive long enough to permit
subsequent binding of additional actin
molecules
Proteins, such as Arp2/3 complex,
regulate nucleation of actin filaments.
Treadmilling – Monomeric actin
molecules (containing ATP) adding for
elongating filament:
Monomer rapid addition at “+” 
Growing filaments, ATP-actin hydrolysis
to form likely dissociated ADP-actin
within filament’s helical lattice  Active
filaments reach steady-state length 
ADP-actin released at “-” at about the
same rate as new ATP-actin monomers
added to “+”
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Treadmilling
Actin filaments assemble and
disassemble very rapidly
regulated by actin-binding
proteins (α-actinin)  Bind
to sides of actin filaments, and
link them into bundles
(Crosslinking creates rigid
structures for cell to resist
physical forces, Ex: fluid force
exerted on endothelial cells
covering lumen of blood
vessels)  Some actinbinding proteins “cap” the
“+” ends to prevent
depolymerization, and
others sequester G-actin to
prevent polymerization
J. Baum, Nature Reviews Microbiology 4, 2006
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Fibrous Actin
Fibrous actin: found in muscle cell in association with regulatory
proteins tropomyosin and troponin
Thin filaments of muscle cells consist of 2 actin strands twisted
into double helix together with troponin and tropomyosin.
Thin filaments hardly change length during muscle contraction
or stretching, but slide past each other to alter the length of
muscle cells.
Cells suspended in fluid are spherical shape (existence of uniform
surface tension); but compose tissues deviate from spherical
shape (forces cell-cell and cell-substratum adhesion pull cells in
different directions) – Cytochalasin B lose cell shape and resemble a plastic bag
Microtubules and Tubulin
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Microtubules: hollow tubes ~ 20 nm in diameter composed of αtubulin and β-tubulin, each contains 13 strands of protofilaments
(polymerized tubulin dimers, α-tubulin and β-tubulin interact head to
tail)  Protofilaments form a sheet, then fold to form hollow
microtubule. Functions:
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Transport of vesicles and other organelles such as those that pass through
Golgi apparatus during protein sorting
Components of cell appendages such as flagella used to propel
spermatozoa: stable configuration of microtubules, beating motion is from
sliding of microtubules along one another)
Mitotic spindle during cell division: remarkably dynamic, grow and shrink at
the same time as they move chromosomes and segregate daughter cells
Microtubules associate with ATP-hydrolyzing motor proteins kinesin and
dynein.
Centrosome
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Centrosome: microtubules nucleated and anchored in a region of cell, also
called microtubule-organizing center (MTOC)
Polarized with “+”  Grow from MTOC into cytoplasm
Microtubules grow by the reversible addition of subunits catalyzed by
GTP-nucleotide hydrolysis.
Dynamic instability: “+” end of microtubules switch from rapidly growing
state to rapidly shrinking state
β-tubulin bound to GTP assembles with other dimers during polymerization
 GTP hydrolysis after polymerization and “cap” of GTP-bound subunits
found at “+” of growing microtubules; size of cap depends on rate of new
subunit addition  Rate at GTP-bound tubulin formed or added to growing
microtubule is reduced, size of GTP
cap ↓, and GDP-tubulin is exposed
Microtubule catastrophe: GDPtubulins dissociate more readily than
GTP-tubulin, microtubule
depolymerizes rapidly  Enzyme
then let GDP-tubulin converts to
GTP- tubulin  Capture “+” (stable)
Implications: cell division, cancer, neurobiology, and cell motility