selected cytoplasmtic processes review semiar cell ... · selected cytoplasmtic processes review...

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Selected cytoplasmtic processesReview semiar

based on

Essenial Cell Biology - Alberts et all Chapters – 11,12, 7, 17

Medical Cell Biology – GoodmanChapters 2, 3, 4, 5, 6

Cell and Molecular Biology- RewiewChabdar and Viselli (Lippincott’s Ilustrated Rewiew)Chapters- 3, 4, 5, 9, 11, 12, 13, 14, 15, 16

Cell membranes and transport

Cellular membranes

Plasma membraneIntracellar membranes

ERGolgi apparatuslysosomesperoxysomesendosomesTransport vesicles

Nuclear envelopeMitochondrial membranes

A biological membrane or biomembrane is an enclosing or separating membrane that acts as a selectively permeable barrier within living things.

Biological membranes consist of a phospholipid bilayer with embedded, integral and peripheral proteins used in communication and transportation of chemicals and ions

Cell membranes

plasma membrane

inner membranes

Characteristics of the plasma membrane:

Fluidity

Selective Permeability

Asymmetry

General schema of membrane compositionFluid mosaic model

Figure 11-4 Essential Cell Biology (© Garland Science 2010)

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Nie można wyświetlić połączonego obrazu. Plik mógł zostać przeniesiony lub usunięty albo zmieniono jego nazwę. Sprawdź, czy łącze wskazuje poprawny plik i lokalizację.Lipids

Phospholipids glycolipids

Esters of Glycerol or Sphingosine

Phosphatiyl-cholineserine,etanoloamine,inositol

Sphingolyelin

Cholesterol

Lipids

Phosphatidylinositol

Types of motions in the membrane

The flip-flopmovements are catalyzed by an enzyme flip-ase, using ATP


Phospholipids as a source of mediators released from plasma membranes

PL A2Removes the fatty acid at 2nd

positionArachidonic acid C20 a substrate for eikosanoids production

PL CRemoves phosorylated 3rd

residue and diacyl-glycerol (DAG) – a second messenger

Phospholipase A A1 A2

Phospholipase B

Phospholipase C

Phospholipase D

Eikosanoids productionArachidonic acid

Cyclooxygenase (COX) lipooxygenase

Prostaglands Leukotriens

Mediators of inflammation

The main COX inhibitors are the non-steroidal anti-inflammatory drugs (NSAIDs)-

acetylsalicylic acid (ASA)- (Aspirin)

PGE1

Prostaglandins

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TXA2

PGI2

Increases platelets aggregation and blood vessels contraction

Tromboxanfrom platelets

Prostacyclinform endothelial cells

Eikosanoids in circulatory system

Decreases platelets aggregation and blood vessels contraction

Low-dose, long-term ASA administration irreversibly blocks the formation of thromboxane A2 in platelets, decreasing platelet aggregation.

Leukotriens

LTB4

Leukotriens are mediators of allergic processesChemical substances inhibiting action of leukotriens are used as anti-alergic drugs

Cholesterol and membrane fluidity


More cholesterol= less fluidMore unsaturated fatty acid = more fluid

Lipid raftPlasma membrane microdomain

with lower lateral diffusion due to increased amount of cholesterol

Lipid raft contains combinations of glycosphingolipids (phosphatidyl-inositol) and protein receptors organized in glycolipoprotein microdomains.

These specialized membrane microdomains compartmentalize cellular processes by serving as organizing centers for the assembly of signaling molecules, influencing membrane fluidity and membrane protein trafficking, and regulating neurotransmission and receptor trafficking.

The caveolin protein in lipids rafts is involved in small invigilation formation know n as ceveolae.

ceveolaeMembrane proteins


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Myristic acidG-proteins

PrenylationRas-protein

Lipid anchored proteins display a fast lateral movement in the plasma membrane

Lipid modifications anchoring protein in the plasma membranes:

Dwuwarstwa lipidów

Glikokaliks

Plasma membrane asymmetryGlycocalycs


Asymmetry of lipids

E

P

Asymmetry of lipids

Lipids %(total) E (outer) P (inner)Cholesterol 23% 50% 50%Phosphatidyl- inositolol 1% - 100%Phosphatidyl- etanolammine 18% 20% 80%Phosphatidyl- choline 17% 80% 20%Phosphatidyl- serine 7% - 100%Sphingomyelin 18% 90% 10%Glycolipids 3% 100% -

Selective Permeability

Figure 12-2 Essential Cell Biology (© Garland Science 2010) Table 12-1 Essential Cell Biology (© Garland Science 2010)

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Types of transport


Types of transporter mediated transport


Active transport

Secondary active transport

Figure 12-8 Essential Cell Biology (© Garland Science 2010) Figure 12-18 Essential Cell Biology (© Garland Science 2010)

Symport glukozy z Na+ do enterocyta wbrew gradientowi stężeń glukozy

GLUT

SGLT

Glucose transporters

Main in RBC

Main in neurons

Insulin and GLUT-4

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Glucose entering the beta-cells though GLUT-2 stimulates

insulin release

Insulin dependent and independent tissues

Primary active transport

Type of transporters

Sodium-potassium ATP-ase


Na+ K+ ATP-ase

1 ATP-ase 300 Na+ and 200 K+ in one sec.

ATP-ase generates the eletrochemical gradient of sodium and potassium though the plasma membrane that is required for membrane resting and action potential;

Calcium pump transport calcium form cytozol to ER


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H+ATPase transpots H+ tolysosomes

Essential Cell Biology (© Garland Science 2010)

Ion channels

inactiveEssential Cell Biology (© Garland Science 2010)


Some potassium channels are always open in the plasma membrane

The out-flow of potassium (plus) ions is stoppedby the driving force of the generated potential (minus)equilibrium potential

The resting potential of the plasma membrane id closed to the equilibrium potential to potassium ions.

It can be calculated using Nernst Equation:

Ek = 62 log ([K+zewn]/[K+

wewn])

Calculated value for neurons is -90mVReal value is -70mV

Protein synthesis and traffing and sortingMembrane enclosed compartment

Figure 7- 23a Essential Cell Biology (© Garland Science 2010)

Summary of transcription and RNA processing in Eukaryotic cell

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The mature mRNA is exported from nucleus into cytoplasm

Successfully processed mature mRNA is recognized by Cap-binding protein, Poly-A-binding protein and Exon Junction Complexprotein that designate mRNA for nuclear export by nuclear pore complex into cytoplasm for translation at ribosomes.

Figure 7-23b Essential Cell Biology (© Garland Science 2010)

In bacteria no RNA processing occurs and no nuclear export

Translation begins before transcription is completedBoth processes takes place in cytoplasm, there is no nucleusThere is only one RNA polymerase for synthesis of all types of RNA

From RNA to Protein

Translation = protein biosynthesis* takes place at ribosomes in cytoplasm* requires mRNA as a template, and t-RNA to transport amino acids


Proteins are polymers of 20 naturally occurring amino acids

The chain of amino acids linked by a peptide bond is named polypeptide chain or polypeptide

Proteins forms higher structuresLevels of Protein Organization

Primary Structure= sequence: order of AA in polypeptide chain i.e. …-Asp-Val-Glu-Gly-…

Secondary Structure: organization of polypeptide chain into special structures: α-helix or β-sheet

Tertiary structure: full 3D structure of protein

Quaternary structure: (only proteins having more than one polypeptide chain) orientation of protein subunits to each other

Primary Structure= sequence:order of AA in polypeptide chain

i.e. …-Asp-Val-Glu-Gly-…• Each protein has an unique amino acid

sequence• Amino acids are connected by peptide

bounds• forming the polypeptide chainThe information about amino acids sequence

is coded in DNA in genes

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Primary Structure= sequence:order of AA in polypeptide chain


N-end C-endMet-Asp-Leu-TyrFigure 4-10d–f Essential Cell Biology (© Garland Science 2010)

Secondary Structure:organization of polypeptide chain into special structures: α-helix or β-sheet

Stabilized by by hydrogen bonds between amino acids


Tertiary structure: full 3D structure of protein

Polypeptide chains folds into a conformation of lowest energy


Quaternary structure:orientation of protein subunits to each other

(only proteins having more than one polypeptide chain)


The structure of Eukaryotic ribosome

60S 40S

80S

Ribosome is a complex of several rRNAs and proteins

Small subunit is responsible for t-RNA binding

Large subunit is responsibleFor synthesis od a peptide bound in synthesized protein

18S rRNA

28S5,8S5S

Table 7-1 Essential Cell Biology (© Garland Science 2010)

Revision

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rRNA processing

Common precursor 45S rRNA pol RNA I

5S RNA pol RNA III

Transcription and processing of rRNA and assembly of ribosome subunitstake place in the nucleolus.

The rRNA genes are located in NOR (nucleoli organizing regions) of some chromosomes

The structure of nucleus and nucleolus

Nucleolus

1.fibrilar center-rRNA genes and Pol RNA I

2.Dense fibrilar component –nascent rRNA and its processing

3. Granular component –assembly of ribosomal subunits

NucleusNuclear envelope with poresNuclear lamina – lamins IF

Euchromatin

Heterochromatin


Back to ribosome

Each ribosome has 3 distinct sides for t-RNA bindingA - aminoacyl, P – peptidyl,and E – exit sideDuring the protein synthesis only 2 of these side can bye occupied by T-RNA at the same time


The information of amino acid sequence in proteinis coded by triplets of nucleotides in mRNA

- codones

Initiation codone

Terminationcodone

Each codon codes only one amino acidOne amino acid can be coded by more than one codon


tRNA (transfer RNA) transport the AA to ribosome and translate the tri-nucleotide code in mRNA

Pseudouridine loop

Dihydrouridine loop

Pseudouridine, Dihydrouridine –modified bases

Complemantary to codon in mRNA

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Figure 7-29 (part 1 of 2) Essential Cell Biology (© Garland Science 2010)

Decoding genetic code 1st stepCharging

aminoacyl-tRNA synthetase attaches a particular amino acid to the t-RNA with appropriate anti-codon


Decoding genetic code 2nd step

Anti-codon recognizes the appropriate codon in mRNA bycomplementary base paring

The protein is always being synthesized from the N- treminus or end (amino-terminus) protruding from the ribosome.

Translation of mRNA begins with initiator codon AUG recruiting Metionine -tRNA

Thereby newly synthesized protein has metionine on the N-terminus.

This metionine is removed later by specific protease

Some important data about protein synthesis at ribosomes Initiation of translation

• Initiation of translation requires special initiation factors

• Only the initiator t-RNA with metionin can bind the P side of ribosome small unit

• Metionine codon AUG is a signal for start of translation

• AUG codon enables also reading of the m-RNA massage in a proper reading frame

• without START signal mRNA can be read in 3 reading frames for 3 different amino sequences


START signal is necessary to choose a proper reading frame


1. The initiator t-RNA binds to the P-side of the small ribosomal subunit

2. The Initiator tRNA and small ribosomal subunit binds to mRNA

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3. Initiator tRNA and small ribosomal subunit moves along mRNA to find First AUG codon

4. Finding of first AUG codon, - stop movingFigure 7-35 (part 3 of 5) Essential Cell Biology (© Garland Science 2010)

5. After binding first AUG codon initiation factors dissociate

6. Recruiting and binding large ribosomal subunit


8. The full ribosome with initiator Met-tRNA at P-side

9. The next AA-tRNA binds to the A side of the ribosome


10. Formation of the first peptide bound between Metionine and the next amino acid

11. Metionine is translocated to the next AA at A-side of the ribosomeSynthesis od a peptide boundElongation of the peptide chain

Elongation of the peptide chain

The synthetized peptitdeIs attached to tRNA at A side


Peptide is attached to tRNAAt P side

Free A side

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Free A side bindsnewly charged tRNAWith amino acid

Complementary base paringCodon-Anticodon

Free tRNA is enjected From E side


STEP 1

Syntesis of new peptide boundPeptide chain is translocatedfrom tRNA at P side to Amino acid charged to tRNA at A side

New peptide boundElongation of a polypeptide chain


Elongation of the peptide chain - summary


TerminationSTOP codon reaches A sideNo Complementary tRNA

Release factor bindsTo A side


Termination

The –OH group from H2O moleculeis added to C-terminus of the polypeptide

The polypeptide is realized

Large subunit translocates


The ribosome dissiociates into subunits

END of translation

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Prokaryota

Prokaryota

EukaryotaProkaryota

Prokaryota

Figure 7-38a Essential Cell Biology (© Garland Science 2010)

More ribosomes can perform protein synthesis on the same m-RNAforming polyribosomes

Translation ihbibitors


Proteins exported from the cell to extra-cellular matrix are synthesized at ribosomes bounded to RER

Protein traffic after synthesis

Membrane enclosed compartment

Cytosol and Other Compartments

Protein traffic in the membrane enclosed compartment

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Nascent proteins with a signal sequence enter the ER


Signal peptidase removes the signal sequence

Proteins undergo posttranslational modifications to obtain their proper function and structure

Molecular help nascent proteins to chaperonsobtain the proper structure – folding process


In the ER proteins undergo N-glycosylation


From the ER proteins are transported into Golgi apparatus in vesiclesAs well as between all components of membrane enclosed compartment


In the Golgi apparatus porteins undergo further maturation and sorting

O-glycosylation

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Signal sequences for protein sorting

KDEL

MTS

NLSPTS

To Lysosomes mannose 6-phosphate

Figure 15-19a Essential Cell Biology (© Garland Science 2010)

Formation of coated vesicles


Docking of vesicles with the target compartment


To lysosome

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Endocytosis, endosomes and lysosomesProtein degradation in a membrane enclosed compartment


Phagocysosis and autophagocytosis

Non- vesicular protein traffic

Cell nucleus – native proteins

Mitochondria – unfolded proteinsPeroxisomes - unfolded proteins

Cytozol – free ribosomes

Degradation - Proteasomes


Mitochondria – transport of unfolded proteinsVia TOM/TIM trnspoters

Protein must undergo re-foldingin mitochondrial matrix (CHAPERONS)

Transport to peroxisomes

Defect in the transport to peroxisomes results in a fatal disease– Zellweger syndrome


Nuclear pore complex – transport of native proteins

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Cytosolic Protein Degradation

Ubiquitin – Proteasome SystemLysosomal degradation of cytosolic protins

Selective ribosomal degradation of cytosolic proteins (during starvation) requires unfolding of a protein and its tranlocation into lysosome

The Cytoskeletonand cell adherence

CytoskeletonComponents

• Microtubules- Tubulin;

• Actin filaments (thin filaments)- Actin;

• Intermediate filaments- keratin, vimentin or laminfilaments

Accessory proteins- linker, controller for assembly, and motor

In muscle cells - myosin filaments (thick filaments)

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CytoskeletonFunction

• Microtubules- movement of organelles, chromosomes (mitotic spindle) and vesicles inside the cell;

• Actin filaments (thin filaments)- movement of the whole cell, muscle contraction, movement of some vesicles inside the cell

• Intermediate filamentsGive the shape to cellsProtects from mechanical stress

Microtubules Actin filaments Intermediate filaments

- At the center of cells; made of tubulin- Finding the center of the cell- Motor Proteins Use the Microtubule Network as a Scaffold to Position Membrane-bounded Organelles

- beneath the plasma membrane

-Generate Cell Polarity

-Are involved in the movement of the cell

Mechanical Stress


Organization of microtubulesMicrotubules are hollow cylinders25nm in diameterComposed of protein called tubulin

forming tublin dimmers. Dimmers of tubulin are made of and

tubulin.

Localized mainly in the center of the cell protruding from microtubule organizing center

Take the role in the movement ofchromosomes OrganellesForm also:

Cilia Flagella

Tubulin and form a dimmerTubulin dimmers are polymerizedin protofilament13 parallel protofilaments are arranged in a helicoid, hollow microtubule Essential Cell Biology (© Garland Science 2010)

Microtubules are very dynamic structuresthey polymerize and depolymerize all the time

Each microtubule contains two and ends :puls end where

microtubule growths(new tubulin dimmers with GTP are added )

and minus end where microtubule gets shorter(shrink) (tubulin dimmers are released into cytoplasm)

Microtubules protrudes from centrosome into the cytoplasm

Centrosome contains two centroils

The minus end is located to the centrosome

The plus end to the cytoplasm

Microtubules are organized at centrosome

A centrosome w ith protruding microtubules


Microtubule-Organizing Centers – (MTOCs)-places where microtubule start assembling

• All MTOCs contain -tubulin• MTOCs are:

– Centrosomes containing• 2 centriols• PCM Pericentriolar material – amorphous matrix with-tubulin rings initiating tubulin polymerization at

nucleating sitesmicrotubule minus end in centriosome plus enlongates to

cytoplasm– Basal Bodies

• At Cilia & Flagella• Identical in structure to centrioles

Centrosome represent Microtubule-Organizing Centers

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Centrosome = two centriolsCentriol = 9 triplets of microtubules and

To perform their function in intracellular movmemt of organelles microtubules cooperate with two motor proteins that moves organelles, vesicles and chromosomes among microtubule:

There are to microtubule motor proteins:Dynein and Kinesin

Dynein – moves along microtubules from the + to – endKinesin – moves along microtubules from the – to + end

Motor proteins use ATP for energy to drive movements along microtubulesDynein – movement along microtubules from the + to – end

= to centrosome

Kinesin – movement along microtubules from the – to + end

= from the centrosome into the cytoplasm

ATP ADP


Microtubules anchored to centromere region chromosome by kinetochore


Movement of chromosomes is mediated by dynein as a motor protein moving

chromatides along microtubule

Microtibules bind to kinetochore (a protein ring surrounding centromere)

And dynein moves chromarides

Mitotic spindle

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Drugs acting on microtubules are used as anticancer drugs

Colchicine,colcemidVincrisine, vinblasintNocodasole-bind to the plus end and prevent tubulin polymerization

Taxol-Binds to mictotubuleand stabilizes them

By preventing depolymerization

Axonal transport of neurotransmiters in vesicles is mediated by microtubules

Anterograde transport ( form cell body to the synapse) = kinesinRetrograde transport (back to the cell body) = dynein

Microtubule based structures-Cilia and flagella

• Cilia line the epithelial tissue of the respiratory tract

• Cilia in the oviduct to push the egg

• Flagella allow sperm to move

Cilia and flagella

Bending movement

Basal body as a MTOC of cillia


Flagella and cillia are specialized microtubule-based structures

structure– Core – axoneme– Composed of – 9 peripheral doublets of microtubules + one

central pair– Dynein arms- movment– Nestin conections

Dynein causes the movement of cilia and flagella

Nestin connections tranform the slying movment of Dynein arms into bending mowment of cilium or flagemmum


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Actin filaments are thin and flexible

• 7 nm in diameter• Less rigid than

microtubules• Plus end - fast growing• Minus end - slow

growing• Monomers polymerize

into a helical chain


Actin polymerization requires ATPActin and microtubules polymerize using

similar mechanisms

• Monomeric actin binds to ATP• Upon polymerization, actin ATPase activity cleaves ATP

to ADP• ATP hydrolysis acts as a molecular “clock”• Older actin filaments with ADP are unstable and

disassemble

Myosin I can carry organelles or slide actin filaments along the membrane

Miosin I does not form any filaments


Myosin II slides actin filamentsMiosin II expressed only in muscles and forms myosin filaments moving along actin


Some of actin-binding proteinsPlus end

Minus end

Drugs acting on actin filaments

Cytochalasins - prevents polymerization of plus end

Phalloidin - prevents depolymerization -bind to the whole actin filament

Latrunculins - induces depolymerization on minus end

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• Structures formed by Microfilaments

Microvilli Stress f ibers contractile ring Migratory protrusions (podia)And cell cortex


• Mechanizm of cell migration

Special structures formed by actin filamentsThe microvilli are actin-based structures

They are tiny, hairlike structures on the surface of epithelial cells

involved in absorption and secretion

Microvilli• Microvilli are cellular extensions covered by plasma membrane,

which encloses cytoplasm and microfilaments.

• Each microvillus has a dense bundle of cross-linked actin filaments , which serves as its structural core .

• 20 to 30 tightly bundled actin filaments are cross-linked by bundling proteins fimbrin and villin to form the core of the microvilli.

• Bundle of a acitn filaments from microvilli are anchored in cytoplasm in the terminal web filaments .

• Thousands of microvilli form a structure called the brush border that is found on the apical surface of some epithelial cells, such as the small intestinal enterocyte and the kidney proximal tubule.

Microvilii are composed of actin filaments bundle and accessory proteins

VillinFimbrin - linking proteins

Myosin I - motor protein

Calmodulin -regulatory protein

Formin - capping protein

Summary of chemical agents affecting cytoskeleton


Anticancer drug

Anticancer drug

Clinical usage

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Myosins are actin-based motor proteins

• Myosins convert ATP hydrolysis into movement along actin filaments

• Many different classes of myosins (>30 in humans)

• Some myosins move cargoes, other myosins slide actin (as in muscles)

• Actin & ATP binding sites in N-termial head domain

Intermediate Filaments

• prevent the cell from mechanical stress and disruption of tissues

Intermediate Filaments

• The protein composition of IF varies with different tissue types.

•• They help maintain shape.

• Protect the cell from mechanical stress

• They attach cells together (cell to cell linkage).

• Intermediate Filaments– All classes have

• Central, rod-shaped -helical domain

• Flanked by variable globular domains

• rod-shaped -helical domains

– Spontaneously form coiled coils

• Both with same polarity– Dimer has polarity

Cytoskeleton

• Intermediate FilamentsCytoskeleton

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The nuclear lamina

IF composed of laminsNuclear lamina is crucial for integration of the nucleus


Nuclear lamina disrupts during mitosis

During M-phaselamins undergo phosphorylation leading to disrupture of nuclear lamina and thereby the nucleus

During thelophase lamins are dephosphorylated and nuclear lamina restores


Cell adherence and adhesion molecules

• Cell to cell junctions– Cadheris– Selectins– Immunoglobin-like molecules– Others

• Cell to ECM connections– integrins

Cell to cell adherence in the epithelial tissueby cadherins


• DESMOSOME (type of adherens junctions)

– Special cadherins- desmogleins – Interacting with IF (via adaptor proteins forming

plaque) within the cell and cadherin from adjacent cell


Strong bridge betw een IF f ilaments protecting disrupture of tissue upon stretching forces

• DESMOSOME


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Classical adhesion junctions: i.e. adhesion belts-classical cadherins-interacting with actin filaments

• Other type of junctionsOccludes junctions (thigh junctions)– Prevent passage of substances across cell layer (in

the space between cells)– Composed by occludis and claudins


• Other type of junctions• Gap junctions – communicating junctions or nexus

– Allow fast flow of ions between adjacent cells– Build electrical synapses– Composed of connecin forming connexons

• Cell to ECM connections– Mainly integrins– Epithelium to basal lamina

– Fibroblasts to ECM

• Epithelium to basal lamina• Hemidesonome – Integrins binding to laminin in basal membrane– Interacts with IF (via adaptor proteins)

lamininEssential Cell Biology (© Garland Science 2010)

• Connective tissue• Fibroblasts to collagen fibers via fibronectin

Integrins interacting with actin filaments via addaptor proteins in the cell and binding fibronectin in ECM

Fibronectin binds to collagen


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• Adhesion molecules are also involved in signal transduction

• Cells loosing their connections undergo apoptosis (cell death)


• Transient cell to cell connections by selectins• Selectins bind to oligosacharides (sugars) i.e.

during leukocyte rolling in blood vessels and diapedesis


• Transient cell to cell connections by Immunoglobulin superfamily cell adhesion molecules (IgSF CAMs)

• They interact either homophilic (binding to other IgSF CAM) or heterophilic (i. e. binding to integrins)

Summery of cell adhesion molecules

Families of CAMs• Calcium-dependent

– Integrins (heterotropic – to another molecule)– Cadherins (homotropic – to cadherin)– Selectins (heterotropic – to oligosacharides)

• Calcium-independent– IgSF CAMs (homotropic and heterotropic)

Summery of cell junctions


•END

selected cytoplasmtic processes review semiar cell ... · selected cytoplasmtic processes review...

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