the typical cell

The Typical CellThe Typical Cell• typical cell: 1. nucleus

2. cell membrane 3. cytoplasm -cytosol

-cytoskeleton 4. cytoplasmic organelles

-membranous-non-membranous

The Eukaryotic cell contains The Eukaryotic cell contains a nucleus and a cytoplasma nucleus and a cytoplasm

CytoplasmCytoplasm

• semi-fluid-like jelly within the cell• division into three subdivisions:

•1. fluid component: cytosol •2. supportive framework of proteins: cytoskeleton

•3. organelles – membranous and non-membranous

The CytosolThe Cytosol

•eukaryotic cells – cytosol is part of the cytoplasm

•fluid surrounding the organelles◦ about 55% of the cell’s volume◦ mostly water - 70-90% ◦ PLUS

◦ ions◦ dissolved nutrients – e.g. glucose◦ soluble and insoluble proteins◦ waste products◦ macromolecules and their components - amino acids, fatty acids◦ ATP

The CytosolThe Cytosol

•the cytosol has a unique composition with respect to extracellular fluids

Cytosol•higher K+•lower Na+•higher concentration of dissolved and suspended proteins (enzymes, organelles)•lower concentration of carbohydrates(due to catabolism)•larger reserves of amino acids (anabolism)

ECF•lower K+•higher Na+•lower concentration of dissolved and suspended proteins

•higher concentration of carbohydrates

•smaller reserves of amino acids

Cytoskeleton:Cytoskeleton:

•part of the cytoplasm•internal framework of the cell•gives the cell its shape and size•gives the cytoplasm flexibility and mechanical strength and support•anchorage points for organelles and cytoplasmic enzymes•also plays a role in cell migration and movement by the cell

•three major components1. microfilaments2. intermediate filaments3. microtubules

Cytoskeleton:Cytoskeleton:

Column of tubulin dimers

Tubulin dimer

25 nm

Actin subunit

7 nm

Keratin proteins

812 nm

Fibrous subunit (keratinscoiled together)

10 m 10 m 5 m

1. microfilaments = thin filaments made up of a protein called actin

-solid rods of about 7nm -twisted double chain of G-actin subunits-forms a dense network immediately under the PM and

throughout the cytoplasm

1. microfilaments = -function: 1. anchors integral proteins and attaches them to the cytoplasm

2. interacts with myosin 3. mechanical strength 4. cell shape5. forms cellular extensions called microvilli

2. intermediate filaments = more permanent part of the cytoskeleton than other filaments• range from 8 to 12 nm in diameter• five types of IF filaments – type I to type V• each cell type has a unique complement of IFs in their cytoskeleton• some cells also have specific IFs

• type I IFs = acidic keratins• type II IFs = basic keratins• type III IFs = desmin, vimentin• type IV IFs = neurofilaments• type V IFs = nuclear lamins

kidney cell - vimentin

-all cells have lamin IFs – but these are found in the nucleus

2. intermediate filaments = function: 1. give strength to the cytoskeleton

2. support cell shape3. anchors & stabilizes organelles4. transports materials

-tubulin

-tubulin

3. microtubules = hollow rods or “straws” of 25 nm in diameter

• made of repeating units of proteins called tubulin• tubulin is a heterodimer – two slightly different protein subunits• the basic microtubule is a hollow cylinder = 13 rows made up of tubulin dimers

3. microtubules - function: 1. cell shape & strength

2. organelles: anchorage & movement

3. mitosis - form the spindle 4. form many of the non-

membranous organelles- cilia, flagella,

centrioles

3. microtubules•in animal cells – microtubule assembly occurs in the MTOC (microtubule organizing center or centrosome)

-area of proteins located near the nucleus-within the MTOC :1. tubulin dimers and other proteins2. assembling MTs 3. modified MTs - called a centriole

3. Microtubules:• microtubules can be assembled as:

• a. singlet – hollow cylinder• b. doublet• c. triplet

• the microtubule is the singlet• modified microtubules are doublets and triplets –

specific functions

A. Centrioles: two modified microtubule structures at right angles to each other

-each centriole half is made up of 9 microtubule triplets -called a 9+0 array

-located in the heart of the centrosome -possible role in MT assembly???

-has role in mitosis - spindle and chromosome alignment

Non-membranous OrganellesNon-membranous Organelles

B. Cilia & Flagella

• cilia = projections off of the plasma membrane of eukaryotic cells

• exposed area is covered with plasma membrane - BUT NOT A MEMBRANOUS ORGANELLE

• about 0.25 um in diameter and only 20 um long• beat rhythmically to transport material • found in linings of several major organs covered with

mucus where they function in cleaningTrachea

B. Cilia & Flagella

• cytoskeletal framework of a cilia or flagella = axoneme

• contain 9 groups of microtubule doublets surrounding a central pair of singlets = called a 9+2 array

• cilia is anchored to a basal body just beneath the cell surface

• doublets and singlets are connected to each other

•flagella = resemble cilia-much larger 9+2 array-found singly per cell-functions to move a cell through the ECF-DO NOT HAVE THE SAME STRUCTURE AS BACTERIAL

FLAGELLA

B. Cilia & Flagella

Membranous OrganellesMembranous Organelles

•completely surrounded by a phospholipid bilayer similar to the plasma membrane surrounding the cell•allows for isolation of each individual organelle - so that the interior of each organelle does not mix with the cytosol

-known as compartmentalization •BUT THAT’S A PROBLEM•cellular compartments must “talk” to each other

Membranous OrganellesMembranous Organelles•therefore the cell requires a well-coordinated transport system in order for the organelles to communicate and function together

-“vesicular transport”

Membranous OrganellesMembranous Organelles

•major functions of membranous organelles

•1. protein synthesis & secretion – ER and Golgi•2. energy production – mitochondria•3. waste management – lysosomes and peroxisomes

• series of membrane-bound, flattened sacs in communication with the nucleus and the PM

• each sac or layer = cisternae• hollow interior of each sac = lumen (10% of total cell volume)• distinct regions of the ER are functionally specialized – Rough vs.

Smooth ER

1. Endoplasmic reticulum (ER)1. Endoplasmic reticulum (ER)

1. synthesis – phospholipids, lipids and proteins•proteins = transmembrane, secreted proteins & ER, Golgi and lysosomal proteins•phospholipids & lipids = for most of the organelles2. storage – intracellular calcium•presence of calcium pumps in the membrane for calcium uptake3. transport – site of transport vesicle production

1. Endoplasmic reticulum (ER)1. Endoplasmic reticulum (ER)

Rough Endoplasmic reticulum Rough Endoplasmic reticulum (RER)(RER)• outside studded with docked ribosomes

• continuous with the nuclear membrane • protein synthesis, phospholipid synthesis

Rough Endoplasmic Reticulum Rough Endoplasmic Reticulum (RER)(RER)

• two kinds of proteins enter the RER:1. ER proteins – retained in the ER2. proteins destined for the Golgi

ApparatusPlasma Membrane

Modifications in the RERModifications in the RER 1. folding of the peptide chain1. folding of the peptide chain 2. formation of disulfide bonds 2. formation of disulfide bonds 3. addition and processing of carbohydrates = 3. addition and processing of carbohydrates = glycosylationglycosylation

4. breakage of specific peptide bonds – proteolytic proteolytic cleavagecleavage

5. assembly into globular proteins assembly into globular proteins (more than one chain)

http://sumanasinc.com/webcontent/animations/content/proteinsecretion_mb.html

Import of Proteins into the RER• certain proteins need to get into the ER• transport across the ER membrane requires the

presence of an ER signal sequence (red in the figure)

• signal sequence is the first series of AAs in the polypeptide

http://www.rockefeller.edu/pubinfo/proteintarget.html

the signal sequence is translateda complex of proteins will bind this signal in the cytoplasm = signal recognition particle/SRPthe SRP/ribosome is bound by an SRP receptor in the ER membranethe ribosome is “delivered” to a “hole” in the ER membrane = translocon

Import of Proteins into the RER

http://www.rockefeller.edu/pubinfo/proteintarget.html

•the translocon recognizes the signal in the polypeptide and binds it

•rest of the translating polypeptide can now be “guided” into the ER lumen

•once the polypeptide is fed into the ER lumen – a peptidase cleaves the signal sequence off

•the polypeptide continues to be made & is modified

Import of Proteins into the RER

http://www.rockefeller.edu/pubinfo/proteintarget.html

• a non-membranous organelle – not surrounded by a phospholipid bilayer membrane

• 2 protein subunits in combination with RNA-large subunit = ribosomal RNA + ~50 proteins-small subunit = rRNA + ~33 proteins

•found in association with the ER = where the peptide strand is fed into from the ribosome•also float freely within the cytoplasm as groups = polyribosomes

2. Ribosomes2. Ribosomes

• extends from the RER• free of ribosomes• many enzymes found on the surface of the SER

1. lipid synthesis for membranes2. steroid biosynthesis 3. detoxification 4. transport vesicle formation5. cleaves glucose

Smooth Endoplasmic Reticulum Smooth Endoplasmic Reticulum (SER)(SER)

The ER- Golgi Pathway

Proteins that traffic through the ER-Golgi have three ultimate destinations:

1.Outside the cell = secreted proteins2.Plasma membrane 3.Lysosome = lysosomal enzymes

• stack of 3 to 20 flattened membrane sacs/cisternae• receives transport vesicles containing proteins from the RER • proteins travel through the stacks via transport vesicles• definite orientation: first stack = cis-face

middle stack = medial-face last stack = trans-face

3. Golgi Apparatus3. Golgi Apparatus

• definite orientation: cis face trans- face• the cis face is preceded by a cisterna called the cis

Golgi network• the trans face is followed by a cisterna called the

trans-Golgi network

3. Golgi Apparatus3. Golgi Apparatus

Named after Camillo Golgi in 1897

•site of final protein modification and packaging of the finished protein•functions:

•1. major site of carbohydrate addition to proteins = glycosylation•2. site for phosphate addition to proteins = phosphorylation•3. production of sugars•4. formation of the lysosome•5. packaging of proteins and transport to their final destination

•Golgi acts as a sorting station for transport vesicles

3. Golgi Apparatus3. Golgi Apparatus

Modifications in the Golgi = Modifications in the Golgi = GlycosylationGlycosylationglycosylation = addition of saccharides to specific amino acidsproduces a glycoprotein most plasma membrane and secreted proteins have one or more carbohydrate chains that help target them to the correct location◦ O-linked sugars are added to the polypeptide one at a time in the Golgi

◦ N-linked sugars are added as a group in the ER

Glycoprotein

Modifications in the GolgiModifications in the Golgi

◦ glycosylation starts in the ER◦ N-linked glycosylation – addition of N-

linked oligosaccharides◦ for the proper folding of the protein

◦ glycosylation continues in the Golgi◦ addition of O-linked oligosaccharides

to proteins◦ the sugars are found in the

cytoplasm but are transported into the ER & Golgi by specific transporters

◦ added by transferase enzymes

Medical Application: Medical Application: GlycosylationGlycosylation

O-linked glycosylation in the Golgi and blood type◦ sugars are added one at a time to the amino acids serine, threonine or lysine (one to four saccharide subunits total)◦ added on by enzymes called glycosyltransferases◦ human A, B and O antigens are sugars added onto the plasma

membrane of the RBC◦ gene for the glycosyltransferase has several “versions” or alleles◦ located on chromosome 9

Medical Application: Medical Application: GlycosylationGlycosylation

O-linked glycosylation in the Golgi and blood type

◦ everyone makes RBCs with the O antigen

◦ those with blood type A have a version of the glycosyltransferase which makes the A antigen by modifying this O antigen

◦ a different glycosyltransferase version is required to make the B antigen

◦ both glycosyltransferases are required for the creation of the AB antigen

some PM proteins and most secretory proteins are synthesized as larger, inactive pro-proteins that will require additional processing to become active◦ e.g. albumin, insulin, glucagon

this processing occurs very late in maturation◦ processing is catalyzed by protein-specific enzymes called proteases◦ occurs in secretory vesicles that bud from the trans-Golgi face

Modifications in the Golgi: Protein Trimming

targets:1. secretory vesicles for

exocytosis2. membrane vesicles

for incorporation into PM

3. transport vesicles for the lysosomee.g. digestive enzymes

SO - WHERE DO SO - WHERE DO PROTEINS GO AFTER PROTEINS GO AFTER THE GOLGI???THE GOLGI???

-proteins budding off the Golgi have three targets:

ER proteins stay in the ER◦ never traffic to the Golginever traffic to the Golgi◦ these ER proteins will have a retention signal

Ribosomal proteins◦ translation of ribosomal proteins are done in the cytoplasmdone in the cytoplasm by by

polyribosomespolyribosomes◦ imported into the nucleus for assembly with rRNA into large and

small subunits

mitochondrial proteins◦ the mitochondria has its own DNA, transcribes its own mRNA and the mitochondria has its own DNA, transcribes its own mRNA and

has its own ribosomes for translationhas its own ribosomes for translation

WHAT IF YOU ARENWHAT IF YOU AREN’’T ONE OF THESE PROTEINS??T ONE OF THESE PROTEINS??

• “garbage disposals”-dismantle debris, eat foreign invaders/viruses/food taken in by endocytosis or phagocytosis-also destroy worn cellular parts from the cell itself and recycles the usable components = autophagy-form by budding off the trans-Golgi network and then fusing?

4. Lysosomes4. Lysosomes

4. Lysosomes4. Lysosomes

-contains powerful enzymes to breakdown substances into their component parts-over 40 kinds of hydrolytic enzymes -these enzymes are collectively known as acid hydrolases

e.g. nucleases = breakdown RNA & DNA into nucleotides

e.g. proteases = breakdown proteins into amino acids

4. Lysosomes4. Lysosomes

• acidic interior - critical for function of these acid hydrolases

• lysosomal enzymes need to be cleaved in order to become enzymatically active

• done by the acidity of the lysosome interior

• acidic interior created and maintained by a hydrogen pump (H+ ATPase) that pumps H+ into the interior via Active transport

• chloride ions that diffuse in passively through a chloride channel forms hydrochloric acid (HCl)

5. Peroxisomes5. Peroxisomes::

• found in all cells but abundant in liver and kidney cells

• may arise from pre-existing peroxisomes or may bud from the ER

5. Peroxisomes5. Peroxisomes::

• major function is oxidation (breakdown) of long chain fatty acids (beta-oxidation)

• results in the conversion of the fatty acid into acetyl coA Kreb’s cycle

• beta-oxidation is done by oxidases = enzymes that use oxygen to oxidize substances

• generates hydrogen peroxide (H2O2)

• PROBLEM#1: H2O2 is very corrosive-therefore peroxisomes also contain an enzyme called

catalase to break this peroxide down into water and oxygen

• PROBLEM #2: the electron transport chain in mitochondria produces superoxide radicals (O2-) as a normal consequence of electrons “leaking” (from complex I)-peroxisomes also contain anti-oxidant enzymes to break down other dangerous oxidative chemicals made by the cell during metabolism

-other functions of peroxisomes:1. synthesis of bile acids2. breakdown of alcohol by liver cells

5. Peroxisomes5. Peroxisomes::

• site of energy production (ATP production)-via Cellular Respiration

- breakdown of glucose results in the production of ATP-initial glucose breakdown occurs in the cytosol =

Glycolysis-terminal stages occur in the mitochondria = Oxidative

Phosphorylation

-has its own DNA - maternal-reproduce themselves via dividing

6. Mitochondria6. Mitochondria

6. Mitochondria6. Mitochondria

-surrounded by two phospholipid bilayers•an outer mitochondrial membrane•an inner mitochondrial membrane•a fluid-filled space = mitochondrial matrix (contains ribosomes)

-the inner membrane is folded into folds called cristae – increased surface area for enzymes of the Electron Transport Chain and Oxidative Phosphorylation-the matrix contains enzymes for the Kreb’s Cycle

Cellular Respiration

http://biology.about.com/gi/dynamic/offsite.htm?site=http://www.sp.uconn.edu/%7Eterry/images/anim/ETS.htmlhttp://biology.about.com/gi/dynamic/offsite.htm?site=http://www.biocarta.com/pathfiles/krebPathway.asphttp://vcell.ndsu.nodak.edu/animations/etc/movie.htm

-glycolysis-transition phase-citric acid cycle-electron transport chain

Glycolysis

http://web.indstate.edu/thcme/mwking/glycolysis.htmlhttp://science.nhmccd.edu/biol/glylysis/glylysis.html

•literally means “splitting sugar”

•conversion of glucose (6 carbon sugar) into 2 molecules of pyruvate pyruvate (3 carbon sugar)

•results in the production of 2 ATP and 2 NADH molecules

•reactions of glycolysis take place in the cytosolcytosol

phosphorylation(ATP used)

isomerization

phosphorylation(ATP used)

2 ATP consumedno energy created

cleavage

NADH

http://web.indstate.edu/thcme/mwking/glycolysis.htmlhttp://science.nhmccd.edu/biol/glylysis/glylysis.html

•known as an electron carrier•produced through the produced through the reduction of NAD+ = reduction of NAD+ = nicotinamide adenine nicotinamide adenine dinucleotidedinucleotide

•reduced through the reduced through the addition of 2 electrons addition of 2 electrons

•electrons are added one at a electrons are added one at a timetime

•11stst electron electron negative negative chargecharge• this results in the addition of 1 this results in the addition of 1

H+H+

•22ndnd electron electron negative negative chargecharge• no place for the 2no place for the 2ndnd H+ to go H+ to go

•NADNAD++ + 2e- + 2H + 2e- + 2H++ NADH + NADH + HH++

•reaction is performed by a reaction is performed by a dehydrogenase enzymedehydrogenase enzyme

GlycolysisGlycolysis

http://web.indstate.edu/thcme/mwking/glycolysis.htmlhttp://science.nhmccd.edu/biol/glylysis/glylysis.html

•under aerobic conditions - pyruvate is converted into acetyl-coenzyme Aacetyl-coenzyme A (Acetyl-CoA) which then enters the citric acid cycle/Kreb’s Kreb’s cyclecycle

•under anaerobic conditions pyruvate is converted into lactate lactate (lactic acid)

Transition Phase: Oxidation of Transition Phase: Oxidation of Pyruvate to Acetyl CoAPyruvate to Acetyl CoA•before the citric acid cycle can begin- pyruvate must be converted to acetyl coenzyme A (acetyl CoA)

◦ links glycolysis to the citric acid cycle

•pyruvate is pumped into the matrix of the mitochondria by a transport protein

•then converted into acetyl coA by a large protein complex called the pyruvate dehydrogense complex• one portion removes a CO2 to make acetic acid; another portion

reduces the acetic acid; the third portion attaches coA acetyl coA

Pyruvate

Transport protein

CYTOSOL

MITOCHONDRION

CO2 Coenzyme A

NAD + HNADH Acetyl CoA

1

2

3•results in the creation of 2 more NADH + 2H+

Pyruvate processing

•pyruvate can be processed in many ways other than acetyl coA

•pyruvate can also be processed to form:◦ 1. lactate1. lactate – by animal cells in the absence of oxygen

◦ also produces NAD+ ◦ 2. ethanol2. ethanol – by yeast and bacteria

◦ pyruvate pyruvate acetylaldehyde acetylaldehyde ethanol + NAD+ ethanol + NAD+◦ catalyzed by alcohol dehydrogenase

◦ chemically a dehydrogenase removes 2 electrons and 2H+ from one substrate and adds it to another

◦ biologically, the dehydrogenase removes 2 electrons and 2 H+ and adds it to NAD+ NADH + H+

Medical Application: EthanolMedical Application: Ethanol

◦ in animals: ethanol ethanol aldehyde aldehyde ◦ also catalyzed by alcohol dehydrogenase alcohol dehydrogenase (ADH)(ADH)◦ there are at least 7 genes for synthesis of ADH◦ there are 5 classes of ADH genes ◦ breakdown of alcohol is done by ADH in the liver and the

lining of the stomach◦ this ADH is made of 3 subunits – encoded for by three genes:

ADH1, ADH2, ADH3 ◦ ADH2 and ADH3 genes show polymorphism – different

forms and activities found in different populations◦ expression of ADH differs according to sex and age◦ increases in women as they age; decreases in men as they

age◦ unprocessed alcohol has multiple targets

◦ the overall effect is to slow the functional processes of the brain cell

◦ inhibits production of GABA - commonly known as the brain's "brake" mechanism.

◦ toxic effects = drunk

state of California legal intoxication = 0.08%

Medical Application: EthanolMedical Application: Ethanol

Citric Acid cycleCitric Acid cycle

•named after Hans Adolf Krebs•Acetyl-CoA is combined with oxaloacetic acid -> citric acid

•the citric acid is converted into a series of compounds that eventually regenerates the oxaloacetic acid

•Cycle “turns” twice – one for each pyruvate

•while this cycle only runs in the presence of oxygen – no no oxygen is usedoxygen is used

Citric Acid cycleCitric Acid cycle

•conversion of succinyl coA results in a transfer of a phosphate group from succinyl coA to GDP GTP

•the phosphate group is then removed from GTP and transferred to ADP ATP

•cycle produces two kinds of electron carriers• 1. NADH • 2. FADH2

•2 “turns” results in the creation of: 6 NADH, 2 FADH2 and 4 CO2 + 2 ATP

Electron transport chainElectron transport chain

•electrons are electrons are transferred to oxygen transferred to oxygen - addition of H+ - addition of H+ forming water forming water

•electrons are transferred by a series of protein complexes in the inner mitochondrial membrane

•these complexes also serve as proton pumps – pump protons into the space between the two mitochondrial membranes

cytochrome coxidase

Electron transport chainElectron transport chain

electronsprotons

NADH dehydrogenase

cytochrome creductase

cytochrome coxidase

•three complexes• Complex 1 = NADH Dehydrogenase• Complex 3 = Cytochrome c

Reductase• Complex 4 = Cytochrome c Oxidase

•NADH transfers 2 electrons to Complex 1Complex 1

• the electrons are then moved from Complex 1 to Complex 2 by Complex 2 by a carrier called Q = a carrier called Q = ubiquinoneubiquinone

•electrons are then transferred electrons are then transferred then to Complex 3 by the Complex 3 by the carrier cytochrome ccarrier cytochrome c

•each of these enzyme complexes pump protons into the intermembrane space -creates a proton gradientproton gradient = source of potential energy

Electron transport chain

•as electrons flow through these complexes, energy is released

•this energy turns each of these three enzyme complexes into proton pumps

•complexes pump protons into the intermembrane space - to create a proton gradient proton gradient = source of potential energy

•as protons flow down their gradient back into the matrix, they pass through an enzyme complex called ATP synthaseATP synthase – which synthesizes ATP

Electron transport chainElectron transport chain

ATP-synthase – comprised of a:1.stator – two “½ channels” for H+ binding 2.rotor – multiple H+ binding sites3.internal rod4.catalytic knob

http://www.youtube.com/watch?v=3y1dO4nNaKY

Electron transport chainElectron transport chain

1. H+ ion flowing down its gradiententers the 1st half-channel in the stator2. H+ ions enter binding sites within therotor-binding of the H+ ions changes the rotorsshape so it rotates3. each H+ ion makes one complete turn before leaving the rotor and passing throughthe second half-channel within the stator4. spinning of the rotor, rotates the rod and then theknob below it5. rotation of the knob activates catalytic sites thatadd a P group to ADP

http://www.youtube.com/watch?v=3y1dO4nNaKY

INTERMEMBRANE SPACE

Rotor

StatorH

Internalrod

Catalyticknob

ADP+P i ATP

MITOCHONDRIAL MATRIX

ETC animations http://www.youtube.com/watch?v=xbJ0nbzt5Kw&feature=relmfu

http://www.youtube.com/watch?v=3y1dO4nNaKY

http://biology.about.com/gi/dynamic/offsite.htm?site=http://www.sp.uconn.edu/%7Eterry/images/anim/ETS.html

Preference for fatsPreference for fats

•in response to hormones like adrenalin – fats are hydrolyzed in adipocytes to form free fatty acids and glycerolform free fatty acids and glycerol

•the fatty acids are released into the blood where they are taken up easily by most cells and oxidized by the mitochondria

•in humans the oxidation of free fatty acids is quantitatively more important than the oxidation of glucose

Preference for fatsPreference for fats

•cytosol: cytosol: free fatty acids + coenzyme A = fatty acyl fatty acyl CoA CoA ◦ this fatty acyl CoA is converted into one molecule of acetyl CoA

and regenerates a new fatty acid that is short 2 carbon regenerates a new fatty acid that is short 2 carbon moleculesmolecules

◦ reduces one molecule of NADH and two molecules of FADH2 one molecule of NADH and two molecules of FADH2 electron transport chain

◦ the shortened fatty acid then recombines with coenzyme A and produces more acetyl CoA and a new shortened fatty acid

◦ the cycle repeats itself until only acetyl CoA is produced◦ this produces a tremendous amount of ATP