Eukaryotic organelles are not present in prokaryotes.
Summary of Eukaryotic Organelles (list format)
Summary of Eukaryotic Organelles (table format)
| Organelle | Role | Membranes |
| Nucleus | Contain & protect DNA. Site of transcription and partial assembly of ribosomes | 2 |
| Mitochondria | Produce ATP via Krebs Cycle and oxidative phosphorylation | 2 |
| Ribosomes | Synthesize proteins | 0 |
| Rough Endoplasmic Reticulum (RER) | Synthesis & modification of secretory, membrane-bound & organelle proteins | 1 |
| Smooth Endoplasmic Reticulum (SER) | Detoxification & glycogen breakdown in liver; steroid synthesis in gonads | 1 |
| Golgi Apparatus | Modification & sorting of protein, some protein synthesis | 1 |
| Lysosomes | Contain acid hydrolases which digest various substances | 1 |
| Peroxisomes | Metabolize lipids & toxins using H2O2 (peroxide) | 1 |
Protoplasm is the fluid within plant and animal cells. The protoplasm surrounding the nucleus is known as the cytoplasm. The protoplasm within the nucleus is the nucleoplasm. The protoplasm is mostly water, and its average elemental composition is:
| Oxygen | ………………….. | .75 + | |
|---|---|---|---|
| Carbon | ………………….. | .10 + | |
| Hydrogen | ………………….. | .10 | |
| Nitrogen | ………………….. | .02 + | |
| Sulfur | ………………….. | .002 | |
| Phosphorous | ………………….. | .003 | |
| Potassium | ………………….. | .003 | |
| Chlorine | ………………….. | .001 | |
| Sodium Calcium Magnesium Etc. |
………………….. | < .001 |
Most cells are between 10 and 100 micrometers. 1 micrometer is 10,000 angstrom units.
Structural Features of All Cells |
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| Chromosome | The chromosome is cDNA in prokaryotes. For eukaryotes, there are two categories: introns and exons. Introns are the noncoding regions of DNA. The chromosome is stored within the nucleus. The chromosome is divided into supercoiling domains (10-100 kb) and macrodomains (800-1000 kb). House-keeping genes essential for biosynthesis. | ||||||
|---|---|---|---|---|---|---|---|
| Cytoplasm | The cytoplasm contains salt, sugar, RNA, DNA, amino acids, ribosomes, and protein. It is made of 75% Oxygen, 10% Carbon, 10% Hydrogen, 2% Nitrogen, .2% Sulfure, .3% Phosphorous, .3% Potassium, .1% Chlorine. In prokaryotes, there is not a nucleus; therefore, transcription and translation occur in the cytoplasm. | ||||||
| Cell Membrane | The cytoplasmic Membrane is a permeable phospholipid bilayer. It is non-covalent, flexible, 8nm thick and as viscous as light-grade oil. To strengthen it are rigid planar molecules: sterols for eukaryotes and hopanoids for prokaryotes. It consists of glycerol, phosphate and fatty acids. Cations like Magnesium and Calcium stabilize the negatively charged phosphates. Primary function is to control movement of materials from one place to another. Hydrophobic bonds occur between nonpolar groups in water. The lipid Bilayer contains a strongly polar phosphate- or sugar-containing head of each molecule associating with water and nonpolar alkyl tails of the fatty acyl groups aggregating by hydrophobic interactions. | ||||||
| Membrane Proteins |
Membrane proteins are proteins embedded in the lipid bilayer.
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Structural Features of All Eukaryotes |
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| Mitochondria | |||||||
| Nuclear Envelope | |||||||
| Nucleolus | |||||||
| Nucleus | |||||||
| Smooth ER | |||||||
| Rough ER | |||||||
| Golgi Complex | |||||||
| Secretory Vesicles | |||||||
| Peroxisomes | |||||||
| Cytoskeleton | (cytoskeletal fibers) | ||||||
| Cell Wall | |||||||
Structural Features of Animal Eukaryotes |
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| Microvilli | |||||||
| Lysosomes | |||||||
Structural Features of Plant Eukaryotes |
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| Plant | |||||||
| Cell Wall | |||||||
| Vacuole | |||||||
| Chloroplast | |||||||
The surface area to volume ratio restricts cell size. Large cells have less surface relative to a small cells. Large cells produce more waste, but have proportionately less surface area through which to expel that waste. This means that waste will build up inside the cell and kill the cell. In addition, large cells need more nutrients, but have proportionately less surface area through which nutrients can diffuse. This means that large cells get proportionately less nutrients and can starve to death.
Cell size is restricted by surface area to volume ratio. Cells become large only when they are able to expel their waste quickly, and obtain nutrients readily. There are some cells which at first seem to contradict this rule:
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Cell Morphology
Biochemical Conditions
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The lipid bilayer consists of phospholipids. Phospholipids consist of a nonpolar alkyl attached to a phosphate. The nonpolar alkyl resembles a tail. These nonpolar alkyls are hydrophobic, meaning they repel water. As a result, when phospholipids are mixed into water, the nonpolar alkyls will join together and the attached phosphates will have contact with water. The result looks like:
The head of each molecule associates with water, while nonpolar alkyl tails of fatty acyl groups aggregate hydrophobically.
| Glycerophospholipids | A glycerol is attached to 2 fatty acyl groups and one phosphate group. The phosphate may in turn be linked to further groups: ethanolamine (phosphatidyl etholamine), choline (phosphatidyl choline), serine (phosphatidyl serine) or inositol (phosphatidyl inositol). |
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| Sphingolipids | A sphingosine linked to 1 fatty acyl group. Sphingolipids are usually linked to a phosphate plus a choline (sphingomyelin), sugar (ceramides) or a complex oligosaccharide (gangliosides). Sphingolipids are absent in most prokaryotes, but are oftentimes present in the outer face of the eukaryotic plasma membrane. |
| Lysophospholipids | Are phospholipids with 1 fatty acyl group removed. This promotes conversion of phospholipid bilayers into micelles, and may destabilize membranes. Substituting cis-unsaturated fatty acids decreases closeness of packing in the nonpolar layer. This increases fluidity and thereby increases movement of small polar molecules across the layer. Cholesterol reduces fluidity and penetration of small polar molecules. |
In the fluid mosaic model, proteins are able to move freely around in the lipid bilayer.
Some membrane proteins are able to move within the plane of the membrane, while other membrane proteins (particularly receptors) are restricted or can be clustered in response to stimuli. This model of membrane organization is called the fluid mosaic model because of the freedom of movement of lipids and some proteins in the membrane.
| Integral Membrane Proteins | Cannot be released from a membrane without breaking covalent bonds or disrupting the lipid bilayer. |
|---|---|
| Peripheral membrane proteins | Attached to integral membrane components (lipids or proteins) by noncovalent bonds. Peripheral proteins may be removed from a membrane by milder treatments than those needed to remove integral membrane proteins. |
| Transmembrane integral membrane proteins |
Contain at least one protein domain extended across the lipid bilayer. Most transmembrane domains adopt alpha helical secondary structure and consist primarily of amino acids with hydrophobic side chains. Some transmembrane integral membrane proteins form ion channels across the membrane; others are active transport or facilitated diffusion carriers; still others are receptors for growth factors or hormones. |
| Lipid Rafts | Lipid rafts are mobile membrane microdomains (small parts of the membrane) which are rich in sphingomyelin, glycosphingolipids and cholesterol. They can contain membrane proteins. |
The nuclear envelope consists of a lipid bilayer.
Long and fibrous lamin proteins form a layer of structural support for the nuclear envelope. Lamin is phosphorylated in prometaphase, causing a conformational change and the loss of laminal structural properties. Without laminal support, the nuclear membrane breaks apart and absorbs into the smooth endoplasmic reticulum. The endoplasmic reticulum breaks apart, but is bound to the lamin via the inner nuclear membrane Lamin B Receptor; and the lamin binds to chromatin.
As anaphase ends, dephosphorylation of existing lamin begins. Once the genetic material has fully segregated at the completion of anaphase, production of new lamin is well underway. The new lamin drags tubes of smooth endoplasmic reticulum across the surface of the chromatin; these tubes flatten and merge, forming a solid nuclear membrane. The endoplasmic reticulum and lamin detach themselves from the chromatin. In the mature daughter cell, the lamina is a continous layer that is bound to the inner membrane of the nuclear envelope by emerin proteins.
Eukaryotic cells are defined as having a nucleus, thus distinguishing eukaryotes from prokaryotes. The nucleus is an organelle containing the genome and complex machinery to control gene expression, and is separated from the cytoplasm by a double-membrane. From the nucleus, genetic information flows to the cytoplasm for utilization. In contrast, while eukaryotes encase their genome in a double-membrane, prokaryotes allow their genome to float in the cytoplasm (sometimes localized to one part of the cell).
| Event | Eukaryotes | Prokaryotes |
| Replication | Nucleus | Cytoplasm |
|---|---|---|
| Transcription | Nucleus | Cytoplasm |
| Splicing | Nucleus | Cytoplasm |
| Translation | Cytoplasm | Cytoplasm |
The nucleus is surrounded by a double-membrane (aka nuclear membrane, nuclear envelope and nucleolemma) and structural scaffolding (the nuclear lamina). This double-membrane keeps DNA and proteins that function in the nucleus segregated from the cytoplasm. Some argue that the nuclear envelope originated as an endosymbiont; others argue the nuclear envelope originated as an invagination of the cellular membrane. The nuclear membrane is contiguous with the endoplasmic reticulum membrane and is reinforced by a cytoskeletal scaffold called the nuclear lamina. Also, the nuclear membrane is laden with huge protein complexes that create nuclear pores that control the passage of molecules in and out. The nucleus also contains specialized structures such as: the nucleolus, a large dense structure where rRNA is transcribed and processed and where ribosomes are assembled; the smaller cajal body, where snRNPs are assembled.
Prokaryotic mRNAs are polycistronic, meaning they encode multiple proteins and do not require a special structure to specify the correct reading frame. However, eukaryotic mRNAs are monocistronic, meaning they only encode a single protein and require a special 5’ cap structure to initiate translation. In eukaryotes, the DNA is transcribed into precursor RNA; pre-mRNA is processed to form mRNA; and the finished mRNA proceeds to the cytoplasm for translation. Translation of unprocessed RNA is detrimental. The nucleus is essential for eukaryotes, separating this unprocessed RNA from the translation machinery in the cytoplasm.
Hydrogenosomes metabolize carbohydrates into ATP and H2. Metabolism in the hydrogenosome is similar to anaerobic bacteria (via enzymes including PFO and ferredoxin) and mitochondria (via Krebs cycle enzymes that convert acetyl CoA into acetate and succinyl CoA which is then converted to succinate and ATP).
Mitochondria and hydrogenosomes likely share an ancestral organelle: similar machinery used for protein translocation; similar signals used for protein translocation; phylogenetically related proteins (Hsp60); and a phylogenetically related ADP/ATP carrier protein. Techniques to explore this theory are shown below.
There are three different theories as to how the hydrogenosome could have arisen: as converted mitochondria; from a common ancestor with mitochondria; or arose independently from mitochondria through different endosymbionts. Hydrogenosome origins are difficult to pinpoint because unlike mitochondria it has no genome. Over time the endosymbiont that evolved into the hydrogenosome transferred all of its genes to the nucleus.
Hydrogenosome function can be characterized as follows: isolate hydrogenosomes; fractionate samples; run on a 1D gel, using Zn chelating chromatography or Na2CO3 extraction; perform a gel trypsin digest; recover the tryptic peptides; use mass spectrometry to get the protein sequence; and run the sequence through databases. From this, a pie chart can be made of hydrogenosomal proteins’ function, revealing most to be small GTP-ases.
| Technique | Overview |
|---|---|
| Phylogenetics | It turns out that the Hsp60 protein in the hydrogenosome branches with a monophyletic group (99%) composed exclusively of mitochondrial homologues and this branches right next to the proteobacteria group (73%) from which the mitochondria are thought to have arisen. |
| Characterization | Organelles with a common origin are predicted to have common protein translocation signals and machinery. Incidentally, hydrogenosomal matrix proteins have mitochondrial-like targeting presequences. To determine if this signal is necessary for organelle targeting in vitro and in vivo, membrane translocation components may be characterized. These components must have evolved as the endosymbiont was converted to an organelle, revealing the evolutionary history. |
The apicoplast (aka plastid) is an organelle found exclusively in the apicomplexan phylum. The apicoplast has a 35kb genome and is surrounded by 4 membranes. Although its genome can be isolated and sequenced, the apicoplast itself cannot be isolated. The apicoplast is also known as a plastid, as drugs against chloroplasts and prokaryotes also kill apicomplexan parasites.
Phylogenetics and GFP tagging reveal that nuclear-encoded proteins of apicoplast origin localize to the apicoplast. Thus, localization of apicoplast proteins is regardless of where they are encoded. Apicoplast proteins have three domains: hydrophobic signal sequence; transit peptide; and mature protein domain. Localization requires the signal sequence and transit peptide.
Identifying protein function via proteomics requires isolated organelles. Unfortunately, the apicoplast cannot be isolated. Thus a common sense approach has been used: all the proteins required for fatty acid synthesis were found in the apicoplast; thus, the apicoplast can probably synthesize fatty acids.
The apicoplast likely became encased in four membranes via a double endosymbiotic event. The chloroplast arose by engulfment of a cyanobacteria by a plant/algae ancestor. An algae was then engulfed by the ancestor of all apicomplexans. Thus an apicoplast organelle arose with four membranes.
The apicoplast genome was sequenced and found to be plastid-like. It encodes rRNA, tRNAs, ribosomal proteins and 5-6 genes related to chloroplast genes. Furthermore, drugs targeting prokaryotic and chloroplast enzymes also kill apicomplexans. Thus, it seems that the apicoplast arose from a chloroplast. Also, nuclear-encoded plastid-like proteins — ie, acyl carrier protein (ACP) or p59 — localize to the apicoplast. The same goes for proteins of plastid origin. But how?
Deletion and restoration identified an evolutionarily conserved apicoplast targeting signal at the N-terminus. Known as the ACP, this bipartite signal contains: a signal sequence to engage secretion; and a plastid-targeting domain to target the plastid. Fusing GFP to ACP targeted it the plastid. Analyzing numerous ACPs led to a consensus amino acid sequence. All translated proteins were screened for this motif at their N-terminus. This identifies putative apicoplast proteins.
Nuclear genes, morphology, biochemistry and pharmacology places apicomplexans with ciliates and dinoflagellates. However, presence of plastids suggest placement with plants and algae. This paradox is resolved by two stage lateral genetic transfer: an ancestral plant/algae cell engulfed a cyanobacteria; this evolved into a free-living algae; this algae was engulfed by an ancestral apicomplexan. Plastids and mitochondria arose via engulfment of eubacteria by eukaryotes.
Cells move to find food, shelter and safety.
| Flagellated | Flagella are polar, bipolar, lophotrichous (bunch at 1 end), monotrichous, amphitricious and petrichous (E. coli). To view with high contrast, use die, electric microscope, or dark field. Help w/ attachment.
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| Random Walk | Cells move toward attractants (c-source), from repellent (organo acid) and indifferently to control (media). Requirements are (a) sense external signal, (b) respond to signal (internal signal), (c) modify behavior and (d) scalable response. E. coli: Tumble, run, tumble. Tumble every 10th sec, run 10 secs, T req of both 13 /sec. Random walk. The random walk is biased. As concentration of attractant goes up, the tumble frequency goes down. E. coli run ccw (bundle) and then unbundle and go cw to tumble. When the attractant concentration is high, the cw frequency goes down, unbundled is less likely to occur, and running (ccw) happens more often. Is the propellor or the whip model correct? Howeder saw that flagellum spin ccw, stop, cw, stop, ccw, etc. Algae is a good model organism for studying motility. Cilia are on protozoans (paramecium). Microtubule-based, extend from basal body, surrounded by cell membrane, mechanism=sliding & bending of microtubules. Running is more often in presence of attractant. |
| Ameboid Motion | Extend pseudopod…mechanism: actin, controlled polymerization of actin filaments at leading edge pseudopod….used by entamoeba protozoan for dyssentary, slime molds. |
| Gliding Motility | Smooth gliding with no apparent change in cell morphology. Example: toxoplamsagondii (very important)…malaria plasmoduan. Gliding motility somehow involves actin. Demonstrate via mutation to actin. |
| Length | # Per Cell | Motion | |
| Flagella | Long; > 5µm | 1-2/cell | Whiplike |
|---|---|---|---|
| Cilia | Short; <5µm | 100s/cell | Breast stroke |
Axoneme (9+2 structure, MT bundle) is 9 pairs of microtubules around central pair. Microtubules are made of a- and B-tubulin). Surrounded by cell membrane. Dynein, ATP-dependent molecular motor, attached to tubulin. Whip-like motion. Cilia are structurally the same.
1) Isolate intact flagellum
2) Remove membrane with detergent
3) Left with flagellic cytoskeleton.
4) Flagella still moves (sliding filament model)
Mutagenize wildtype cells so they cannot move. You can find the tightest colonies, or you can put them in a solution and find which ones sink to the bottom. Isolate a mutant, grow it up, and then grow up the ones from the bottom yet again. Transfer bottoms to fresh flask, and if they are motility mutants then all should settle. You then study those under a microscope. The mot(-) cells sometimes had no, stubby or rigid flagella. The ones with rigid flagella lacked radial spokes, so those are required for flagellic motility.
To determine which flagellar component was most important, the following experiment was performed.
There is another experiment possible, although it is not as reliable, where you screen for small colonies after transposon tagging.
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