# Structural Biochemistry/Prokaryotes and Eukaryotes
## Eukaryotes Originated from Prokaryotes

Similar gene sequences between prokaryotes and eukaryotes suggest that they originated from a universal ancestor and evolved into separate domains billions of years ago. Prokaryote evolved to eukaryote through several stages. An ancestral anaerobic (without air) eukaryote cannot metabolize efficiently due to its inability to oxidized fuel completely. To improve its metabolism, the ancestral eukaryote ingests a bacterial genome that is aerobic (with air). An aerobic metabolism is more efficient because fuel is oxidized to carbon dioxide. Once the bacterium is engulfed by the eukaryote, it uses the cell for replication. This symbiotic system can now carry out aerobic catabolism; thus, transforming anaerobic eukaryote to aerobic eukaryote. There are three major changes that occurred as prokaryotes evolved to eukaryotes. First, the mechanism needed to fold DNA into compact structure containing specific proteins and the ability to divide equally between daughter cell during cell division became more elaborate. Since cell are now larger, system intracellular membranes developed to create a double membrane to surround the DNA. Lastly, early eukaryotes were incapable of carrying out photosynthesis or aerobic metabolism until an aerobic bacterium is introduced to form endosymbiotic and to eventually form plastids. They are similar in their metabolic reactions and in the way they produce energy, as well as in regards to what both prokaryotic and eukaryotic cells are composed of. To name some of their similarities, both have their cells surrounded by plasma membranes, both contain cytoplasm, and they both contain structures of RNA and protein called ribosomes. Though variations are present, their distinct differences result from DNA mutations that have occurred over time.

### Eukaryotic Cells Evolved from Simple Precursors

Major changes of the simple cells lead to the development of Eukaryotic Cells
1. Cells were able to acquire more DNA, therefore mechanisms that required to fold DNA strands into complexes with more specific proteins and divide into daughter cells (cell division)
2. Growth of Cells- the cells grow larger in size allowed intramolecular membranes to develop, which led the development of double membrane surrounding DNA -RNA synethsis on DNA template from cytoplasmic process of protein synthesis on ribosomes became possible

### Prokaryotes

* Domain
** in the domains Bacteria and Archaea.
* Structure:
** Cell membrane: phospholipid bilayer that encloses the cytoplasm, serves as attachment point for the intracellular cytoskeleton and cell wall.
** Cell wall: rigid, outside of the plasma membrane. Its function is to determine the shape of the organism and to act as a vessel pressure, preventing over-expansion when water enters the cell.
** Nucleoid: analog to nucleolus of eukaryotes, nucleoid contains DNA, genetic material of the cell, but it is not enclosed by any membrane.
** Chromosomes: contains genetic information. Chromosomes make up nucleoid. Prokaryotic cells are haploid.
** Flagella: tail-like organelles in charge of movements of cells.
** Pili: shorter and thinner than flagella, used also for motility and adherence.
* Morphology of prokaryotic cells
Prokaryotic cells have a variety of shapes. These shapes are to describe, classify and identify micro-organism. Some common shapes are:
** Cocci: spherical shape
** Bacilli: cylindrical or rod shape
** Spirilla: a curves rod long enough to form spirals
** Vibrio: a short curved rod (comma) shaped
** Spirochete: long helical shape
* Cell division
** Prokaryotic cells reproduce through asexual reproduction. They usually are divided by binary fissions (breaking in half, forming two identical daughter cells) or budding (daughter cells grow out of the parent and gradually increase in size)
** Prokaryotic cells have their genes passed out completely to their daughter cells through mitosis. Genome is stored in chromosome.
* Energy intake
* Bacteria and Archaea are the main branches of prokaryote evolution.
** Generally, Bacteria and Archaea are quite similar in size and shape. They share the characteristics of prokatyotes but are different in many key structural, biochemical, and physiological characteristics.
Characteristics Bacteria Archaea Nuclear envelope Absent Absent
Membrane-enclosed organelles Absent Absent
Peptidoglycan in cell wall Present Absent
Membrane lipid Unbranched hydrocarbon Some branched hydrocarbons
RNA polymerase One kind Many kinds
Initiator amino acid for start of protein synthesis Formyl-methionine Methionine
Response to antibiotics Growth-inhibited Growth not inhibited
Histones associated with DNA Absent Present
Circular chromosome Present Present
Ability to grow at temperature >100C No Some species

#### Prokaryotes vs. Eukaryotes Cell

| | Eukaryotic Cell | Prokaryotic Cell |
| Nucleus | Present | Absent (nucleoid) |
| # of Chromosomes | More than one | One - but not a true chromosome; Plasmids present |
| Cell Type | May be unicellular or multicellular | Unicellular |
| True Membrane-bound Nucleus | Present (Lysosomes, Golgi-complex, Endoplasmic Reticulum, Mitochondria, Chloroplasts) | Absent |
| Telomeres | Present (Linear DNA) | Circular DNA; does not need telomeres |
| Genetic Recombination | Mitosis, fusion of gametes | Partial, un-directional transfer of DNA |
| Lysosomes/Peroxisomes | Present | Absent |
| Microtubules | Present | Absent (rare) |
| Edoplasmic Reticulum | Present | Absent |
| Mitochondria | Present | Absent |
| Cytoskeleton | Present | Present |
| DNA associated with proteins | Yes | No |
| Ribosomes | Larger (80S); 70S in organelles due to symbiosis | Smaller (70S) |
| Vesicles | Present | Present |
| Golgi Apparatus | Present | Absent |
| Mitosis | Yes | No; binary fission |
| Chloroplasts | Present in plants | Absent; chlorophyll is scattered in the cytoplasm |
| Cell Size | 10-100 µm | 1-10 µm |
| Permeability of Nuclear Membrane | Selective | not present in cell |
| Cell Wall | Present on Plant and Fungi cells (chitin) | Present (peptidoglycan) |
| Vacuoles | Present | Present |
| Flagella | Present; for movement | Present; for propulsion |
Campbell NA, Reece JB. 2008. Biology. 8th ed. San Francisco (CA): Pearson/Benjamin Cummings.
There are many difference between prokaryote and eukaryote cell. In nuclear body of prokaryote, the nuclear body is not bounded by a nuclear membrane while eukaryotic cell have a nuclear that is bounded by a nuclear membrane having pores connecting it with the endoplasmic reticulum. In prokaryote, the cell is covered by cell envelope, a structure varies with type of bacteria, while in eukaryote cell, there is cell membrane to separate the cell from outside environment and regulates movements of materials in and out of the cells. Circular, unorganized DNA molecule is located in nucleoid of prokaryote; on the other hand, linear DNA that is organized by histones is located in nucleus of eukaryote which the protector of nuclear envelope. In prokaryotes, the nuclear body contains a circular chromosome with the lack of histones (unwounded DNA). There is no nucleolus eukaryotic chromosome but a nucleolus, which is present with one or more paired, linear chromosome containing histones. This says that the DNA of eukaryotic cells are organized in nucleus and the DNA of prokaryotes cells are unorganized and floats free in the nucleolus. Eukaryotes sex cell and prokaryotes cell both have flagella, organelle that helps the cell move. Prokaryote's flagella is consist of two protein building block while eukaryote's flagella is complex and consisting of multiple microtubules. Eukaryotes have many organelles in cells such as mitochondria, golgi, lysosomes.... besides ribosomes, there is no organelles in prokaryotes. Prokaryotic cell on average are usually ten times smaller than eukaryotic cell. Cell division in prokaryotic cell and eukaryotic cell is also different. In prokaryotic cell, the cell divided by binary diffusion and prokaryotic cell are haploid. In eukaryotic cell, cell division follows process of mitosis; haploid sex cells in diploid. Cell membrane in prokaryotic cell is a phospholipid bilayer which usually lacking sterols while eukaryotic cell membrane contains sterols. Eukaryotic cell membrane is capable of endocytosis and exocytosis while prokaryote cell is not. Cell wall is present in plant cell, algea, and fungi which belong to eukaryote. Cell wall of eukaryotic cell never composed of peptidoglycan. In prokaryotic cells, a few member of domain bacteria have cell walls which composed of peptydoglycan. Member of domain Archae have cell wall composed of protein or unique molecules resembling but not the same as peptidoglycan. In cytoplasmic structures of eukaryote, the ribosomes are composed of a 60S and a 40S subunit forming an 80S ribosome. Internal membrane-bound organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are present. Chloroplasts serve as organelles for photosynthesis. A mitotic spindle involved in mitosis is present during cell division. A cytoskeleton is present. It contains microtubules, actin micofilaments, and intermediate filaments. These collectively play a role in giving shape to cells, allowing for cell movement, movement of organelles within the cell and endocytosis, and cell division. In prokaryote, the ribosomes are composed of a 50S and a 30S subunit forming an 70S ribosome. Internal membrane-bound organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes are absent. There are no chloroplasts. Photosynthesis usually takes place in infoldings or extensions derived from the cytoplasmic membrane. There is no mitosis and no mitotic spindle in prokaryote but fission and budding only. They may contain only actin-like proteins that, along with the cell wall, contribute to cell shape.

### Eukaryotes

* Domain
** in the domain Eukarya
* Structure
** Plasma membrane: A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems.
** Mitochondrion: Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.
** Cytoskeleton
*** Microfilaments
*** Intermediate filaments
*** Microtubules
** Nucleus: double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome.
*** Nuclear envelope: doubled membrane, enclosing the nucleus.
*** Nucleolus
*** Chromatin: contains genetic information of cells (DNA)
**** Chromosomes: only visible during cell divisions.
** Endoplasmic Reticulum (ER)
*** Rough ER: A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes.
*** Smooth ER: A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides.
** Golgi apparatus: A series of stacked membranes.
** Lysosome: A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell.
** Ribosome: Protein and RNA complex responsible for protein synthesis
* Cell division
* Energy intake
Eukaryotes that live in extreme environments tend to be microbial. Microbial life is present in all extreme environment with enough energy to support life. Eukaryote cells are very adaptable, but prokaryotes are a little bit more so. This is not conclusive due to many environments that have yet to be explored. Anaerobic environments lack oxygen, but eukaryote cells still manage to survive.
Thermophile eukaryote cells are resistant to high temperatures. These cells must adapt by modifying their lipid and cell walls. The heat is dangerous so modifications to resist heat are necessary.
Psychrophiles are cells that have adapted to extremely cold temperatures. An example would be Heteromita globosa, which is a heterotrophic flagellate that lives in Antarctica. Psychrophiles face an extra challenge in that they must make modifications to the lipid and cell walls in order to maintain fluidity. The cold temperatures cause cell walls to become rigid.
Acidophiles are cells that can survive in extremely acidic conditions. Until recently, there were only four organisms, all eukaryotic that could survive in near 0 pH conditions. The way acidophiles can survive in such low pH levels is not known, but it is suggested that it could be due to a strong proton pump or low proton membrane permeability.
Alkalophiles are cells that can survive in high pH levels. Some of these Alkalophiles can also be stable at neutral pH also which leads us to believe that the internal chemistry is highly resistant to environmental influence. Possible compartmentalization of eukaryotic cells could help this.
Barophiles are cells that survive in high pressure conditions.
Xerophiles are cells that survive in dry conditions.
Halophiles are cells that live in high saline conditions. These cells must face the problem of drying out by osmotic pressure. Eukaryotes such as flagellates thrive in such conditions.
* ↑ extreme conditions, November 20, 2012.