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

Similar gene sequences between prokaryotes and eukaryotes suggests 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 ingest 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 then multiples within it. 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 bacteria 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 they are not alike in many other ways, 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 domain Bateria 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 microorganism. 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
There are many difference between prokaryote and eukaryote cells. The nuclear body of prokaryotes is not bounded by a nuclear membrane while eukaryotic cell have a nuclear body that is bounded by a nuclear membrane connected through pores with the endoplasmic reticulum. In prokaryotes, the nuclear body contains a circular chromosome and there is no nucleolus while in side eukaryotic cell, a nucleolus is present with one or more paired, linear chromosomes. Cell division in prokaryotic cell and eukaryotic cell is also different. In prokaryotic cells, the cell divides by binary diffusion and prokaryotic cells are haploid. In eukaryotic cells, cell division follows the process of mitosis; haploid sex cells in diploid. The cell membrane in prokaryotic cells is a phospholipid bilayer which usually lacks sterols while eukaryotic cell membranes contain sterols. The eukaryotic cell membrane is capable of endocytosis and exocytosis while prokaryote cell is not. A cell wall is present in plant cells, algea, and fungi which belong to the eukaryotes. The cell wall of eukaryotic cells never contains peptidoglycans. In prokaryotic cells, a few members of domain bacteria have cell walls which are composed of peptydoglycans. Member of the domain Archae have cell walls composed of proteins 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. Eukaryotes posses membrane-bound organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, and lysosomes. Chloroplasts serve as organelles for photosynthesis n eukaryotes. 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 prokaryotes, 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. Prokaryotes have actin-like proteins that contribute to cell shape and are involved in cell wall syntehsis.

### Eukaryotes

* Domain
** in the domain Eucaryota
* 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