All mammalian cells are eukaryotic, and whilst the eukaryotic type of cell is not exclusive to mammals, mammalian cells differ from other eukaryotic cells because of the organelles that are or are not present. For instance some plant cells have chloroplasts which are not present in mammalian cells, but both plant cells and mammalian cells are eukaryotic in nature. The term eukaryotic refers to the cell having specific membrane bound organelles, which are not present in prokaryotic cells. The defining feature of a eukaryotic cell is usually its membrane bound nucleus (the exception being the red blood cell) .
Because of the sheer number of organelles in eukaryotic cells I will not be describing each independently and fully in this essay. Instead I will first provide an overview of the organelles involved in protein synthesis so as to give a logical order and clearer picture of each independent organelles specific function, and then move on to some of the most important organelles with a more independent function. The membrane that bounds the organelles into specific space is called a phospholipid bilayer.
As shown in Fig 1, the bilayer is permeated with different types of protein, glycolipid etc. These allow the transmembrane movement of molecules that would otherwise be unable to permeate the phospholipid bilayer. This is necessary for the correct flow of molecules from one side of the membrane to the other, so the organelle is not starved of vital nutrients or unwanted electrochemical gradient is made, for example.
The nucleus usually the largest organelle in a mammalian cell, and like almost all other organelles is encased within a phospholipid bilayer. The phospholipid bilayer, as can be seen in Fig. 1 has different channels and routes which different molecules can diffuse or be transported through. Unlike most other organelles, which have a single phospholipid bilayer, the nucleus is double layered.
At points this double membrane touches, forming nuclear pore complexes. This double membrane is necessary due to the need for macromolecular exchange through these pores that a normal phospholipid bilayer inhibits . The outer bilayer of the nuclear envelope is partially made up of endoplasmic reticulum, an organelle I will come onto later .
The nucleus is where the genetic code for the production of different proteins is stored, therefore controlling the enzymes present and thus regulating the activity of the cell. These genes are encoded in a long series of different combinations of the 4 DNA bases; adenine, thymine, guanine and cytosine. The long series of bases are attached to each other by hydrogen bonds, and each end has a pentose phosphate backbone that twists round into the double helix structure discovered by Crick and Watson in the late 60’s.
Within the nucleus is where chromatin is found. Chromatin is DNA strands wound around histones . Many chromatin fibres further condensed make up chromosomes. It is these chromosomes that hold the genetic code for that particular cell, and is the site for one of the first steps of protein synthesis. This is known as transcription.
The nucleolus is a non-membrane bound structure in the nucleus of eukaryotic cells. It is made up of proteins and nucleic acid. The nucleolus is responsible for ribonucleoprotein maturation, where ribosomal RNA is transcribed and combined to proteins to form nearly complete ribosomes .
The ribosome is made up of large complexes of RNA and protein. They are the most abundant RNA-protein complex in the cell. A ribosome is composed of two parts; the small subunit, and the large subunit. The function of the ribosome as a whole is to translate the genetic information in the form of RNA (gathered via transcription) into a chain of amino acids.
This chain will later become a protein. The large ribosomal subunit is responsible for the catalysis of the formation of the peptide bonds needed to bond amino acids to make a polypeptide. The small ribosomal subunit, amongst other things, is initiates the engagement of the mRNA and is responsible decoding the genetic information during translation .
The endoplasmic reticulum is specialised for protein processing and lipid biosynthesis. One of its primary functions is to regulate the ionic concentration in the cytoplasm via the movement of Ca2+, via ionic pumps and channels. It also contains enzymes responsible for the metabolising of drugs. Endoplasmic reticulum (ER) can come in two forms. As depicted in Fig. 2 Rough ER has ribosomes present as part of the membrane of the organelle and together with these ribosomes takes polypeptides and amino acids from the cytosol and synthesises proteins destined for attachment to cell membranes.
It is in the lumen of the rough ER that the proteins are folded into the specific three dimensional shapes that are so important for biochemical recognition and linking sites . It is called rough because of the presence of ribosomes makes the surface of the membrane look rough, unlike smooth ER, which lacks the ribosomes so the membrane looks smooth. Rough ER is composed of a large but convoluted flattened sac.
The main function of the smooth ER is the production of lipids and the metabolism of compounds (such as the breakdown of glycogen into glucose). Because of the different functions between the rough and smooth ER, different specialised cells will have different amounts of each; for example, hepatic cells have large amounts of smooth ER due to its role in the detoxification of excess alcohol and barbiturates from the blood . The release of calcium ions required for muscle contraction, in accordance with the sliding filament theory, also comes from the smooth ER.
The Golgi apparatus is a stack of flattened, membrane bound sacks, and has many vesicles associated with it. Due to the ability of phospholipid bilayers to fuse, soluble proteins and membrane molecules can pass from one side of the Golgi apparatus to the other, through the stacks of membranes . Enzymes, anchored within specific layers of the Golgi apparatus by transmembrane anchors, modify the amino acid chains into a tertiary structure. The modified proteins are then separated depending on where their final destination is.
The mitochondria are organelles separate from the synthesis of proteins, but they are still large, both in importance, complexity and actual size. The number of mitochondrion in a cell differs dependent of independent cell function, for example a goblet cell will use lots of ATP in the secretion of mucus, and will there for have a large amount of mitochondria in the cell. A single mitochondrion itself has two structurally and functionally distinct membranes. The outer membrane is a smooth phospholipid bilayer which envelopes the entire organelle.
The inner membrane, whilst following the outer membrane around the majority of the organelle, has lots of cristae. These cristae are long finger-like extensions from the inner membrane into the centre of the organelle. This causes the inner membrane to have a large surface area, thus increasing the efficiency of the mitochondrion (the inner membrane can have up to 500% more surface area than the outer membrane). Between the inner and outer membrane is the intermembrane space, and inside the inner membrane is called the matrix. As hinted at before, the function of mitochondria is the production of ATP, which is the almost universal macromolecule used for the release of energy in eukaryotic cells.
As can be seen from the summary of the biochemical process, Fig.3, which that occurs throughout the mitochondria to produce ATP is quite intricate and complex. In an extremely concise summary I will outline the key features of ATP production and where in the mitochondria that these stages occur. The first step is for a pyruvate molecule and an acetyl fatty acyl coenzyme A molecule (the products of a reaction with glucose that occurs in the cytosol) to enter through the outer membrane into the intermembrane space. These molecules pass through two separate transporter proteins embedded in the intermembrane membrane, and thus enter the inner mitochondrial matrix.
A series of reactions that occur in the matrix (called fatty acid metabolism and the citric acid cycle) ends with products that can be used in the synthesis of ATP from ADP + PI, via a series of oxidation and reduction reactions of differing energy levels along the electron transport chain, which is embedded in the inner membrane. This reaction is catalysed by the enzyme ATP synthase, which is also present in the inner membrane.
 – Molecular Cell Biology, 7th edition 2012, Harvey Lodish, Chris A. Kaiser, Anthony Bretscher, et al. Macmillian Higher Education.  – The structure of the nuclear pore complex, The Annual Review of Biochemistry 2011, Hoelz A, Debler EW, Blobel G  – http://www.ibiblio.org/virtualcell/textbook/chapter3/nucs2.htm  – Frank Schluenzen et al, Structure of Functionally Active Small Ribosomal Subunit at 3.3A Resolution  – http://www.unitus.it/scienze/corsonew/lezione11.html
 – Cell Biology, second edition. Thomas D. Pollard and William C. Earnshaw. Saunders Elsevier.  – http://biology.about.com/od/cellanatomy/ss/endoplasmic-reticulum.htm  -http://www.bscb.org/?url=softcell/er
 – Structure and Function of the Nucleolus, Current opinions in cell biology June 11th 1999, Scheer U, Hock R,  – http://www.ncbi.nlm.nih.gov/books/NBK21624/figure/A4351/?report=objectonly