Organization of Eukaryotic Cells

The eukaryotic cell contains organelles, which are defined as membrane-bound structures such as nucleus, mitochondria, chloroplasts, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, peroxisomes, etc.  Prokaryotic cells do not have organelles.

For animal cells, the cell surface consists of the plasma membrane only, but plant cells have an additional layer called cell wall, which is made up of cellulose and other polymers.

The nucleus is the largest organelle in an eukaryotic cell.   It is not part of the cytoplasm.  By definition, cytoplasm is everything inside the plasma membrane except the nucleus.

Under microscope, the nucleus shows two distinct areas.  The darker area is called nucleolus, and the lighter area is known as nucleoplasm.

Cytosol is the cytoplasm excluding organelles.   It contains cytoskeleton, ribosomes, proteins and other smaller molecules.

Figure 1-A-3.  The organization of animal and plant cells.  Red color indicates the difference between them.

All biological membranes, including plasma membranes and all organelle membranes, contain lipids and proteins.   The lipids found in biomembranes are mainly phospholipids and cholesterol.  In the plasma membrane and some of organelle membranes, proteins and phospholipids are attached to carbohydrates, forming glycoproteins and glycolipids, respectively.

Figure 1-B-1.  Schematic drawing of a typical plasma membrane.

 Phospholipids

A phospholipid molecule consists of a hydrophilic polar head group and a hydrophobic tail.  The polar head group contains one or more phosphate groups.  The hydrophobic tail is made up of two fatty acyl chains.  When many phospholipid molecules are placed in water, their hydrophilic heads tend to face water and the hydrophobic tails are forced to stick together, forming a bilayer.

(a)

(b)

Figure 1-B-2.  Structure of a phospholipid (phosphatidylcholine). (a) Chemical structure. (b) A computer model.

 

Polar head groups:

Most phospholipid head groups belong to phosphoglycerides, which contain glycerol joining the head and the tail.  Examples of phosphoglycerides include phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, phosphatidylinositol, etc.

Fatty acyl chains:

The fatty acyl chain in biomembranes usually contains even number of carbon atoms. They may be saturated (neighboring C atoms are all connected by single bonds) or unsaturated (some neighboring C atoms are connected by double bonds). 

Table 1-B-1.  Cellular fatty acids.

Chemical Formula Name

Saturated fatty acid  

CH3(CH2)10COOH Lauric

CH3(CH2)12COOH Myristic

CH3(CH2)14COOH Palmitic

CH3(CH2)16COOH Stearic

CH3(CH2)18COOH Arachidic

CH3(CH2)22COOH Lignoceric

Unsaturated fatty acid  

CH3(CH2)5CH=CH(CH2)7COOH Palmitoleic

CH3(CH2)7CH=CH(CH2)7COOH Oleic

CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH Linoleic

CH3(CH2)4(CH=CHCH2)3CH=CH(CH2)3COOH Arachidonic

CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH Linolenic

     Note: In the bond-line representation,

Palmitic acid is represented as

Arachidonic acid is represented as

Cholesterol and Steroids

Cholesterol is absent from most prokaryotic cells, but abundant in the plasma membrane of mammalian cells.  It is used as a precursor to generate other important steroids.

Figure 1-B-3.  Structures of cholesterol and other important steroids.  They are characterized by four hydrocarbon rings, designated as A, B, C, and D.  Although cholesterol is made up of almost entirely hydrocarbons, it is still an amphipathic molecule (with both hydrophilic and hydrophobic parts) because it contains a hydroxyl group (OH).

 

Glycoproteins and Glycolipids

Glycoproteins are the proteins covalently attached to carbohydrates such as glucose, galactose, lactose, fucose, sialic acid, N-acetylglucosamine, N-acetylgalactosamine, etc.  Glycolipids are carbohydrate-attached lipids.  Their role is to provide energy and also serve as markers for cellular recognition.

The antigens which determine blood types belong to glycoproteins and glycolipids.  Click here for more information.

 

Blood Group Antigens

The antigens which determine blood types belong to glycoproteins and glycolipids.  There are three types of blood-group antigens: O, A, and B.  They differ only slightly in the composition of carbohydrates.

Figure 1-B-5.  Blood-group antigens.  All humans contain enzymes which catalyze the synthesis of the O antigen.  Humans with A-type blood also contain an additional enzyme (called A-type enzyme here) which adds N-Acetylgalactosamine to the O antigen.  Humans with B-type blood contain another enzyme (called B-type enzyme here) which adds Galactose to the O antigen.  Humans with AB-type blood contain both A-type and B-type enzymes while humans with O-type blood lack both types of enzymes.

The Nucleus

The cell nucleus consists of nuclear envelope, nucleolus and nucleoplasm.    Most chromosomes are located in the nucleoplasm, but portions of several chromosomes containing clusters of rRNA genes may get together in the nucleolus, forming the nucleolar organizing region.  The major role of the nucleolus is to produce rRNA.

Figure 1-C-1.  Schematic drawing of the nuclear envelope which contains two lipid bilayers.  A mammalian nucleus has about 4000 nuclear pores, each is formed by over 100 different proteins.  

 

Chromosomes and Karyotype

In a non-dividing cell, chromosomes are not visible by light microscopy, because chromatin spreads throughout the nucleus.  During the metaphase of cell division, the chromatin condenses and becomes visible as chromosomes.  At this time, each chromosome has been duplicated.  A chromosome becomes two sister chromatids attached at the centromere.

Figure 1-C-2.  Schematic drawing of chromosomes.   (a) During the metaphase of cell division, a chromosome becomes two sister chromatids attached at the centromere.  (b) Notations about the chromosome bands.  This figure uses human chromosome 17 as an example.

 

Chromosome banding

To see chromosomes by microscope, they are normally treated with chemical dyes, such as Giemsa.  The chromosome will appear as a series of alternate dark and light bands.  If Giemsa is used, the dark band is called G-band or G-positive band, and the light band is named G-negative band.   Similar banding patterns can be observed by using another dye, Quinacrine.   However, if chromosomes were treated in a hot alkaline solution before staining with Giemsa, a reverse pattern will be observed, namely, the original dark band will become light band, and vice versa.  For this reason, the G-negative band is also known as the R-band. 

Chromosome bands are named as follows.  Each chromosome consists of two arms separated by the centromere. The long arm and short arm are labeled q (for queue) and p (for petit), respectively.  At the lowest resolution, only a few major bands can be distinguished, which are labeled q1, q2, q3; p1, p2, p3, etc., counting from the centromere.  Higher resolution reveals sub-bands, labeled q11, q12, q13, etc.  Sub-sub-bands identified by even higher resolution are labeled q11.1, q11.2, q11.3, etc.  Traditionally, the short arm (p) is displayed on top of the long arm (q).  See Figure 1-C-5 for the banding pattern of the entire human chromosomes.  

Karyotype

Karyotype is the representation of entire metaphase chromosomes in a cell, arranged in order of size.

Figure 1-C-3.  The karyotype of human somatic cells.  A human somatic cell contains two sets of homologous chromosomes, which may be divided into two types: autosomes and sex chromosomes.  Autosomes are further divided into seven groups: A to G.  During the metaphase of cell division, each chromosome has been duplicated.   Therefore, this karyotype consists of 92 chromosomes.

 

Chromosome Numbers

A germ cell (sperm or egg) contains only one set of chromosomes.  It belongs to haploid, represented as 1n.  Somatic cells (cells other than germ cells) of sexually reproducing organisms are diploid, denoted by 2n.   In humans, the haploid chromosome number is 23, but the diploid chromosome number is 46. 

Table 1-C-1.  Chromosome numbers of common species.

Extremes:

Smallest number: The female of a subspecies of the ant, Myrmecia pilosula, has one pair of chromosomes per cell.  Its male has only one chromosome in each cell.

Largest number:  In the fern family of plants, the species Ophioglossum reticulatum has about 630 pairs of chromosomes, or 1260 chromosomes per cell.

 

Organelles in the Cytoplasm

By definition, organelles are the membrane-bound structures in a cell.  The nucleus is an example.  Other organelles are located in the cytoplasm such as mitochondria,  chloroplasts, endoplasmic reticulum, Golgi apparatus, peroxisomes, lysosomes, vacuoles and glyoxisomes.

Mitochondria

An eukaryotic cell contains many mitochondria, occupying up to a quarter of the cytoplasmic volume.  The size of a mitochondrion is about 1.5-2 m in length, 0.5-1 m in diameter, approximately the same as E. coli.  It has two membranes: outer membrane and inner membrane.   Mitochondria also have their own DNA (represented as mtDNA),

which encodes some of the proteins and RNAs in mitochondria.  However, most proteins operating in mitochondria still originate from nuclear DNA.

The major role of mitochondria is to produce ATP (adenosine triphosphate), which carries high energy to power most cellular processes.  Such energy is stored in the phosphoanhydride bonds of ATP (Figure from Lodish et al.).  During ATP hydrolysis, the bond is broken, releasing 7.3 kcal/mole of energy.  Many cellular processes can utilize the released energy by coupling with the ATP hydrolysis.

In animal cells, the major sources for the synthesis of ATP are fatty acids and glucose. Oxidation of an 18-carbon fatty acid can make 146 ATP molecules. By contrast, oxidation of one glucose molecule (6 carbons) can generate only 36 ATP molecules. 

The generation of ATP involves a series of electron transport. Inevitably, electrons may leak from the electron transport chain, producing free radicals.  This has been suggested to be the major mechanism involved in the aging process.  See "Mitochondria, Apoptosis and Aging".

Site of Interest:

 

Chloroplasts

Like mitochondria, a chloroplast also contains both outer and inner membranes on its surface.  Inside the chloroplast, there are many thylakoids, each is enclosed by a membrane.  Chlorophylls are located on the thylakoid membrane to absorb light for photosynthesis.

In the first step of photosynthesis, light energy is used to split water into hydrogen ions and oxygen molecules. The generated hydrogen ions will create a concentration gradient across the thylakoid membrane.  Movement of hydrogen ions through the membrane is coupled to ATP synthesis. The overall reactions can be written as

Like mitochondria, chloroplasts also have their own DNA, but most chloroplast proteins are still encoded by nuclear DNA.

 

Endoplasmic reticulum

Endoplasmic reticulum (ER) can be divided into rough ER and smooth ER.  The major role of rough ER is to process the newly synthesized peptides from ribosomes.  Therefore, the surface of rough ER is usually associated with ribosomes and thus appears "rough".  Smooth ER is involved in the synthesis and metabolism of lipids.   Hepatocytes are abundant in smooth ER.

Golgi apparatus

Golgi apparatus is a major site for sorting and modifications of proteins and lipids.   After proteins are sorted at rough ER, they are enclosed in transport vesicles and carried to the Golgi apparatus.  Some proteins could be modified into glycoproteins and then transported to other destinations.

 

Peroxisomes

Peroxisomes contain enzymes for degrading amino acids and fatty acids.  These reactions produce harmful hydrogen peroxide.  Hence, peroxisomes also contain catalase to convert hydrogen peroxide into water and oxygen: