Introduction to the Study of Cell Biology

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Introduction to the Study of Cell Biology

Cell is the smallest basic unit of a plant and animal. This is the definition defined

according to Cambridge Dictionaries Online

(http://dictionary.cambridge.org/dictionary/british/cell_1?q=cell). However, this definition

does not include other life forms such as bacteria, yeast, fungi, protozoa and algae, although

these organisms consist of single or multiple unit of cell. Also the definition does not state

the function of a cell. In biology, cell can be defined as “small, membrane-enclosed units

filled with a concentrated aqueous solution of chemicals and endowed with the

extraordinary ability to create copies of themselves by growing and dividing in two” (Albert

et al., 2010). This gives more details about cell physiology and its ability to regenerate.

As you can imagine about complexity in structure and function of human body, similar

condition can be found in the structure and function of our cells. However, complexity in

structure and function of cells is also depending on whether the cell belongs to prokaryote

or eukaryote. Generally, eukaryotic cell structures are more complex than those of

prokaryote. Furthermore, there are some differences in plant cells structures compared with

that of animal cells. Bacterium, a prokaryotic microorganism, is probably the simplest type of

cells. Great diversity is also found in size and appearance of cells as shown in figure 1.

Figure 1 Size and Shape of different cells (Albert et al., 2010)

Question: Is there so much variation of cells and tissues in terms of size, shape, and

organization in the past billion years compared with the present day? And why?

Structure of animal, plant, algal, bacterial, yeast and fungal cells

Animal, plant, algae, bacteria, yeast and fungi compose of cells. Each cell type has some

specific structures and functions. For example, flagellum is commonly found in organisms

that are able to move. Plant cell wall composes of polysaccharide such as cellulose. There

is no nucleus and nucleus membrane in a bacterial cell. Chloroplast is a common energy-

producing unit in a plant cell. This structure is not observed in yeast, fungal and animal

cells. It is also possible to detect variation in cellular structure within the same species.

However, there are some common structures among the mentioned organisms.

Structure of bacterial cell

A good resource about details of bacterial cell structure can be found online at Todar’s

Online Textbook of Bacteriology (http://textbookofbacteriology.net/structure.html). Figure 2

shows drawing of a typical bacterial cell. Table 1 gives function of some bacterial structures.

Figure 2 drawing of bacterial cell structure

(http://textbookofbacteriology.net/schematic_bacterium.jpg)

Not all bacteria have all these cell structures. Some may not have flagellum while others

may have more than one flagella. The composition of cell wall of Gram’s positive differs

from Gram’s negative bacteria. Some bacteria have large inclusion.

Table 1 function of bacterial structures

Structure Function(s) Predominant chemical composition

Flagella Swimming movement Protein

Pili

Sex pilus Stabilizes mating bacteria during DNA

transfer by conjugation

Protein

Common pili or

fimbriae

Attachment to surfaces; protection against

phagotrophic engulfment

Protein

Capsules (includes

"slime layers" and

glycocalyx)

Attachment to surfaces; protection against

phagocytic engulfment, occasionally killing

or digestion; reserve of nutrients or

protection against desiccation

Usually polysaccharide; occasionally

polypeptide

Cell wall

Gram-positive

bacteria

Prevents osmotic lysis of cell protoplast

and confers rigidity and shape on cells

Peptidoglycan (murein) complexed with

teichoic acids

Gram-negative

bacteria

Peptidoglycan prevents osmotic lysis and

confers rigidity and shape; outer membrane

is permeability barrier; associated LPS and

proteins have various functions

Peptidoglycan (murein) surrounded by

phospholipid protein-lipopolysaccharide

"outer membrane"

Plasma membrane Permeability barrier; transport of solutes;

energy generation; location of numerous

enzyme systems

Phospholipid and protein

Ribosomes Sites of translation (protein synthesis) RNA and protein

Inclusions Often reserves of nutrients; additional

specialized functions

Highly variable; carbohydrate, lipid, protein

or inorganic

Chromosome Genetic material of cell DNA

Plasmid Extrachromosomal genetic material DNA

Structure of algal cells

Algae are classified as a eukaryotic organism. There are both unicellular and multi-cellular.

There is a great diversity within algae. Some are unicellular organism; others are plant-like

organism, like seaweed. However, algae derive energy from sun light through photosynthetic

process. Although algae are similar to plants, they lack structures such as root, xylem and

phloem. Some algae do not have chlorophyll. They use other types of pigment to produce

energy. The structure and function of organelle in an algal cell is presented in Figure 3.

Figure 3 a Unicellular alga (a) and Yeast cell structure (b) (Talaro, 2002)

Structure of a yeast cell

Yeast is a microorganism which belongs to eukaryote. The structure of a yeast cell is

represented in Figure 3. A number of organelles inside the yeast cell can be observed

including vacuole, nucleus, endoplasmic reticulum, mitochondria, centrioles, etc. This is

typical of the eukaryotic organism. As yeast reproduce asexually by budding, there is a bud

scar left on the surface of cell wall.

Cellular structure of fungi

Fungi are multicellular organisms in the form of filament. Septum is a cellular structure that

separates two adjacent fungal cells from each other. Some species of fungi lacks this

structure. Asexually, the growth of fungi is at the tip of hyphae. A special cellular structure

of fungi is spore. There are many types of spores depending on the specie of fungi.

Internally, the ultrastructures are similar to that of other eukaryotes and presented in Figure

4. The growth of fungi is active at their tips. On the contrary, the aged hyphae may break

due to autolysis.

Figure 4 Ultrastructure of fungal hyphae (Deacon, 2006)

Cellular structure of animal and plant cells

The structures of animal and plant cells are similar because both of them are eukaryotic

cell. Plant cells tend to be bigger. They consist of membrane-bound organelles such as

nucleus, mitochondria, endoplasmic reticulum, etc. The functions of organelles of the two

are similar. However, they do have some differences. This includes the lacks of cell wall,

vacuoles and chloroplast in animal cells compared with plant cells. Figure 5 shows

structural details of animal and plant cells.

Figure 5 The structure of bacteria, animal and plant cells (Albert, 2003)

Basic structure of prokaryotic and eukaryotic cells

The previous section gives examples of cell components of bacteria, fungi, yeast, algae,

animal and plant. Several analogous components can be observed, although there are some

variations. As we know now, cells can be classified into either prokaryotic or eukaryotic type.

The first one is simpler. It consists of a single closed compartment that is surrounded by the

plasma membrane, lacks a defined nucleus, and has a relatively simple internal

organization. Prokaryote can be either single (bacteria) or multi-cellular organisms (some

cyanobacteria). On the other hand, eukaryotic cells are commonly larger and more complex.

Structurally, they contain membrane-enveloped nucleus and the organelles. Both types of

organisms contain significant amount of water inside their cells, cytosol. Figure 6 shows basic

structures of prokaryotic and eukaryotic cells.

Figure 6 Basic structures of prokaryotic and eukaryotic cells

Question: Structurally, how are prokaryotes differ from eukaryotes?

Question: What is the function of each cell component?

Origin of life

A cell is the basic unit of life. One of the most skeptical questions is where the cell comes

from. In the cell theory of Schlieden and Schwan, a cell must comply with three principles

including

1. All living organisms are composed of one or more cells

2. The cell is the most basic unit of life.

3. All cells arise from pre-existing, living cells.

Based on this theory, the first and the second principles are true. However, the third

principle cannot be applied with the first cell on Earth. This raises the question “How is the

first cell occur on Earth?”. In 1950s, Stanley Miller and the colleges showed that they can

synthesize amino acids by charging atmosphere consisting of H2, CH4 and NH3 in the

presence of water. Although this is not the precise condition of primitive Earth, they clearly

show that simple molecules can be created spontaneously by nature. Similarly, the

occurrence of macromolecules such as proteins and DNA should be the same scenario.

Apart from these two components, proteins and DNA or RNA, primitive cells must consist of

at least cell membrane to protect and enclose pools of enzyme, DNA or RNA and those

necessary for cell replication inside. In order for cell to thrive and self-replicate, it must have

some mechanisms to generate energy. It is expected that there is no oxygen in the

atmosphere of Earth at the beginning. Therefore, the energy-generating reaction should

involve the breakdown of organic molecules in the absence of oxygen. This is similar to

glycolysis. The next evolution of origin of life is photosynthesis reaction. This reaction

produces oxygen and change Earth’s atmosphere. Later, oxidative metabolism (respiration)

evolves. Another critical in cell evolution is acquisition of membrane-enclosed sub-cellular

organelles, especially mitochondria and chloroplast, by endosymbiosis. This is supported by

the evidence that both mitochondria and chloroplast have their own DNA and systems for

self-replication. Multicellular organisms, then, evolve from aggregation of unicellular

organisms (eukaryote). Complexity of multicellular organisms increases as a result of cell

specialization. This is the case for animal cells, which has several types of cells. The first

cells seem to emerge on Earth around 3.8 billion year ago.

Question : What is endosymbiosis?, Please explain the evolution of mitochondria and

chloroplast?

Surprisingly, researchers at J. Craig Venter Institute in United State of America have

successfully created a chemically synthesized genome that can control cells of

Mycobacterium mycoides in their laboratory

(http://en.wikipedia.org/wiki/Mycoplasma_laboratorium). This proves that DNA can be

created from a chemical synthesis. Their work is very useful for the future applications. For

example, bacteria that have a specific function might be created such as biogas producing-

or carbon dioxide absorbing bacteria.

.

Figure 7 Spontaneous formation of organic molecules (Cooper and Hausman, 2007)

History and progress of cell studies

Initially, the history of cell studies closely associates with the invention of

microscope. The first compound microscope is invented in 1950 by Francis Janssen and

Zacharias Janssen. Their microscope can magnify only at 10x to 30x. During 1564 – 1642,

Galileo Galilei invented a simple microscope having only single lens. The use of microscope

to study biological samples such as tissues of kidney, brain, liver, spleen, etc. is done by

Marcello Malpighi (1628 – 1694). However, the first scientist which was the first to define the

word “cell” is Robert Hooke (1635 – 1703). Then, in 1675, Anton van Leeuwenhoek was the

first to examine free-living cell by using his microscope. During 19th century, cell theory has

been formulated through many discoveries. Mathias Jacob Schleiden and Theodor Schwan

postulated that a cell is basic unit of life during 1838 and 1839. Then, K. Nageli as well as

Rudolf Virchow suggested that cells arise from the division of the pre-exist cells. Since then,

numerous discoveries in cell biology have been made as shown in the table below (Verma

and Agarwal, 2005). These findings correlate with the advances in novel technologies such as

electron microscope, fluorescence microscopy, X-ray diffraction, immune-technology,

chromatography and electrophoresis. Some of microscopic instruments commonly used to

study cell are reviewed in the following section.

Microscope

Prior to go to the detail of each microscope, it is worth to look into the scale of

things, especially cells. The scale of things is presented in Figure 8. Individual cell of

organisms is generally small that hardly be seen by unaided eye because human eye can

see the smallest objects no less than 0.1 mm long

(http://learn.genetics.utah.edu/content/cells/scale/). The first invented compound

microscope belongs to light microscope classification. Its magnification is very low, ~ 9x

(http://www.history-of-the-microscope.org/history-of-the-microscope-who-invented-the-

microscope.php). To date, modern light microscopes can magnifiy object up to 2000x

(Talaro, 2002). In detail, the limitation is not about the magnification power. The limitation

depends on resolution. Resolution or resolving power is defined as the ability of an optical

system to separate two objects from one another (Talaro, 2002). Resoving power of any light

microscopic system can be calculated from an equation provided below.

푟푒푠표푙푣푖푛푔 푝표푤푒푟 = 휆

2 × 푁. 퐴.

This means that resolving power of a microscope system can be decreased by decreasing

wavelength or increasing numerical apperture of objective lens.

As we all know, microscopes are invented to help researchers to study detail of minuscule

objects. Light microscopes use light as a light source with broad spectrum of wavelength. To

use this microscope effectively, samples are needed to be prepared as thin as possible.

Staining helps researchers to see objects clearer. Nevertheless, some specific details inside a

cell, expecially for the very tiny one, can not be seen or differentiated from other

components. There are other types of light microscopes such as dark field-, phase contrast-,

and differential interference microscopes.

Figure 8 Size of object and tools commonly used to study (http://micro.magnet.fsu.edu/cells/)

Fluorescence microscope

Fluorescence microscope can be classified as one type of light microscope. Fluorescence

microscope use UV light as their light source. It is a sensitive method to study intracellular

structure of cells. Generally, fluoresence occur when high energy light (a wavelength) is

radiated on some substances that absorb light energy making a shift in electron to an exited

state and then release energy as emission light or fluorescence out (another wavelength).

The electron come back to their normal state. Fluorescence dyes coupling with antibodies

are used to stain or fix on the specific structure of a cell. This is very useful. The staining can

be used with living cells as well. With an advance in DNA recombinant and green

fluorescence protein (GFP), the DNA sequence of this protein can be fused into DNA

segement of the target protein which when expressed, it can be seen by fluorescence

microscope. Nevertheless, the images obtained by fluorescence microscope are not clear as

a result of out-of-fucus fluorescence. Confocal microscopy solves this problem by detecting

fluorescence signal from only a single point at a time. Laser is used as a light source. The

image from confocal microscope is very clear compared to that of fluorescence microscope.

Nevertheless, both of them still have limitation of resolution as a result of light diffraction

which both of them still use light source. Recently, there is a break through in fluorescence

microscopy. The new technique is collectively called super-resolution fluorescence

microscopy. This techninue solves the problem of light diffraction by various methods

including SNOM/NSOM, TIRFM, SIM, STED or PALM (Schermelleh et al., 2010). In principle, the

fluorescence signal from fluorephore dyes is reduced to that of single spot of single

molecule. Each method have their own principle and limitation. Nevertheless, the resolution

of these super-resolution fluorecence microscopy is much better than normal fluorescence

microscopy. For example, STED and PALM give images with the lowest resolution (xy) at 20

nm. Figure 9 shows pictures taken by super-resolution fluorescence microscopy compared

with other methods. It can be seen that the details of images taken by super-resolution

fluorescence microscopy is much better than the conventional methods. Apart from its

specificity, which is one of many advantages, it can be use to study structures and well as

interaction between structures of living cells.

Electron microscope

Electron microscope or EM is pobably one of the most powerful microscopes. Instead of

light, EM use electron which have very short wavelength, 0.004 nm. This value should give

vaery low resolution. Another factor affecting resolution is numerical apperture of lens. In

EM, electromegnetic lens is used instead of glass lens. The numerical apperture of

electromegnetic lens is 0.01. Theoretically, the limitation in resolution of images taken by

EM is at 0.2 nm. In reality, it is 1-2 nm. There are two types of EM; Scanning electron

microscope (SEM) and Transmission electron microscope (TEM). In TEM, the sample is

prepared as thin as possible using a microtome and stained with salt of heavy metals. The

beam of electron that pass through the stained sample is collected and the signal is used to

create an image (apear white). The stained components appear dark as a result of electron

scattering. The chemicals commonly that are used as stains are osmium tetroxide, uranyl

acetate, and lead citrate. Apart from these chemicals, Antibodies labelled with heavy metal

salts can also be used similar to that used in fluorescence microscopy. For SEM, it is used to

study 3 dimentional structure of a sample. The electron beam does not pass through the

sample as in TEM. The samples in SEM have to be coated with heavy metal, so the scatter

electron from the surface is then collected and use to create an image. The resolution of

SEM is about 10 nm, therefore it is suitable to study structure of whole cell instead of detail

structure inside. The drawnbacks of the EM are the incapability in studying live cells as well

as the tedious sample preaparation and costs compared with light microscopy.

Scanning probe microscopy

Scanning probe microscopy was invented in 1981. It uses several kinds of probes to examine

the surface of a specimen by using specially design probes. Its resolution is very high to an

atomic level. In addition, there is no need for sample preparation. Scanning tunnelling

microscopy and atomic force microscopy are two examples of scanning probe microscopy.

Question: What kind of instrument that is suitable for investigating the structure and

function of mitochondria, cell surface, flagella, microtubule? And Why?

Figure 9 Images talen by super-resolution fluorescence microscopy (Schermelleh et al.,

2010)