Introduction - University of Tokyocsls-text.c.u-tokyo.ac.jp/pdf/Chap_01.pdfChapter 1 Diversity and...

Chapter 1 Diversity and Universality of Organisms

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CSLS / THE UN IVERS ITY OF TOKYO 11

Introduction

Chapter 1Diversity and Universality of Organisms

It is hard to give a concise definition of exactly what life is. One might define it

as the dynamic equilibrium of “living” itself, while others might say it consists of

entities with the hierarchy of substances, cells, tissues and individuals. Some may

even identify it as a machine coded by DNA or a vague existence with the soul.

To allow the simplest possible expression of the basics of life science, this chapter

deals with the following topics: what organisms are; how they came into existence

and evolved into their current diversity of biotic groups; the principles common to

all organisms; and the constituents and functions of cells, which represent the

smallest unit of an organism (in other words, the substances that constitute cells

and what their functions are). The account places particular focus on the diversity,

uniformity and hierarchy of organisms.

I . Diversity and Universality of Organisms

Organisms have long been classified by differences in morphology and lifestyle.

Higher animals provide a good example; variations in skeletal fossils have shown

that rabbits and mice, as well as elephants and dugongs, have evolved from

common ancestors, and that horses have evolved in a unilinear manner (in

accordance with orthogenetic theory). With this methodology, however,

variations that cannot be gleaned from skeletal morphology, such as skin color

and intelligence, have been overlooked.

All humans have different faces, skin colors and personalities, and these

characteristics are strongly influenced by genetic base-sequence differences. Just

one base-sequence difference results in significant variations in morphology and

phenotype (i.e., traits), as demonstrated by the occurrence of hereditary diseases.

In humans, polydactylism, achondroplasia and color blindness are examples of

this. In mice, a mutation in the hairless gene is known to produce hairless mice.

However, as genome analysis advances into the 21st century, it is becoming

increasingly clear that the diversity of organisms is determined by the organization

of genes and their expression patterns. It is interesting that genes are not the only

determinant. As an example, identical human twins have the same gene



composition but not the same personality; this stems from differences in the

expression pattern of genes among individuals. It is known that if one twin is

infected with a disease, the expression pattern of antibody genes in that twin

changes, resulting in a difference in resistance to the illness between the two

siblings. It is also clear that one twin mastering the piano at a certain stage of life

results in differences in the range of the motor and auditory areas of the brain. A

simpler example is that identical twins are born with different weights; this is

believed to be caused by a difference in nutritional balance between the two in

the mother’s body.

Humans, despite the varying appearance of different races, constitute a single

species as far as the reproductive pattern is concerned. This universality in

humans is obvious when compared with other primates; differences in intra-

species variation and inter-species gaps in terms of traits are clear between

humans and other primates, indicating the importance of understanding the extent

to which genes influence traits in defining species.

I I . What are Organisms?

Organisms have the following characteristics:

• They are made of units known as cells, each of which is surrounded by a

phospholipid bilayer.

• They self-replicate through DNA, a genetic material.

• They respond to stimuli from the surrounding environment.

• They synthesize adenosine triphosphate (ATP), an energetic material, and use

the energy produced for life and growth.

Let’s look at these characteristics more closely.

Organisms and Cells

The fact that all organisms are made of cells, the minimum unit of life, is of

enormous importance. It is believed that the first organisms to emerge on earth

some 3.8 billion years ago were anaerobic unicellular organisms, which

depended on organic compounds in the ocean rather than oxygen. Then came

photosynthetic bacteria and cyanobacteria, which were capable of synthesizing

organic matter from carbon dioxide, thus gradually increasing the amount of

oxygen in the air. This oxygen was gradually transformed into ozone in the


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stratosphere 10 to 50 km above the ground by ultraviolet rays. The ozone layer

blocked these harmful ultraviolet rays, thus allowing the emergence of organisms

on the planet. The first organisms found on the ground surface were plants, which

began to grow approximately 400 million years ago. This marked the start of an

explosive diversification of life on earth.

Take a moment to look around you. What you see are very complex and diverse

biotic communities. An adult human is made of some 60 trillion cells. All organisms

consist not of uniform cells but of specialized versions with many different

functions. In other words, cell differentiation is needed for the creation of complex

organisms (see Chapter 10). For groups of differentiated cells to be highly

organized in a spatial sense and become an organism, another step known as

cell-to-cell interaction is required (see Chapter 11). This mechanism is called

hierarchization, and is essential for the creation of higher organisms.

Self-replication

Another characteristic of organisms is that they produce offspring that are visually

similar to them. Unicellular cells procreate by asexual reproduction such as

division (e.g., in paramecia) and budding (e.g., in baker’s yeast) (see Chapter

12), and the offspring cells have the same traits as the parent cells provided no

mutation occurs in their DNA. On the other hand, multicellular organisms

procreate by sexual reproduction, and the offspring inherit half their genes from

each parent. Although different species do not result from this method of

reproduction, any DNA mutation that occurs during the process of self-replication

can be reflected in the traits of the offspring. This is called evolution. Mutation

occurs in DNA bases at a certain frequency, meaning that evolution may be

observed in the characteristics of reproduced organisms.

Response to Stimuli

One of the key characteristics of organisms is that they respond to stimuli from the

surrounding environment (i.e., the outside world). The cell membrane has

receptors – proteins that receive stimuli. When these receptors are stimulated by

some external influence, a cascade of chemical reactions is triggered in the

cytoplasm, leading to the synthesis of new proteins via DNA transcription. This

chain reaction mechanism is called the signal transduction pathway (see Chapter

9). Various types of receptor are coded into the genes of all organisms, from E.



coli to humans, and many such receptors are common to all organisms. This

indicates that organisms on earth have evolved from the same protobionts.

ATP – Currency of Energy Transfer

The last characteristic of organisms discussed here is their capacity for metabolic

activities (i.e., synthesis and degradation of substances) within their cells. During

these processes, ATP (see Chapter 2) – an energetic material – is synthesized, the

resulting energy is used to produce heat, and metabolic activities are retained

(see Chapters 7 & 8).

I I I . Phylogeny of Organisms

Classification by the Phylogenetic Tree

Figure 1-1 shows the phylogenetic tree of all organisms currently known. The

classification is primarily based on differences in DNA sequence. Here, organisms

are divided into three main categories (i.e., domains) – bacteria, archaea and

eukarya (or eukaryotes). The former two do not have a clearly defined nucleus,

and are also known as prokaryotes. Bacteria and archaea not only have different

lipid compositions in the cell membrane, but also have clearly different gene

compositions. As for eukaryotes, which include humans and plants, there is

mounting evidence suggesting their evolution from the branch of archaea rather

than that of bacteria.

Figure 1-1 Phylogenetic tree of all organismsThe phylogenetic tree of all organisms on earth estimated based on genome sequence. Eukaryotes are closer to archaea than to bacteria.


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Viruses generally have a simple structure; their nucleic acids (gene segments),

DNA and RNA are surrounded by proteins, and they do not have a cell

shape. Although viruses self-replicate, they cannot do so using only their

intrinsic components, and must rely on the materials of the host organism. In

addition, viruses themselves do not respond to external stimuli and do not

have the ability to synthesize ATP.

Viruses do not satisfy the definition of organisms outlined in II. Column Figure

1-1 shows the gene structure of the Rous sarcoma virus. In 1911, Peyton

Rous demonstrated that sarcomas are caused by elements on a sub-cell

scale. To do this, he mashed and filtered sarcoma tissue and injected the

extract into healthy chickens, which subsequently developed sarcomas. The

relevant element was later found to be an RNA-genome-based virus with a

typical retrovirus structure. It has only four genes coded into its genome, of

which v-src – an oncogene – causes sarcomas in chickens.

Another molecule with odd properties is the prion. Prions were isolated as

elements that cause transmissible spongiform encephalopathy in cattle and

humans, and are made of one type of protein. It has also been shown that

infectious prions are not derived from other organisms and that the gene

coding them exists in the human genome, and that normal prion proteins are

expressed in our brains. Since both normal and infectious prions have

identical primary protein structures, it has been suggested that the infection

mechanism follows the path shown in Column Figure 1-2 (Prion hypothesis).

Although prions multiply, they are a single protein t ype and do not satisfy

the definition of organisms shown in II.

Column Viruses and Prions

Column Figure 1-2 Prion hypothesis

Column Figure 1-1 Gene structure of the Rous sarcoma virus



Classification Based on Organelles

Turning our attention to organelles, not all eukaryotes have mitochondria, and

some protista also lack them. Since mitochondria are surrounded by double

membranes and have circular DNA, it is believed that aerobically respiring

bacteria began to live symbiotically with primitive eukaryotes and subsequently

adapted to an intracellular environment by discarding unnecessary genes, thus

becoming organelles (Endosymbiotic hypothesis: see Column [P.104] in Chapter

5). Similarly, chloroplasts found in plant cells are believed to have originated as

cyanobacteria that were able to photosynthesize while living symbiotically with

plants (Table 1-1).

The earliest stage of eukaryotes is protista, which include mastigotes, plasmodia

and red-tide-causing dinoflagellates. Protista also include euglena, which perform

photosynthesis, and slime molds, which differentiate and change shape despite

being unicellular organisms.

From this stage, the group of organisms known as plants was diverged. Plants are

multicellular organisms that have cells surrounded by cell walls and perform

photosynthesis. Plants are autotraphs, meaning that they can synthesize organic

matter from carbon dioxide and water. As producers, plants provide nutrients to

all other organisms on earth.

Then, fungi (such as molds and mushrooms, nutritionally classified as decomposers)

with cell walls but no photosynthesis (i.e., heterotrophs) were diverged, followed

Figure 1-2 Sizes of biological materialsThis figure shows the general scheme of the size order for biological components, organelles, cells and individuals. The resolutions of the naked eye and light microscopes are 100 μm and a few micrometers, respectively, whereas that of electron microscopes is a few nanometers.


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finally by animals. Animals neither have cell walls nor perform photosynthesis,

making them heterotrophs, and are nutritionally classified as consumers.

Sizes of Biological Materials

Figure 1-2 shows the sizes of cells and the organelles they contain.

The naked eye enables observation of specimens as small as 0.1 mm (100 μm)

in size, which includes the diameter of a human egg (ovum), a human hair and

a paramecium (200 μm). The resolution of light microscopes allows the subjects

of just a few micrometers to be viewed. The average size of bacteria is 0.5–5μm,

and the size of mitochondria in higher animals is slightly larger than that.

Generally, eukaryotic cells are larger – up to 40 μm in diameter – and their

volume is 1,000 to 10,000 times that of prokaryotic cells. Some cells are very

long; sciatic nerve cells in humans, for example, are nearly 1 m in length. Cells

smaller than 1 μm can be observed only by electron microscopes. The diameter

of DNA molecules in a cell is 2 nm, the thickness of the cell membrane is 10 nm,

and the diameter of ribosomes is 20 nm.

IV. Biological Materials

Among the materials that constitute a cell, water is the most abundant – normally

representing approximately 70–80% of the total volume – and has many

substances dissolved in it. After water, proteins and lipids are the most common

cell materials (Table 1-2).

Table 1-1 Similarit ies between organelles and prokaryotes

Table 1-2 Cellular components



(A)

(B)


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Proteins

Proteins are long molecules built from 20 different amino acids linked by peptide

bonds. Figures 1-3A and B show the structures of amino acids. Those that constitute

most of the proteins found in organisms on earth are L-amino acids, while D-amino

acids are found only in the cell walls of bacteria and some other organisms. The

sequential order of amino acids (i.e., primary structures) is determined by DNA,

and the higher-order structure (i.e., the 3-D structure) is determined from this order.

For example, main-chain structures include alpha helices and beta sheets, and

main chains with no fixed structure are called random coils (i.e., secondary

structures). A three-dimensional structure consisting of a protein chain is called a

tertiary structure. Sometimes, multiple protein chains together form a complex that

performs functions; this is known as a quaternary structure (Fig. 1-3C).

Proteins with certain shapes have specific functions. They work as enzymes to

control biological reactions in the living body, as structural and cytoskeletal

proteins to support cellular structures, and as receptors to receive external stimuli

inside the cell membrane. Most hereditary diseases in humans are caused by

functional changes in proteins due to DNA mutation.

(C)

Figure 1-3 Amino acids and proteins(A) Differences between D- and L-amino acids.

Most amino acids on earth, except those that constitute the cell walls of bacteria and some other exceptions, are L-amino acids.

(B) The 20 amino acids and their abbreviations. Among amino acids that make up proteins in humans, leucine (L) is the most abundant, and tryptophan (W) is the least abundant.

(C) An example of a peptide. This peptide is abbreviated as AYDG (the N-terminus is always drawn on the left-hand side). The amino acid sequence at the top is the primary structure, followed in descending order by the second structure (the main chain), the tertiary structure (a three-dimensional structure) and the quaternary structure (intersubunit interaction).



Lipids

Lipids are important components of biological membranes, which consist of a

phospholipid bilayer intertwined with mobile proteins. A phospholipid is a

molecule in which two hydrophobic fatty acid chains and a hydrophilic chain

with phosphorus are linked to a glycerol backbone and form a bilayer with its

hydrophobic parts facing inward and its hydrophilic parts in contact with the

water surface (see Chapter 5). Ions and polar substances can barely penetrate

this structure. The ratio of proteins to lipids changes depending on the biological

membrane, and the proportion of proteins increases progressively in the order of

myelin, red cells, hepatocytes and inner mitochondrial membrane. In triglycerides,

all hydroxyl groups form ester bonds with fatty acids, and play an energy-storage

role. The body fat percentage in humans is normally 21% in men and 26% in

women; the higher ratio for females explains their better survival rate during

famines. Various steroid hormones are synthesized from cholesterol.

Let’s look at the structure of fatty acids. A fatty acid is a carbon chain with a

carboxyl group located at its end (Fig. 1-4). Those that do not contain double

bonds are saturated fatty acids, and those with double bonds are unsaturated.

For example, ω-3 fatty acids have a double bond on the third carbon counting

Figure 1-4 Fatty acidsω-3 fatty acids have a double bond located on the third carbon from the left. ω-6 amino acids have a double bond located on the sixth carbon. C22:6 means that the amino acid has 22 carbons and 6 double bonds. In organic chemistry terms, linoleic acid is known as 9, 12-octadecadienoic acid because the double-bond location is counted from the carboxyl-group side. EPA is eicosapentaenoic acid, and DHA is docosahexaenoic acid.


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from the terminal carbon, and C20:5 means that the fatty acid has 20 carbon

atoms and 5 double bonds. ω-6 fatty acids, which are abundant in the fat found

in the flesh of terrestrial animals, have a double bond on the sixth carbon from the

end; arachidonic acid, an important component of the cell membrane in humans,

can therefore be termed a ω-6 fatty acid and C20:4. ω-3 and ω-6 are also

expressed as n-3 and n-6, respectively.

Carbohydrates

Carbohydrates are an important energy source. Glucose is derived from glycogen

and starch – both energy reserves – in animals and plants, respectively. ATP is

synthesized, while glucose is broken down into water and carbon dioxide through

Figure 1-5 Examples of carbohydrate structures(A) Glucose is commonly drawn using Haworth’s cyclized

structural formula.(B) Structure of maltose(C) Structural differences between starch (amylose) and cellulose(D) Structure of lactose

(B)

(D)

(C)(A)



the glycolytic pathway, the citric acid cycle and the electron transport system.

Carbohydrates are also constituents of materials such as nucleic acid (deoxyribose

and ribose), glycoprotein (mannose, glucosamine, etc.) and cell walls (cellulose).

Figure 1-5 shows the structure of glucose. Maltose is a disaccharide formed from

two units of α-D-glucose joined with an α (1→4) glycosidic linkage because

water is removed from -OH groups at C-1 and C-4. Looking at the location of the

-OH group at C-1, the difference between α-D-glycosidic linkage and β-D-

glycosidic linkage can be seen. Starch (amylose) is a long molecule consisting of a

large number of glucose units joined together mainly by α-D-glycosidic bonds, and

cellulose is a long molecule consisting of a large number of glucose units linked by

β-D-glycosidic bonds. Lactose is sometimes abbreviated as Galβ (1→4) Glc.

In the main text, we learned that amino acids have amino and carboxyl

groups, and that there are 20 amino acid t ypes. Here are some other

important aspects of amino acids.

Looking at the structure of lysine, we see it has a carbon linked with the

amino and carboxyl groups (α-carbon), followed by β-, γ-, δ- and

ε-carbons, in that order. Since amino group is linked to ε-carbon, this

group is known as a ε-amino group. You might remember the ornithine

cycle for urea synthesis from high school biology class. Did you know that

Column More on Amino Acids

Column Figure 1-3 Examples of amino acids


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ornithine has an amino group linked to δ-carbon?

Let’s look at the structure of glutamic acid. The carboxyl group is linked to

γ-carbon. γ-aminobutyric acid (GABA) is synthesized when an

α-carboxyl group is decarboxylated by the decarboxylase. In other

words, an excitatory transmitter is quickly transformed into an inhibitory

transmitter in the brain. Now, let’s look at the structure of histidine. How

will decarboxylase change it?

Minerals

Living bodies utilize other minerals in addition to elements such as C, H, O, N,

P and S that are found in proteins, lipids, nucleic acids, carbohydrates and other

materials. Na, K and Cl are necessary for homeostasis (i.e., the maintenance of

osmotic pressure and generation of potential difference), Zn is a constituent of

enzymes, Fe is a constituent of hemoglobin, Mn is involved in oxygen generation

during photosynthesis, and Mg is a constituent of chlorophyll and involved in the

ATP hydrolysis reaction. Additionally, Ca is important for Ca-dependent enzymatic

reactions and coagulation as well as being a constituent of bone, and Co and I

(iodine) are essential elements of vitamin B12 and thyroid hormones, respectively.

Se, a trace component, is sometimes incorporated into an amino acid called

selenocysteine, and plays a role in enzymatic activities.



• The diversity of organisms is determined by the organization of their

genes and their expression patterns.

• Organisms share characteristics; they consist of units called cells, each of

which is surrounded by a membrane consisting mainly of a phospholipid

bilayer; they self-replicate using a genetic material called DNA; they

respond to external stimuli; they synthesize adenosine triphosphate (ATP),

an energetic material, and live and grow using the energy thus produced.

• Organisms are roughly classified into the three categories (i.e., domains)

of bacteria, archaea and eukarya (eukaryotes). The former two do not

have a clearly defined nucleus, and are also known as prokaryotes.

• It is believed that during the process of evolution, bacteria capable of

aerobic respiration and cyanobacteria with photosynthetic ability started

living symbiotically with primitive eukaryotes, subsequently adapted to the

cellular environment of these eukaryotes by discarding their unnecessary

genes, and finally became organelles – mitochondria and chloroplasts –

respectively (as per endosymbiotic theory).

• Among the materials that make up cells, the most abundant is water

(normally representing 70–80% of the total volume), in which many

substances are dissolved. The next most common are proteins and lipids,

while carbohydrates and minerals also play important roles.

Summary Chapter 1


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[1] List the four characteristics that define an organism, and

describe the cellular structural differences between

prokaryotes and eukaryotes.

[2] Draw a phylogenetic tree that includes animals, plants,

fungi, archaea and bacteria. Name one species of

eubacterium and one species of fungus.

[3] In an ideal environment, E. coli bacteria multiply every 20

minutes. Assuming that no bacteria die, calculate the time

taken for one E. coli bacterium in a medium (1 ml) to reach

10 billion/ml.

[4] Respond to the following protein-related tasks:

1) Explain the primary, secondary and tertiary structures.

2) Name some typical examples of secondary structures.

3) Identify the forces that contribute to the stabilization of

secondary and tertiary structures.

4) Explain the quaternary structure.

[5] List the three main functions that proteins perform within cells.

[6] Mark the following with ○ (Yes) or × (No). If your answer is

×, give one or two lines explaining the reason.

1) A hydrogen bond is a bond between hydrogen atoms

formed on the surface of protein molecules in a solution.

2) Glucose is a constituent of nucleic acid.

3) When a translated protein forms a higher-order structure,

a structural change occurs so that the hydrophobic

residues of the protein are positioned on its inner side.

4) The peptide tyrosine-glycine-glycine-phenylalanine-leucine

is known as an enkephalin. A peptide whose amino acid

sequence is opposite to this (i.e., leucine-phenylalanine-

glycine-glycine-tyrosine) has the same functions as an

enkephalin.

5) DNA consists of four bases: A, G, U and C.

Problems

(Answers on p.250)

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