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1 The Cell as the Basic Unit of Life

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Michael Wink

Heidelberg University, Institute of Pharmacy and Molecular Biotechnology (IPMB), Im Neuenheimer Feld 329, 69120 Heidelberg, Germany

The base unit of life is the cell. Cells constitute the base element of all prokaryotic cells (cells without a cell nucleus, e.g. Bacteria and Archaea) and eukaryotic cells (or Eukarya) (cells possessing a nucleus, e.g. protozoa, fungi, plants, and animals). Cells are small, membrane‐bound units with a diameter of 1–20 μm and are filled with concentrated aqueous solutions. Cells are not created de novo, but possess the ability to copy themselves, meaning that they emerge from the division of a previous cell. This means that all cells, since the beginning of life (around 4 billion years ago), are connected with each other in a continuous lineage. In 1885, the famous cell biologist Rudolf Virchow conceived the law of omnis cellula e cellula (all cells arise from cells), which is still valid today.

The structure and composition of all cells are very similar due to their shared evolution and phylogeny (Figure 1.1). We see an astonishing constancy in fundamental structures and mechanisms. Owing to this, it is possible to limit the discussion of the general characteristics of a cell to a few basic types (Figure 1.2):

 Bacterial cells

 Plant cells

 Animal cells


Figure 1.1 Tree of life – phylogeny of life domains.


Figure 1.2 Schematic structure of prokaryotic and eukaryotic cells. (a) Bacterial cell, (b) plant mesophyll cell, and (c) animal cell.

Nucleotide sequences from 16S rRNA, amino acid sequences of cytoskeleton proteins, and characteristics of the cell structure were used to reconstruct this phylogenetic tree. Prokaryotes are divided into Bacteria and Archaea. Archaea form a sister group with eukaryotes; they share important characteristics (Tables 1.1 and 1.2). Many monophyletic groups can be recognized within the eukaryotes (diplomonads/trichomonads, Euglenozoa, Alveolata, Stramenopilata [heterokonts], red algae and green algae/plants, fungi and animals; see Tables 6.3–6.5 for details).

Table 1.1 Comparison of important biochemical and molecular characteristics of the three domains of life.

Character Prokaryotes Eukaryotes
Archaea Bacteria
Organization Unicellular Unicellular Unicellular or multicellular
Cytology
Internal membranes Rare Rare Always (Table 1.2)
Compartments Only cytoplasm Only cytoplasm Several (Table 1.2)
Organelles No No Mitochondria; plastids
Ribosomes 70S 70S 80S (mt, cp: 70S)
Membrane lipids Ether lipids Ester lipids, hopanoids Ester lipids, sterols
Cell wall Pseudopeptidoglycan, polysaccharides, glycoproteins Murein (peptidoglycan), polysaccharides, proteins PL: polysaccharides, cellulose F: chitin A: no
Cytoskeleton FtsZ and MreB protein FtsZ and MreB protein Tubulin, actin, intermediary filaments
Cell division Binary fission Binary fission Mitosis
Genetics
Nuclear structure Nucleoid Nucleoid Membrane‐enclosed nucleus with chromosomes
Recombination Similar to conjugation Conjugation Meiosis, syngamy
Chromosome Circular, single Circular, single Linear, several
Introns Rare Rare Frequent
Noncoding DNA Rare Rare Frequent
Operon Yes Yes No
Extrachromosomal DNA plasmids (linear) Plasmids (circular) mtDNA, cpDNA, plasmids in fungi
Transcription/translation Concomitantly Concomitantly Transcription in nucleus, translation in cytoplasm
Promotor structure TATA box −35 and −10 sequences TATA box
RNA polymerases Several (8–12 subunits) 1 (4 subunits) 3 (with 12–14 subunits)
Transcription factors Yes No (sigma factor) Yes
Initiator tRNA Methionyl‐tRNA N‐Formylmethionyl‐tRNA Methionyl‐tRNA
Cap structure of mRNA polyadenylation No No Yes

PL, plants; F, fungi; A, animals; mt, mitochondria; cp, plastid.

Table 1.2 Compartments of animal and plant cells and their main functions.

Compartment Occurrence Functions
Nucleus A P Harbors chromosomes, site of replication, transcription, and assembly of ribosomal subunits
Endoplasmic reticulum (ER)
Rough ER A P Posttranslational modification of proteins
Smooth ER A P Synthesis of lipids and lipophilic substances
Golgi apparatus A P Posttranslational modification of proteins, modification of sugar chains
Lysosome A Harbors hydrolytic enzymes, degrades organelles and macromolecules, macrophages eat invading microbes
Vacuole P Sequestration of storage proteins, defense and signal molecules, contains hydrolytic enzymes, degrades organelles and macromolecules
Mitochondrium A P Organelle derived from endosymbiotic bacteria; contains circular DNA, own ribosomes; enzymes of citric acid cycle, β‐oxidation, and respiratory chain (ATP generation)
Chloroplast P Organelle derived from endosymbiotic bacteria; contains circular DNA, own ribosomes; chlorophyll and proteins of photosynthesis, enzymes of CO2 fixation and glucose formation (Calvin cycle)
Peroxisome A P Contains enzymes that generate and degrade H2O2
Cytoplasm A P Harbors all compartments, organelles, and the cytoskeleton of a cell; many enzymatic pathways (e.g. glycolysis) occur in the cytoplasm

A, animal; P, plant.

A highly resolved tree of life is based on completely sequenced genomes (Ciccarelli 2006). The image was generated using Interactive Tree Of Life (iTOL) (Letunic 2007), an online phylogenetic tree viewer and Tree of Life resource. Eukaryotes are colored red, archaea green, and bacteria blue.

The most important biochemical and cell biological characters of Archaea, Bacteria, and Eukarya are summarized in Table 1.1.

As viruses and bacteriophages (Figure 1.3) do not have their own metabolism, they therefore do not count as organisms in the true sense of the word. They share several macromolecules and structures with cells. Viruses and bacteriophages are dependent on the host cells for reproduction, and therefore their physiology and structures are closely linked to that of the host cell.


Figure 1.3 Schematic structure of bacteriophages and viruses. (a) Bacteriophage T4 and (b) structure of a retrovirus (human immunodeficiency virus causing AIDS).

Eukaryotic cells are characterized by compartments that are enclosed by biomembranes (Table 1.2). As a result of these compartments, the multitude of metabolic reactions can run in a cell at the same time.

In the following discussion on the shared characteristics of all cells, the diverse differences that appear in multicellular organisms should not be forgotten. The human body has more than 200 different cell types, which show diverse structures and compositions. These differences must be understood in detail if cell‐specific disorders, such as cancer, are to be understood and consequently treated. Modern technology with Next‐Generation Sequencing (NGS) allows a study of single cells at a genomic and transcriptomic level.

Before a detailed discussion of cellular structures and their functions (see Chapters 35), a short summary of the biochemical basics of cellular and molecular biology is given in Chapter 2.

Progress in cell biology and biotechnology largely depends on innovative methods, as new methods often open windows to look deeper into biology and to solve old questions. Table 1.3 summarizes some of the important tools, which are important for cell and molecular biology today.

Table 1.3 Important methodological tools of modern biology.

Problem Technique/instrument Remarks
Structure elucidation of proteins Protein isolation, column chromatography (gel filtration, ion exchange, affinity) Chapter 7
Gel electrophoresis Chapter 7
Protein–protein interactions (FRET, two hybrid systems, FRAP) Chapters 19 and 23
Crystallization
X‐ray diffraction
NMR
Cryoelectron microscopy
Mass spectrometry Chapter 8
Protein sequencing
DNA PCR and quantitative PCR (qPCR) Chapter 13
DNA/RNA isolation Chapter 9
DNA hybridization Chapter 11
Sanger sequencing Chapter 14
Restriction enzymes Chapter 12
Gel and capillary electrophoresis Chapter 10
Next generation sequencing Chapter 14
Microsatellite analysis Chapter 11
SNP analysis Chapters 14 and 21
FISH Chapter 11
In situ hybridization Chapter 11
RNA (transcriptomics) RNA‐seq (NGS) Chapters 14 and 21
DNA microarrays Chapter 11
In situ hybridization Chapter 11
Cell and tissue culture Cells with reporter genes
Cell sorting
Organoid cultures
Stem cells
Cancer cells
Hybridoma cells for production of monoclonal antibodies
Cell cycle analysis Chapter 18
Patch clamp recording Chapter 17
Microscopy Light microscope (bright field, dark field, phase contrast, differential interference contrast) Chapter 19
Fluorescence microscope (confocal) Chapters 19 and 20
Immunofluorescence and GFP fusion proteins Chapter 19
Super‐resolution microscopy (STED, SIM, PALM, STORM) Chapter 19
Atomic force microscopy Chapter 19
Electron microscope Chapter 19
Scanning electron microscope (SEM)
Cryoelectron microscopy Chapter 19
Image processing
Cloning and expression Plasmid and viral vectors Chapter 15
Expression vectors Chapters 15 and 16
Fermenters
Genomic and cDNA libraries Chapter 21
Reverse genetics
Genetic engineering Transformation Chapter 15
Transfection Chapter 15
RNAi
CRISPR–Cas gene editing
Transgenic organism
New active agents Recombinant antibodies Chapter 16
Recombinant vaccines Chapter 16
Recombinant enzymes Chapter 16
Information DNA sequences Chapter 24
Genomes Chapter 24
Proteins Chapter 23
System biology Chapter 23

Abbreviations: SNP, single nucleotide polymorphism; GFP, green fluoresecnt protein; NGS, next generation sequencing.

An Introduction to Molecular Biotechnology

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