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Molecular Biology of the Cell, 5 ed.

© Garland Science 2008

Chapter 1:

Cell and Genomes

ALL LIVING ORGANISMS ARE MADE OF CELLS

• Plants, Animals, Bacteria, etc. share many differences (diversity) but also many similarities (unity). – The diversity and unity of all of life is the result of evolution– Unity is due to having common ancestors and inheriting

common traits– Diversity is due to accumulated differences in the

instructions for life (DNA)

• A striking example of unity is that all living organisms are made of cells

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ALL LIVING ORGANISMS ARE MADE OF CELLS

• Many organisms are single cells• Even multicellular organisms start as

single cells (all of them)• All cells share many characteristics

– All cells have certain structures in common– All cells have certain functions and

mechanisms in common


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Figure 1-1 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

THE UNIVERSAL FEATURES OF CELLS ON EARTH

• All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA)

• All Cells Replicate Their Hereditary Information by Templated Polymerization


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• All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form (RNA)

• All Cells Use Proteins as Catalysts


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Figure 1-7a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)


• All Cells Translate RNA into Protein in the Same Way

• The Fragment of Genetic Information Corresponding to One Protein Is One Gene


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• Life Requires Free Energy

• All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks


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• All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass

• A Living Cell Can Exist with Fewer Than 500 Genes


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Figure 1-13b Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

Shared DNA sequences between organisms

(Outdated Methodology)- The Human genome is around 3 billion base long.

- Only 2% are genes that produce RNA or protein products. 98% “Junk” though we continually find more and more important functions in regions of that “junk”

- Genome-wide variation from one human being to another can be up to 0.5% (99.5% similarity)

- Chimpanzees are 96% to 98% similar to humans, depending on how it is calculated.

- Cats have 90% of homologous genes with humans,.

- Cows (Bos taurus) are 80% genetically similar to humans

- 75% of mouse genes have equivalents in humans, 90% of the mouse genome could be lined up with a region on the human genome 99% of mouse genes turn out to have analogues in humans

- The fruit fly (Drosophila) shares about 60% of its DNA with humans

- About 60% of chicken genes correspond to a similar human gene.

…SO IF SO MUCH IS SIMILAR, WHY ARE WE DIFFERENT?

• Even in our own bodies, all of our cells contain 100% the same genetic information, yet many different cell types with a wide range of different functions.

• The differences between genetically identical cells and differences in organisms with many shared genetic sequences is due to gene regulation– Not all genes are expressed at all times– Controlling which genes are expressed in which cells and at which time

determines the distinct characters of cells, tissues, organs and organisms. © Garland Science

2008

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GENOMES

• Genome: All of a species genetic material.– Not all of the genetic material is in functional

genes – Not all the functional genes are expressed at all

times. • Gene regulation controls which genes are expressed

– Genes are not only turned “on” or “off” they can be turned up or turned down

• Complex interaction of many molecules involved in the regulation of many eukaryotic genes

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THE DIVERSITY OF GENOMES AND THE TREE OF LIFE

• All cells require energy to maintain order and perform functions of life but– Different cells can be powered by a variety of free energy

sources

• Cells require material to build into molecules important for life– Some cells fix nitrogen and carbon dioxide

• Fixation is the process of incorporating elements from inorganic material into organic material

• Other cells rely directly or indirectly on these important fixating cells.

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• The Greatest Biochemical Diversity Exists Among Prokaryotic Cells


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Molecular Evolution

•The Tree of Life Has Three Primary Branches called Domains: Bacteria, Archaea, and Eucaryotes

Example:

Bacteria and Archaea

Physically look very

similar

Molecularly:

Archaea similar to Bacteria – metabolism, energy conversion

Archaea similar to Eukarya – DNA, RNA, protein

mechanisms

Molecular Evolution

ArchaebacteriaBacteria – Cholera

http://commons.wikimedia.org http://filebox.vt.edu


• Some Genes Evolve Rapidly; Others Are Highly Conserved

• Most Bacteria and Archaea Have 1000–6000 Genes


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• New Genes Are Generated from Preexisting Genes– Can be harmful to function– Can have not effect– Can be beneficial to function– Harm and benefit only determined through natural

selection

• Gene Duplications Give Rise to Families of Related Genes Within a Single Cell


Chapter 1 Mutations and Evolution

Regions within genome change at different rates

Noncoding/nonregulatory DNA – rate same as error rate

Coding DNA – rate lower

Conserved Genes

Low mutation rate

Similar between different organisms

Represent evolutionary relationships

Genes can be:

Essential (lack of gene = lethal)

Non-essential, but can be important

Comparison of Genomes

• Evolution of Genomes– Conserved genes

– Genes lost

– Genes acquired

– Some genomes become very complex: • coding sequence less condensed

• more modular

• Evolution of new Genes– Ancestor genes

– Evolution is evolution of DNA seqences

Figure 1-23 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Figure 1-25c Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

Evolution ofNew Genes

Related genes

Shared ancestor gene

Figure 1-25a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)


Different organisms

Shared ancestor gene

Very similar functions

Figure 1-25b Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)


Same genome

Same ancestor gene

Different functions


• The Function of a Gene Can Often Be Deduced from Its Sequence

• More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life


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Table 1-2 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

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