CHAPTER 1 CELLS AND GENOMES

THE UNIVERSAL FEATURES OF CELLS ON EARTH

The basic unit of life is the cell. Fig. 1-1

Most forms of life are just a single cell.

Humans have 10¹³ cells, all derived from a single cell!

Cells must consume energy in order to grow and multiply.

All Cells Store Their Hereditary Information in the Same Linear

Chemical Code (DNA)

DNA: A, T, C, G (each is called a nucleotide)

computer: 0, 1

All Cells Replicate Their Hereditary Information by Templated

Polymerization

Each nucleotide is composed of three parts: phosphate, sugar, and a base. Fig. 1-2

Only the base is different between A, T, C, G.

A polymer of nucleotides is called a polynucleotide.

The unique arrangement of nucleotides forms the genetic code.

The genetic code provides all the information necessary to make an organism.

When cells grow and multiply, they must duplicate the genetic code.

The polynucleotide provides a template for its own replication.

A only pairs with T

C only pairs with G

All Cells Transcribe Portions of Their Hereditary Information into the

Same Intermediary Form (RNA)

In order to use the information in the genetic code, the DNA must be ‘read’. Fig. 1-4

Transcription is the process by which parts of the DNA are ‘read’.

Transcription is similar to DNA replication, except that an RNA polynucleotide is made.

DNA: A, T, C, G

RNA: A, U, C, G (a ‘U’ is used instead of a ‘T’).

Same pairing rules apply.

(RNA also has an extra –OH group on each sugar.)

RNA and DNA are two different kinds of polynucleotides.

Different RNAs have different sequences of nucleotides.

Some RNAs direct chemical reactions (more on this later). Fig. 1-6

Messenger RNA (mRNA) codes for the production of proteins.

Translation is the process by which mRNA is ‘read’ into protein. Fig. 1-4

All Cells Use Proteins as Catalysts

Proteins do almost all the work in the cell.

Proteins make each cell different.

Proteins are made up of a linear polymer of amino acids.

Proteins range in size (~100-1000 amino acids).

There are 20 different kinds of amino acids.

The arrangement of the amino acids is dictated by the DNA à RNA nucleotide sequence.

A protein is also called a polypeptide.

Polypeptides fold up into very precise 3-dimensional structures. Fig. 1-7a

Proteins that catalyze (facilitate) chemical reactions are called enzymes. Fig. 1-7b

Other proteins also serve as signaling molecules and provide structure to the cell.

All Cells Translate RNA into Protein in the Same Way

Three nucleotides at a time are translated into one amino acid. Fig. 1-9

A group of three nucleotides that code for an amino acid is called a codon.

There are 64 possible codons (4x4x4), that code for 20 amino acids.

Codons are translated by transfer RNAs (tRNA).

The anticodon part of the tRNA pairs with the codon.

So, there are many different kinds of tRNAs

Each kind of tRNA is attached to a particular amino acid.

The ribosome uses mRNA as a template to align the tRNAs, which then allows the amino acids to be stitched together. Fig. 1-10

The ribosome is composed of mostly ribosomal RNA (rRNA) and ribosomal protein.

The Fragment of Genetic Information (DNA) Corresponding to One Protein (or One Functional RNA) Is One Gene

Not all of the DNA has genes.

Certain stretches of DNA regulate the ‘expression’ of genes.

When the cell needs to make a particular protein, it ‘read’ or ‘expresses’ the corresponding gene.

The entire sequence of DNA of an organism is called a genome.

Life Requires Free Energy

Cells take energy (food) from its environment and use it to build more of itself.

Fig. 1-13

It is composed of lipids (fats).

A Living Cell Can Exist with Fewer Than 500 Genes Fig. 1-14

Humans have over 30,000 genes.

Summary

The cell is the minimal operational unit.

All info to make a cell is stored in DNA.

Central Dogma: DNA makes RNA makes protein.

Proteins do much of the work in the cell.

THE DIVERSITY OF GENOMES AND THE TREE OF LIFE

Most of life on earth is microorganisms (single-celled),

Cells Can Be Powered by a Variety of Free Energy Sources

Where do cells get their energy to make more of themselves?

Inorganic chemicals

The sun

Other organisms

Some Cells Fix Nitrogen and Carbon Dioxide for Others

The Greatest Biochemical Diversity Is Seen Among Procaryotic Cells

Prokaryotes have no nucleus. Fig. 1-18

They live in a wide variety of habitats (hydrothermal vents, Arctic, bogs, sea, dirt, other organisms)

Are microorganisms.

Eukaryotes have a nucleus. Fig. 1-43b

A nucleus is an intracellular compartment that houses DNA.

Eukaryotes can be microorganisms or multicellular.

The Tree of Life Has Three Primary Branches (domains): Bacteria, Archaea, and

Eucaryotes Fig. 1-21

Bacteria and Archaea are prokaryotes.

Note how diverse the prokaryotes are.

Note that plants, animals, and fungi are highly related!

Some Genes Evolve Rapidly; Others Are Highly Conserved

When DNA is replicated, mistakes are made (albeit very rarely).

Most mistakes (mutations) have little effect on the organism.

Some are detrimental to the organism. Fig. 1-22

Such mutant organisms are eliminated by natural selection (ability/inability to thrive or compete with other organisms for survival).

Therefore the mutation is also lost.

Such regions of DNA are therefore highly conserved and are indicative of important genetic information.

In rare cases, the mistake changes the genetic code for a protein in a beneficial way.

This is the core of evolution.

Most Bacteria and Archaea Have 1000–4000 Genes.

Natural selection favors those organisms that can reproduce the fastest.

Small size

Small genome

Specific environmental niche

New Genes Are Generated from Preexisting Genes Fig. 1-23

Mutation

Nucleotides within a gene can mutate.

Happens very frequently with HIV (as an example).

Duplication

Duplicating a gene allows one to mutate, while the other provides the essential function.

Segment shuffling

Two or more genes can be broken up and pieced back together differently.

Horizontal transfer

A gene from one organism can be transferred to a related or unrelated organism.

Humans have bacterial DNA in their genomes!!

Gene Duplications Give Rise to Families of Related Genes Within

a Single Cell

Related organisms have related genes. The related genes are said to be orthologs.

When a gene is duplicated within the same cell, allowing them to evolve separately, then these genes are paralogs.

Homologs refer to both orthologs and paralogs.

All homologs form a gene family. Fig. 1-26

Genes Can Be Transferred Between Organisms, Both in the Laboratory

and in Nature

Bacterial viruses (bacteriophages) are mobile genetic vehicles that allow genes to move horizontally.

Bacteria can also take up DNA from their environment.

This and the rapid rate of replication, allow bacteria to evolve rapidly. Fig. 1-21

Think antibiotic resistance.

Horizontal Exchanges of Genetic Information Within a Species Are

Brought About by Sex

Primordial life may have extensively used horizontal transfer.

Groups of genes might have moved together.

Bacteria and Archaea but not Eukaryotes have similar metabolic genes

Metabolic genes are involved in getting food

Archaea and Eukaryotes but not Bacteria have similar genes that control information flow

DNA replication, transcription, translation

Horizontal gene transfer is essentially bacterial sex.

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

Genes with similar sequence have similar function.

If you know the function of one homolog, you then know the function of all homologs.

More Than 200 Gene Families Are Common to All Three Primary

Branches of the Tree of Life Table 1-2

Mutations Reveal the Functions of Genes

How do we figure out what the function of any given gene is?

Isolate the protein coded for by a gene, and determine what chemical reaction it carries out.