Chapter 25: The History of Life on Earth

3 Main Questions:

-What is ribozymes?

An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing.

- What is protobiont?

A collection of abiotically produced molecules surrounded by a membrane or membrane-like structure.

- What is half-life?

The amount of time it takes for 50% of a sample of a radioactive isotope to decay.

5 Main Facts:

- The earliest evidence of life on Earth comes from fossils of microorganisms that are about 3.5 billions years old.

- There is scientific evidence that Earth and the other planets of the solar system formed about 4.6 billion years ago, condensing from a vast cloud of dust and rocks that surrounded the young sun.

- As the bombardment of early Earth slowed, conditions on the planet were extremely different from those of today.

- It is unclear whether the atmosphere of young Earth contained enough methane and ammonia to be reducing.

- The presence of small organic molecules, such as amino acids, is not sufficient for the emergence of life as we know it.

Diagram:

The proposed ancestors of mitochondria were aerobic, heterotrophic prokaryotes (meaning they used oxygen to metabolize organic molecules obtained from other organisms). The proposed ancestors of plastids were photsynthetic prokaryotes.

Summary:

Conditions on early Earth made the origin of life possible. The earliest evidence of life on Earth comes from fossils of microorganisms that are about 3.5 billion years old. The hypothesize that chemical and physical processes on early Earth, aided by the emerging force of natural selection, could have produced very simple cells.

For the first few hundred million years, life probably could not have originated or survived on Earth because the planet was still being bombarded by huge chunks of rock and ice left over from the formation of the solar system.

Video:

http://www.youtube.com/watch?v=uVrzNR_UK_4

Chapter 24: The Origin of Species

3 Main Questions:

- What is speciation?

An evolutionary process in which one species splits into two or more species.

- What is macroevolution?

Evolutionary change above the species level, including the origin of a new group of organisms or a shift in the broad pattern of evolutionary change over a long period of time.

- What is biological species concept?

Definition of a species as a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but do not produce viable, fertile offspring with members of other such groups.

5 Main Facts:

- A species may originate from an accident during cell division that results in extra sets of chromosomes, a condition called polyploidy.

- A second form of polyploidy can occur when two different species interbreed and produce hybrid offspring.

- Many hybrid zones are stable in the sense that hybrids continue to be produced.

- The fossil record includes many episodes in which new species appear suddenly in a geologic stratum, persist essentially unchanged through several strata, and then dissappear.

- The punctuated pattern suggests that once the process begins, speciation can be completed relatively repidly a suggestion confirmed by a growing number of studies.

Diagram:

A mutation in one gene cayses the shell of the Japanese land snail (a) to spiral in the opposite

direction from others. Snails with opposite spirals cannot mate, resulting in reproductive isolation.

Summary:

The "mystery of mysteries" that captivated Darwin is speciation, the process by which one species

Speciation fascinated Darwin and many other biologists because it is responsible for the tremendous

diversity of life, repeatedly yielding new species that differ from existing ones.

Speciation also forms a conceptual bridge between mocroevolution, changes over time in allele

frequencies in a population, and macroevolution, the broad pattern of evolution over the long time

spans.

Video:

http://www.youtube.com/watch?v=vfmOaAz371M

Chapter 23: The Evolution of Populations

3 Main Questions:

- What is microevolution?

Evolutionary change below the species level; change in the allele frequencies in a population over generations.

- What is mutation?

A change in the nucleotide sequence of an organism's DNA, ultimately creating genetic diversity. Mutations also can occur in the DNA or RNA of a virus.

- What is a gene pool?

The aggregate of all of the alleles for all of the loci in all individuals in a population. The term is also used in a more restricted sense as the aggregate of alleles for just one or a few loci in a population.

5 Main Facts:

- Character that vary within a population may be discrete or quantitative.

- Average heterozygosity is often estimated by surveying the protein products of genes using gel electrophoresis.

- Nucleotide variability is measured by comparing the DNA sequences of two individuals in a population and then averaging the data from many such comparisons.

- Chromosomal changes that delete, disrupt, or rearrange many loci at once are almost certain to be harmful.

- In organisms that reproduce sexually, most of the genetic variation in a population results fromthe unique combination of alleles that each individual receives.

Diagram:

The small wildflower population has a stable size of ten plants. Suppose that by chance only five plants (those in white boxes) of generation 1 produce fertile offspring. This could occur, for example, if only those plants happened to be grow in a location that preovided enough nutrients to support the production of offspring. Again by chance, only two plants of generation 2 leave fertile offspring. As a result, by chance alone, the frequencies of the a allele first increases in generation 2, then falls to zero in generation 3.

Summary:

One common misconception about evolution is that individual organisms evolve. Focusing on evolutionary change in populations, we can define evolution on its smallest scale, called microevolution, as change in allele frequencies in a population over generations.

Natural selection is not the only cause of microevolution. In fact there are three main mechanisms that can cause allele frequencies change: natural selection, genetic drift(chance events that alter allele frequencies), and gene flow (the transfer of alleles between populations).

Video:

http://www.youtube.com/watch?v=MzKQfrb8Dh4

Chapter 23: The Evolution of Populations

Chapter 22: Descent with Modification a Darwinian View of Life

3 Main Questions:

- What is evolution?

Descent with modification; the idea that living species are descendants of ancestral species that were different from the present day one.

- What is strata?

A rock layer formed when new layers of sediment cover older ones and compressed them.

- What is uniformitarianism?

The principle stating that mechanisms of change are constant over time

5 Main Facts:

- During the voyages of the Beagle, Darwin observed many examples of adaptions, characteristics, of organisms that enhance their survival and reproduction in specific environment.

- Darwin viewed the history of life as a tree, with multiple branchings from a trunk out to the tips of the youngest twigs.

- Darwin proposed a mechanism, natural selection, to explain the observable patterns of evolution.

- An organism's trait can influence not only its own performance, but also how well its offspring cope with environmental challenges.

- One subtle but important point is that although natural selection occurs through interactions between individual organisms and their environment, individuals do not evolve.

Diagram:

This evolutionary tree of insect and plant eater and thier relatives is based mainly on fossils - their anatomy, older of appearance in strata, and geographic distribution. Most branches of descent ended in extinction.

Summary:

A century and a half ago, Charles Darwin was inspired to develope a scientific explanation for these three broad observations. When he published his hypothesis in The origin of species, Darwin ushered in a scientific revolution the era of evolutionary biology.

Evolution as descent with modification, a phrase Darwin used in proposing that Earth's many species are descendants of ancestral species that were differnent from the present day species.

Video:

http://www.youtube.com/watch#!v=GcjgWov7mTM&feature=related

Chapter 21: Genomes and Thier Evolution

3 Main Questions:

- What is genomic?

The study of whole sets of genes and their interaction.

- What is bioinformatics:

The use of computers, software, and methematical models to process and itegrate biological from large date sets.

- What is Human Genome Project?

An international collaboartive effort to map and sequence the DNA of the entire human genome.

5 Main Facts:

- The chimpanzee is our closest living relative on the evolutionary of life.

- Using available DNA sequences, geneticists can study genes directly, without having to infer genotype from phenotype, as in classical genetics.

- The identities of about half of the human genes were known before the Human Genome Project began.

- Sometimes a newly identified sequence will match, at least partially, the sequence of a gene or protein whose function is well known.

- Genomics and proteomics are enabling biologists to approach the study life from an increasingly global prespective.

Diagram:

Whole genome shotgun approach to sequencing. In this approach, developed by Craig Venter and colleagues at the company he founded, Celera Genomics, random DNA fragments are sequenced and then ordered relative to each other.

Summary:

The chimpanzee is our closest relative on the evolutionary tree of life. Its genome was sequenced in 2005, two years after sequencing of the human genome was largely completed. Now that we can compare our genome with that of the chimpanzee base by base.

We can tackle the more general issue of what differences in the genetic information account for the distinct characteristics of these two species of primates. With the genomes of many species fully sequences, scientist can study whole sets of genes and their interactions, an approach called genomics.

Video:

http://www.youtube.com/watch?v=XuUpnAz5y1g

Chapter 21: Genomes and Thier Evolution

Chapter 20: Biotechnology

3 Main Questions:

- What is genetic engineering?

The direct manipulation of genes for practical purposes.

- What is biotechnology?

The manipulation of organisms or their components to produce useful products.

- What is recombinant DNA?

A DNA molecule made in vitro with segments from differents sources.

5 Main Facts:

- Naturally occuring DNA molecules are very long, and a single molecule usually carries many genes.

- Most methods for cloning pieces of DNA in the laboratory share certain general features.

- Gene cloning is useful for two basic purposes: to make many copies of a particular gene and to produce a protein product.

- Gene cloning and genetic engineering rely on the use of enzymes that cut DNA molecules at a limited number of specific locations.

- The most useful restriction enzymes cleave the sugar-phosphate backbones in the two DNA strands in a staggered manner.

Diagram:

Using a restriction enzyme and DNA ligase to make recombinant DNA. The restriction enzyme in this example recognizes a specific six base pair sequence, the restriction site, and makes staggered cuts in the sugar phosphate backbones within this sequence, producing fragments with sticky ends.

Summary:

Researchers had sequenced the entire genome of a free living organism, the bacterium Haemophilus influenzae. This news electrified the scientific community. Ultimately, these achievements can be attributed to advances in DNA technology methods of working with and manipulating DNA that had their roots in the 1970s.

A key accomplishment was the invention of techniques for making recombinant DNA, DNA molecules formed when segments of DNA from two different sources often different species are combined in vitro (in a test tube).

Video:

http://www.youtube.com/watch?v=rrT5BT_7HdI

Chapter 19: Viruses

3 Main Questions:

- What is capsid?

The protein shell enclosing the viral genome.

- What is phages?

A virus that infects bacteria; also called a bacteriophage.

- What is viral envelope?

A membrane that cloaks the casid that in turn encloses a viral genome.

5 Main Facts:

- Some viruses have accessory structures that heko them infect their hosts.

- A viral infection begins when a virus binds to a host cell and the viral genome makes its way inside.

-Phages are the best understood of all viruses, although some of them are also among the most complex.

- There are many variations on the simplified viral reproduction cycle we have traced in this general description.

- Most DNA viruses use the DNA polymerases of the host cell to synthesize new genomes along the templates provided by the viral DNA.

Diagram:

Viruses are made up of nucleic acid (DNA or RNA) enclosed in a protein coat (the capsid) and sometimes further wrapped in a membranous envelope. The individual protein subunits making up the capsid are called capsomeres. Although diverse in size and shape, viruses have common structural features, most of which appear in the diagram.

Summary:

To large extent, molecular biology was born in the laboratories of biologists studying viruses that infect bacteria. Beyond their value as experimental systems, viruses have unique genetic mechanisms that are interesting in their own right.

Experiments with viruses provided imoportant evidence that genes are made of nucleic acids, and they were critical in working out the molecular mechanisms of the fundamental processes of DNA replication, transcription, and translation.

Video:

http://www.youtube.com/watch?v=Rpj0emEGShQ

Chapter 18: Regulation of Gene Expression

3 Main Questions:

- What is an operator?

In bacterial DNA, a sequence of nucleotides near the start of an operon to which an actice repressor can attach. The binding of the repressor prevents RNA polymerase form attaching toe hte promoter and transcribing the genes of the operon.

- What is operon?

A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator and a coordinately regulated cluster of genes whose products function in a pathways.

- What is repressor?

A protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators form binding to DNA.

5 Main Facts:

- When glucose and lactose are both present in its environment, E. coli prefertentially uses glucose.

- If the amount of glucose in the cell increases, the cAMP concentration falls, and without cAMP, CAP detaches from the operon.

- For the lac operon, the inducer is allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell.

- A typical human cell probably expresses about 20% of its genes at any given time.

- Almost all the cells in an organism contain an identical genome.

Diagram:

In the pathway for trytophan synthesis, an abundance of trytophan can both (a) inhibit the activity of the first enzyme in the pathway (feedback inhibition), a rapid response, and (b) repress expression of the genes encoding all subunits of the enzymes in the pathway, a long term response. Genes trpE and trpD encode the two subunits of enzyme 1, and gene trpB and trpA encode the two subunits of enzyme 3.

Summary:

Cells intricately and precisely regulate their gene expression. Both prokaryotes and eukaryotes must alters their patterns of gene expression in reponse to changes in environmental conditions. Multicellular eukaryotes must also develop and maintain multiple cell types.

Each cell type contains the same genome but expresses a different subset of genes, a significant challenge in gene regulation. At every stage, gene expression is carefully regulated, ensuring that the right genes are expressed only at the corrected time and place.

Video:

http://www.youtube.com/watch?v=OEWOZS_JTgk

Chapter 17: From Gene to Protein

3 Main Questions:

- What is transcription?

Transription is the synthesis of RNA under the direction of DNA.

- What is translation?

Translation is the synthesis of a polypeptide, which occurs under the direction of mRNA.

-What is mRNA?

A type of RNA, synthesized using a DNA template, that attaches to ribosomes un the cytoplasm and specifies the primary structure of a protein.

5 Main Facts:

- Genes provide the instruction s for making specific proteins.

- The basic mechanics of transcription and translation are similar for bacteria and eukaryotes, but there is an important difference in the flow of genetic information within the cells.

- Transcription and translation occurs in all organisms.

- In DNA or RNA, the monomers are the four types of nucleotides long, which differ in their nitrogenous bases.

- Genes are typically hundreds or thousands of nucleotides long, each gene having a specific sequence of bases.

Diagram:

As a molecule of mRNA is moved through a ribosome, codons are translated into amino acids, one by one. The interpreters are tRNA molecules, each type with a specific anticodon at one end and a corresponding amino acid at the other end. A tRNA adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogen-bonds to a complementary codon on the mRNA.

Summary:

Genes provide the instructions for making specific proteins. But a gene does not build a protein directly. The bridge between DNA and a protein synthesis is the nucleic acid RNA. Thus, nucleic acids and proteins contain information written in two different chemical languages.

Getting from DNA to protein requires two major stages: transcription and translation. Transcription is the synthesis of RNA under the direction of DNA. Translation is the synthesis of a polypeptide, which occurs under the direction of mRNA.

Video:

http://www.youtube.com/watch?v=5bLEDd-PSTQ

Chapter 16: The Molecular Basis of Inheritance

3 Main Questions:

- What is transformation?

The conversion of a normal animal cell to a cancerous cell. A change in genotype and phenotype due to the assimilation of external DNA by a cell.

- What is a double helix?

The form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape.

- What is helicase?

An enzyme that untwists the double helix of DNA at the replication forks, separating the two strands and making them available as template strands.

5 Main Facts:

- The relationship between structure and function is manifest in the double helix.

- The replication of a DNA molecule begins at special sites called origins of replication.

- Enzymes called DNA polymerase catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain.

- At each end of a replication bubble is a replication fork, a Y-shpaed region where the parental strands of DNA are being unwound.

- Most DNA polymerase require a primer and a DNA template strand, along which complenmentary DNA nucleotides line up.

Diagram:

The diagram shows the base pairing in DNA. The pairs of nitrogenous bases in a DNA double helix are held together by hydrogen bonds, shown here as dotted line. The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.

Summary:

James Watson and Francis Crick shook the scientific world with an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA. Of all nature's molecules, nucleic acids are unique in their ability to dsirect thier own replication from monomers.

The replication of a DNA molecule begins at special sites called origins of replication, short stretches of DNA having a specific sequence of nucleotides. DNA replcation recognize this sequence and attach to the DNA, separating the two strands and opening uo a replication "bubble".

Video:

http://www.youtube.com/watch?v=teV62zrm2P0

Chapter 14: Mendel and the Gene Idea

3 Main Questions:

- What is true breeding?

Refering to plants that produce offspring of the same variety when they self-pollinate.

- What is trait?

Any detectable variant in genetic character.

- What is hybridization?

In genetics, the mating, or crossing, of two true-breeding varietites.

5 Main Facts:

- An organism that has a pair of identical alleles for a character is said to be homozygous.

- An organism that has two different alleles for a gene is said to be heterozygous.

- Because of the different effects of dominant and recessive alleles, an organisms's trait do not always reveal its genetic composition.

-Alleles can show different degrees of dominance and recessiveness in relation to each other.

- We can not predict with certainty the exact numbers of progeny of different genotypes resulting from a genetic cross.

Diagram:

Group F2 offspring from a cross for flower color according to phenotype results in the typical 3:1 phenotypic ratio. In terms of genotype, however there are actually two categories of purple flowered plants, PP(homozygous) and Pp(heterozygous), giving a 1:2:1 genotypic ratio.

Summary:

The explaination of heredity most widely in favor during the 1800s was the "blending" hypothesis, the idea that genetic material contributed by the two parents mixes in a manner analogous to the way blue and yellow blend to make green.

Mendel discovered the basic principles of heredity by breeding garden peas in carefully planned experiments. The results of Mendel's dihybrid experiments are the basis for what we now call the law of independent assortment, which states that each pair of alleles segregates independently of each other pair of alleles during gamete formation.

Video:

http://www.youtube.com/watch#!videos=_fSyRniZiY4&v=d4izVAkhMPQ

Chapter 15: The Chromosomal Basis of Inheritance

3 Main Questions:

- What is the chromosome theory of inheritance?

It is a basic principle in biology stating that genes are located on chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns.

- What is sex-linked gene?

A gene located on either sex chromosome.

- What is hemophilia?

It is a sex-linked recessive disorder defined by the absence of one or more of the proteins required for blood clotting.

5 Main Facts:

- Whether we are male or female is one of our more obvious phenotypic characters.

- In humans and other mammals, there are two varieties of sex chromosomes, designated X and Y.

- In both testes nd ovaries, the two sex chromosomes segregate during meiosis, and each gamete receives one.

- In humans, the anatomical signs of sex begin to emerge when the embryo is about 2 months old.

- The inactive X in each cell of a female condenses into a compact object called a Barr body, which lies along the inside of the nuclear envelope.

Diagram:

The tortoiseshell gene is on the X chromosome, and the tortoiseshell phenotype requires the presence of two differnt alleles, one for orange fur and one for black fur. Normally, only females can have both alleles, because only they have two X chromosomes. If a female is heterozygous for the tortoiseshell gene, she is tortoiseshell. Orange patches are formed by populations of cells in which the X chromosome with the orange allele is active; black patches have cells in which the X chromosome with the black allele is active.

Summary:

Gregor Mendel's "hereditory factors" were purely an abstract concept when he proposed their existence. At that time, no cellular structure were known that could house these imaginary units. Today, we can show that genes Mendel's factors are located along chromosomes.

Whether we are male or female is one of our more obvious phenotypic characters. Although the anatomical and physiological differnces between woman and men are numerous, the chromosomal basis for determining sex is rather simple.

Video:

http://www.youtube.com/watch#!videos=6b322RVU5O4&v=dOs6tLAYcUQ