Chapter 14: The Origin of Species

Three questions about the chapter:
1.What is taxonomy?
Taxonomy is the branch of biology that names and classifies species and groups them into broader categories.
2.How many types of reproductive barriers are there?
There are two types of reproductive barriers - prezygotic and postzygotic.
3.Who were the people who most recently studied the evolution of Darwin's finches?
Peter and Rosemary Grant were the most people who studied the evolution of Darwin's finches most recently.

Five main facts about the chapter:
1.The origin of species is the source of biological diversity.
2.There are several ways to define a species.
3.Reproductive barriers keep species separate.
4.In allopatric speciation, geographic isolation leads to speciation.
5.Most plant species trace their origin to polyploid speciation.
 

Diagram:

This diagram shows the evolution of wheat.



















 Link: http://www.flickr.com/photos/monado/sets/72157625811571540/detail/


Summary:
The introduction of the chapter talked about the rise and fall of cichlids, who live in Lake Victoria. Biologists often define a species as a group of organisms whose members can breed and produce fertile offspring, but who do not produce fertile offspring with members of other groups. Speiation is the emergence of a new species-is the bridge between microevolution and macroevolution. Next the chapter talked about that the origin of species is the source of biological diversity. There are sevral ways to define a species. Taxonomy is the branch of biology that names and classifies species and groups them into broader categories. The biological species concept was described in 1942 by biologist Ernst Mayr. It defines a species as a group of populations whose members have the potential to interbreed in nature and produce fertile offspring. Members of different species do not usually mate with each other. And, if members of one species do mate with members of anther species, the offspring will probably not be fertile. In effect, reproductive isolation prevents genetic exchange and maintains the gap between species. Other definitions of species are the morphological species concept, which has been used to identify most of the 1.8 million species that have been name to date, the ecological species concept, and the phylogenetic species concept. Reproductive barriers keep species separate. There are two main types of reproductive barriers - prezygotic, which prevent mating or fertilization between species, and postzygotic, which operate after hybrid zygotes are formed. In allopatric speciation, geographic isolation leads to speciation. In sympatric speciaton, speciation takes place without geographic isolation. New species formed in this way are polyploid. Most plant species trace their origin to polyploid speciation. Reproductive barriers may evolve as populations diverge. Hybrid zones provide opportunities to study reproductive isolation. Peter and Rosemary Grant study the evolution of Darwin's finches on Galapagos. Adaptive radiation may occur when new opportunities arise. Speciation can occur rapidly or slowly. 

Key Terms:
1.Species - a group of organisms whose members can breed and produce fertile offspring, but who do not produce fertile offspring with members of other groups.
2.Speciation - the emergence of new species.
3.Taxonomy - the branch of biology that names and classifies species and groups them into broader categories.
4.Biological species concept - defines a species as a group of populations whose members have the potential to interbreed in nature and produce fertile offspring.
5.Reproductive isolation - prevents genetic exchange and maintains the hap between species.
6.Reproductive barrier - a biological feature of the organism itself to prevent individuals of closely related species from interbreeding when their ranges overlap.
7.Prezygotic barriers - prevent mating or fertilization between species.
8.Postzygotic barriers - operate after hybrid zygotes are formed.
9.Adaptive radiation - the evolution of many diverse species from a common ancestor
10.Hybrid zones - regions in which members of different species meet and mate, producing at least some hybrid offspring.

Chapter 13: How Populations Evolve

Three questions about the chapter:
1.Where did Charles Darwin made most of his observation in order to come with the theory of evolution?
He did most of his observations in Galapagos.
2.What is the fossil record?
It is the sequence in which fossils appear within layers of sedimentary rocks-provides some of the strongest evidence of evolution.
3.What are some evidence that reinforce the evolutionary view of life?
Some of the evidence that reinforce the evolutionary of life are biogeography, comparative anatomy, and molecular biology.


Five main facts about the chapter:
1.Charles Darwin proposed natural selection as the mechanism of evolution.
2.Scientists can observe natural selection in action.
3.The study of fossils provides strong evidence for evolution.
4.Homologies indicate patterns of descent that can be shown of an evolutionary tree.
5.Populations are the units of evolution.




Diagram:

This diagram shows homologous structures: vertebrate forelimbs.


































Link: http://www.myspace.com/roiscience




Summary:

The introduction of this chapter talked about the blue-footed boobies, which are well adapted and very interesting birds. Their big webbed feet, stream-lined shape, large tail, and specialized salt-excreting glands are all good examples of evolutionary adaptations. Charles Darwin came up with the study of evolution - the core theme of biology. A sea voyage helped Darwin frame his theory of evolution. The most important things that helped Darwin to form his theory of evolution were his cultural and scientific context, his sea voyage, his writings, and the study of fossils. Darwin also proposed natural selection as the mechanism of evolution. Darwin devoted much of On the Origin of Species to how organisms become adapted to their environment. First, he discussed familiar examples of domesticated plants and animals. Humans have modified other species by selecting and breeding individuals that possess desired traits - a process called artificial selection. Darwin then explained how a similar selection process could occur in nature, a process he called natural selection. Scientists can observe natural selection in action. The study of fossils provides strong evidence for evolution. Many of the fossils that paleontologists find in their digs are not the actual remnants of organisms at all, but are replicas of past organisms. The fossil record - the sequence in which fossils appear withing layers of sedimentary rocks-provides some of the strongest evidence of evolution. A mass of other evidence reinforces the evolutionary view of life. Some of them are biogeography, comparative anatomy, and molecular biology. Homologies indicate patterns of descent that can be shown on an evolutionary tree. Populations are units of evolution. In other words, a population is a group of individuals of the same species living in the same place at the same time. In studying evolution at the population level, biologists focus on what is called the gene pool, the total collection of genes in a population at any one time. Mutation and sexual reproduction produce genetic variation, making evolution possible. The Hardy-Weinberg equation can be used to test whether a population is evolving. It is also useful in public health science. Natural selection, genetic drift, and gene flow can alter allele frequencies in a population. Natural selection is the only mechanism that consistenly leads to adaptive evolution. It also can alter variation in a population in three ways: stabilizing selection, directional selection, and disruptive selection. Sexual selection may lead to phenotypic differences between males and females. Darwin was the first to explore the implications of sexual selection, a form of natural selection in which individuals with certain characteristics are more likely than other individuals to obtain mates. The evolution of antibiotic resistance in bacteria is a serious public health concern. Diploidy and balancing selection preserve genetic variation. Balancing selection occurs when natural selection maintains stable frequencies of two or more phenotypic forms in a population. Natural selection cannot fashion perfect organisms.


Key Terms
1. Evolution - the core theme of biology.
2.Artificial selection - the process by which humans have modified other species by selecting and breeding individuals that possess desired trait. 
3.Fossil record - the sequence in which fossils appear within layers of sedimentary rocks-provides some of the strongest evidence of evolution.
4.Biogeography - the geographic distribution of species.
5.Vestigial organs - structures that are of marginal or perhaps no importance to the organism.
6.Population - a group of individuals of the same species living in the same place at the same time.
7.Mutation - a change in the nucleotide sequence of DNA.
8.Genetic drift - a change in the gene pool of a population due to chance.
9.Founder effect - differences in a gene pool of a small colony compared with the original population.
10.Sexual dimorphism - the distinction in appearance.

Chapter 12: DNA Technology and Genomics

Three questions about the chapter:
1.When was the first time when a DNA sample solved a criminal case?
It happened in 1986, when professor Alec Jeffrey compared two samples of DNA and solved the case.
2.What are enzymes used for in DNA process?
Enzymes are used to "cut and paste" DNA.
3.What organisms have been cloned already?
Many plant and animal species have been already cloned, but a human being has not, and probably will not in the close future, due to ethical issues.




Five main factors from the reading:
1.Genes can be cloned in recombinant plasmids.
2.Cloned genes can be stored in genomic libraries.
3.Reverse transcriptase can help make genes for cloning.
4.Nucleic acid probes identify clones carrying specific genes.
5.Recombinant cells and organisms can mass-produce gene products.


Diagram:

 This is an example of real RFLP analysis.














Link: http://www.cdc.gov/ncidod/eid/vol4no2/kordick.htm


Summary:


The introduction of the chapter talked about DNA and crime scene investigations. It gave us the first case in which DNA solved a criminal case, by comparing a sample of DNA left at the crime and a sample taken from the person who did it. It also explained us what DNA technology is. It is the methods for studying and manipulating genetic material and it has rapidly revolutionized the field of forensics, the scientific analysis of evidence for legal investigations. The next part of the chapter talked about that genes can be cloned in recombinant plasmids. Although it may seem like a modern field, biotechnology, the manipulation of organisms or their components to make useful products, actually dates back to the dawn of civilization. In the 1970s, the uses of biotechnology exploded with the invention of methods for making recombinant DNA in the laboratory. Recombinant DNA is formed when scientists combine nucleotide sequences (pieces of DNA) from two different sources-often different species-to form a single DNA molecule. To manipulate genes in the laboratory, biologists often use bacterial plasmids, which are small, circular DNA molecules that replicate separately from the much larger bacterial chromosome. Because plasmids can carry virtually any gene and are passed on from one generation of bacteria to the next, they are key tools for gene cloning, the production of multiple identical copies of a gene-carrying piece of DNA. Gene-cloning methods are central to genetic engineering, the branch of biotechnology that involves the direct manipulation of genes for practical purposes. Enzymes are used to "cut and paste" DNA. In the gene-cloning procedure, a piece of DNA containing the gene of interest must be cut out of a chromosome and "pasted"into a bacterial plasmid. The cutting tools used are bacterial enzymes called restriction enzymes. Cloned genes can be stored in genomic libraries. Most bacterial clones consist of identical cells with recombinant plasmids carrying one particular fragment of target DNA. The entire collection of all the cloned DNA fragments from a genome is called a genomic library. Reverse transcriptase can help make genes for cloning. The DNA that results from such a procedure, called complementary DNA, represents only the subset of genes that had been transcribed into mRNA in the starting cells. Nucleic acid probes identify clones carrying specific genes. Recombinant cells and organisms can mass-produce gene products. DNA technology has changed the pharmaceutical industry and medicine. It is mostly used for therapeutic hormones, such as insulin, diagnosis and treatment of disease, and vaccines. Genetically modified organisms are transforming agriculture. Genetic engineers have produced many varieties of genetically modified organisms, ones that have acquired one or more genes by artificial means. If the newly acquired gene is from another species, the recombinant organism is called a transgenic organism. However, genetically modified organisms raise concerns about human and environmental health. Gene therapy may someday help treat a variety of diseases. One reason to tamper with the human genome is the potential for treating a variety of diseases by gene therapy - alteration of an afflicted individual's genes. The analysis of genetic markers can produce a DNA profile. The most important application of biology to forensics is DNA profiling, the analysis of DNA fragments to determine whether they come from a particular individual. The PCR method is used to amplify DNA sequences. Cloning DNA in host cells is often the best method for preparing large quantities of DNA from a particular gene. However, when the source of DNA is scanty or impure, the polymerase chain reaction (PCR) is a much better method. Gel electrophoresis sorts DNA molecules by size. Many approaches for studying DNA molecules make use of gel electrophoresis. This technique uses a gel as a molecular sieve to separate macromolecules - usually proteins or nucleic acids-on the basis of size, electrical charge, or other physical properties. STR analysis is commonly used for DNA profiling. Repetitive DNA consists of nucleotide sequences that are present in multiple copies in the genome; much of the DNA that lies between genes in humans is of this type. DNA profiling has provided evidence in many forensic investigations. RFLPs can be used to detect differences in DNA sequences. Genomics is the scientific study of whole genomes. The Human Genome Project revealed that most of the human genome does not consist of genes. The whole-genome shotgun method of sequencing a genome can provide a wealth of data quickly. Proteomics is the scientific study of the full set of proteins encoded by a genome. Genomes hold clues to the evolutionary divergence of humans and chimps.


Key Terms:


1.Biotechnology - the manipulation of organisms or their components to make useful products.
2.DNA technology - methods for studying and manipulating genetic material.
3.Plasmids - small, circular DNA molecules that replicate separately from the much larger bacterial chromosome.
4.Gene cloning - the production of multiple identical copies of a gene-carrying piece of DNA.
5.Genetic engineering - the branch of biotechnology that involves the direct manipulation of genes for practical purposes.
6.Restriction site - the DNA sequence recognized by a particular restriction enzyme.
7.Genomic library - the entire collection og all the cloned DNA fragments from a genome.
8.Vaccine - a harmless variant or derivative of a pathogen that is used to stimulate the immune system to mount a defense against the pathogen.
9.Gene therapy - alteration of an afflicted individual's genes.
10.DNA profiling - the analysis of DNA fragments to determine whether they come from a particular individual.

Chapter 11: How Genes Are Controlled

Three questions about the chapter:
1.What is gene expression?
It is the overall process by which genetic information flow from genes to proteins-that is, from genotype to phenotype.
2.What are the histones used for?
Histones are small proteins that help DNA packing by supporting the shape of the DNA.
3.Do small RNAs have a role in gene expression?
Yes, they do. The micro RNAs can bind to complementary sequences on mRNA molecules. They can degrade mRNA or block its translation.




Five main factors from the reading:
1.Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes.
2.DNA packing in eukaryotic chromosomes helps regulate gene expression.    
3.In female mammals, one X chromosome is inactive in each somatic cell.
4.Cascades of gene expression direct the development of an animal.
5.DNA micro-arrays test for the transcription of many genes at once.


Diagram:

 This diagram represents the processes of turning on and off the lac operon.





















Link: http://www.accessexcellence.org/RC/VL/GG/induction.php


Summary:

The introduction of the chapter was talking cloning. A clone is an individual created by asexual reproduction and thus genetically identical to a single parent. After this we learned that proteins interacting with DNA turn prokaryotic genes on or off in response to environmental changes. Gene regulation - the turning on and off of genes - can help organisms respond to environmental changes. The overall process by which genetic information flows from genes to proteins-that is, from genotype to phenotype-is called gene expression. The control of gene expression makes it possible for cells to produce specific kinds of proteins when and where they are needed. The turning on and off of transcription is the main way that gene expression is regulated in all organisms.The chapter talked about the lac operon and the trp operon. Adjacent to the group of lactose enzyme genes are two control sequences, short sections of DNA that help control the enzyme genes. One stretch of nucleotides is a promoter, as site where the transcription enzyme, RNA polymerase, attached and initiates transcription. Between the promoter and the enzyme genes, a DNA segment called an operator acts as a switch. The operator determines whether RNA polymerase can attach to the promoter and start transcribing the genes. Such a cluster of genes with related functions, along with a promoter and an operator, is called an operon. A gene called a regulatory gene, located outside the operon, codes for the repressor. Another type of operon control involves activators, proteins that turn operons on by binding to DNA. Differentiation is the process by which cells become specialized in structure and function. Differentiation results from the expression of different combinations of genes. DNA packing in eukaryotic chromosomes helps regulate gene expression. A crucial aspect of DNA packing is the association of the DNA with small proteins called histones. In fact, histone proteins account for about half the mass of eukaryotic chromosomes. In female mammals, one X chromosome is inactive in each somatic cell. Female mammals, including humans, inherit two X chromosomes. So why don;t females make twice as much of the proteins encoded by genes on the X chromosome compared to the amount in males? it turns out that in female mammals, one X chromosome in each somatic cell exists in a highly compacted and almost entirely inactive form. This X chromosome inactivation is initiated early in embryonic development, when one of the two X chromosomes in each cell is inactivated at random. The inactive X in each cell of a female condenses into a compact, called a Barr body. Complex assemblies of proteins control eukaryotic transcription. In order to function, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. Eukaryotic RNA may be spliced in more than one way. With an alternative RNA splicing, an organism can get more than one type of polypeptide from a single gene. Small RNAs play multiple roles in controlling gene expression. Translation and later stages of gene expression are also subject to regulation. After a eukaryotic mRNA is fully processed and transported to the cytoplasm, there are additional opportunities for regulation. These include mRNA breakdown, initiation of translation, protein activation, and protein breakdown. Cascades of gene expression direct the development of an animal. A homeotic gene is a master control gene that regulates batteries of other genes that actually determine the anatomy of parts of the body. DNA microarrays test for the transcription of many genes at once. A DNA microarray is a glass slide with thousands of different kinds of single-stranded DNA fragments fixed to it in a tightly spaced array, or grid. Signal transduction pathways convert messages received at the cell surface to responses within the cell. Cell-to-cell signaling, with proteins or other kinds of molecules carrying messages from signaling cells to receiving cells is a key mechanism in the coordination of cellular activities. In most cases, a signal molecule acts by binding to a receptor proteins in the plasma membrane of the target cell and initiating a signal transduction pathway in the cell. Cell-signaling systems appeared early in the evolution life. Plant cloning shows that differentiated cells may retain all of their genetic potential. Nuclear transplantation can be used to close animals. Reproductive cloning has valuable applications, but human reproductive cloning raises ethical issues. Therapeutic cloning can produce stem cells with great medical potential. Cancer results from mutations in genes that control cell division. Multiple genetic changes underlie the development of cancer. Faulty proteins can interfere with normal signal transduction pathways. Lifestyle choices can reduce the risk of cancer.


Key Terms:
1.Clone - an individual created by asexual reproduction.
2.Operon - a cluster of genes with related functions, along with a promoter and an operator.
3.Differentiation - an individual's cells become specialized in structure and function.
4.Homeotic gene - a master control gene that regulates batteries of other genes that actually determine the anatomy of parts of the body.
5.DNA microarray - a glass slide with thousands of different kinds of single-stranded DNA fragments fixed to it in a tightly spaced array, or a grid.
6.Nuclear transplantation - the technique used to achieve animal cloning.
7.Reproductive cloning - a type of cloning, which results in birth of a new individual.
8.Therapeutic cloning - when the major aim is to produce embryonic stem cells for therapeutic treatments.
9.Adult stem cells - cells that are able to give rise to many but not all cell types in the organism.
10.Oncogene - a gene, which can cause cancer when present in a single copy in the cell. 

Chapter 10: Molecular Biology of the Gene

Three questions about the chapter:
1.What contains the genetic material?
Experiments showed that DNA is the genetic material.
2.What are the four nucleotides found in DNA?
They are thymine (T), cytosine (C), adenine (A), and guanine (G).
3.What are the four nucleotides found in RNA?
They are uracil (U), cytosine (C), adenine (A), and guanine (G).


Five main facts from the reading:
1.DNA is a double-stranded helix.
2.DNA replication depends on specific base pairing.
3.Genetic information written in codons is translated into amino acid sequences.
4.Transcription produces genetic messages in the form of RNA.
5.Transfer RNA molecules serve as interpreters during translation.

Diagram:

  
  This diagram represents the process of DNA transcription to RNA.














Link: http://www.sequencing-gene.com/sequencing-gene/dna-transcription


Summary:
  The introduction of this chapter talked about the way viruses enter a host, and start multiplying and making new copies of themselves, based on the host's provisions. A virus is simply nucleic acid wrapped in a coat of protein and for herpesviruses and some other animal viruses, a membranous envelope. This chapter taught us about molecular biology, the study of DNA and how it serves as the chemical basis of heredity. In the past scientists had hard time to find out which part was the genetic material. They were in front of a dilemma between the DNA and the protein. However, experiments showed that DNA is the genetic material. We can trace the discovery of the genetic role of DNA back to 1928. British medical officer Frederick Griffith was studying two strains of a bacterium: a harmless strain and a pathogenic strain that causes pneumonia. Griffith was surprised to find that when he killed the pathogenic bacteria and then mixed the bacterial remains with living harmless bacteria, some living bacterial cells were converted to the disease-causing form. Most biologists doubted that DNA could be Griffith's transforming factor, primarily because there was not a lot of information for DNA. However, in 1952, Alfred Hershey and Martha Chase performed a set of experiments, which shows that DNA is the genetic material of a virus called T2, which infects the bacterium E. coli. Bacterial viruses are called bacteriophages or just phages. DNA and RNA are polymers of nucleotides. One year after Hershey and Chase published their results, scientists figured out the three-dimensional structure of DNA and the basic strategy of how it works. The four nucleotides found in DNA differ only in their nitrogenous bases. Thymine (T) and cytosine (C) are single-ring structures called pyrimidines. Adenine (A) and guanine (G) are larger, double-ring structures called purines. The one-letter abbreviations can be used for either the bases alone of for the nucleotides containing them. In RNA, instead of thymine, RNA has a nitrogenous base called uracil (U). James Watson and Francis Crick discovered that the DNA is a double-stranded helix in 1953. DNA replication depends on specific base pairing. The most famous model for DNA replication is knows as semi-conservative model, because half of the parental molecule is maintained in each daughter molecule. This model was confirmed by experiments performed in the 1950s. DNA replication proceeds in two directions at many sites simultaneously. Each strand has a 3' end and a 5' end. The enzymes that link DNA nucleotides to a growing daughter strand called DNA polymerases, add nucleotides only to the 3' end of the strand, never to the 5' end. So, a daughter DNA strand can only grow in the 5' to 3' direction. Another important enzyme, called DNA ligase, links the separated pieces together into a single DNA strand. The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits. The two main stages that take place after replication are transcription, the transfer of genetic information from DNA into an RNA molecule, and translation, the transfer of the information in the RNA into a protein. Genetic information written in codons is translated into amino acid sequences. Experiments have verified that the flow of information from gene to protein is based on a triplet code: The genetic instructions fro the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of three-base words, called codons. The genetic code is the set of rules giving the correspondence between codons in RNA and amino acids in proteins. The Genetic code is also called the Rosetta stone of life. Transcription produces genetic messages in the form of RNA. The "starting transcribing" signal is a nucleotide sequence called a promoter. Eukaryotic RNA is processed before leaving the nucleus. The kind of RNA that encodes amino acid sequences is called messenger RNA (mRNA) because it conveys genetic information from DNA to the translation machinery of the cell. The RNA has internal noncoding regions called introns, and coding regions called exons. Before the RNA leaves the nucleus, the introns are removes, and the exons are joined to produce an mRNA molecule with a continuous coding sequence. This cutting-and-pasting process is called RNA splicing. Transfer RNA molecules serve as interpreters during translation. To convert the three-letter words (codons) of nucleic acids to the one-letter, amino acid words of proteins, a cell employs a molecular interpreter, a special type of RNA called transfer RNA (tRNA). Ribosomes build polypeptides. A ribosome consists of two subunits, each made up of proteins and a kind of RNA called ribosomal RNA (rRNA). An initiation codon marks the start of an mRNA message. Transcription and translation have three stages: initiation, elongation, which adds amino acids to the polypeptide chain until a stop codon terminates translation, and termination. Mutations can change the meaning of genes. Any change in the nucleotide sequence of DNA is called a mutation. Viral DNA may become part of the host chromosome. Many viruses cause disease in animals and plants. bacteria can transfer DNA in three ways: transformation, transduction, and conjugation. Also bacterial plasmids can serve as carriers fro gene transfer.


Key Terms:
1. Virus - simply nucleic acid wrapped in a coat of protein.
2. Molecular biology - the study of DNA and how it serves as the chemical basis of heredity.
3.  Nucleotides - long chains of chemical units.
4. DNA Polymerases - the enzyme that links DNA nucleotides to a growing daughter strand.
5. DNA Ligase - the enzyme that links the pieces together into a single DNA strand.
6. Transcription - the transfer of genetic information from DNA into an RNA molecule.
7. Translation - the transfer of the information in the RNA into a protein.
8. Genetic code - the set of the rules giving the correspondence between codons in RNA and amino acids in proteins.
9. RNA splicing - the process of cutting-and-pasting introns and exons.
10. Mutation - any change in the nucleotide sequence of DNA.