Chapter Thirteen

Key Terms:
Natural selection: the differential survival and reproduction of individuals within a population
Biogeography: the geographic distribution of species, suggested to Darwin that organisms evolve from common ancestors
Comparative anatomy: is the comparison of body structures in different species
Homology: is the similarity in characteristics that result from common ancestry
Molecular biology: comparisons of DNA and amino acid sequences between different organisms reveal evolutionary relationships
Population: a group of individuals of the same species living in the same place at the same time
Evolution: the change in heritable traits in a population over generations
Gene Pool: the total collection of genes in a population at any one time
Microevolution: a change in the relative frequencies of alleles in a gene pool over time
Population genetics: studies how populations change genetically over time

Reading Journal: 1) What is artificial selection? artificial selection is a process in which humans have modified other species by selecting and breeding individuals that possess desired traits.
2) Who are paleontologists? they are scientists who basically study fossils.
3) What is the Hardy-Weinburg equilibrium? The principle that the frequency of each allele in the gene pool will remain constant unless other factors are operating.
Five Facts: 1) In the mid-1700s, the study of fossils revealed fossil forms in layers of sedimentary rock that differed from current life forms.
2) Fossil records is the sequence in which fossils appear within layers of sedimentary rocks. They provide some of the strongest evidence of evolution.
3) Vestigial organs are structures that are of marginal or no importance to the organisms. They are remnants of structures that served important functions in the organism's ancestors.
4) Darwin's boldest hypothesis is that all life-forms are related.
5) In The Origin of Species, Darwin provided evidence that life on Earth has evolved over time, and natural selection was the primary mechanism for the change.

Adaptations are inherited characteristics that enhance organism's ability to survive and reproduce in a particular environment. In natural selection individuals that are well suited to the environment tend to leave more offspring, while those who are not well suited eventually decline. In Darwin's theory of evolution, living species are descended from earlier life-forms that differed from present day organisms. There has been evidence of natural selection in the populations of birds, insects, and other organisms. Fossil records are able to reveal the historical sequence that organisms have evolved and many fossils linking ancestral species with those living today.
Evidence of evolution comes from sources of biogeography, molecular biology, comparative anatomy, etc. Homologous structures and DNA sequences also provide evidence of evolutionary relationships.
Allele frequencies change due to natural selection, genetic drift, and gene flow. The bottle neck effect occurs when a population’s size is reduced for at least one generation. Founder's effect occurs when a new colony is started by a few members of the original population. The new colony may have a reduced genetic variation from the original population and a non-random sample of the genes in the original population. They both may lead to genetic drift as well.
Sexual selection leads to the evolution of secondary sex characteristics, which give individuals an advantage in mating. An example include the male peacock showing his big and colorful feathers.
There has been much concern over the evolution of antibiotic resistance in bacteria. An antibiotic resistance results from excessive or incorrect use of antibiotics.
Many may think that natural selection fashions perfect organisms, but it does not. Selection can only act on existing variations. Evolution is limited by historical constraints; adaptations are often compromises; and chance, natural selection, and the environment interact.


This is an example of human population in North America. People are most likely to choose mates locally. For humans and other species, individuals in one population are generally more closely related than to other members in other populations.


Youtube video Natural selection:
http://www.youtube.com/watch?v=oCXzcPNsqGA

Chapter Twelve

Key terms:
Genetic engineering- involves manipulating genes for practical purposes
Gene cloning- leads to the production of multiple identical copies of a gene-carrying piece of DNA
Plasmids- small, circular DNA molecules independent of the bacterial chromosome
Restriction enzymes- cut DNA at specific sequences
Restriction fragments- single stranded ends called "sticky ends"
Genomic library- is a collection of all the cloned DNA fragments from a target genome
Biotechnology- the manipulation of organisms or their components to make useful products
Gene cloning- the production of multiple identical copies of a gene-carrying piece of DNA.
Reverse transcriptase- an enzyme which is obtained from retroviruses.
Complementary DNA (cDNA)- represents the only subset of genes that had been transcribed into mRNA in the starting cells.

Reading Journal:
1) What is a plasmid library? genomic DNA which are carried by plasmids
2) What are advantages of cloning with cDNA? you are able to study genes responsible for specialized characteristics of a particular cell type, and you are able to obtain gene sequences without introns.
3) What are some products of DNA technology? therapeutic hormones, such as insulin and human growth hormones; it also helps the diagnosis and treatment of disease.


Five Facts:
1) DNA ligase DNA fragments together.
2) Cells and organisms containing cloned genes are used to manufacture large quantities of gene products.
3) Recombinant DNA is formed when scientists combine nucleotide sequences from two sources to form a single DNA molecule.
4) Plasmids are key tools for gene cloning, because they are able to carry virtually any gene and are passed on from one generation of bacteria to the next.
5) phages can also serve as vectors, which are DNA carriers, when cloning genes.

Biotechnology, which is the manipulation of multiple organisms or their components to make useful products. Biotechnology has been used for almost thousands of years.
Gene cloning, is the production of multiple identical copies of a gene-carrying piece of DNA. Some applications of gene cloning include mass production of gene products for medical and other uses. Researchers also use gene cloning to produce hormones to diagnose and treat diseases, and produce vaccines. Some examples include insulin for diabetes and growth hormone for those who have growth disabilities. Recombinant DNA technology can be used to produce new genetic varieties of plants and animals. Many important crop plants are genetically modified to be immune to the chemicals that are sprayed to protect from diseases and insects. There are many risks, especially ecological damage, from genetic engineering.
DNA profiling is the analysis of DNA fragments can determine whether two samples of DNA come from the same individual. DNA profiling is most frequently used in solving crimes and finding suspects. Some methods include using a thumbprint and gel electrophoresis.
Genomics is the study of whole genomes, and has advanced rapidly in recent years. Nonhuman genomes can be compared with the human genome. Information from the Human Genome Project revealed that the haploid human genome contains about 21,000 genes and a huge amount of non coding DNA. The Human Genome Project used genetic and physical mapping of chromosomes along with DNA sequencing. Genomic data provides insight into recent and ancient evolution.



Here are steps of Gel electrophoresis. Once the aragose gel is prepared, the DNA sample is added into lane 2. The gel runs through an electric current, which separates the DNA band into size. The dye is then added the DNA and exposed under UV light, which makes the DNA visible.









Youtube video of DNA technology:
http://www.youtube.com/watch?v=Nc3jArZXHjs

Chapter Eleven

Key Terms:
Gene Expression- the overall process of gene flow from genes to proteins
Operon- a group of genes under coordinated control in bacteria
Regulatory gene- codes for a repressor protein
Activators- enhance RNA polymerase binding to the promoter
Differentiation- involves cell specialization, in structure and function
Nucleosomes- formed when DNA is wrapped around histone proteins
Barr Body- inactivated X chromosome
Transcription factors- promote RNA polymerase binding to the promoter
Silencers- repressors that inhibit transcription
Homeotic genes- master control genes that determine the anatomy of the body

Reading Journal:
1) How does differentiation work? Differentiation works by turning specific sets of genes either on or off.
2) What is a lac operon? it is an active repressor that binds to the operator; the inducer, which is lactose, binds and inactivates the repressor.
3) What is a signal transduction pathway? it is a series of molecular changes that converts a signal at the cell's surface to a response within a cell.

Five facts:
1) Most differentiated cells retain a full set of genes, even though only a subset may be expressed.
2) Cloned animals can show differences from their parent due to a variety of influences during development.
3) Tumor-suppressor genes promote cancer when both copies are mutated.
4) Carcinogens are cancer-causing agents that damage DNA and promote cell division.
5) Cloning does not increase genetic diversity, but can be used to help save endangered species.


in prokaryotes, genes for related enzymes are often controlled together in units called operons. gene regulation can help organisms respond to environmental changes. regulatory proteins bind to control sequences in the DNA. In multicellular eukaryotes, cells differentiate, or specialize in a specific task. A chromosome contains DNA that goes around clusters of histone proteins, forming a string of beadlike nucleosomes. DNA packing sometimes block gene expression, preventing access of transcription proteins to the DNA. A variety of regulatory proteins interact with DNA and with each other to turn the transcription of eukaryotic genes on or off.
The lifetime of an mRNA molecule helps determine how much protein is made, as do protein factors involved in translation. A protein may need to be activated, and eventually the cell will break it down.
Gene expression controls the development of an animal from a fertilized egg. Signal transduction pathways convert molecular messages to cell responses. Some similarities in organisms have suggested the signal transduction pathways evolved early.
In cloning, a clone is an individual created by asexual reproduction and is genetically identical to a single parent. nuclear transplantation is used to clone animals. The goal of therapeutic cloning is to produce embryonic stem cells. Embryonic stem cells have not differentiated yet, thus they are more diverse with applications. In adult stem cells, they normally have a limited range of cell types.
Cancer cells divide uncontrollably, which result from mutations in genes. a mutation can change into an oncogene. An oncogene is a normal gene that promotes cell division and divide excessively. Cancer result form a series of genetic changes in a cell lineages. Reducing exposure to carcinogens and making other lifestyle changes can help reduce cancer risks.



Here is an illustration of cloning. An unfertilized egg's nucleus is taken out of the egg, and replaced with a cell to be cloned. Once they develop to a certain stage, they are implanted into the organism.










Youtube video on Gene expression:
http://www.youtube.com/watch?v=OEWOZS_JTgk

Chapter Ten

Key Terms:
Viruses- Invaders that sabotage our cells.
Bacteriophages- Viruses that infect bacterial cells.
Nucleotide- The monomer unit of DNA and RNA which contains a nitrogenous base, 5-carbon sugar, and a Phosphate group.
Sugar-phosphate backbone- formed by covalent bonding between the phosphate of one nucleotide and the sugar of the next nucleotide.
DNA polymerase- adds nucleotides to a growing chain
DNA ligase- joins small fragments into a continuous chain
RNA polymerase- catalyzes reaction
Transcription- Process in which DNA is transcribed in to RNA
Translation- Process in which RNA is transcribed into protein
RNA splicing- removal of introns and joining of exons to produce a continuous coding sequence
Reading Journal:
1) How do viruses work? viruses have genetic material that is surrounded by a protein coat. the proteins bind to receptors on a host's target cell, and the viral nucleic acid enters the cell, which it may choose to remain dormant or activate. Once it is activated, the host cell is destroyed, and the viruses are released to continue.
2) What was the semiconservative model? It is a model for DNA replication. Basically, two DNA strands separate and each strand is used as a pattern to produce a complementary strand. Each DNA helix has one old strand with a new strand.
3)What proteins are involved in DNA replication? DNA polymerase, which adds nucleotides, and DNA ligase which joins small fragments in a continuous chain.

Five Facts:
1) James D. Watson and Francis Crick deduced the secondary structure of DNA.
2) A nucleotide contains a nitrogenous base, a phosphate group, and a 5-carbon sugar.
3) DNA is composed of two polynucleotide chains joined together by hydrogen bonding between bases that is twisted in a helix.
4)DNA replication occurs in a 5' to 3' direction.
5) There are three stages in transcription and translation which include initiation, elongation, and termination.

Viruses are invaders that have the ability to sabotage our cells by destroying and taking over the host cell. Viral proteins are able to bind to receptors on a host's target cell, and once the nucleic acid enters the cell, it will remain dormant. When activated, viral DNA triggers viral duplication, which uses the host's molecules and organelles. Once the host cell is destroyed the, the replicated viruses are released to continue the infection.
Frederick Griffith discovered that "transforming factor" could be transferred in a bacterial cell.
Alfred Hershey and Martha Chase also showed that if they used bacteriophages, it could show that DNA was the genetic material. Bacteriophages are viruses that infect bacterial cells. A nucleotide is a monomer unit of either a DNA or RNA. It contains a phosphate group, a nitrogenous base, and a 5-carbon sugar. DNA and RNA are also polymers called polynucleotides. DNA is composed of two polynucleotide chains that are joined together by hydrogen bonds between bases. Specific base pairings give the helix a uniform shape (A with T, G with C).
In DNA replication, DNA unwinds at the origin, and replication proceeds in both directions from the origin, in a 5' to 3' direction. Replication ends when products form the bubbles merge with each other. Transcription is when DNA is being transcribed to RNA. Transcription has three steps, initiation, which is when RNA polymerase binds to a promoter; Elongation, in which RNA nucleotides are added to the chain. Last is termination, which is when RNA polymerase reaches a terminator sequence and detaches from the template. Translation is when RNA is translated into a protein. Translation has very similar steps as well, and occurs on the surface of a ribosome.
There are three mechanisms which allow the transfer of bacterial DNA: Transformation, Transduction, and Conjugation. Transformation is the uptake of DNA from surrounding environment, while transduction is gene transfer through bacteriophages, and conjugation is the transfer of DNA from a donor to a recipient bacterial cell through cytoplasmic bridge. There are also infectious agents that are made only of RNA or Protein. Viroids, which are circular RNA molecules that infect plants; and Prions, which are infectious proteins that cause brain diseases in animals.





This is an example of an HIV cell, which causes AIDS. The HIV is a retrovirus, containing two copies of its RNA genome and an enzyme that produces DNA from an RNA template, which is called reverse transcriptase. In HIV duplication, the enzymes(Reverse transcriptase) uses RNA to produce one DNA strand, and also produces the complementary DNA strand. The viral DNA enters the nucleus and integrates into the chromosome. This then becomes a provirus, which is used to produce mRNA, which is translated to produce viral proteins. These viral particles are assembled and leave the host cell.




Youtube Overview video of Trascription and Transcription:
http://www.youtube.com/watch?v=XIG_KCAUWPI