Chapter 14 - Origin of Species

Q: What is the difference between micro and macroevoltuion?
A: Microevoltuion is the changes in a singel gene pool where as macroevoltion deals with patterns of evolutionary change over long periods of time.
Q: What is a species?
A: A species is a kind of organism.
Q: How does environment affect evolution?
A: Evolution is affected by environment because in some cases a population may be secluded from outside contact.

Five main facts:
1) Reproductive barriers keep species separate.
2) In allopatric speciation, geographic isolation leads to speciation.
3) Reproductive barriers may evolve as a population diverges.
4) Most plant species trace their origin to polyploid speciation.
5) Hybrid sones provide opportunities to study reproductive isolation.

This diagram shows polyploid speciation. Polyploid speciation is where organisms with more then two sets of homologuous chromosomes are able to breed.

Chapter 14 focuses on how species have evolved over time. This is partially due to natural selection but other variables are present. Speciation allows for new species to diversify. Reproductive barriers have also lead to a very diverse set of species because only certain organisms are able to breed together. Environment also affects how species have evolved over time. 

Key Terms:

1) Taxonomy: branch of biolgy that names and classifies species

2) biological species concept: primary definition for species

3) Reproductive isolation: prevents genetic exchange and maintains the gap between species

4) Reproductive barrier: biological feature of the organism itself

5) Prezygotic barriers: prevent mating or fertilization between species

6) Postzygotic barriers: operate after hybrid zygotes are formed

7) Allopatric speciation: initial block of gene flow due to geographic barrier

8) Sympatric speciation: new speices that arise within the same geographic area as a parent species

9) Polyploid: cells have more then two complete sets of chromosomes

10) Adaptive radiation: evolution of many diverse species from a common ancestor 

http://www.youtube.com/watch?v=YCoEiLOV8jc

Chapter 13 - How Populations Evolve

Q: What is Darwins theory of evolution?
A: He felt that evolution was by means of descent with modification.
Q: What is natural selection?
A: A natural process that results from evolution for those best suited for their environment.
Q: What is homology?
A: Homology is the similarities in different species due to evolution from a common ancestor.

Five main facts:
1) Darwin theorized evolution.
2) Scientists are able to observe natural selection while it is in action.
3) Fossils provide strong evidence for evolution.
4) Homologies indicate patterns of descent that can be shown on an evolutionary tree.
5) Sexual selection can lead to phenotypic differences between males and females.

This diagram shows a stabilizing selection. This favors intermediate phenotypes. 

This chapter talks about evolution and how it came about. Darwin is the father of evolution and he came about this theory when he traveled to the Galapagos Islands. Adaptations of species allows for them to be better suited for their environment. Natural selection plays a major role in evolution. Populations are said to evolve and Hardy-Weinberg showed this through his theory of equilibrium.

Key Terms:

1) Artificial selection: modified species by selecting and breeding individuals to possess desired traits

2) Natural selection: natural process that results from evolution for those best suited for their environment

3) Extinction: when a species no longer exists

4) Paleontologists: scientists who study fossils

5) Fossil record: sequence in which fossils appear within layers of sedimentary rock

6) Strata: layers of rock

7) Homology: similarity in characteristics that results from common ancestory

8) Vestigial organs: structures that are of marginal or perhaps no importance to an organism

9) Evolutionary tree: patterns of descent in evoltuion

10) Mutation: change in the nucleotide sequence of DNA

http://www.youtube.com/watch?v=vss1VKN2rf8

Chapter 12 - DNA Technology and Genomics

Q: Why does the rapid reproduction of bacteria make them suitable choices for cloning foreign genes?
A: They are suitable because they are located within plasmid DNA which can be replicated each time the cell divides which results in man copies of the same gene.
Q: What are "sticky ends"?
A: These are single-stranded regions with unpaired bases that can hydrogen-bond to the complementary sticky ends of fragments made by restriction enzymes.
Q: What is DNA profiling?
A: This the analysis of DNA fragments to determine whether they come from a particular individual or not.

Five main facts:
1) Enzymes are used to essentially "cut and paste" DNA.
2) Cloned genes are able to be stored in a genomic library.
3) Nucleic acid probes help identify clones carrying certain genes.
4) The PCR method is used to amplify DNA sequences.
5) DNA profiling has aided in many investigations by use of forensics.

This depicts the PCR method. This method is used when the source of DNA is scanty or impure. IT allows for a specific gene segment to be targeted and amplified. 

This chapter focuses on DNA technology. There are several ways in which this is applied. One is through the research on cloning. Other ways include genetically modified organisms, for example the corn many of us eat. It had been modified genetically to be more resistant to certain diseases and to produce more corn itself. DNA profiling has aided in many forensic cases.

Key Terms:

1) Plasmids: small, circular DNA molecules that replicate separately from the much larger bacterial chromosome

2) Gene cloning: production of multiple identical copes of a gene-carrying piece of DNA

3) Genetic engineering: branch of biotechnology that involves the direct manipulation of genes for practical purposes

4) Vector: gene carrier

5) Clone: group of identical cells descended from a single ancestral cell

6) Genomic library: entire collection of all the cloned DNA fragments from a genome

7) Nucleic acid probe: complementary molecule

8) Vaccine: harmless variant or derivative of a pathogen that is used to stimulate the immune system to mount a defense against that pathogen

9) Gene therapy: alteration of an afflicted individual's genes

10) Primers: short, chemically synthesized single-stranded DNA molecules with sequences that are complementary to one strand at one end of the target sequence

http://www.youtube.com/watch?v=eEcy9k_KsDI

Chapter 11 - How Genes are Controlled

Q: How is it that densely packed DNA prevents gene expression?
A: RNA polymerase and other proteins necessary for transcription do not have viable access to DNA that is tightly packed.
Q: How is alternative RNA splicing used to enable a single gene that will encode more than one kind of polypeptide?
A: A polypeptide is encoded by a mRNA molecule that contains different combinations of exons.
Q: What can be learned from a DNA microarray?
A: In a DNA microarray it can be inferred what genes are active in a particular sample of cells.

Five main facts:
1) Proteins that interact with DNA turn prokaryotic genes on or off in response to outside changes such as environment.
2) Differentiation can result from the expression of many combinations of genes.
3) DNA packing in eukaryotic cells help regulate how genes will be expressed.
4) Eukaryotic RNA can be spliced in several different ways.
5) In the later stages of translation, gene expression may be subject to regulation.

This diagram shows the packing of DNA into a chromosome. It shows how spacers are used to keep genes from interfering with one another. 

In chapter 11 the main focus is how genes are expressed. There is a control in both prokaryotic and eukaryotic cells. This allows for certain genes to be expressed that will benefit an organism. Also the cloning fo plants and animals is talked about and can be regulated by scientists through differentiated cells and nuclear transcription. 

Key Terms:

1) Differentiation: when cells become specialized in structure and function

2) Histones: association of the DNA with small proteins

3) Barr body: the inactive X in each cell of a female condenses into this compact object

4) Transcription factors: assistance given from proteins in order for eukaryotic RNA to function

5) Enhancers: binding of activator proteins to DNA sequences 

6) Silencers: proteins that may bind to DNA sequences and inhibit the start of transcription

7) RNA interface: procedure in which researchers can take advantage of miRNA mechanisms to artificially control gene expression

8) Hometic gene: master control gene that regulates batteries of other genes that actually determine the anatomy of parts of the body

9) DNA microarray: glass slide with thousands of different kinds of single-stranded DNA fragments fixed to it in a tightly spaced array or grid

10) Adult stem cells: cells that are able to give rise to many but not all cell types in an organism 

http://www.youtube.com/watch?v=mUcE1Y_bOQE

Chapter 10 - Molecular Biology of the Gene

Q: What does a DNA polymerase do in the process of DNA replication?
A: DNA polymerase is used to line up new nucleotides on the already existing strand in terms of the base-pairing rules.
Q: What do transcription and translation do?
A: Transcription is where information is transfered from DNA to RNA and translation is where RNA is used to aid in the process of making a new protein.
Q: What is a promotoer?
A: A promoter is a certain nucleotide sequence of bases that starts off a strand of DNA.

Five main facts:
1) Transcription produces genetic messages in the form of RNA.
2) Ribosomes are what aid in the building up of polypeptides.
3) There are certain codons that initiate as well as marks the start of an mRNA message.
4) Mutations change genes.
5) A virus may use a host cell so that it may implement its own DNA into that of the host's cell DNA.

This is a model of mRNA. As you can see there is only one side of the helix. Also note that instead of T, in place there is instead U. This is an easy way to tell whether or not it is a normal DNA strand or and that of RNA.

This chapter focuses on how DNA, RNA is used in the cell. DNA holds genetic coding that allows for genes to be passed on through the process of DNA replication. RNA comes into play during the actual DNA replication process. DNA controls both phenotype as well as genotype. All living organisms are able to replicate their genes and even viruses are able to put their DNA into a host cell so that more of that virus may be made. 

Key Terms:

1) Molecular biology: study of DNA and how it serves as the chemical basis of heredity

2) Bacteriophages: a type of bacterial virus

3) Polynucleotides: a type of polymer that is in DNA

4) Double helix: two strands that make up the structure of DNA

5) DNA polymerase: enzymes that link DNA nucleotides to a growing daughter strand

6) DNA ligase: enzyme that links two polynucleotides together to form a single strand of DNA

7) Transcription: transfer of genetic information from DNA to RNA

8) Translation: transfer of information from RNA into a protein

9) Triplet code: flow of information from genes to proteins

10) Codons: genetic instructions for amino acid sequence of a polypeptide chain 

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