The Origin of Species

Again, how awesome was Charles Darwin?

Extremely awesome. Like extremely awesome. On a whim he decided to go on a lengthy sea voyage instead of become a minister. This voyage took him to the Galapagos islands, and it was there Darwin discovered his passion and goal of proving evolution. Instead of just accepting that the Earth was 6,000 years old and that species were static in their evolution, he studied fossil and geological records to discover they were not

What is the significance of Daphne Major?


It's an isolated, uninhabited island in the Galápagos in which 60 different types of ground finches were living. This inspired much work with small populations in evolutionary study.

What is the significance of Cichlids? 


Over 1000 species of Cichlids live in Lake Victoria. They are a study in sexual reproduction and inbreeding because there are many cichlids that differ in only color, not anything biological, but they don't seem to interbreed. In a few studies, it is shown that the fish have certain color receptors that signal them to mate with only the colors they are sensitive to.

The Facts:

-Biological species concept: It defines a species as a group of populations whose members have the potential to interbreed in nature and produce fertile offspring

-Reproductive isolation: prevents genetic exchange and maintains the gap between species by isolating those that are genetically similar from those who are different

-Morphological species concept: classification is based mainly on observable and measurable physical traits such as shape, size and other features of form

-Ecological species concept: Identifies species in terms of their ecological niches

-Phylogenetic species concept: defines a species as the smallest group of individuals that shares a common ancestor that forms one branch on the tree of life

-Reproductive barrier: a biological feature of the of the organism itself that prevents fertilization between species

-Prezygotic barriers: Prevent mating or fertilization between species

-Postzygotic barriers: After hybrid zygotes are formed, most offspring will not survive. 

-Reduced hybrid fertility: A type of postzygotic barrier that produces infertile offspring.

-Punctuated equilibria: Used to describe long periods of little change evolutionarily

Some Key Terms:

-Speciation: the emergence of new species

-Taxonomy: the branch of biology that names and classifies species and groups into broader categories

-Sympatric speciation: a new species arises within the same geographic area as a parent species
-Allopatric speciation: Formation of many species living today by changing of allele frequencies
-Adaptive Radiation: The evolution of many species from a common ancestor
-Temporal isolation: Mating or flowering occurs at different times of day or seasons
-Habitat isolation: Populations live in different habitats and do not meet

-Behavioral isolation: There is little or no sexual attraction between different species

-Mechanical isolation: Structural differences in genitalia or flowers to prevent copulation or pollen transfer

-Gametic isolation: Male and/or female gametes dies before uniting or fail to unite

Diagram:

This is a diagram of the 3 Domains: Archaea, Bacteria and Eukarya. Domain is the highest taxonomic classification, and within the Domain Archaea you have the kingdom archaeobacteria (which are prokaryotes), and in Bacteria you have Eubacteria. The Domain Eukarya is the broadest, having 4 kingdoms: Protista, Fungi, Plantae, and Animalia

Summary:

A Cool Video:

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

How Populations Evolve

How awesome was Charles Darwin?

So awesome. Like you wouldn't believe. He wrote the Origin of species. He proposed evolution in ways no one ever had before- generations upon generations of adaptation (Suck it, Lamark), using fossil and geological records (the church has nothing on this guy), and of course: the theory of natural selection.


What is natural selection?

Natural selection is the theory that those that have an advantage to life, such as a helpful mutation, will live, and thus will be able to pass this trait on to their offspring. Those that don't may or may not be less favorable for breeding, but if they are not because they do not possess this mutation, they will naturally die out or become less common.

What is the Hardy-Weinberg Equation?

p + q = 1

p^2  + 2pq + q^2 = 1

p = homozygous dominant
q = homozygous recessive
pq = heterozygous

The Facts:

-The Hardy-Weinberg equilibrium is the state in which evolution is static and the gene pool remains constant unless other factors are at work

-The Hardy-Weinberg equation only works if the population involved has 5 very specific criteria:

-1. Very large population

-2. No gene flow between populations
-3. No mutations

-4. Random Mating

-5. No natural selection

-A genetic drift is a change in the gene pool of a population due to chance, the smaller the population, the more impact the genetic drift will have

-The bottleneck effect refers to when a population is reduced down to very little, leaving only those that were most frequent, unless they had a trait that allowed them to survive the near-extinction

-The founder effect refers to when a few individuals colonize an island or new habitat and genetic drift takes place.

Some Key Terms:

-Adaptations: Inherited traits that enhance an organism's ability to live.

-Extinction: An irrevocable loss of species

-Fossil record: The sequence in which fossils appear in sedimentary rocks

-Strata: Layers

-Homology: Similarity in characteristics that results from a common ancestry

-Vestigial organs: Structures that are of marginal or perhaps no importance to the organism

-Mutation: A change in the nucleotide sequence

-Heterozygote advantage: Heterozygous organisms having greater reproductive success than homozygous

-Fitness: the contribution an individual makes to the gene pool of the next generation relative to that of others

-Sexual dimorphism: The secondary sexual characteristics that differ in males and females

Diagram:

Here you can see different colored marbles. Imagine the marbles are different species. In an event of mass death within this species, the most common (or most advantageous) will survive, albeit only a few of them. But we find in the next generation, there are only those genetically similar to those that survived, deteriorating the gene pool.

Summary:

This chapter was about the awesomeness of Darwin. Maybe not completely about him at all times, but it ties back to him a lot. First it talks about natural selection, which is just the process of the most desirable traits living on, and thus making for speedy evolution. It touches on how many animals probably had a common ancestor at one point, seeing as we have homologous structures to many of them. Although wings are a question, since they evolved in separate species in a different way. Then it talks about the Hardy-Weinberg equation, which is commonly used to gauge evolution in a population, since it rarely meets all the requirements.
It goes on to talk about sexual selection in animals, with sexual dimorphism and sexual selection. This means that the most genetically appealing (in a sense) will most likely attract mates.

A Cool Video:

http://www.youtube.com/watch?v=06hGNM9M6Fs

How Genes Are Controlled

What is one of the main concerns with cloning?


Clones are usually less healthy and shorter than the original. The cells in the clone are "older" than those of the originals'. They would be prone to diseases that are more commonly seen in older specimens, including obesity, pneumonia, liver failure and premature death

Why are calico cats only female?

In all female mammals, only one X chromosome is active in each cell. In cats, there is an X chromosome for black fur, and one for orange. In a female, one finds that if each X is a different color, different X's could be active, thus creating patches of orange and black.

Why do cloned specimens look and act different than their parent?


Cloning makes the offspring genetically the same as the parent, but appearance and behavior are largely environmental factors


The Facts:
-Cloning could provide an answer to endangerment
-The problem with cloning is that you are taking DNA that is already relatively old, and thus your clones have much older bodies
-The lac operon deals with lactose and allows for digestion
-The trp operon is made from E. coli
-Female mammals have two X chromosomes, one of which is inactive in each cell
-mRNA are broken down after they have created enough proteins
-Insect antenna are more similar to their leg parts
-In crustaceans, their mouth parts are homologous to their leg parts
-A DNA microarray is a glass slide with strands of DNA on it, each carrying thousands upon thousands of genes
-A signal transduction pathway is a series of molecular changes that coverts a signal on a target cell's surface to a specific response

Some Key Terms:
-Clone: An individual created by asexual means and genetically identical to the parent
-Gene Expression: The expression of genes into physical characteristics
-Differentiation: Individual cells becoming specialized in structure
-Histones: Small proteins packaged in the DNA
-Barr Body: The inactive X chromosome in a female
-Alternative RNA Splicing: A way by which an organism can get more than one type of polypeptide from a gene
-Homeotic Gene: Master control gene that regulates batteries of other genes and determine the anatomy of parts of the body
-Embryonic Stem Cells: "Blank" cells found in embryos that have the potential to become any type of cell
-Oncogene: A gene that could potentially make a cell cancerous
-Proto-Oncogene: A gene that has the potential to become an Oncogene

Diagram:

This is a diagram of reproductive and therapeutic cloning. You can see that you take the nucleus out of the cell you want to clone, remove the nucleus from your egg cell, and you'll eventually have the start of a clone. In reproductive cloning, these cells are put into a surrogate mother, in therapeutic cloning, these will be used in a tissue culture to be used in the organism.









Summary: 


This chapter, as the name suggested, talking about how genes are controlled and regulated. The first step in protein creation and control are the transcription factors that initiate the RNA polymerase. Silencers will repress protein production once finished. Keeping that in mind, only 1.5% of the human genome codes for proteins.

A Cool Video:


http://www.thedailyshow.com/watch/tue-march-27-2007/cloned-meat

DNA Technology and Genomics

What was the Human Genome Project?

The goals of the HGP were to determine the nucleotide sequence of all DNA in the human genome. As of 2007, there remain many gaps unknown still. However, for the most part, it has been determined within 99.9999% accuracy.

What is genetic engineering?

The branch of biotechnology dealing in manipulating the DNA of organisms for practical purposes. For example, a few years back they genetically engineered a type of potato that grew leaves with a bacteria that killed potato bugs, making them pest-resistant and thus decreased their need for pesticides.

What happened to smallpox?

Smallpox was virtually eradicated from the world due to effective vaccines. This was made possible by using a harmless variant. But not only that, now that they have made this harmless variant, they are able to genetically alter it to induce immunity to other diseases.


The Facts:
-Recombinant DNA is formed when scientists combine nucleotide sequences from two different sources to form a single DNA strand
-Complementary DNA represents only the subset of genes that had been transcribed into mRNA in the starting cells.
-Nucleic acid process are used to find a specific gene or other nucleotide sequence within a mass of DNA
-Insulin is made in E. coli
-A vaccine is made of a harmless variant of a harmful pathogen
-Genetically modified organisms have acquired genes by artificial means
-DNA profiling is what finally convicted Clinton of his affair
-Genomics is the study of a complete set of genes
-Whole-genome shotgun method is a method that skips right from mapping to sequencing
-Ti Plasmids are used to introduce new genes into plant cells 



Some Key Terms:
-Biotechnology: the manipulation of organisms or their components to make useful products
-Plasmids: Small, circular DNA molecules that replicate separately from the much larger bacterial chromosome
-Gene therapy: Alternation of afflicted individual's genes
-Forensics: The scientific analysis of evidence for crime scene investigations
-DNA profiling: The analysis of DNA fragments to determine whether they come from a particular individual
-DNA ligase: an enzyme that joins two DNA molecules by covalent bonds
-Restriction Site: A DNA sequence is recognized by this enzyme
-Gel electrophoresis: A technique of studying DNA with gel used as a molecular sieve to separate macromolecules on the basis of size
-Polymerase chain reaction: A specific segment of a DNA molecule can be targeted and amplified in a test tube
-Repetitive DNA: DNA that consists of nucleotide sequences that are present in multiple copies in the genome

Diagram:

This is a picture roughly describing the process of gene therapy. In this particular instance, a helpful gene has been placed in a virus with an extreme capacity for reproduction. Then this is placed in a human cell, which is then duplicated to a point where it helps whatever problem that existed.










Summary:

This chapter was about how we've essentially "figured out" DNA and the benefits that come from that. Mostly it talks about practical application such as in crime scene investigation. It talks a lot about different techniques such as gel electrophoresis, STR analysis and the whole-genome shotgun method.
But it moves on to talk about the Human Genome Project, and while the entire genome may still have some gaps in it, it is still very helpful now that we have much of it mapped. Having the genome mapped may shed some light on the divergence of human and primate evolution.


A Cool Video:


http://www.youtube.com/watch?v=vl7ggCqr79s

Molecular Biology of the Gene

What is Transcription?

The transfer of genetic information from DNA into an RNA molecule



What is Translation?


The transfer of the information in the RNA into a protein


What are the base nucleotides for DNA and RNA?

DNA: Adenine, Cytosine, Guanine and Thymine
RNA: Adenine, Cytosine, Guanine and Uracil


The Facts:
-DNA is arranged in a double helix shape (a sort-of molecular ladder), twisted.
-DNA nucleotides are only attached to the 3' end of a strand
-Daughter DNA can only grow in the 5' --> 3' direction
-The two main stages of RNA protein synthesis are Translation and Transcription
-In RNA protein synthesis, the only start codon is AUG
-The stop codons in RNA synthesis are: UAA, UAG, UGA
-tRNA matches amino acids to the correct codons to form new polypeptide chains
-The P Site on the ribosome is where the growing polypeptide is being held
-The A Site on the ribosome is vacant and ready for the next tRNA
-The most common method of mutagens come from radiation


Some Key Terms:
-Bacteriophages: Infects bacterial viruses
-Nucleotides: Chemical monomers
-Sugar-phosphate backbone: a repeating pattern of sugar-phosphate-sugar-phosphate
-Double Helix: Two strands of DNA
-Semiconservative model of DNA: Half of the parental molecule is maintained in each daughter molecule
-DNA Polymeras: Enzyme that links nucleotides to a growing daughter strand
-Triplet Code: The genetic information for an amino acid codes in chunks of three nucleotides
-Introns: Internal non-coding regions
-Exons: The parts of the genes that are expressed in the amino acids
-RNA Splicing: Introns are removed, exons are joined to form mRNA before leaving the nucleus


Diagram:

This is a diagram of DNA replication. As you can see on the side, the 4 monomers are labelled. You can also see the parent strands prior to splitting, in the process while the free monomers attach, and finally being coupled with a new complimentary strand.















Summary:


This chapter was about the molecular level of genetics, explaining replication of DNA as well as RNA replication and the production of amino acids.
Transcription occurs, translating a strand of DNA into RNA via free RNA monomers attaching. These are then Translated into amino acids through triplet codes, becoming a poly peptide chain of acids. But before leaving the nucleus, Eukaryotic RNA has its' introns removed and its' exons spliced as a coding sequence. The anticodon is the base triplet of a tRNA strand and couples the tRNA to the correct codon in the mRNA.
The chapter ends talking about viral DNA and how it integrates itself with the host chromosomes. It can either go through the lytic or lysogenic cycle. The lytic cycle destroys the cell shortly after infection, while the lysogenic cycle lets the cell divide a few times, letting the DNA copy itself before multiplying.

A Cool Video:


http://www.thedailyshow.com/watch/wed-july-10-2002/ted-williams--resurrection

Patterns of Inheritance

Who was Gregor Mendel?
Gregor Mendel was the first "geneticist" to figure out a concrete law on inheritance. He was a monk in what was then Austria, working with the inheritance of pea plants. 

Are there diseases that are genetically transmittable?
Yes, many in fact. Thankfully most are recessive, due to evolution, ones that are dominant have mostly killed off their hosts.

What is incomplete dominance? 
A condition in genetics that causes both, blended or some traits of the parents to appear in the offspring.

The Facts: 
-The Law of Segregation is: A sperm or egg carriers only one allele for each inherited character because allele pairs separate from each other during the production of gametes
-The Law of Independent Assortment is: Each pair of alleles segregates independently of other pairs of alleles during gamete formation.
-The Rule of Multiplication is: 1/2*1/2 = 1/4, which is true for genetics when it comes to recessive traits
-The Rule of Addition is used to figure out the probability of certain phenotypes (Aa and AA produce the same phenotype)
-"Carriers" refers to those who carry a recessive gene for a disorder, but do not show signs of said disorder
-Cystic fibrosis is one of said diseases, which causes mucus to be produced in excess in many places in the body, including the lungs
-Chromosome Theory of Inheritance: Genes occupy specific loci on chromosomes and chromosomes that undergo segregation and independent assortment during meiosis.
-Recombination frequency is when the offspring have the phenotype of the parent.
-Sex-linked genes are ones that are specifically on the sex chromosomes, usually on the X
-Red-Green Color blindness is attached to the X, and is much more common in males, since they only have one. Females, having two, have the chance of having a non-affected X, which allows them full color vision.

Some Helpful Terms:
-Character: A heritable feature that varies among individuals
-Trait: A variant of a character
-Homozygous: Two of the same allele
-Heterozygous:  Two different alleles
-Phenotype: The physical traits
-Genotype: The genetic make-up
-Testcross: Mating between an individual of unknown genotype and homozygous recessive to figure out the genetic make up of the other
-Inbreeding: Mating of closely related organisms
-Codominant: Both alleles are expressed in a heterozygous individual
-Pleiotropy: Genes that affect more than one character

Diagram:

This is an example of a Punnett square, for the shape and color of peas. It is apparent that green and wrinkled are the recessive traits, while smooth and yellow are dominant. About 1/4 will be green, and 1/4 will be wrinkled- this being an example of the rule of addition. On that note, only 1/16 will be green AND wrinkled (rule of multiplication).








Summary:
This chapter discusses one of the coolest facets of biology- genetics and inheritance. GO GENETICS! But it starts off talking about Gregor Mendel, and how he came to study genetics. He was very meticulous in controlling which plants bred with which, giving some very concrete data. The punnett square was crucial in the field of genetics, giving us a good way of seeing how genetic variation operates.
Not only that, but it goes on to talk about the things that Mendel didn't know, such as incomplete dominance, co-dominance and sex linked genes.

A Cool Video:
http://www.youtube.com/watch?v=oVl8OH_7QSc

Photosynthesis: Using Light to Make Food

What is the equation for photosynthesis?

6CO2 + 6H2O --> (Light Energy) --> C6H12O6 + 6O2

What is the difference between photosynthesis and the Calvin cycle?

The Calvin cycle doesn't require sunlight.

What does the Calvin cycle produce?

Sugars: Cellulose, Starch and other organic compounds.

The Facts:

-The Calvin cycle doesn't require sunlight
-Plants are known as producers because they create their own energy
-Another word for producers is autotrophs
-Photosynthesis is similar to cell respiration in that it's how the cell produces energy
-Without photosynthesis, cell respiration couldn't occur, as photosynthesis creates oxygen for it
-Similarly, without cell respiration, photosynthesis couldn't occur, as it requires the carbon dioxide that cell respiration gives off
-The energy released by electrons is conserved as it is passed from one molecule to another.
-Cellular respiration uses redox reactions to harvest the chemical energy stored in a glucose molecule.
-Chemiosmosis is the mechanism that not only is involved in oxidative phosphorylation in mitochondria but also generates ATP in chloroplasts
-ATP synthase couples the flow of H+ to the phosphorylation of ADP.

Some Helpful Terms:

-Autotrophs: Organisms that make their own food, sustaining themselves
-Producers: Organisms that make up the food supply
-Photoautotrophs: Organisms that produce organic materials from inorganic molecules using light energy
-Chlorophyll: Light-absorbing pigment in chloroplasts that converts solar energy into chemical energy
-Mesophyll: The green tissue in the interior of the leaf where chloroplasts are concentrated
-Stomata: Pores in the lead in which CO2 enters
-Stroma: Thick fluid inside the chloroplasts
-Thylakoids: Sacks suspended in in the stroma
-Grana: Stacks of thylakoids
-Photosystem: A light-center complex consisting of light-harvesting complexes.

Diagram:

The plant that contains chlorophyll is absorbing the light energy from the sun. Not only that, but it also takes in the CO2. Within the plant, photosynthesis occurs, releasing oxygen and creating glucose.














Summary:
This chapter was about photosynthesis, which is another way that cells harvest energy, but this is exclusively to plants and other organisms that contain chloroplasts and chlorophyll. Plants are known as the producers, as they create their own food, and consumers eat them for their energy.
Photosynthesis consumes sunlight and water and produces O2 and carbohydrates for the plant. There are two types of energy cycles for plants- one is the light cycle (photosynthesis) and the dark cycle (the calvin cycle).


A Cool Video:
http://www.youtube.com/watch?v=C1_uez5WX1o