June 1st blog

What was your favorite topic this semester? Why?
What was your least favorite?
What would you change about this class if you could?
What do you feel is your biggest accomplishment in biology this year?

1) My favorite topic in this semester was ecology because it expanded my knowleged on the natural world.
2) My least favorite topic was dissection. I have no interest in exploding the external and internal parts of organisms.
3) I would prefer study from our biology text book instead.
4) My biggest accomplishment in biology this year was maintaining an A throughout the semester.

Endanger Species - Panda

     I am a Panda,  and I am a symbol for international wildlife conservation since 1936.  Unfortunately, I am in a serious problem right now.  My favorite food, bamboo, is getting less and less, it will be hard to find any food for me and my friends to eat.  As a result, bamboo takes about twenty years before it can support our population.  We keep moving to new areas to search foods.  We afraid that we might die of starvation someday. 

     Even though we want to have babies, it's hard for us to find a perfect mate since we are a little picky about choosing mates.  However, we are slow to reproduce too.  Furthermore, many people are trying to kill us and sell our furs.  That's why we are near extinction line.   So, please save us!

(http://www.theinsite.org/earth/earth_es_panda.html)

Virtual worm lab

Parts of a worm

nternal anatomy of an earthworm (lateral section): small, long, cylindrical animal without legs or hard body parts.
Mouth cavity: entrance to the digestive tract of an earthworm.
Pharynx: part of the digestive tract of an earthworm just after its mouth.
Ventral nerve cord: set of nerves in the abdomen of an earthworm.
Seminal receptacle: pocket related to the semen of an earthworm.
Ventral blood vessel: blood vessel situated in the front part of an earthworm.
Nephridium: organ of an earthworm that performs the functions of kidneys.
Gizzard: pocket used as the stomach of an earthworm.
Dorsal blood vessel: blood vessel situated in the rear part of an earthworm.
Crop: bulge of the esophagus of an earthworm.
Seminal vesicles: small hollow organs that carry the semen of an earthworm.
Lateral heart: blood-pumping organ of an earthworm.
Esophagus: part of the digestive tract of an earthworm between the pharynx and the crop.
Brain: brain of an earthworm.

parts of a flower

           an imperfect flower does not have a male and female part in the same flower.

           a perfect flower contains male and female reproductive systems.

           a complete flower is a perfect flower that has petals and sepals.

a flower lacking one or more of the four parts found in a complete flower: sepals, petals, stamens, and pistils

Biogeochemical cycle

Biogeochemical cycle connects with biological, geological, and chemical.

Bio: Living things are involved in the cycle.  The cycle might limit the organisms on earth.
Geo: Rocks, nonliving things, and evironments are part of the cycles.
Chemical:  oxygen, carbon, hydrogen, and nitrogen cannot be used unless the elements are in a chemical form that cells can take up.

http://www.geography4kids.com/files/cycles_intro.html

Ecological footprint

BOW Go to http://www.myfootprint.org/ and calculate your ecological footprint. What are some areas that you can improve in?


My ecological footprint is 4.64 Earth.  I can improve it by shorten the shower time since I usually took more than 30 minutes for shower.  Lowering my shower time to 20 minutes can save water.  Also, I should turn off the light when no one is in the house or my room.  I often left the lights on at night.  Furthermore, I should recycle all the bottles and papers.

BOW Becoming Human

Go to BECOMING HUMAN Click on interactive timeline. Click on 5 different hominids. Get a picture and a general description of each. Where was it found? How old is it? What did it look like?
Write one paragraph summarizing how the hominids changed from oldest to newest

            1) Sahelanthropus tchadensis
   

Found: 2001, in Toros-Manalla site 266, Chad Old: 7 to 6 million years info.: The fossil specimen that was found by Brunet’s team was a badly crushed and distorted cranium.     2)  Ardipithecus kadaba           Found:1997      Old: 5.7 to 5.2 million years      Info.: Ardipithecus kadabba is an early hominin species recovered from sediments in the Middle Awash Valley of Ethiopia dated to between 5.2 and 5.8 million years ago. These fossils are of particular importance because fragments from both the skull and body have been found and are argued to demonstrate some of the earliest signs of bipedalism and hominin dental morphology. As one of the oldest species of human ancestors, Ar. kadabba helps to push back the origin of hominins into the late Miocene Epoch (roughly 11.6 to 5.3 million years ago).    3) Australopithecus afarensis     Found: November 1974, Hadar, Ethiopia and other sites in Ethiopoia, Kenya, Tanzania     Old: 3.9 tp 3.9 million years     Info. : The first specimens attributed to Australopithecus afarensis were discovered in the 1970’s by Donald Johanson working in the Afar Triangle of Ethiopia at the site of Hadar. A succession of spectacular discoveries, including a knee joint, the famous Lucy skeleton, and the remains of a family group, ensured that Au, afarensis would come to occupy a prominent place on the hominin family tree. In addition to the impressive finds located by Johanson and his international team of scientists, further amazing discoveries were uncovered by Mary Leakey and her team, four years later and far to the south of Ethiopia, at the site of Laetoli, on the edge of the Serengeti Plains in Tanzania. Leakey’s team discovered trace fossils of footprints of hundreds of animals, preserved in an ash layer that was securely dated to 3.6 ma. Amongst the animal footprints were some 70 footprints of hominins, captured as they walked bipedally across a wet, muddy plain.

4) Australopithecus africanus     Found: October 1924, Taung also Sterkfontein and Makapansgat, South Africa     Old: 3.0 to 2.0 million years old     Info.: The first member of its genus to be discovered, Australopithecus africanus is the oldest species of hominin to be found in southern Africa. Cave sites where it is found have been dated approximately to 3-2.0 ma based mostly on biochronological methods (dating methods utilizing the relative chronologies of non-hominin animal fossils). Its morphology is similar to Australopithecus afarensis, but it has important differences in the skull and teeth. The fact that Au. africanus shares some morphological features with Au. afarensis, others with members of the Paranthropus genus, and others with early Homo species makes it a difficult species to place in the hominin lineage. Thus, understanding Au. africanus is central to understanding early hominin phylogeny.



                   5) Homo heidelbergensis
                       
                       Found: October 1907, Mauer, Germany also Europe generally, Africa, Asia
                       Old: 800-350 thousand years

                       Info.: Fossils assigned to Homo heidelbergensis (named for a mandible found near Heidelberg, Germany) are found throughout the Old World from tropical to temperate zones at sites dating to the Middle Pleistocene dated (Approximately) between 800,000 and 125,000 years ago. These sites include Bodo and Kabwe in Africa, Petralona, Arago and Sima de los Huesos in Europe, Dali and Jinnishuan in Asia. H. heidelbergensis displays traits that are primitive (traits shared with its ancestor, in this case, Homo erectus); however, it also possesses many derived traits (traits different from those found in the ancestral species, in this case, traits that are more similar to those found in Homo sapiens). There is evidence H. heidelbergensis made fairly sophisticated stone tools and hunted large animals, suggesting an advanced ability to engage in cooperative social activities. Because the size of the sample of H. heidelbergensis fossils is small and many fossils have not been precisely dated, the relationships between this species and those that came before and after (as well as the cohesiveness of the species itself) is the source of substantial debate among scientists. Paleoanthropologists often refer to the uncertainties surrounding the specimens, their dating and morphology, as “the muddle in the middle.”

Bow 9 3/29/12 predator/prey, parasitim, mutualism, commensalism

BOW 9 Find an example of each kind of symbiosis. Get a picture and write a definition for: predator/prey, parasitim, mutualism, commensalism

A predator is an organism that eats another organism. 

The prey is the organism which the predator eats.

(http://necsi.edu/projects/evolution/co-evolution/pred-prey/co-evolution_predator.html)

Parasitism is a type of non mutual relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host.

(http://en.wikipedia.org/wiki/Parasitism)

Mutualism is the way two organisms of different species biologically interact in a relationship in which each individual derives a fitness benefit.

(http://en.wikipedia.org/wiki/Mutualism_(biology))

commensalism is a class of relationship between two organisms where one organism benefits but the other is neutral (there is no harm or benefit). There are two other types of association: mutualism (where both organisms benefit) and parasitism (one organism benefits and the other one is harmed).

(http://en.wikipedia.org/wiki/Commensalism)

Norman Bird

When the "pet" bird is hungry, it likes to eat insects and has a beak like a chisel to hammer away at the bark of trees to expose the insects underneath.Its body has a tail it uses as a prop for better balance and has feet with two toes that face forward and two toes that face backward for climbing up and down tree trunks.

Food web in a Forest

Producers: Green plants

Primary consumers: Mouse

Secondary consumers: Rabbit, Goat.

Tertiary consumers: Owl, Snake, Wild Cat, Jackal

Quaternary consumers: Kite, Lion

Blog 6Geographic distribution

One example of geographic distribution for evolution was the beaver and the capybara. They are similar species that that inhabit similar environments of North America and South America. As Charles Darwin proposed, similar animals in different locations were the product of different lines of evolutionary descent.

Blog5 geologic periods

Describe on of the geologic periods what organisms dominated, what was introduced, what died out? Be sure to include pictures.

The Mesozoic Era is an interval of geological time from about 250 million years ago to about 65 million years ago. It is one of three geologic eras of the Phanerozoic Eon. It is often referred to as the age of reptiles because reptiles, namely dinosaurs, were the dominant terrestrial and marine vertebrates of the time.   There were three geologic periods in the Mesozoic Era -Triassic,Jurassic, and Cretaceous.


Triassic: The Triassic is a geologic period and system that extends from about 250 to 200 Mya(million years ago).   It is the first geologic period of the Mesozoic era.The first true mammals also evolved during the Triassic, as well as the first flying vertebrates, the pterosaurs. The vast supercontinentof Pangaea existed until the mid-Triassic, after which it began to gradually rift into two separate landmasses, Laurasia to the north and Gondwana to the south.The Triassic period ended with a mass extinction, which was particularly severe in the oceans; the conodonts disappeared, and all the marine reptiles except ichthyosaurs and plesiosaurs. Invertebrates like brachiopods, gastropods, andmolluscs were severely affected. In the oceans, 22% of marine families and possibly about half of marine genera went missing according to University of Chicago paleontologist Jack Sepkoski.

Jurassic: The Jurassic is a geologic period and system that extends from about 199.6± 0.6 Mya(million years ago) to 145.5± 4 Mya. The Jurassic constitutes the middle period of the Mesozoic era, also known as the age of reptiles. The dinosaurs continued to dominate the land, and reached their peak in this period as they diversified into a wide variety of groups, ranging from the carnivorous theropods to the massive, herbivorous sauropods. The first birds appeared during the Jurassic, having evolved from a branch of theropod dinosaurs. Marine reptiles such as ichthyosaurs and plesiosaurs ruled the oceans, while the flying reptiles called pterosaurs continued to dominate the skies.  There was a minor mass extinction toward the end of the early Jurassic period (roughly 190-183 million years ago) in which more than 80% of marine bivalve species (like many clams) and many other shallow-water species died out. The cause of this extinction is unknown, but there is some speculation (by sedimentologist Stephen P. Hesselbo et al.) that it was triggered by the release of huge methane deposits from within the Earth (these deposits formed beneath the seabed as surface algae dies and sinks to the sea floor).


Cretaceous :The Cretaceous was a period with a relatively warm climate and high eustatic sea level. The oceans and seas were populated with now extinct marine reptiles, ammonites and rudists; and the land by dinosaurs. At the same time, new groups of mammals and birds as well asflowering plants appeared. The Cretaceous ended with one of the largest mass extinctions inEarth history, the K–T extinction, when many species, including non-avian dinosaurs,pterosaurs, and large marine reptiles, disappeared.

BOW-Natural selection and exaptation

BOW What is natural selection? How does it relate to mutations, genotypes and phenotypes? What is an exaptation.


Natural selection is the gradual, nonrandom process by which biological traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution.  natural selection is dependent on the existence of mutations in the genes coding for different characteristics of an organism. Most mutations in DNA are spontaneous and random, sometimes caused by passing cosmic rays or other exposure to radiation. Mutations may also be caused by errors in the formation of the genes in the parents' gametes in sexual organisms. Additionally, "proofreading" enzymes built into many higher organisms sometimes fail, leaving an incorrect version of an organism's DNA.

Furthermore, Natural selection occurs through the mutation and recombination actions on the genome of the organism, whether through its plasmids or itself. Bare in mind that genotype, the combination of alleles of the genome, affects the phenotype, the physical appearance as a result of the genotype. Therefore, because natural selection initially occurs through the changes in the genome, natural selection acts on genotypes which may or may not have visible phenotypes.

Exaptation is a feature that performs a function but that was not produced by natural selection for its current use. Perhaps the feature was produced by natural selection for a function other than the one it currently performs and was then co-opted for its current function. For example, feathers might have originally arisen in the context of selection for insulation, and only later were they co-opted for flight. In this case, the general form of feathers is an adaptation for insulation and an exaptation for flight. (http://evolution.berkeley.edu/evosite/evo101/IIIE5cExaptations.shtml)

http://library.thinkquest.org/C004367/be2.shtml

Sem two Week Three Computer Lab - cloning

Should cloning research be regulated? How, and by whom?
     Cloning research shouldn't be regulated because without regulation scientists would be free to make advances in cloning research that would benefit society.  Since the discovery of DNA, scientific technologies have been moving forward to find ways to benefit society with its knowledge. The medical benefits of cloning have the potential to bring society to a whole new level of physical wellness.  Stem cell research promises to make way for the treatment of many disorders by replacing damaged or diseased cells with cells that are genetically compatible with the person being treated.

http://web.gccaz.edu/~mdinchak/101online_new/argument_essay_example1.htm

BOW 2 Mutations

Biology BOW
Describe the different types of mutations: sense, non-sense, deletion, insertion, framshift, point and translation.


Sense mutation: A mutation that results in a new codon still coding for the same amino acid in a polypeptide or protein. Usually due to a substitution mutation.

Non-sense mutation: A mutation that results in transcription of a nonsense codon and terminates the polypeptide or protein prematurely.

Deletion mutation: a mutation in which a part of a chromosome or a sequence of DNA is missing.   Deletions can be caused by errors in chromosomal crossover during meiosis. This causes several serious genetic diseases. Deletion also causes frame shift.

Insertion mutation:  the addition of one or more nucleotide base pairs into a DNA sequence. This can often happen in microsatellite regions due to the DNA polymerase slipping. Insertions can be anywhere in size from one base pair incorrectly inserted into a DNA sequence to a section of one chromosome inserted into another.

Frameshift mutation: a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides that is not evenly divisible by three from a DNA sequence. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is.

Point mutation: or single base substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA.

Transition mutation: a point mutation that changes a purine nucleotide to another purine (A ↔ G) or a pyrimidine nucleotide to another pyrimidine (C ↔ T). Approximately two out of three single nucleotide polymorphisms (SNPs) are transitions.Transitions can be caused by oxidative deamination and tautomerization. Although there are twice as many possible transversions, transitions appear more often in genomes, possibly due to the molecular mechanisms that generate them.

Extra credit blog

     The topics that confused me the most were Fungi and Protist.  The topic that I feel very clear on was Genetics.  My favorite lab was burning cheetos and find the calories for it, because I was curious about how much calories  does each cheetos contained.  My least favorite lab was the onion lab; because I couldn't see a cell through the microscope.  One thing that I would like to change in this class was to have less reading quiz.  I prefer to take the quizlet  online instead.  Overall, I think the last semester was pretty good, and I learned lots of things from it.

2nd Semester BOW #1 (transcription, translation, protein synthesis)

BOW 1
Get a picture of transcription, translation or protein synthesis
Explain in as much detail as you can what is happening.




Transcription:    
Transcription may be broken into three major steps: 1) The DNA unwinds and unzips in the area of the gene. Enzymes match RNA nucleotides to the unzipped nitrogen bases of the gene, forming a single strand of mRNA.  2) The strand of mRNA detaches from the gene and goes out of the nucleus through one of the pores in the nuclear envelope. The DNA zips back together and winds back up.  3) The mRNA finds a ribosome where protein synthesis will happen.

Translation  :  Translation involves taking the message that's in the messenger RNA and in a sense decoding the message from the language of nucleic acids to the language of proteins or polypeptides. For translation to happen, the messenger RNA goes to the cytoplasm where it is attached to a cellular structure called a ribosome. Ribosomes are two part molecular assemblies consisting of various proteins plus a special kind of RNA called ribosomal RNA. Ribosomal RNA is involved in catalyzing some of the chemical reactions of translation.
In addition to the ribosome, another kind of RNA called tRNA carries amino acids to the mRNA when it is attached to a particular part of the ribosome's small subunit, called a binding site. A critical feature of mRNA and how it is translated is the fact that each three nucleotides in the mRNA is called a codon and it is the codon that is translated. Thus the sequence of codons corresponds to the sequence of amino acids in the polypeptide. You will see that the tRNA molecules have a set of three nucleotide bases at one end that are complementary to a corresponding codon. The bases on the tRNA are called the anti codon. This is critical because the anti codons make the connection between the codons and the correct amino acids that go with each codon.

Protein synthesis:  The first step in protein synthesis is the transcription of mRNA from a DNA gene in the nucleus. At some other prior time, the various other types of RNA have been synthesized using the appropriate DNA. The RNAs migrate from the nucleus into the cytoplasm.   In the cytoplasm, protein synthesis is actually initiated by the AUG codon on mRNA. The AUG codon signals both the interaction of the ribosome with m-RNA and also the tRNA with the anticodons (UAC). The tRNA which initiates the protein synthesis has N-formyl-methionine attached. The formyl group is really formic acid converted to an amide using the -NH₂group on methionine.  

2nd Semester BOW #1 (4 Gene Sequences)

Gene 1:
Huntingtin is a disease gene linked to Huntington's
disease, a neurodegenerative disorder characterized by loss of

            striatal neurons. This is thought to be caused by an expanded,
            unstable trinucleotide repeat in the huntingtin gene, which
            translates as a polyglutamine repeat in the protein product. A
            fairly broad range in the number of trinucleotide repeats has been
            identified in normal controls, and repeat numbers in excess of 40
            have been described as pathological. The huntingtin locus is large,
            spanning 180 kb and consisting of 67 exons. The huntingtin gene is
            widely expressed and is required for normal development. It is
            expressed as 2 alternatively polyadenylated forms displaying
            different relative abundance in various fetal and adult tissues.
            The larger transcript is approximately 13.7 kb and is expressed
            predominantly in adult and fetal brain whereas the smaller
            transcript of approximately 10.3 kb is more widely expressed. The
            genetic defect leading to Huntington's disease may not necessarily
            eliminate transcription, but may confer a new property on the mRNA
            or alter the function of the protein. One candidate is the
            huntingtin-associated protein-1, highly expressed in brain, which
            has increased affinity for huntingtin protein with expanded
            polyglutamine repeats. This gene contains an upstream open reading
            frame in the 5' UTR that inhibits expression of the huntingtin gene
            product through translational repression. [provided by RefSeq, Jul
            2008].

Gene 2:  

This gene encodes a protein that is one of the two

components of elastic fibers. The encoded protein is rich in
            hydrophobic amino acids such as glycine and proline, which form
            mobile hydrophobic regions bounded by crosslinks between lysine
            residues. Deletions and mutations in this gene are associated with
            supravalvular aortic stenosis (SVAS) and autosomal dominant cutis
            laxa. Multiple transcript variants encoding different isoforms have
            been found for this gene. [provided by RefSeq, Jul 2008].

Gene 3:  

Alzheimer's disease (AD) patients with an inherited form

of the disease carry mutations in the presenilin proteins (PSEN1 or
            PSEN2) or the amyloid precursor protein (APP). These disease-linked
            mutations result in increased production of the longer form of
            amyloid-beta (main component of amyloid deposits found in AD
            brains). Presenilins are postulated to regulate APP processing
            through their effects on gamma-secretase, an enzyme that cleaves
            APP. Also, it is thought that the presenilins are involved in the
            cleavage of the Notch receptor such that, they either directly
            regulate gamma-secretase activity, or themselves act are protease
            enzymes. Two alternatively spliced transcript variants encoding
            different isoforms of PSEN2 have been identified. [provided by
            RefSeq, Jul 2008].

Gene 5:     

This gene encodes a member of the fibrillin family. The
            encoded protein is a large, extracellular matrix glycoprotein that
            serve as a structural component of 10-12 nm calcium-binding
            microfibrils. These microfibrils provide force bearing structural
            support in elastic and nonelastic connective tissue throughout the
            body. Mutations in this gene are associated with Marfan syndrome,
            isolated ectopia lentis, autosomal dominant Weill-Marchesani
            syndrome, MASS syndrome, and Shprintzen-Goldberg craniosynostosis
            syndrome. [provided by RefSeq, Jul 2008].