Monday, June 4, 2012

Last Blog of the Year

What was your favorite topic this semester? Why?
-My favorite topic this semester would have to be animal anatomy. It was interesting to see what features distinguish certain types of animals. The dissections helped me visualize the different structures of different animals and compare them to others. I particularly enjoyed the shark dissection! It was something very different from the normal frog or worm dissections I've done since I never thought I would be opening up a shark's body!

What was your least favorite?
-My least favorite topics were photosynthesis and cellular respiration. I've always struggled with understanding the number of products and what products show up at the various parts of each process. I just find this part of biology dry even though it's one of the most important topics.

What would you change about this class if you could?
-I would probably change the amount of computer work students get. It can get very confusing and the simulations usually end up not working out the way they should. I know these are meant to help us understand the topics we are learning better but the confusion causes the opposite result. Additionally, it causes students to neglect doing notebook work and end up with less work to turn in.

What do you feel is your biggest accomplishment in biology this year?
-I believe my biggest accomplishment this year was...well...surviving! This was my first year of having AP classes so it was really hard to adjust at first. The lack of sleep drove me nuts but I eventually got used to it (not saying I like going without sleep though). I thought I couldn't get through this class alive and I dreaded the AP test. But after the test, I felt pretty relieved and confident that I scored well enough to make sure this year didn't go to waste. I do want to say that I appreciate having you, Ms. Malonek, as my teacher. You went out of your way to help us, your first ever AP class (A.K.A. the Guinea Pigs), understand the complexities of biology and prepare us for our future college lives. Thanks for everything!

Thursday, March 8, 2012

3 Invertebrates Comparison

Differences
Grasshopper
(Arthropod- Insect)
Lobster
(Arthropod- Crustacean)
Spider
(Arthropod- Arachnid)
-3 body segments: head, thorax, & abdomen.
-2 large jumping legs & 4 walking legs. 6 legs total.
-Pair of wings attached at the thorax.
-Mandibles (jaws) are used for chewing.
-2 sets of eyes: 1 pair of large compound eyes under the antennae and 3 ocelli, which detect light & dark, in between the compound eyes.
-Sensory organ: Antennae. Used to touch and smell.
-2 body segments- Cephalothorax and abdomen.
-10 walking legs; the front 3 pairs bear claws.
-Largest of the 3 clawed legs are the chelipeds.
-Cheplipeds = Prey-capturing body part.
-2 simple eyes.
-Small, leg-like structures called swimmerets are located under the abdomen.
-Swimmerets used to move, hold eggs/young, and transfer sperm.
-Sensory organ: Antennae.
-2 body segments- Cephalothorax (head+thorax) and abdomen.
-8-legged invertebrate.
-8 ocelli eyes. No compound eyes.
-Body segments are connected by the pedicel, the spider’s waist.
-Sensory organ: Pedipalps. They resemble short legs at the front of the spider.
-Jaws are called chelicera, with poison-injecting fangs.
-Jaws = Prey-capturing body part.
Similarities
-Hard exoskeleton made of chitin.
-Segmented bodies (3 segments for insects, 3 for crustaceans and spiders).
-Have 3 kinds of appendages: mouthparts, sensory organ, and legs.
-Bilaterally symmetrical.

Grasshopper

Image from: http://www.enchantedlearning.com/ggifs/Grasshopper_bw.GIF

Lobster
Image from: http://www.gma.org/lobsters/images/lobsterbottomview.gif

Spider
Image from: http://www.bumblebee.org/invertebrates/images/spider.gif

Friday, March 2, 2012

Intelligence Blog-Related to Genome Chapter 6

Intelligence can apply to several different definitions. Intelligence, in my opinion, is not something that necessarily determines a person's intellectual capabilities in school. Intelligence can be defined in terms of street smarts, academics, natural intelligence, and more. It is important to debate over what intelligence really is because we must establish a solid understanding of one another's "intelligence". It prevents us from labeling a person as "stupid" or "dumb" because even though they show a weakness in one aspect of intelligence, they show extreme strength in another (as does everyone).
But where does our intelligence come from? It's a constant debate over if it comes from our genes (nature) or the influences we encounter (nurture). I stand strongly behind my opinion that intelligence is shaped by means of nurture. We can't allow ourselves to think that our genes alone are what influence our capabilities of intelligence. However, I don't rule out the fact that they may possibly have influence (science has it's unpredictability at times). The stimuli we encounter each day is what really shapes our intelligences. For example, the learning environment a student is in can really cause a difference in how they absorb whatever is being taught. Noises can be distractions to some while to others it may somehow be a tool that helps.
The debate over intelligence's origin really matters because it does shape our opinions of others. Being a high school student, it's common to encounter those who think a particular student is smart just because his mom is a rocket scientist and his dad is an engineer (something along the lines of that...). In reality, we should look past the family tree and notice how this person takes in whatever information he/she encounters.
As you can see, the debate over intelligence's definition and it's origin really matters to me. I know for a fact that I'm quite a mathematical and visual learner (Just a note I really don't like math even if it's my learning/thinking strength). At the same time, I tend to lack common sense and think critically when I really don't have to. I have my strengths, and I have my weaknesses. Everyone has them. Intelligence isn't something that should limit and label us. So even if someone may be the lowest scoring student in a class, he/she may be the smartest kid in regards to the streets or has a knack for thinking outside the box.

Genome Chapter 3- History

This chapter of Genome mainly revolved around the history behind the start of genetics. It elaborated on Mendel's famous pea-plant experiment, in which he discovered the characteristics of dominant and recessive alleles in genes. Mendel's discoveries challenged the long-accepted ideas of Darwinism at this time. The chapter also noted Hermann Joe Muller's discovery on genes being artificially mutable. His Nobel prize-winning discovery basically answered the question if mutation is "unique among biological processes in being itself outside the reach of modification or control" (46). His answer showed that mutation "does not stand as an unreachable god playing its pranks upon us from some impregnable citadel in the germplasm".
I thought it was interesting how this chapter was titled "History". At first I thought it just referred to the fact that there is a lot of history that backs up the creation the study of modern genetics. Then I realized that it is connected to genes themselves. Genes are passed down from parent to offspring, being the history that determines our phenotypes and genotypes. Our genes are the combinations of various histories from all of our ancestors and relatives.

Nephrons: How they work and their relation to counter currents or hydrostatic skeletons.

The nephron is the basic unit of the kidney that serves a role in filtering blood. It's structure is comprised of a long, thin tube that is closed at one end, has two twisted regions interspaced with a long hairpin loop, ends with a long straight portion, and is surrounded by capillaries. The parts of a nephron are broken down into the following: the Bowman's capsule, the proximal convoluted tubule or proximal tubule, the Loop of Henle, the distal convoluted tubule or distal tubule, and the collecting duct. Each have different types of cells with different properties, which is important in understanding how the kidney regulates the composition of blood. Along with these parts, the nephron includes a variety of arteries, capillaries, and veins that connect the parts of the nephron, giving it a unique blood supply compared to other organs.
In the nephron, about 20% of the blood is filtered under pressure through the cell walls of the glomerular capillaries and Bowman's capsule. Filtration is carried out at a rate of approximately 125 mL/min. or 45 gallons (180 L) each day. The amount of any substance that gets filtered is the product of the concentration of that substance in the blood and rate of filtration. Small molecules, such as ions, glucose, and amino acid, are reabsorbed from the filtrate inside the lumen of the nephron by specialized proteins called transporters. Any excess is goes through secretion, which means they will be excreted into urine and eliminated from the body.
The movement of fluid and substances through pressure that is involved in the work of nephrons is similar to the role of hydrostatic skeletons in many cold-blooded organisms. In a hydrostatic skeleton, the pressure of the fluid and action of the surrounding circular and longitudinal muscles are used to change an organism's shape and cause movement, like burrowing or swimming.

Thursday, February 16, 2012

Starfish Description

Starfish are classified under the phylum Echinodermata. They exhibit 5 rayed radial symmetry, or sometimes bilateral symmetry, characteristic that developed through evolution. The body wall consists of three germ cell layers. The outer layer, the epidermis,  is a single layer of cells that covers the entire animal including its various spines. The middle layer, the dermis, is much thicker. This layer is composed of connective tissue and contains the organism's exoskeleton. For Starfish, the exoskeleton is a set of free moving small plates called ossicles. The third layer is also a single layer of ciliated cells that encloses the animal's coelom, separating the animal's internal organs from the skin. This is related to the phylum's characteristic of having a body cavity of a true coelom. The third layer creates what is known as the "coelomic lining".
Starfish possess a through gut with an anus with a headless body that can vary in shape. They have a poorly defined open circulatory system but a fairly good nervous system with a circum-oesophageal ring.  Starfish feed on fine particles of the water, detritus, or even other animals. Their diet includes oysters and clams and proves to make Starfish a pest of commercial clam and oyster beds. Interestingly, species of the phylum Echinodermata possess no excretory organs. Species of Starfish can reproduce by means of sexual reproduction and gonochoristic reproduction.
There are five living classes:
Crinoidea: Includes Sea lilies, Feather stars, and comatulids.

Image of Crinoidea structure from http://tolweb.org/tree/ToLimages/crinoid.gif

Ophiocistioidea: A class of extinct echinoderms from the Palaeozoic. They had a body structure similar to that of a sea urchin.

Image of Ophiocistioidea fossil from http://www.geomuseum.uni-goettingen.de/people/mreich/pdf/images/neuweb_seegurken11.gif

Astroidea: Harmless algal grazers and detrivores. Includes Starfish.
astroidea starfish
Image of Astroidea Starfish from http://www.reefs.org/hhfaq/starfish/star.jpg/view

Echinoiudea: Includes Sea urchins, which are spiny, globular animals. Sand dollars are closely related.

Image of Sea urchin from http://upload.wikimedia.org/wikipedia/commons/thumb/4/4b/Riccio_Melone_a_Capo_Caccia_adventurediving.it.jpg/250px-Riccio_Melone_a_Capo_Caccia_adventurediving.it.jpg

Holothuoidea: Includes Sea cucumbers, which have leathery skin and an elongated body containing a single, branched gonad.
File:Espardenya (animal).jpg
Image of Sea cucumber from http://en.wikipedia.org/wiki/File:Espardenya_(animal).jpg

Sunday, February 12, 2012

Genome Chapter 2- Species

This chapter of Genome begins by explaining how people had mistaken the human genome to have 24 chromosomes. Later studies have shown that humans have only 23 chromosomes due to the fact that Chromosome 2  is actually the fusion of two medium sized chromosomes. Chromosome has been subject to much speculation, with some believing that at some part of the chromosome near the centromere lies the code that creates the human soul. The chapter further explores the slight difference in genes that exists between humans and chimps, with only about a 2% difference in the genes. At some point in time a population of chimpanzees was isolated and a genetic mutation occurred. This mutation created a new species, hence the chapter title, and prevented the new species from breeding with the chimps. Ridley concludes the chapter pondering at the possibility that genes have some sort of influence over behavior. He explains that in the end he isn't sure how genes can play a role in behavior but he is open to the possibility that genes are not constrained to only determining anatomy.

Genome Chapter 1- Life

Chapter 1 of Genome looks into the "word" that builds up the world. Ridley points out that many would mistaken DNA as this word when in reality, the word is RNA. He describes RNA as a kind of bridge between DNA and proteins worlds. Its presence is extremely necessary in the most primitive and basic functions of a cell, acting as catalyst or replication device. Another important topic brought up in the chapter was the discussion on LUCA, the Last Universal Common Ancestor. LUCA is first described as an organism that looked like a bacterium that lived in a warm pond, possibly near a hot spring. However, it is later revealed that LUCA was most likely a protozoan.
The reason I believe this chapter is titled "Life" is that it still amazes us how our lives are basically determined by genetic code. Our lives literally hang by a thread of four letters put into specific sequences that map out our appearance and ability to carry out vital processes.

Tuesday, February 7, 2012

Double Fertilization

Double fertilization is an essential characteristic in the sexual reproduction of angiosperms. In sexual reproduction, a haploid sperm cell fuses with a haploid egg cell, forming a diploid zygote that soon develops into an embryo. Following this fertilization process is a second event that involves another sperm cell and a second cell found in the female's reproductive tissue creating a triploid cell as a product. This product develops into what would be the embryo's food supply. Without double fertilization, angiosperms would be incapable of successfully reproducing due to an inability to fertilize and a lack of resources for the embryo.

Fertilization starts between sperm cells, which are transferred through pollen grains produced in the anthers, and two cells within an ovule, the reproductive organ of the female. The reproductive cell found in the ovule is a diploid (2n) megaspore mother cell, which eventually undergoes meiosis to produce four haploid (n) megaspores. Only one of the four megaspores remain in most species while the other three degenerate. The surviving megaspore goes through three rounds of mitosis to form eight haploid nuclei that share the same cytoplasm, forming the embryo sac. Cell walls form between the nuclei to form three antipodal cells opposite the micropyle and near the micropyle; the ones near the micropyle are distinguished as two synergids and an egg. The two remaining nuclei, called polar nuclei, remain together in a single large central cell.

Before the two polar nuclei can take place in double fertilization, the sperm must travel within the female's reproductive organs to the cells. A pollen grain lands on the stigma and begins to germinate, sending a long pollen tube through the style and ovary. The generative cell, a haploid, travels down the pollen tube behind the tube nucleus and divides by mitosis to form two haploid sperm cells.

After the pollen tube reaches the micropyle and makes its way into one of the synergids, the sperms cells are released, which degenerates the synergid and sends one of the two sperm cells to fertilize the egg cell. The second sperm cell fuses with both of the polar nuclei, forming a triploid cell. This cell develops into the endosperm and serves as the embryo's food supply as the zygote develops into an embryo.

Sunday, February 5, 2012

Genome Chapter 4- Fate

This chapter of Genome focused on chromosome 4. Chromosome 4 is linked to degenerative diseases such as Wolf-Hirschhorn syndrome and the notorious Huntington's disease. Both of these diseases are caused by a gene that contains the repetition of the "word" CAG (glutamine). The chapter focuses mainly around Huntington's disease, which is caused by a mutation of the previously mentioned gene. Usually the longer the repetition, the more prone you are to the disease. The Huntington gene was actually located quite recently by a woman named Nancy Wexler. Finding the gene was compared to "looking for a needle in a haystack the size of America" but Wexler pushed herself to locate that needle.

Going back to the disease itself, Huntington's disease is known to strike at earlier ages in people with longer repetitions of glutamine. The disease is extremely destructive, causing a loss of muscle control and, inevitably, control of your mind. Symptoms as usually not apparent until it is too late. The inevitable result: Death. No case of Huntington's has been cured at the moment.
The chapter is titled "Fate" for a very obvious reason. It is constantly repeated that no one can escape their fate even if what will happen is known. The Greek allusion to Tiresias, the blind seer, caught my attention. The allusion spoke the fact that knowing the future (or fate) is truly not a gift since nothing can be done to change it. In this case, a person who has Huntington's disease knows that he/she has the inescapable fate of a slow but premature death, whether it be by their own hand or by the disease itself.

Thursday, January 12, 2012

Extreme Organism: Acetobacter aceti (Acidophile)

An acidophilic organism can thrive in environments of extremely low pH (usually of a pH of 2.0 or below). These organisms have evolved highly efficient mechanisms to help pump protons out of the intracellular space in order to maintain a pH that is near or at neutral pH. This mechanism is what allows acidophilic organisms to tolerate being in such highly acidic conditions. Additionally, the intracellular proteins are not required to develop acid stability due to this evolved mechanism.

Acidophiles can be found in conditions of acidic pH. Pictured here is an acidic mud pot in Yellowstone Park, which contains the acidophile Sulfolobus acidocaldarius. Found on http://www.daviddarling.info/encyclopedia/A/acidophile.html

Acetobacter aceti is an example of an acidophile that has proteins that have been forced to develop acid stability. This organism has an acidified cytoplasm which forces the proteins to evolve this way. Acetobacter species have the ability to convert ethanol to acetic acid in the presence of oxygen. It's commercial uses can vary. Acetobacter species are known to be used in the production of vinegar, during which ethanol is intentionally converted into acetic acid in wine, and the maturation of certain  beers, during which they are intentionally used to acidify beer. However, acetobacter have the potential to destroy wine they infect by producing an overabundance of acetic acid or ethyl acetate, both of which can cause the wine to be unpalatable.

Acetobacter used to produce vinegar and the acid in beer. Found on http://indokombucha.wordpress.com/2009/12/29/scoby/

Sources:
http://en.wikipedia.org/wiki/Acetobacter
http://microbewiki.kenyon.edu/index.php/Acetobacter
http://library.thinkquest.org/CR0212089/acid.htm
http://en.wikipedia.org/wiki/Acidophile_(organisms)

Saturday, January 7, 2012

Cell Metabolism Wordle

http://www.wordle.net/show/wrdl/4642806/Cell_Metabolism

The key terms I chose in this wordle were terms that I found to break down the basic concept of metabolism. Metabolism can follow one of two pathways: catabolic, which involves the release of energy by breaking down complex molecules to simple compounds, and anabolic, in which energy is consumed to build complicated molecules from simpler ones. Energy is a very important term due to the fact that all metabolic processes depend on energy. Energy comes in different forms: kinetic energy, which is the energy of motion; potential energy, which is the stored energy matter possesses  because of its location or structure; and chemical energy, which is a form of potential energy stored in molecules as a result of the arrangement of atoms in those molecules. Energy can also be described in terms of free energy, which is the portion of a system's energy that can  perform work when there is a uniform temperature in the system, or activation energy, which is the energy required to start a reaction.

The laws of thermodynamics explains the limits of energy transformation. The first law of thermodynamics explains that energy is constant and cannot be created or destroyed. The second law of thermodynamics every energy transfer or transformation increases the entropy, a measure of disorder or randomness, of the universe. Chemical reactions can either be endergonic or exergonic. In an endergonic reaction, free energy is absorbed from the surrounding environment. In contrast, an exergonic reaction involves a net release of free energy.

Another important factor in metabolic processes is the use of a catalyst or enzyme. Catalysts are chemical agents that changes the rate of a reaction without being used up in the process. Catalysts help lower the amount of activation energy needed to start a reaction.  Enzymes are a type of catalytic protein. They function in a similar manner to that of a key and a lock; the enzyme binds to its substrate in a region known as the active site, which is typically a pocket or groove on the surface of the protein. The fit must be compatible in order for the reaction to be carried out. The enzyme can manipulate its shape so that the active site fits around the substrate. This is known as an induced fit.