Ch.10 Molecular Biology of the Gene

HOW DO BACTERIOPHAGES EAT BACTERIA?
A bacteriophage has a head, containing DNA and a hollow tail with six jointed fibers extending from it. Bacteriophage attaches to bacterial cell, and injects DNA. It can reprogram its host cell to produce new pages, by their proteins. When the bacteria had been infected with T2 phages containing labeled protein, the radioactivity ended up mainly in the liquid, which contained phages but not bacteria. This result suggested that the phage phage protein did not enter the cells. But when the bacteria had been infected, then most of the radioactivity was in the bacteria pellet. When these bacteria were returned to liquid growth medium, the bacterial cells were destroyed, lysing and releasing new phages that contained radioactive phosphorus in their DNA but no radioactive sulfur in their proteins.

WHAT IS NUCLEOTIDE MADE OF?
DNA nucleotide is a long molecule of nucleotides, consisting of 3 parts. These 3 parts include a pentose sugar, a phosphate group, and a nitrogenous base. The nitrogenous bases include purines (adenine and guanine) and pyrimidines (cytosine and thymine). DNA includes adenine, guanine, cytosine, and thymine. RNA includes adenine, cytosine, guanine, and uracil instead of thymine.

WHAT ARE THE DIFFERENCES BETWEEN DNA AND RNA?
DNA and RNA are slightly different. In the cell RNA is usually single stranded, while DNA is double stranded. RNA nucleotides contain ribosome while DNA contains deoxyribose, which is a type of ribose that lacks one oxygen atom. In RNA the nucleotide uracil substitutes for thymine, which is present in DNA. DNA can be found in nucleus, but RNA can be found in nucleus and cytoplasm. A job of DNA is medium of long-term storage and transmission of genetic information. THe main job of RNA is to transfer the genetic code need for the creation of proteins from the nucleus to the ribosome. This process prevents the DNA from having to leave the nucleus, so it stays safe. Without RNA protein would never be made.



SUMMARY:
Frederick G. discovered that a transforming factor could be transferred into a bacterial cell. Alfred Hershey and Martha Chase used bacteriophages to show that DNA is the genetic material. DNA and RNA is the nucleotide, which contains 1) nitrogenous base, 2) 5-carbon sugar, and 3) phosphate group. DNA is a double-stranded helix, and it is composed of two polynucleotide chains joined together by hydrogen bonding between bases, twisted into a helical shape. DNA replication follows a semiconservative model. It begins at the origins of replication. It always occurs in the 5' to 3' direction. A gene is a sequence of DNA that directs the synthesis of a specific protein. DNA is transcribed into RNA, and RNA is translated into protein. The sequence of nucleotides in DNA provides a code for constructing a protein. Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence. Transcription rewrites the DNA code into RNA, using the same nucleotide language. Each word is a codon, consisting of three nucleotides. Translation involves switching from the nucleotide language to amino acid language. The basic steps of transcription is, 1) the two DNA strands separate, this stage is called initiation 2) One strand is used as a pattern to produce an RNA chain, using specific base pairing, this stage is called elongation 3) RNA polymerase catalyzes the reaction, this stage is called termination.
Translation occurs on the surface of the ribosome.  During initiation, mRNA binds to a small ribosomal subunit and the first tRNA binds to mRNA at the start codon. And a large ribosomal subunit joins the small subunit, allowing the ribosome to function. During elongation, next tRNA binds to the mRNA at the A site. And joining of the new amino acid to the chain occurs. tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site. Elongation continues until the ribosome reaches at stop codon. Mutations can be spontaneous, and induced by mutagens. Viruses have two types of reproductive cycles, lytic cycle and lysogenic cycle. Both DNA viruses and RNA viruses cause disease in animals. Some animal viruses reproduce in the cell nucleus. Aids is caused by HIV, human immunodeficiency virus. HIV is a retrovirus, containing two copies of its RNA genome, and reverse transcriptase. Three mechanisms let transfer of bacterial DNA, transformation, transduction, and conjugation.

KEY TERMS:
1) Bacteriophages: bacterial viruses that eat bacteria
2) Nucleotides: chemical units that DNA and RNA are consisting of
3) Semiconservative model: When each strand separates and each has one old strand with one new strand
4) DNA polymerases: the enzymes that link DNA nucleotides to a growing daughter strand
5) Promoter: a nucleotide sequence of the "start transcribing" signal
6) RNA splicing: the cutting-and-pasting process
7) Mutation: any change in the nucleotide sequence of DNA
8) Mutagen: a source of mutation is a physical or chemical agent
9) Plasmid: a small, circular DNA molecule separate from the bacterial chromosome
10) Conjugation: the physical union of cells and the DNA transfer between them

This is a diagram of DNA transcription. The first step, initiation, the attachment of RNA polymerase to the promoter and the start of RNA synthesis. The second step, elongation, the RNA elongates. As RNA synthesis continues, the RNA strand peels away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed. The third step, termination, finally the RNA polymerase reaches a sequence of bases in the DNA template called a terminator. At that point, the polymerase molecule detaches from the RNA molecule and the gene, sense it signals the end of the gene.

http://www.youtube.com/watch?v=ztPkv7wc3yU&feature=related



5 FACTS:
1) Central dogma shows the processes of replication/transcription/translation to make DNA to protein.
2) During DNA replication, DNA strands separate and random nucleotides come in so they can make two identical daughter molecules of DNA
3) During transcription, as DNA strands separate, RNA nucleotides come in so they can make RNA strand
4) During translation, anticodon with amino acid come in to make polypeptide and the anticodon leaves, so they can make protein
5) DNA nucleotides: A bonds with T, T bonds with A, G bonds with C, and C bonds with G.
RNA nucleotides: A bonds with T, U bonds with A, G bonds with C, and C bonds with G.

Ch.9 Patterns of Inheritance

WHAT WERE EXPERIMENTS MENDEL CONDUCT AND WHAT WERE HIS RESULTS?
Mendel conducted pea plant experiment. He crossed different plants and came out mostly with the same result, but some had different phenotypes. Je experimented with thousands of pea plants and recorded the phenotypic and genotypic traits of both using Punnet Squares. Mendel's finding showed that phenotypic traits in pea plants were inherited in discrete packages and at predictable frequencies. Mendel stated two laws, law of independent segregation, which states that a parent plant passed only one copy of a trait to the offspring. His second law was the Law of independent assortment that states that these traits met randomly in the offspring. 

WHY DO MORE MEN THAN WOMEN HAVE COLOR BLINDNESS?

Women have the sex chromosomes XX, while men have the chromosomes XY. The gene for normal color vision is found on the X-chromosome. If a woman has one X-chromosome with the gene and one without it, she will not be color blind. On the other hand, a man with an X-chromosome that is missing the gene has no backup. He will be color blind. Color blind women have both X-chromosomes missing the color vision gene. This has less probability than having just one X-chromosome missing the gene.

WHAT ARE THE MENDELIAN LAWS?
1) Law of segregation: pair of characteristics only one can be represented in a gamete. In another words,  for any pair of characteristics there is only one gene in a gamete even though there are two genes in ordinary cells.
2) Law of independent assortment: two characteristics the genes are inherited independently.
 If you had the genotype AaBb, you would make four kinds of gametes: they would contain the combinations of either AB, Ab, aB, or ab.

SUMMARY:
Genetic materials are only transported to offsprings. In another words, no matter how hard you work out to build your arm muscles, the offsprings will not get the muscle unless you have muscle cells that build muscles faster and easier than normally. In 1859, Mendel published a paper that says that the heritable factors retain their individuality generation after generation. He choose garden pea flower to study, using method that prevented fertilization, to cross fertilize the stamenless flower the carpel developed into a pod, and he planted. The seeds grew into offspring plants. Through these methods, Mendel was always sure of the parentage of new plants. He worked until he was sure he had true-breeding varieties. Mendel's law of segregation describes the inheritance of a single character. This starts with a cross between two parents and cross them to expect how offsprings are going to look like, using punnett square. We are able to describe phenotype and genotype of offsprings. Mendel's law of segregation states that pairs of alleles segregate during gamete formation. Homologous chromosomes state that alleles of a gene reside at the same locus on homologous chromosomes. Mendel's law of independent assortment states that each pair of alleles segregates independently of other pairs of alleles during gamete formation. From crossing P generations using punnett square, we are able to distinguish the percentage of phenotype and genotype of offsprings that will be born.
Genetic traits in humans can be tracked through family pedigrees. To analyze the pedigree, the geneticist applies logic and the Mendelian laws. Dominant traits are usually easier to occur, such as having freckles, widow's peak, and free earlobe. However people do have recessive traits, opposite of dominant traits, such as no freckles, straight hairline, and attached earlobe. Many inherited disorders in humans are controlled by a single gene. For example of recessive disorders, if both parents have gene of deaf, 25% of offsprings have possibilities to be deaf. The most common fatal genetic disease in the United states is cystic fibrosis. The CF allele is carried by about one in 25 people of European ancestry. The probability increases greatly if close relatives marry and have children. People with recent common ancestors are more likely to carry the same recessive relatives, called inbreeding, which is more like to produce offspring many types of inbred animals.
New technologies are able to provide insight into someone's genetic legacy. Genetic testing, fetal testing, fetal imaging, and ethical considerations are used. There is an incomplete phenotype. For example, if you cross red flower and white flower, there are probabilities of pink flower to be born between them.
Many genes have more than two alleles in the population. Most genes can be found in populations in more than two versions, known as multiple alleles. Although any particular individual carries, at most, two different alleles for a particular gene, in cases of multiple alleles, more than two possible alleles exist in the wider population. For example, blood group phenotype. There are four blood types, A, B, O, and AB. These letters refer to two carbohydrates, designated A and B, that may be found on the surface of red blood cells. Genotypes will be ii for O, IAIA or IAiA for A, IBIB or IBiB for B, and IAIB for AB. If I is a capital, it is a codominant; both alleles are expressed in heterozygous individuals.
Chromosome behavior accounts for Mendel's laws. The chromosome theory of inheritance was emerging. It states that genes occupy specific loci on chromosomes and it is the chromosomes that undergo segregation and independent assortment during meiosis. Thus, it is the behavior of chromosomes during meiosis and fertilization that accounts for inheritance patterns. Genes located close together on the same chromosome tend to be inherited together and they are called linked genes. They do not generally follow Mendel's law of independent assortment. Crossing over is very useful. They are used to produce new combinations of alleles, see the percentage of it, and also its data can be used to map genes.
Many animals have a pair of sex chromosomes, designated X and Y that determine and individual's sex. A gene located on either sex chromosome is called a sex-linked gene. By using punnett square, whether an individual is a male or a female is also able to be determined. Disorders can affect mostly males. For example, hemophilia, red-green color blindness, and duchenne muscular dystrophy.


KEY TERMS:
-self-fertilize: sperm-carrying pollen grains released from the stamens land on the egg containing carpel of the same flower.
-cross-fertilization: fertilization of one plant by pollen from a different plant.
-hybrids: the offspring of two different varieties
-P generation: the true-breeding parental plants
-F1 generation: true-breeding parental plants' hybrid offsprings
-F2 generation: offsprings of when F1 plants self-fertilizeor fertilize each other
-testcross: a mating between an individual of unknown genotype and a homozygous recessive individual
-phenotype: offsprings' composition, geneticists distinguish between an organism's expressed, or physical, traits
-genotype: genetic makeup such as PP, Pp, pp
-rule of addition: the probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways.

This punnett square shows that both parents have gametes that can be showed as  RrYy cross over. And it shows the probabilities of offspring whether if it is going to have round yellow, round green, wrinkled yellow, or wrinkled green. In this punnett square, 1/16 have RRYY, RRyy, rrYY, or rryy, 2/16 have RRYy, rrYy, Rryy, or RrYY, and 4/16 have RrYy. This is genotype of offsprings. And 9/16 have round yellow, 3/16 have round green, or wrinkled yellow, and 1/16 have wrinkled green. It is phenotype of offsprings. 
http://www.youtube.com/watch?v=-2YPAt8hOmE

5FACTS:

1) Phenotype shows the physical looking of organism, and genotype shows the alleles.

2) Mendel's laws are valid for all sexually reproducing species, but genotype often does not dictate phenotype in the simple way his laws describe.

3) Sex chromosomes determine sex in many species. If a specie has Y, it is a male, and if it has XX, it is a female.

4) Genes are located on chromosomes, whose behavior during meiosis and fertilization accounts for inheritance patters.

5) Crossing over can separate linked alleles, producing gametes with recombinant chromosomes.

Ch.8 The Cellular Basis of Reproduction and Inheritance

HOW DO PROKARYOTIC CELLS PERFORM CELL DIVISION WITHOUT NUCLEUS?
--> Cell division in prokaryotic organisms is simpler than in eukaryotes. This is because prokaryotes have much less complex DNA, and they don't have to worry about ensuring that each of the new cells receives an approximately equal number of organelles. All cells reproduce by dividing the middle until the cell membrane pinches closed and two new daughter cells are formed. In prokaryotes,once the DNA of the cell is replicated, each copy moves toward an opposite side of the cell by attaching to the cell membrane. The cell then elongates until it is approximately double its original size. At the end, the cell membrane on either side pinches inward and forms two new cells. 

WHY CAN'T PROKARYOTIC CELLS PERFORM MITOSIS?
--> Prokaryotic cells cannot go through mitosis. This is because mitosis is a division of nucleus into nuclei containing the same number of chromosomes. However, prokaryotic cells do not have nucleus, thus making it impossible.


WHAT HAPPENS TO THE NUMBER OF CHROMOSOMES WHEN FERTILIZATION HAPPENS?
--> A sperm has 23 chromosomes, and an egg also has 23 of them. When they fertilize, there will be 46 chromosomes. An offspring that is going to be made will have 46 chromosomes at the end. But its sex will only have 23 of them. That is how a human is like. This offspring will have 46 chromosomes but they are all mixed of 23 chromosomes from the sperm, and the other 23 from the egg. Also when meiosis occurs, all the chromosomes perform cross over, so it all depends on which sperm and egg fertilizes. This is why there is no identical people in the world because the possibility is almost 0%. It is almost impossible to happen to make two identical people.


SUMMARY:
There are two ways of reproduction for living things. Asexual reproduction, offsprings are identical to the original cell or organism. It only requires one parent, and sexual reproduction, it requires two parents and offsprings get genes from both of the parents. Cell division is the reproduction of cells. Roles of Asexual reproduction are reproduction of an entire single-celled organism, growth of a multicellular organism, growth from a fertilized egg into an adult, and repair and replacement of cells in an adult. For sexual reproduction is that sperm and egg production.
Binary fission is a type of cell division which occurs in prokaryotic cells. Two identical cells arise from one cell. Cell cycle consists of two stages. Interphase, duplication of cell contents, which includes G1, S, and G2, and mitotic phase, the division of duplicated contents, which includes mitosis and cytokinesis.
There are two types of reproduction of eukaryotic cells. Mitosis and Meiosis. Mitosis progresses through a series of stages. Interphase, prophase, prometaphase, metaphase, anaphase, telophase. Cytokinesis often overlaps telophase. During interphase, cytoplasmic contents are duplicated and two centrosomes form in the cytoplasm, and in the nucleus, chromosomes duplicate during the S phase. During prophase, in the cytoplasm, microtubules begin to emerge from centrosomes, forming the spindle. In the nucleus, chromosomes coil and become compact, and nucleoli disappears. During metaphase, spindle is fully formed, and chromosomes align at the cell equator, kinetochores of sister chromatids are facing the opposite poles of the spindle. During anaphase, sister chromatids separate at the centromeres, daughter chromosomes are moved to opposite pole of the cell, and the cell elongates due to lengthening of nonkinetochore microtubules. During telophase, the cell continues to elongate, the nuclear envelope forms around chromosomes each pole, establishing daughter nuclei, the spindle disappears, and chromatin uncoils. In cytokinesis, cytoplasm is divided into separate cells. Cleavage furrows is formed for animal cells for division, and cell plate is formed for plant cells.
Cancer cells escape controls on the cell cycle. They divide quickly. often in the absence of growth factors. They spread to other tissues through the circulatory system. Tumors get formed. There are three classifications of cancer by origin, carcinomas, sacromas, leukemias, and lymphomas.
Meiosis is a reproduction of sex cells. It also consists a series of stages but they perform twice. During prophase I, contents in nucleus duplicate. During metaphase I, tetrads align at the cell equator. During Anaphase I, homologous pairs separate and move toward the end of the cell. During telophase I, duplicated chromosomes have reached the poles and a nuclear envelope forms around them. Next stage is meiosis II, which follows meiosis I without chromosomes duplication. During metaphase II, duplicated chromosomes align at the cell. During anaphase II, sister chromatids separate and chromosomes move toward opposite poles. During telophase II, chromosomes have reeached the poles of the cell, and a nuclear envelope forms around each set of chromosomes.

KEY TERMS:
-chromatin: DNA+ proteins
-centromere: a join of sister chromatids. Made of protein
-cell cycle: an ordered sequence of events for cell division
-mitosis: division of the nucleus
-cytokinesis: division of cytoplasm
-mitotic spindle: composed of microtubules, produced by centrosomes to divide the chromosomes
-centrosomes: structures in the cytoplasm that organize microtubule arrangement, only in animal cells
-growth factor: proteins that stimulate division
-cell cycle control system: a set of molecules, including growth factors, that triggers and coorinates events of the cell cycle
-carcinomas: a type of cancer that arise in external or internal body coverings
-sarcomas: a type of cancer that arise in supportive and connective tissue
-leukemias/lymphomas: a type of cancer that arise from blood-forming tissues

This diagram shows movement of chromosomes during mitosis. The first step is prophase, when the chromosomes are form and nuclear envelope begins to dissolve. The second step is metaphase, when chromosomes line up in the middle of the cell. Spindles get attached to the centromere. During anaphase, the chromosomes are pulled apart from each other toward the end of the cell. During the last step, telophase, cleavage furrows are formed, and at the same time nuclear envelope begin to reform. The result of this step is two identical daughter cells.

http://www.youtube.com/watch?v=3kpR5RSJ7SA

This video shows more details about mitosis.

5 FACTS:
1) Mitosis is a reproduction of cells, and meiosis is a reproduction of sex cells.
2) Cytokinesis is division of cytoplasm.
3) Cells control how many cells they will reproduce, but cancer cells do not.
4) Animal cells form cleavage furrow, and plant cells form cell plate.
5) There are 46 chromosomes in human cells. After duplication it will go up to 92, and after division of sex cells, each will have 23.

Ch.7 Photosynthesis: Using Light to Make Food

WHAT IS RUBISCO?
Rubisco is used from the beginning of the calvin cycle. From the second that CO2 is taken in by the plants, Rubisco starts the process. Starting with phase 1; carbon fixation which is where ATP, and NADPH are produced. The second phase; reduction, is where glucose is produced. In the final cycle, regeneration of CO2 acceptor, ribulose bisphosphate is produced. And the the calvin cycle continues all over again, producing more and more ATP and glucose. The reason that Rubisco is so important to our world is that it acts as a catalyst for the Calvin Cycle, therefore making sure that the cycle can metabolize ATP from glucose (sugar). This also makes it the most abdunent protein on earth.

HOW IS PHOTOSYNTHESIS RELATED TO CELLULAR RESPIRATION?
In photosynthesis, plants use the sun's energy as light to transform carbon dioxide and water into glucose. In cellular respiration, glucose is ultimately broken down to yield carbon dioxide and water, and the energy from this process is stored as ATP molecules. They are the opposite process of each other. Animals need oxygen to breathe in order to perform cellular respiration, and plants need CO2 to perform photosynthesis. If those process didn't happen, there would be no living things in universe.

HOW DOES PHOTOSYNTHESIS AFFECT GLOBAL WARMING?
Photosynthesis reduces the amount of carbon dioxide in the air. This is the difference between plants and animals. The carbon dioxide is stored in the plants until they decompose or they are burned. For example, each fall when the trees lose their leaves and the plants die the level of carbon in the atmosphere goes up. The rest of the tree, bark etc.., does not continue to absorb carbon. Plants only take in carbon so long as they are growing and not after they have reached their natural height. Planting trees and other plants is one component of the solution to global warming, but the number of plants we have now cannot consume more carbon than they already do, and there is some evidence that warmer temperatures make photosynthesis more difficult.

SUMMARY:
Photosynthesis is a totally opposite process of cellular respiration. Plants produce a simple sugar and oxygen, using water and carbon dioxide.
Formula of Photosynthesis:
6CO2 + 6 H2O --(light energy)--> C6H12O6 + 6O2
The most important organelle in photosynthesis is chloroplast. It is consisting of photosynthetic pigments, enzymes, and other molecules grouped together in membranes. Stomata are tiny pores in the leaf that allow carbon dioxide to enter and oxygen to exit. Photosynthesis occurs in thylakoids, which segregates the stroma from another compartment. Photosynthesis is a redox process. Light energy is converted to chemical energy, which is stored in the chemical bonds of sugar molecules, as a result of this process. There are two stages in photosynthesis, light reactions and calvin cycle.
In the light reactions, light energy is converted in thylakoid membranes to chemical energy and O2. Water is split to provide the O2 as well as electrons. Reactants are water, light, NADP+ and ADP. Products are ATP, NADPH, and O2. Light and water go into the second photo system. While that is happening, they excite electrons and electrons move because of electron transport until first photo system Once they get to this point, light comes through to excite the electrons to produce NADPH. The hydrogen gradient is inside the membrane. Hydrogens move through ATP synthase to produce ATP.
In Calvin cycle, which occurs in the stroma of the chloroplast, it builds sugar molecules from CO2 and the products of the light reactions. Reactants are CO2, ATP, and NADPH. Products are glucose, NADP+, and ADP. CO2 bonds with rubisco to form two 3-carbons. ATP and NADPH are oxidized which reduces two 3-carbons. One of them leaves the cycle and the other five form rubisco.
The light behaves as photons. Chloroplasts contain several different pigments all absorb light of different wavelengths. For example, chlorophyll is a absorbs blue violet and red light and reflects green. Chlorophyll b absorbs blue and orange and reflects yellow-green. The carotenoids absorb mainly blue-green light and reflect yellow and orange. Also they are responsible for absorbing photons, capturing solar power in another words, causing release of electrons.
Within the photosystem, the energy is passed from molecule to molecule. At the end, it reaches the reaction center where a primary electron acceptor accepts these electrons and consequently becomes reduced. There are two types of photosystems. Photosystem I(P700) and photosystem II(P680). II is the first one because its pigment absorbs light with a wavelength of 680 nm.  I is the second one because it absorbs light with a wavelength of 700 nm. During the light reactions, light energy is transformed into the chemical energy of ATP and NADPH. Electrons are removed from water pass from photosystem II to I and are accepted by NADP+. Electron transport chain works as a bridge between I and II.

KEY TERMS:
1) Autotrophs: living things that can make their own food without using organic molecules derived from any other living things
2) Chlorophyll: important light absorbing pigment in chloroplasts. Responsible for the green color of plants.
3) Electromagnetic spectrum: the full range of electromagnetic wavelengths
4) Photon: a fixed quantity of light energy, and the shorter the wavelength, the greater the energy.
5) Photosystems: light harvesting complexes surrounding a reaction center complex.
6) Photophosphorylation: the chemiosmotic production of ATP in photosynthesis.
7) Photorespiration: a process that rubisco adds oxygen instead of carbon dioxide to RuBP and produces a two-carbon compound.
8) C4 plants: the plants that first fix carbon dioxide into a four-carbon compound
9) CAM plants: the plants that conserve water by opening their stomata and admitting CO2 only at night
10) Carbon fixation: a process that during the calvin cycle, CO2 is incorporated into organic compounds.

http://www.youtube.com/watch?v=hj_WKgnL6MI
Light reaction produces ADP and Pi from ATP, using light from the sun. It occurs in chloroplast. It has photo system I and II. They excite electrons to produce ATP. NADPH is produced by NADP+ bonding with hydrogen, which are in hydrogen gradient. It is simpler than cellular respiration.

5 FACTS:
1) The products of the light reactions are NADPH, ATP, and O2.
2) There are two stages in photosynthesis, the light reactions, and Calvin cycle.
3) There are two types of photosystems, photosystem I and photosystem II. Photosystem II comes first and I comes the next.
4) Photosysthesis is a opposite process of cellular respiration. It produces sugar and O2, using CO2 and light and water.
5) Chrolophyll is responsible for the color of the leaves. Green color is represented by them.

Ch.6 How Cells Harvest Chemical Energy

WHAT ARE THE DIFFERENCES BETWEEN FAST AND SLOW TWITCH MUSCLE FIBERS?
Because fast fibers use anaerobic metabolism to create fuel, they are much better at generating short bursts of strength or speed than slow muscles. However they get tired more quickly. Fast fibers generally produce the same amount of force per contraction as slow muscles, but they get their name because they are able to fire faster. Having more fast fibers can be an asset to a sprinter since she needs to quickly generate a lot of force. Olympic sprinters are supposed to have about 80 % fast fibers, while those who excel in marathons tend to have 80% slow fibers. Slow fibers are more continuous and are able to keep making ATP since they take oxygen more. They are smaller in diameter, red in color, they depend on oxidative phosphorylation for their ATP supply, they have better blood supply, they have more mitochondria, and more myoglobin.

HOW DOES ATP WORK IN THE BODY?
ATP is stored in chemical bonds and is released when the last phosphate is lost and ATP becomes ADP. It is used to do work in the cell by a reaction that removes one of the phosphate-oxygen groups, leaving ADP. When ATP converts to ADP, the ATP is spent. Then the ADP is usually immediately recycled in the mitochondria where it is recharged and comes out again as ATP. The total human body content of ATP is only about 50 grams, which must be constantly recycled everyday. The ultimate source of energy for constructing ATP is food. ATP is the carrier and regulation-storage unit of energy. The average daily intake of 2500 food calories translates into a turnover of a whopping 180 kilograms of ATP.

WHAT IS THE RELATIONSHIP BETWEEN GLUCOSE, NADH AND FADH2?
Glucose has the most energy and during cellular respiration, it is broken down. The energy that is in glucose is stored in many molecules of NADH and a few of FADH2. NADH is able to store more energy than FADH2. This is why it is more abundant electron carrier. Also NADH can be synthesized from scratch or from tryphtophan. FADH2 has accommodation for two hydrogens while NAD accepts one hydrogen molecule. In NAD, an electron pair one hydrogen are transferred, with a second hydrogen released into the medium. Electron transfer by FADH2 produces less ATP than by NADH.

SUMMARY:
This chapter discusses about how ATP is produced, and how cells work for the process. There are two types of muscle fibers, slow and fast. Slow fibers such as marathoners make ATP using oxygen, aerobically. Fast fibers, such as sprinters, make ATP without oxygen anaerobically. Energy is essential for life processes. Photosynthesis make glucose from CO2 and H2O and releases O2. Other organisms need O2 and energy and release CO2 and H2O. Animals perform cellular respiration and plants perform both photosynthesis and cellular respiration since they have mitochondria. Breathing is the key of cellular respiration. The equation of cellular respiration is; C6H12O6 + 6O2 --> 6CO2 + energy. This tells that the atoms of the starting molecules glucose and O2 regroup to form the products CO2 and H2O. In this exergonic process, the chemical energy of the bonds in glucose is transferred and stored (banked). Cellular respiration can produce up to 38 ATP molecules for each glucose molecule. During cellular respiration, carbon-hydrogen bonds of glucose get broken, and electrons will be transferred to oxygen. Dehydrogenase (enzymes) remove hydrogen from an organic molecules. They also use NAD+ to shuttle electrons. NADH will be formed by transferring electrons to NAD+.
There are 3 stages in order to produce ATP in cellular respiration.
1) Glycolysis: Begins respiration by breaking glucose, a six carbon molecule, into two molecules of a three-carbon compound called pyruvate. It occurs in cytoplasm.
2) The citric acid cycle: Breaks down pyruvate into carbon dioxide and supplies the third stage with electrons. It occurs in mitochondria.
3) Oxidative phosphorylation: Electrons are shuttled through the electron transport chain. ATP is generated through oxidative phosphorylation associated with chemiosmosis. It occurs in inner mitochondrion membrane.
In glycolysis, glucose will be cut in half to produce two molecules of pyruvate. Two NAD+ are reduced to two NADH. At the same time, two ATP are produced by substrate-level phosphorylation. The pyruvate formed in glycolysis is transported the mitochondria, where it is prepared for entry into the next level. With the help of CoA, the acetyl enters the citric acid cycle. Oxidative phosphorylation requires the involvement of electron transport and chemiosmosis and also adequate supply of oxygen. NADH and FADH2 are involved as well.
There are three different categories of cellular poisons that affect cellular respiration.
1) Blocking of the electron transport chain, such as cyanide and carbon monoxide.
2) Inhibiting ATP synthase, such as oligomycin
3) Production of the membrane leaky to hydrogen ions, such as dinitrophenol
Muscles are able to oxidize NADH through lactic acid fermentation. NADH is oxidized to NAD+ when pyruvate is reduced to lactate. Pyruvate is serving as an electron sink, a place to dispose of the electrons generated by oxidation reactions in glycolysis.



KEY TERMS:
-kilocalorie: the quantity of heat required to raise the temperature of 1 kilogram of water by 1C.
-redox reaction: the movement of electrons from one molecule to another. Oxidation-reduction reaction.
-chemiosmosis: process that the potential energy of this concentration gradient is used to make ATP
-substrate-level phosphorylation: process that an enzyme transfers a phosphate group from a substrate molecule to ADP, forming ATP
-fermentation: an anaerobic energy-generating process taking advantages of glycolysis, which is producing two ATP and reducing NAD+ to NADH
-yeasts: single-called fungi that not only can use respiration for energy but can ferment under anaerobic conditions
-dehydrogenase: an enzyme that is used in the process of oxidizing glucose
-intermediates: compounds that form between the initial reactant, glucose, and the final product, pyruvate
-obligate anaerobes: prokaryotes that live in stagnant ponds and deep in the soil.
-facultative anaerobe: process that is able to make ATP either by fermentation or by oxidative phosphorylation, depending on whether O2 is available.

http://www.youtube.com/watch?v=iXmw3fR8fh0

Glycolysis produces 2 ATP molecules by substrate level phosphorylation. Also it makes 2 pyruvate. In energy investment phase, it starts with one molecule of glucose and hexopkinase breaks down the bonds.  Then in this stage, dihydroxyacetone phosphate and G3P are produced, but isomerase converts them into two G3P. Next payoff phase, NADH is made and at the end, pyruvate will be made and 4 ATP produced at the same time. It happens in the cytoplasm.
In the citric acid cycle, reactants are acetyl CoA. ATP and NADH and FADH2 are produced. 2 molecules are created in net amount and 6 molecules of NADH and 2 molecules of FADH2 are produced as well. CO2, oxaloacetate, as if combines with acetyl in the first step. It occurs in the mitochondria.
In oxidative phosphorylation, NADH and FAOH2, which give away their electrons to the electron transport chain as reactants. The reactants of chemiosmosis are ADP and phosphate, which form ATP as the products. They produce water molecules in the electron transport chain. Oxygen and hydrogen are two important molecules as are the mulriprote, complexes in the energy transport chain. 32 to 34 molecules of ATP are produced while no new NADH or FADH2 are formed. It happens in the inner membrane of the mitochondria.

5 FACTS:
1) Although glucose is considered to be the source of sugar for respiration, carbohydrates, proteins, and fats are the actual three sources for generation of ATP
2) Glycolysis is the universal energy-harvesting process of living organisms
3) The statement "plants perform photosynthesis and animals perform cellular respiration." is wrong, because plants do perform cellular respiration with mitochondria as well.
4) There are three stages of producing ATP, glycolysis, the citric acid cycle, and oxidative phosphorylation.
5) The total number of ATP molecules per a glucose molecule produced are 32 to 34. This is about 40% of a glucose molecule potential energy.

Ch.5 The Working Cell

WHY DO CELLS USE ATP WHEN SUGAR MOLECULES HAVE MORE ENERGY?

Cells use sugars because all of energy origins are from glucose. However the cell breaks down the glucose and stores the energy in ATP. The reason why it stores energy in ATP is that because the cell can only use a little bit of energy to work at one time. Therefore, if it just directly uses glucose to do work, there will be a large amount of energy released, and all the energy it cannot use will just escape as heat. So by storing the energy in smaller amounts in ATP, not as much energy is wasted as heat.

HOW DO ANIMALS AND PLANTS PERFORM OSMOREGULATION?
Osmoregulation keeps the body's fluids from becoming too concentrated. Animals must maintain the right concentration of solutes and amount of water in the body fluids. There is no specific osmoregulation organs in higher plants. Control of water intake and loss means those internal and external factors, which affect the rate of transpiration. Plants share with animals the problems of obtaining water and in disposing of the surplus. Some plants develop methods of water conservation. Xerophytes are plants in dry places. They have better qualities of osmoregulation. Cactus have water stored in large parenchyma tissues so they can get more water. Other plants have leaf modifications to keep water.


WHAT ARE THE DIFFERENCES BETWEEN EXOCYTOSIS AND ENDOCYTOSIS?
Exocytosis is the process by which a cell expels molecules and other objects that are too large to pass through the cellular membrane. Endocytosis is the process by which a cell takes in molecules and other objects that are too large to pass through the cellular membrane. The basic mechanism of those are pretty much the same. Both make use of vesicles for their molecular transport. Vesicles are used for storage and transport. Since they are enclosed by a membrane, inside they can have a completely different composition than that of their cell.

KEY TERMS:
-Diffusion: the tendency for particles of any kind to spread out evenly in an available space, moving from where they are more concentrated to regions where they are less concentrated
-Passive Transport: diffusion across a cell membrane does not require energy
-Fluid Mosaic: the surface appears mosaic because of the protein embedded in the phospholipids and fluid because the proteins can drift about in the phospholipids
-Osmosis: a physical model of the diffusion of water molecules across a selectively permeable membrane
-Aquaporins: the very rapid diffusion of water into and out of certain cells, such as plant cells, kidney clls and red blood cells, is made possible by transport proteins
-Active Transport: moving a solute against its concentration gradient using energy
-Thermodynamics: the study of energy transformations that occur in a collection of matter
-Cellular Respiration: a chemical process that uses oxygen to convert the chemical energy stored in fuel molecules to a form of chemical energy that the cell can use to perform work
-Energy Coupling: the use of energy released from exergonic reactions to drive essential endergonic reactions. It is a crucial ability of all cells
-Cofactors: many enzymes that require nonprotein helpers

SUMMARY:
Membranes are composed of phospholipids and proteins and they are described as fluid mosaic. Phospholipids are made of fatty acids kinks which are unsaturated. Membranes exhibit selective permeability. Non polar molecules cross more easily than polar molecules because polar molecules are not soluble in lipids. Phospholipids can spontaneously self-assemble into simple membranes. Particles move in concentration gradient to less concentration gradient. This movement without energy is called passive transport. Osmosis moves water across a membrane down its concentration gradient until the concentration of solute is equal on both sides of the membrane. Animal cells can maintain their water balance by osmoregulation. However plant and prokaryotic, and fungal cells have different issues because of their cell walls. Cells don't let any substances across the membrane. They require the help of aquaporins. They assist in facilitated diffusion, which is a type of passive transport. In active transport, they move particles against its concentration gradient. They always require the energy in the form of ATP. When cells move large molecules across membrane, they use exocytosis to export bulky molecules, and endocytosis to import substances useful to the livelihood of the cell.
There are two kinds of energy for the capacity to do work and cause change. Kinetic energy for motion and potential for resulting of its location. There are two important laws of thermodynamics. The first law is energy in universe is constant. It cannot be created or destroyed. The second law is energy conversions increase the disorder of the universe. So it cannot be recycled. Exergonic reaction is a chemical reaction that releases energy. Also cellular respiration releases energy and heat and produces products but is able to use the released energy to perform work.
Living things produce many endergonic and exergonic chemical reactions. Those are all called metabolism. One cell mainly does three types of cellular work; chemical work, transport work, and mechanical work. ATP is used when a cell needs energy immediately. It is  renewable source of energy. Energy that is available to break bonds and form new ones is called EA. EA can be speed up by enzymes. They require the certain conditions for them such as temperature, and pH. They also need cofactors and coenzymes. They can be inhibited by competitive inhibitors and noncompetitive inhibitors.

This is a diagram of endocytosis. The plasma membrane takes a particle into a cell, and it will turn a food valuole. Those are the main functions of endocytosis.
-Receive nutrients
-Entry of pathogens
-Cell migration and adhesion
-Signal receptors

This is a diagram of exocytosis. It releases enzymes, hormones, proteins, and glucose to be used in other parts of the body. Also those are the main functions of exocytosis.

• 
  
• -Neurotransmitters (in the case of neurons)
• -Communicate defense measures against a disease
• -Expel cellular waste

5 FACTS:

1) To make the concentration equal, passive transport and active transport occur. Active transport requires energy.

2) Tonicity describes the ability of a solution to cause a cell to gain or lose water.

3) Many substances are necessary for viability of a cell do not freely diffuse across the membrane. 

4) Kinetic energy performs work by transferring water. Example, heat is a kinetic energy associated with the random movement of atoms.

5) The first law of thermodynamics: energy in the universe is constant. It cannot be created or destroyed. The second law of thermodynamics: energy conversions increase disorder of the universe. 

Ch.4 A Tour of the Cell

WHAT ARE THE PROBLEMS WITH SPERM MOTILITY?

Sperm motility is a problem. For example, his sperm shape is different from the other sperm shape, he has too much sperm, and how his sperms move is not right. When he as a fertility problem, it can cause a severe loss of self esteem, not to mention the frustration involved with not being able to have a baby. Knowing what can cause low sperm motility and other fertility problems for men can, however, help a man to know how to proceed with addressing the problem.

WHY DO NOT  ANIMALS PHOTOSYNTHESIZE?

Because if animals do photosynthesize, food chain will not work. Also animals can get energy from eating other organisms. That is why animals don't have cell wall so we can move easily. Plants cannot move, so they need to photosynthesize to get energy. Also animals need O2 to breathe. If we could photosynthesize, we will need CO2, which we produce now, but not use. There would be no O2 for animals to breathe. That is why I think that animals don't photosynthesize, because we don't need to.

WHAT HAPPENS IF A CELL GETS DISEASE?
There are some cell diseases. I am going to answer one of them, Leukemia. Leukemia is a disease that number of white blood corpuscle increases more than number of red blood corpuscle. The numbers those two blood cells will be unbalanced. Thus losing hair, having a fever, out of breath, feeling of less blood, and etc. It is usually caused from smoking, and some how.  There are many cell diseases like that. The reasons why those happen are mostly from genetic.



SUMMARY:
     Robert Hooke first observed cells in 1665. As we know about cells, we developed the microscopes. We have basically 4 kinds of microscopes. Light microscope, works by passing visible light through a specimen which can magnify objects about 1000 times, Electron microscope, uses a beam of electrons, which can magnify up to 100,000 times, Scanning Electron microscope, which can show a specimen with 3D, and Transmission Electron microscope, used to study the details of internal cell structure. Cell theory states that al living things are composed of cells and that all cells come from other cells.
     There are two types of cells. Prokaryotic cells, and eukaryotic cells. Prokaryotic cells compose bacteria and archaea, and eukaryotic cells compose other forms of life. The surface area of a cell is important for carrying out the cell's functions. Cells are all bounded by a plasma membrane. All have chromosomes carrying genes made of DNA. And they all contain ribosomes, tiny structures that make proteins according to instructions from the genes. The entire region between the nucleus and the plasma membrane is called the cytoplasm. There are various organelles in an eukaryotic cell. There are four different life processes in eukaryotic cells; 1) manufacturing 2) breakdown of molecules 3) energy processing, 4) structural support, movement, and communication.
     Phospholipids are the main components of biological membranes. It has two distinct regions; a negatively charged and thus hydrophilic phosphate group and two non-polar, hydrophobic fatty acid tails. Non-polar molecules such as O2 can easily pass through its hydrophobic interior. Some of these proteins form channels that allow specific ions and other hydrophilic molecules to cross the membrane.
     During a cell reproduction, as a cell prepares to divide, the DNA is copied and the thin chromatin fibers coil up. Nuclear envelope controls the flow of materials into and out of the nucleus. It connects with ER. Ribosomes are found in two locations. Free ribosomes are in the fluid of the cytoplasm, while bound ribosomes are attached to the outside of ER or nuclear envelope. Smooth ER is important in the synthesis of lipids. It is a detoxification in liver cells and also a calcium ion storage. Rough ER is a synthesis of membrane lipids and proteins, secretory proteins, and hydrolytic enzymes. It is also a formation of transport vesicles. Cell's structure and activities are organized by internal skeleton. Cytoskeleton supports the cell structure and cell motility. Microfilaments form a 3D network just inside the plasma membrane that helps support the cell's shape. Intermediate filaments serve mainly to reinforce cell shape and to anchor certain organelles. It holds nucleus as well. Microtubules are readily disassembled in a reverse manner and the tubulin subunits can then be reused in the cell. They can grow out from a centrosome. They shape and support the cell and also act as tracks along which organelles equipped with motor proteins can move. Cells have an ability to move. They have cilia which sweep.
     Three types of cell junctions are found in animal tissues. At tight junctions, the membranes of neighboring cells are every tightly pressed against each other, knit together by proteins. Anchoring junctions function like rivets, fastening cells together into strong sheets. Gap junctions are channels that allow small molecules to flow through protein-lined pores between neighboring cells.

KEY TERMS:
-Nucleoid: the region where the DNA of a prokaryotic cells is coiled
-Flagella: longer projections that help attach prokaryotes to surfaces
-Cellular metabolism: many of the chemical activities of cells that occur within organelles
-Chromatin: a material that makes up eukaryotic chromosomes
-Vesicles: the transfer of membrane segments that connect physically the membranes such as endo-membrane system
-Golgi apparatus: a structure of a cell that packages substances and send them out
-Lysosome: a digestive system of a cell
-Vacuole: digestion; storage of chemicals; cell enlargement; controls water balance
-Endosymbiosis: hypothesis of it proposes that mitochondria and chloroplasts were formerly small prokaryotes that began living within larger cells
-Granum: a stack for thylakoids

This is a diagram of a cell. As you can see, there are various structures in a cell. Those structures are grouped in four types as I mentioned in summary.

1) Manufacturing

-Nucleus: DNA synthesis; RNA synthesis. Nucleolus is inside.

-Ribosomes: protein synthesis. 

-Smooth ER: produces lipid. Detoxification in liver cells. Calcium ion storage.

-Rough ER: produces mainly protein. Has ribosomes attached. 

2) Breakdown

-Lysosomes: only in animal cells. Digestive system of cells. Recycles food.

-Vacuoles: Digestion. Storage of chemicals, cell enlargement, water balance.

-Peroxisomes: Diverse metabolic processes with breakdown of H2O2 by-product.

3) Energy Processing

-Mitochondria: makes chemical energy. 

-Chloroplasts: only in plant cells and some protists. produces light energy to chemical energy sugars

4) Support, Movement, and Communication Between Cells

-Cytoskeleton: including cilia, flagella, and centrioles in animal cells. maintains cell shape. anchorage for organelles: movement of organelles within cells and also cell itself. mechanical transmission of signals from exterior of cell to interior. communication between cells.

-Extracellular Matrix: only in animal cells. Binding of cells in tissues; surface protections; regulation of cellular activities.

-Cell junctions: communication between cells. binding of cells in tissues

-Cell walls: only in plants, fungi, and some protists. maintains the cell shape and skeletal support. protects surface. binding of cells in tissues.


5 Facts:
1) There are many structures in a cell. They all perform the important functions for a cell.
2) There are two different kinds of cell. Prokaryotic, and Eukaryotic. Prokaryotic cells are simpler than Eukaryotic.
3) Manufacturing, breaking down of molecules, energy processing, and structural support, movement, and communication are the main life process for eukaryotic cells.
4) Animal cells have lysosome and they do not have cell wall. Not having cell walls make it easier for animals to move. They have plasma membrane instead.
5) Plant cells have chloroplast, and cell wall.