Unit two: professor's response

Re: question about biology‏
From:
Lewis Cantley (lewis_cantley@hms.harvard.edu)
Sent:
Mon 11/30/09 7:30 PM
To:
vivian zhang (princesszhang@live.com)
Cc:
kuhn (kip.kuhn@wasatchacademy.org)
Vivian
Enzymes create an environment for the reactants that make the transition state more stable compared to an aqueous environment.
Lew
On Nov 30, 2009, at 9:58 PM, vivian zhang wrote:
Dear Dr Cantley,I am a student from Wasatch Academy in Utah, and I am studing AP Biology now. I am very intereted in this course and I also want to major in biochemistry or pharmacy in collage. I have a question about enzyme while I am studing. Chemical reactions sometimes have to go to a transition state to react. enzyme can lower the state in order to catalyze the reaction. My question is how enzyme can lower the state. I will be very appreciate if you have time to answer my question.From, Vivian Zhang

Chapter Thirteen: Meiosis and Sexual Life Cycles

Q1: why do we need meiosis not only mitosis?
A1: during sexual reproduction, both parents pass their chromosomes to offspring. if only mitosis occures, there will be double chromosomes of parents' chromosomes which cannot exist.
Q2: what is the different between meiosis and mitosis?
A2: 1. meiosis has two divisions;mitosis has only one division.
2. during mitosis, DNA replication occure in interphrase; in meiosis before meiosis I
3. meiosis has crossing over during prophrase I
4. mitosis has two daughter cells, each diploid; meiosis has four haploid
5. mitosis raise from zygote; meiosis raise from gametes
Q3: what is the main stage of meiosis?
A3: Meiosis I: prophase I, Metaphase I, Anaphase I, Telophase I and cytokinesis
Meiosis II: prophase II, Metaphase II, Anaphase II, Telophase II and cytokinesis


Five Facts:
1. offspring acquire genes from parents by inheriting chromosomes
2. fertilization and meiosis alternate in sexual life cycles
3. meiosis reduces the number of chromosome sets from diploid to haploid
4. genetic variation produced in sexual life cycles contributes to evolution
5. genetics is the study of heredity and hereditary variation


Figure:

the number of chromosomes in a single set is haploid, two sets is diploid. meiosis reduces the number of chromosomes sets from diploid to haploid.

Summary:

The transmission of traits from one generation to the next is called inheritance, or heredity. Coded information in the form of hereditary called genes. Gametes are the vehicles that transmit genes from one generation to the next. DNA packaged into chromosomes which include several hundred genes. A gene's specific location along the length of a chromosome is called the gene's locus. In asexual reproduction, a single individual divide itself by mitosis or clone. Both parent and offspring have same genes. However, in sexual reproduction, two parents give conbinations of genes to offsprings by meiosis and mitosis. A life cycle is the generation-to-generation sequence of stages in the reproductive history of an organism, from conception to production of its own offsprong. Somatic cell is any cell except gamete has 46 chromosomes. Homologous chromosomes, or homologs are two chromosomes in a pair have same length, centromere position, and staining pattern. X and Y are sex chromosomes. Female has XX; Male has XY. others are autosomes. 46 chromosomes are two sets of 23 chromosomes-a maternal set and a paternal set. Chromosomes in single set called haploid cell; two sets called diploid cell(2n). Fertilized egg, or zygote, is diploid. The germ cells first do meiosis and half the number of chromosomes.After fertilization, diploid zygote do mitosis.

Meiosis has two divisions: meiosis I and meiosis II. Result in four daughter cells. DNA replication occure in interphase. During prohase I, homologous chromosome pair held together by chiasma and sister chromatid cohesion. Chromosomes line up at metaphase plate. Homologs separate during anaphase I; sister chromatids remain attached at centromere. Sister chromatids separate during anaphase II. Synapsis is the proces that pair up the homologos. Genetic rearrangement between nonsister chromatids known as crossing over. X-shaped region called a chiasma. Independent Assort,emt of chromosomes, crossing over, and random fertilization make variation and evolution.

Key Terms:

1. alternation of generations-A life cycle in which there is both a multicellular diploid form, the sporophyte, and a multicellular haploid form, the gametophyte; characteristic of plants and some algae.
2. gametophyte-In organisms (plants and some algae) that have alternation of generations, the multicellular haploid form that produces haploid gametes by mitosis. The haploid gametes unite and develop into sporophytes.
3. karyotype-A display of the chromosome pairs of a cell arranged by size and shape.
4. recombinant chromosome-A chromosome created when crossing over combines the DNA from two parents into a single chromosome.
5. spore-(1) In the life cycle of a plant or alga undergoing alternation of generations, a haploid cell produced in the sporophyte by meiosis. A spore can divide by mitosis to develop into a multicellular haploid individual, the gametophyte, without fusing with another cell. (2) In fungi, a haploid cell, produced either sexually or asexually, that produces a mycelium after germination.
6. sporophyte-In organisms (plants and some algae) that have alternation of generations, the multicellular diploid form that results from the union of gametes. The sporophyte produces haploid spores by meiosis that develop into gametophytes.
7. autosome- A chromosome that is not directly involved in determining sex; not a sex chromosome.
8. haploid cell- A cell containing only one set of chromosomes (n).
9. somatic cell-Any cell in a multicellular organism except a sperm or egg.
10. synapsis-The pairing and physical connection of replicated homologous chromosomes during prophase I of meiosis.

Video:

http://www.youtube.com/watch?v=D1_-mQS_FZ0

Chapter Twelve: the cell cycle

Q1: how important is reproduction?
A1: the ability of organisms to reproduce their own kind is the one characteristic that best distinguishes living things from nonliving matter. living things reproduce to pass their gene to their offsprings so that they won't be extinct.
Q2: what is the difference between cell cycle and cell division?
A2: cell division is an integral part of cell cycle. cell division is the cell reproduction. cell cycle is the life of a cell from the time it is first formed from a dividing parent cell until its own division into two cells.
Q3: what is the difference between unicellular and multicellular organism reproduction?
A3: a unicellular organism reproduces the entire organism; in multicelllar organimsm, by producing eggs and sperms.

Five Facts:
1. the continuity of life is based on the reproduction of cells, or cell division
2. the cell division process is an integral part of the cell cycle, the life of a cell from the time is first formed from a dividing parent cell until its own division into two cells.
3. cell division results in gentically identical daghter cells
4. the mitotic ohase alternates with interphase in the cell cycle
5. the eukaryotic cell cycle is regulated by a molecular control system.

Figure:







DNA and histone proteins are packaged into structures called chromosomes. each chromosome has two sister chromatids. centromere between two sister chromatids connects them.

Summary:
Most cell division involves the distribution of identical genetic material-DNA-to two daughter cells. a cell's endowment of DNA, its genetic information, is called its genome. the replication and distribution of so much DNA is manageable because the DNA molecules are packaged into chromosomes. reproductive cells, or gametes-sperm and eggs-have one set of 23 chromosome in humans. eukaryotic chromosomes are made of chromatin, a complex of DNA and associated protein molecules. each duplicated chromosome has two sister chromatids. the two chromatids, each containning an identical DNA molecule, are initially attached all along their lengths by adhesive protein complexes called cohesins. Mitosis is the division of the nucleus is usually followed immediately by cytokinesis, the division of the sytoplasm. producing gametes-eggs or sper- by a variation of cell division called meiosis, which yields nonidentical daughter cells that have only one set of cell.
in one cell cycle, interphase has 90%, which includes G1 phase, S phase, and G2 phase. chromosomes are suplicated only during the S phase. the mitotic(M) phase, which includes both mitosis and cytokinesis, is usually the shortest part of the cell cycle about 10%. Mitosis has five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Many of events of mitosis deoent on the mitotic spindle, which begins form in the cytoplasm during prophase. it consisits of fibers made of microtubules and associated proteins. centrosome is a subcellular region containing material that functions throughout the cell cycle to orgaize the cell's microtubules. A pair pf centrioles is located at the center of the centrosome. In animal cells, cytokinesis occurs by a process know as cleavage. Cell cycle control system is a cyclically operating of molecules in the cell that both triggers and coordiantes key events in the cell cycle. a checkpoint is a control point were stop and go-ahead signals can regulate the cycle: G1, G2, and M phrase. the G1 point is the restriction pont will switch to a nondiving state called Go phase. the regulartory molecules are mainly proteins of teo types: protein kinases and cyclins.

Key Terms:

1. anchorage dependence-The requirement that a cell must be attached to a substratum in order to divide.
2. aster-A radial array of short microtubules that extends from each centrosome toward the plasma membrane in an animal cell undergoing mitosis
3. benign tumor-A mass of abnormal cells that remains at the site of its origin.
4. binary fission-A method of asexual reproduction by “division in half.” In prokaryotes, binary fission does not involve mitosis; but in single-celled eukaryotes that undergo binary fission, mitosis is part of the process.
5. cell plate-A double membrane across the midline of a dividing plant cell, between which the new cell wall forms during cytokinesis.
6. cleavage-(1) The process of cytokinesis in animal cells, characterized by pinching of the plasma membrane. (2) The succession of rapid cell divisions without significant growth during early embryonic development that converts the zygote to a ball of cells.
7. cleavage furrow-The first sign of cleavage in an animal cell; a shallow groove in the cell surface near the old metaphase plate.
8. cyclin-dependent kinase (Cdk)-A protein kinase that is active only when attached to a particular cyclin.
9. density-dependent inhibition-The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another
10. somatic cell-Any cell in a multicellular organism except a sperm or egg.

Video:

http://www.youtube.com/watch?v=VlN7K1-9QB0

Chapter Eleven: cell communication

Q1: why do cells need to communicate?

A1: for growth, metablolism, regulation, evalution.etc.
Q2: how do cells communicate?
A2: cells send signals to other cells, bu a process of recceptor-transduction-response.
Q3: how often do cells do communication?
A3: Depends on different types of cells. skin cells do very often, but brain and nerve cells never do.



Five Facts:
1. external signals are converted to responses within the cell
2. reception: A signaling molecule binds to a receptor protein, causing it to chnge shape
3. transduction: cascades of molecular interactions relay signals from receptions to target molecules in the cell.
4. response: cell signaling leads to regulation of transcription ot cytoplasmic activities
5. apoptosis (programmed cell death) integrates multiple cell-signaling pathways



Figure:




































cell communication between two yeast cells. Cells of the yeast Saccharomyces cerevisiae use chemical signaling to identify cells of opposite mating type and to initiate the mating process. First cells of mating type A release a-factor, which binds to receptors on nearby cells of mating type B. Meanwhile, B cells release b-factor, which binds to specific receptors on A cells. Both these "factors" are small proteins of about 20 amino acid in length. Binding of these factors to the receptors induces changes in the cells that lead to their fusion, or mating. The resulting A/B cell combines in its nucleus all the genes from both A and B cells, (diploid).



Summary:
In local signaling, animal cells may communicate by direct contract or by secreting local regulators, such as growth factor(paracrine signaling) or neurotransmitters(synaptic signaling). For signaling over long distances, both animals and plants use homones; animals also signals along nerve cells. Sutherland discovered how the hormone epinephrine acts on cells, by receptor-transduction-response.The signal is transmitted by successive shape changes in the receptor and relay molecules.
The binding between signaling molecule(ligand) and receptor is highly specific. There are three types of receptors in plasma membrane. 1. G protein-coupled receptor with help of a G protein, a protein that binds the energy-rich molecule GTP. Ligand binding activates the receptor, which then activetes a specific Gprotein, which activates yet another protein. 2. receptor tyrosine kinases react to the binding od singlaing molecules by forming dimers and then adding phosphate groups to tyrosines. 3. ion channel receptors have a gated-protein close or open for ions. intracellular receptors are cytoplasmic or nulcear proteins. singaling molecules that are small or hydrophobic and can readily cross the plasma membrane use these recptors. Many signal transduction pathways include phosphorylation cascades, in which a serise of protein kinase each add phosphate group to a next one in line, activating it. Phosphatase enzymes soon remove the phosphates. Second messengers, such as cyclic AMP(cAMP) and Ca2+, diffuse readily through the cytosol and thus help broadcast siganls quickly. many G proteins activate adenyly cyclase, which makes cAMP from ATP. cells use Ca2+ as a second messenger in both G-protein and tyrosine knase pathways. The tyrosine kinase pathways also involve two other second messengers, DAG and IP3 can trigger a subsequent increase in Ca2+ levels.some pathways regulate genes by protein turning specific genes on or off. Apoptosis is type of programmed cell death in which cell components are disposed of in an orderly fashionm without damage to neighboring cells.

Key Terms:

1. adenylyl cyclase-An enzyme that converts ATP to cyclic AMP in response to a signal.
2. amplification-The strengthening of stimulus energy during transduction.
3. apoptosis-A program of controlled cell suicide, which is brought about by signals that trigger the activation of a cascade of suicide proteins in the cell destined to die.
4. cyclic AMP (cAMP)-Cyclic adenosine monophosphate, a ring-shaped molecule made from ATP that is a common intracellular signaling molecule (second messenger) in eukaryotic cells. It is also a regulator of some bacterial operons.
5. diacylglycerol (DAG)-A second messenger produced by the cleavage of a certain kind of phospholipid in the plasma membrane.
6. growth factor-1) A protein that must be present in the extracellular environment (culture medium or animal body) for the growth and normal development of certain types of cells. (2) A local regulator that acts on nearby cells to stimulate cell proliferation and differentiation.
7. inositol trisphosphate (IP3)-A second messenger that functions as an intermediate between certain nonsteroid hormones and a third messenger, a rise in cytoplasmic Ca2+ concentration.
8. ligand-A molecule that binds specifically to another molecule, usually a larger one.
9. protein kinase-An enzyme that transfers phosphate groups from ATP to a protein, thus phosphorylating the protein.
10. epinephrine-A catecholamine that, when secreted as a hormone by the adrenal medulla, mediates “fight-or-flight” responses to short-term stresses; also released by some neurons as a neurotransmitter; also known as adrenaline.

Video:

http://www.youtube.com/watch?v=NMeBZlbs2dU

Chapter Ten: Photosynthesis

Q1: why is photosynthese important?

A1: Photosynthses produces oxygen and food by plants as producers, so cunsumers can use these to live.

Q2: where does photosynthesis take place?

A2: In chloroplast

Q3: what is major process of photosynthsis?

A3: 1. the light reaction in which solar energy is captured and transformed into chemical energy 2. calvin cycle in which chemical energy s used to make organic molecules of food.

Five Facts:

1. photosynthesis converts light energy to the chemical energy of food

2. the light reactions convert solar energy to the chemical energy of ATP and NADPH

3. the calvin cycle uses ATP and NADPH to convert CO2 to sugar

4. alternative mechanisms of carbon fixation have evolved in hot, arid climates

5. 6CO2+12H2O+light energy=C6H12O6+6O2+6H2O

Figure:

In certain climates sunlight is very abundant, and seldom if ever becomes limiting to photosynthesis. However, such climates as found in dry, hot regions can produce another limiting factor "CO2".One can think of it in terms of availability of H2O and the loss of H2O.
When the plant is photosynthesising in bright sun, the CO2 must enter the leaves through the stomata. But when these holes are "open" H2O can also escape therefore, the plant dehydrates. If you close the stomata CO2 becomes limiting. In these C4 plants, CO2 is bound into phosphenol pyruvate (pep), (recall glycolysis) in cells in the leaf known as "mesophyll cells". As CO2-pep and The CO2 is released into the bundle sheath cells, which surround the vascular bundle. In these bundle sheath cells the CO2 enters the Calvin cycle as usual. In effect the mesophyll cells of a C4 plant pump CO2 into the bundle sheath cells, keeping the CO2 concentration in the bundle sheath cells high enough for RUBISCO to fix CO2 rather than Oxygen. In this way C4 plants can minimise photorespiration and maximise sugar production.

Summary:

Plants are autptrphs which can produce organic molecules from CO2 and inorganic. consumers are heterotrophs unable to make own food. Photosynthsis takes place in chloroplasts which contain chlorophyll, green pigment can absorb light energy. Chloroplast has bilayer. stoma is the liquid inside the membrane. thylakoids are sacs stack to grana. NADPH is energy carrier like NADH in CR. light is a form of energy known as electromagnetic energy travels in rhythmic waves. the distance between crests of electomagnetic waves is called wavelength. the entire range is electromagnetic spectrum. the radiation between 380nm to 750nm is visible light. photons are particles of light. substances that absorb visible light are known as pigments. different types of pigments make more efficient. chlorophyll molecule put electron from groud state to excited state more energy. a photosystem is composed of a protein complex called a reaction-center complex surrounded by several light-harvesting complexes. the reaction-center complex contains a molecule capable of accepting electrons and becoming reduced called primary electron acceptor.

Light reaction occurs in thylakoids of photosystemII and photosystemI. it requires light, water,ADP, NADP+;it produces oxygen, ATP,NADHP. photon first goes into photosystemII. water split into oxygen, hydrogen ions, and electons. Photon put electrons to primary acceptor have higher energy. then electron goes down to electron trasport chain and form ATP. then it goes into photosystemI. photon from light again push it to primary acceptor. it then goes down electron trasport chain and stored in NADPH. since light reaction needs light, also called light dependent reaction. Calvon cycle, also called dark reaction happens in stroma. it requires carbon dioxide, ATP,NADPH; it produces glucose. 6O2 first catalyzed byrubisco, rearranged. one G3P comes out from 6G3P as a sugar. However, the climate gonne be super hot. if stoma open, dehydration. if it closes, CO2 limited. C4 plants and CAM plants can still survive in that stuiation. CAM plants open their stomata at night, incorporation CO2 into organic acids, which are atored in mesophyll cells. during daytime, the stomata close, and the CO2 is released from th eorganic acids for use in the calvincycle.

Key Term:

1. absorption spectrum-The range of a pigment’s ability to absorb various wavelengths of light; also a graph of such a range.
2. action spectrum-A graph that profiles the relative effectiveness of different wavelengths of radiation in driving a particular process.
3. bundle-sheath cell-in C4 plants, a type of photosynthetic cell arranged into tightly packed sheaths around the veins of A leaf.
4. C3 plant-A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material, forming a three-carbon compound as the first stable intermediate.
5. carbon fixation-The initial incorporation of carbon from CO2 into an organic compound by an autotrophic organism (a plant, another photosynthetic organism, or a chemoautotrophic prokaryote).
6. carotenoid-An accessory pigment, either yellow or orange, in the chloroplasts of plants and in some prokaryotes. By absorbing wavelengths of light that chlorophyll cannot, carotenoids broaden the spectrum of colors that can drive photosynthesis.
7. chlorophyll a-A photosynthetic pigment that participates directly in the light reactions, which convert solar energy to chemical energy.
8. cyclic electron flow-A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or O2.
9. mesophyll cell-In C4 plants, a type of loosely arranged photosynthetic cell located between the bundle sheath and the leaf surface.
10. linear electron flow-A route of electron flow during the light reactions of photosynthesis that involves both photosystems (I and II) and produces ATP, NADPH, and O2. The net electron flow is from H2O to NADP+.

Video:

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