Chapter Fourteen: Mendel and the Gene Idea

Q1: why did Mendel use pea?

A1: Short life span, bisexual, many traits known and cross- and self-pollinating.
Q2: how did Mendel work on peas?
A2: he controled other characters but make one variable, by cross-pollination, then record the data.
Q3: why did Mendel record so many data?
A3: for the sake of geting accurate datas



Five Facts:
1. Mendel used the scientific approach to identify two laws of inheritance
2. the laws of probability govern Mendelian inheritance
3. inheritance patterns are often more complex than predicted by simple Mendelian genetics
4. many human traits follow Mendelian patterns of inheritance
5. inheritance is pretty random but follow laws



Figure:


Gnotype A&B are dominate than O.

Summary:
in the 1860s, Gregor Mendel formulated a theory of inheritance based on experiments with garden peas, proposing that parents pass on to their offspring discrete genes that retain their identity through generations. In a diploid organism, the two allels of a gene segregate(separate)during gamete formation; each sperm or egg carries only one allele of each pair. ratio of F2 3:1. In heterozgotes, the two alleles are different , and the dominant allel phenotypic effect of the recessive allele. Homozygotes have identical allels of a given gene and are ture-breeding. Each pair of alleles segregates into gametes independently of the pair of allels for any other gene. in a cross between dihybrids, the offspring have fou phenotypes in a 9:3:3:1 ratio.
The expresiion of a genotype can be affected by environmental influences. the phenotypic range of a particular genotype is called its norm of reaction. Polygenic characters that are also influenced by the environment are called multifactorial character.

Key Term:

1. allele- Any of the alternative versions of a gene that produce distinguishable phenotypic effects.
2. amniocentesis- A technique of prenatal diagnosis in which amniotic fluid, obtained by aspiration from a needle inserted into the uterus, is analyzed to detect certain genetic and congenital defects in the fetus.
3. codominance-The situation in which the phenotypes of both alleles are exhibited in the heterozygote because both alleles affect the phenotype in separate, distinguishable ways.
4. dihybrid-An organism that is heterozygous with respect to two genes of interest. All the offspring from a cross between parents doubly homozygous for different alleles are dihybrids. For example, parents of genotypes AABB and aabb produce a dihybrid of genotype AaBb.
5. Huntington’s disease-A human genetic disease caused by a dominant allele; characterized by uncontrollable body movements and degeneration of the nervous system; usually fatal 10 to 20 years after the onset of symptoms.
6. incomplete dominance-The situation in which the phenotype of heterozygotes is intermediate between the phenotypes of individuals homozygous for either allele
7. monohybrid-An organism that is heterozygous with respect to a single gene of interest. All the offspring from a cross between parents homozygous for different alleles are monohybrids. For example, parents of genotypes AA and aa produce a monohybrid of genotype Aa.
8. pedigree-A diagram of a family tree showing the occurrence of heritable characters in parents and offspring over multiple generations.
9. polygenic inheritance-An additive effect of two or more genes on a single phenotypic character.
10. testcross-Breeding an organism of unknown genotype with a homozygous recessive individual to determine the unknown genotype. The ratio of phenotypes in the offspring reveals the unknown genotype.

Video:

http://www.youtube.com/watch?v=EvR_Sdm1orU

mendel rap

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

Chapter Nine: Cellular Respiration: Harvesting Chemical Energy

Q1: where does cellular respiration take place?

A1: in mitochrondia, prokaryotic cell in cytoplasm.
Q2: why is cellular respiration important?
A2: Living cells require transfusions of energy from outside sources to perfirm their many tasks. and cellular respiration is the process that living things can change sources to energy.
Q3: what's the defference between fermentation and anaerobic?
A3: fermentation only get through glycolysis, only produce a few ATP. anaerobic respiration takes place in centain prokaryotic organisms do not use oxygen as a final electron accepetor.



Five Facts:
1. glycolysis harvests chemical energy by oxidizing glucose to pyruvate
2. the citric acid cycle completes the energy yielding oxidating of organic molecules
3. during oxidative phosphorylation. chemiosmosis couples electron transport to ATP synthesis
4. fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen
5. catabolic pathways yield energy by oxidizing organic fuels



Figure:





























Substrate-level phosphorylation is a type of chemical reaction that results in the formation and creation of adenosine triphosphate (ATP) by the direct transfer and donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) from a reactive intermediate. While technically the transfer is PO3, or a phosphoryl group, convention in biological sciences is to refer to this as the transfer of a phosphate group. In cells, it occurs primarily and firstly in the cytoplasm (in glycolysis) under both aerobic and anaerobic conditions.

Summary:
Oxidation-reduxtion reaction, or redox reaction is the electron transfers. Redox reaction loss elelctrons from one substance called oxidation, and addition of electrons to another substance reduction. NAD+ is electron carrier coenzyme. Electron transport chain breakdown electrons in many steps in order to control the release of energy. C6H12O6 (aq) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l) is the whole process of cellualr respiration which require oxygen. Anaerobic respiration and fermentation don't need oxygen. fermentation only get through glycolysis, only produce a few ATP. anaerobic respiration takes place in centain prokaryotic organisms do not use oxygen as a final electron accepetor.Cellular respiration can be diveded into three processes:glycolysis, citric acid cycle, and oxidative phosphorylation.
Glycolysis breakdown glucose into two three-carbon pyruvates. It occures in cytosol. Its reactants are glucose, 2ATP, NAD+; products are 2pyruvate, 2H2O, 4ATP, and 2NADH. It has energy investment and energy payoff. By the end of energy investment, glucose breakdown to Glyceraldehyde-3-phosphate. Citric acid cycle complete breakdown and take place in mitochrondia matrix. It needs pyruvate, coe A, 4NAD+, 1ATP, and 1FAD and produces 3CO2, 1ATP, 4NADH, and 1FADH2. Oxidative phosphorylation is in mitochrondia cristae. It requires NADH, FADH2, ATP, and oxygen, and produces NAD+, FAD, ATP, and water. It has electron transport chain and chemiosmosis. Hydrogen ions from NADH and FADH2 go out then flow back by ATP synthase. The whole energy sequence is: glucose-NADH-electorn transport chain-proton motive force-ATP.

Key Term:

1. acetyl CoA-Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.
2. alcohol fermentation-Glycolysis followed by the conversion of pyruvate to carbon dioxide and ethyl alcohol.
3. chemiosmosis-An energy-coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP. Most ATP synthesis in cells occurs by chemiosmosis.
4. facultative anaerobe- An organism that makes ATP by aerobic respiration if oxygen is present but that switches to anaerobic respiration or fermentation if oxygen is not present.
5. obligate anaerobe-An organism that only carries out fermentation or anaerobic respiration. Such organisms cannot use oxygen and in fact may be poisoned by it.
6. oxidizing agent-The electron acceptor in a redox reaction.
7. ATP synthase-A complex of several membrane proteins that provide a port through which protons diffuse. This complex functions in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion (proton) concentration gradient to make ATP. ATP synthases are found in the inner mitochondrial membrane of eukaryotic cells and in the plasma membrane of prokaryotes.
8. lactic acid fermentation-Glycolysis followed by the conversion of pyruvate to lactate, with no release of carbon dioxide.
9. substrate-level phosphorylation-The formation of ATP by an enzyme directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.
10. cytochrome-An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells.

Video:

http://www.youtube.com/watch?v=_hGW6NjCUSs

Chapter eight: introduction of metabolism

Q1: what is metabolism?

A1: The totality of an organism’s chemical processes.

Q2: how does metabolism work in living things?

A2: catabolic and anabolic pathway that release or gain energy.

Q3: what is energy?

A3: the ability of work

Five Facts:

1. an organism's metabolism transforms matter and energy, subject to the laws of thermodynamics.

2. the free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

3. ATP powers cellular work by coupling exergonic reactions to endergonic reactions

4. enzymes speed up metabolic reactions by lowering energy barries

5. regulation of enzyme activity helps control metabolism

Figure

if the reaction goes from higher free energy to lower free energy, there will be a negative ΔG, and the reaction will be spontaneous. However, if the reactants have a lower ΔG than the products, there will be an increase in free energy, and the reaction is nonspontaneous. In this situation, some form of energy (in the form of heat, light, etc.) will be required for the reaction to take place. It should be noted that a spontaneous reaction will not necessarily occur on its own. This is because an initial activation energy is needed in order to start the reaction and thus even a spontaneous reaction may need some form of energy input. A good example of this is the very exergonic combustion of octane, which still needs a flame in order to initiate.

Summary:

Metabolism is the totality of an organism’s chemical processes, concerned with managing the material and energy resources of the cell.A metabolic pathway begins with a specific molecule, which is then altered in a series of defined step, resulting ina centain product. Catabolic pathway is breakdown pathway. Anabolic pathways consume energy to build complicated molecules from ones. Also called biosynthetic pathway. energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways.

Kinetic energy is energy of motion. Potential energy is stored enegy or th ecapacity to work. Activation energy needed to convert potential energy into kinetic energy. The study of the energy transformation that occur in a collection of matter is called thermodynamics: 1)Energy can be transferred and transformed, but it cannot be created or destroyed.2)Each energy transfer or transformation increases the entropy of the universe.Entropy is the measure of disorder. Free energy is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system. If the system has more free energy, it is less stable, it has greater work capacity. Exergonic reaction is chemical reactions with a net release of free energy. Endergonic: chemical reactions that absorb free energy from the surroundings. Living cell is not in equilibrium. ATP contains sugar ribose, adenine, and three phosphate groups. Atp can be broken by hudrolysis. Energy released from ATP drives anabolic reactions.Energy from catabolic reactions “recharges” ATP. enzymes cause rate of a chemical reaction to increase and lower the activation energy for a chemical reaction to take place. environment, cofactors, coenzymes, and inhibitor are some factors can effect enzyme.

Key Terms:

1. active site-The specific portion of an enzyme that binds the substrate by means of multiple weak interactions and that forms the pocket in which catalysis occurs.
2. allosteric regulation-The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
3. catalyst-A chemical agent that increases the rate of a reaction without being consumed by the reaction.
4. coenzyme-An organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.
5. cofactor-Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.
6. competitive inhibitor-A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.
7. feedback inhibition-A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.
8. induced fit-Induced by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate
9. noncompetitive inhibitor-A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme’s shape so that the active site no longer functions effectively
10. bioenergetics-(1) The overall flow and transformation of energy in an organism. (2) The study of how energy flows through organisms.

Video:

http://www.youtube.com/watch?v=V4OPO6JQLOE

enzyme

Chapter seven: membrane structure and function

Q1:what is plasma membrane's structure?
A1: phospholipid bilayer and protein.
Q2: what's plasma membrane's function?
Q2: controls traffic into and out of the cell it surrounds.
Q3: why does plasma membrane have that structure?
A3: cell membrane is a boundary the separates cell from its surrounding. it has hydrophobic layer outside so that it won't be dissolved in its surrounding. the mosaic protein help substances transport.

Five Facts:
1. cellular membrane are fluid mosaics of lipids and proteins
2. membrane structure results in selective permeability
3. passive transport is diffusion of a substance across a membrane with no energy investment
4. active transport uses energy to move solutes against their gradients
5. bulk transport across the plasma membrane occurs by exocytosis and endocytosis

Figure

mosaic proteins in phospholipids help select substances tranport. it has integral protein and peripheral protein. Because phospholipids are hydrophilic inside and hydrophobic outside, the hydrophobic part of protein is inside the lipids.

Summary:
The plasma mambrane is the edge of life, the boundary that separates the living cell from its surrounding. It exhibits selective permeability which allows some substances to cross it more easily than others. Lipids and protein are the staple ingredients of membrane. The phospholipids are amphipathic which has both hydrophobic and hydrophilic parts. In fluis mosaic model, the membraen is a fluid structure with mosaic proteins in bilayer. Membranes are not static, it can move laterally, flip-flop. Low temperature can cause unsaturates hydrocarbon tails. Cholesterol will also add to the membrane. Integral protein penetrate the hydrophobic core of th elipid bilayer. Peripheral proteins are appendages loosely bound to the surface of the membrane. Membrane carbohydrates are glycolipids or glycoproteins.
Cell membrane are permeable to apecific ions and a variety of polar molecules. Hydrophlic substances can avoid contact with the lipid bilayer by passing through transport proteins. The selective permeability of a membrane depends on both the discriminating barrier of the lipid bilayer and the specific transport proteins. Passive transport is the movement across membranes that does NOT require cellular energy.Diffusion is the net movement of atoms, ions or molecules down a concentration gradient. Osmosis is the diffusion of water.Tonicity is the concentration of water relative to a cell.Osmoregulation is the control of water balance.Facilitated diffusion has transport protein that helps materials through the cell. Active transport is movement across membranes that DOES require cellular energy. Electrogenic pump is a transport protein that generates voltages across a membrane.Sodium-potassium pump is themajor electrogenic pump of animals.Proton pump is the main electrogenic pump of plants, fungi, and bacteria.Exocytosis is the movement of bulk material out of cells.
Endocytosis is the movement of bulk materials into cells.

Key Term:

1. aquaporin-A channel protein in the plasma membrane of a plant, animal, or microorganism cell that specifically facilitates osmosis, the diffusion of water across the membrane.


2. concentration gradient-A region along which the density of a chemical substance increases or decreases


3. electrogenic pump-An ion transport protein that generates voltage across a membrane.


4. hypertonic-Referring to a solution that, when surrounding a cell, will cause the cell to lose water.


5. hypotonic-Referring to a solution that, when surrounding a cell, will cause the cell to take up water.


6. isotonic- Referring to a solution that, when surrounding a cell, has no effect on the passage of water into or out of the cell.


7. receptor-mediated endocytosis-The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances.


8. tonicity-The ability of a solution surrounding a cell to cause that cell to gain or lose water.


9. turgid-Swollen or distended, as in plant cells. (A walled cell becomes turgid if it has a greater solute concentration than its surroundings, resulting in entry of water.)


10. ligand-A molecule that binds specifically to another molecule, usually a larger one.

Video:

http://www.youtube.com/watch?v=s0p1ztrbXPY

Chapter six: A tour of the cell

Q1: What's cell's component?
A1: prokaryotic: capsule, cell wall, plasma membrane, cytoplasm, DNA, ribosomes
eukaryotic: cell wall, membrane, cytoplasm, DNA, ribosome, cytoskeleton, nucleus, ER, golgi apparatus, lysosome, vacuoles and vesicles, peroxisome, mitochodria, chloroplast
Q2: what's cell's function?
A2: passing genetic information, regulation, metabolism, etc, cells are basic units of all living things.
Q3: how do people study the tiny cell?
A3: by improving and using microscope.

Five Facts:
1. to study cells, biologists use microscopes and the tools of biochemistry.
2. eukaryotic cells have internal membrane that compartmentalize
3. the endomembrane system regulates protein traffic and perfroms metabolic functions in the cell
4. the cytoskeleton is a network of fibers that organizes structures and activities in the cell
5. extracellular components and connections between cells help coordinate cellular activies.

Figure

chloroplast has bilayer, outer membrane and inner membrane. Between these two is the intermembrane space. The inner membrane is convoluted so that it has more surface. The folding of inner membrane is called cristae. Mitochondrial matrix is enclosed by the inner membrane. Free ribosomes are in the mitochondrial matrix.

Summary:
Scientists use light microscope to study most cells and bacterias and electron microscope to study bacteria, viruses, macromolecules, and atoms.Cytology is the study of cell structure. Both prokaryotic and eukaryotic have plasma membrane, cytosol, chromosomes, ribosome, ad cytoplasm. Prokaryotic cell has nucleoid instead of nucleus.
The nucleus contains most of the genes in the eukaryotic cell. Nuclear envelope encloses the nucleus, separating its contents form the cytoplasm. It is a double membrane, inner membrane supported by a protein matrix which gives the shape to the nucleus. Nucleolus storage ribosomes. chromatin form chromosomes, a complex of protein and DNA. Free ribosome in cytosol; bound ribosome in ER. Endoplasmic reticulum fold sheet or tubes of membranes. Smooth ER lacks ribosome and uses for lipid synthesis, carbohydrate storage, and detoxification of poisons. Rough ER has ribosomes, adn makes secretory proteins. Golgi apparatus package products of ER for transport. It has vesicles. Lysosome is digestive compartments. It can so phagocytosis and antophagy. Vacuoles has single membrane in plant's cell. Mitochondria are the sites if cellular respiration, the metablic process that generates ATP by extracting energy from sugarsm fats, and other fuels with help of oxygen; Chloroplasts found in plants and algae, are the sites of photosynthesis. Peroxisome use hydrogen peroxide.Cytoskeleton help cell strucure, shape, movement, and division. Three types: microtubules, microfilaments, and intermediate filaments. Cell wall supports and protects cell. it has primary and secondary walls. middle lamella connect cells. Extracellular matrix helps cells together. Intercellular junction in plant is plasmodesmata. in animals are tight junction, desmosome, and gap junction.

Key term:

1. cell fractionation-The disruption of a cell and separation of its parts by centrifugation.


2. scanning electron microscope (SEM)-A microscope that uses an electron beam to scan the surface of a sample to study details of its topography.


3. transmission electron microscope (TEM)-A microscope that passes an electron beam through very thin sections and is primarily used to study the internal ultrastructure of cells.


4. thylakoid-A flattened membranous sac inside a chloroplast. Thylakoids exist in an interconnected system in the chloroplast and contain the molecular “machinery” used to convert light energy to chemical energy.


5. stroma-Within the chloroplast, the dense fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.


6. phagocytosis-A type of endocytosis in which large particulate substances are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells).


7. integrin-in animal cells, a transmembrane receptor protein that interconnects the extracellular matrix and the cytoskeleton.


8. dynein-In cilia and flagella, a large contractile protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella.


9. collagen-A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom.


10. basal body-A eukaryotic cell structure consisting of a 9 + 0 arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.

Video:

http://www.youtube.com/watch?v=GW0lqf4Fqpg&feature=related

cell membrane

Unit One: professor's response

Re: question about gene‏
From:
Angela DePace (Angela_DePace@hms.harvard.edu)
Sent:
Mon 10/05/09 6:35 AM
To:
vivian zhang (princesszhang@live.com)
Dear Vivian
Glad to hear that biology has sparked your interest! How gene evolution contributes to organism diversity is a big question, still unanswered in many ways. There is a wonderful book that could help you begin to understand the issues involved - it's called "Endless Forms Most Beautiful" by Sean Carroll. Here's a link to it on Amazon.
http://www.amazon.com/gp/product/0393327795/ref=pd_luc_sim_01_02
Best of luck with your studies!
Angela
................................................................
Angela DePace
Dept. of Systems Biology
Harvard Medical School
200 Longwood Avenue WA452A
Boston, MA 02115
(617) 432-7410
Angela_DePace@hms.harvard.edu
http://depace.med.harvard.edu
On Oct 4, 2009, at 9:13 PM, vivian zhang wrote:
Dear professor DePace, I am a high school student from Utah, and I just learnt about the feritable information from AP biology. I have a question that I really want know how gene evolution contribute to organism diversity. I will be very appreciate if you have time to answer my question.
From,Vivian Zhang

Chapter Five: the structure and funcion of large biological molecules

Q1: what are the large biological molecules?
A1: carbohydrates, lipids, proteins, and nucleic acids.
Q2: why are they defined as large biological molecules?
A2: they are macromolecules which are built from monomers.
Q3: how are the large molecules formed?
A3: monomers form by dehydration.



Five Facts:

1. macromolecules are polymers, built from monomers
2. carbohydrates serve as fuel and building material
3. lipids are a diverse group of hydrophobic molecules
4. proteins have many structures, resulting in a wide range of functions
5. nucleic acids store and transmit hereditary information



Figure

Phospholipids can be bilayer of cells. It is compounded by fatty acids, phosohate, glycerol, and choline. Fatty acids which are carbon and hydrogen bond together are hydrophobic, and the head is hydropilic. When the phospholipids form the bilayer, the heads are in contact with water , and the hydrophobic tails are in contact with each other and remote from water.

Summary:
Carbohydrates, lipids, proteins, and nucleic acids are macromolecules, which are polymers built from monomers. Dehydration reaction, which means lost water molecules, help bond monomers together. Hydrolysis is the opposite. Monosaccharides are the monomers of carbohydrates. Disaccharide consists two monosaccharides. Polysaccharides consist alot. Fats, phospholipids, and steroids are types of lipids. Fatty acid and glycerol make fat. Oil is unsaturated fat. Phospholipids have hydropilic head and hydrophobic tail.
Protein consists one or more polypeptides which are polymers of amino acids. Amino acids have carboxyl, amino group, alpha carbon, and R group. Primary structure is sequence of amino acids. Secondary structure is the coils and folds. Tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids. Quaternary structure is the result from aggregation of these polypeptide subunits.Because of pH, salt concentration, temperature, etc, the protein may lose its shape, which is called denaturation. Nicleic acids are DNA and RNA. They are polymers of nucleotide, which conclude sugar, phosphate group, and nitrogeous base. Both DNA and RNA are important meterial of gene.

Key Terms:

1. cellulose-A structural polysaccharide of plant cell walls, consisting of glucose monomers joined by β glycosidic linkages.


2. chitin-A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.


3. starch-A storage polysaccharide in plants, consisting entirely of glucose monomers joined by a glycosidic linkages.


4. triacylglycerol-Three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride


5. steroid-a type of lipid characterized by a carbon skeleton consisting of four rings with various chemical groups attached.


6. catalyst-A chemical agent that increases the rate of a reaction without being consumed by the reaction.


7. disulfide bridge-A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.


8. peptide bond-The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction


9. alpha (α) helix-A spiral shape constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding.


10. beta (β) pleated sheet-One form of the secondary structure of proteins in which the polypeptide chain folds back and forth. Two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

Video:

http://www.youtube.com/watch?v=ha-DNTOooXk

Chapter four: carbon and the molecular diversity of life

Q1: what is the structure of carbon atom?
A1:carbon has 6electrons, with 2 in first electron shell and 4 in the second shell.
Q2: How does carbon exist in biosphere?
A2: Carbon enters the biosphere through the action of plants, which use solar energy to transform atmospheric CO2 into the molecules of life.
Q3: What common things are made of carbon element?
A3: Proteins, DNA, carbohydrates, and other molecules.

Five Facts:
1. Compounds containing carbon are said to be organic, and the study of carbon compounds is callded organic chemistry.
2. carbon can bond with hydrogen, oxygen, nitrogen, and carbon.
3. The carbon skelectons of organic molecules vary in length and shape and have bonding sites for atoms of other elements.
4. The distinctive properties of an organic molecule also depend on the molecular components attached to that skeleton.
5. ATP is an important source of energy for cellular processes.

Figure

Miller set up a simulate condition of origin earth. He evaporated water and mixed gas of water with hydrogen, methane, and ammonia. Under the lightning and cooling, some simple organic molecules were formed. As a result, organic molecules may have been synthesized abiotically on the early earth.

Summary:
Compounds containing carbon are said to be organic, and the study of carbon compounds is callded organic chemistry. Vitalism, the belief in a life force outside the jurisdiction of physical and chemical laws, provided the foundation for the new discipline of organic chemistry. Stanley Miller made the organic compound acetic from inorganic substances that could be prepared directly from pure elements.
Carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms in covalent bonds. Tetrahedron is the shape of four single covalent bonds. When two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane. The shape pf a molecule often determines its function. CO2 is inorganic. Urea is both single and double bonds. Carbon skelectons vary in length, straight, branched, or arranged in closed rings, or vary in number and location. Hydrocabons, organic molecules consisting of only carbon and hydrogen, are hydrophobic. The distinctive properties of an organic molecule also depend on the molecular components attached to that skeleton. Seven most important chemical group are hydroxyl, carboxyl, amino, sulfhydryl, phosphate, and methy groups.


Key Terms:

1. isomer- One of several compounds with the same molecular formula but different structures and therefore different properties.


2. geometric isomer-One of several compounds that have the same molecular formula and covalent arrangements but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds.


3. enantiomer-One of two compounds that are mirror images of each other.


4. functional group-A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.


5. amino group-A chemical group consisting of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of 1+.


6. carbonyl group-A chemical group present in aldehydes and ketones and consisting of a carbon atom double-bonded to an oxygen atom.


7. carboxyl group-A chemical group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group.


8. hydroxyl group-A chemical group consisting of an oxygen atom joined to a hydrogen atom. Molecules possessing this group are soluble in water and are called alcohols.


9. methyl group-A chemical group consisting of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom.


10. phosphate group-A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; important in energy transfer.


11. sulfhydryl group-A chemical group consisting of a sulfur atom bonded to a hydrogen atom.

Video:

http://www.youtube.com/watch?v=qOhEJK4Umds

Isomers of Hexane

Chapter three: Water and the fitness of the environment

Q1: How does the water affect the environment?
A1: Almost all the living things contain water. They release and gain energy by transfer water. Water can control climate by evaporating.
Q2: How is water compounded?
A2: A water molecule has one oxygen atom and two hydrongen atoms. And hydrogen bonds between eater molecules.
Q3: How important is water of the planet Earth?
A3: Three-quater of earth surface is coverd with water. Water is the resource of living things.Living things can not live without water.

Five Facts:
1. Because oxygen is more electronegative, hydrogen bonds are founded.
2. heat is form of energy measured by volume.
3. evaporation is a process that from liquid to air gas
4. hyfrophilic is something likes water; hydrophobic is something repel water
5. acid has high hydrogen concentration; base reduces hydrogen concentration

Figure

Because of the cool environment, ice crystal is founded. All the hydrogen bonding in specific shape, so the dense is less than liquid. So the ice can float above the liquid water. If the environment becomes warmer, hydrogen bonds break and re-from in free.

Summary:
Water has three phsical states: solid, liquid, and gas. Hydrogen bond has cohesion to transfer water against gravity. And water has strong surface tension. Kinekic energy is the energy of motion. Heat is form of energy. A calorie is the amount of heat it takes the temperature of 1g of water by 1℃. Water's specific heat is 1cal. Heat must be absorbed in order to break hydrogen bonds, and released by bonds form. Water evaporation can help cool down. Heat of vaporization is the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gas. At 4℃, water has the biggest density. A solution is a liquid with solvent and solute. An aqueous solution is one in which water is the solvent. Molecular mass is the sum of its atomic mass.
Hydrogen ion, H+. Hydroxide ion OH-. Hydronium ion H3O+. ph is scale of acid and base. H+ and OH- concentrations at 10-14. So the ph is 1-14. 7 is neutral at 25℃. Buffers can control changes of H+ and OH- in blood.

key terms:

1. buffer-A substance that consists of acid and base forms in a solution and that minimizes changes in pH when extraneous acids or bases are added to the solution.


2. calorie (cal)-The amount of heat energy required to raise the temperature of 1 g of water by 1°C; also the amount of heat energy that 1 g of water releases when it cools by 1°C. The Calorie (with a capital C), usually used to indicate the energy content of food, is a kilocalorie.


3. cohesion-The binding together of like molecules, often by hydrogen bonds.


4. evaporative cooling-The process in which the surface of an object becomes cooler during evaporation, owing to a change of the molecules with the greatest kinetic energy from the liquid to the gaseous state.


5. heat of vaporization-The quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state.


6. hydrophilic- Having an affinity for water.


7. hydrophobic-Having an aversion to water; tending to coalesce and form droplets in water.


8. polar molecule-A molecule (such as water) with opposite charges on different ends of the molecule.


9. specific heat-The amount of heat that must be absorbed or lost for 1 g of a substance to change its temperature by 1°C.


10. surface tension-A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules.

video:

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

hydrogen bond

Chapter two: The chemical context of life

Q1: how do chemicals relate to biology?
A1: Biology is a multidiscplinary science. And chemistry is applied to solve nature problems.
Q2: what are some important matters we should know in chemistry?
A2: compounds, atoms, molecules, and chemical bonds,etc.
Q3: what does make matter?
A3: elements

Five facts:
1. matter is made up of elements; atom is unit of an element; compound contains two or more elements.
2. atom conclude electrons, protons, and neutrons.
3. orbitals: 1s 2s 2p
4. covalent bonds share electrons; electrons transfer in ionic bonds
5. chemical reactions change reactants into products.

Figure

The valence shell of chlorine has 7 electrons. So it needs one more electron from sodium to keep balance. As a result, chlorine and sodium can bond together as ionic bond.

Summary:
Organisms are composed of matter; matter is made up of elements. Carbon, oxygen, hydrogen, and nitrogen make up 96% of living matter. Trace elements are needed rarely by organism. Atomic number is the number of protons; mass number is the sum of protons and neutrons. Isotopes are same element atoms have different neutrons. Potential energy is caused by location and structure. Electrons are founded in different electron shells. The farthest shell is valence shell.
Chemical bond is stoms staying close together. Single bond shares a pair of electrons; double bond shares two. The same atoms are equally electronegative, and the bond is nonpolar covalent bond. Ion is charged atom: cation is positive, anion is nagative. Molecules sharpded as tetrahedron. If the rates of the forward and reverse reactions are equal, the reaction reaches equilibrium.

key terms:

1. atomic mass-The total mass of an atom, which is the mass in grams of 1 mole of the atom.


2. atomic number-The number of protons in the nucleus of an atom, unique for each element and designated by a subscript to the left of the elemental symbol.


3. chemical bond-An attraction between two atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells.


4. chemical equilibrium-In a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so that the relative concentrations of the reactants and products do not change with time.


5. covalent bond- A type of strong chemical bond in which two atoms share one or more pairs of valence electrons.


6. electronegativity-The attraction of a given atom for the electrons of a covalent bond


7. hydrogen bond-A type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.


8. ionic bond-A chemical bond resulting from the attraction between oppositely charged ions.


9. isotope- One of several atomic forms of an element, each with the same number of protons but a different number of neutrons, thus differing in atomic mass.


10. van der Waals interactions-Weak attractions between molecules or parts of molecules that result from localized charge fluctuations.

Video:

http://www.youtube.com/watch?v=2mzDwgyk6QM&feature=related

sodium chloride

Chpter One: Intronduction: Themes in the study of life

Q1: why is evolution the core theme of biology?
A1: Because evolution is the change of early life to the living things today. We can learn a lot about diversity of organisms from evolution.
Q2: what are the themes of biology?
A2: 1.properties emerge 2.organisms interact with their environments, exchanging matter and energy 3.structure and function are correlated 4. cells are basic units 5. information DNA 6.feedback
Q3: what is the main way to study biology?
A3: Inquiry is the heart of science. Discovery science and hypothesis-based science are two main types.

Five Facts:
1.properties emerge;organisms interact with their environments, exchanging matter and energy;structure and function are correlated;cells are basic units;information DNA;feedback are the themes connect the concepts of biology.

2. evolution accounts for the unity and diversity of life, and also for the match of organisms to their environments
3.contemporary living things are all evolve from their ancetors
4.organisms evolve to adapt to environment
5. dicovery science and hypothesis-based science are the main forms of inquiry



Figure

The tree interact with its environment. It uses energy from sunlight and chemical energy; it produces heat and chemical nutrients to the environment.



Summary:
The evolution is the overarching theme of biology. The level in biological hierarchy is biosphere-ecosystem-community-population-organism-organ system-organ-tissue-cell-organelle-molecule-atom. Reductionism is reduction of complex systems to simpler components that are more manageable to study. In system biology, models are uesed for the dunamic behavior of whole biological systems. Cycling of nutrient and one-way flow of energy from sunlight are two major processes.Eukaryotic cell has nucleus, while prokarytic cell does not. High-throughout, bioibformatics, and development are key research. In negative feedback, accumlation of an end product slows the process that makes that product, on the contract the positive feedback.
Domain bacteria and domain archaea consist of prokaryotes. Domain eukarya includes kingdoms plantae, fungi, and animalia.Charles Darwin found the theory of natural selection. Organisms evolve to adapt to environment. Hypothesis must be testable and falsifiable. Controlled experiment is to keep all constant except one being teated.

key terms:

1. biology-The scientific study of life.


2. controlled experimet-An experiment in which an experimental group is compared with a control group that varies only in the factor being tested.


3. deductive reasoning-A type of logic in which specific results are predicted from a general premise.


4. emergent properties-New properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases.


5. genome-The genetic material of an organism or virus; the complete complement of an organism’s or virus’s genes along with its noncoding nucleic acid sequences.


6. inductive reasoning-A type of logic in which generalizations are based on a large number of specific observations.


7. inquiry-The search for information and explanation, often focused by specific questions.


8. negative feedback-A primary mechanism of homeostasis, whereby a change in a physiological variable triggers a response that counteracts the initial change.


9. positive feedback-A physiological control mechanism in which a change in a variable triggers mechanisms that amplify the change.


10. system bioligy-An approach to studying biology that aims to model the dynamic behavior of whole biological systems.

Video:

http://www.youtube.com/watch?v=GfQcOZXBBb8

about natural selection