Chapter Sixteen: the molecular basis of inheritance

Q1: who found the model of double helix?

A1: James watson and francis crick

Q2: what did Griffth find in his work?

A2: Some sustance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic.

Q3:Is RNA also shaped helix?

A3: yes, because it needs hyrophobic nitrogenous bases in the molecule's interior.

Five Facts:

1. DNA ias the genetic material

2. Many protein work together inj DNA replication and repair

3. A chromosome consists of a DNA molecule packed together with proteins.

4. DNA replication copy gene from parental to offspring.

5. RNA is made based on DNA

Figure:

Structurally, DNA is usually found as a double helix, with two strands wrapped around one another. However, DNA can adopt other configurations and it can also exist in single-stranded forms.

Summary:

Experiments with bacteria and with phages provided the first strong evidence that the genetic material is DNA. Waston and Crick deduced that DNA is a double helix. Two antiparallel sugar-phosphate chains wind around the outside of the molecule; the nitrogenous bases project into the interior, where they hydrogen-bond in specific pairs, A with T, G with C. The Meselson-Stahl experiment showed that DNA replication is semiconservation: the parent molecule unwinds, and each strand then serves as a template for the synthesis of a new strand according to base-pairing rules.

DNA replication:1. helicase unwinds the parental double helix.

2. moelcules of single-strand binding protein stabilize the unwound tamplate strands

3. the leading strand is synhesized continously in the 5-3direction by DNA pol III

4. primase begins synthesis of the RNA primer for the fifth Okazaki fragment

5. DNA pol III is completing synthesis of the fouth fragment. When it reaches the RNA primer on the third fragment, it will dissociate, move to the replication fork, and add DNA nuclrotides to the 3 end of the fifth fragment primer.

6. DNA pol I remove primer with DNA.

7. DNA ligase bonds the 3 end of the second fragment to the 5 end of the first fragment.

In missmatch repair, enzymes correct errors that persist. The ends of eukaryotic chromosomal DNA get shorter with each round of replication. Telomerase catalyzes the lengthening of telomeres in germ cells. The bacterial chromosome is usually a circular DNA molecule with some associated protein. Eukaryotic chromatin making up a chromosome is composed mostly of DNA, histones, and other proteins.

Video:

http://www.youtube.com/watch?v=teV62zrm2P0

Chapter Fifteen: the chromosomal basis of inheritance

Q1: What's that structure of chromosome?

A1: Each chromosome consists two sister chromotids, connecting by centremere.

Q2: Where are Mendel's hereditary factors located in the cell?

A2: DNA

Q3: What lead to genetic variation?

A3: Law of segregation and law of independent assortment

Five Facts:

1. Mendelian inheritance has its physical basis in the behavior of chromosomes.

2. Sex-linked genes exhibit unique patterns of inheritance.

3. Linked genes tend to be inherited together because they are locaed near each other on the same chromosome.

4. Alterations of chromosome number or structure cause some genetic disorders

5. some inheritance patterns are exceptions to the standard chromosome theroy.

Figure:

nondisjunction in which the members of a pair of homologous chromosomes do not move apart properly during meiosis I or sister chromatids fail to separate during meiosis II

Summary:

Chromosomes and genes are both pressent in pairs in diploid cells; homologous chromosomes separate during the process of meiosis; and fetilization restores the paired condition for both chromosomes and genes. The behavior of chromosomes during meiosis accounts for Mendel's laws of segregation and independent assortment. Sex is an inherited phenotypic character usually determined by which sex chromosomes are present. A gene located on either sex chromosome is called a sex-linked gene. X chromosome has more genes than Y chromosome. In females, one of two X chromosome is radonly inactivate, which is called barr body.

Genes located on the same chromosome that tend to be inherited together in genetic crosses are said to be linked genes. Genetic recombination is the production of offspring with combinations of traits that differ from those found in either parent. A genetic map based on recombination frequencies is called a linkage map. The father apart genes are, the more likely their allele combinations will be recombined during crossing over. If either of the aberrant gametes unites with a normal one at fertilization, the zygote will also have an abnormal number of a chromosome, a condition known as aneuploidy. missing one is monosomic; triplicate is trisomic. Polyploidy have more than two complete chromosome sets. Chromosome breakage can result in deletions, inversions. duplications, and translocations.

video:

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

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