Chapter twenty: Biotechnology

Q1: what's biotechnology?

A1: the manipulation of organisms or their components to make useful products.

Q2: what's recombinant DNA?

A2: DNA molecules formed when segments of DNA from two different sources-often different species-are combined in vitro.

Q3: what's genetic engineering?

A3: the direct manipulation of genes for practical pruposes.

Five Facts:

1. DNA cloning yields multiple copies of a gene or other DNA segment

2. DNA technology allows us to study the sequence, expression, and function of a gene

3. cloning organisms may lead to productino of stem cells for research and other applications

4. the practical applications of DNA technology affect our lives in many ways

5. biotechnology is the manipulation of organisms or their components to make useful products.

Figure:

In presence of polymerase enzyme (heat resistant) separation of a double stranded DNA (parentral strands) by heat at 95 degrees.
o Annealing: Synthetic pair of oligonucleotide probes are allowed to attach to their matcing base sequences on the separated DNA helicals.
o Since DNA polymerase is not denaturated by heat, its presence will allow the small synthesized oligonucleotide probe to extend along the specific DNA fragment – sort of replication-.
o This 3 step cycle is repeated 25 to 35 times.

Summary:

Plasmids are small circular pieces of DNA in bacterial cells that are used to insert pieces of foreign DNA.The DNA is cut using restriction enzymes. The collection of thousands of clones of bacteria containing recombinant plasmids is called a genomic library. Nucleic Acid Hybridizaion is used to detect genes. The DNA of the cell is denatured to produce single stranded DNA. The radioactive probe will hybridize with complementary bases if present. Probes can be radioactive isotopes or flourescent dyes. PCR is used to amplify DNA. Gel electrophoresis is a technique to separate DNA based on the movement of DNA fragments from neg to pos. Smaller fragments travel farther. Samples are placed in gels. Organismal cloning produce genetically identical individuals from a single somatic cell of a multicellular organism. Stem cells are relatively unspecialized cells that continue to reproduce themselves and can be induced to form specialized cells. Therapeutic cloning uses stem cells to replace organs and tissues. Reproductive cloning uses stem cells to reproduce new organisms.

DNA technology identify of human genes in which mutation plays a role in gentic diseases. Single nucleotide polymorphisms(SNPs) are useful genetic markers. When a restriction enzyme is added, SNPs result in DNA fragments with different lengths, or restriction fragment length polymorphisms(RFLP). Gene therapy is the alteration of an afflicted individual's genes. Vectors are used for delivery of genes into specific types of cells.

Video:

http://www.youtube.com/watch?v=mUcE1Y_bOQE

Chapter ninteen: viruses

Q1: is viruse alive?

A1: no, because viruses have to inject to a host cell to live and work.
Q2: what's the basic structure of viruses?
A2: viruse contain geetic materials DNA and RNA, and enclosed by protein.
Q3: who was the first person come up with the idea of viruses?
A3: Wendell Stanley.


Five Facts:
1. a virus consists of a nucleic acid surrounded by a protein coat.
2. viruses reproduce only in host cells
3. viruses, viroids, and prions are formidable pathogens in animals and plants
4. lytic cycle and the lysogenic cycle are two alternative way of reproduction
5. researches discovered viruses in the late 1800s by studying a plant disease, tobacco mosaic disease


Figure:
bacteriophage T4, like other "T-even: phages, has a complex capsid consisting of an icosahedral head and a tail apparatus.


Summary:
Many viruses' genomes consist of double or single-stranded DNA or RNA, depending one the kind of virus. The protein shell enclosing the viral genome is called a capsid. Capsids are built from a large number of protein subunits called capsomeres. Some viruses have accessory structure that help them infect their hosts. Viral envelope, which are derived form the membane of the host cell, contain host cell phopholipids an membrane protein.Many of the most complex capsods are found among the viruses that infect bacteria, called bacteriophage, or phage. Each type of virus can infect cells of only a limited variety of hosts, called the host range of the virus. This host specificity results from the evolution of recognition systems by the virus. Virus identify host cells by a "lock and key" fit.

A phage reproductive cycle that culminate in death of the host cell id known as a lytic cycle. A phage that reproduces only by a lytic cycle is a virulent phage. When phage DNA successfully enters a bacterium, the DNA often identifitied as foreign and cut up by cellular enzymes called restriction enzymes. The lysogenic cycle allows replication of the phage genome without destroying the host. Phage capable of using both modes of reproduing within a bacterium are called temperate phage. The RNA animal viruses with the most complicated reproductive cycles are the retroviruses. These viruses are equipped with an enzyme called reverse transcriptase, which transcrbes an RNA template into DNA, providing an RNA-DNA information flow. The integrated viral DNA, called a provirus, never leaves the host;s genime, remaining a permanent resident of the cell.

A vaccine is a harmless variant or derinative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen. Virods are circular RNA molecules tha infect plants. Prions appear ro cause a number of degenerative brain diseases in various animal species.



Video:
http://www.youtube.com/watch?v=41aqxcxsX2w

Chapter Eighteen: regulation of gene expression

Q1: what regulate expression of the different genes?

A1: enzyme protein.

Q2: why does expresion of gene need to be regulated?

A2: to perform right role in body; to regulate life acticity.

Q3: what is the different between positive and negative gene regulation?

A3: negative redulation control of gene: the operons are switched off by the active form of th erepression protein. positive only when a regulatory protein interacts direactly with the genome to switch transcription on.

Five Facts:

1. bacteria often respond to environmental change by regulating transcription.

2. eukaryotic gene expression can be regulated at any stage

3. noncoding RNAs play multiple roles in controling gene expression

4. a program of differential gene expression leads to the different cell types in a multicellular organism

5. cancer results from genetic changes that affect cell cycle control

Figure:

overwhole view of eukaryotic gene expression.

Summary:

Every cell in a human contains exactly the same sequences of DNA. One way in which cells with Identical DNA become different is by regulationg gene expression through the activatio of only selected genes. The DNA of bacteria contain sequence of DNA, called operons.

1. a regulatory gene produces a repressor protein, a substance that can prevent gene expression by blocking the action of RNA polymerase.

2.promoter region is a sequence of DNA to which the RNA polymerase attaches to begin transcription

3. operator region can block action of the RNA polymerase if teh regionis occupied by a repressor protein

4. structual genes contain DNAsequences that code for several related enzymes that direct the production of some particular end product

The lac operon controls the breakdown of lactos. The regulatory gene in the lac operon produces an active repressor that binds to the operator region. When the operator region is occupied by the repressor, RNA polymerase is unable to transcribe several strnctural genes that code for enzymes that control the uptake and subsquent breakdown of lactose. When lactose is available, however, some of the lactose combines with the repressor to make it inactive. When the repressor is inactived, RNA polymerase is able to transcribe the genes. Since a substance is required to induce the operon, the enzymes that the operon produces are said to be inducible enzymes.

Another operon is trp operon, produces enzymes for the synthesis of the amino acid tryptophan. The regulatory gene produces an inactive repressor that does not bind to the operator. As a result, the RNA polymerase proceeds to transcribe the structural genes necessary to pruoduce enzymes that synthesis tryptophan. When tryptophan is available from environment, the bacteria no longer eed to manufacture its own tryptophan. In this case, rising levels of tryptophan is acting as a corepressor. The active repressor now binds to th e operator region, which, in turn, prevents the transcription of the stuctural genes. Since these structural genes stop producing enzymes only in the presence of an active repressor, they are called repressible enzymes.

Video:

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

Chapter seventeen: from gene to protein

Q1: how does gene to protein?
A1: transcription and translation
Q2: what's the central dogma of life?
A2: From gene to protein; from genotype to phenotype
Q3: what does DNA make?
A3: mRNA

Five Facts:
1.transcription is the DNA directed synthesis of RNA
2. eukaryotic cells modify RNA after transcription
3. translation is the RNA directly synthesis of a polypeptide
4. point mutations can affect protein structure and function
5. while gene expression differs among the domains of life, th econcept of a gene is universal

Figure:
Translation is the process where the copied stretch of mRNA is translated into proteins.This occurs in ribosomes, either free floating in cells or bound to the endoplasmic reticulum.An enzyme called RNA polymerase catalyses the reaction. A tRNA triplet code lines up alongside the single stranded mRNA molecule. tRNA has an amino acid binding site attached, and the amino acid that binds is dependent on the codon of the tRNA molecule.When two amino acids are next to each other on the tRNA then a peptide bond forms between them and the first amino acid breaks free of the tRNA.

Summary:
Gene expression is the process by which DNA directs the synthesis of proteins. A, G, U, C are the nucleotides of RNA. An RNA molecule is a single strand.
Transcription begins with initiation, the RNA polymerase attaches to promoter regions on the DNA and begins to unzip the DNA in to two strands. A promoter region for mRNA transcriptions contains the sequence TATA box.Elongation occurs as the RNA polymerase unzips the DNA and assembles RNA nuceotides using one strand of the DNA as a template. As in DNA replication, elongation of the mRNA molecule occurs in the 5-3 direction. Termination occurs when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes, the termination region often contains the DNA sequence AAAAA.
Before a mRNA leaves nucleus, it undergoes two kinds of alternations. The first modification adds special nucleotude sequence to both ends of the mRNA. GTP is added to 5 end to form 5'cap. poly-A tail is added to 3 end. The tail provide stability and also appears to controlo the movement of the mRNA across the nuclear serve to regulate gene experssion. A transcribed DNA segmant contains teo kinds of sequences0exons, which are sequence that express a code for a polyprptide, and intons, intervening sequences that are noncoding. Before the RNA moves to the cytoplasm, snRNPs, delete out the introns and splce the exons.
A cell translations an mRNA binding message into protein using tRNA. After binding specific amino acidds, tRNA lines up via their anticodons at complementary codons on mRNA. Ribosomes help facilitate this coupling with binding sites for mRNA and tRNA. The formation of peptide bonds between amino acids is catalyzed by rRNA.

Videos:
http://www.youtube.com/watch?v=l96PKVfGh-0&feature=related

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