Saturday, September 13, 2008

COMPENDIUM II



COMPENDIUM II






TABLE OF CONTENTS:



I. Chromosome Inheritance




A. Mitosis and Meiosis




B. Chromosomes/Karotype




C. Diseases with Chromosomes




II. CANCER




A. Cancer cells




B. Causes & Prevention




C. How Cancer is diagnosed




D. Treatments available




III. GENETIC INHERITANCE




A. One & two trait inheritance




B. Genotype & phenotype




C. Gametes




D. Genetic Disorders






E. Polygenic Inheritance




F. Sex-linked inheritance




G. X-linked disorders




IV. DNA BIOLOGY & TECHNOLOGY




A. Structure and Function of DNA RNA and Protein




B. Translation and Transcription




C. Regulation of gene expression




D. Gene Isolation & cloning




E. Genome Project








CHROMOSOMAL INHERITANCE








Chromosomes are what we inherit from generation to generation, because of the genes expressed in each chromosome. Humans have 46 chromosomes that occur in 23 pairs. 22 of these pairs are called autosomes. All of these genes control traits, except gender. The gender are determined by the one pair of chromosomes called the sex chromosomes. Males have the XY chromosome and the female has the XX chromosome. Also, an important note is the Y chromosome also contain the SRY gene that causes the male testes to develop. Chromosomes are found in out DNA. They are packaged into chromatins and when the cell divide they unravel and become chromosomes.











A Karotype is basically a picture of numbered chromosomes.
http://www.nature.com/cr/journal/v15/n5/fig_tab/7290307f2.html









Mitosis is the process of cell division during which the cell nucleus divides.











nte-serveur.univ-lyon1.fr/.../mitosis1.gif














As you can see mitosis goes through stages. Prophase is the first stage in which the chromosomes become visible. The centerioles, located in the cytoplasm near the nuclear envelop separate and take up positions on opposite sides of the nucleus. The centerioles lie in the centrosome that help to organize the spindle, a microtubule structure that helps separate the chromosomes. Then the condensed chromosomes become attached to fibers in the spindle at a point near the centromere of each chromatid. Next is metaphase. In metaphase, the chromosomes line up across the center of the cell, microtubules connect the centromere of each chromosome to the poles of the spindle. Third is Anaphase. During ananphase the centromeres that join the sister chromatids separate letting the sister chromosomes continue to move until the have seperated into two groups near the poles of the spindle. It ends when the chromosomes stop moving. The last phase is telophase. In telophase, the chromosomes which were condensed begin to disperse into a tangle of dense material. A nuclear envelop reforms around each chromosome, the spindle begins to break apart and a nucleolus becomes visible in each daughter nucleus.















Meiosis also has stages. Meiosis is the process of reduction division in which the number of chromosomes per cell is cut in half through the separation of homologous chromosomes in a diploid cell.





























kenpitts.net/hbio/8cell_repro/meiosis_pics.htm




























Before meiosis 1 occurs each chromosome is replicated. The cell begin to divide and kind of looks like mitosis, but each chromosome pairs with its homologous chromosome to form a structure called a tetrad. There are 4 chromatids in a tetrad. This is where they may exchange portions of their chromatids in a process called crossing over. Next is metaphase and this is when the spindle fibers attach to the chromosomes. Anaphase is when the fibers pull the homologous chromosomes toward opposite ends of the cell. After the chromosomes separate two new cells are formed. Each cell contains four chromatids. But neither one of the daughter cells has two complete sets of chromosomes.




























Second stage is meiosos II.














With meiosis II the two cells produced in meiosis one enter a second meiotic division. This has the four stages just like mitosis. Prophase cells have one chromosome from each homologous pair. In metaphase, two chromosomes line up in the center of each cell. In Anaphase the paired chromatids separate. Each of the four daughter cells produced is receives 2 chromatids. Four daughter cells now contain the haploid number.














Diseases can result from having to many or too few chromosomes. This can occur during the two cell divisions with I explained above. One example is non disjunction that happens during meiosis when both of a homologous pair go into the same daughter cell. Normal development relies on two of each kind of chromosomes. One disease is Down Syndrome. This is when there is an extra chromosome on chromosome 21. They say you have a better survival rate with an extra chromosome then you do with a deficiency. Another disease is Turner syndrome. This is when a child is born with only one sex chromosome. They will need hormonal supplements because they do not go through puberty or menstruate.














CANCER This is a picture of a brain cancer cell

www.alternative-cancer.net/Cell_photos.htm










Cancer cells are invasive. They have no function and look abnormal. They have a abnormal nuclei. They are large and may contain chromosomes. In a normal human cell, chromosomes end with special repetitive DNA sequences called telomeres. After binding with the correct protein the cell undergoes a process called apopstosis in which the cell dies. With cancer cells, a special enzyme telmerase continues the telomere sequences so that the cancer cell can keep growing, and growing. The cells eventually make up a tumor, they pile on top of each other and grow in layers. There are 2 types of cancers. benign is is a tumor that is encapsulated and will not invade adjacent tissue. Malignant is more serious. They can invade and destroy surrounding healthy tissue. In order for cancer cells to grow they need a well developed capillary network. Angiogenesis is the formation of new blood vessels. Cancer cells can also metastasize, meaning it can spread rapidly and invade other organs. This is terminal!! Cancer is a genetic disease. When cancer develops, the cell cycle occurs repeatedly due to mutations in two types of genes:












1. Proto-oncogenes - they code for proteins that promote the cell and prevent apotosis.












2. Tumor-suppressor genes - they code for proteins that inhibit the cell cycle and promote apoptosis.












There are several types of cancer. Most can be treated, but if it metastasizes then there is usually nothing doctors can do. Tumors are related to the organ it is associated with or has invaded. One example is leukemia. This particular cancer is associated with white blood cells. Another cancer is breast cancer. Very common in women, but men can get breast cancer too. Cancer can be hereditary. Some parents can be carriers. For example, with breast cancer scientist have found genes BRCA1 and BRCA2. These are tumor-suppressor genes that follow a particular inheritance pattern. Another type of tumor suppressor is RB gene. This is retinoblastoma, when a tumor develops in the eye. Others causes of cancer are environmental carcinogens. A carcinogen is a chemical that causes cancer. One example is radiation, like, ultraviolet rays (sun), x-rays and radon gas. These interfere with a persons DNA causing mutations. Smoking is also environmental. You don't even have to be a smoker to get cancer. People need to make healthy choices, not to smoke, eat a good diet with less red meat, and exercise. Also, people need to get regular checkup because sometimes cancer can go undetected. Women need regular pap smears and mammograms. Men need to have a prostate test done and yes some need mammograms. The American Cancer Society has seven warning signs which spells out CAUTION. C= change in bowel or bladder habits. A= a sore that does not heal. U= unusual bleeding or discharge. T= thickening or lump in breast or elsewhere. I= indigestion or difficulty swallowing. O= obvious change in wart or mole. N= nagging cough or hoarseness. Another important thing people can prevent is skin cancer. People can die from it. Melanoma is very dangerous and can start with just a small mole on your back that grows to the size of a half dollar. Keep checking moles!! Other tests that can be performed are Cat scans, MRI's, Pet scans and colonoscopy. Treatments for cancers are surgery to remove a cancerous tumor, radiation and chemotherapy. The radiation treatment causes chromosomal breakage and cell cycle disruption. People in low cancer stages are usually treated with radiation. Chemotherapy is a way to catch cancer cells that have spread throughout the body. Chemotherapy is usually given intravenously. one example of a chemotherapy drug is Alkylating agents - these medications interfere with the growth of cancer cell by blocking the replication of DNA. There are also newer therapies. One is immunotherapy, which refers to our immune system. The immune system is compromised when cancer cells attack. A vaccine called Melacine, which contains broken melanoma cells from two different sources in being studied for prevention of melanoma. There will be a lot of new therapies, as scientists keep up the research. It will never end!!









GENETIC INHERITANCE









We inherit our genes obviously from our parents. There are genotypes and phenotypes. The genotypes is generally your genetic makeup, the "genes" that you inherit. For you to inherit certain genes they have to be on the same chromosome and affecting the same trait, known as an alleles. These alleles are recognized by dominant or recessive. To separate the two they are categorized into letters. The dominant get capital letters, whereas the recessive gets lower case letters. For example, unattached earlobes are dominant over attached earlobes, so the dominant "E" for unattached and "e" for attached. There are two alleles for a given trait. Also, if the alleles is dominant; ie., EE this is considered a homozygous dominant and if it is recessive; ee it is homoozygous (meaning same) recessive. If the alleles are Ee then this is considered heterozygous. This would be considered dominant because of the leading E. Phenotype is what physical characteristics you inherit from our parent. Phenotypes can also be inheriting a disorder such as color blindness. There is also one and two trait cross inheritance, which involves gamates. Gametes are the specialized sex cells, which are the sperm of a male and an egg of a female. The gametes start out with 23 pairs of chromosomes. These chromosomes separate during meiosis. One trait crossing involves parents wanting to know if their child will a certain genotype or phenotype; ie freckles. Only "one" parent has freckles. This would depend on the allele pairing and if a parent carries this particular gene. Depending how the alleles pair there are sometimes a 50% chance that the child will have freckles. This is where the Punnett square is a useful tool in determining what the chances are a child would have freckles or unattached earlobes. The square combines all possible gametes and determine the genotype and the phenotypes of all offspring. The child or children can be homologous or heterozygous. Heterozygous refers to monohybirds in regards to having one pair of alleles. There are also two trait crosses. This involves meiosis and the gamete formation when a cross involves two traits. The alleles, of course, plays a key role in this process. What chromosomes you are inheriting from your parents, is homologue of each pair is the parental (father) chromosome and the maternal (mother) chromosome. All possible combinations of alleles occur in the gametes. Genetic disorders can occur if a parent is a carrier and some parents can be unaware that they are carriers if genetic testing is not done. One genetic disorder can be autosomal dominant in someone who has alleles AA or Aa and they will have the disorder. Someone with the recessive alleles aa will have the disorder. So a child born to heterozygous parents, has a 25% chance of having a disorder. Examples of genetic disorders are Tay-Sachs disease. This disease is an autosomal recessive disorder. It is a lack of an enzyme hexosaminidase A (Hex A) and storage of its substrate glycophingolipid in lyosomes. Occurs mainly in the brain. The symptoms are not apparent at first, but the child's development slows between four and eight months. Also has neurological impairment. These children eventually become blind, has seizures and becomes paralyzed. There are Polygenetic inheritance. Polygenic traits are skin color and height. Several sets of alleles are involved. The polygenic inheritance is like phenotype that is inherited from your parents. Skin color and height are multifactual traits because they both can effected by the environment. For example with skin color; the sun can make you darker due to the pigment in the skin. With height; if you are not the nutrition needed you could stop growing properly. Next six-linked inheritance which are controlled by genes on the sex chromosomes. An allele on the X chromosome is X-linked (mom) and the Y chromosome is Y-linked. These determine if you will be male or female when you are born. Many sex-linked genes are found on the X chromosome. The Y chromosome is much smaller then the X chromosome therefore it can carry more. Colorblindness is one of traits carried. There are three genes associated with color vision which lies on the X chromosome. In males a defective version of any one of these genes produces colorblindness. The most common form of colorblindness is not seeing the red-green colors. Males have just one X-chromosome so all the X-linked alleles are expressed in males even if they are recessive. For the female to express for colorblindness there must be two copies of the allele one on each of the two X chromosomes. There are sex-linked disorders. One example is Hemophilia. There are two important gens that are carried on the X-chromosome that help control blood clotting. A recessive allele in either of the two genes may produce this disease.








DNA BIOLOGY AND TECHNOLOGY








DNA(deoxyribnucleic acid) is the genetic material housed in the nucleus of a cell. The structure is similar to a ladder when replication is taking place. Originally, it is a double helix and is composed of two strands, each strand is a polynucleotide. The nucleotide is composed of a phosphate, deoxyribose sugar, and nitrogenous base. The phosphate-sugar combination is the backbone !! The base pairing is held together be hydrogen bonding, which are weak bonds. The bases are what is important in the functioning of DNA. The bases for DNA are Adenine and Guanine, which are purine (two rings) and Tymine and cytosine (one ring). In replication(also known as semiconservative), (one function of DNA), the cell divides and each new cell get an exact copy of DNA. In replication the one strand of DNA is separated and the base pairing, because they are held together with weak hydrogen bonds are separated. Then complementary base pairing is started. A-T always and C-T. These bases are joined together by an enzyme DNA polymerase. The DNA is originally unzipped by an enzyme helicase. The replication is complete when an enzyme seals any breaks in the sugar-phosphate backbone. I believe the enzyme is called ligase. Structure and function of RNA. RRNA (ribonucleic acid) is made up of nucleotides and the sugar ribose. The nucleotides are similar to DNA's nucleotides, except Urasil takes the place of Thymine. RNA still has Adenine, Cytosine, and Guanine. RNA has a single strand. RNA is made with help of DNA and is used for protein synethesis. There are 3 forms of RNA. mRNA is messenger RNA, used to carry genetic information from the DNA to the ribosomes, where protein synethesis occurs. Next, is tRNA, transfer RNA, is produced in the nucleus also with the help of DNA and tRNA is responsible for transferring amino acids to the ribosomes. The last RNA is rRNA, ribosomal RNA, this is made up in the nucleolus of a nucleus and DNA is used to help produce it. rRNA is involved with the ribosome where protein synthesis occurs. Transcription is when RNA molecules are produced by copying part of the nucleotide sequence of DNA into a complementary sequence in RNA. During transcription RNA polymerase binds to DNA and seaprates the DNA strands. RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA. mRNA is produced when the RNA nucleotides joins with RNA polymerase. With translation, the ribosome binds to the mRNA at the start codon,AUG, that is reconized only by the iniator tRNA. Amoni acids are linked to tRNA and bind to the appropiate codon in mRNA by forming completmentary base pairing withe tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one translated into a polypeptidic sequences dictated by DNA and represnted by RNA. At the end a release factor binds to to the stop codon terminating translation and reelasing the completed polypeptide from the ribosome. Proteins are macromolucules that contain a nitrogen as well as carbon, hydrogen, and oxygen. Proteins are also polymers of amino acids. There are more the 20 different amino acids. Protein help to carry out chemical reactions, transport small molecules in and out of cell and fight diseases.

molbioandbiotech.wordpress.com/.../ This is a picture of gene expression.


About replication, I would like to break it down.................................


Replication fork: point of unwinding DNA


Primer: starts thing off or gets things going


DNA is tightly coiled and must be uncoiled to begin replication


Uncoiling done by enzymes


DNA is made in a 5'-3' direction




Replication enzyme is DNA polymerase


DNA synthesizes enzyme


Makes new strand by finding base pair


It can find, bond to, modify at the rate of 1000 nucleotides per second


DNA polmerase can only make DNA in a 5'-3' direction


To make a new base it needs something to bond too


Can't seal gapping holes made in lagging (3'-5') strand it goes in the oppisite direction then 5'-3'


RNA polymerase makes RNA primer to sart so DNA polymerase can continue


DNA ligase fills hole in DNA replication on lagging strand created when Okazaki fragments made


Helicase is the enzyme that unwinds or flattens out DNA helix


If DNA can't be unwound by helicase, topisomerase (also an enzyme) breaks DNA backbone so helicase can unwind it


Single strand binding proteins keep DNA from recoiling after helicase unwinds it


Leading stand is made continuously


Lagging strand is similar to road under construction (analogy)


RNA polymerase makes RNA primer so DNA polymerase has a starting point


Okazaki fragment is added onto primer


DNA has to get rid of primer (RNA)




Genome Project
http://en.wikipedia.org/wiki/Genome
This is a picture of multiple chromosome making up a genome. A genome is from an organism and its whole hereditary information encoded in DNA. DNA fingerprinting uses the genome of an organsim to identifiy individuals. It does not analyze the cells most imortant genes, which are almost identical in most people. DNA fingerprinting analyzes sections of DNA that have little or no known function bt var from one person to another. How it works.....A small sample of DNA is cut with a restrction enzyme. The fragments that are left are seperated by size using gel electrophoresis (The migration of electrically charged molecules through a fluid or gel under the influence of an electric field. Electrophoresis is used especially to separate combinations of compounds, such as fragments of DNA, for the purpose of studying their components). Fragments containing these variable regions are the detected with a DNA probe, revealing a series of DNA bands of various sizes. If enough combinations of restriction enzymes and probes are used, a pattern of bands is produced that can be distinguished from the pattern of any othr individual in the world. DNA samples can be taken from blood, sperm and hair follicles. With the Genome project Dr. Francis Collins and Dr Craig Venter attempted to sequence all human DNA. They were successful. The genome project is similar to what I've just explained about DNA fingerprinting. Scientisit use the autosomal chromosomes and the 2 sex chromosomes. They can locate genes in several ways. An open reading frome is a series of DNA bases that can produce part of a working mRNA sequence. The mRNA coding regions of most genes are interrupted by introns, but scienctists also have to find the special DNA sequences that mark the boundaries between intron and exonsin order to follow the gene through its complete length. When the process is complete the scietists can can pinpoint the gene's promotor and the start and stop sites for transcription. The Genome project continues today, as scientiss are still analyzing the huge amount of information in the DNA sequence looking for gene's that might provide clues to some of the basic properties of life. Also, Biotechnology companies are working on finding genetic information that could be useful in developing new drugs and treatments for diseases.
Conclusion:
Well, three of these chapters were a great explanation of how we were really built. We are all very unique individuals due to what we inherit. This can be good and bad because of the diseases carried in some genes. Scientists around the world have a never ending job because of DNA sequences. Obviously, science is limitless in its findings. You hear it every day about new discoveries or a cure for a certain disease. The chapter on cancer is a wake up call for people to take better care of themselves. Some diseases are preventable and others are inherited.

































































































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