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genetics the science of heredity; it includes the study of what genes are, how they carry information, how they are replicated and passed to subsequent generations of cells or passed between organisms, and how the expression of their information within an organism determines the particular characteristics of that organism. genome The genetic information in a cell. A cell's WHAT includes its chromsomes and plasmids chromosomes structures containing DNA that physically carry hereditary information; the chromosomes contain the genes genes segments of DNA that code for functional products DNA The WHAT within a cell exists as long strands of nucleotides twisted together in pairs to form a double helix. Each strand has a string of alternating sugar and phosphate groups and a nitrogenous base is attached to each sugar in the backbone. The two strands are held together by hydrogen bonds between their nitrogenous bases base pair The WHAT always occur in a specific way: adenine always pairs with thymine, and cytosine always pairs with guanine. complementary Because of this specific base pairing, the base sequence of one DNA strand determines the base sequence of the other strand. The two strands of DNA are thus WHAT? genetic information WHAT is encoded by the sequence of bases along a strand of DNA genetic code The WHAT, set of rules that determines how a nucleotide sequence is converted into the amino acid sequence of a protein mRNA A gene usually codes for a WHAT molecule, which ultimately results in the formation of a protein. Alternatively, the gene product can be a ribosomal RNA or transfer RNA genotype The WHAT of an organism is its genetic makeup, the information that codes for all the particular characteristics of the organism. The WHAT represents potential properties, but not the properties themselves. phenotype WHAT refers to actual, expressed properties, such as the organism's ability to perform a particular chemical reaction. It is the manifestation of genotypes. genotype WHAT is its collection of genes, its entire DNA? phenotype WHAT is its collection of proteins. Most of a cell's properties derive from the structures and functions of its proteins genomics The sequencing and molecular characterization of genomes is called WHAT? DNA replication WHAT makes possible the flow of genetic information from one generation to the next. The DNA of a cell replicates before cell division so that each offspring cell receives a chromosome identical to the parent's. Within each metabolizing cell, the genetic information contained in DNA is transcribed into mRNA and then translated into protein DNA replication In WHAT, one "parental" double-stranded DNA molecule is converted to two identical "daughter" molecules. DNA polymerase Once bases are aligned, the newly added nucleotide is joined to the growing DNA strand by an enzyme called WHAT? DNA replication The double helix of the parental DNA separates as weak hydrogen bonds between the nucleotides on opposite strands break in response to the action of replication enzymes. Next, hydrogen bonds form between new complementary nucleotides and each strand of the parent template to form new base pairs antiparallel The two strands of DNA are WHAT. The sugar-phosphate backbone of one strand is upside-down relative to the backbone of the other strand. semiconservative replication Because each new double-stranded DNA molecule contains one original (conserved) strand and one new strand, the process of replication is referred to as WHAT? How is the information in DNA used to make the proteins that control cell activities? How is the information in DNA used to make the proteins that control cell activities?: Int he process of transcription, genetic information in DNA is copied, or transcribed, into a complementary base sequence of RNA. The cell then uses the information encoded in this RNA to synthesize specific proteins through the process of translation transcription WHAT is the synthesis of a complementary strand of RNA from a DNA template mRNA WHAT in transcription carries the coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized. transcription The process of WHAT allows the cell to produce short-term copies of genes that can be used as the direct source of information for protein synthesis. mRNA acts as an intermediate between DNA and translation translation Protein synthesis is called WHAT because it involves decoding the "language" of nucleic acids and converting that information into the "language" of proteins. codons The language of mRNA is in the form of WHAT, groups of three nucleotides, such as AUG, GGC, or AAA. The sequence of codons on an mRNA molecule determines the sequence of amino acids that will be in the protein being synthesized. Each codon "codes" for a particular amino acid. degeneracy Codons are written in terms of their base sequence in mRNA. Notice that there are 64 possible codons but only 20 amino acids. This means that most amino acids are signaled by several alternative codons, a situation referred to as the WHAT of the code. degenerate The genetic code is WHAT? Ex.) Degeneracy allows for a certain amount of change, or mutation, in the DNA without affecting the protein ultimately produced. central dogma DNA->RNA->protein= flow of genetic information or WHAT? sense codons Of the 64 codons, 61 are sense codons and 3 are nonsense codons. WHAT code for amino acids? nonsense codons WHAT do not code for amino acids rather, UAA, UAG, and UGA signal the end of the protein molecule's synthesis. The start codon that initiates the synthesis of the protein molecule is AUG, which is also the codon for methionine. translation The codons of mRNA are converted into protein through the process of WHAT? The codons of an mRNA are "read" sequentially; and, in response to each codon, the appropriate amino acid is assembled into a growing chain. tRNA The site of translation is the ribosome and WHAT molecules both recognize the specific codons and transport the required amino acids. anticodon Each tRNA molecule has an WHAT, a sequence of three bases that is complementary to a codon. process of translation process of translation: The overall goal of translation is to produce proteins using mRNAs as the source of biological information. The ribosome acts as the site where the mRNA-encoded information is decoded, as well as the site where individual amino acids are connected into polypeptide chains. The tRNA molecules act as the actual "translators" one end of each tRNA recognizes a specific mRNA codon, while the other end carries the amino acid coded for by that codon. summary summary: Genes are the units of biological information encoded by the sequence of nucleotide bases in DNA. A gene is expressed, or turned into a product within the cell, through the process of transcription and translation. The genetic information carried in DNA is transferred to a temporary mRNA molecule by transcription. Then, during translation, the mRNA directs the assembly of amino acids into a polypeptide chain: mRNA attaches to a ribosome, tRNAs deliver the amino acids tot he ribosome as directed by the mRNA codon sequence, and the ribosome assembles the amino acids into the chain that will be the newly synthesized protein. mutation A WHAT is a change int he base sequence of DNA neutral Mutations may be beneficial, harmful, or WHAT: The change in DNA base sequence causes no change in the activity of the product encoded by the gene. Silent mutations commonly occur when one nucleotide is substituted for another in the DNA base substitution The most common type of mutation involving single base pairs is WHAT in which a single base at one point in the DNA sequence is replaced with a different base. Ex.) AT might be substituted for GC. If a base substitution occurs within a gene that codes for a protein, the mRNA transcribed from the gene will carry an incorrect base at that position. missense mutation When the mRNA is translated into protein, the incorrect base may cause the insertion of an incorrect amino acid in the protein. If the base substitution results in an amino acid substitution in the synthesized protein, this change in the DNA is known as a WHAT? nonsense mutation A base substitution resulting in a nonsense codon is thus called a WHAT? frameshift mutations Besides base-pair mutations, there are also changes in DNA called WHAT, in which one or a few nucleotide pairs are deleted or inserted int he DNA. This mutation can shift the "transitional reading frame". Ex.) Deleting one nucleotide pair int he middle of a gene causes changes in many amino acids downstream from the site of the original mutation. spontaneous mutations Base substitutions and frameshift mutations may occur spontaneously because of occasional mistakes made during DNA replication. These WHAT apparently occur in the absence of any mutation-causing agents. mutagens Agents in the environment, such as certain chemicals and radiation, that directly or indirectly bring about mutations are called WHAT? ionizing radiation X-rays and gamma rays are forms of radiation that are potent mutagens because of their ability to ionize atoms and molecules. The rays of WHAT cause ions that combine with nucleotide bases in DNA, resulting in errors in DNA replication. An even more serious outcome is the breakage of covalent bonds in the sugar-phosphate backbone of DNA, which causes physical breaks in chromosomes. thymine dimers Another form of mutagenic radiation is ultraviolet (UV) light. The most mutagenic component of UV light is screened out by the ozone layer of the atmosphere. The most important effect of direct UV light on DNA is the formation of harmful covalent bonds between certain bases. Adjacent thymines in a DNA strand can cross-link to form WHAT? These can cause serious damage or death to the cell because it cannot properly transcribe or replicate such DNA. photolyases Bacteria and other organisms have enzymes that can repair UV-induced damage. WHAT, also known as light-repair enzymes, use visible light energy to separate the dimer back to the original two thymines. nucleotide excision repair WHAT is not restricted to UV-induced damage; it can repair mutations from other causes as well. Enzymes cut out the incorrect base and fill in the gap with newly synthesized DNA that is complementary to the correct strand. mutation rate WHAT is the probability that a gene will mutate when a cell divides. The rate is usually stated as a power of 10, and because mutations are very rare, the exponent is always a negative number. Ex.) If there is one chance in 10,000 that a gene will mutate when the cell divides, the mutation rate is 1/10,000, which is expressed as 10^-4. spontaneous mutation WHAT in DNA replication occurs at a very low rate, perhaps only once in 10^9 replicated base pairs (a mutation rate of 10^-9). Because the average gene has about 10^3 base pairs, the spontaneous rate of mutation is about 10^6 replicated genes. mutagen A WHAT usually increases the spontaneous rate of mutation, which is about one in 10^6 replicated genes, by a factor of 10-1000 times. Int he presence of a mutagen, the normal rate of 10^-6 mutations per replicated gene becomes a rate of 10^-5 to 10^-3 per replicated gene. positive selection (direct) involves the detection of mutant cells by rejection of the unmutated parent cells. Ex.) suppose we were trying to find mutant bacteria that are resistant to penicillin. The few cells in the population that are resistant will grow and form colonies, where as the normal, penicillin-sensitive parental cells cannot grow. (detects mutant cells bc they grow or appear different) negative selection (indirect) The process selects a cell that cannot perform a certain function, using the technique of replica planting. Ex.) suppose we wanted to use replica plating to identify a bacterial cell that has lost the ability to synthesize the amino acid histidine. First, 100 bacterial cells are inoculated onto an agar plate. Then each cell forms a colony. Then a pad of sterile material is pressed over the master plate, and some of the cells from each colony adhere to the velvet. Next, the pad is pressed down onto two or more sterile plates. One plate contains a medium without histidine, and one contains a medium with histidine. Any colony that cannot synthesize its own histidine will not be able to grow on the medium without histidine. (detects mutant cells bc they do not grow) carcinogens Many known mutagens have been found to be WHAT, substances that cause cancer in animals, including humans. Ex.) Ames test Ames test A faster and less expensive procedure for the preliminary screening of potential carcinogens. One of these is called WHAT and uses bacteria as carcinogen indicators. ames test can identify a mutant by cutting a well into a special agar that contains the chemical mutagen, if bacteria grow, the chemical was a mutagen. 90% of carcinogens are mutagenic in amines test. genetic recombination WHAT refers to the exchange of genes between two DNA molecules to form new combinations of genes on a chromosome. In eukaryotes, genetic recombination is an ordered process that usually occurs as part of the sexual cycle of the organism. Recombination generally takes place during the formation of reproductive cells. Like mutation, genetic recombination contributes to a population's genetic diversity, which is the source of variation in evolution. vertical gene transfer WHAT occurs when genes are passed from an organism to its offspring. Plants and animals transmit their genes by vertical transmission. horizontal gene transfer Bacteria can pass their genes to other microbes of the same generation transformation During the process of WHAT, genes are transferred from one bacterium to another as "naked" DNA in solution. competence When a recipient cell is in a physiological state in which it can take up the donor DNA, it is said to be competent. WHAT results from alterations int he cell wall that make it permeable to large DNA molecules. conjugation Another mechanism by which genetic material is transferred from one bacterium to another is known as WHAT? WHAT is mediated by one kind of plasmid, a circular piece of DNA that replicates independently from the cell's chromosome. Plasmids differ from bacterial chromosomes in that the genes they carry are usually not essential for the growth of the cell under normal conditions. conjugation vs transformation Conjugation differs from transformation in two major ways: 1.) conjugation requires direct cell-to-cell contact 2.) the conjugating cells must generally be of opposite mating type; donor cells must carry the plasmid, and recipient cells usually do not. F factor The WHAT was the first plasmid observed to be transferred between cells during conjugation. Donors carrying F factors (F+ cells) transfer the plasmid to recipients (F- cells), which become F+ cells as a result. Hfr cell In some cells carrying F factors, the factor integrates into the chromosome, converting the F+ cell into a WHAT (high frequency of recombination). When conjugation occurs between an Hfr cell and an F- cell, the Hfr cell's chromosome replicates, and a parental strand of the chromosome is transferred to the recipient cell. transduction A third mechanism of genetic transfer between bacteria is WHAT? In this process, bacterial DNA is transferred from a donor cell to a recipient cell inside a virus that infects bacteria, called a bacteriophage. transduction steps transduction steps: 1.) The phage attaches to the donor bacterial cell wall and injects its DNA into the bacterium. 2.) The phage DNA acts as a template for the synthesis of new phage DNA. The bacterial chromosome is broken apart by phage enzymes 3.) Some pieces of bacterial DNA are mistakenly packaged inside phage protein coats. The resulting phage particles then carry bacterial DNA inside of phage DNA. 4.) When the released phage particles later infect a new population of bacteria, bacterial genes will be transferred to the newly infected recipient cells 5.) Transduction of cellular DNA by a virus can lead to recombination between the DNA of the donor host cell and the DNA of the recipient host cell. genetic diversity All these processes (mutation, transportation, and recombination) provide WHAT in the descendants of cells. Diversity provides the raw material for evolution, and natural selection provides its driving force. Natural selection will act on diverse populations to ensure the survival of those fit for that particular environment.