Applying Conservation of Mass
A water storage tank initially contains 100,000 gal of water. The average daily usage is 10,000 gal. If water is added to the tank at an average rate of 5000[exp(−t/20)] gallons per day, where t is time in days, for how many days will the tank contain water?
1 • Friedrich Miescher investigated the chemical composition of the nucleus. • DNA must meet the following criteria: • information- must contain the information to construct the entire organism • replication- must be accurately and precisely copied • transmission- must be able to be passed on (or inherited) from cell to cell and parent to offspring • variation- differences in the genetic material must account for known variations within each species and among different species • purines- two-ringed structures; adenine and guanine • pyrimidines- single-ringed structures thymine and cytosine • DNA has different structural levels of complexity • nucleotides- the building blocks of DNA • strand- nucleotides that are covalently linked to one another • double helix- two strands of DNA that are bound to each other via hydrogen bonds and twist to form a helix • chromosomes- double stranded, helical DNA, associated with different proteins to form a more compact structure • genome- the complete complement of an organism’s genetic material • handrails (or sides) of the “ladder”- sugar-phosphate component • The staircase/ladder twists at every 10 bases. • Bases pair with hydrogen bonds. • Adenine pairs with thymine. • Guanine pairs with cytosine. • One end of the DNA ends in a 3’ OH and the other ends in a 5’ PO . 4 2 • The complementary strands of DNA run antiparallel; one end of the DNA is available at the phosphate group attached to carbon #5 (5’) and the other end is available at carbon #3 (3’). • DNA structure is essential for function. • The DNA molecule stores an organism’s genetic information. • DNA is precisely replicated. • DNA is susceptible to mutation. • DNA is expressed as the phenotype. • DNA is passed on from parent to offspring. • When a cell copies a DNA molecule, the two strands separate and each strand serves as a template for ordering new nucleotides into a new complementary strand. One at a time nucleotides line up along the template strand according to the base-pairing rules, and are joined by a phosphodiester bond. • E. coli can copy each of the 5 million base pairs in its single chromosome and divide to form two identical daughter cells in less than an hour. • A human cell can copy its 6 billion base pairs and divide into daughter cells in approximately 24 hours. • DNA replication 1. unwinding and separation of the two strands of DNA (denaturation) • occurs by DNA topoisomerase and DNA helicase - topoisomerase untwists the DNA while helicase pulls apart the two strands from each other • special proteins called DNA single-strand binding proteins bind to the separated strands to keep them from re-forming the double helix • this results in two single strands of DNA that are ready to be replicated 3 • once the strands are separated, DNA polymerase is able to catalyze the elongation of new DNA • as nucleotides align with complementary bases along the template strand, they are added to the growing end of the new strand by polymerase - DNA polymerase cannot initiate synthesis of new DNA on a bare template strand; it can only add nucleotides to the end of and existing chain that is base-paired with the template strand - starting a new chain requires a primer, a short segment of RNA - the primer is about 10-12 nucleotides long - primase, RNA polymerase, makes he primer • after the primer forms, DNA polymerase can start adding nucleotides to the 3’ end of the chain • Another DNA polymerase later replaces the RNA primer with DNA nucleotides that are complementary to the template • The sugar phosphate backbones run in opposite directions (antiparallel) • DNA polymerase can only add nucleotides to the free 3’ end of a growing DNA strand. • DNA can only elongate in the 5’ to 3’ direction. • Okazaki fragments- the lagging strand is copied in short segments; each one is about 100-200 nucleotides, they are joined by the enzyme ligase to form the sugar-phosphate backbone of a single DNA strand Proteins Involved in DNA Replication separates double-stranded DNA into single DNA helicase strands binds to single-stranded DNA and prevents it from Single-strand binding protein re-forming a double helix Removes tightened coils ahead of the replication Topoisomerase fork 4 Proteins Involved in DNA Replication DNA primase synthesizes short RNA primers synthesizes DNA in the leading and lagging DNA polymerase strands, removes RNA primers, and ﬁlls in gaps DNA ligase covalently attaches adjacent Okazaki fragments in the lagging strand • DNA replication is very accurate, but it’s not 100% accurate. • errors can occur naturally or by other means such as UV light, X-rays, and chemicals. These are known as mutagens. • an error in replication can be minor but it can also be deadly. • it has been estimated that DNA polymerase makes uncorrected errors at the rate of 1 per 100,000 nucleotides added to the chain. • At the end of chromosomal DNA molecules, are telomeres. • telomeres protect genes from being eroded through multiple rounds of DNA replication • the enzyme telomerase uses a short molecule of RNA as a template to extend the 3’ end of the telomere. • telomerase is not present in most cells of multicellular organisms • therefore, the DNA of somatic cells gets shorter and shorter after every DNA replication • thus, telomere length is a limiting factor in the life span of certain tissues and of the organism • telomerase is present in germ-line cells (sperm and egg) and also some cancerous somatic cells. • Humans contain 46 chromosomes (23 “identical” pairs) • Each chromosome consists of a long, linear, double-stranded DNA molecule. 5 • histones- about 60% of a chromosome; help maintain the structure and help control gene activity • The blueprint of every protein comes from DNA. • gene expression- the process by which information from a gene is used in the synthesis of a functional gene product • Two speciﬁc steps involved in gene expression • transcription- DNA is copied into RNA in the nucleus, then RNA moves into the cytoplasm • translation- RNA is converted to form polypeptide chains in the cytoplasm, polypeptide chains fold to form proteins • RNA is chemically similar to DNA except • it contains ribose sugar instead of deoxyribose sugar • it has uracil instead of thymine • generally a single strand instead of a double • there are many different forms of RNA that each have a different function • Three main classes of RNA • messenger RNA (mRNA)- the transcript of the coding strand of DNA involved in “carrying” the protein-building instruction • acts as the bridge between DNA and protein synthesis • serves as the template for the synthesis of proteins • ribosomal RNA (rRNA)- the major component of ribosomes involved in the process of assembling amino acids into proteins • transfer RNA (tRNA)- delivers amino acids to ribosomes for the process of assembling amino acids into proteins 6 • transcription- the process of using DNA as a template to synthesize mRNA • similar to DNA replication except that only a small stretch of DNA is used as a template (i.e. gene) and only one strand of the DNA is used to synthesize RNA • Transcription makes an RNA copy of DNA • initiation- several different transcription factors (proteins) bind to a speciﬁc nucleotide sequence before the beginning of the gene, called the promoter • promoter- initiates the binding of RNA polymerase to begin transcription of the gene • elongation- as RNA polymerase moves along the DNA, it unwinds the double helix about 10 base pairs at a time, adding on RNA nucleotides to the 3’ end of the growing strand • RNA polymerase does not proofread the RNA and thus mistakes occur at a rate of 1 per 10,000-100,000. • termination- transcription proceeds until after the RNA polymerase transcribes a terminator nucleotide sequence found at the end of the gene in the DNA • The order of nucleotides in DNA determines the order of amino acids in proteins. • The genetic code is read in increments of three bases called codons. • Each codon speciﬁes which of the 20 amino acids will be incorporated at the corresponding position along a polypeptide. • The number of nucleotides must be three times the number of amino acids making up the protein. (it would take 300 nucleotides to code for a protein that is 100 amino acids long) • the code is degenerate but very speciﬁc • 61 out 64 codons specify an amino acid • There are 3 “stop” codons and the codon AUG codes for methionine and “start”. 7 • translation- the process of making a polypeptide chain • the tRNA are attached to speciﬁc amino acids on one end of the molecule and have an “anticodon” at the other end. • anticodon- is complementary to codons in the mRNA sequence and can thus base pair with the mRNA • Once it reaches the cytoplasm, each tRNA is used to repeatedly: • pick up its designated amino acid • deposit the amino acid at the ribosome return to the cytosol to pick up another copy of that amino acid • the stages of translation • initiation- brings together mRNA, a tRNA with the ﬁrst amino acid, and the ribosome at the start codon • elongation- consists of a series of cycles as each amino acid is added to the proceeding one • termination- occurs when one of the three stop codons is reached resulting in the release of the translation complex • Additional alterations may occur to the newly synthesized polypeptide to make it functional • many enter the ER and move through the endomembrane system (made from “bound” ribosomes • some will enter the cytoplasm where they will perform their function (made from “free” ribosomes • Post translational modiﬁcations • removal/addition of some amino acids as well as sugars, lipids, and/or phosphates • modiﬁed, packaged, and shipped to their ﬁnal destination inside or outside the cell 8 • mutation- a heritable change in the genetic material • good mutations: evolution from chimp to human • bad mutations: extinction or genetic disorder • point mutation- a mutation that alters a single base • base substitution: when one base is wrongly paired with another base during DNA replication • silent- has no effect on the amino acid sequence because the new codon still translates into the same amino acid • missense- codes for an amino acid but translates into a different amino acid; changes a single amino acid • nonsense- a base substitution that changes an amino acid codon into a stop codon • frameshift: addition or deletion of single base • A mutation may alter the sequence within a promoter and affect the rate of transcription. May also enhance or inhibit transcription. • Four categories of structural changes • deletion- loss of some portion of the chromosome; most are lethal or cause serious disorder • duplication- gene sequence that is repeated two or more times in a row can occur in normal and abnormal chromosomes. • inversion- occurs when a segment of a chromosome is broken in two places, reversed, and put back together • translocation- a piece of one chromosome is broken off and becomes attached to a different chromosome 9 • mutagens- a chemical or physical agent that interacts with DNA to cause mutations • ex.- many chemicals such as nicotine and benzopyrene; ionizing and nonionizing radiation such as X-rays and UV light; some viruses like papilloma virus and hepatitis B • some chemicals act as base analogs that can be substituted into DNA, but par incorrectly during DNA replication • some interfere with DNA replication by inserting into DNA and distorting the double helix • carcinogens- mutagens that lead to cancer • Mutations can be spontaneous or induced. • spontaneous- occur as a result of problems during DNA replication or repair; can also occur “spontaneously” as a result of metabolic processes within the cell that produce toxic chemicals • induced- occur as a result of exposure to mutagens; can enter cell and alter DNA • All cells have the ability to recognize and repair damage to DNA in order to minimize mutation. • direct repair- a repair enzyme recognizes an incorrect structure in the DNA and directly converts it back • nucleotide excision repair- portion of DNA strand containing an abnormal nucleotide is removed and replaced 10 • cancer- a disease caused by random spontaneous mutations to environmental inﬂuences such as physical mutagens or chemical carcinogens that causes cells to divide excessively and invade other tissues • oncogenes- cancer-causing genes that have the capacity to stimulate cell division, but are normally tightly regulated in non-dividing cells • tumor-suppressor genes- involved with regulating cell division by acting as a “brake” or inhibitor • p53- a transcription factor that promotes synthesis of growth-inhibiting proteins • Mutations in the p53 tumor suppressor gene occur in 50 % of human cancer. • Ras- a protein that relays a growth signal from the outside of the cell to the inside • Mutations in the Ras oncogene occur in 30% of human cancer. • Modern genetics began with Gregor Mendel. • We knew that sperm and egg carried info but we didn't know how. • Mendel tested his hypothesis with pea plants. • He used pea plants because they are available in many varieties with distinct heritable features (ﬂower color) with different variants (purple or white). • He also had strict control over which two plants ma ted to produce offspring. • genes- organized units of heredity, comprised of DNA, that code for info about speciﬁc traits • genome- the complete genetic composition of a cell species • diploid organisms- each individual carries two genes for a given character • alleles- different versions of a speciﬁc gene • gene’s locus- the physical location of a gene on a chromosome • homozygous- both alleles of a gene are the same • heterozygous- both alleles of a gene are different • genotype- the genetic composition of an organism 11 • phenotype- the manner in which each combination of alleles are expressed; the physical appearance • dominant- allele whose phenotypic trait is expressed; capital letter • recessive- the allele which is masked an not expressed; lowercase letter • only expressed if there are two; aa • Mendel would cross true-breeding pea varieties. • Parental generation (P) —> First ﬁlial (F1)—> Second ﬁlial (F )2 • monohybrid cross- a cross that follows only two variations of a single character Mendel’s Law of Segregation- the two alleles of a gene separate (segregate) during the • formation of gametes so that every gamete receives only one allele • Punnet square- a way to predict the outcome of a simple genetic cross between individuals of known genotype • EXAMPLE Punnet Square combining: Aa x Aa A=purple ﬂowers a=white ﬂowers monohybrid A a cross A AA Aa a Aa aa • dihybrid cross- a cross that follows two different characters 12 • EXAMPLE dihybrid cross combining: AaBb x AaBb dihybrid cross AB Ab aB ab AB AABB AABb AaBB AaBb Ab AABa AAbb AaBB Aabb aB AaBB AaBb aaBB aaBb ab AaBb Aabb aaBb aabb • Mendel’s Law of Independent Assortment- the alleles of each gene assort independently of each other during gamete formation • chromosomes- contain genetic material and are replicated and passed from parent to offspring; found in the nucleus of a diploid cell • sex chromosomes- XX=female XY=male 13 • Heritable variations are often more complex than predicted • pleiotropy- a term used to describe the multiple effects that a gene may have on the phenotype • PKU- one of the most common inherited disorders, occurring in approx. 1 in 10,000 babies born in the US • occurs in babies who inherit two mutant genes (homo recessive) for the enzyme PAH • incomplete dominance- results when one allele of a pair is not fully dominant over its partner, so the phenotype of the heterozygote is a combination of the phenotypes • multiple alleles and codominance- sometimes there are more than two alleles for a particular gene, and depending upon which of those alleles you inherit, will determine your phenotype • skin color in humans and coat color in rabbits are examples of multiple alleles • Sometimes the environment determines whether or not a trait is expressed. • Autosomal recessive inheritance- both parents are heterozygous, child has 25% chance of being affected • cystic ﬁbrosis • sickle cell anemia • Tay-Sachs disease • X-linked recessive inheritance • males show disorder more than parents • son cannot inherit from his father • hemophilia • Duchenne muscular dystrophy 14 • Autosomal dominant inheritance • XXX syndrome- 3+ X chromosomes • generally normal • Klinefelter’s syndrome- XXY male • have male sex organs but are infertile • Turner syndrome- only one X chromosome • 98% spontaneously aborted • survivors are short, infertile females • XYY condition (Jacob syndrom)- males can have an extra Y chromosome • generally normal