Pennsylvania has a flat-rate personal income tax. It can be represented as T(I) 0.0307I, where I is the income in dollars and T(I) is the tax owed in dollars. a. What is the income tax rate in Pennsylvania? b. What is the input? The output? c. Estimate T(35,000). What is its meaning? d. Estimate I if T(I) 1535. What is its meaning?
• All living cells are surrounded by a plasma membrane. • This membrane separates internal contents of the cell from external environment. • cell membranes- thin structures made mainly of phospholipids, proteins, and carbohydrates. • Phospholipids are amphipathic; have hydrophilic and hydrophobic regions. • The plasma membrane functions as a selectively permeable barrier that allows passage of oxygen, nutrients, and wastes for the whole volume of the cell. • extracellular ﬂuid- outside of cell • intracellular ﬂuid- inside the cell • The membrane is not just phospholipids; many other molecules makeup the cell membrane. • The overall structure of membranes is referred to as the ﬂuid-mosaic model. • Membranes are mainly composed of: phospholipids, carbohydrates, and proteins. • The proteins can span across the membrane and/or loosely bound to the outside or inside of the membrane and thus not part of the membrane structure. • phospholipids- structurally similar to triglycerides, but phospholipids have 2 fatty acid chains and a phosphate group where as triglycerides have three fatty acid chains. • The phosphate group on the end of the phospholipid is negatively charged causing that end to form a polar covalent bond with glycerol. • One end of the phospholipid id polar and the other is non-polar. • The polar end of the molecule is negatively charged and the non-polar end is positively charged. • Since water is also polar, the polar end of the phospholipid is attracted to the positive ends of water molecules. (hydrophilic) • The neutral end of the phospholipid is non-polar and is repelled by the water molecules. (hydrophobic) • The plasma membrane isn't rigid. It moves and sways. Imagine a water bed. This is called ﬂuidity. • The individual molecules remain close but can readily move within the membrane. • These molecules are held together with relatively weak hydrophobic interactions. • Most lipids can drift laterally through the membrane but they can also ﬂip-ﬂop. • lipid component in the membrane- synthesized in the smooth ER, transported by the Golgi, lysosomes, vacuoles, or plasma membrane • lipid exchange proteins- can take a lipid from one protein to another • protein component in the membrane- comes from the endomembrane system organelles • rough ER-> Golgi-> plasma membrane • Cells have to transport materials (nutrients and waste) in and out to survive. • Transport mechanisms • passive transport (by diffusion) + + 2+ • facilitated transport- large molecules, such as K , Na , and Ca , diffuse passively through channel transport proteins • osmosis- diffusion of water • active transport- movement of a solute across a membrane against its concentration gradient, uses energy • primary active transport- requires energy to move solute against concentration gradient secondary active transport- pre-existing gradient drives active transport of • another solute • exocytosis- involves packaging material inside the cell into vesicles and the excrete the material outside the cell • endocytosis- plasma membrane folds inward to form a pocket, resulting in an internalized vesicle that brings substances into the cell • three types of endocytosis • receptor-mediated endocytosis • pinocytosis (“cell- drinking”) • phagocytosis (“cell-eating”) • aA+bB=cC+dD • A and B are reactants • C and D are products • a, b, c, and d are the number of moles • energy- the ability to promote change or to do work • two forms of energy • kinetic energy- energy associated with movement • potential energy- stored energy due to structure or location • chemical energy is a form of potential energy contained within covalent bonds • thermodynamics- the study of energy • 1st law- energy can neither be created nor destroyed • 2nd law- any energy transfer or transformation from one form to another increases the degree of disorder of a system • entropy- the measure of randomness of molecules in a system • The sun provides energy (light energy) to all living systems on the planet. • Cells do three main types of work • mechanical work- movement of cilia and ﬂagella, contraction of muscle cells, and movement of chromosomes • transport work- pumping substances across membranes against the direction of spontaneous movement • chemical work- involving stockpiling, building, rearranging, and breaking apart substances • ATP- energy that powers cellular work; a nucleotide consisting of ribose, adenine, and a chain of three phosphates; can be broken into ADP • The phosphate bonds of ATP are weak covalent bonds. • The ATP Cycle- ATP is a renewable that is continually regenerated by adding a phosphate group to ADP • enzymes- catalysts that speed up the rate of chemical reactions that perform at normal body temperature • Enzymes DON’T change anything other than the time it takes for a reaction to occur. They just make it faster! • activation energy- needed to initiate a chemical reaction • active site- a speciﬁc location on the enzyme for the reactants to bind to • enzyme inhibitors- prevent enzymes from catalyzing reactions • Enzymes are affected by concentration, temperature, and pH. • Temperature has a major impact on reaction site. • metabolism- the sum total of all chemical reactions that occur within an organism • metabolic pathway- a sequence of steps that chemical reactions happen in • Two types of metabolic pathways involving energy • catabolic pathways- breakdown larger molecules into smaller ones to produce energy (hydrolysis) • cellular respiration • anabolic pathways- synthesize larger molecules from smaller ones and requires energy to do so (dehydration) • photosynthesis • Metabolic pathways are tightly regulated in three ways • gene regulation- allows cells to make or inhibit enzymes involved in metabolic pathway • cellular regulation- environmental signals activate/inactivate cell • biochemical regulation- a molecule noncovalently binds to enzyme to activate or inhibit that enzyme • All living organisms require a constant supply of energy to sustain life. • energy from sun -> chemical energy via photosynthesis • Complex chemical reactions occur in a number of separate stages. • Each reaction is catalyzed by a speciﬁc enzyme. • Metabolic pathways are similar in all organisms, from bacteria to humans. • oxidation-reduction (redox) reactions- break down organic molecules; transfer one or more electrons from one reactant to another • oxidation- loss of electrons • reduction- addition of electrons • Ae- + B -> A + Be- (redox reaction)- A, the electron donor, is the reducing agent and reduces B. B, the electron recipient, is the oxidizing agent and oxidizes A. The transfer electron carries energy with it. • In cellular respiration, glucose and other fuel molecules are oxidized, realizing energy. • As glucose is oxidized, the electrons get passed to a ﬁnal electron acceptor. • Cellular respiration doesn’t transfer hydrogen from glucose to oxygen all at one time. Hydrogen atoms are stripped from glucose and transferred to electron carriers. • electron carriers- NAD+ (nicotinamide adenine dinucleotide) and FAD+ (ﬂavin adenine dinucleotide) • Electron carriers deliver hydrogen to the ﬁnal step of the respiration process resulting in the majority of ATP. • Oxidation reactions occur in a speciﬁc order; it begins in the cytoplasm and is completed in the mitochondria. • Three main stages and one intermediate stage: • glycolysis- begins the breakdown of glucose; occurs with or with out oxygen • breakdown of pyruvate via oxidation (intermediate stage) • citric acid cycle (Kreb’s cycle or TCA (tricarboxylic acid cycle)) • oxidative phosphorylation via electron transport chain • cellular respiration- involves the breakdown of glucose (and other organic molecules) in the presence of oxygen (aerobic) • simpliﬁed equation of cellular respiration: glucose + oxygen -> -> -> -> carbon dioxide + water + energy • Glycolysis • As glucose is broken down, hydrogen atoms are stripped from glucose and passed to NADH. • energy investment phase- ATP energy activates glucose and its six-carbon derivatives • pyruvate- 6-carbon glucose is broken down into 2 three-carbon molecules in the cytoplasm • energy liberation phase- the products of the ﬁrst part are split into three-carbon pyruvate molecules; 4 ATP formed by substrate-level phosphorylation, 2 NADH formed • If oxygen is present, pyruvate is transported into the mitochondrion where enzymes of the Kreb’s cycle complete the oxidation of glucose to carbon dioxide. • Citric Acid Cycle • begins when the acetyl group from acetyl CoA combines with oxaloacetate to form citrate. • each cycle produces 1 ATP by substrate-level phosphorylation, 3 NADH, and 1 FADH2 per acetyl CoA • The Electron Transport Chain • All the NADH and FADH2 produced in glycolysis go to the electron transport chain. • vast majority of ATP produced from the oxidation of glucose comes from the energy in the electrons carried by NADH and FADH2 • the ETC generates no ATP directly • ATP Synthase- the only way for H+ to get back into the matrix; as H+ passes through, it leads to generation of ATP by ATP Synthase • chemiosmosis- the movement of ions across a selectively permeable membrane, down the electrochemical gradient. • ATP yield- the theoretical yield of ATP is 36-38; the actual yield is closer to 30 • regulation of aerobic respiration • negative inhibition- the end product feedbacks and inhibits an enzyme that catalyzes an early str in that pathway • ATP and citrate • positive feedback- the reactant activates an enzyme that catalyzes an early step in that pathway • AMP • Molecules such as proteins, fats, and nucleic acids can also be used as sources of energy. • proteins are broken down into their individual amino acids • fats are broken down into glycerol and fatty acids • nucleic acids are broken down into nucleotides • DON’T FORGET… polysaccharides are broken down into glucose • anaerobic respiration- absence of oxygen, sugars can occur by fermentation • examples of fermentation • lactate or lactic acid fermentation- the pyruvate from glycolysis is converted to lactate/lactic acid • some fungi and bacteria used to make cheese, yogurt, and sour cream • causes our muscles to be fatigued and sore • ethanol fermentation- pyruvate is covered to ethanol and carbon dioxide • some yeast and plant cells use in the absence of oxygen • used in brewing, wine-making, and bread- making • photosynthesis- plants, algae, and some bacteria can convert light energy to chemical energy; takes place in the chloroplasts • Sugar made in the chloroplasts supplies the entire plant with chemical energy and carbon skeletons to synthesize all the major carbon-containing molecules for its cells • Photosynthetic organisms produce their own organic molecules (carbs) and use them to make ATP. • Photosynthesis takes place in two stages: • capturing energy from sunlight and using this energy to make ATP, NADPH, and O2. • using the ATP, NADPH, and CO2 to power the synthesis of organic molecules • Pigments inside the chloroplasts capture light energy and use it to drive photosynthesis • chlorophyll a and b- green • other pigments- carotenoids and xanthophylls • Two pathways of photosynthesis • light reactions: driven by light energy- produces ATP and NADPH + H+ • the Calvin Cycle: does not use light directly (sometimes called dark reactions)- uses ATP, NADPH + H+ and CO2 to produce sugars • the two are linked by the exchange of ATP, ADP, NADP+, and NADPH • The Greenhouse Effect • CO2 released into the atmosphere acts like glass in a greenhouse; it allows solar energy to pass through and reach the Earth’s surface, but it absorbs and is heated by the energy that radiates back from the Earth’s surface • As CO2 levels increase, so does the Earth’s temperature • CO2 is produced from fossil fuels used in power plants, factories, and automobiles. • cellular reproduction- essential for replacing dead cells, growth of an organism, and wound healing • Four events must occur for cell reproduction • reproductive signal • DNA replication • distribution or segregation DNA • physical division of cells (cytokinesis) • Chromosomes are inherited in sets; after replication chromosomes consist of two sister chromatids which contain identical copies of the chromosome’s DNA • as they condense, the region where the strands connect shrinks to a narrow area, called the centromere • Humans have 23 pairs of chromosomes that vary in shape and size • karyotype- visualization of the different numbers, shapes, and sizes of chromosomes • Every eukaryotic species has a characteristic number of chromosomes in the nucleus. • humans have 46; we inherit 23 from each parent • Sperm or egg cells only have one set of chromosomes: 22 autosomes and 1 sex chromosome (X or Y) • haploid- cell with a single set of chromosomes; n=23 for haploid number for humans • a fertilized egg has two haploid sets of chromosomes (one from each parent) • diploid cells- cells with two sets of chromosomes; 2n=46 for humans • Cell division requires the distribution of identical genetic material, DNA, to two daughter cells. • mitosis- the process of cell division in somatic (body) cells • meiosis- cell division in sex cells (cells that produce gametes, egg and sperm) • Cell division is part of a larger pathway called the cell cycle. • Interphase- ﬁrst step of the cell cycle; cells are engaged in their metabolic activities such as photosynthesis, muscle cell contractions, etc.; cell prepares for the cell division phase; the longest part of the cell cycle • G1- RNA molecules, proteins, and enzymes are being made; cell is growing • S- DNA replication • G2- the ﬁnal preparations for mitosis • preparation for cell division- prior to DNA replication, the DNA of each eukaryotic chromosome consists of a linear DNA doubt helix that is found in the nucleus and is not highly compacted; when a cell is ready to divide, the sister chromatids become tightly packed and readily visible under microscope • Mitotic/Meiosis- second step of the cell cycle; consists of sub phases involved in the physical process of one cell producing two or four daughter nuclei. • prophase • duplicated chromosomes are condensed and become visible • nuclear envelope begins to disappear • spindle microtubules begin to form and capture chromosomes • chromatids are still attached to the centromere • centrioles move to opposite poles • metaphase • nuclear envelope has disappeared • centrioles are at opposite poles • chromosomes are attached to the spindle causing them to be lined up at the metaphase plate • each chromosome still has two chromatids • in human cells there are 46 chromosomes, or 92 chromatids • anaphase • centromeres split and chromatids separate • each chromatid is now termed a chromosome • chromatids move to opposite poles by spindle ﬁbers • each chromatid moving to the opposite pole is the exact copy of the other one • telophase • each set of chromosomes decondense/unwinds • spindles disassemble • nuclear envelope re-forms around each of the two sets of chromosomes • cytokinesis or equal division of the cell cytoplasm takes place • each of the daughter cells formed can now inert G1 stage of interphase and the cycle repeats. • cytokinesis- the division of the cell to form daughter cells; division of the cytoplasm • For the most part, plant and animal cells have very similar cell division cycles • plant cells do not have centrioles, but are still able to produce the spindle ﬁbers • there is a difference in the process of cytokinesis; animal cells form a cleavage furrow and plant cells form a cell plate • The cell cycle is highly regulated and the frequency of cell division varies with cell type. • Three irreversible checkpoints: • G1- determines if conditions are favorable for cell division • G2- makes sure that the DNA was replicated and there is no damage • Metaphase- senses the integrity of the spindle apparatus and all chromosomes attached • the cell cycle can be put on hold at checkpoints • Meiosis is a reduction division (2n -> n) • Meiosis starts with replicated chromosomes composed of two chromatids that go through two consecutive divisions that end with four haploid cells • meiosis 1 • prophase 1 • individual chromosomes become visible • nuclear envelope begins to breakdown • centrioles move to opposite poles • spindles begin to form • homologous chromosomes pair with one another (synapsis) • crossing over may occur • metaphase 1 • synapsed pairs of chromosomes move to the equatorial plate • centromeres of each chromosome are attached to the spindle • the differences from mitosis is that the homologous chromosomes are still attached • chromosomes randomly align along the metaphase plate • anaphase 1 • during this stage, the chromosome number is reduced from diploid to haploid • each pair of homologous chromosomes move to opposite poles • each chromosome is independently attached to a spindle at the centromere • the centromeres do not replicate at this stage • telophase 1 • chromosomes uncoil and become long, thin threads • the nuclear envelop reforms around each new set of chromosomes • cytokinesis divides the cell into two daughter cells • meiosis 2 • the two daughter cells formed in meiosis 1 undergo another division in meiosis 2 • prophase 2 • the nuclear envelope breaks down • the spindles are formed • metaphase 2 • this will be typical metaphase because the chromosomes are attached by their centromeres to the spindle • the chromosomes move to the equatorial plate • pairs of chromosomes are not attached, therefore, each chromosome moves as a separate unit • chromosomes randomly align • anaphase 2 • the difference between anaphase 1 and 2 is in anaphase 2, the centromere of each chromosome divides • the chromatids (daughter chromosomes) move to the opposite poles as in mitosis • there are no paired homologous at this stage • telophase 2 • nuclear envelope forms • chromosomes uncoil, nuclei reform • the spindles disappear • cytokinesis occurs • four haploid cells are formed (egg or sperm) • in humans and other organisms only one functional egg is produced; the other three (known as polar bodies) disintegrate. • nondisjunction- failure of chromosomes to move to opposite poles during anaphase 1 or 2 • Downs Syndrome- an extra 21 chromosome • Klinefelter’s Syndrome- XXY in males; have male sex organs but are infertile • XYY condition- males can have an extra Y chromosome; generally normal (can be taller) • XXX Syndrome- generally normal; can be taller • Turner Syndrome- inheritance of only one X • 98% spontaneously aborted • survivors are short, infertile females • Differences in mitosis and meiosis • chromosome number is halted in meiosis • mitosis produces genetically identical daughter cells • meiosis produces cells that are different from parent cells and each other • mitosis- one division resulting in two genetically identical cells • meiosis- two consecutive divisions resulting in four cells that are not genetically identical • 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 • 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 • 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 the 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 DNA primase synthesizes short RNA primers synthesizes DNA in the leading and lagging DNA polymerase strands, removes RNA primers, and ﬁlls in gaps covalently attaches adjacent Okazaki fragments in DNA ligase 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. • 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 • 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”. • 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 • 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 • 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 • 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 • 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 • 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 • 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 • 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 syndrome)- males can have an extra Y chromosome • generally normal • spontaneous generation- living organisms arise from inanimate material • biogenenis- life-from-life • Spontaneous generation was disproved which cause for new theories to come about. • big bang- 13.7 billion years ago, a dense mass of matter exploded in a “big bang”, resulting in the formation of atoms • solar nebular- the solar system was formed from large cloud gases and elements formed from previously existing stars • extraterrestrial- life came from other planets • deep-sea vent- key organic molecules originated from deep-sea vents • creationism- humans, life, the earth, and/or the universe as a whole were created by a supreme being or by another deity’s supernatural intervention • The Four Overlapping Stages Hypothesis • Stage 1: nucleotides and amino acids were produced prior to the existence of cells • Stage 2: nucleotides become polymerized to form RNA and/or DNA, and amino acids become polymerized to form proteins • Stage 3: Polymers became enclosed in membranes • Stage 4: Polymers enclosed in membranes acquired cellular properties • the fossil record • fossils are preserved remnants left by organisms that lived in the past • the relative ages of fossils can be determined by their locations in the rock layers • radiometric dating- can be used to get a more accurate age of fossils • Earth was formed about 4.55 billion years ago (bya) • Prokaryotes appeared about 3.5 bya • Prokaryotes that produced oxygen appeared about 2.4 bya • Single-celled eukaryotes evolved about 1.8 bya • multicellular eukaryotes appeared about 1.5 bya • all the major phyla of animals evolved about 630 million years ago (mya) • Plants and fungi colonized land, amphibians evolved from ﬁsh, and vertebrate life moved onto land about 520 mya • Environmental changes on earth have inﬂuenced the types of organisms that have existed during different periods of time • temperature- not only changes over time, but is also not uniform across the planet • atmosphere- started out with little to no oxygen and then about 2.4 bya, O 2 levels began to rise signiﬁcantly • landmasses- formation of landmasses surrounded by water resulted in two different environments, terrestrial and aquatic • ﬂoods and glaciations- effect living organisms in the vicinity of these events • volcanic eruptions- not only effects living organisms in the vicinity, but also can cause formation of new landmasses, such as islands • meteorite impacts- large meteorites can also effect living organisms in the vicinity, but can also effect surrounding landmasses and environment • Living things have several levels of organization • atoms > molecules > (organelles) > cells • tissues > organs > organisms • population > community > ecosystem > biosphere • atom- the smallest unit of an element; all matter is composed of atoms • molecule- a group of two or more atoms • organelle- structures or “organs” of the cell • cell- the simplest unit of life • tissue- many similar ells that perform a speciﬁc function • organ- several tissues performing a speciﬁc function • organism- an individual living “thing” made up of a collection of different organs • population- groups of interacting individuals of one species occupying the same environment/area • community- all organisms that interact with one another in a particular environment/ area • ecosystem- interactions of a community of organisms with their physical environment • biosphere- the worldwide ecosystem including the air, bodies of water, on the land, and in the soil • evolution- results from heritable changes in one or more characteristics of a population from one generation to the next • The better adapted individuals tend to survive and reproduce. • ﬁtness- a measure of an individual’s ability to survive and reproduce • natural selection- the process of differential survival and reproduction that inevitably leads to changes in allele frequencies over time as those individuals who are the most “ﬁt” survive and leave more offspring • phylogenetics- the study of evolutionary “relatedness” between different organisms • Evidence that supports the theory of evolution • fossils- provide information regarding evolutionary change in a series of related organisms • biogeography- the study of the geographical distribution of extinct and modern species • endemic- naturally found only in a particular location • convergent evolution- two different species from different lineages show similar characteristics because they occupy similar environments • selective breeding- programs and procedures designed to modify traits in domesticated species • homologies- fundamental similarity due to descent from a common ancestor • anatomical homology- the comparison of body structure between different species • developmental homology- the comparison of structures that appear during the development of different organisms • molecular homology- the comparison of cells and molecular information (DNA, RNA, and proteins) of different organisms • population genetics- the study of genes and genotypes in a population • gene pool- all of the alleles for every gene in a given population • polymorphism- traits display variation within a population • polymorphic gene- two or more alleles • monomorphic gene- predominantly single allele • single nucleotide polymorphisms (SNPs)- smallest type of genetic change in a gene; most common, 90% of variation in human gene sequence • Four evolutionary mechanisms that effect microevolution and bring the most genetic change • natural selection- the process in which individuals with certain heritable traits tend to survive and reproduce at higher rates than those without those traits • directional selection- shifts the frequency curve for variations in some phenotypic character in one direction or another; from rare to average • stabilizing selection- acts against extreme phenotypes; favors the survival of the more common intermediate variants (maintains the “status quo”) • diversifying selection- favors the survival of two or more variants of opposite extremes over the intermediate individual • balancing selection- does not favor the survival of one over the other, but maintains genetic diversity • sexual selection- results from individuals with certain traits being more likely to successfully reproduce than others • intrasexual selection- between members of the same sex; males compete • intersexual selection- between members of the opposite sex; female choice • genetic drift- the genetic ﬂuctuation due to random chance from one generation to the next • bottleneck effect- a sudden change in the environment (earthquake, ﬂoods, drought, etc) may drastically reduce the size of a population • founder effect- when a few individuals become isolated from a larger population and form a new colony in a new location • migration- the movement of individuals in or out of a population • gene ﬂow- genetic exchange due to the migration of fertile individuals or gametes between populations • nonrandom mating- occurs when the probability that two individuals in a population will mate is not the same for all possible pairs of individuals • inbreeding- individuals are more likely to mate with close relatives than with distant relatives • outbreeding- individuals are more likely to mate with distant relatives than with close relatives • species- a group of related organisms that share a distinctive set of attributes in nature • speciation- the formation of a new species • allopatric speciation- gene ﬂow is interrupted or reduced when a population becomes isolated from other populations • sympatric speciation- speciation takes place in geographically overlapping populations • Biologists use characteristics to identify a species • morphological traits- physical characteristics • reproductive isolation- prevents one species from successfully interbreeding with other species • prezygotic- before formation of a zygote • habitat isolation- two species encounter each other rarely, or not at all, because they occupy different habitats • temporal isolation- species that breed at different times of the day, different seasons, or different years • behavioral isolation- courtship rituals and other behaviors unique to a species act as reproductive barriers • mechanical isolation- morphological differences prevent successful mating • gametic isolation- two species attempt to interbreed, but the gametes one species may not be able to fertilize the gametes of another species • postzygotic- block development of a viable and fertile individual after fertilization • hybrid inviability- gamete of one species is fertilized by gamete from another species, but fertilized egg can’t develop past early embryonic stages • hybrid sterility- hybrid is viable, but sterile (mule) • hybrid breakdown- some ﬁrst-generation hybrids are fertile, but when they mate with another species or with either parent species, offspring of the next generation have genetic abnormalities that are lethal • molecular features- compare features to identify similarities and differences among different populations • ecological factors and evolutionary relationships- variety of factors related to an organism’s habitat can be used to distinguish one species from another • ecology- the study of the interactions of organisms with each other and their environment • abiotic interactions- between organisms and non-living environment • biotic interactions- all interactions between organisms • organismal ecology- individual organisms’ behavior, physiology, morphology, etc. in response to interactions with the abiotic environment • physiological ecology- how organisms are physiologically adapted to there environment and how the environment impacts the distribution of species • behavioral ecology- how the behavior of individual organisms contributes to their survival and reproductive success • population ecology- the factors which affect population composition, growth, size, and density • density- the number of organisms in a given unit, area, or volume • dispersion- the way individuals are spaced within the population’s living area • growth rate- the overall number of individuals (birth v death) • community ecology- interactions between populations of different species in a given area and their effects on structure and organization • ecological succession- the gradual and continuous change in a species composition of a community following a disturbance • primary succession- plants and animals invade on newly exposed sites where soil has not yet formed • secondary succession- occurs when a site has previously supported life but has undergone a disturbance that leaves soil intact/ present • ecosystem ecology- the responses and changes in the community as a result of interactions between • Hierarchical organization of living systems • atom > molecule > organelle > cell > tissue > organ > organism > population > community > ecosystem > biosphere • biome- a large, relatively distinct terrestrial region with speciﬁc characteristics • terrestrial biomes • tropical forests- warm and rainy, near equator • temperate forests- cold to hot, well deﬁned seasons • temperate coniferous forests- also known as taiga, largest; cold, short, wet seasons • grassland- dominated by grass • desert- hot days and cold nights • tundra- coldest of all biomes • mountain ranges- mountainous • aquatic biomes • marine- saltwater • the open ocean- largest, deep ocean • pelagic zone- includes those waters further from the land, basically the open ocean • benthic zone- the area below the pelagic zone, does not include the deepest parts of the ocean • abyssal zone- the deep ocean • intertidal zone- beach • coral reef- tropical, warm shallow waters • freshwater • lentic habitats- lakes (bigger) ponds (smaller) • lotic habitats- rivers and streams • wetlands- marshes, swamps, and bogs • biogeography- the study of geographic distribution of extinct and living species • populations can have different levels of dispersion • clumped distribution- individuals live close together in groups; this is the most common pattern • ransom distribution- individuals live at variable and random distances from one another; rare • key factor in population growth is how they reproduce • semelparity- “big bang” reproduction in which an individual produces a large number of offspring and then dies • iteroparity- individual produces only a few offspring during repeated reproductive episodes • Population growth depends on: • age of ﬁrst reproduction • frequency of reproduction • number of offspring produced • life span • death rate • ecological footprint- the environmental impact of an individual or a population • Population interactions help limit population growth • intraspeciﬁc- interactions between individuals of the same species • interspeciﬁc- interactions between individuals of different species • Several types of interactions • competition- an interaction between two or more species in which both organisms rely and compete for the same resources and are harmed to some extent • predation- the action of the predator results in the death of the prey • herbivory- the consumption of plant material by animals • symbiotic relationship- involves a symbiont, which lives off another species, called the host • parasitism- the symbiont feeds off another; beneﬁts at the host’s expense • mutualism- both species beneﬁt from one another • commensalism- one species beneﬁts and the other is unaffected • biodiversity- the diversity of life forms in a given location • genetic diversity- consists of the amount of genetic variation occurring within and between populations • species diversity- the number and relative abundance of species in a community • ecosystem diversity- the diversity of structure and function within an ecosystem • extinction- the process by which a species dies out • Four main human-induced threats to species • introduced species- those species moved by humans from a native location to another location • direct exploitation- hunting and ﬁshing of animals, birds, and ﬁsh • habitat destruction- altering the normal habitat by deforestation, agriculture crops, buildings, etc. • climate change- altering climate, atmosphere, and ecological systems reduce Earth’s capacity to sustain life • bioremediation- use of living organisms to detoxify polluted habitats