Compute the total energy of the signal f (t) = H(t)e2t .
BIOL 1362 Exam 3 Review Chapters 14, 15.1, 16.1, 20, and 21 Chapter 14 Gene transcription and translation Fig. 14.24 pg 287 T ranscription (prokaryotic cell) 1. Initiation • After RNA polymerase binds to the promoter, the DNA strands unwind and the polymerase initiates RNA synthesis at the start point on the template strand 2. Elongation • The polymerase moves from 3’5’ of template DNA strand, unwinding the DNA and elongating the RNA transcript 5’3’. • In the wake of transcription, the DNA strands re-form a double helix 3. Termination • Eventually the RNA transcript is released and the polymerase detaches from the DNA T ranscription (eukaryotes) 1. Initiation • Eukaryotic promoter usually includes a TATA box about 25 nucleotides from the transcriptional start point (TATA is the nucleotide sequence of the NONtemplate strand) 2. Elongation • Several transcription factors, one recognizing the TATA box, must bind to the DNA before RNA polymerase II can bind in the correct position and orientation 3. Termination • Additional transcription factors bind to the DNA along with RNA polymerase II forming the transcription initiation complex. RNA polymerase II then unwinds the DNA double helix, and RNA synthesis begins at the start point on the template strand T ranslation 1. Initiation • Small ribosomal subunit binds to a molecule of mRNA • An initiator tRNA with the anticodon UAC base pairs with the start codon AUG. this tRNA carries the amino acid methionine (Met) • required to bring all the translation components together; hydrolysis of GTP provides the energy for the assembly • The initiator tRNA is in the P site, the A site is available for the tRNA bearing the next amino acid 2. Elongation • The anticodonof an incoming tRNA base-pairs with the comp. mRNA codon in the A site; hydrolysis of GTP increases accuracy and efficiency of this step • An rRNA molecule of the large ribosomal subunit catalyzes formation of a peptide bond between the amino step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site • The ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA mofes along with its bound tRNAs, bringing the next codon t be translated into the A site. • Ribosome moves 5’3’ on mRNA 3. Termination • When a ribosome reaches a stop codon on the mRNA, the A site of the ribosome accepts a “release factor” (a protein shaped like a tRNA) instead of an aminoacyl tRNA • the polypeptide->freeing the polypeptide from the ribosome subunits dissociatete and the last amino acid of Limiting molecules-T ranscription • If RNA polymerase was limited, mRNA could not be made (as much) nucleotides complementary to the DNA template strandg would be adding • If there were no transcription factors in a eukaryotic cell, there would be nothing to mediate the binding of RNA polymerase and the initiation of transcription; without the transcription factors attached to the promoter, RNA polymerase II will not bind to it. RNA polymerase II unwinds the DNA double helix, which is needed to start RNA synthesis • If there is no polyadenylation signal (AAUAAA) in the pre-mRNA, RNA polymerase will not stop adding nucleotides to the mRNA and transcription keeps going Limiting molecules-T ranslation • Transfer RNA is needed to bring the corresponding anticodon/amino acid combination to the ribosomal complex to create the polypeptide chain, so tRNA is necessary for translation to even occur; limited amounts of tRNA would mean less polypeptide chains that would become proteins • Ribosomes are needed to be in abundance to aid translation of the mRNA; the more ribosomes, the more copies of the proteins Misc. • Multiple copies of a protein molecule can be made from one molecule of mRNA if there are multiple ribosomes attached to it at the same time forming polyribosomes • Transcription and translation occur in all organisms Chapter 15.1 and 16.1 Gene expression Gene regulation • Changing transcription changes amount of mRNA and potentially amount of protein • Changing translation changes amount of protein • Enzymes, cytoskeleton, receptors for chemical signals, signaling molecules (ex. Glucose changeinsulin) are all made of proteins Inducible Regulation in Prokaryotes • Inducible: transcription of the operon occurs when environmental conditions induce (turn ON) transcription • Ex. Lactose • Gene expression is usually “off” because a repressor protein is present attached to operator, blocking transcription • If an inducer binds to the repressor protein, it can no longer attach to the operator • Gene expression now “on” and transcription of genes in the operon proceeds Gene Regulation in Eukaryotes • 3 ways to change Eukaryotic gene expression 1. Chromosome structure • Chemical changes to histone proteins or to DNA can alter transcription rate • Htranscription- DNA unfolds, allows RNA polymerase to start transcriptionbinding between nucleosomes INCREASES • DNA methylation: enzymes add methyl groups to cytosine in DNA DECREASE transcription of heavily methylated genes 2. Transcription Factors • Proteins that interact with control elements of genes • Can enhance or reduce rate of transcription • General transcription factors needed for all promoters • Activators and enhancers are specific transcription factors • Transcription factors present differ between cell types which results in cell type-specific gene expression 3. Translation (Post-transcriptional regulation) • Regulation occurs most commonly at initiation stage of translation • The initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structures within the 5’ to 3’ UTR, preventing the attachment of ribosomes T ranscription Factors • Proteins that interact with control elements of genes • General transcription factors needed for all promoters in eukaryotes • Activators and enhancers are specific transcription factors • for transcription factorsach to DNA at control elements (response element)- specific binding sites • Enhance or reduce interaction of RNA polymerase with the promoter • General transcription factors: can interact with promoters of any protein-coding genes • Specific transcription factors: works only on specific promoters • Transcription factors differ between cell types which results in cell-type specific gene expression • Ex. Gene for albumin expressed in liver cells but not in lens in eye due to which transcription factors are there • Homeotic genes=hox genes- genes that control anterior-posterior position of limbs, development of digits and organs • domain in the transcription factor proteince that codes for the homedomain which is the DNA binding Gene expression • The example in class was the girl eating the donut so her blood glucose level went up so insulin needed to be made to counteract this physiological change and return the body to homeostasis Chapter 20 Phylogeny Structurally similar characteristics • Homology- share recent common ancestor which is why they share the characteristic • Analogy- have similar characteristic developed by similar selection pressures, NOT due to a recent common ancestor (2 unrelated organisms having same structure due to a similar need for the same structure) Chapter 21 Population Evolution Natural Selection Conditions for microevolution Microevolution- change in allele frequency in a population over generations • Genetic variation • Random selection • Genetic drift • Gene flow • Natural selection • Sexual selection Random vs. Adaptive Evolution Natural Selection Random Evolution • Those who inherit traits that are • A random event/cause that does suitable to the current, local not choose a trait most suitable environment strive and for the environment; purely a reproduce more than those who chance type of evolution do not have traits favorable to the environment the population is in Sources of Genetic Variation • Mutation- a change in the nucleotide sequence of an organism’s DNA or in the DNA or RNA of a virus • Creates a new allele for a certain character in a population • Independent assortment at metaphase I- the position homologous chromosomes align at the metaphase plate in meiosis • Gives many possibilities for offspring depending on which way the chromosomes are lined up • Crossing over- the reciprocal exchange of genetic material between nonsister chromatids during prophase I of meiosis • Creates genetic variation through exchange of genes so every chromosome is different • Fertilization- the union of haploid gametes to produce a diploid zygote •(parents) a unique combination of genetic material from 2 separate organisms Alleles in a population vs Individual • A diploid organism can only have 2 alleles for any gene, no matter how many alleles in the population there are. • For example, hair color: one person can have blonde, another brown, another red, black, etc. but each person will only have 2 alleles that code for one of those specific colors. • A redhead could have RR while someone with brown hair could have Bb • Even though they are the same gene, there are 3 different alleles right there but each person can only have 2 Genetic drift • Random events that change allele frequency without regard to whether traits provide a reproductive advantage [sudden environmental change] • Hurricane • Fire • Isolation from other members of same species • Founder effect: portion of a population found in a new colony • Alleles in founding population are present by chance • Bottleneck effect: population size is drastically reduced • Allele frequency changes drastically from 1 generation to the next • Population stays in the same place Chapter 23 Macroevolution: the broad pattern of evolution above the species level Radiometric Dating • A method for determining the absolute age of rocks and fossils, based on the half-life of radioactive isotopes • Half-life: time for 50% of a substance to decay • Half life of carbon-14: 5,730 years • up to 75,000 years oldarbon-14 to carbon-12 in an organism to tell its age • longer half lives75000 years old, use isotopes with • U-238 decomposes to Pb-206; half life= 4.5X10^9 yr • Organisms don’t contain U-238use sandwich dating by dating rocks above and below fossil • K-40 decomposes to Ar-40; half life=1.5X10^9 yr Oxygen Production- Cambrian explosion • Fossils from Cambrian explosion are bilaterians • Arose sometime between 670 and 635 million years ago • Diversified explosively during the Cambrian and beyond possibly aided by rise in atmospheric concentration of oxygen • Entirely new sorts of animals “made their debut” during the explosion • Adaptive changes to some species occurred • Changes set the stage for many key events in the history of life over the last 500 million years • Decline in diversity of Ediacaran life-forms • increase of atmospheric oxygen preceded the Cambrian explosion • More plentiful oxygen would have enabled animals with higher metabolic rates and larger body size to thrive while potentially harming other species 3 Domains of life Endosymbiont Theory • Mitochondria and plastids (chloroplasts and related organelles) were formerly small prokaryotes that began living within larger cells • Archael host cell ingested but did not digest another cell (alpha proteobacterium) • 2 cells formed a symbiotic relationship • Evidence: • Replication, transcription, and translation are similar in Archaea and Eukarya • Mitochondrial genome and translation system similar to proteobacteria Shared derived Characteristics- Plants Shared derived characteristics- Animals 1. Collagen 2. Gastrulation 3. Radial symmetry 4. Bilateral symmetry 5. Digestive tract forms from mouth (1 ) to anus (2 ) = protostome 6. Digestive tract forms from anus (1 ) to mouth (2 ) = deuterostome 7. Grow by shedding exoskeleton = ecdysis (molting) Vocabulary • Pyrimidine- single ring nitrogenous base • Purine- double ring nitrogenous base • 3’ end of nucleotide- OH end • 5’ end of nucleotide- free end • Anti-parallel- oriented in opposite directions as each other • Transcription- synthesis of RNA using DNA template • RNA polymerase- an enzyme that links ribonucleotides into a growing RNA chain during transcription, based its 5’3’ direction but it doesn’t need a primer like DNA polymerase doesy assemble a polynucleotide in • Translation- synthesis of a polypeptide using the genetic information encoded in an mRNA molecule; there is a change of “language” from nucleotides to amino acids • Codon- a 3-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code • Transfer RNA- an RNA molecule that functions as a translator between nucleic acid and protein languages by carrying specific amino acids to the ribosome, where they recognize the appropriate codons in the mRNA. • Ribosome- a complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large subunit and a small subunit; in eukaryotic cells, each subunit is assembled in the nucleolus • Acomplementary codon on an mRNA moleculeend of a tRNA molecule that base-pairs with a particular • Operon- a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway • Operator- in bacterial and phage DNA, a sequence of nucleotides near the start of an operon which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon • Enhancer- a segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates • Transcription factor- a regulator protein that binds to DNA and affects transcription of specific genes • Cytoplasmic determinant- a maternal substance, such as protein or RNA, that when placed into an egg influences the course of early development by regulating the expression of genes that affect the developmental fate of cells • Inductive signal- chemical signals secreted by neighboring cells that continue the process of cell differentiation by turning on transcription of specific genes, providing position information to each cell, influencing its differentiation into a specific type of cell • Morphogenesis- the development of the form of an organism and its structures • Evolution- descent with modification; the idea that living species are descendants of ancestral species that were different from the present-day ones; also defined more narrowly as the change in the genetic composition of a population from generation to generation • Homology- similarity in characteristics resulting from a shared ancestry (recent common ancestor) • Analogy- similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait • Biogeography- the scientific study of the past and present geographic distributions of species • Gene pool- the aggregate of all copies of every type of allele at all loci in every individual in a population; also used in a more restricted sense as the aggregate of alleles for just one or a few loci in the population • Locus- a specific place along the length of a chromosome where a given gene is located • Gene- a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses) • Allele- any of the alternative versions of a gene that may produce distinguishable phenotypic effects • Selection pressure- condition that affects survival and reproduction • Stabilizing selection- natural selection in which intermediate phenotypes survive or reproduce more successfully than do extreme phenotypes • Disruptive selection- natural selection in which individuals on both extremes of a phenotypic range survive or reproduce more successfully than do individuals with intermediate phenotypes • Directional selection- natural selection in which individuals at one end of the phenotypic range survive or reproduce more successfully than do other individuals • Gone generation to the next; effects of genetic drift are most pronounced in small populationsquencies from • Founder effect- genetic drift that occurs when a few individuals become isolated from a larger population and form a new population whose gene pool composition is not reflective of that of the original population • Bottleneck effect- genetic drift that occurs when the size of a population is reduced, as by a natural disaster or human actions; typically, the surviving population is no longer genetically representative of the original population • Parsimony- simplest explanation, fewest changes • Sclosest relativess of organisms that share an immediate common ancestor and hence are each other’s • Outgroup- a species or group of species from an evolutionary lineage that is known to have diverged before closely related to the group of species being studied, but not as closely related as any study-group memberse are to each other • Shared ancestral character- a character that is shared by members of a particular clade but that originated in an ancestor that is not a member of that clade • Shared derived character- an evolutionary novelty that is unique to a particular clade • Cyanobacteria- photoautotrophs that are the only prokaryotes with plantlike, oxygen-generating photosynthesis • Radiometric dating- a method for determining the absolute age of rocks and fossils based on the half-life of radioactive isotopes • Half-life- the amount of time it takes for 50% of a sample of radioactive isotope to decay • Endosymbiosis- a mutually beneficial relationship between 2 species in which one organism lives inside the cell or cells of another organism • Archea- one of the 2 prokaryotic domains, the other one being Bacteria Transcription Translation Where it occurs Nucleus Cytoplasm Molecules • RNA polymerase • mRNA • DNA template strand (transcription unit) • Ribosomes • Promoter • tRNA • Terminator • Amino acids • Enzyme for termination in eukaryotes Template Molecule DNA Template strand mRNA New molecule made mRNA Amino acids Purpose Make RNA from DNA template that will Produce polypeptide chain of amino eventually code for a protein acids (protein) Phase of cell cycle where itInterphase- G’s (G1 and G2) occurs Chromosome structure Extended during process