Consider a solution prepared by mixing a weak acid HA and HCl. What are the major species? Explain what is occurring in solution. How would you calculate the pH? What if you added NaA to this solution? Then added NaOH?
genes & Evolution Chapters 14, 15.1 & 16.1, 20, 21, Chapter 14 Central Dogma of Molecular Biology Eukaryote Transcription occurs in the nucleus, translation occurs in the cytoplasm Deoxyribose Gene expression Is the process by which DNA directs the synthesis of proteins ( or in some cases, just the RNAs) Facts! ● Archibald Garrod was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell. ● The term codon is also used for the DNA nucleotide triplets along the nontemplate strand ● The ﬁrst codon was deciphered in 1961 by Marshall Nirenberg (UUU) The one gene–one protein hypothesis Based on results from work in their lab on nutritional mutants, Beadle and Tatum proposed that the function of a speciﬁc gene is to dictate production of a speciﬁc enzyme that catalyzes a particular reaction. states that the function of a gene is to dictate the production of a speciﬁc enzyme Transcription is the synthesis of RNA using information in the DNA. The two nucleic acids are written in diﬀerent forms of the same language, and the information is simply transcribed, or “rewritten,” from DNA to RNA messenger RNA (mRNA) because it carries a genetic message from the DNA to the proteinsynthesizing machinery of the cell. Translation is the synthesis of a polypeptide using the information in the mRNA.The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide Ribosomes are the translation sites primary transcript. The initial RNA transcript from any gene, including those specifying RNA that is not translated into protein is called primary transcript Triplet code The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, threenucleotide words. template strand it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript. codons The mRNA nucleotide triplets are called codons, and they are customarily written in the 5′→ 3′ direction RNA polymerase An enzyme called an RNA polymerase pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand. THEY DON’T NEED A PRIMER Promoter The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter terminator the sequence that signals the end of transcription transcription unit The stretch of DNA that is transcribed into an RNA molecule Facts! Bacteria have single type of RNA polymerase that synthesis not only mRNA but also other types In contrast, eukaryotes have at least three types of RNA Polymerase Transcription factors In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Transcription initiation complex The whole complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex RNA splicing A stage of RNA processing in the eukaryotic nucleus is the removal of large portions of the RNA molecule that is initially synthesized—a cutandpaste job Introns The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences, or introns. Exons The regions that code are called exons. THey are called exons because they are eventually expressed. Spliceosome The removal of introns is accomplished by a large complex made of proteins and small RNAs. Transfer RNA The message is a series of codons along an mRNA molecule, and the translator is called transfer RNA (tRNA). Main function is to transfer amino acids from cytoplasmic pool to growing polypeptide. Anticodon The particular nucleotide triplet that basepairs to a speciﬁc mRNA codon. Signalrecognition particle (SRP) The signal peptide, a sequence of about 20 amino acids at or near the leading end (Nterminus) of the polypeptide, is recognized as it emerges from the ribosome by a proteinRNA complex called a signalrecognition particle (SRP). This particle functions as an escort that brings the ribosome to a receptor protein built into the ER membrane. Mutations Responsible for the huge diversity of genes found among organisms because mutations are the ultimate source of new genes Point Mutations changes in a single nucleotide pair of a gene. Nucleotidepair Substitution replacement of one nucleotide and its partner with another pair of nucleotides Substitution Silent mutation which has no observable eﬀect on the phenotype Missense mutations Substitutions that change one amino acid to another one Nonsense Mutation a point mutation can also change a codon for an amino acid into a stop codon. Insertion or deletion Insertions and deletions are additions or losses of nucleotide pairs in a gene Frameshift The # of nucleotides inserted or deleted is not a multiple of three Immediate ( 1 pair insertion) Extensive (1 pair deletion) No frameshift (missing amino acid) Spontaneous mutations The incorrect base will be used as a template in the next round of replication, resulting in a mutation. Such mutations are called spontaneous mutations. The P site (peptidyltRNA binding site) holds the tRNA carrying the growing polypeptide chain, while the A site (aminoacyltRNA binding site) holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the E site (exit site). The nucleotide base triplets UAG, UAA, and UGA do not code for amino acids but instead act as signals to stop translation. ● In a bacterium, the RNA transcript is immediately usable as mRNA; in a eukaryote, the RNA transcript must ﬁrst undergo processing. ● eukaryotic promoter commonly includes a TATA box, ● During RNA processing, both ends of the primary transcript are altered. ● The 5′ end is synthesized ﬁrst; it receives a 5′ cap, a modiﬁed form of a guanine ● At the 3′ end, an enzyme adds 50–250 more adenine (A) nucleotides, forming a polyA tail. Chapter 15.1 and 16.1 This picture is about the tryptophan First, cells can adjust the activity of the enzymes that are already present Second, cells can adjust the production level of certain enzymes; that is, they can regulate the expression of the genes encoding the enzymes. One basic mechanism for this control of gene expression in bacteria, described as the operon model, was discovered in 1961 by François Jacob and Jacques Monod Operator The switch is a segment of DNA called an operator. Positioned within the promoter or, in some cases, between the promoter and the enzymecoding genes, the operator controls the access of RNA polymerase to the genes. Enchancer In genetics, an enhancer is a short (501500 bp) region of DNA that can be bound by proteins (activators) to activate transcription of a gene. These proteins are usually referred to as transcription factors. Operon DNA sequence on a prokaryotic chromosome including (in 3’ to 5’ order): a promoter, operator, enzymes Repressor The operon can be switched off by a protein called repressor Regulatory gene Changing the transcription or translation changes amount of mrna and potentially amount of proteins Inducible Gene Expression Transcription of the operon occurs when environmental conditions induce( turn on) transcription corepressor a small molecule that cooperates with a repressor protein to switch an operon oﬀ. Inducer Differentiation the process by which cells become specialized in structure and function. morphogenesis, The physical processes that give an organism its shape constitute morphogenesis, the development of the form of an organism and its structures. Cytoplasmic determinants Maternal substances in the egg that influence the course of early development Induction Such signals cause changes in the target cells, a process called induction Chapter 21 Microevolution We can deﬁne evolution on its smallest scale, called microevolution, as a change in allele frequencies in a population over generations. Genetic Variation Diﬀerences among individuals in the composition of their genes or other DNA sequences. HardyWeinberg principle Describes the expected frequency of genotype in a population for a single locus only with 2 alleles This principle states that the frequencies of alleles and genotypes in a population will remain constant from generation to generation, provided that only Mendelian segregation and recombination of alleles are at work(textbook version) Population A group of individuals of the same species that live in the same area and interbreed, producing fertile oﬀspring. Gene Pool consists of all copies of every type of allele at every locus in all members of the population. If only one allele exists for a particular locus in a population, that allele is said to be ﬁxed in the gene pool, and all individuals are homozygous for that allele. If multiple are present then individuals might be either homozygous or heterozygous. Conditions for HardyWeinberg Equilibrium Conditions for Microevolution Change in allele frequency in a population over generation A. Genetic Variation B. Random selection a. Genetic drift b. Gene flow C. Natural selection D. Sexual selection Genetic Variation Individuals of a population differ in their genetic make up 1. Mutation 2. Sexual reproduction a. Crossing Over b. Independent assortment of homologous chromosomes c. fertilization. Gene drift Random events that change allele frequency without regard to whether traits provide a reproductive advantage. 1. Genetic drift is significant in small populations 2. Can cause allele frequencies to change at random 3. Can lead to loss of genetic variation within populations 4. Can cause harmful alleles to become fixed founder eﬀect When a few individuals become isolated from a larger population, this smaller group may establish a new population whose gene pool diﬀers from the source population bottleneck eﬀect A sudden change in the environment, such as a ﬁre or ﬂood, may drastically reduce the size of a population. A severe drop in population size can cause the bottleneck eﬀect, so named because the population has passed through a “bottleneck” that reduces its size ● Bottlenecking a population tends to reduce genetic variation. Gene flow The transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes Occurs when conditions favor individuals at one extreme of a phenotypic range, thereby shifting a population’s frequency curve for the phenotypic character in one direction or the other Directional selection Disruptive selection Occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes Stabilizing selection Acts against both extreme phenotypes and favors intermediate variants. This mode of selection reduces variation and tends to maintain the status quo for a particular phenotypic character Selection pressure some aspect of the env’t that reduces survival & repro of a phenotype Chapter 20 Phylogeny Evolutionary relationships among organisms Inferred by comparing traits between potential close relatives classification Hierarchy of more inclusive categories Taxon Named unit at any level of hierarchy Kingdom > Phylum > Class > Order > Family > Genus > Species Sister Taxa groups of organisms that share an immediate common ancestor and hence are each other’s closest relatives Basal Taxa refers to a lineage that diverges early in the history of a group and hence, lies on a branch that originates near the common ancestor of the group. homologies phenotypic and genetic similarities due to shared ancestry are called homologies analogy A potential source of confusion in constructing a phylogeny is similarity due to convergent evolution Inferring relationships Comparing traits between potential close relatives 1. Morphology 2. Biochemistry 3. Pattern of embryonic development 4. DNA sequence data Basal Taxon outage Taxa that are each other's closest relatives because they share an immediate common ancestor. Cladistics common ancestry is the primary criterion used to classify organisms. Using this methodology, biologists attempt to place species into groups called clades, each of which includes an ancestral species and all of its descendants Shared ancestral character a character that originated in an ancestor of the taxon. Shared derived character an evolutionary novelty unique to a clade Characters different from ancestors and unique to the clade. Clade Complete group of descendents from a single ancestor. Outgroup An outgroup is a species or group of species from an evolutionary lineage that is known to have diverged before the lineage Parsimony Simplest explanation is the most likely