Final Exam Study Guide PDF

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Final exam study guide for bio 2...

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Exam 1 Chapter 13: Experiments Revealed the Function of DNA as Genetic Material ● Summary 13.1 ○ Griffith's Experiments ■ Done in the 1920’s, demonstrated that some substance in cells can cause heritable changes in another ○ Location and quantity of DNA suggested that DNA might be the genetic material ■ Avery and colleagues isolated the transforming principle from bacteria and identified as DNA ○ Hershey-Chase Experiments ■ Established conclusively that DNA (and not protein) is the genetic material, by tracing the DNA of radioactively labeled viruses, which were used to infect bacterial cells ○ Transfection (Insertion of recombinant DNA into animal cells) ■ Tra Genetic information and transfection can be studied with the aid of a genetic marker gene that confers a known and observable phenotype ● Summary 13.2: DNA has a structure the suits its function ○ Chargaff’s Rule ○ X-Ray diffraction ■ Shows the DNA molecule is a double helix ■ Watson and Crick proposed DNA is antiparallel ○ Reactive groups are exposed in the base pairs, allowing for recognition by other molecules such as proteins ● Summary 13.3: DNA is replicated semiconservatively ○ Meselson and Stahl ■ Showed DNA undergoes semiconservative replication ○ DNA Replication ■ The enzyme DNA polymerase catalyzes the addition of nucleotides to the 3’ end of each strand ■ The pre-replication complex is a huge protein protein complex that attaches to the chromosome at the ori ■ Replication proceeds from the ori on both strands in the 5’-3’ direction, forming a replication fork ■ Primase catalyzes the synthesis of a short RNA primer to which nucleotides are added by DNA polymerase ■ Telomeres ● Repetitive DNA sequences ○ Unless telomerase is present, a short segment at the end of each telomere is lost each time the DNA is replicated ● Summary 13.4: Errors in DNA can be Repaired ○ DNA polymerases make about one error in 1000,000 bases replicated ○ DNA can be repaired by: ■ Proofreading

■ Mismatch repair (mispaired bases) ■ Excision repair (removes damaged DNA and replaces it) ● Summary 13.5: The PCR Chain Amplifies DNA ○ Makes multiple copies of DNA ○ Used in fingerprinting Chapter 14 ● Summary 14.1 ○ Bread mold experiment led to the one-gene, one-enzyme hypothesis ■ Each gene only encodes a single polypeptide ● We now know this is a one-gene, one polypeptide relationship ● Summary 14.2: Information Flow from Genes to Proteins ○ Central Dogma ■ DNA encodes RNA, and RNA encodes proteins. Proteins don’t encode jawn. ○ DNA → RNA is transcription ○ RNA → Protein is translation ○ The product of transcription is messenger RNA. tRNA translate the genetic information in the mRNA into a corresponding sequence of amino acids to produce a polypeptide (in the ribosome) ○ Retroviruses don’t apply to the central dogma, they do reverse transcription ● Summary 14.3: DNA Is Transcribed to Produce RNA ○ RNA polymerase is the catalyst for transcription ■ RNA transcription from DNA proceeds in three steps: Initiation (the start), Elongation (the addition of monomers), and Termination (end) ○ Initiation requires a promoter, where RNA polymerase binds. This includes the initiation site ○ Elongation proceeds from 5’ to 3’ end ○ Particular bases specify termination ● Summary 14.4: Eukaryotic Pre-mRNA Transcripts Are Processed prior to Translation ○ Eukaryotic genes contain introns, which are non coding (these are transcribed, not translated) ○ Modified with 5’ cap and 3’ poly A tail ○ Pre-mRNA introns are removed via RNA splicing ● Summary 14.5: The information in mRNA is Translated into Proteins ○ Translation ■ Amino acids are ordered by the codons in mRNA ● This task is achieved by tRNA’s, each of which binds to a specific amino acid and has an anticodon complementary to an mRNA codon ○ Ribosome Sites ■ A site ● Where the charged tRNA anticodon binds ■ P site

● Where the tRNA adds it’s growing amino acid chain E site ● tRNA is released ○ Initiation Complex ■ Consists of tRNA bearing the first amino acid, small ribosomal unit, and mRNA ○ rRNA makes the peptide bonds between amino acids ○ Polysome: more than one ribosome moves along a strand of mRNA at one time ● Summary 14.6: Polypeptides Can Be Modified and Transported during or after Translation ○ Signal Sequences ■ Directs the protein to a specific organelle ○ Posttranslational Modifications ■ Proteolysis ● Polypeptide is cut into smaller fragments ■ Glycosylation ● Sugars are added ■ Phosphorylation ● Phosphate groups are added Chapter 15 ● Summary 15.1: Mutations Are Heritable Changes in DNA ○ Point mutations ■ Result from alterations in single base pairs of DNA ○ Silent mutations ■ Can occur in non coding or coding DNA regions ■ Do not affect the amino acid sequence ○ Missense ■ Changes the amino acid at that site ○ Nonsense ■ Prematurely terminates ○ Frameshift mutation ■ The addition or deletion, changes the whole protein ○ Chromosomal mutations ■ Deletions ● Loss of a segment, these will never revert to wild type ■ Duplications ● Segment is duplicated, often by a segment lost from its homolog ■ Inversion ● 180 degree reversal ■ Translocation ● In genetics, a rare mutational event that moves a portion of a chromosome to a new location, generally on a nonhomologous chromosome. ■

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Summary 15.2: Mutations in Humans Can Lead to Diseases ○ Point mutations, deletions and chromosome abnormalities are associated with genetic disease ○ Fragile X= expanding triplet repeat

Exam 2 Chapter 15: Mutations Can Be Detected and Analyzed ● Cleavage of DNA by restriction enzymes can be used to rapidly detect mutations ○ Bacteria defend themselves with restriction enzymes ■ Break the bonds of DNA backbone between the 3’ hydroxyl group of one nucleotide and the 5’ phosphate group of the next nucleotide ○ Recognition sequence or a restriction site ■ Usually palindromic (read the same way backwards and forwards) ● DNA Fingerprinting combines PCR with restriction analysis and electrophoresis ○ DNA Fingerprinting ■ Identifies individuals based on differences in DNA sequences ● Works best with sequences that are highly polymorphicsequences have multiple alleles ○ Single Nucleotide Polymorphisms ■ Inherited variations involving a single nucleotide base ■ Point mutations ○ Short Tandem Repeats ■ Short, repetitive DNA sequences that occur side by side on the chromosomes, usually in noncoding regions ● Contain 1 to 5 base pairs ● PCR is used to amplify both of these polymorphisms to distinguish individuals ● DNA analysis can be used to identify mutations that lead to disease ○ Clinical phenotypes of inherited diseases could be traced to individual proteins ■ The genes are then identified ● DNA testing is the most accurate way to detect abnormal genes ○ DNA testing: the direct analysis of DNA for a mutation ○ Only a couple cells are needed ○ Preimplantation screening is done rarely ● Genetic diseases can be treated ○ Diseases can be treated by modifying the phenotype ■ Done one of three ways: ● Restricting the substrate of a deficient enzyme ○ What they do for newborns with PKU

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Deficient enzyme: phenylalanine hydroxylase, and the substrate is phenylalanine ○ So, they go on a low phenylalanine diet ● Inhibiting a harmful metabolic reaction ○ Drugs used to treat symptoms ○ Targeted therapies ● Supplying a missing protein product ○ Human clotting proteins can be recreated through recombinant DNA Chapter 16: Regulation of Gene Expression ● Prokaryotic Gene Expression is Regulated in Operons ○ Gene expression begins at the promoter ■ This is where the RNA polymerase binds to initiate transcription ■ Not all promoters are active all the time ● Suggests that gene transcription must be selective ● The decision regarding which genes to activate involves two types of regulatory proteins that bind to DNA: repressor proteins and activator proteins ○ Negative regulation: ■ Binding of a repressor protein prevents transcription ○ Positive regulation ■ An activator protein binds DNA to stimulate transcription ● Operons are units of transcriptional regulation in prokaryotes ○ Structural Genes ■ Primary structures (amino acid sequences) of protein molecules that act as enzymes or cytoskeletal proteins ○ Operion ■ A cluster of genes with a single promoter ■ Regulated by an activator protein ● Regulating gene transcription conserves energy ○ Lactose is a B-galactosidase- disaccharide containing galactose B-linked to glucose ○ Three proteins are involved with the initial uptake and metabolism of lactose by E.coli ■ B-galactoside permease, a carrier protein in the bacterial cell membrane, moves sugar into the cell ■ B-galactoside is an enzyme that hydrolyses lactose to glucose and galactose ■ B-galactoside transacetylase transfers acetyl groups from acetyl CoA to certain B-galactosides

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When the cell has plenty of glucose, the levels of these proteins are very low But, if there is no glucose, all three will start to be made after a short lag period The response of the bacterial cell to lactose is at the level of transcription

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Inducers ■ Compound that stimulates the synthesis of a protein ● Proteins that are produced are called inducible proteins ● Proteins produced all the time at a constant rate of constitutive proteins Operator-Repressor interaction control transcription in the lac and trp operons ○ Lac Operon ■ Repressor protein binds ● When repressor is bound, the transcription of the operon is blocked ● Negative regulation ● Repressor proteins have two binding sites: ○ One for the operator and one for the inducer (allolactose) ■ Summary: ● When lactose is absent, the synthesis of enzymes for its metabolism is inhibited ● Lactose (the inducer) leads to the synthesis of the enzymes in the lactose-metabolizing pathway by binding to the repressor protein and preventing its binding to the operator ○ Other pathways are repressible ■ The repressor is not normally bound to the operator ● But if a co repressor binds to the repressor, the repressor changes shape and binds to the operator, thereby inhibiting transcription ● Ex. Trp ○ Trp operon is always going, but if you get enough from food, it can be repressed ■ In inducible  systems, the substrate of a metabolic pathway (the inducer) interacts with a regulatory protein (the repressor), rendering the repressor incapable of binding to the operator and thus allowing transcription. ● ■

Control catabolic pathways

In repressible systems, the product of a metabolic pathway (the co-repressor) binds to a regulatory protein, which is then able to bind to the operator and block transcription. ●

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Control anabolic pathways

Protein synthesis can be controlled by increasing promoter efficiency

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Negative control: transcription is decreased in the presence of a repressor protein

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Positive control: Increase transcription through the presence of an activator protein

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Second messengers increase the signal ■

Ex. cyclic amp

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Binds to cAMP receptor protein, producing a conformational change in CRP that allows it to bind to the lac promoter

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RNA polymerases can be directed to particular classes of promoters ○

Sigma factors ■

Proteins in prokaryotic cells that bind to RNA polymerase and direct it to specific classes of promoters

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General Transcription Factors Act at Eukaryotic Promoters ○

TATA Box ■

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Transcription Factors ■

Regulatory proteins that help control transcription

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General transcription factors allow RNA polymerase to bind

Specific protein-DNA interactions underlie binding ○

How does a protein recognize a sequence in DNA? ■

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Site where DNA begins to denature

Points exposed in the major and minor grooves

The Expression of sets of Genes can be Regulated by Transcription Factors

Exam 3 Chapter 20 ● Summary 20.1: Evolution is Both Factual and the Basis of Broader Theory

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Evolution is the genetic in populations over time. Evolution can be observed directly or with fossil evidence ● Summary 20.2: Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution ○ Mutation is the source of genetic variation ○ Adaptation: refers to both a trait that evolves through natural selection adn to the process that produces such traits ○ Gene Flow: Movement of individuals or gametes between populations ○ Bottleneck Effect: Occurs when few individuals survive a random event ○ Founder Effect: A population established by a small number of individuals colonizing a new region may lose ○ Non random mating results in changes in genotype and allele frequencies ● Summary 20.3: Evolution Can Be Measured by Changes in Allele Frequencies ○ Allele frequencies measure the amount of genetic variation in a population ○ Genotype frequencies show how a population’s genetic variation is distributed among its members ■ These together create a population’s genetic structure ○ Hardy Weinberg ● Summary 20.5: Multiple Factors Account for the Maintenance of Variation in Populations ○ What maintains a population? ■ Neutral mutations ● Neutral alleles do not affect the fitness or an organism, are not affected by natural selection, and may accumulate or be lost due to genetic drift ■ Sexual Recombination ● Countless genotypes ■ Frequency-dependant selection ● Polymorphism may be maintained by this ● When the fitness of a genotype depends on its frequency in the population ■ Heterozygote Advantage ● Fitness exceeds homozygotes ○ Clinical Variation: Changes in phenotype across a geographical area ● Summary 20.6: Evolution Is Constrained by History and Trade-Offs ○ Developmental processes constrain ○ Adaption impose costs as well as benefits Chapter 21: Reconstructing and Using Phylogenies ●

Summary 21.1: All of Life is Connected Through Its Evolutionary History ○ Taxa: Named species and groups ■ A taxon consists of an ancestor and all of its evolutionary descendants ● Called a clade^^ ○ Homologies: Similar traits that have been inherited from their common ancestor

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Synapomorphy: A derived trait that is shared by two or more taxa and is inherited from their common ancestor ○ Homoplasie: Not inherited from a common ancestor ■ Results from convergent evolution Summary 21.2: Phylogeny Can be Reconstructed From Traits of Organisms ○

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