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Final Exam Study Guide

by: Danielle Thomas

Final Exam Study Guide BIOSC 0160

Marketplace > University of Pittsburgh > Biology > BIOSC 0160 > Final Exam Study Guide
Danielle Thomas
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Foundations of Biology 2
Dr. Hale
Study Guide
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This 10 page Study Guide was uploaded by Danielle Thomas on Sunday April 24, 2016. The Study Guide belongs to BIOSC 0160 at University of Pittsburgh taught by Dr. Hale in Spring 2016. Since its upload, it has received 7 views. For similar materials see Foundations of Biology 2 in Biology at University of Pittsburgh.


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Date Created: 04/24/16
▯ ▯ ▯ DNA SYNTHESIS ▯ Hershey Chase experiment – all radioactive protein was outside the cell in the capsid and radioactive DNA was inside the cell  genes are made from DNA ▯ Semi-conservative replication: each parental strand from DNA separates and is used as a template to make new daughter strands ▯ DNA Polymerase 3: only works in 5’  3’ direction, new nucleotides added to 3’ end  DNA Polymerase 1: uses RNA primer on lagging strand to add new DNA, removes primer on Okazaki fragment and adds DNA ▯ Replication fork: where parent DNA is split into two single strands ▯ DNA Helicase: breaks hydrogen bonds ▯ Single Stranded DNA-Binding Proteins (SSBPs): attach to single DNA strands to prevent them from snapping back together ▯ Primase: RNA Polymerase that synthesizes short stretch of RNA to act as a prime for DNA Polymerase 1 ▯ Leading Strand: toward the replication fork, continually synthesized ▯ Lagging Strand: away from the replication fork  DNA Polymerase 1  Okazaki Fragments: short DNA fragments that have primers  DNA ligase: binds together Okazaki fragments ▯ Replisome: macromolecule machine for DNA synthesis ▯ Telomere: end of eukaryotic chromosome  Telomerase: adds DNA to the end of a chromosome to prevent shortening, only in cells that make gametes  Somatic cell chromosomes shorten as someone ages  Prokaryotes don’t have this because their chromosomes are circular ▯ Nucleotide Excision Repair: works on DNA damaged by ultraviolet light  UV causes Thymine to pair with itself instead of Adenine ▯ If there are repeats in the DNA sequence, there could be loops that make DNA Polymerase skip the loop and cause deletions ▯ ▯ Start Codon: AUG, Methionine ▯ Stop Codon: UAA, UAG, UGA ▯ Point mutation: single base change  Missense mutation: changes amino acid sequence – can be beneficial, deleterious or neutral  Silent mutation: does not change amino acid sequence, neutral ▯ Frameshift mutation: single addition or deletion, changes the reading frame, always deleterious ▯ Nonsense Mutation: amino acid is changed by a mutation that changes it to a stop codon, makes nonfunctional proteins, always deleterious ▯ Chromosome mutations  Inversion: chromosome segments break, flip and rejoin the chromosome  Translocation: chromosome segments detach and add to a different chromosome  Deletion  Duplication ▯ ▯ ▯ ▯ TRANSCRIPTION – DNA  RNA ▯ Coding Strand: RNA sequence that codes for a polypeptide ▯ Transcription in Bacteria  Initiation Phase: sigma must bind to DNA first and RNA Polymerase to begin transcription o Sigma guides RNA Polymerase to promoters to start transcription o Promoters: section of DNA that promotes the start of transcription  -35 Box TTGAC, -10 Box TATAAT o Transcription only begins in bacteria when sigma binds to the -35 and -10 boxes  Elongation Phase: RNA Polymerase begins moving along the DNA template, synthesizing RNA  Termination Phase: forms hairpin and RNA Polymerase is interrupted  Produces mature RNA – ready for translation ▯ Transcription in Eukaryotes  RNA Polymerase 2 transcribes protein coding genes  TATA box: basal transcription factor, promotes transcription o Basal transcription factor: assemble at the promoter, followed by RNA Polymerase, non-specific  Primary Transcript: initial product of transcription, must undergo processing before translation – Pre-mRNA o RNA Processing: modifications to RNA to convert pre-mRNA to mature mRNA  Splicing: introns are removed, happens in the nucleus  Exons: genes that are part of the mature mRNA  Introns: sections of genes that are removed before mature mRNA is made  snRNPs: catalyzes splicing of pre-mRNA  Spliceosome: complex of snRNPs o Mature mRNA: has 5’ cap and 3’ tail to protect mRNA from being degraded  5’ cap: modified Guanine  3’ tail: repeating Adenines ▯ ▯ Control of Gene Expression in Bacteria ▯ Transcriptional control: affect RNA Polymerase’s ability to bind to a promoter that stops transcription  make no mRNA ▯ Translational control: regulatory molecules alter the length of time an mRNA survives to affect translation or elongation  prevent mRNA from being translated to a protein ▯ Post-Translational control: chemical modifications of proteins  turn off protein ▯ Constitutively: transcribed all the time – proteins always needed ▯ Inducer: triggers transcription of a specific gene  Ex: high levels of lactose trigger B-galactosidase to be made in E.Coli – controlled by lacZ gene in the lac operon ▯ Negative control of transcription: repressor binds to DNA and shuts down transcription ▯ Positive control of transcription: activator binds to DNA and triggers transcription ▯ Operon: set of coordinately regulated Bacterial genes – transcribed together into one mRNA  Lac operon: involved in lactose metabolism  Operator: where repressor binds o Lactose is the repressor in the lac Operon  Ara operon: example of positive control for arabinose o araC: activator and repressor ▯ Cotranscription: adjacent genes and are transcribed into one mRNA and initiated from one promoter – coordinated expression ▯ Inducer exclusion: prevents transport of inducer into the cell ▯ Regulon: set of separate genes that contain the same regulatory sequence and are controlled by the same regulatory protein ▯ ▯ Control of Gene Expression in Eukaryotes ▯ Differential gene expression: creates different cell types ▯ Control in the nucleus – Transcriptional Control  1. Chromatin Remodeling: promoter must be released from chromatin to start transcription o Nucleosome: DNA wrapped around histones o Chromatin must be decondensed to expose the promoter  When DNA is in chromatin, genes are turned off o Methylation: trigger chromatin condensation  No methyl = decondensed, transcribed  Methyl = condensed, not transcribed o Acetylation: trigger decondensation  No acetyl = condensed, not transcribed  Acetyl = decondensed, transcribed o Epigenetic inheritance – DNA methylation and histone modifications are inherited due to something other than DNA differences  Allows a cell to pass on its modifications so the same cell type is produced  2. Transcriptional Control o Promoter-Proximal Elements: close to the promoter and bind to regulatory proteins o Regulator Transcription factors: enhancers and silencers are places for activators and repressors to bind, specific to a gene  Enhancers: far from the promoter, activate transcription  Transcriptional activators: bind to enhancers and begin transcription – positive control  Silencers: inhibit transcription, repressors bind and stop transcription – negative control o Basal transcription factors: interact with the promoter but are not specific to particular genes – TATA binding protein  3. RNA Processing – Post-Transcriptional Control o Splicing o Alternative Splicing: splicing the same primary transcript in different ways to make different mature mRNA that makes different proteins  90% of Human genes have alternative splicing – allows one sequence of gene to make many different proteins – why Eukaryotes don’t need more genes than Prokaryotes ▯ ▯ ▯ TRANSLATION – mRNA  PROTEIN ▯ Translation in Bacteria – can happen at the same time as translation because bacteria do not have a nuclear envelope to separate the two events  Polyribosome: multiple ribosomes attach to each mRNA to synthesize proteins ▯ ▯ ▯ ▯ Translation in Eukaryotes – transcription is inside the nucleus and translation is in the cytoplasm Initiation Phase o Shine Dalgarno Sequence: mRNA where rRNA in the small ribosomal subunit binds o Initiation factors: bind first aminoacyl tRNA to the ribosome Elongation Phase o P site is filed by the start codon o Translocation: elongation factors move the ribosome in the 5’  3’ direction of the mRNA Termination Phase o Release factor: when translocation reaches a stop codon it fills the A site so the polypeptide is freed  tRNA: transfer RNA, transfers amino acids to growing polypeptide, interpreter during translation o CCA Sequence: allows amino acid attachment, at the 3’ end o Anticodon: ribonucleotides that form base pairs with the mRNA codon o Aminoacyl tRNA: catalyze the addition of amino acids to tRNA  There are different synthases for each of the 20 amino acids  Wobble hypothesis: nonstandard base pairs with tRNA in the third position of the codon – G-U or C  Ribosomal RNAs: in the ribosome  Ribosomal Synthesis of Protens o 1. Aminoacyl enters the A site, anticodon matches codon in mRNA  A site: receptor for aminoacyl tRNA, carries amino acid o 2. Peptide bond forms between the amino acid held by the aminoacyl tRNA in the A site and the polypeptide chain in the P site  P site: peptide bond formation o 3. Ribosome moves down the mRNA by one codon  E site: exit o Starts at N-terminus (amino) and ends at C-terminus (carboxyl)  Molecular chaperones: fold a new protein into a shape so it can function ▯ Control in the Cytoplasm – Post-Transcriptional Control  1. mRNA Stability o RNA interference: destruction of mRNA or blocks translation o RNAi: interference RNA  Exact match = cut RNA in two  Not exact match = inhibit translation  2. Translational Control  3. Post-Translational Control – Modifications o Chaperone proteins, phosphorylation ▯ ▯ Shotgun sequencing: break a genome and sequence fragments, look for overlapping parts and put the fragments back together to get the entire genome ▯ ▯ Genome Annotation ▯ In bacteria  Identify open reading frames – look for start codon, promoters, regulatory sites  Homology: similar base sequences equal genes in different species due to a common ancestor ▯ In Eukaryotes  Make Expressed Sequence Tag (EST) – isolate mRNA, use reverse transcriptase, make cDNA, sequence a portion, find the matching sequence in the DNA and find the gene ▯ Prokaryotic Genomes  Linear relationship between genome size and gene number  Lateral Gene Transfer: movement of DNA from one species to another o Genes are more similar to genes in distantly related species than closely related ones ▯ Eukaryotic Genomes  Larger than bacteria  Have introns – not uninterrupted coding sequences  Transposable elements: segments of DNA that are capable of being inserted into new locations in a genome o Long Interspersed Nuclear Element (LINEs): use reverse transcriptase  Microsatellites: repeating unit 2-6 bases long  Minisatellites: repeating units 6-100 bases long  Unequal crossover: micro/minisatellites have many different alleles o Homologs line incorrectly during prophase of meiosis 1  DNA Fingerprinting: identifying individuals based on unique features of their genomes – use micro/minisatellites ▯ ▯ Population: individuals of the same species living in the same area at the same time ▯ Homology: similarity due to a common ancestory  Genetic homology: similarity in DNA/RNA/amino acids  Developmental homology: vestigial traits o Vestigial traits: incompletely developed structure that has no function but is similar to a functioning structure in a relative  Structural homology: similarity in adult morphology ▯ Fitness: ability of an individual to produce surviving, fertile offspring relative to the population ▯ Adaptation: heritable trait, increases fitness ▯ ▯ Evolution: change in allele frequency over time  1. Natural Selection  2. Gene Flow: leaving one population, reproducing and joining another  3. Genetic Drift: change in allele frequencies randomly  4. Mutation: makes new alleles ▯ Hardy-Weinberg Hypothesis – tests whether evolution is occurring  Allele frequencies – # copies of allele of interest / total # alleles o P+Q=1  Genotype frequencies – # individuals with genotype / total # individuals o P^2 + 2PQ + Q^2 = 1  Assumptions o 1. Random mating o 2. No natural selection o 3. No genetic drift o 4. No gene flow o 5. No mutation  Ways to violate o 1. Nonrandom mating  Inbreeding – changes genotype frequencies, not allele frequencies, increases homozygosity  Sexual selection – changes allele frequencies and genotype frequencies, females invest more into offspring so they are picky with their mate o 2. Natural Selection: certain characteristics produce more offspring than individuals without those characteristics  1. All individuals do not look alike  2. Trait differences are heritable  3. Resources are finite  4. Certain variations will reproduce and survive better than others  Makes change in frequency of alleles  Directional Selection: change average value of trait – decreases genetic diversity, selection for extreme phenotype


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