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Exam Study Guide

by: Nicole Hinds

Exam Study Guide BIL 250

Marketplace > University of Miami > Biology > BIL 250 > Exam Study Guide
Nicole Hinds
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Study Guide for Exam 1.
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Study Guide
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This 14 page Study Guide was uploaded by Nicole Hinds on Thursday October 23, 2014. The Study Guide belongs to BIL 250 at University of Miami taught by a professor in Fall. Since its upload, it has received 145 views. For similar materials see Genetics in Biology at University of Miami.

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Date Created: 10/23/14
21 Original thoughts o Pangenes Darwin thought genetic was circulated throughout the blood a Knew that genetic material must be a Stable source of info a Ability to repilicate accurately o Capable of change important Important Experiments ldentifvind Genetic material 0 Griffiths Transformation experiment 1928 0 transforming principle heat killed virulent mixed with non virulent still gives virulent o Wrong bc he thought the transforming agent was a IIIS protein a Oswald T Avery s Transformation experiment 1944 o Found that DNA was responsible for Griffith s results not RNA c When DNA was removed the IIIS wasn39t present in the product a RNAse and DNase used to cut RNA and DNA a Hersey and Chase Bacteriophage experiment 1953 0 Bacteriophage virus composed of DNA and protein that attacks bacteria and uses machinery to replicate a Found DNA 32P was the genetic material not protein 358 o More protein in chromosomes than DNA still the protein not found in the new phages o Hersey Nobel Prize in Physiology or medicine a Gierer and Schramm Tobacco Mosaic Virus experiment 1956 o Showed that RNA not protein was the viral genetic material No prokaryotes or eukaryotes use RNA was their genetic material a Ends are not the same 5 carbon on one end and 3 on the other 23 a Based on Chargaff s Base pair rules a GC vs AT varies less balances in humans a more GC means harder to separate strands influences gene expression usually balanced a g 50 and c t 50 differs because the less GC the easier it is to evolve Or express genes which is why humans are nice A binds T or U in RNA with 2 Hbonds while G binds C with 3 Hbonds 24 RNA is different from DNA is three ways 1 the sugar in RNA is ribose not dioxyribose 2 RNA is generally single stranded and not doublestranded and 3 RNA contains uracil in place of thymine DNA has adenine not 25 DNARNA Organization a Genome set of chromosomes containing all DNA of an organism o C value total amount of DNA in haploid 1 N genome of a species 0 Conserved in closely related organisms most mammals around 34 billion bp s a Not necessarily related to structure or organizational complexity a Viral chromosomes 0 Single or double stranded RNA or DNA can be circular or linear o Surrounded by proteins a Prokaryotic chromosomes a Double stranded usually circular chromosomes 0 Arranged in a dense clumped region called nucleoid no nucleus 0 Structure solutions for prokaryotes to compensate for no chromatin 0 Supercoilingz topoisomerases twist double helix around its own axis to relax or coil a T1 loosens with negative coils a T3 tightens with positive coils o Must be relaxed for replication andor transcription o Looped domains loops attached at base in unknown way a Eukaryotic chromosomes o Chromatin complex of DNA plus much more protein a Histones most abundant positive charge to bind to DNA charge 0 Involved with DNA expression a Evolutionarily conserved equal in mass to DNA 5 types a Non histones other proteins associated with DNA a Involved with chromatid structure and maintain protein scaffold o Packing of DNA in chromosomes a Level 1 wind DNA around histones to create nucleosomes a Level 2 nucleosomes connected by linker DNA like strings on a bead a Level 3 nucleosomes packed into chromatin fiber a Level 4 formation of looped domains Genes that are actively expressed have looser chromosomal structure Important regions of DNA highly conserved middle and ends a Centromeric DNA specialized sequenced at center of chromosome o Microtubules and spindle apparatus during mitosismeiosis o Telomeric DNA tandem repeats at ends of DNA a For replication and stability o More about DNA a Unique sequence single copy usually coding for a gene a Repetitive sequence can be short long or microsatellite o Microsatellitez common marker for genotyping for polymerase ex TTATTA 26 27 A List Eukaryotic cells have a true nucleus bound by a double membrane Prokaryotic cells have no nucleus The purpose of the nucleus is to sequester the DNArelated functions of the big eukaryotic cell into a smaller chamber for the purpose of increased efficiency This function is unnecessary for the prokaryotic cell because its much smaller size means that all materials within the cell are relatively close together Of course prokaryotic cells do have DNA and DNA functions Biologists describe the central region of the cell as its quotnuceoidquot oidsimiar or imitating because it39s pretty much where the DNA is located But note that the nucleoid is essentially an imaginary quotstructurequot There is no physical boundary enclosing the nucleoid Eukaryotic DNA is linear prokaryotic DNA is circular it has no ends Eukaryotic DNA is complexed with proteins called quothistonesquot and is organized into chromosomes prokaryotic DNA is quotnakedquot meaning that it has no histones associated with it and it is not formed into chromosomes Though many are sloppy about it the term quotchromosomequot does not technically apply to anything in a prokaryotic cell A eukaryotic cell contains a number of chromosomes a prokaryotic cell contains only one circular DNA molecule and a varied assortment of much smaller circlets of DNA called quotplasmidsquot The smaller simpler prokaryotic cell requires far fewer genes to operate than the eukaryotic cell Prokaryotic cells Most primitive earliest form of life Do not have a predefined nucleus Chromosomes are dispersed in the cytoplasm Contain no membranebound organelles Have circular chromosomes and lack histone proteins Most metabolically diverse Small typically 0220 micrometers in diameter Have a primitive cytosketetal structures or don39t have a cytoskeleton at all Smaller 708 ribosomes Don39t undergo meiosis but reproduce sexually by the transfer of DNA fragments through conjugation Eukaryotic cells More complex evolved organsims Contain true nuclei in which chromosomes are compacted as chromatin Contain membranebound organelles Have linear DNA and contain histone proteins Larger typically 10100 micrometers in diameter Have a complex cytosketeton Larger 808 ribosom Reproduce sexually with the use of meiosis 0 Meselon and Stahl experiment 1958 31 32 0 0 42 Started with heavy 15N for first generation then switched to light 14N DNA separates into bands in cesium chloride gradient After 1 cycle all had intermediate density excluding conservative model After 2 cycles half intermediate density and half light excluding dispersive model Semiconservative model proved However it quickly became apparent that 0 More than one gene can control each step in a pathway enzymes can be composed of two or more polypeptide chains each coded by a separate gene Many biochemical pathways are branched Modifications to Beadle Tatum formulation 0 One gene one polypeptide still not true 0 One gene can code several different polypeptides or RNA subunits Alternative splicing of exons 43 0 Some gene products transcribes to RNA tRNA rRNA snRNA and not proteins a RNA sequences also important for gene expression miRNA and siRNA o Noncoding sites for gene function ex Binding sites for transcription etc c Number of genes not important but expression is more essential Beadle Tatum experiment only represents the complex link between genes and gene products Sicklecell anemia OMIM141900 51 First described by J Herrick 1910 discovered that red blood cells RBCs change shape to form a sickle under low oxygen pressure Sickleshaped RBCs are fragile and less flexible than normal RBCs resulting in anemia blocking capillaries and damaging tissues One common form of the disease results from an amino acid substitution in the 6th amino acid of the chain of the hemoglobin molecule hemoglobins are composed of four polypeptides 2 and two chain each associated with a my Effects include anemia damage to the extremities heart lung brains kidney GI tract muscles and joints Heterozygotes produce both normal and sickleshaped RBCs and show a sicklecell trait but it is a much milder form of the disease Sicklecell trait also protects heterozygotes against malaria when the malarial parasite Plasmodium falciparum infects a sicklecell the RBC and parasite are destroyed resulting in a lower parasite count In tropical Africa as many as 2040 of people are heterozygotes Significance of ntrons lntrons are notjunk DNA They have important regulatory functions One of their primary attributes is that they enable the differential splicing of different exons result in different protein variants with different functional properties Multiple proteins from a single gene These patterns of gene regulation are as important as the genes themselves They can also regulate the rate of transcription and function as a point for recombination They can also be lost and gained making them a type of mobile genetic element External transcribed spacer ETS refers to a piece of nonfunctional RNA closely related to the internal transcribed spacer which is situated outside structural ribosomal RNAs rRNA on a common precursor transcript Internal transcribed spacer ITS refers to a piece of nonfunctional RNA situated between structural ribosomal RNAs rRNA on a common precursor transcript Read from 539 to 339 this polycistronic rRNA precursor transcript contains the 539 external transcribed sequence 539 ETS 18S rRNA ITS1 58S rRNA TS2 28S rRNA and finally the 339 ETS During rRNA maturation ETS and ITS pieces are excised and as nonfunctional maturation byproducts rapidly degraded Genes encoding ribosomal RNA and spacers occur in tandem repeats that are thousands of copies long each separated by regions of nontranscribed DNA termed intergenic spacer IGS or nontranscribed spacerNTS Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because it a is easy to amplify even from small quantities of DNA due to the high copy number of rRNA genes and b has a high degree of variation even between closely related species This can be explained by the relatively low evolutionary pressure acting on such nonfunctional sequences Spacer DNA are regions of nontranscribed DNA between tandemly repeated genes such as ribosomal RNA genes in eukaryotes Its function most likely involves ensuring the high rates of transcription associated with these genes In bacteria spacer DNA sequences are only a few nucleotides long In eukaryotes they can be extensive and include repetitive DNA comprising the majority of the DNA of the genome The term is used particularly for the spacer DNA between the many tandemly repeated copies of the ribosomal RNA genes 52 Posttranscriptional modification mRNA editincl o Adds or deletes nucleotides from a preRNA or chemically alters the bases so the mRNA bases do not match the DNA sequence Can results in the substitution addition or deletion of amino acids relative to the DNA template Generally cell or tissue specific Examples occur in protozoa slime molds plant organelles and mammals 54 mRNA differences between prokaNotesa1nd eukarvotg Prokaryotes o mRNA transcript is mature and used directly for translation without modification 0 Since prokaryotes lack a nucleus mRNA also is translated on ribosomes before it is transcribed completely ietg1nscription and translation are coupled 0 Prokaryote mRNAs are polycistronic they contain amino acid coding information for more than one gene Eukamotes o mRNA transcript is not mature premRNA must be processed 0 Transcription and translation are not coupled mRNA must first be exported to the cytoplasm before translation occurs 0 Eukaryote mRNAs are monocistronic they contain amino acid sequences forjust one gene In a prokaryotic cell transcription and translation are coupled that is translation begins while the mRNA is still being synthesized In a eukaryotic cell transcription occurs in the nucleus and translation occurs in the cytoplasm 61 Degeneracy is basically things that are different structurally but create the same results One of the reasons why the genetic code is degenerate is to allow for quotmistakesquot or quotmutationsquot from being fatal In some of the mutations sometimes you land on a amino acid with the same charge as before Hence degenerate code may minimize effect of a mutation on protein degenerate ie more than one codon specifies the same amino acid A practical consequence of redundancy is that errors in the third position of the triplet codon cause only a silent mutation or an error that would not affect the protein because the hydrophilicity or hydrophobicity is maintained by equivalent substitution of amino acids 62 Amino Acid Contains the following bonded to a central carbon atom 0 Amino group NH2 0 Carboxyl group COOH 0 Hydrogen atom 0 R group different in each amino acid 20 different amino acids occur in livinq cells 0 Abbreviated with 3 and 1letter codes 0 Classified into four chemical groups based on the composition of the R group 0 Acidic n 2 0 Basic n 3 0 Neutral and polar hydrophilic n 6 0 Neutral and nonpolar hydrophobic n 9 It is not known at least by me why there are 3 stop codons and why they are UAA UAG and UGA Code has start and stop signals ATG codes for E and is the usual start signal TAA TAG and TGA are stop codons and specify the the end of translation of a polypeptide 64 Proteins show four hierarchical levels of structural organization a Primam structure amino acid sequence Determined by the genetic code of the mRNA a Secondary structure folding and twisting of a single polypeptide chain Result of weak Hbonds and electrostatic interactions eg helix coiled and pleated sheet zigzag o Tertiary structure three dimensional shape or conformation of a single polypeptide chain Results from the different R groups 0 Quaternary structure association between polypeptides in multisubunit proteins eg hemoglobin Occurs only with two or more polypeptides 65 A frameshift mutation also called a framing error or a reading frame shift is a genetic mutation caused by indels insertions or deletions of a number of nucleotides in a DNA sequence that is not divisible by three Due to the triplet nature of gene expression by codons the insertion or deletion can change the reading frame the grouping of the codons resulting in a completely different translation from the original The earlier in the sequence the deletion or insertion occurs the more altered the protein A frameshift mutation will in general cause the reading of the codons after the mutation to code for different amino acids The frameshift mutation will also alter the first stop codon quotUAAquot quotUGAquot or quotUAGquot encountered in the sequence The polypeptide being created could be abnormally short or abnormally long and will most likely not be functional 66 According to the genetic code the cell would need tRNAs with 61 different anticodons to complement the available 61 codons However due to the degeneracy of the genetic code the third base is less discriminatory for the amino acid than the other two bases This third position in the codon is referred to as the wobble position At this position Us and Cs may be read by a G in the anticodon Similarly As and Gs may be read by a U or y pseudouridine in the anticodon 67 68 71 Lamarck thought adaptations could be passed on through inheritance but they cant Danvin knows it was passed down through genesinheritable traits 72 73 What is a mutation o Substitution deletion or insertion of a base pair Chromosomal deletion insertion or rearrangement Two tvloes of point mutations a Base pair substitutions o Transitions o Convert a purinepyrimidine to the other purinepyrimidine o 4 types of transitions A G and T C 0 Most transitions results in synonymous substitution because of the degeneracy of the genetic code a Transversions 0 Convert a purinepyrimidine to a pyrimidinepurine o 8 types of transversions A T G C A C and G T o Transversions are more likely to result in nonsynonomous substitution a Base pair deletions and insertions Terminoloqv describinq mutations in protgn codinq sequences Nonsvhonvmouslmissense mutation Base pair substitution results in substitution of a different amino acid Nonsense mutation Base pair substitution results in a stop codon and shorter polypeptide Neutral nonsvhonvmous mutation Base pair substitution results in substitution of an amino acid with similar chemical properties protein function is not altered Svnonvmou ent mutatii Base pair substitution results in the same amino acid Fimeshift mutations Deletions or insertions not divisible by 3 result in translation of incorrect amino acids stops codons shorter polypeptides or readthrough of stop codons longer polypeptides 74 Suppressor mutation Occur at sites different from the original mutation and mask or compensate for the initial mutation without reversing it 0 lrilqenic suppressors occur on the same codon eg nearby addition restores a deletion o rqenic suppressors occur on a different gene lnterqenic suppressor genes 0 Many function in mRNA translation 0 Each suppressor gene works on only one type of nonsense missense of frameshift mutation 0 Suppressor genes often encode tRNAs which possess anticodons that recognize stop codons and insert an amino acid a Three classes of tRNA nonsense suppressors one for each stop codon UAG UAA UGA tRNA suppressor genes coexist with wild type tRNAS tRNA suppressors compete with release factors which are important for proper amino acid chain termination 0 Small number of readthrough polypeptides are produced tandem stop codons UAGUAG are required to result in correct translation termination 77 Base analogs 0 Similar to normal bases incorporated into DNA during replication o Some cause mispairing eg 5bromouracil a Not all are mutagenic Base modi ing aqents act at anv stage of the cell cvcle o Deaminating agents a Hydroxylating agents a Alkylating agents lntercalating agents 0 Thin platelike hydrophobic molecules insert themselves between adjacent basepairs o Mutagenic intercalating agents cause insertions during DNA replication a Loss of intercalating agent can result in deletion o Examples proflavin ethidium bromide 78 DNA repair mechanisms Enzymebased repair mechanisms prevent and repair mutations and damage to DNA in prokaryotes and eukaryotes Tvpes of mechanisms a DNA polvmerase proofreadinq 3 5 exonuclease activity corrects errors during the process of replication 0 Photoreactivation also called light repair photolyase enzyme is activated by UV light 320370 nm and splits abnormal base dimers apart Demethvla ncl DNA reoair enzvmes repair DNAs damaged by alkylation Nucleotide excision repaiI39 NER Damaged regions of DNA unwind and are removed by specialized proteins new DNA is synthesized by DNA polymerase o Methvldirected mismatch repair removes mismatched base regions not corrected by DNA polymerase proofreading Sites targeted for repair are indicated in E coli by the addition of a methyl CH3 group at a GATC sequence


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