Bio Exam 3

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Bio Exam 3
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2010-11-22 00:59:17
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Exam 3
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  1. Griffith (1928)
    showed evidence of a 'transforming principle'
  2. Avery, et al (1944)
    followed up on this to find that the 'transforming principle' was DNA
  3. Chargaff (1950)
    discovered the startling ratio of A:T and G:Cs
  4. Hershey and Chase (1952)
    provided additional evidence that DNA was genetic material (at least in T2 bacteriophages!)
  5. Watson and Crick (1953)
    developed DNA double helix model based on others'evidence
  6. Helicase
    unwinds the DNA
  7. Primase
    creates a short RNA fragment called a "primer"
  8. DNA polymerase
    synthesizes new DNA by connecting nucleotides into a chain
  9. Ligase
    joins the new DNA strands together
  10. What kinds of bonds is the helicase breaking?
    hydrogen bonds
  11. What is the advantage of multiple origins of DNA replication in eukaryotes?
    Faster
  12. Topoisomerase
    untangles the DNA (specifically, DNA gyrase in bacteria)
  13. What unwinds the DNA?
    helicase
  14. What creates a short RNA fragment called a "primer"?
    primase
  15. What synthesizes new DNA?
    polymerase
  16. What joins the new DNA strands together?
    ligase
  17. What untangles the DNA as it's being unwound?
    Topoisomerase (gyrase in bacteria)
  18. The DNA polymerase requires a...
    template
  19. The DNA polymerase synthesizes in what direction?
    5' to 3'
  20. Why does the DNA polymerase synthesize in the 5' to 3' direction?
    Can only add nucleotides to the 3'OH
  21. In bacteria, DNA Polymerase III does...
    replication synthesis
  22. In bacteria, DNA Polymerase I does...
    repair synthesis
  23. How do cells stitch together Okazaki fragments?
    • by DNA ligase
    • joins the 5' phosphate of one DNA molecule to the 3' OH of another to seal fragments together
    • seals the backbone between the two Okazaki fragments on the lagging strand
  24. What two enzymes are required to join Okazaki fragments into a single DNA strand?
    ligase and polymerase
  25. Why are gyrases required in bacterial replication?
    • untangle the DNA strang
    • example of a topoisomerase
    • present in bacteria cells
  26. In what direction does DNAP synthesize DNA?
    5' to 3'
  27. How many replication forks are in a replication bubble?
    one
  28. Beadle and Tatum's hypothesis
    one gene-one enzyme
  29. Beadle and Tatum's experiment
    • 1. Mutigenized bread mold spores by emitting them with xrays which caused mutations
    • 2. Grew the spores in a complete medium
    • 3. Grew them in a minimum medium to try to identify the spores mutated in the ability to create life; if the cell cannot make an amino acid, it is dead
    • 4. Added amino acid to the minimum medium; which amino acid, when present, allows them to live?
  30. What is the difference between RNA and DNA?
    • The sugar in the backbone: RNA lacks the hydroxyl (-O) on 2'
    • DNA is a double helix, RNA is a single strand
    • DNA uses ATGC, RNA uses AUGC
  31. Transcription
    RNA is synthesized using DNA as a template
  32. Translation
    mRNA message is "read" by the ribosome, which directs protein synthesis
  33. Codon
    group of three nucleotides of mRNA specifies one amino acid
  34. Genetic code
    The three-nucleotide combination that specifies a given amino acid
  35. Start codon
    AUG
  36. Stop codons
    UAA, UGA, UAG
  37. Gene expression
    process by which DNA directs protein synthesis
  38. The Central Dogma of Genetic Coding
    • DNA is transcribed to make RNA
    • RNA is translated to make protein
  39. Explain how Beadle and Tatum illustrated that one gene codes for one protein. What are the exceptions to this rule?
    • quaternary structure means multiple polypeptides
    • Ex: hemoglobin is two different genes
    • DNA always codes for protein, final product of gene is RNA
  40. DNA is _______to make RNA. RNA is _____ to make protein.
    transcribed; translated
  41. What is a codon?
    group of three nucleotides of mRNA that specifies an amino acid
  42. The genetic code is redundant and unabiguous. Explain.
    • redundant: many codons will specify the same amino acids
    • unambiguous: every time we have GGG, we have glysine no matter what
  43. What polypeptide can be made given the following DNA sequence: 3' - TTC TAC GGC ACC CAG AGA - 5'
    • Transcribe to RNA= 5' - AAG AUG CCG UGG GUC UCU - 3'
    • Start codon = AUG...Met Pro Trp Val Ser
  44. 3 stages of transcription
    • Initiation
    • Elongation
    • Termination
  45. Three parts of modifying pre-mRNA in Eukaryotes
    • 5' CAP
    • 3' Poly A tail
    • RNA splicing
  46. Replication
    • duplication of the entire genome, occurs in S phase
    • DNA Polymerase makes DNA from DNA template
    • every cell in your body have the same genome but don't express the same genes (ex: Liver cells only express genes for liver cells, skin cells express genes for skin)
    • a genome is all the DNA in the cell, a transcriptome is all the genes that are expressed
  47. Transcription
    • only parts of the genome are transcribed
    • "transcriptome"
    • RNA polymerase makes RNA using DNA template
  48. We don't need a sperate helicase during transcription initiation because
    RNA polymerase is capable of opening the DNA itself
  49. We don't need a primase during transcription initiation because
    RNA polymerase is capable of beginning transcription without a free 3' end, it can start from scratch
  50. Two things we don't need during transcription initiation:
    Helicase and primase
  51. The template strand in transcription elongation is also known as the
    "Noncoding" strand
  52. The nontemplate strand in transcription elongation is also known as the
    "coding" strand
  53. During transcription elongation the new RNA strand will look identical to the
    "coding"/nontemplate strand
  54. RNA moves in what direction on the template DNA strand?
    3' to 5'
  55. Transcription Initiation
    RNAP binds promoter and opens up helix, begins synthesizing RNA
  56. Transcription Elongation
    • RNAP continues to synthesize RNA
    • reads template strand
    • RNA made is almost identical to coding strand (nontemplate)
  57. Transcription Terminatino
    RNAP reaches specific sequence that prompts the RNAP to fall off DNA
  58. Promoter
    • sequence where RNA Polymerase first attaches to DNA
    • 'upstream' sequence that specifies which strand is template (in both prok/euk)
    • Eukaryotic promoters have a 'TATA' box motif
  59. TATA box
    indicates which strand is the template strand (not the coding strand)
  60. Transcription factors
    guild the RNAP to the correct location on the promoter
  61. Introns
    intervening sequences spliced out of transcript
  62. Exons
    expressed sequences that are joined during modification
  63. Why are the 5'CAP and poly-A sequence and tail important?
    • Helps the export of mRNA from the nucleus
    • Protects mRNA from degradation
    • Helps ribosomes attach for translation
  64. Pre-mRNA is spliced by
    snRNPs
  65. snRNPs
    • recognize sequences of ends on introns
    • snips out intron and ligates exons
  66. What is a promoter? What is its purpose?
    • Attachment of RNAP to DNA
    • Determines which DNA strand is the template
  67. Why is only part of the genome transcribed?
    • all the cells in your body have the same genome but don't express the same genes
    • Ex: Liver cells only express genes for liver cells, skin cells express genes for skin
  68. How is a mRNA modified after it has been made?
    • 5' CAP
    • 3' Poly A tail
    • RNA splicing
  69. Where does transcription occur in eukaryotic cells; in prokaryotic cells?
    in the nucleus; in the cytoplasm
  70. How is replication and transcription similar and different?
    • Replication: duplication of the entire genome, occurs in S phase; DNA Polymerase makes DNA from DNA template
    • Transcription: only parts of the genome are transcribed ("transcriptome"); RNA Polymerase makes RNA using DNA template
    • Both: enzymes move in 5'-3' direction, adding nucleotides to the 3' end while reading a DNA template
  71. Two functions of tRNA
    • binds RNA
    • carries aminio acid specified by the codon
  72. What kind of function does each of these RNAs have?--mRNA, tRNA, rRNA, snRNA, SRP RNA, miRNA, siRNA
    • mRNA, tRNA: informational
    • rRNA, snRNA: catylitic/structural
    • SRP RNA: structural
    • miRNA, siRNA: regulatory
  73. Describe how amino acids are attached to produce a polypeptide chain in translation.
    Translator binds RNA; carries amino acid specified by the codon (aka binds the codon and carries appropriate amino acid as specified by that codon)
  74. What is an anticodon? Where is is found?
    complementary to the mRNA codon; when anticodon pairs with codon, it brings with it the appropriate amino acid; attached to the tRNA
  75. What is the third base wobble?
    third nucleotide in a codon often doesn't matter as much, primary reason why you can get away with 45 tRNAs to bind with 61 codons, third nucleotide doesn't always matter
  76. If an antibiotic bound the A site, which phase of translation would be affected first?
    Elongation
  77. How do tRNAs become 'loaded' with their amino acids?
    The P site amino acid is attached to the A site amino acid. Then mRNA + tRNAs move one codon over. This continues until a STOP codon is reached. Translation terminations
  78. How are membrane proteins localized?
    • targeted to specific locataions
    • Signal peptide recognized by SRP (signal-recognition particle) guides ribosome to ER
  79. Five types of mutations
    • Chromosomal rearrangements
    • insertions
    • deletions
    • substitutions
    • point mutations
  80. Chromosomal rearrangement
    • entire pieces of chromosome misplaced or attached to another chromosome (dramatic)
    • Ex: down syndrome-caused by three copies of chromosome 21
  81. Point mutations
    • affect one base pair in a gene
    • change of a single nucleotide
  82. Two types of point mutations and their results
    • Base pair substitution, base pair insertion or deletion
    • Result in: silent mutations, missense mutations, nonsense mutations (all on amino acid level)
  83. Silent mutation
    • arises from base substitution
    • no affect on the amino acid sequence because the new nucleotide still codes for the same amino acid, therefore the protein is not affected
  84. Missense mutation
    • arises from base substitution
    • one nucleotide changed that doesn't code for the same amino acid
    • can have dramatic consequences (death, cystic fibrosis, sickle cell anemia, etc.)...disease causing
  85. Sickle cell anemia
    • missense mutation of the amino acid Glu to Val
    • Glu is charged/hydrophilic, Val is hydrophobic (carbons in side chain)
    • completely changes the shape of the protein (shape is dictated by R groups)
    • protein is hemoglobin which carries oxygen around the body shape changed so oxygen is not moved around as efficiently
    • odd shape of the hemoglobin makes them stick together to change the shape of the actual cell
    • the new shape of the cell doesn't allow it to move through the veins as easily
  86. Nonsense mutation
    • arises from base substitution
    • premature stop codon being specified (translation stopped, not transcription)
    • the protein doesn't get made
  87. Frame shift mutation
    insertion or deletion of a nucleotide shifts the frame one basepair, resulting in an 'in frame' stop codon
  88. Nucleotide excision repair after mutation caused by DNA damage (sun exposure)
    • Thymine dimer distorts DNA
    • Nuclease cuts out damaged DNA
    • DNA pol I repair synthesis
    • DNA ligase seals the backbone
  89. How might a missense mutation change the structure of a protein?
    • changes the shape of the protein if a different amino acid is sensed from a new nucleotide in the sequence
    • may go from being hydrophilic to hydrophobic or vice versa
  90. What are thymine dimers and how are they repaired?
    • UV light causes thymine dimers
    • when two adjacent T's bind to each other instead of across
    • nuclease repairs that bulge
  91. Are point mutations always bad? Explain.
    no, they can also be a source of genetic variability in nature and allows animal to adapt to new environments
  92. How would an insertions or deletions cause a nonsense mutation?
    a premature stop codon is specified so that translation is stopped and the protein doesn't get made
  93. operon
    • one promoter for multiple genes
    • set of genes coordinately regulated by a single promoter--produces a polycistronic message (one mRNA for more than one gene)
  94. promoter
    DNA sequence that recruites DNA polymerase
  95. beta-galactosidase
    enzyme that breaks down lactose into glucose and galactose
  96. bacteria breaks down lactose into
    monosaccharides
  97. permease
    makes membrane permeable to lactose
  98. allolactose
    • inducer that binds the repressor when lactose is present
    • changes the shape and function so that the repressor no longer fits on the DNA and falls off and the RNA polymerase is able to express the transcript
    • produced by lacZ (converted by B-gal)
    • 1'-4' glycosidic linkage converted to 1'-6' linkage
  99. lacI
    binding site for the repressor (operator)
  100. When no lactose is present, the lac operon is
    repressed by lacI repressor protein bound to operator
  101. When lactose is present, what happens with the lac operon?
    • inducer (allolactose) binds repressor and changes its shape
    • Repressor falls off the DNA and some low level of gene expression takes place
  102. How does the cell know if glucose is present or absent
    Glucose inhibits adenylyl cyclase activity resulting in low cAMP levels
  103. What happens when glucose levels are low?
    • cAMP levels are high and bind with CAP to the promoter (at a specific site) which keeps the RNA polymerase on the DNA
    • promotes transcription
  104. What proteins are on the lac promoter when only lactose is present?
    • RNA polymerase (bound to promoter)
    • cAMP levels high (glucose levels low)
  105. Why does the lac operon require an activator?
    RNA pol falls off all the time, transcription won't be very robust without an activator
  106. How does the cell know when glucose is present?
    cAMP levels are low
  107. What is the function of B-galactosidase (B-gal)?
    • breaks down lactose into glucose and galactose
    • rearranges lactose to form allolactose, the inducer
  108. Ways in which gene expression is regulated (4)
    • DNA packaging (access to promoter region is controlled)
    • Regulation of transcription initiation
    • Post-transcriptional regulation
    • Protein degradation
  109. Most common mechanism of gene regulation in prokaryotes and eukaryotes
    Transcriptional regulation because it saves energy to stop the synthesis of a protein early
  110. Five levels of DNA package
    • 1. DNA, the double helix
    • 2. "beads on a string"-DNA wrapes around histones=nucleosome
    • 3. 30-nm fiber
    • 4. Looped domains (300-nm fiber)
    • 5. Metaphase chromosome
  111. Heterochromatin
    DNA that is always tightly packaged, highly condensed
  112. Euchromatin
    relatively loosely packaged DNA
  113. Would actively transcribed genes be within euchromatin or heterochromatin?
    Euchromatin
  114. Would telomeres be located in euchromatin or heterochromatin?
    heterochromatin
  115. How does packaging of DNA affect transcription?
    • Histone tailes can be modified to allow access of RNAP to a gene's promoter
    • Tails have a positive charge, DNA has a negative charge creating an electrostatic interaction between these proteins and the DNA
    • if we change the charge of the tailes to be negative (acetylation), they repel from the DNA and we now have access to the DNA polymerase
    • Add methyl groups to repress expression (makes the DNA pol inaccessible by condensing the DNA (30-nm fiber)
  116. Enhancers
    DNA sequences that bind specific transcription factors (like activators) to increase gene expression
  117. Ways transcription is regulated
    • Specific transcription factors bind to the enhancer to stimulate transcription
    • General transcription factors bind to proximal control elements to initiate transcription
  118. Types of Post-transcriptional regulation
    • Alternative splicing (shuffling exons/introns to create more than one peptide from the same gene)
    • Control of mRNA degradation (mRNA stability/RNAi mechanisms)
  119. mRNA degradation occurs when
    • polyA tail is chewed up, CAP is removed, nuclease degrades mRNA
    • The untranslated region can contain "instability factors" which promote mRNA degradation (when we only need proteins for a short period of time)
  120. RNAi
    • controls half of all gene expression
    • Single stranded RNA (called microRNA or small interfering RNA) binds complementary sequences in mRNA
    • Results in the repression of translation of mRNA
  121. Ways in which gene expression is regulated
    • Histone tails can be modified to allow access of RNAP to a gene's promoter
    • Presence or absence of specific transcription factors control which genes get expressed
    • The stability of the transcript and how the transcript is spliced
    • Protein (e.g. repressors) can also be degraded if they are no longer needed
  122. How does the acetylation of histone tails affect gene expression?
    loosens association of DNA with histones and allows transcription
  123. Why would you not expect to see the same collection of activator proteins in skin and liver cells?
    some not necessary in others
  124. What are two ways RNAi affects gene expression?
    can block or degrade the translation of specific mRNAs
  125. What mechanism allows the cells to 'shut down' a protein once it is no longer needed?
    "instability factors" in the untranslated region promotes mRNA degradation
  126. If the DNase-treated extract had killed the mice
    • Protein is the heritable material
    • Protein was transferred from the killed S cells to the R cells
    • S cell protein transformed R cells to a virulent strain.
  127. If 35S had been detected in the pellet instead of 32P, what would have been concluded from the Hershey-Chase experiments?
    Protein is the heritable material
  128. A fly as the following percentages of nucleotides in its DNA: 27.3% A, 27.6% T, 22.5% G, and 22.5%C. How do these numbers demonstrate Chargaff's rules?
    Chagraff's rules state that in DNA, the percentages of A and T and of G and C are essentially the same, and the fly data are consistent with those rules.
  129. How did Watson and Crick's model explain the basis for Chargaff's rules?
    In the Watson-Crick model, each A hydrogen-bonds to a T, so in a DNA double helix, their numbers are equal; the same is true for G and C
  130. In his work with pneumonia-causing bacteria and mice, Griffith found that
    some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic
  131. In analyzing the number of different bases in a DNA sample, which results would be consistent with the base-pairing rules?
    A + G = C + T
  132. DNA polymerase attaches nucleotides together. Describe this process
    An anabolic reaction, creating phosphodiester bonds
  133. What type of bond is formed between Okazaki fragments by ligase activity?
    phosphodiester
  134. Why do eukaryotic chromosomes shorten with each replication cycle? Why do bacterial chromosomes not have this problem?
    • Ultimately, it's because DNA Poly cannot add to the 5' end so the 5' DNA is never replaced in most cells (a shortened 5' end is produced when primers are removed).
    • Bacteria chromosomes are circular, so there's always a free 3' end to which DNA Polymerase can add nucleotides
  135. What direction does DNA polymerase synthesize DNA?
    5'-3' on the newly synthesized DNA
  136. Explain how Beadle and Tatum illustrated that one gene codes for one protein. What are the exceptions to this rule?
    sometimes more than one polypeptide is required to make the final protein (so more than one gene is required for a given protein), also sometimes an RNA is the final product of the gene (ex. tRNA or rRNA)
  137. What is a codon?
    a three nucleotide unit in mRNA that specifies an amino acid
  138. The genetic code is redundant and unambiguous.Explain.
    • There is more than one codon per amino acid (redundant)
    • but each codon codes for the same amino acid each time (unambiguous)
  139. What is a promoter? What is its purpose?
    a DNA sequence that binds RNA polymerase and initiates transcription
  140. Why is only part of the genome transcribed?
    Only a subset of genes are required at any given time
  141. How is replication and transcription similar and different?
    • Both use polymerases that must add nucleotides to the 3' end.
    • Replication and Transcription use different enzymes.
    • Replication duplicates DNA during S phase of the cell cycle.
    • Transcription makes an RNA copy of a gene.
  142. The synthesis of proteins is endergonic or exergonic?
    Endergonic
  143. What is the third base wobble?
    • Pairing at the 3rd position of the codon to the anticodon isn't always strict.
    • Inosine in the tRNA can pair with A, C or U.
    • Sometimes G's pair with U's.
    • The 3rd base wobble is the reason we can get away with 45 tRNAs for 61 codons.
  144. How do tRNAs become 'loaded' with their amino acids?
    through the action of aminoacyl-tRNA synthetases
  145. How are membrane proteins localized?
    a signal peptide in a newly synthesized protein targets the protein to the ER lumen, where it enters the endomembrane system and from there, is targeted to the membrane
  146. If you grow E.coli in both lactose and glucose
    • Cells will use glucose first
    • Glucose is a monosaccharide
  147. What proteins are on the lac promoter when only lactose is present?
    RNA polymerase, cAMP/CAP complex
  148. Why does the lac operon require an activator?
    because RNA polymerase doesn't stay on the DNA very well by itself, so transcription efficiency is relatively low
  149. What is the function of B-galactosidase (B-gal)?
    • two functions:
    • a) break down lactose into glucose and galactose
    • b) convert lactose into allolactose by rearranging the glycosidic bonds. (B-gal carries out this second function only occasionally)
  150. Actively transcribed genes would mostly like be....
    located in euchromatin
  151. RNAi
    • requires double stranded RNA
    • can degrade target mRNAs
  152. Ubiquitin....
    tags proteins for degradation
  153. What genes may be on in a skin cell but off in a liver cell?
    • an example: the proteins that produce skin pigments (melanin) would not be on in the liver cells.
    • Proteins that are involved in alcohol detoxification would not be on in skin cells (at high levels)
  154. How does the acetylation of histone tails affect gene expression?
    acetylation opens up DNA, and promotes gene expression
  155. Why would you not expect to see the same collection of activator proteins in skin and liver cells?
    because activators turn on specific genes found only in certain cells
  156. What are two ways RNAi affects gene expression?
    RNAi can degrade mRNAs or prevent translation of mRNAs
  157. What mechanism allows the cells to 'shut down' a protein once it is no longer needed?
    tagging proteins with ubiquitin, which leads to protein degradation
  158. What enzyme describes separation of the DNA strands?
    Helicase
  159. What enzyme describes requirement of a free 3'OH to synthesize new DNA?
    DNA polymerase III
  160. What enzyme describes synthesis of short segments of RNA?
    primase
  161. What enzyme describes untangling of knots?
    topoisomerase
  162. Contrast DNA replication and transcription. You must include two (2) general ways in which the process of replication and transcription differ.
    • Replication: whole genome (DNA to DNA); DNA pol used; uses nucleotides A,T, C, G;
    • Transcription: part of the genome; RNA pol used; uses nucleotides A, U, C, G;
  163. Give two specific ways in which DNA pol function differs from RNA pol function
    • DNA pol: used to synthesize DNA; does not require helicase; binds to promoters; A, U, C, G
    • RNA pol: used to synthesize RNA; requires helicase to unwind DNA; bind to origins of replication; A, T, C, G

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