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2012-07-19 12:52:23
DNA bio

EK Bio Lecture 2
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  1. If hemoglobin's noncovalent bonds are dissociated, what would the isolated alpha chains act like?
    Myoglobin (high oxygen affinity)
  2. Define osmolarity
    Osmolarity is molarity times the number of particles per molecule.

     Ex. NaCl has two particles, H3PO4 has four particles.
  3. What are the four DNA nucleotides? Which bind together? How many hydrogen bonds between complimentary nucleotides?
    Purines: Adenine, Guanine; Pyrimidines: Cytosine, Thymine

    A2T, C3G.
  4. How are nucleotides bound? (direction + type of bond)

    Creates what kind of backbone? Directionality?
    Phosphodiester bonds bt C3 and C5, creating a sugar-phosphate backbone with 5'--> 3' directionality.

  5. What are three words that describe DNA replication really well?
    • 1. Semi-conservative
    • 2. Semi-discontinuous
    • 3. Accurate
  6. What are the major enzymes involved in DNA replication and roles? (4) Other important helpers? (
    • Enzymes:
    • 1. DNA Helicase - unwinds double helix
    • 2. DNA Polymerase - builds new DNA strand, proofreading (exonuclease)
    • 3. DNA Primase - create primer so DNA pol can replicate
    • 4. DNA Ligase - joins Okazaki fragments

    • Other helpers:
    • 1. Replisomes - group of proteins that govern replication
    • 2. SSB Tetramer Proteins - single strand binding proteins - stabilize unwound helix.
    • 3. Telomeres - repeated six nucleotide units that protect chromosomes from erosion from multiple replications.
  7. Define the origin of replication

    Eu vs Pro?
    the particular sequence in a genome at which replication is initiated.

    Eukaryotes can have multiple  OOR, whereas prokaryotes only have one.
  8. DNA Directionality:

    1. How DNA is read by DNA Pol
    2. How DNA is assembled by DNA Pol
    3. How DNA is written by convention
    • 1. 3'--> 5' (reading is the hard part)
    • 2. 5'-->3'
    • 3. 5'-->3'
  9. Where does energy for DNA replication come from?
    Removal of pyrophosphate group from nucleotide triphosphates
  10. What are the five differences between RNA and DNA?
    • 1. C2 is not deoxygenated (has hydroxyl group)
    • 2. Single-stranded
    • 3. Uracil instead of Thymine
    • 4. Not confined to nucleus like DNA (can move through nuclear pores)
    • 5. 3 types - mRNA, rRNA, tRNA
  11. What are the three major steps of transcription? Where does it take place in eukaryotes?
    • 1. Initiation
    • 2. Elongation
    • 3. Termination

    In nucleus/mitochondrial matrix
  12. What are the steps in initiation in transcription? (2)

    Needs?! Provide def as well.
    • 1. Initiation factors find promoter on DNA strand and assemble transcription initiation complex (includes RNA pol)
    • 2. RNA Pol unzips DNA double helix creating the transcription bubble.

    NEEDS PROMOTER - sequence of DNA nucleotides that designate the beginning pt of transcription
  13. What are the steps in elongation in translation? Enzyme?
    What does termination require?

    - which DNA strand is transcribed? (two names)
    - Similarities with DNA Pol?
    - Differences with DNA Pol? (2) - 2nd- why is it ok?
    RNA pol transcribes one DNA strand into complementary nucleotide sequence.

    • - "DNA template strand" or "antisense strand"
    • - Similarities: Directionality - reads 3'-->5' and assembles 5'-->3'
    • - Differences: 10x slower and no proofreading - okay, because RNA errors are not called mutations and generally aren't harmful.

    Termination - requires special termination sequence and proteins to dissociate bubble.
  14. Gene Regulation:

    1. Primary function of gene regulation?
    2. Genes are regulated:
    - at which level?
    - by which two factors? (2 facts for each factor)
    • 1. Primary function - to respond to environmental changes to maintain homeostasis
    • 2. Genes are regulated at the level of transcription; (1) by DNA-binding proteins (activators/repressors), which are generally allosterically regulated by small molecules (2) mRNA - decides how much of a type of protein in present in cell (mRNA half-life; amount of mRNA transcribed - amplifying effect)
  15. What do T lynphotocyte-derived effector cells do? (4 types)
    • 1. Helper T-cells activate B-cells and other T-cells through secretion of lymphokines.
    • 2. Cytotoxic T-cells destruct infected self cells
    • 3. Suppressor T-cells downregulate B- and T-cell activity against antigens.
    • 4. Memory T-cells - proliferate and produce a large number of cytotoxic T-cells upon 2ndary exposure.
  16. What is the final electron acceptor in the electron transport chain?
    O2 - why oxygen is needed.
  17. Define polycistronic and monocistronic - which characterizes pro and which euk?
    Polycistronic - multiple genes per mRNA transcript (pro)

    Monocistronic - one gene per mRNA transcript (eu)
  18. Define operon - define each piece.
    Operon - sequence of bacterial DNA that contains operator, promoter, and genes.

    Operator - where activators/repressors can bind to affect transcription.

    Promoter - sequence where transcription begins

    Genes - series of DNA nucleotides coding for a single polypeptide or RNA.
  19. What is the difference between an activator/repressors and enhancers?
    Same function, but enhancers are located much farther from the promoter.
  20. Basic description of how lac operon works
    A way for bacteria to use monosaccharides available. If glucose is low, then activates lac operon, but cannot be used until there is lactose present to inactive lac repressor protein.
  21. RNA post-transcriptional processing:

    1. What type of cells (pro or eu) & which type of RNA
    2. What is a benefit of posttranscriptional processing?
    3. Posttranscriptional processing for mRNA?
    - name of initial mRNA nucleotide?
    - processed in which general ways? (3)
    - specific types of modification: 3 1-energy type; 3-proteins needed
    • 1. Both cells, but in prokaryotes, only tRNA and rRNA undergo post-transcriptional processing. (Eu - all 3)
    • 2. More gene regulation
    • 3. (1) addition of nucleotides (2) deletion of nucleotides (30 modification of N bases

    • (1) 5' cap - attachment site in protein syn and protects against degradation from exonucleases ( uses GTP)
    • (2) 3' cap - polyadenylation to protect from exonucleases.
    • (3) Cleaved into exons and introns - snRNPs (small nuclear ribonucleoproteins) recognize introns, connect exons, and snip out introns (using spliceosomes).
  22. What determines the number of mitochondria a certain cell has?

    Name a cell that doesn't have mitochondria.
    Purely based on energy requirements.

    Red blood cells (erythryocytes)
  23. What is an obligate anaerobe?
    An organism that can only live without oxygen.
  24. Which proteins are responsible for cleaving primary transcripts into exons and introns? What specifically do they do? (3)
    small nuclear ribonucleoproteins (snRNPs)

    recognize and snip out introns (using spliceosomes) and connect exons.
  25. Which of the following cell types does NOT contain the diploid number of chromosomes?

    A. Spermatogonium
    B. Zygote
    C. Primary Oocyte
    D. Spermatid
    D. Spermatid - haploid
    (this multiple choice question has been scrambled)
  26. What does it mean when DNA has been denatured? Under what conditions does this happen? (2)
    Denatured - when H bonds have been degraded.

    Under high salt concentrations and high pH.
  27. What is the purpose of hybridization techniques? (nucleic acid hybridization) What does it use?
    Because DNA prefers to be double stranded, it can be used to identify nucleotide sequences by binding a known sequence with an unknown sequence to find a particular gene in a library.

    Uses a probe
  28. What is cDNA?  What is the benefit of using cDNA?
    cDNA = complementary DNA. It's just DNA reverse transcribed from mRNAcDNA lacks introns that would be normally found in eu DNA.
  29. How can you screen for clones with the intended DNA fragment in the original vector? Why is this necessary?
    • Necessary b/c not all bacteria take up vectors and not all vectors take up DNA including a gene for resistance to an antibiotic or adding in the lacZ gene in the original vector1) Clones that have orignal vector: resistance to antibiotic means vector was uptaken2)
    • Clones that have the DNA fragment: use endonuclease that cuts lacZ
    • rendering it inactive. If inactive, will not turn blue when placed in
    • medium. If inactive, it means that the intended DNA fragment made it in.
  30. How do you make a clone of bacteria with a certain DNA fragment? (5 steps)
    1) Restriction enzymes will cut at a restriction site2) Two DNA fragments cleaved by same restriction enzyme (endonuclease) can be joined together (regardless of origin of DNA) = recombinant DNA3) Lengthening - recombinant DNA can be made long enough for bacteria to replicate 4) Placed in bacteria (using a vector/plasmid)5) Clone - grow bacteria in large quantities to have lots of cells with the vector containing the recombinant DNA fragment.
  31. What is PCR?
    Polymerase Chain Reaction - fast way to "clone/amplify" DNA by denaturing target DNA and mixing it with complementary primers, annealing primers with DNA fragments, and using specialized polymerase to replicate DNA fragments to make millions of copies.
  32. What is Southern blotting?

    - purpose?
    - uses what important things?
    Southern - used to identify target fragments of known DNA seq in a large population of DNA by DNA nucleic acid hybridization

    Uses electric field to separate DNA fragments by side and radioactive probe, visualized with radiographic film.
  33. What is the Western Blot used for?
    detecting a protein with antibodies
  34. What is a Northern Blot?
    Just like a Southern Blot, but it identifies RNA fragments instead of DNA fragments.
  35. What is RFLP?
    - stands for?
    - uses what type of blotting?
    - identifies what instead of what?
    - how does it work?
    Restriction Fragment Length Polymorphisms. Uses Southern Blot and identifies individuals (DNA fingerprints) instead of genes.

    RFLP works b/c DNA of individuals have differnet restriction sites and varying distances between restriction sites (polymorphic).
  36. Where is ribosomal RNA synthesized?
    All ribosomal RNA is synthesized in the nucleolus in the nucleus.
  37. hat is the difference between exocrine and endocrine glands?
    WExocrine glands excrete its products into tubes/ducts that typically empty onto epithelial tissue, whereas endocrine glands release hormones directly into bloodstream.
  38. What are the exocrine and endocrine (list enzymes) roles of the pancreas?
    Exocrine: secretes insulin, glucagon, and somatostatin

    Endocrine: releases enzymes to small intestine for digestion of carbs, proteins, and lipids.

    • Enzymes: pancreatic amylase hydrolyzes starch to maltose; trypsin hydrolyzes peptide bonds and converts chymotrypsinogen to chymotrypsin; chymotrypsin and carboxypeptidase hydrolyze peptide bonds; lipases break down lipids.
  39. cDNA:

    What does it stand for?
    What can it be used for?
    Complementary DNA.

    cDNA is used to find ds complementary DNA.

    Benefit: Reverse transcription of mRNA to produce DNA without introns!!
  40. What are the four parts of the operon?
    operon (seq of bacterial DNA containing the rest)

    Operator - where activators/repressors to affect transcription

    promoter - sequence where transcription begins

    Genes - series of DNA nucleotides coding for a single polypeptide or RNA.
  41. What happens at termination of translation?
    • 1) Stop (nonsense) codon reaches A site
    • 2) Release factors bind to A site
    • 3) Polypeptide is released and ribosome breaks down for recycling
  42. Where does translation take place?
    Translation begins on free floating ribosome in cytosol or may attach to rough ER to inject proteins into ER lumen.
  43. After translation, where can proteins go? (3)

    • 1. Cytosolic proteins
    • 2. Membrane bound proteins (nuclear envelope, ER, Golgi, lysosomes, plasma membrane)
    • 3. Secreted from cell
  44. What is a signal peptide?
    Sequence near front of polypeptide that carries:

    • 1) ribosomal complex to receptor protein on ER
    • 2) polypeptides to target them to mitochondria, nucleus, etc.
  45. Define mutation
    Def: Any alteration in the genome that's not genetic recombination.
  46. What are the two largest categories of mutations and what effect do they have?
    • 1) chromosomal - affects structure of chromosome
    • 2) gene - alteration in sequence of DNA nucleotides
  47. What are the two general causes of mutagens?
    • 1. Spontaneous
    • 2. Induced
  48. How agent causes mutagens? Define that agent.
    Mutagens - any phys/chem agent that increases the frequency of mutations above the frequency of spontaneous mutations.
  49. What is a mutation called if it changes a single base-pair of nucleotides in dsDNA?
    Point mutation
  50. What is a frameshift mutation?
    insertion or deletion of nucleotides in multiples other than 3
  51. What is it called if multiples of 3 nucleotides are inserted or deleted?

    What is the consequence of this?
    Nonframeshift mutation

    Partially/completely active protein
  52. What is a nonsense mutation?

    How serious is the effect?
    If basepair sub or insertion/deletion creates a STOP codon

  53. What is a missense mutation? What are two specific types?
    A missense mutation is a basepair mutation that occurs in the amino acid coding sequence of thet gene.

    • 1. Silent - no change in AA
    • 2. Neutral - no change in protein function
  54. What are chromosomal structural changes caused by? (4)
    • 1. Deletions - portion of chromsome breaks off/lost during homologous recombination/crossing over
    • 2. Duplications - a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome
    • 3. Translocations - segment of DNA in one chromosome is inserted in another chromosome
    • 4. Inversions - orientation of DNA section is reversed in a chromosome
  55. What is transposition? Does it take place in Eu or Pro cells? What does transposition cause? (2)
    Transposition is when DNA segments called transposons/transposable elements excise themselves from a protein and insert them somewhere else.

    Takes place in both eu and pro cells.

    Transposition can cause translocation and inversion.
  56. What terms refer to an already mtuated organism that is mutated again?
    forward mutation or backward mutation, meaning the organism is mutated closer to its original state (wild type) or farther from its original state.
  57. What is the wild type?
    Wild type is the original state of an organism prior to mutation.
  58. Mutation diagram (12)
  59. Define proto-oncogenes

    What can they be converted to? By what cause?
    Genes that stimulate normal growth in cells.

    They can be converted to  oncogenes (genes that cause cancer) by mutagens.
  60. Describe how DNA is coiled into chromosomes? 6
    (1) DNA wraps around 8 histones to form (2) nucleosomes which coil to form (3) chromatin fiber (4) chromatin (5) supercoil within chromosome (6) chromosomes
  61. What are homologous chromosomes? What's another word for them?
    In humans, each chromosome has a partner that codes for the same traits as itself.

  62. Diploid chromosomes vs haploid?
    • Diploid - contains homologous pairs
    • Haploid - does not contain homologous pairs.

  63. A. Bohr effect
    B. Cooperative binding of oxygen to myoglobin
    C. Different in PO2 between blood and muscle.
    D. Cooperative binding of oxygen to hemoglobin
    D. Cooperative binding of oxygen to hemoglobin.

    You can tell from the S-shape/sigmoid shape of hemoglobin's O2 dissociation curve, which reflects that the saturation of hemoglobin depends on [O2] as well as # of subunits that are occupied with O2 molecules.
    (this multiple choice question has been scrambled)
  64. Do viruses have photosynthetic pigments? What about bacteria? What types of bacteria? Are they infectious in humans?
    • No.
    • Some do, but not all.
    • Cyanobacteria (blue-green algae)
    • Not infectious in humans.
  65. Do viruses have DNA or RNA?
    They can have either DNA or RNA, but not both!!
  66. Do viruses have protein?
  67. What would be more effective for helping an epidemiologist determine that the infectious disease was viral instead of bacterial?
    A) Hybridize the infectious agent with radiolabeled probes specific for the genes encoding viral caspids; only viral genes would hybridize.

    B) Analyze a patient's serum in spectrophotometer to measure absorption wavelength; the photosynthetic pigments found in all bacteria would distinguish them from viruses, which lack such pigments.

    Why and why not the other choice?
    The answer is A, because all viruses have a caspid (protein coat). All viruses are closely related, so there will be homology in viral genes coding for the protein coats of different viruses.

    B doesn't work because though there are no photosynthetic viruses, not all bacteria are photosynthetic (only cyanobacteria) and they are not infectious in humans.
  68. Where is bacterial chromsome located in the cell?
    In the nucleoid.
  69. Do all bacteria have cell walls?
  70. In a healthy individual, which of the following blood vessels has the highest partial pressure of carbon dioxide?

    A. Coronary arteries
    B. Aorta
    C. Pulmonary arteries
    D. Pulmonary veins
    D. Pulmonary veins

    (this multiple choice question has been scrambled)
  71. What does coccus mean?
  72. What does enterokinase do? Where is it secreted from? What does it act on?
    Enterokinase converts chymotrypsinogen to chymotrypsin. It is secreted from the small intestine .
  73. If the pancreas is impaired, which macronutrient absorption would be most affected?
    Lipid absorption - because of bile and pancreatic lipase.
  74. An amino acid is subjected to electrophoresis at pH 8.5 and is observed to migrate to the anode. The isoelectric point of this amino acid is:

    A. less than 8.5
    B. more than 8.5
    C. equal to 8.5
    D. cannot be determined without more information
    A. Less than 8.5

    When an amino acid reaches its isoelectric point, it is in the form of a zwitterion.

    If an amino acid migrates to the anode at pH 8.5, it means that the A.A. has a net negative charge. So, to attain neutrality, the ammonium group has to be protonated by lowering the pH.
    (this multiple choice question has been scrambled)
  75. In what type of organism does oxygenated and deoxygenated blood coexist within same chambers of heart?
    in mammalian fetal circulation.
  76. What are the four stages of interphase of the cell cycle?
    - G1 (first growth phase): - cell has just split and grows in size (heterochromatin --> euchromatin; new organelles, RNA synthesis, protein synthesis)

    Next step: If cytoplasm:DNA ratio & protein numbers are sufficient, will go into S1. Otherwise, G0.

    G0: (nongrowing state distinct from interphase) - allows for differences in length of cell cycle for different cells.

    S1 (Synthesis): DNA production; organelles and proteins produced more slowly.  Each chromosome is exactly duplicated to form sister chromatids (2n)

    G2: Cell prepares for division - organelles keep duplicating, RNA & protein (esp tubulin for microtrublin are actively synthesized). This is also the checkpoint for mitosis promoting factor (MPF) - if high enough, mitosis happens.
  77. What are examples of cells that stay in G0 permanently? (2)
    Mature neurons & muscle cells
  78. What happens to during the growth phases (G1 & G2)  of the cell cycle?
    Both identical - heterochromatin --> euchormatin, RNA/protein syn, and organelle synthesis
  79. Is G0 part of interphase?
    No, it's a nongrowing phase distinct from interphase.
  80. What happens in the four stages of mitosis? Name and describe.

    1-4; 2-3 - NOT FINISHED!!!
    1. Prophase: chromatin condenses, centrioles move to opposite sides of cell, spindle fibers form as microtubules grow from centrioles.

    2. Metaphase: double-stranded chromosomes line up at equator; spindle fully formed; microtubules from centrioles are attached to each sister chromatid.