4 Written Questions

1. 
   DNA denaturation (melting):
   In vitro: increased temperature breaks double bonds, 2 DNA strands separate driven by repulsion of "-" charged backbone
   In vivo: enzyme helicase
   DNA renaturation: single strand molecules anneal to form
   double strand
   
   *Monitoring melting DNA by UV light absorption at 260 nm
   *ds DNA absorbs less UV light than ss DNA due to stacking interactions
   *At Tm (melting temperature) ½ of the bases in ds DNA have denatured
2. 
   Most RNA in a cell: single stranded
   Secondary structures: form a DNA type double helices
   Hairpins: 5-10 nucleotides involved in base pairing
   Stem loops: similar to hairpin but the loop is much longer
3. 
   *The most common form of DNA: right handed helix
   *The strands are antiparallel
   *Complementarity: A pairs with T; G pairs with C
   *B DNA: 3.4 nm per turn
   *Minor and major groove: bases are exposed and are typical protein binding sites
4. 
   *Melting temperature Tm depends on GC content as 3 H-bonds connect base pairs stronger than 2 H-bonds in AT
   *Thus the higher % of GC the higher Tm

4 Multiple Choice Questions

1. 
   Tertiary structure: 3D
   Pseudoknot: found in human telomerase RNA, other examples include rRNA and tRNA
   Ribozymes: have catalytic capacities, such as self splicing
   1. DNA protein interaction
   2. nucleic acids
   3. RNA conformation
   4. DNA double helix
2. Deoxyribonucleic acid (DNA)
   Stable (can be recovered from fossils)
   Repair mechanisms
   Base pairs in human genome: 3 x 109
   Found in all forms of life
   Information stored in hereditary units: genes
   
   Ribonucleic acid (RNA)
   Messenger ribonucleic acid (mRNA)
   Copied from DNA (transcription)
   Directs synthesis of a particular protein (translation)
   Transfer RNA (tRNA)
   Reads nucleotides of mRNA
   Ribosomal RNA (rRNA)
   Part of ribosomes along with other proteins
   1. structure of nucleic acids
   2. nucleic acids
   3. RNA conformation
   4. DNA double helix
3. 
   *No H-bonds parallel to DNA axis allows for DNA bending
   *DNA can pack tightly in chromatin
   *Proteins can interact with DNA
   *TATA box binding protein (TBP) binds to minor groove of DNA
   1. nucleic acids
   2. RNA conformation
   3. DNA protein interaction
   4. DNA double helix
4. 
   *Circular DNA (mt, procaryotic genomes) with no free ends can twist itself forming supercoils (supercoils can also be found in eukaryotic chromosomes during replication)
   *Topoisomerase I: enzyme binds to DNA and breaks phosphodiester bonds in 1 DNA strand causing loss of supercoil, eventually the 2 ends of DNA are joined (ligated) by the same enzyme
   *Topoisomerase II: breaks phosphodiester bonds in 2 DNA strands
   1. DNA protein interaction
   2. DNA denaturation and renaturation
   3. structure of nucleic acids
   4. Torsional stress and supercoiling

4 True/False Questions

1. structure of nucleic acids → Deoxyribonucleic acid (DNA)
   Stable (can be recovered from fossils)
   Repair mechanisms
   Base pairs in human genome: 3 x 109
   Found in all forms of life
   Information stored in hereditary units: genes
   
   Ribonucleic acid (RNA)
   Messenger ribonucleic acid (mRNA)
   Copied from DNA (transcription)
   Directs synthesis of a particular protein (translation)
   Transfer RNA (tRNA)
   Reads nucleotides of mRNA
   Ribosomal RNA (rRNA)
   Part of ribosomes along with other proteins

   True        False

2. base catalyzed hydrolysis of RNA →
   *The most common form of DNA: right handed helix
   *The strands are antiparallel
   *Complementarity: A pairs with T; G pairs with C
   *B DNA: 3.4 nm per turn
   *Minor and major groove: bases are exposed and are typical protein binding sites

   True        False

3. Other forms of DNA include: →
   A DNA: exists in vitro when water is removed, shorter and wider
   Z DNA: right handed helix, may occur in cells

   True        False

4. Basic molecular genetic processes, know figure →
   *RNA is less stable than DNA:
   *2' OH group on ribose can participate in OH- catalyzed hydrolysis of phosphodiester bonds in RNA
   *2' OH is absent in DNA (deoxyribose)
   *DNA is less reactive and therefore more stable molecule for long term storage of genetic information

   True        False