nucleic acids hl Flashcards
Directionality of RNA and DNA
- Include 5’ to 3’ linkages in the sugar–phosphate backbone and their significance for replication, transcription and translation.
HINT: defined direction/additional nucleotide
- The DNA and RNA strands have a defined direction with the 5’ end at the top and 3’ end at the bottom.
- Any additional RNA or DNA nucleotide in a strand can only attach to the 3’ end of a previous nucleotide. For pairing in DNA between purines and pyrimidines to occur, the two strands must run in antiparallel directions.
- why is directionality important (think: The linking…)
- RNA vs. DNA directionality
important b/c:
- The linking of nucleotides between the 3rd carbon and the 5th carbon results in a directionality of the sugar-phosphate backbone – it is said to go from 5’ (“prime”) to 3’ direction.
- Each strand has a 5’ end with a terminal phosphate group and a 3’ end with a terminal hydroxyl group.
- RNA shows the same directionality as DNA. The phosphate groups act as connectors between the sugar rings, by forming covalent phosphodiester bonds between the 3rd carbon atom of the one sugar ring and the 5th carbon atom of the second sugar ring in the growing strand of RNA.
importance of directionality in replication, transcription,, and translation
- In replication, DNA nucleotides can only be added on to the 3’ end of the growing polymer of nucleotides. The 5’ end is already bonded to a phosphate group. Both DNA strands acts as templates.
- In transcription, the 5’ ends of free RNA nucleotides are only be added on to the 3’ end of the growing polymer of mRNA nucleotides. Only one of the two strands is used as a template.
- TRANSLATION: A molecule of RNA carries the sequence information for making a polypeptide by linking amino acids together. The ribosome moves along the mRNA towards the 3’ end. Translation is in 5’ -> 3’ direction.
Purine-to-pyrimidine bonding as a component of DNA helix stability
- Adenine–thymine (A–T) and cytosine–guanine (C–G) pairs have equal length, so the DNA helix has the same three-dimensional structure, regardless of the base sequence.
- Purine-purine pair? not enough space
- Pyrimidine-pyrimidine pair? too much space
- DNA is composed of an equal number of purines (A + G) and pyrimidines (C + T) and X-ray diffraction studies showed that the DNA helix was tightly packed. This tight packing is only possible if a pyrimidine is paired with a purine… and if the bases are upside down in relation to one another.
- Only purine – pyrimidine pairs fit inside the double helix without leaving a gap or bulge. This is responsible for complementary base pairing between A – T and G – C and allows tight packing of the DNA helix.
- Tight bonding between complementary base pairs is enhanced through electrochemical attraction and the formation of hydrogen bonds
- The number of partial positive and negative charges between pairs of complementary bases determine the number of hydrogen bonds between them.
- The number of H-accepting and H-donating pairs of complementary bases determine the number of hydrogen bonds between them
Structure of a nucleosome
- Limit to a DNA molecule wrapped around a core of eight histone proteins held together by an additional histone protein attached to linker DNA.
- When eukaryotic DNA is more closely examined under the microscope, it looks like beads on a string.
- Each ”bead” represents a nucleosome. Nucleosomes are the basic units of eukaryotic DNA and are composed of packaging proteins called histones, and which hold the DNA together to form the frame of chromosomes.
- The DNA double strand coils around histone proteins to form nucleosomes. This process of (called supercoiling) makes DNA denser, so takes up less space in the nucleus. Nucleosome packing and supercoiling only takes place in eukaryotic cells and usually during prophase of mitosis/meiosis.
why are nucleosomes useful?
- Nucleosomes are useful, because they help to pack the long strands of DNA composed of billions of base-pairs into the nucleus of a size between 5 – 10µm.
structure of nucleosome (quick)
- The core is composed of 8 histone proteins with a positively charge. This structure is called an octamer.
- Each octamer consists of two copies of 4 different types of histones.
- Nucleosomes are linked by an additional histone protein (H1 histone)
- The “linker “ DNA connects one nucleosome to the next
- The histone contains high concentrations of amino acid residues with additional base groups (NH2), such as lysine and arginine.
purpose of nucleosome (3)
- Nucleosomes help to supercoil and package the DNA into a smaller volume to fit in the cell, resulting in a greatly compacted structure that allows for more efficient storage
- Supercoiling helps to protect the DNA from damage and allows chromosomes to be mobile during mitosis and meiosis.
- It helps to control gene expression and DNA replication – for a gene to be transcribed it must be uncoiled.
Evidence from the Hershey Chase experiment for DNA as the genetic material
- Students should understand how the results of the experiment support the conclusion that DNA is the genetic material.
NOTE:
Proteins: Composed of amino acids – some of which contain sulfur. None of them contains phosphorus.
DNA: Contains phosphorus, but no sulfur
- In their experiment, Hershey and Chase took advantage of radioactive isotopes of Sulfur (35S) and phosphorus (32P), knowing that DNA and proteins could be distinguished that way. While isotopes have the same chemical properties, the stability of them might be different. Unstable isotopes release energy in the form of radiation.
Chargaff’s data on the relative amounts of pyrimidine and purine bases across diverse life forms
- For a long time scientists thought that DNA contains a repeating sequence of four bases – with an equal number of nucleotides, which would allow little room for variation. This hypothesis was referred to as the tetranucleotide hypothesis.
- The Austrian biochemist Erwin Chargaff analysed DNA samples from different species to find their nucleotide composition and to disprove the tetranucleotide hypothesis.
