A1.2 Nucleic Acids PDF

A1.2 Nucleic Acids Components of Nucleotides Each DNA molecule has three parts: – A sugar – 5 carbon atoms (Pentose sugar) – A phosphate – negatively charged (Polar) – A base – contains Nitrogen (one or two rings)  Components of Nucleotides The chemical bonds occur at specific...

A1.2 Nucleic Acids Components of Nucleotides Each DNA molecule has three parts: – A sugar – 5 carbon atoms (Pentose sugar) – A phosphate – negatively charged (Polar) – A base – contains Nitrogen (one or two rings)  Components of Nucleotides The chemical bonds occur at specific locations in order to produce a functional unit. Be able to draw this!!!! All bonds within the nucleotide involve sharing electrons and are therefore COVALENT BONDS!  Sugar – Phosphate Bonding – The pattern (Pentose (sugar) - Phosphate- Pentose (sugar) - Phosphate) This is called – Pentose Phosphate Backbone – The nucleotides are always added the same way The phosphate of the nucleotide being added is linked by covalent bond to the pentose sugar of the previous nucleotide. Sugar – Phosphate Bonding  A1.2.11 - DNA - Nucleotides Nitrogenous Base – 4 nucleotides found in DNA differ only in their nitrogenous bases All bases contain Nitrogen thus the name. Pyrimidines: single ring structure Thymine (T) Cytosine (C) Purines: double ring structure Adenine (A) Guanine (G) A1.2.11 - DNA - Nucleotides This makes the structure of DNA more stable.  Nitrogenous Base Any base sequence is possible along a DNA or an RNA molecule The number of possible sequences is almost infinite. The sequence of basis is how information is stored This is a universal code shared by all organisms.  RNA as a Polymer of Condensation RNA is a single unbranched polymer of nucleotides. – Nucleotide is a subunit of a polymer thus a monomer They are linked by a condensation reaction  DNA - Structure DNA is made of polymers of nucleotides. The sugar in DNA is deoxyribose The Nitrogenous base pairs are: – Adenine – Cytosine – Guanine – Thymine AT CG At Coral Gables  DNA Structure The 2 strands are parallel to each other. – But they run in opposite direction called Antiparallel – One end ends with a phosphate group – One ends with a deoxyribose If the 2 strands were oriented in the same direction the bases would not be able to form hydrogen bonds with each other. DNA is double helix – Constant diameter of 2 nm Antiparallel The 2 single strands that make up the double- stranded molecule run in opposite directions to each other. A1.2.10 Direction of RNA and DNA 3’ - The pentose sugar of the nucleotide at one end is unlinked. – The carbon number 3 is available for linkage to another nucleotide 5’ - The phosphate group of the nucleotide at the other end of the strand is unlinked. – The phosphate group is attached to carbon number 5  DNA Structure Base Pairing Rules A with T (2 hydrogen bonds) C with G (3 hydrogen bonds) AT CG (Coral Gables) Bonded by weak Hydrogen Bonds  DNA vs. RNA The nucleic acid sugar is ribose rather than deoxyribose (DNA) Another difference is that the Nitrogenous Base Thymine is replaced by Uracil (U) – Similar to thymine – Also, Pair with Adenine RNA forms single strands NOT a double helix (like DNA) – RNA can twist  Base pairing in Allowing Genetic Information to be Passed On DNA replication occurs before cell division This ensures that cells carry the same genetic information This is also the method for inheritance.  Base pairing in Allowing Genetic Information to be Passed On The 2 strands of DNA are separated by breaking the hydrogen bond between their bases. New polymers of nucleotides are assembled on each of the 2 single strands – A strand of DNA on which a new strand is assembled is called a template strand. Complimentary base pairing guarantees the new strand has the same base sequence as the old strand – The two DNA strands produced this way are identical to each other and the original parent DNA molecule Semi-conservative because half is new and have is old. DNA Replication  Base pairing in Allowing Genetic Information to be Passed On Gene – sections of DNA containing genetic information Each gene contains information for a particular purpose Gene Expression - when a gene has an affect on a cell – Coping the base sequence to make RNA is the first step – This process is called Transcription Base pairing in Allowing Genetic Information to be Passed On  Base pairing in Allowing Genetic Information to be Passed On RNA created may have a regulatory role of a structural role – To synthesis protein the base sequence of the RNA molecule is Translated into the amino acid sequence of a protein.  Diversity of Possible DNA Base Sequences Genetic information is stored in the base sequences of one of the 2 strands of a DNA molecules. – There are 4 possibilities for each base sequence A,C, G, or T – There are 4² or 16 possibilities for a sequences of 2 bases – AA. AC, AG …. – There are 4³ or 64 possibilities for a sequence of 3 bases – AAA, AAC, AAG … – With n bases there are 4 possible sequences. As n increases the number of possibilities increases. 10 bases has a million possibilities. Possible sequences are limitless This feature makes DNA ideal to store information Conservation of Genetic Code Across All Life Forms DNA and RNA contains information in a coded form. This is decoded during protein synthesis The 3 bases are called codons – There are 64 different codons Most codons represent one particular amino acid One codon signals that protein synthesis should START Three codons signal that protein should STOP A1.2.10 Direction of RNA and DNA The directionality of RNA and DNA affects the processes carried out by enzymes or ribozymes RNA and DNA strands and nucleotides must be facing in the correct direction to fit the active sites of enzymes and ribozymes. – Replication, transcription and translation A1.2.10 Direction of RNA and DNA We will talk about this again later but….. All processes Replication Transcription and Translation occur 5’ to 3’. A1.2.10 Direction of RNA and DNA Notice in BOTH processes the template strand is copied 3’ to 5’ The new strand is created 5’ to 3 ‘ The mRNA segment in Translation is copied 3’to 5’ but the Amino Acid is made 5’ to 3’  A1.2.13 Nucleosomes DNA in eukaryotes is associated with proteins to form nucleosomes. – These are globular structures that have a core of 8 histone proteins with DNA wrapped around. – Another histone protein called H1 binds the DNA to the core. – A short DNA connects one nucleosomes to the next  A1.2.13 Nucleosomes Eukaryotes have nucleosomes. Prokaryotes (bacteria) do not www.rcsb.org – Do using molecular visualization software page 27  A1.2.14 Hershey and Chase 1950’s – Alfred Hershey – Martha Chase – Worked with viruses that infected bacterial cells (E.coli) to investigate this. Bacteriophage – Viral proteins start being made in the cytoplasm of E. coli showing that the viral genes have entered the bacteria – T2 Virus  A1.2.14 Hershey and Chase The coat of the virus they chose is composed entirely of protein. The DNA is inside the coat DNA contains phosphorus but not sulfur Proteins contain sulfur but not phosphorus They cultured viruses with proteins that had radioactive sulfur Other viruses were cultured with DNA with radioactive phosphorus Then they infected separate groups of bacteria with the respecting radioactive material.  A1.2.14 Hershey and Chase For both groups of bacterial cells they used a blender to sperate the non-genetic component of the virus. They centrifuged the culture solution to concentrate the cells in a pellet The cells had the radioactive genetic material of the virus The radioactive sulfur coated protein viruses retained most of the radioactive material. A1.2.14 Hershey and Chase A1.2.15 Chargaff’s Data on Relative amounts of Pyrimidine and Purine Bases. 1910 – Tetranucleotide hypothesis – Scientist believed that DNA contained repeating sequences of the 4 bases – That would mean that the 4 nucleotides would occur in equal numbers. – This would not vary enough so scientist believe the 20 amino acids were the genetic material. Erwin Chargaff analyzed the composition of nucleotides per species this helped to disprove the tetranucleotide hypothesis. – Page 30 -31 Data based questions