Nucleic Acids Lecture Notes PDF

Nucleic Acids Dr Charlotte Lawson School of Pharmacy and Biomedical Sciences [email protected] Where opportunity creates success Learning Outcomes Understand the basic structure of a nucleotide Outline the structure of the DNA double helix Explain the structure and funct...

Nucleic Acids Dr Charlotte Lawson School of Pharmacy and Biomedical Sciences [email protected] Where opportunity creates success Learning Outcomes Understand the basic structure of a nucleotide Outline the structure of the DNA double helix Explain the structure and function of mRNA and tRNA for protein Appreciate the role of the ribosome for protein translation Questions? Please use the TEAM! No such thing as a stupid question! If you wondered, then so did someone else! I will post emailed questions on the Team so please save us both a job! If you know the answer to the question, please feel free to post – we are all in this together! Biomolecules Organic molecules that are formed by living organisms – Consists majorly of Carbon, Hydrogen, Oxygen and Nitrogen Four major classes Lipids Proteins Carbohydrates Nucleic acids The Central Dogma Nucleic acids DNA – Deoxyribonucleic Acid RNA – Ribonucleic Acid BOTH Long biopolymers Structural similarities Carriers of Information BUT Individual roles Nucleic acids are polymers Polymers = large molecules that consist of similar smaller molecules (monomers) linked together Monomers of nucleic acid = nucleotides BASE Phosphate Each nucleotide has 3 components : 1. Nitrogenous SUGA base R 2. Pentose sugar 7 3. Phosphate Nucleotide A nucleotide is one of the structural components (building blocks) of DNA and RNA. It consists of a base, sugar (pentose) and a phosphate. Sugar: Pentose- Ribose 5’ Penta- (Greek suffix for 4’ 1’ five) 1’ = (one prime) 3’ 2’ Sugar: RNA or DNA DNA – Deoxyribonucleic Acid RNA – Ribonucleic Acid Nitrogen bases There are five bases in DNA and RNA Two classes: Bases: Purines Bases: Pyrimidines Nucleosides and Nucleotides A nucleoside consists of a base that bound to C1’ of sugar. A nucleotide is a nucleoside bound to a phosphate group on –OH on C5’ Names of nucleosides and nucleotides Bases It is the order of these bases – A, T(U), C and G which forms the basis for the genetic code DNA structure Primary structure of nucleic acids is represented by the sequence of nucleotides They are bound together via phosphodiester bonds to form a single strand of nucleic acid -OH group on C3” in sugar of the first nucleotide will interact with the phosphate group bound to C5” in the other nucleotide. Polynucleotides Long chains of nucleotides – i.e. RNA and DNA Nucleotides  Polynucleotides Long chains of nucleotides – i.e. RNA and DNA Phosphodiester bond (O-P) 3’ Polynucleo tide 3’ Polynucleotides Long chains of nucleotides – i.e. RNA and DNA PHOSPHATE- SUGAR BACKBONE DNA structure Single strand of DNA has a free phosphate group on the 5’ end and a free hydroxyl group on the 3’ end. The sequence is read starting from the 5’ end using letters designating the nitrogen bases in the nucleotides. Here, the sequence reads: 5’—A—C—G—T— 3’ RNA - presence of ribose instead of deoxyribose, and the presence of uracil (U) instead of thymine (T) The DNA Double Helix DNA exists as double stranded helix (the double helix) The 2 strands wind around each other. Phosphate-sugar backbone on outside. Bases aligned inside helix Hydrogen Bonding stabilises helix Base-Pairing Hydrogen bonding between bases inside the helix holds the strands together This is how bases are paired: Base pairing Base- Pairing 5’ to 3’ Strands are antiparallel (3`-5` and 5`-3`) Strands run in opposite directions – complementary Genetic information is carried on one strand (template) while the other strand (anti- template) (eukaryote) 3’ to 5’ Base-Pairing in the DNA double helix The DNA Double Helix Phosphate-sugar backbone is orientated to the outside of the helix Negative charge = hydrophilic Uncharged, Hydrophobic bases hidden inside Helps further stabilise double-helix Van der Waal’s between stacked bases Helix Dimensions Base pairs 0.34nm apart Complete turn – 3.4nm 10bp per turn External diameter – 2nm The helix is imperfect  Grooves 2 types of grooves as a result of DNA winding, - Major groove - Minor groove Grooves facilitate the binding of regulatory protein on specific sites on DNA strand (transcription factors, repressor proteins, silencers) DNA Denaturation DNA double strands can be separated by breaking hydrogen bonds (change pH or heating). Does not break phosphodiester bonds. Temperature of Melting (Tm) is defined as the temperature at which 50% of double stranded DNA is changed to single- stranded DNA The higher the Tm, the greater the G-C content of the DNA ouble helical DNA can be denatured DNA strands can be reversibly separated by: Extreme heat (>80oC) pH Disruption of H bonds and base stacking Renaturation – disordered The Genetic Code AUG START CODON The Genetic Code...some rules Codon usage bias 64 codons 61 code for amino acids 3 code for stop codons There are 20 amino acids so there is redundancy But The Genetic code of different organisms are often biased towards using one codon over the others There are many theories as to why! RNA Synthesis & Function DNA Gene Transcription RNA Leaves nucleus Translation Machinery Protein  RNA Structure Polymer of nucleotides joined by phosphodiester bonds (similar to DNA). Differences: - Sugar: ribose not deoxyribose - Nitrogen bases: A, G, C, U - RNA is a single stranded not double stranded as DNA RNA: messenger mRNA, transfer tRNA and ribosomal rRNA… and others  Types of RNA ypes of RNA you may read about include miRNA, siRNA, piRNA, lncRNA some viruses carry genetic material as RNA  RNA messenger-mRNA mRNA is a copy of a piece of DNA (transcription). Carries genetic information required to make a protein. Post transcriptional modifications (exons, poly A tail etc.) It leaves the cell nucleus and moves to the cytoplasm where proteins are made mRNA is a complementary strand to the template DNA strand. RNA Synthesis & Function DNA Gene Transcription RNA Leaves nucleus Translation Machinery Protein  Ribosomal RNA-rRNA Ribosomes are the structures where proteins are synthesized Found in the cytoplasm. Ribosomes are 65% rRNA and 35% proteins. Role in binding mRNA  Transfer RNA - tRNA Role in transferring amino acids to the ribosome when mRNA is being translated to synthesize proteins. 23-45 types of tRNA, one for each amino acid (varies between organisms) clustered in anti- codons Special shape Protein translation https://youtu.be/gG7uCskUOrA Summary Nucleotide = monomers formed of nitrogenous base, pentose sugar and phosphate groups Four bases – purines: adenine and guanine - pyrimidines: cytosine, thymine (DNA), uracil (RNA) - base pairing in DNA A/T C/G Phosphodiester linkages join nucleotides together to form nucleic acids Base-pairing, base stacking and hydrophobic/hydrophilic interactions stabilise the double helix We read DNA sequence 5’ to 3’ RNA is short and single stranded and is transcribed from DNA forming the complementary strand Translation occurs in ribosomes in the cytoplasm tRNA brings amino acids to the ribosome to form the growing polypeptide chain There are other forms of RNA that serve regulatory purposes Further reading Voet D & Voet J (2013) Biochemistry Chapter 3. Nucleotides, Nucleic Acids, and Genetic Information 5th edition. ISBN 13 978-0470-54784-7 Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell New York: Garland Science; 2002. https://www.ncbi.nlm.nih.gov/books/NBK26887/