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Structure and Function Of 8/5/2019 DNA and RNA The Code of Life The Human Genome Project Gene Expression Genetic code The alphabet of the genetic code contains Genes are DNA sequences that encode proteins (the gene product) only four letters (A,T,G,C). Gene expression refers to the process A number of experiments confirmed that the whereby the information contained in genes genetic code is written in 3-letter words, each begins to have effects in the cell. of which codes for particular amino acid. DNA encodes and transmits the genetic A nucleic acid word (3 nucleotide letters) is information passed down from parents to offspring. referred to as a codon. 1 8/5/2019 Nucleic acids Nucleotides Principle information molecule in the Nucleotides are the unit structure of cell. nucleic acids. Nucleotides composed of 3 All the genetic codes are carried out on components: the nucleic acids. Nitrogenous base (A, C, G, T or U) Pentose sugar Nucleic acid is a linear polymer of Phosphate nucleotides Nucleotides Nitrogenous bases There are four nitrogen bases making up four different nucleotides. There are 2 types: Purines(pyoo r-een): Adenine A Two ring structure Purines Adenine (A) and Guanine (G) Guanine G Pyrimidines(pahy-rim-i-deen,): N base Single ring structure Cytosine (C) and Thymine (T) or Uracil (U). Thymine T Pyrimidines Cytosine C 2 8/5/2019 A NUCLEOTIDE Nucleotide bases 1. Phosphate Group 2.3. 5Nitrogen-Carbon BaseSugar 1. Phosphate Group 2. 5-Carbon Sugar (Dexoyribose or Ribose) 3. (Dexoyribose or Ribose) 1. 3. Nitrogen Base 2. 3. Nucleotides, too O 1. 2. O P O C H3 O C C O C H2 O C H N H C H H C N C H C H C O H O H O 3 8/5/2019 Role of Nucleotides Role of Nucleotides They carry packets of chemical energy—in They carry packets of chemical energy—in the form of the nucleoside triphosphates the form of the nucleoside triphosphates ATP(Adenosine triphosphate) ATP(Adenosine triphosphate) GTP(Guanosine triphosphate GTP(Guanosine triphosphate CTP(Cytidine triphosphate) CTP(Cytidine triphosphate) Role of Nucleotides Types of Nucleic acids throughout the cell to the many cellular There are 2 types of nucleic acids: functions that demand energy 1. Deoxy-ribonucleic acid (DNA) Pentose Sugar is deoxyribose (no OH at 2’ position) synthesizing amino acids Bases are Purines (A, G) and Pyrimidine (C, T). synthesizing proteins cell membranes and parts Moving the cell and moving cell parts internally and intercellularly Dividing the cell Participate in cell signaling (cGMP and cAMP 4 8/5/2019 2. Ribonucleic acid (RNA) Polymerization of Nucleotides Pentose Sugar is Ribose. Bases are Purines (A, G) and Pyrimidines (C, U). The formed polynucleotide chain is formed of: Negative (-ve) charged Sugar-Phosphate backbone. Free 5’ phosphate on one end (5’ end) Free 3’ hydroxyl on other end (3’ end) Nitrogenous bases are not in the backbone Attached to the backbone Free to pair with nitrogenous bases of other polynucleotide chain Example of DNA Primary Structure Polymerization of Nucleotides In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between deoxyribose and phosphate Nucleic acids are polymers of nucleotides. The nucleotides formed of purine or pyrimedine bases linked to phosphorylated sugars (nucleotide back bone). The bases are linked to the pentose sugar to form Nucleoside. The nucleotides contain one phosphate group linked to the 5’ carbon of the nucleoside. Nucleotide = Nucleoside + Phosphate group 5 8/5/2019 Example of DNA Primary Structure In DNA, A, C, G, and T are linked by 3’-5’ ester bonds N.B. between deoxyribose and phosphate The polymerization of nucleotides to form nucleic acids occur by condensation reaction by making phospho-diester bond between 5’ phosphate group of one nucleotide and 3’ hydroxyl group of another nucleotide. Polynucleotide chains are always synthesized in the 5’ to 3’ direction, with a free nucleotide being added to the 3’ OH group of a growing chain. Chargaff’s Base Pair Rules Complementary base pairing Adenine always bonds with thymine. A = T It is the most important structural feature of nucleic acids It connects bases of one polynucleotide A T chain (nucleotide polymer) with complementary bases of other chain The lines between the bases represent hydrogen bonds Complementary bases are bonded together via: Double hydrogen bond between A and T (DNA), A and U (RNA) (A═T or A═U) Triple H-bond between G and C in both DNA or G C RNA (G≡C) Guanine always bonds with Cytosine. G C 6 8/5/2019 Base pairing Base pairing in DNA: 5’End 3’End Pairing DNA Nucleotides What iswould athe nucleotide? base be the pairing complementary rule? nucleotide pairing? P Nucleotide N-b S C ladder G shaped molecule Rule A A to T A C to G T DNA DOUBLE HELIX DOUBLE DNA G 3’End 5’End 7 8/5/2019 How Do Nitrogen Bases Pair Up? T A single strand •Adenine(A) pairs up w/ Thymine(T) of DNA •Guanine(G) pairs up w/ Cytosine(C) A Example: Sugar- C 3’ A G C T A C G C A 5’ phosphate 3’ backbone 5’ T C G A T G C G T G Structure of DNA Fig 10.2 Nucleotide Hydrogen bonds Sugar-phosphate backbone Key Adenine (A) Thymine (T) Cytosine (C) Guanine (G) 8 8/5/2019 DNA is like a rope ladder twisted into a spiral Significance of complementary base pairing DNA Structure • Consists of 2 The importance of such complementary base pairing is that each strand of DNA can act as strands joined template to direct the synthesis of other strand together by weak similar to its complementary one. hydrogen bonds • Rungs of the Thus nucleic acids are uniquely capable of ladder are directing their own self replication. hydrogen bonded N-bases The information carried by DNA and RNA direct the synthesis of specific proteins which control most cellular activities. Fig 10.4 Twist Artificial Nucleotides Artificial Nucleotides 1989 Steven Benner 2002 Swiss Federal Institute of Technology Ichiro Hirao’s group, Japan Modified forms Unnatural base pair between 2-amino-8 Cytosine 2006 Guanine 7-(2-thienyl)imidazo DNA molecules in vitro 2013 Applied the Ds-Px pair to DNA in vitro 9 8/5/2019 Artificial Nucleotides 2012 American scientists led by Floyd R • The two new artificial nucleotides or 2014 Unnatural Base Pair (UBP) A team synthesized a stretch of circular • d5SICS and dNaM DNA known as a plasmid containing • Bearing hydrophobic nucleobases natural T-A and C-G base pairs along with • team designed a variety of in vitro the best-performing UBP (Unnatural Base Pair). Artificial Nucleotides DNA structure 2014 DNA is a double stranded molecule consists of 2 inserted it into E. coli (intestines) polynucleotide chains running in opposite directions. that successfully replicated the unnatural base pairs through multiple generations. Both strands are complementary to each other. The bases are on the inside of the molecules This is the first known example of a living and the 2 chains are joined together by double organism passing along an expanded genetic H-bond between A and T and triple H-bond code between C and G.. 300 variants to refine the design of nucleotides 10 8/5/2019 DNA structure Forms of DNA The base pairing is very specific which make the 2 strands complementary to Minor groove each other. The minor groove is generated by the smaller angular distance between sugars. So each strand contain all the required information for synthesis (replication) of a Major groove new copy to its complementary. major groove: The larger of the two grooves that spiral around the surface of the B-form of DNA. DNA structure: Lecture 7: 2 Secondary Structure: alternative conformations 1 0 / 4/2006 Forms of DNA 1- B-form helix: It is the most common form of DNA in cells. Right-handed helix Turn every 3.4 nm. Each turn contain 10 base pairs (the distance between each 2 successive bases is 0.34 nm) Contain 2 grooves; Major groove (wide): provide easy access to bases Minor groove (narrow): provide poor access. 11 8/5/2019 2- A-form DNA: Less common form of DNA , more common in RNA Denaturing and Annealing of DNA Right handed helix Each turn contain 11 b.p/turn The DNA double strands can denatured if Contain 2 different grooves: heated (95ºC) or treated with chemicals. Major groov e: v ery deep and narrow AT regions denature first (2 H bonds) Minor groov e: v ery shallow and wide (binding site f or RNA) GC regions denature last (3 H bonds) DNA denaturation is a reversible process, as 3- Z-form DNA: denatured strands can re-annealed again if Radical change of B-form cooled. Left handed helix, very extended It is GC rich DNA regions. The sugar base backbone form Zig-Zag shape This process can be monitored using the The B to Z transition of DNA molecule may play a role in hyperchromicity (melting profile). gene regulation. Properties of a DNA Hyperchromicity (melting profile) double helix It is used to monitor the DNA denaturation and annealing. The strands of DNA are antiparallel It is based on the fact that single stranded (SS) The strands are complimentary DNA gives higher absorbtion reading than double stranded (DS) at wavelength 260º. There are Hydrogen bond forces Using melting profile we can differentiate between single stranded and double stranded DNA. 12 8/5/2019 8.3 DNA Replication Schematic representation of the strand separation in duplex DNA resulting from its heat denaturation.
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