DNA and RNA Chemical Structure PDF

DNA and RNA chemical structure DR SAFA HAMID L Learning Objectives: o DNA and RNA chemical structure and the different between them o Organization of Eukaryotic DNA o Steps of backing DNA into chromosomes o Understand what is denaturation, renaturation and...

DNA and RNA chemical structure DR SAFA HAMID L Learning Objectives: o DNA and RNA chemical structure and the different between them o Organization of Eukaryotic DNA o Steps of backing DNA into chromosomes o Understand what is denaturation, renaturation and hybridization and the difference between them. Nucleic acids o Principle information molecule in the cell. o All the genetic codes are carried out on the nucleic acids. o Nucleic acid is a linear polymer of nucleotides Types of Nucleic acids There are 2 types of nucleic acids: 1. Deoxy-ribonucleic acid (DNA) Pentose Sugar is deoxyribose (no OH at 2’ position) Bases are Purines (A, G) and Pyrimidine (C, T). 2. Ribonucleic acid (RNA) Pentose Sugar is Ribose. Bases are Purines (A, G) and Pyrimidines (C, U). Base pairing Nucleic acids are polymers of nucleotides. The nucleotides formed of purine or pyrimidine 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 The polymerization of nucleotides to form nucleic acids occur by condensation reaction by making phosphodiester 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  The DNA Duplex Two antiparallel strands of DNA are paired by hydrogen bonds between purine and pyrimidine bases Remember DNA is a double stranded molecule consists of 2 polynucleotide chains running in opposite directions. Both strands are complementary to each other. The bases are on the inside of the molecules and the 2 chains are joined together by double H-bond between A and T and triple H-bond between C and G. The base pairing is very specific which makes the 2 strands complementary to each other, So each strand contain all the required information for synthesis (replication) of a new copy to its complementary. Tertiary structure of DNA It is a specific 3-dimensional shape. The tertiary arrangement of DNA's double helix in space includes three forms of DNA 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. 2- A-form DNA: Less common form of DNA , more common in RNA Right handed helix Each turn contain 11 b.p/turn Contain 2 different grooves: Major groove: very deep and narrow Minor groove: very shallow and wide (binding site for RNA) -3Z-form DNA: Radical change of B-form Left handed helix, very extended It is GC rich DNA regions. The sugar base backbone form Zig-Zag shape The B to Z transition of DNA molecule may play a role in gene regulation. Comparison of A, B, and Z forms of DNA Denaturing and Annealing of DNA Definition: Denaturation is the loss of helical structure of DNA. The two strands are separated by breaking of the hydrogen bonds between the paired bases. (Phosphodiester bonds are not broken) The DNA double strands can denatured if heated (95ºC) or treated with chemicals. AT regions denature first (2 H bonds) GC regions denature last (3 H bonds) DNA denaturation is a reversible process, as denatured strands can re- annealed again if cooled. This process can be monitored using the hyperchromicity (melting profile).  Melting temperature (Tm): the temperature at which one half of the helical structure of DNA is lost. DNA that contains high concentrations of A and T denatures at a lower temperature (because A and T bind by two hydrogen bonds) than G and C-rich DNA where they bind by three hydrogen bonds  Melting temperature (Tm): the temperature at which one half of the helical structure of DNA is lost. DNA that contains high concentrations of A and T denatures at a lower temperature (because A and T bind by two hydrogen bonds) than G and C-rich DNA where they bind by three hydrogen bonds Hyperchromicity (melting profile It is used to monitor the DNA denaturation and annealing. It is based on the fact that single stranded (SS) DNA gives higher absorption reading than double stranded (DS) at wavelength 260º. Using melting profile we can differentiate between single stranded and double stranded DNA. Hyperchromicity(melting profile) Using melting profile we can differentiate between SS DNA and DS DNA SS SS Ab260 DS Tm Temperature Tm (melting temp.): temp. at which 50% of DS DNA denatured to SS Heating of SS DNA: little rise of Ab reading Heating of DS DNA: high rise of Ab reading  Melting profile continue….. Melting profile can be also used to give an idea about the type of base pair rich areas using the fact that: A═T rich regions: denatured first (low melting point) G≡C rich regions: denatured last (higher melting point) SS AT rich DNA Tm1: Small melting temp. of AT rich GC/AT DNA DNA GC rich DNA Tm2: higher melting temp. of AT/GC equal DNA Tm3: Highest melting temp. of GC rich DS DNA Tm1 Tm2 Tm3 Difference between denaturation, renaturation and hybridization Denaturation: is the loss of helical structure in DNA. The two strands are separated by breaking of the hydrogen bonds between the paired bases (Phosphodiester bonds are not broken)  *Renaturation: reanneal of the separated strands of DNA by gradual decrease of the temperature. Base pairs reform and the complementary strands of DNA come back together *Hybridization: A single strand of DNA pairs with complementary base sequences on another strand of DNA or RNA. Comparison between Prokaryotic and Eukaryotic DNA Prokaryotic DNA Eukaryotic DNA Main chromosome is Each chromosome is circular linear molecule of DNA DNA DNA is naked DNA is linked with histone proteins DNA is free within the DNA is Enclosed within cell the nucleus No introns Introns are present Plasmid is present Plasmid is absent  STRUCTURE OF RNA RNA is a polymer of ribonucleotides linked together by phosphodiester bonds The pentose sugar is Ribose Uracil (U) replace Thymine (T) in the pyrimidine bases. RNA structure RNA is a single stranded polynucleotide molecule. It can take 3 levels of structure; Primary: sequence of nucleotides Secondary: hairpin loops (base pairing) Tertiary: motifs and 3D folding RNA function The Main function of RNA It retrieves the protein code from DNA and carry out the processes needed to produce proteins. RNA is found It is found both inside and outside of the nucleus. Nucleus, ribosome, mitochondria and cytoplasm. Classes of RNA: There are four major classes of RNA : 1- Messenger RNA (mRNA). 2-Ribosomal RNA (rRNA). 3-Transfer RNA (tRNA). 4-Small RNAs such as: Small nuclear RNA and micro RNA. Messenger RNA (mRNA): Carries genetic information copied from DNA in the form of a series of 3- base code, each of which specifies a particular amino acid It is synthesized in the nucleus from DNA by a process called transcription and translocated to the cytoplasm In prokaryotes:- mRNA is polycistronic i.e. mRNA carries genetic information from more than one gene. In eukaryotes:- mRNA is monocistronic i.e. mRNA carries information from just one gene  Types of RNA Transfer RNA (tRNA):. It is the smallest one of the three major types of RNA molecules Its adapter. There is at least one specific type of tRNA molecule for each of the 20 amino acids commonly found in proteins. tRNAs make up about 15% of the total RNA in the cell It is the key that read the code on the mRNA. Each amino acid has its own tRNA ,it transferring amino acids to the ribosomes when needed. The structure of tRNA: It consists of single strand folded to have the shape of clover leaf appearance Ribosomal RNA (rRNAs) Ribosomal RNA (rRNA) is RNA component of ribosome. It is synthesized in the nucleus and pass to the cytoplasm where they bind to several proteins to form a nucleoprotein called ribosomes. rRNAs make up about 80% of the total RNA in the cell and is has a key role in the binding of mRNA to ribosomes and its translation Small RNA Small nuclear RNA (SnRNA) are large number of small stable RNA species found in eukaryotic cells. Most of them are complexed with proteins to form ribonucleoproteins. They are distributed in the nucleus, cytoplasm or both. Functions: They are involved in mRNA processing and gene regulation. Differences between RNA and DNA S.NO. RNA 1) Single stranded m except when self complementary sequences are th forms a double st structures (Hair pin structure) 2) Ribose is the main 3) Pyrimidine compo differ. Thymine is n found ( Except tR 4) Being single stran structure – it does follow Chargaff's THANK YOU