Molecular Biology Notes PDF

# DNA - Structure, Properties, Types, and Functions - DNA stands for Deoxyribonucleic Acid, which is a molecule that contains the instructions an organism needs to develop, live, and reproduce. - These instructions are found inside every cell and are passed down from parents to their children. - It...

# DNA - Structure, Properties, Types, and Functions - DNA stands for Deoxyribonucleic Acid, which is a molecule that contains the instructions an organism needs to develop, live, and reproduce. - These instructions are found inside every cell and are passed down from parents to their children. - It is a nucleic acid and is one of the four major types of macromolecules that are known to be essential for all forms of life. - DNA is found in the nucleus, with a small amount of DNA also present in mitochondria in the eukaryotes. ## DNA Structure - In 1953, James Watson and Francis Crick discovered the structure of DNA. - The works of Rosalind Franklin lead to Watson and Crick's discovery. Franklin first had pointed out that the DNA is made up of two spirals. - The structure of DNA is a double helix structure because it looks like a twisted ladder. The sides of the ladder are made of alternating sugar (deoxyribose) and phosphate molecules while the steps of the ladder are made up of a pair of nitrogen bases. - There are 4 types of nitrogen bases Adenine (A) Thymine (T) Guanine (G) Cytosine (C). DNA Pairing. - The nitrogen bases have a specific pairing pattern. This pairing pattern occurs because the amount of adenine equals the amount of thymine; the amount of guanine equals the amount of cytosine. - The pairs are held together by hydrogen bonds. ## Detailed Structure and Composition of DNA - DNA is a double-stranded helix. That is each DNA molecule is comprised of two biopolymer strands coiling around each other to form a double helix structure. These two DNA strands are called polynucleotides, as they are made of simpler monomer units called nucleotides. - Each strand has a 5'end (with a phosphate group) and a 3'end (with a hydroxyl group). - The strands are antiparallel, meaning that one strand runs in a 5'to 3'direction, while the other strand runs in a 3' to 5' direction. - The two strands are held together by hydrogen bonds and are complimentary to each other. - Basically, the DNA is composed of deoxyribonucleotides. - The deoxyribonucleotides are linked together by 3' - 5'phosphodiester bonds. - The nitrogenous bases that compose the deoxyribonucleotides include adenine, cytosine, thymine, and guanine. - The complimentary of the strands are due to the nature of the nitrogenous bases. The base adenine always interacts with a thymine (A-T) on the opposite strand via two hydrogen bonds and cytosine always interacts with guanine (C-G) via three hydrogen bonds on the opposite strand. - The shape of the helix is stabilized by hydrogen bonding and hydrophobic interactions between bases. - The diameter of double helix is 2nm and the double helical structure repeats at an interval of 3.4nm which corresponds to ten base pairs. ## Major and Minor Grooves of the DNA - As a result of the double helical nature of DNA, the molecule has two asymmetric grooves. One groove is smaller than the other. - This asymmetry is a result of the geometrical configuration of the bonds between the phosphate, sugar, and base groups that forces the base groups to attach at 120-degree angles instead of 180 degree. - The larger groove is called the major groove, occurs when the backbones are far apart; while the smaller one is called the minor groove, occurs when they are close together. - Since the major and minor grooves expose the edges of the bases, the grooves can be used to tell the base sequence of a specific DNA molecule. - The possibility for such recognition is critical, since proteins must be able to recognize specific DNA sequences on which to bind in order for the proper functions of the body and cell to be carried out. ## Properties of DNA - DNA helices can be right-handed or left-handed. But the B conformation of DNA having the right-handed helices is the most stable. - On heating the two strands of DNA separate from each other and on cooling these again hybridize. - The temperature at which the two strands separate completely is known as melting temperature (Tm). Melting temperature is specific for each specific sequence. - The B sample of DNA having higher melting point must have more C-G content because C-G pair has 3 hydrogen bonds. - The sequence of bases along the DNA molecule encodes for the sequence of amino acids in every protein in all organisms. ## Types of DNA - Eukaryotic organisms such as animals, plants and fungi, store the majority of their DNA inside the cell nucleus and some of their DNA in organelles such as mitochondria. - Based on the location DNA may be: ### Nuclear DNA - Located within the nucleus of eukaryote cells. - Usually has two copies per cell. - The structure of nuclear DNA chromosomes is linear with open ends and includes 46 chromosomes containing 3 billion nucleotides. - Nuclear DNA is diploid, ordinarily inheriting the DNA from two parents. The mutation rate for nuclear DNA is less than 0.3%. ### Mitochondrial DNA - Mitochondrial DNA is located in the mitochondria. - Contains 100-1,000 copies per cell. - Mitochondrial DNA chromosomes usually have closed, circular structures, and contain for example 16,569 nucleotides in human. - Mitochondrial DNA is haploid, coming only from the mother. - The mutation rate for mitochondrial DNA is generally higher than nuclear DNA. ## Forms of DNA - Most of the DNA is in the classic Watson-Crick model simply called as B-DNA or B-form DNA. - In certain condition, different forms of DNAs are found to be appeared like A-DNA, Z-DNA, B- DNA. - This deviation in forms is based on their structural diversity. ### B-DNA - Most common, originally deduced from X-ray diffraction of sodium salt of DNA fibres at 92% relative humidity. ### A-DNA - Originally identified by X-ray diffraction of analysis of DNA fibres at 75% relative humidity. ### Z-DNA - Left-handed double helical structure winds to the left in a zig- zag pattern. ## Functions of DNA - DNA has a crucial role as genetic material in most living organisms. It carries genetic information from cell to cell and from generation to generation. Thus its major functions include: - Storing genetic information - Directing protein synthesis - Determining genetic coding - Directly responsible for metabolic activities, evolution, heredity, and differentiation. - It is a stable molecule and holds more complex information for longer periods of time. # RNA (Ribonucleic Acid) - RNA is a single stranded polymer of ribonucleotides. It occurs in viruses, prokaryotic cells and Eukaryotic cells. It is largely found in cytoplasm. It forms the major constituent of ribosome. - RNA forms in the nucleolus, and then moves to specialized regions of the cytoplasm depending on the type of RNA formed. - RNA, containing a ribose sugar, is more reactive than DNA and is not stable in alkaline conditions. RNA's larger helical grooves mean it is more easily subject to attack by enzymes. - RNA strands are continually made, broken down and reused, and more resistant to damage from UV light than DNA. - RNA's mutation rate is relatively higher, Unusual bases may be present. - The number of RNA may differ from cell to cell. - Rate of renaturation after melting is quick. - RNA is more versatile than DNA, capable of performing numerous, diverse tasks in an organism. - It is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. ## Chemical Composition: - chemically RNA is made up of Ribose sugar, Phosphate and nitrogenous bases like Adenine, guanine, cytosine and Uracil. In RNA, thymine is absent. ## Nucleosides of RNA - RNA has 4 types of nucleosides, they are - Ribose adenosine - Ribose guanosine - Ribose cytidine - Ribose Uridine. - Ribose sugar + Adenine =Riboseadenosine - Ribose sugar + Guanine =Riboseguanosine. - Ribose sugar + Cytogine = Riboge cytidine. - Ribose sugar + uracil = Ribose uridine. ## Nucleotides of RNA - Nucleotides of RNA are Called Ribonucleotides. RNA has four types of nucleotides, they are - Ribose adenylic acid or Ribose adenosine monophosphate (Amp) - Ribose guanylic acid or Ribose guanosine manophosphate (Gmp) - Ribose cytidylic acid or Riboge cytidine monophosphate (cmp) - Ribose uridylic acid or Ribose uridine monophosphate (ump) - i) Ribose Sugar + Adenine + phosphate = Ribose adenylic acid. - ii) Ribose Sugar + Guanine + phosphate = Ribose guanylic acid. - iii) Ribose Sugar + cytodine + phosphate = Ribosecytidylic acid. - iv) Ribose Sugar + Uracil + phosphate = RiboseUridylic acid. ## Salient features of RNA - Genetic RNA and non-genetic RNA - Genetic RNA : The RNA that carry genetic or heredity character & from generation to generation is called genetic RNA. Eg: RNA in Tmv (Tobacco mosaic virus), HIV, Influenza virus, polio virus etc... - Non genetic RNA: It is RNA does not carry genetic character from generation to generation but helps in protein synthesis. - Based on the structure and function, Genetic RNAS are classified into 3 types. They are - mRNA (messenger RNA) - rRNA (ribosomal RNA) - tRNA (transfer RNA). ## Messenger RNA (mRNA) - Like DNA, RNA is a long polymer consisting of nucleotides. - RNA is a single-stranded helix. - The strand has a 5'end (with a phosphate group) and a 3'end (with a hydroxyl group). - It is composed of ribonucleotides. - The ribonucleotides are linked together by 3' - 5' phosphodiester bonds. - The nitrogenous bases that compose the ribonucleotides include adenine, cytosine, uracil, and guanine. - Thus, the difference in the structure of RNA from that of DNA include: - The bases in RNA are adenine (A), guanine (G), uracil (U) and cytosine (C). - Thus thymine in DNA is replaced by uracil in RNA, a different pyrimidine. However, like thymine, uracil can form base pairs with adenine. - The sugar in RNA is ribose rather than deoxyribose as in DNA. - The corresponding ribonucleosides are adenosine, guanosine, cytidine and uridine. - The corresponding ribonucleotides are adenosine 5'-triphosphate (ATP), guanosine 5'-triphosphate (GTP), cytidine 5'-triphosphate (CTP) and uridine 5'-triphosphate (UTP). ## mRNA (Messenger RNA) - mRNA (Messenger RNA) mRNA was discovered by VOLKIN in the term mRNA was Coined by Jacob and Monad. ### Characters of mRNA - It is a linear single stranded polynucleotide chain. It forms about 3 to 5% of the total RNA content. It consists of about 900 to 1500 nucleotides. It has blue print or genetic message for protein synthesis. It has no base pairing. ### Structure - mRNA a linear molecule consists of about 900-1500 ribonucleotides. It has a cap structure at 5¹ end which is a 7' methyl guanosine nucleotide. The cap is followed by the non coding region called leader Sequence. The leader sequence is followed by Coding an initiator codon AUG. It is followed by the coding or sensible region. The triplet codons present in this region Code for aminoacids. The coding region followed by the terminator Codons UAA, UAG or UGA. The coding region followed by the non-coding region. It is followed by the poly A tail (polyadenylate tail) which forms 3' end of the of mRNA, Present in Eukaryotic mRNA but absent in prokaryotic mRNA ### Function - mRNA Carry the genetic information from the DNA in the form codons to the cytoplasm to synthesis protein at the ribosome. ## Transfer RNA (tRNA) - The RNA Carrying aminoacids to the ribosome for protein Synthesis is called tRNA. ### Characters. - It forms about 3 to 15% of the total RNA content. It is shortest RNA consists of about 80 ribonucleotides. tRNA folded itself to produce double stranded regions. The folded regions have base pairing i.e., A=U and C= G. It is also known as Soluble RNA (S RNA) or Adaptor RNA ### STRUCTURE - Robert Holley was proposed Clover leaf model to explain the structure of tRNA. (The folded tRNA appear like clover leaf (Trifolium). - The tRNA shows the following structure. - The t RNA has two ends, 3'end and 5'end. The 3'end has the base Sequence 'CCA' and 5'end has GUA nucleotide. - It has four arms. They named as Acceptor arm, Pseudouridine arm (Tực arm) DHU arm (Dihydrouxidine arm) and Anticodon arm. - Each arm has two parts namely stem and loop, but acceptor arm hat only stem. Acceptor arm has amino acid binding site 1.e., CCA to which amino acid is attached. It consists of 3 unpaired and 7 paired nitrogenous bases. - DHU arm 4 paired and 10 unpaired nitrogenous bases. It is meant for attachment tRNA synthetase during protein Synthesis. - TVC arm has 5 paired and 4 unpaired nitrogenous bases. It is meant for attachment to a ribosome during protein Synthesis. - Anti codon arm have 5 paired and 7 unpaired nitrogenous bases of these three unpaired nitrogenous bases forms anticodon or NODOC. It is Complementary to codon on mRNA. ### Function - tRNA transfer amino acid to ribosome (site of protein synthesis) during protein synthesis. Transfer RNA brings or transfers amino acids to the ribosome that corresponds to each three-nucleotide codon of rRNA. The amino acids then can be joined together and processed to make polypeptides and proteins. ## rRNA (Ribosomal RNA) - It is most abundantly (largely) occurring RNA in the cell. it forms about 80% of the total RNA content. It forms major component of ribosome. it has many folded regions, folded regions have base pairing i e, A=U & C= G. It consists of 120 to 4500 ribonucleotides. It is also known as Structural RNA. - It is a RNA forms the structural Component of the ribosome. Ribosomes consist of two major components: the small ribosomal subunits, which read the RNA, and the large subunits, which join amino acids to form a polypeptide chain. - Each subunit comprises one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins (r-protein or rProtein). - Different rRNAs present in the ribosomes include small rRNAs and large rRNAs, which denote their presence in the small and large subunits of the ribosome. - rRNAs combine with proteins in the cytoplasm to form ribosomes, which act as the site of protein synthesis and has the enzymes needed for the process. - These complex structures travel along the mRNA molecule during translation and facilitate the assembly of amino acids to form a polypeptide chain. They bind to tRNAS and other molecules that are crucial for protein synthesis. ### Functions: - It helps to form the structure of ribosome and helps to bind the mRNA and tRNA to ribosome and rRNA directs the translation of mRNA into proteins. ## General functions of RNA - RNA is a nucleic acid messenger between DNA and ribosomes. - It serves as the genetic material in some organisms (viruses). - Some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. - Messenger RNA (mRNA) copies DNA in the nucleus and carries the info to the ribosomes (in cytoplasm). - Ribosomal RNA (rRNA) makes up a large part of the ribosome; reads and decodes mRNA. - Transfer RNA (tRNA) carries amino acids to the ribosome where they are joined to form proteins. - Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules, and the catalysis of peptide bond formation in the ribosome; these are known as ribosomes. # RNA as the Genetic Material (Fraenkel-Conrat experiment) - The genome of viruses may be DNA or RNA. Most of the plant viruses have RNA as their hereditary material. Fraenkel-Conrat (1957) conducted experiments on tobacco mosaic virus (TMV) to demonstrate that in some viruses RNA acts as genetic material. - TMV is a small virus composed of a single molecule of spring-like RNA encapsulated in a cylindrical protein coat. Different strains of TMV can be identified on the basis of differences in the chemical composition of their protein coats and difference in symptoms on the tobacco leaves. By using the appropriate chemical treatments, proteins and RNA of TMV can be separated. - Fraenkel-Conrat experimentally proved that in the absence of DNA, RNA acts as the genetic material. In one experiment protein and RNA components of the TMV were separated and both were used to infect the tobacco leaf separately. It was observed that in case of protein subunits, there was no symptoms on the leaf and no progeny viruses were obtained. - RNA part caused the infection and symptoms appeared on the tobacco leaf. Fresh progeny of TMV was also obtained. - In the other experiment, two strains of TMV (type A and type B) showing different symptoms (one causing spots in random pattern and the other in a definite ring form) were taken. There Protein and RNA parts were separated and chimera (hybrid) viruses were synthesized using RNA of type A and protein of type B and vice-versa. - These chimera/hybrid viruses were used to infect the tobacco leaves. It was observed that symptoms on the leaf always belonged to the virus strain from which RNA was taken. Fresh progeny also belonged to the same strain. (When the hybrid or reconstituted viruses were rubbed into live tobacco leaves, the progeny viruses produced were always found to be phenotypically and genotypically identical to the parental type from where the RNA had been isolated.) - These experiments proved that the genetic information of TMV is stored in the RNA and not in the protein. ## How DNA/RNA codes for protein? - DNA alphabet contains four letters but must specify protein, or polypeptide sequence of 20 letters. - Trinucleotides (triplets) allow 43 = 64 possible trinucleotides - Triplets are also called codons | First Letter | Second Letter | Third Letter | |---|---|---| | U | U | UUU Phenylalanine | | U | U | UUC Phenylalanine | | U | U | UUA Leucine | | U | U | UUG Leucine | | U | C | UCU Serine | | U | C | UCC Serine | | U | C | UCA Serine | | U | C | UCG Serine | | U | A | UAU Tyrosine | | U | A | UAC Tyrosine | | U | A | UAA Stop codon | | U | A | UAG Stop codon | | U | G | UGU Cysteine | | U | G | UGC Cysteine | | U | G | UGA Stop codon | | U | G | UGG Tryptophan | | C | U | CUU Leucine | | C | U | CUC Leucine | | C | U | CUA Leucine | | C | U | CUG Leucine | | C | C | CCU Proline | | C | C | CCC Proline | | C | C | CCA Proline | | C | C | CCG Proline | | C | A | CAU Histidine | | C | A | CAC Histidine | | C | A | CAA Glutamine | | C | A | CAG Glutamine | | C | G | CGU Arginine | | C | G | CGC Arginine | | C | G | CGA Arginine | | C | G | CGG Arginine | | A | U | AUU Isoleucine | | A | U | AUC Isoleucine | | A | U | AUA Isoleucine | | A | U | AUG Methionine; start codon | | A | C | ACU Threonine | | A | C | ACC Threonine | | A | C | ACA Threonine | | A | C | ACG Threonine | | A | A | AAU Asparagine | | A | A | AAC Asparagine | | A | A | AAA Lysine | | A | A | AAG Lysine | | A | G | AGU Serine | | A | G | AGC Serine | | A | G | AGA Arginine | | A | G | AGG Arginine | | G | U | GUU Valine | | G | U | GUC Valine | | G | U | GUA Valine | | G | U | GUG Valine | | G | C | GCU Alanine | | G | C | GCC Alanine | | G | C | GCA Alanine | | G | C | GCG Alanine | | G | A | GAU Aspartic acid | | G | A | GAC Aspartic acid | | G | A | GAA Glutamic acid | | G | A | GAG Glutamic acid | | G | G | GGU Glycine | | G | G | GGC Glycine | | G | G | GGA Glycine | | G | G | GGG Glycine |