Nucleic Acids And Biotechnology 2021 PDF

Unit 10- Nucleic Acids Nucleic Acids Nucleotide  Nucleotides are the monomers of nucleic acids  They are energy rich compounds  They provide energy for metabolic processes  They are a part of enzyme cofactors e.g. NAD - nicotinamide adenine dinucleotide FAD – flavin adenine dinucle...

Unit 10- Nucleic Acids Nucleic Acids Nucleotide  Nucleotides are the monomers of nucleic acids  They are energy rich compounds  They provide energy for metabolic processes  They are a part of enzyme cofactors e.g. NAD - nicotinamide adenine dinucleotide FAD – flavin adenine dinucleotide  They act as secondary chemical messengers in response to hormones  A nucleotide consist of three portions a) a nitrogenous bases – purine and pyrimidine  common purine bases – adenine and guanine  common pyrimidine bases – cytosine, uracil, thymine  Uracil http://www.uic.edu/classes/bios/bios100/lecturesf04am/nucleotides.jpg  Nucleotides (b) A sugar – deoxyribose or ribose http://www.mun.ca/biology/scarr/Deoxyribose_vs_Ribose.gif  Nucleotides (c) One or more phosphate groups  Nucleotides  Some common nucleotides include- ATP – adenosine triphosphate ADP – adenosine diphosphate AMP – adenosine monophosphate GTP – guanosine triphosphate UTP – uridine triphosphate CTP – cytidine triphosphate  Nucleotides http://www.madsci.org/posts/archives/2001-02/982619379.Bc.1.gif  Nucleosides  A nucleoside consists of a nitrogenous base covalently attached to a sugar(ribose or deoxyribose) but without the phosphate group  When a nucleoside is phosphorylated a nucleotide is formed In naming the nucleosides The purine NSs end in "-sine" : adenosine and guanosine The pyrimidine NSs end in "-dine" : cytidine, uridine, deoxythymidine (NS – nitrogen sugar complex)  Nucleic Acids  There are two types of nucleic acids (a) DNA – deoxyribonucleic acid (b) RNA – ribonucleic acid  They provide genetic information  Both nucleic acids are found in plants and animals  Viruses contain either RNA or DNA but not both  Nucleic Acids – DNA It is found in the chromatin of the cell nucleolus and also outside the nucleus i.e. in the mitochondria and chloroplast  It contains genetic information in a segment called the genes  It contains information (blue print) that is used to construct other cell components  The DNA is made up of nucleotide monomers and the structure consists of two strands that are entwined  The structure is described as a double helix (proposed byWatson and Crick)  The helix is formed through the pairing of the nitrogenous bases in the nucleotide http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg  Nucleic Acids - DNA  The double helix is also called the B-form DNA or B-DNA  This form is very stable  There also exists different variations in DNA helix structure i.e.A-DNA and Z-DNA  Both forms are converted into the B-DNA at normal physiological conditions  Main Differences in Variations A-DNA B-DNA Z-DNA Right handed helix Right handed helix Left handed helix Helix has a hollow core Helix has a solid core Helix has a solid core – more tightly packed Appears when the DNA is Occurs at normal Occurs when there is very dehydrated physiological conditions high salt concentration  Nucleic Acids – DNA Structure  The backbone of the DNA is comprised of a deoxyribose sugar linked by phosphodiester bridges  The 3' hydroxyl group of the sugar is linked to the 5' hydroxyl group of another sugar by a phosphodiester bond  The linking of the sugars maintains the structure of the DNA  The strands run anti parallel to each other, i.e. one strands run in the 3' → 5' direction and the other strand runs in the 5' → 3' direction  Nucleic Acids – DNA Structure The nitrogenous bases found in DNA are adenine (A), thymine (T), cytosine (C) and  guanine (G)  They carry the genetic information  Adenine is paired with thymine and vice versa by 2 hydrogen bonds (double bond) A =T  Guanine is paired with cytosine by 3 hydrogen bonds (triple bond) G C  The GC pair is more strongly held together than the AT pair due to the triple bonds that holds the latter pair together  The pairing of the bases is referred to as complementary base pairing  The two helices are complementary to each other.They are not identical  There must exist equal amounts of complementary bases  Nucleic Acids – DNA Structure  The DNA helix can be bent or super coiled  This flexibility allows DNA to be wrapped around proteins  Allows the DNA to be compact into smaller volumes  Nucleic Acids - RNA  RNA is present in the cytosol of the cell and in the nucleolus  It is formed from DNA by a process called Transcription  The molecule consist of (a) a phosphate group (b) a nitrogenous base – adenine (A), uracil (U), cytosine (C) and guanine (G) (c) sugar – ribose  Similar to DNA, the nitrogenous bases in RNA carries the genetic information and sugar-phosphate serves to maintain the structure of the molecule  Nucleic Acids – RNA Structure  The structure is single stranded and runs in the 5' → 3' direction However because base pairing can occur, the molecule can fold on itself in the form of a hairpin  During base pairing adenine pairs with uracil and guanine with cytosine A U G C  The hairpin formation does not require the molecule to have equal amounts of complementary base pairs Differences Between DNA and RNA  DNA RNA Found in the chromatin of the nucleus Found mainly in the cytoplasm and to a lesser extent in the nucleolus Sugar – 2 deoxyribose Sugar – ribose Nitrogenous bases areA,T, C and G Nitrogenous bases areA, U, C and G Double stranded Normally single stranded TheA/T and G/C ratio is 1 Complementary base pairs ratio not necessary Base pairing occurs throughout the molecule Base pairing occurs at specific locations Can replicate and transcribe Does not replicate or transcribe  Types of RNA There exist three RNA forms ribosomal RNA – rRNA transfer RNA – tRNA messenger RNA – mRNA  They differ from each other by size, function and stability  Types of RNA - rRNA  It is the most abundant and makes up 80% of the RNA in the cells  It is also the most stable form  The molecule has a higher GC content thanAU content  In the cytoplasm rRNA combines with proteins to form ribosomes http://img.sparknotes.com/figures/F/f88cd44dc6a50ffa6b94cdb9d213894e/ribosome.gif  Types of RNA - tRNA  It occupies 15% of the total RNA in the cell  It is the smallest polymeric form  It functions as a carrier of activated amino acids to a growing polypeptide chain (protein synthesis)  It binds to specific amino acids  All tRNA molecules have a three fold clover leaf configuration  Types of RNA - tRNA  The 3' end contains the CCA sequence. Amino acids bind to this end via esterification  The anticodon region base pairs to the corresponding codon region on the mRNA molecule  Each tRNA molecule contains a specific anticodon triplet http://universe-review.ca/I11-21-tRNA1.jpg  Types of RNA - mRNA  Otherwise called template RNA  Comprises 5% of RNA in the cell  It is synthesized on the surface of the DNA template  It carries genetic information from the nuclear DNA to the cytosol  It is used as a template for protein synthesis  If the mRNA carries the code for a single protein it is called monocistronic  If it carries the code for more than one kind of protein it is polycistronic  Genetic Code  The sequence of bases that encodes a functional protein is called the gene  The relationship between the base sequence and the amino acid sequence in a particular  protein is called the genetic code  A codon consists of 3 nucleotides Consequences of Altering the Nucleotide Sequence  Silent Mutation: A silent mutation is a change in the sequence of nucleotide bases which constitutes DNA, without a subsequent change in the amino acid or the function of the overall protein  Nonsense Mutation: A change in a base in the DNA that prematurely stops the translation (reading) of the mRNA resulting in a polypeptide chain that ends prematurely and a protein product that is truncated and incomplete and usually non functional  Missense Mutation: A change in a base that results in the substitution of one amino acid in protein for another  Missense Mutation: SICKLE CELL ANAEMIA 34 Frameshift Mutation Genetic Flow  This is the flow of genetic material form DNA to proteins  It is described as the central dogma  DNA Replication  This is a duplication of genetic material  During replication the hydrogen bonds holding the nitrogenous bases together are broken (helicase) causing separation of the strands  Each separated strand serves as a template for the synthesis of a new strand that is complementary to the parent strand  The enzyme DNA polymerase moves along each template of the open helix reading the nucleotide in the template  The enzyme ligase then joins the complementary nucleotide in the new strand  DNA polymerase is only able to move in the 3' → 5' direction, therefore the enzyme moves in the opposite direction along the two strands  (Remember the strands run opposite to each other, i.e. one strand runs in the 3' → 5' direction and the other in the 5' → 3' direction  DNA Replication  Other proteins are needed in the process -: (a) to unwind the helix (b) to keep the strands separated (c) to join the segments together after into a continuous strand  When the process is completed there would be two identical molecules of double stranded DNA  Each molecule will contain one strand that was obtained from the parent strand  This form of DNA replication is described as semi conservative because half of the DNA molecule comes from the parent http://www.uic.edu/classes/phar/phar331/lecture4/replication2.jpg  DNA Replication The DNA polymerase is a phenomenal enzyme, in that it is able to reduce the number of mistakes made in complementary base pairing  The enzyme contains two active sites i.e. one for polymerization and the other for proof reading  If a strand is being synthesized and a wrong nucleotide is selected by the first active site then the second active site would recognize the error and remove the incorrect nucleotide  If the second active site does not recognize the error then this results in a permanent change or genetic mutation  Transcription This is the process by which RNA is formed from DNA   The information stored in the DNA molecule is carried by the mRNA molecule  During transcription the double helix of the DNA temporarily separates  A complementary strand of mRNA assembles on one of the DNA strand (anti sense strand) which acts as a template  The process is catalyzed by RNA polymerase  A=U G≡C U =A C ≡ G  Transcription  The strand is synthesized in the 5' → 3' direction At the end of the process, the mRNA will contain the complementary genetic information of the DNA  The mRNA then leaves the DNA template where it carries the information to the ribosomes so the synthesis of polypeptides can take place  N.B mRNA is the only RNA synthesized by a cell http://fig.cox.miami.edu/~cmallery/150/gene/c7.17.7b.transcription.jpg  Translation  Every three consecutive nucleotide on the mRNA is called a codon  Each codon codes for a particular amino acid  The mRNA determines the sequence of amino acids in a protein  This occurs in a process called translation  It is the most complex process of the cell  The process requires numerous enzymes, ribosomes, amino acids, mRNA, tRNA and energy (ATP and GTP)  Translation  One of the folds on the tRNA molecule has a specific triplet codon to which an amino acid is attached  The amino acid binds covalently to this region  At least one kind of tRNA is present for each of the 20 amino acid  Some amino acids have more than one tRNA molecules  There is a triplet codon called an anticodon located at another folded end of the tRNA molecule  The anticodon is the complementary code for the amino acid attached  E.g. tRNA with valine (GUA) attached will have an anticodon CAU  When the amino acid is linked to the tRNA molecule, base pairing can occur between the anticodon region of the tRNA and the mRNA molecule  Functional Ribosome http://genomebiology.com/content/figures/gb-2003-4-12-237-1.jpg  Translation  Each triplet codon on the mRNA specifies the insertion of a particular amino acid  The tRNA carrying the appropriate amino acid can become attached to the mRNA  Therefore the message on the mRNA is read codon by codon until the synthesis of a polypeptide chain is completed  Translation involves three main steps (a) Initiation (b) Elongation (c)Termination  Initiation  During the initiation step, the small subunit of the ribosome binds at the start codon (AUG) near the 5' end of the strand  It is then joined by the large subunit of the ribosome and a special initiator tRNA molecule (i.e. one that codes for met)  If the message is read at the wrong nucleotide in the start sequence, then the remaining triplets would be incorrectly read  The wrong amino acid would be inserted producing a useless polypeptide Initiation e.g. correct a.a. order - Met Leu His Pro mRNA sequence - AU CU CA CC G G U A mRNA sequence - AUG CUG CAU CCA Incorrect a.a. order - Ala Ala Ser  Elongation  A tRNA with the amino acid bonded to it then base pairs with the mRNA molecule  This process requires energy  The preceding amino acid (met) is then linked to the incoming amino acid by a peptide bond  The initiator tRNA to which methionine was attached is then released  The ribosome then moves to the next codon where base pairing between tRNA and mRNA molecule occurs  Termination  The end of the translation occurs when the ribosome reaches a stop codon (i.e. either UAA, UAG, UGA)  There exists no tRNA molecule with anticodons for stop codons. Hence there exists no amino acids that codes for these codons  Release factors recognize these codons and releases the polypeptide chain from the ribosome…the process requires energy  The ribosome then split into its subunit which can be reassembled later for another round of protein synthesis  Protein synthesis is an efficient process…i.e. many mRNA molecules can be translated at the same time as there exist numerous ribosomes http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.gif Biotechnology  Discussion  Forensic Science  DNA profiling  Genetically Modified Foods  Biotechnology Applications of Biotechnology https://files.askiitians.com/cdn1/images/2016117-122852838-8469-o17.jpg  Genetic Diagnosis  Haemophilia  HIV  Cystic fibrosis  Huntington's disease  Sickle cell anemia  PKU – phenylketonuria  Multiple sclerosis  Tay-sachs  Alzheimers  Metabolic example: lactose intolerance 56  Genetic Diagnosis  HIV can be diagnosed by actually detecting the genome using the polymerase chain reaction – PCR  Haemophilia can be diagnosed by looking at the genetic area of the genes that should produce certain proteins to detect any differences from the normal pattern of bases  Sickle cell Anaemia can also be detected by how the resulting protein acts in red blood cells  The DNA can be tested by using PCR to produce samples of DNA large enough to be analysed to test for certain genetic coding sequences that are not normal 57  Genetic Diseases  As you see in the sickle cell example, one base in the gene for a protein can cause such a huge difference  Generally there are additional defects in the genetic code that lead to a malfunction/disease, but the result is due to a lacking protein or proteins that do not perform their function 58  Other Applications  Proteins made by genes in bacteria: like insulin, another example is bacterial TPA (Tissue Plasminogen Activator) it is used to dissolve blood clots  Genetically modified plants are produced for food crops  Examples: - soya, corn/maize, tomatoes, rice, sweet potato 59  Genetically Modified Food  Genetically modified organisms are mostly used for food  Examples are:- soybeans, corn and canola are mainly herbicide resistant from bacterial gene  Bt (Bacillus thuringiensis) corn, cotton are resistant to insect pests 60 Genetically Modified Food  Papaya resistant to a virus  Rice and sugar cane improved