Nucleic Acids and Molecular Genetics PDF

Nucleic Acids and Molecular Genetics  Heredity Transfer of characteristics, anatomical and biochemical, from generation to generation  Transmission of Hereditary Information Nucleus Chromosomes Genes Unit of heredity Deo...

Nucleic Acids and Molecular Genetics  Heredity Transfer of characteristics, anatomical and biochemical, from generation to generation  Transmission of Hereditary Information Nucleus Chromosomes Genes Unit of heredity Deoxyribonucleic acid (DNA) Nucleic Acids _________________ Carries hereditary and genetic information for an organism _________________ Interprets hereditary and genetic information into proteins that will carry out essential cellular functions Nucleotide Building block of nucleic acid chains Consists of: Bases Monosaccharide (sugar) Phosphate Bases Purines Pyrimidines  Sugar Sugar for Sugar for RNA: DNA: ________ ________ ________ ________ _ _ Nucleoside ____ + ____ Phosphate  ____ + ____ + ____ Nucleotide Chains linked together Nucleic acid Nucleic Acids Sample Problems Nucleotide structure GTP is important for energy storage. Draw the structure of guanosine triphosphate. Draw the structure of UMP DNA structure Primary structure: __________ Sequence of deoxyribonucleotides Connected by __________ bonds DNA structure Secondary structure Strands of DNA coil around each other in a screw-like fashion → _________________ Based on: __________ rule: quantity of A in moles is approximately equal to the quantity of T and quantity of G in moles is approximately equal to the quantity of C X-ray diffraction photographs from Rosalind Franklin and Maurice Wilkins where two polynucleotide chains run in _________________ DNA structure Secondary structure Base pairs: adenine pairs with __________, and cytosine pairs with __________ via hydrogen bonding The two strands of DNA are both __________ and __________ There are ~10.0 nucleotides in each strand per complete 360° turn of the helix DNA structure Superstructures __________: Consists of a strand of DNA wrapped around a small disk made up of histone proteins __________: A larger structure made of strings of beads of nucleosomes __________: Complex of DNA and proteins __________: pieces of DNA that carry the genes RNA structure Sugar-phosphate backbone: sequence of ribonucleotides connected by 3’-5’ phosphodiester bonds __________ Base pairing: adenine pairs with __________, and cytosine pairs with guanine Classes of RNA Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA) Small nuclear RNA (snRNA) Micro RNA (miRNA) Small interfering RNA (siRNA) Classes of RNA Messenger RNA (mRNA) Carries the __________ for a __________ from DNA to the ribosomes Complementary RNA copy of a gene on the DNA Classes of RNA Ribosomal RNA (rRNA) Structural and functional component of ribosomes “__________” on which __________ occurs Classes of RNA Transfer RNA (tRNA) Transports amino acids to the site of the protein synthesis in ribosomes __________ the genetic code of the mRNA into the __________ of amino acids in the protein Classes of RNA Small nuclear RNA (snRNA) Complexed with proteins to form _________________ Helps with processing of __________ transcribed from DNA in a mature form that is ready for export out of the nucleus Classes of RNA Micro RNA (miRNA) Inhibits __________ of mRNA into protein and promote the __________ of mRNA Can stimulate protein production in cells when cell cycle has been arrested Classes of RNA Small interfering RNA (siRNA) Eliminates expression of an __________ and leads to the degradation of specific mRNA molecules Knocks out known genes  DNA and RNA differences DNA RNA Bases A-T, C-G A-U, C-G Sugar 2-deoxy-D-ribose D-ribose Strand Almost always double- Single-stranded stranded (double helix)  DNA Replication Guide Questions: Answer the following while watching the video on DNA Replication What are the purposes of the following enzymes?: helicase, primase, DNA polymerase, exonuclease, DNA ligase What results from the unzipping of DNA? What is the function of the RNA primer in the replication process? What is the condition of DNA polymerase in replicating? What is the difference between leading and lagging strand? What is the limitation of DNA polymerase in replicating along the lagging strand?  Enzymes of DNA Replication SSB protein: keep the two parent Helicase: _____ the DNA strand by DNA strands separated breaking the H bonds between them DNA polymerase III: binds to the RNA primer to __________ (daughter strand) Topoisomerase: alleviates and prevents _____ of DNA DNA ligase: __________in both replicated strands by _____ strand catalyzing the formation of 5’ – 3’ phosphoester bonds between Primase: creates the RNA primer the fragments _____ strand 3’ – 5’ DNA polymerase I: catalyzes the removal of RNA primers and _____ left behind with DNA Semiconservative Central Dogma of Molecular Biology Replication Replication Transcription Translation DNA RNA Protein Reverse Transcription  Central Dogma of Molecular Biology Guide Questions: Answer the following while watching the video on Central Dogma What is the purpose of RNA polymerase? What happens to the mRNA right after the transcription process? After the post-transcripted mRNA is expelled from the nucleus to the cytoplasm, what happens to it? What is the purpose of the ribosome and tRNA? How does the tRNA interact with the mRNA to provide the correct amino acid?  Transcription Process by which messenger RNA (mRNA) is synthesized based on DNA template One strand of DNA molecule is transcribed Complementary sequence: Initiation C-G, A-U, T-A Termination Elongation  Transcription RNA polymerases RNA polymerase I (pol I): Catalyzes formation of most of the rRNA RNA polymerase II (pol II): Catalyzes formation of mRNA RNA polymerase III (pol III): Catalyzes formation of tRNA, ribosomal subunit, and other small regulatory RNA types  Transcription ____ (expressed sequences): nucleotide sequences in DNA or _____ (intervening sequences): do not code for a protein mRNA that codes for a protein Post-transcription process Capping Splicing  Translation Information encoded in a mRNA molecule is used to assemble a specific protein Ribosomes Where __________ happens Contains rRNA and polypeptide chains Has larger and smaller units mRNA attaches to the smaller unit of the whole ribosome unit  Translation Information encoded in a mRNA molecule is used to assemble a specific protein Aminoacyl-tRNA synthetase tRNA Carries the amino acids as dictated by the ____ from mRNA Has two important segments: The site to which enzymes attach the amino acids Recognition site Anticodon  Translation Genetic code  Translation Activation Amino acid is activated by reacting with a molecule of adenosine triphosphate (ATP)  Translation Initiation Forming the pre-initiation complex Migration to mRNA  Translation Initiation Migration to mRNA Forming the full ribosomal complex  Translation Initiation Forming the full ribosomal complex  Translation Elongation Binding to the A site Forming the first peptide bond Translocation Forming the second peptide bond  Codon in mRNA: GCU CCA Codon in mRNA: GGU  Translation Termination  Translation Termination H2O  Translation Termination Sample Problems Genetic Code Which amino acid is represented by the codon CGU? What is its anticodon? What are the codons for histidine? What are the anticodons? Translation A tRNA has an anticodon, 5’ AAG 3’. Which amino acid will this tRNA carry? What are the anticodons that are linked to the other end of valine-tRNA, in 3’ to 5’ direction? Mutation Error in the __________ of bases Causes Ionizing radiation (x-ray, ultraviolet, gamma rays) Mutagens (carcinogens) Types Point Deletion Insertion Mutation Negative: inborn genetic diseases (ex. Sickle cell anemia) Positive: enhancement of survival rate of species, development of new strains of plants, sterilization of areas (by UV light that causes pyrimidine dimerization) DNA Repair _____ excision repair (BER) pathway: Specific DNA glycosylase recognizes the damaged base _____ excision repair (NER) pathway: Removal of whole nucleotides, as many as 25-32 residue oligonucleotides Manipulating DNA Recombinant DNA techniques Manipulating DNA Recombinant DNA techniques Manipulating DNA Recombinant DNA techniques Sample Problems Restriction endonucleases Two different restriction endonucleases act on the following sequence of a double-stranded DNA: ~~AATGAATTCGAGGC~~ ~~TTACTTAAGCTCCG~~ One endonuclease, EcoRI, recognizes the sequence GAATTC and cuts the sequence between G and A. The other endonuclease, TaqI, recognizes the sequence TCGA and cuts the sequence between T and C. What are the sticky ends that each of these endonucleases will create? Gene Therapy Treatment of genetic diseases through introducing a gene for a missing protein Usually, __________ are used as vectors to alter somatic cells Two types of delivery methods Ex vivo In vivo Ex vivo Somatic cells are __________ from the patient, altered with gene therapy, and returned to the patient Most common vector: _________________ (MMLV) Ex vivo Ex vivo Adenosine deaminase (ADA) deficiency ADA deficiency Affects DNA synthesis in lymphocytes Immune system is Development of severe greatly compromised combined immune deficiency (SCID) David Vetter, the “bubble boy” Ex vivo Adenosine deaminase (ADA) deficiency Get bone marrow cells from SCID patients Introduce gene for ADA using a virus as a vector Reintroduce bone marrow in the body ADA will be produced in the patient’s body In vivo Virus is used to __________ the tissues of the patient Most common vector: __________ Used in clinical trials for cystic fibrosis, and ornithine transcarbamylase deficiency in humans, and in treating diabetes for mice Risks of Gene Therapy Dangerous immunological response to the vector carrying the gene The gene can be incorporated to the host chromosome at a location that activates a cancer-causing gene DNA Amplification Polymerase Chain Reaction (PCR) Used when the _________________, or at least a sequence bordering the desired DNA is known __________: process in which two strands of nucleic acids or segments of nucleic acid strands form a double-stranded structure through hydrogen bonding of complementary base pairs Sequence Denaturation Annealing DNA synthesis DNA Amplification Polymerase Chain Reaction (PCR) Taq DNA polymerase DNA Amplification Polymerase Chain Reaction (PCR) Applications Disease diagnosis DNA fingerprinting DNA Sequencing Guide Questions: Answer the following while watching the video on DNA Sequencing What components are added to the isolated plasmid DNA before sequencing? Why is the isolated DNA exposed to the following temperatures in order?: 96 °C, 50 °C, and 60°C What is the purpose of adding the terminator base after the addition of free DNA bases to create the new strand? After the creation of the new strand, why is the DNA heated again to 96°C? How does gel electrophoresis arrange the new DNA fragments upon going into the capillary tube for analysis? What is the function of the laser at the end of the capillary tube during electrophoresis? DNA Sequencing Involves reactions in which DNA polymerase copies specific DNA sequences. __________ that cause chain termination (dideoxynucleotides) are incorporated randomly into the growing DNA chain. This generates a family of DNA fragments that differ in size by one nucleotide. DNA sequencing _____ separate these fragments and provide DNA sequence data.