MT 6310 LEC Unit 4 - Nucleotides, Nucleic Acids, and Heredity PDF

[LEC] UNIT 4: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY Each cell of our bodies contains thousands of different...

[LEC] UNIT 4: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY Each cell of our bodies contains thousands of different proteins. OUTLINE I. The Molecules of Heredity ○ Nucleic acids guide cells and let them know which proteins to synthesize out of the II. Nucleic Acids extremely large number of amino acid A. DNA vs RNA sequences. B. Purines and Pyrimidines From the end of the 19th century, biologists C. Sugars suspected that the transmission of hereditary D. Nucleosides information took place in the nucleus, more E. Nucleotides specifically in structures called chromosomes. III. DNA Structure The hereditary information was thought to reside in A. Primary genes within the chromosomes. B. Secondary Chemical analysis of nuclei showed chromosomes are C. Superstructure of Chromosomes made up largely of proteins called histones and nucleic 1. Histones 2. Nucleosome acids 3. Chromatin Friedrich Miescher - discovered nucleic acids. ○ Originally called as “nuclein” IV. RNA ○ Found in the nucleus A. Kinds of RNA (tabulated) It was discovered that prokaryotes also have nucleic B. tRNA structure acids. C. rRNA and Ribosome structure Through the work of Oswald Avery, by the 1940s, it V. Genes became clear that deoxyribonucleic acids (DNA) carry A. Genes, Exons, and Introns the hereditary information for transmission and B. Differences in Gene Expression replication. 1. Prokaryotes ○ Other work in the 1940’s demonstrated that 2. Eukaryotes each gene controls the manufacture of one VI. DNA replication protein. A. Replication of DNA ○ Thus the expression of a gene in terms of an B. General Features enzyme protein led to the study of protein C. Molecules involved (tabulated) synthesis and its control. D. Process of DNA replication NOT ALL GENES LEAD TO THE PRODUCTION OF 1. Process PROTEIN; but all genes lead to the production of 2. Reaction Mechanism another type of nucleic acid - RNA. VII. DNA Amplification NUCLEIC ACIDS A. DNA amplification DNA VS RNA B. Polymerase Chain Reaction There are two kinds of nucleic acids in cells: ○ Ribonucleic acid (RNA) IX. DNA Repair ○ Deoxyribonucleic acid (DNA) A. DNA Repair B. Base Excision Repair Both RNA and DNA are polymers built from monomers called nucleotides. THE MOLECULES OF HEREDITY ○ Polymer = set of many molecules linked Heredity is the inheritance of characteristics from together parents to their offspring. ○ Monomer = one molecule Inheritance takes place with the help of biomolecules ○ Monomer of nucleic acids: nucleotides like chromosomes with genes; genes are chemically Nucleotide = base + monosaccharide + phosphate made of nucleic acids. MT 6310 LEC 1  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY Table No.1 DNA vs RNA Table No.3 Pyrimidines DNA RNA Class (and Name Structure mnemonic) BASES Pyrimidines Cytosine (C) Adenine (A) Adenine Guanine (G) Guanine “CUT(e)” Thymine (T) Uracil (U) Cytosine (C) Cytosine SUGAR 2-deoxy-D-ribose: D-ribose: Lacks a hydroxyl on carbon 2 Has hydroxyl on carbon 2 Carbon 4: Amino (-NH2) Less polar; more stable - less More polar; less stable - more susceptibility to hydrolysis susceptibility to hydrolysis Thymine (T) STRUCTURE DOUBLE-STRANDED SINGLE-STRANDED MONOMERS (deoxy)nucleoside-5’ Nucleoside-5’-monophosphate -monophosphate Carbon 4: Oxygen Carbon 5: Methyl (-CH3) dAMP AMP dGMP GMP dCMP CMP Uracil (U) dTMP UMP PURINES AND PYRIMIDINES Serve as the five principle bases of DNA and RNA ○ DNA: Adenine, Guanine, Cytosine, Thymine ○ RNA: Adenine, Guanine, Cytosine, Uracil Purines: two fused rings, Pyrimidines: one ring. Table No.2 Purines Class (and Name Structure Carbon 4: Oxygen mnemonic) Carbon 5: H (implicit) Purines Adenine (A) SUGARS “GA!” Sugars of nucleosides predominantly exist in D-form. RNA: ribose sugar ○ Has hydroxyl on carbon 2 DNA: 2-deoxy-D-ribose sugar ○ No hydroxyl on carbon 2 Carbon 6: Amino (-NH2) Guanine (G) Carbon 6: Oxygen The two sugars of nucleic acids Carbon 2: Amino (-NH2) MT6310 2  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY NUCLEOSIDES EXAMPLES: Nucleoside = base + monosaccharide β-N-glycosidic bond connects the base and sugar. Deoxythymidine-3’-monophosphate (3’-dTMP) Deoxycytidine-5’-diphosphate (5’-dCDP) ○ Purines: Carbon 9 (base)--Carbon 1 (sugar) Deoxyguanosine-5’-triphosphate (5’-dGTP) ○ Pyrimidines: Carbon 1 (base)--Carbon 1 (sugar) There are 8 nucleosides; 4 for DNA, 4 for RNA ○ DNA: deoxyadenosine, deoxyguanosine, deoxythymidine, deoxycytidine ○ RNA: adenosine, guanosine, uridine, cytidine Name of the figure: deoxythymidine-3’-monophosphate Thymine group connected to carbon 1’ One phosphate group connected to carbon 3’ No hydroxyl on carbon 2’ RNA nucleosides (top row) and DNA nucleosides (bottom row) For nucleotides, carbons 1’, 3’, and 5’ are important. ○ Carbon 1’ - β-N-glycosidic bond Carbon 1’ of the nucleoside (which is the same as ○ Carbon 3’ - participate in phosphodiester carbon 1 of the sugar) is anomeric. bonding during polymerization ○ Anomeric: Stereocenter in cyclic form, but not ○ Carbon 5’ - phosphate esters; participate in a stereocenter in linear form. phosphodiester bonding during polymerization NUCLEOTIDES Nucleotide = phosphate + nucleoside Phosphate esters form when phosphoric acid reacts with the hydroxyl (-OH) of the 3’ or 5’ carbon). ○ Monomeric units of nucleic acids have their phosphate groups attached to 5’ carbon. Nucleotides follow their own nomenclature: For D-ribose nucleotides Nucleoside + phosphate ester location + number of phosphate groups EXAMPLES: Adenosine nucleotides Adenosine-5’-triphosphate (5’-ATP) Guanosine-3’-monophosphate (3’-GMP) Adenosine-5’-triphosphate (5’-ATP) serves as a Uridine-5’-monophosphate (5’-UMP) common currency into which energy gained from food is converted and stored. For 2-deoxy-D-ribose nucleotides deoxynucleoside + phosphate ester location + number of phosphate groups MT6310 3  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY DNA STRUCTURE SECONDARY It is observable how they differ in molecular level, thus The ordered arrangement of nucleic acid strands given that difference and magnitude, its function will The double helix model of DNA 2° structure was differ as well proposed by James Watson and Francis Crick in 1953. Provide an idea how molecules do their physiological Double helix: A type of 2° structure of DNA in which part two polynucleotide strands are coiled around each One DNA molecule may have between 1 million and other in a screw-like fashion 100 million bases. ○ They run in opposite directions (antiparallel) ○ Connected by opposite base pairs (A and T; C PRIMARY and G) Nucleic acids are linked together to form a polymer. ○ The sugar-phosphate backbone is hydrophilic Divided into two parts: and exposed to the aqueous environment ○ Backbone - alternating deoxyribose and ○ Bases are hydrophobic and point inward phosphate groups; for structural stability Hydrophobic interactions stabilize ○ Bases - side-chain groups; for genetic the double helix information ○ Stable form: B-DNA (right-handed helix; has a For nucleic acids, the primary structure is the major and minor groove) sequence of nucleotides, beginning with the nucleotide that has the free 5’ terminus ○ The strand and base sequence are read from the 5’ end to the 3’end ○ The four bases are arranged in specific sequences. Three Dimensional structure of the DNA double helix Two grooves are observed when the two strands intertwine to each other and are not equally spaced ○ Minor groove is narrow and shallow ○ Major groove is deep and wide Grooves are present for protein and drug binding Schematic diagram of a nucleic acid molecule purposes. A nucleic acid has two ends: ○ 3’ -OH terminus ○ 5’ -OH terminus Example: Consider the sequence AGT: - Adenine (A) is at the 5’ terminus - Thymine (T) is at the 3’ terminus MT6310 4  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY When nucleosomes condense, it forms a chromatin. It is the “beads of a string” as we call it Nucleosomes are wound in a solenoid fashion, with six nucleosomes forming a repeating unit. Chromatin are further organized into loops, then bands, then chromosomes. Base Pairing Chargaff’s Rule A and T pair by forming two hydrogen bonds. G and C pair by forming three hydrogen bonds SUPERSTRUCTURE OF CHROMOSOMES HISTONES Coiled DNA that serve as the basic foundation structure for chromosomes DNA is coiled around proteins called histones ○ 5 main types - H1, H2A, H2B, H3, and H4. ○ Histones are rich in the basic amino acids Lys and Arg, whose side chains have a positive charge. Basic Amino Acids of Histone + Acidic DNA = strong ionic bonds for nucleosomes. ○ DNA molecules - negatively-charged ○ Histones - positively charged NUCLEOSOME Histones that are arranged forming a unit A core of eight histone molecules around which the 147-base pair DNA helix is wrapped. Nucleosomes are further condensed into chromatin CHROMATIN Chromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of chromosomes MT6310 5  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY Table No. 4 Summary of DNA Structures RNA is an important intermediary for converting the genetic code of DNA to proteins. DNA Structure Key Features/Interactions Three steps: ○ Replication - production of identical molecule Primary Sequence of nucleotides ○ Transcription - 1st step in gene expression; transcribe the genetic sequence DNA Backbone + Bases ○ Translation - converts mRNA to proteins Read from 5’ to 3’ KINDS OF RNA Table No. 5 Roles of Different Kinds of RNA Secondary Right double helix structure (B-DNA) RNA Type Size Function Base pairing Transfer RNA Small Transports amino acids to site (tRNA) of protein synthesis Nucleosome DNA wrapped around eight histones; made possible with ionic interactions between 73 to 93 nucleotides per acidic (-) DNA and basic (+) histones. molecule 147 DNA base pairs per core; 8 histones Does not only contain the per core bases A, U, C, & G, but it also contains nucleotides such as Chromatin “Beads on a string” 1-methylguanosine. Solenoid Six nucleosomes per turn Ribosomal RNA Several Combines with proteins to (rRNA) kinds – form ribosomes, the site of Loop 50 turns per loop variable in protein synthesis size Miniband 18 loops per miniband Messenger RNA Variable Directs amino acid sequence Chromosome Stacked minibands (mRNA) (NOTE: a chromosome still contains 2 super long DNA molecules) Small nuclear Small Processes initial mRNA to its RNA (smRNA) mature form in eukaryotes. RNA Complexed with proteins to INFORMATION TRANSFER form small nuclear ribonucleoprotein particles or “snurps” - function in splicing. smRNA of “snurps” function in catalysis (aka ribozymes) Micro RNA Small Affects gene expression by (miRNA) inhibiting or stimulating protein synthesis; important in growth and development Small interfering Small Affects gene expression; used RNA (siRNA) by scientists to knock out a gene being studied Degrades specific mRNA to control gene activity. MT6310 6  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY Long non-coding Variable Involved in activating or RNA (lncRNA) silencing specific genes Piwi-associated Small Protects animal genomes RNA (piRNA) against transposons Circular RNA Variable Acts as miRNA sponge, controlling the effects of miRNA TRNA STRUCTURE Helps decode a mRNA sequence into a protein Functions at specific sites in the ribosome during translation Eukaryotic ribosomal RNA has 4 types: 18S, 5.8S, 28S, and 5S ○ “S” refers to Svedberg, a measure of density used in centrifugation It has a distinctive fold with 3 hairpin loops that form the shape of a clover leaf One of the hairpin loops contains a sequence called anticodon which can recognize and decode an mRNA codon Each tRNA has its corresponding amino acid attached to its end Outcome of 70S ribosome dissociated into two RRNA AND RIBOSOME STRUCTURE subunits: 30S and 50S rRNA is a catalytic component of the ribosomes ○ One subunit is larger than the other Ribosomes have a small and large subunit ○ Small subunit - 1 large RNA molecule; 20 GENES proteins GENES, EXONS, AND INTRONS ○ Large subunit - 2 to 3 RNA molecules; 35 to Gene: A segment of DNA that carries a base sequence 50 proteins that directs the synthesis of a particular protein, tRNA, When a ribosome is attached to mRNA, it carries out or mRNA. protein synthesis ○ There are many genes in one DNA molecule. ○ In bacteria, the gene is continuous. ○ In higher organisms, the gene is discontinuous - Exons (coding) and introns (noncoding). ○ Few hundred nucleotides that carry one particular message Exon: A section of DNA that, when transcribed, codes for a protein or RNA. MT6310 7  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY ○ A segment of DNA used to transcribe In eukaryotes, the genes are separated by introns and proteins the processes take place in different compartments. ○ The coding sequences are called exons, The DNA is turned into RNA in the nucleus, but then short for “expressed sequences” the initial mRNA, containing introns, is transported to ○ In humans, only 3% of the DNA codes for the cytosol where the introns are spliced out. The final proteins, but it is estimated that over 70% of mRNA is then translated to protein. the DNA does serve a purpose. Intron: A section of DNA that does not code for anything functional. ○ The noncoding sequences are called introns, short for “intervening sequences.” ○ Functions as spacers, or even as enzymes. ○ Can function as satellites - repeated DNA nucleotides Large satellite stretches - appears at ends and centers of chromosomes for stability The properties of mRNA in eukaryotic cells during transcription Mini- or microsatellites - associated and translation with cancer Encounter these when performing analysis in genetic Table No.6 Prokaryotic vs Eukaryotic Gene Expression sequences using BLAST, MEGA or other omni-computational tools Prokaryotic Eukaryotic mRNA are synthesized in the mRNA are synthesized in DIFFERENCES IN GENE EXPRESSION nucleoid region nucleus PROKARYOTES Direct and simultaneous gene Compartmentalized and Prokaryotic mRNA are synthesized in the bacterial expression highly-regulated gene nucleoid in direct contact with cytosol. They are expression immediately available for translation Every region codes for something Most of the regions are In prokaryotes, the genes on a stretch of DNA are next noncoding (introns) to each other. These are turned into a sequence of mRNA, which is then translated by ribosomes to make Transcription and translation occur RNA transcription occurs in the in direct contact with the cytosol nucleus proteins, all of which happens simultaneously. mRNA splicing and translation occurs in the cytosol DNA REPLICATION REPLICATION OF DNA The DNA in chromosomes carries out two functions ○ It reproduces itself; replication ○ It supplies information necessary to make all The properties of mRNA molecules in prokaryotes cells during the RNA and proteins in the body, including transcription and translation. enzymes Replication begins at a point in the DNA called the EUKARYOTES origin of replication or a replication fork. mRNA is produced in the nucleus, it must be transported to the cytosol for translation GENERAL FEATURES The initial product of translation may contain introns, Very organized and sequential which must be removed before translation may occur. Semiconserative: one parent (conserved) and one daughter (new) strand. Occurs at a sequential junction drawn as a fork (replication fork); follows the movement of the helicase enzyme and is initiated by an RNA primer. Replication direction: 5’ to 3’. MT6310 8  UNIT 04: NUCLEOTIDES, NUCLEIC ACIDS, AND HEREDITY ○ DNA nucleotides are only added to the 3’ end will therefore be synthesized this way: ○ The replicate strand has a 3’ to 5’ direction 5’-TCAGCAAT-3’ Has a leading strand and lagging strand. —-------------> Table No. 7 Leading vs Lagging Strand Replication will not be continuous for the strand on the bottom. The complementary strand will primarily exist as Okazaki LEADING LAGGING fragments like this (~ represents fragment): Continuous Discontinuous 3’-A~GT~CGT~TA-5’