DNA Structure & Replication PDF

Concept 1: DNA is the genetic material, Nucleic acids store and transmit hereditary information...

Concept 1: DNA is the genetic material, Nucleic acids store and transmit hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a Presented by Dr Ghada Khawaja gene (or is encoded by a gene) Genes are made of DNA, a nucleic acid DNA Structure & DNA replication Overview: Life’s Operating Instructions The Roles of Nucleic Acids In 1953, James Watson and Francis Crick introduced an elegant double- There are two types of nucleic acids: helical model for the structure of deoxyribonucleic acid, or DNA – Deoxyribonucleic acid (DNA) DNA, the substance of inheritance, is the most celebrated molecule of our time – Ribonucleic acid (RNA) Hereditary information is encoded in DNA and reproduced in all cells of the DNA provides directions for its own replication body – Thus, as a cell divides, its genetic instructions (DNA) are passed to each daughter This DNA program directs the development of biochemical, anatomical, cell physiological, and (to some extent) behavioral traits DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes DNA -Genes in DNA do not build proteins directly Nucleotide Monomers 1 -They work through an intermediary, the second type of nucleic acid, the RNA Synthesis of mRNA in the There are two families of nitrogenous bases: – Pyrimidines (cytosine, thymine, and uracil) have a nucleus mRNA - In the nucleus of a eukaryotic cell, a gene directs the synthesis of an RNA molecule  DNA is transcribed into RNA single six-membered ring - RNA molecules moves out of the nucleus and NUCLEUS CYTOPLASM – Purines (adenine and guanine) have a six- interact with the protein building machinery of the cell called ribosome membered ring fused to a five-membered ring 2 mRNA - There, the gene’s instructions written in Movement of mRNA into cytoplasm Ribosome Sugars nucleic acid language are translated into via nuclear pore protein language, the aa sequence of a polypeptide 3 In DNA, the sugar is - P.S: in prokaryotic cells, which lack nuclei, Synthesis deoxyribose; in RNA, of protein both transcription and translation take place the sugar is ribose within the cytoplasm of the cell Deoxyribose (in DNA) Ribose (in RNA) Amino Polypeptide acids (c) Nucleoside components: sugars 5’ end Nucleotide Polymers Nitrogenous bases Pyrimidines The Structure of Nucleic Acids 5 C 3 C Nucleic acids are polymers called Nucleoside Nitrogenous base polynucleotides Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Each polynucleotide is made of monomers called nucleotides 5 C Phosphate group Sugar (pentose) Each nucleotide consists of a nitrogenous base, Adenine (A) Guanine (G) 3 C (b) Nucleotide Sugars a pentose sugar, and a phosphate group 3’ end (a) Polynucleotide, or nucleic acid The portion of a nucleotide without the - Nucleotide polymers are linked together to build a polynucleotide - Adjacent nucleotides are joined by covalent bonds that form between phosphate group is called a nucleoside the –OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars - These links create a backbone of sugar-phosphate units with nitrogenous bases as attachments (nitrogenous bases are not part of the backbone) - The sequence of bases along a DNA or mRNA polymer is unique for each gene  - DNA is a double helix 5' end 3' end - Because of the base pairing rules, the 2 strands of the double helix are said to be complementary, each a Sugar-phosphate predictable counter part of the other backbones (e.g. If a stretch of nucleotides on one strand has the base Base pair (joined by sequence AGCACT, then the same stretch on the other strand must be TCGTGA) hydrogen bonding) -Complementary base pairing is the key to know a cell makes two identical copies of each of its DNA molecules every time Old strands it divides Nucleotide - Thus, the structure of DNA accounts for its function of about to be transmitting genetic information whenever a cell reproduces. added to a new strand - The same base pairing rules (with the 3' end exception that U nucleotides of RNA pair with A nucleotides of DNA) also account for the precise transcription of information from DNA to RNA. 5' end An organism’s genes determine the proteins and thus the structures and functions of its New body. strands 3' end 5' end 5' end 3' end The DNA Double Helix Concept 2: Many proteins work together in A DNA molecule has two polynucleotides spiraling DNA replication and repair around an imaginary axis, forming a double helix The relationship between structure and function is In the DNA double helix, the two backbones run in manifest in the double helix opposite 5 → 3 directions from each other, an arrangement referred to as antiparallel Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic One DNA molecule includes many genes material The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) The Basic Principle: Base Pairing to a Getting Started Template Strand Replication begins at particular sites called origins of replication, Since the two strands of DNA are complementary, each strand acts as where the two DNA strands are separated, opening up a replication a template for building a new strand in replication “bubble” In DNA replication, the parent molecule unwinds, and two new A eukaryotic chromosome may have hundreds or even thousands of daughter strands are built based on base-pairing rules origins of replication Replication proceeds in both directions from each origin, until the entire molecule is copied (a) Origin of replication in an E. coli cell (b) Origins of replication in a eukaryotic cell Double-stranded DNA Replication: A Closer Look Origin of replication Parental (template) strand Origin of replication DNA molecule Daughter (new) strand Parental (template) Daughter (new) The copying of DNA is remarkable in its speed and Double- Replication fork strand strand stranded accuracy DNA molecule Replication bubble More than a dozen enzymes and other proteins Bubble Replication fork participate in DNA replication Two daughter DNA molecules Two daughter DNA molecules 0.25 m 0.5 m  At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating Helicases are enzymes that untwist the double helix at the replication forks Synthesizing a New DNA Strand Single-strand binding proteins bind to and stabilize single-stranded DNA Topoisomerase corrects “overwinding = overtwisting” ahead of replication forks by Enzymes called DNA polymerases catalyze the elongation of new DNA breaking, swiveling, and rejoining DNA strands at a replication fork Primase Most DNA polymerases require a primer and a DNA template strand The rate of elongation is about 500 nucleotides per second in bacteria 3 and 50 per second in human cells Topoisomerase 5 RNA 3 primer 5 3 Helicase 5 Single-strand binding proteins DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end The initial nucleotide strand is a short RNA primer An enzyme called primase can start an RNA chain from scratch and Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate adds RNA nucleotides one at a time using the parental DNA as a dATP supplies adenine to DNA and is similar to the ATP of energy metabolism template The difference is in their sugars: dATP has deoxyribose while ATP has ribose The primer is short (5–10 nucleotides long), and the 3 end serves as As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a the starting point for the new DNA strand molecule of pyrophosphate Antiparallel Elongation The antiparallel structure of the double helix affects replication Overview DNA polymerases add nucleotides only to the free 3end of a growing Leading strand Origin of replication Lagging strand; therefore, a new DNA strand can elongate only in the strand 5to 3direction Primer Along one template strand of DNA, the DNA polymerase synthesizes a Lagging Leading leading strand continuously, moving toward the replication fork strand strand Overall directions of replication Overview Origin of Leading replication Origin of replication Lagging strand strand 3 Primer 5 Lagging Leading strand Origin of strand Overall directions replication 5 RNA primer of replication 3 3 Sliding clamp 3 5 DNA pol III RNA primer Parental DNA 5 5 3 3 Sliding clamp 3 DNA pol III 5 Parental DNA 5 3 5 5 5 3 3 3 3 5 5  3 Overview 3 5 3 Leading Origin of replication Lagging 5 Template Template 3 strand strand strand RNA primer 5 strand 5 for fragment 1 Lagging strand 3 2 1 5 Leading 1 3 strand Overall directions 5 of replication 3 Okazaki fragment 1 5 1 RNA primer 3 for fragment 2 5 5 3 Okazaki To elongate the other new strand, called the fragment 2 2 lagging strand, DNA polymerase must work 1 in the direction away from the replication 3 5 5 fork 3 The lagging strand is synthesized as a series 2 of segments called Okazaki fragments, 1 3 5 which are joined together by DNA ligase 5 3 2 1 3 5 Overall direction of replication 3 5 3 Template strand 5 3 RNA primer for fragment 1 Overview 5 1 3 5 Leading Origin of replication Lagging strand strand Lagging strand To elongate the other new strand, called the 2 lagging strand, DNA polymerase must work 1 in the direction away from the replication Leading fork strand The lagging strand is synthesized as a series Overall directions of segments called Okazaki fragments, of replication which are joined together by DNA ligase 3 3 5 3 5 3 Template Template strand 5 strand 5 3 RNA primer 3 RNA primer for fragment 1 for fragment 1 5 5 1 3 1 3 5 5 3 Okazaki 3 Okazaki fragment 1 fragment 1 5 5 1 1 3 RNA primer 3 5 for fragment 2 5 5 3 To elongate the other new strand, called the 2 lagging strand, DNA polymerase must work Okazaki fragment 2 1 3 in the direction away from the replication 5 5 fork 3 The lagging strand is synthesized as a series 2 of segments called Okazaki fragments, 1 3 which are joined together by DNA ligase 5 5 3 3 3 5 3 5 3 Template Template strand 5 strand 5 3 RNA primer 3 RNA primer for fragment 1 for fragment 1 5 5 1 3 1 3 5 5 3 Okazaki 3 Okazaki fragment 1 fragment 1 5 5 1 1 RNA primer 3 RNA primer 3 for fragment 2 5 for fragment 2 5 5 5 3 3 2 2 Okazaki Okazaki fragment 2 1 3 fragment 2 1 3 5 5 5 3 To elongate the other new strand, called the 2 lagging strand, DNA polymerase must work 1 3 in the direction away from the replication 5 5 fork 3 The lagging strand is synthesized as a series 2 1 3 of segments called Okazaki fragments, 5 which are joined together by DNA ligase Overall direction of replication  DNA pol III synthesizes DNA pol III leading strand continuously 3 Parental DNA Leading strand 5 5 Parental 5 3 3 DNA DNA pol III starts DNA synthesis at 3 end of primer, 3 Origin of 5 5 continues in 5 3 direction replication 3 5 3 5 Lagging strand synthesized Connecting Helicase in short Okazaki fragments, protein Helicase later joined by DNA ligase 3 5 Lagging DNA strand Primase synthesizes 3 Lagging strand template a short RNA primer 5 pol III 5 3 DNA pol I replaces the RNA primer with DNA nucleotides The DNA Replication Complex Proofreading and Repairing DNA The proteins that participate in DNA replication form a large complex, DNA polymerases proofread newly made DNA, replacing any a “DNA replication machine” incorrect nucleotides The DNA replication machine may be stationary during the replication In mismatch repair of DNA, repair enzymes correct errors in base process pairing DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA 5 3 3 5 Replicating the Ends of DNA Molecules Nuclease Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes 5 3 3 5 Because DNA polymerases can only add nucleotides to the 3 end of a preexisting polynucleotide, the usual replication machinery provides DNA no way to complete the 5 ends, so repeated rounds of replication polymerase produce shorter DNA molecules with uneven ends 5 3 This is not a problem for prokaryotes, most of which have circular 3 5 chromosomes DNA ligase 5 3 3 5 5 Ends of parental Leading strand Evolutionary Significance of Altered DNA DNA strands 3 Lagging strand Nucleotides Last fragment Next-to-last fragment Lagging strand RNA primer Error rate after proofreading repair is low but not zero 5 Sequence changes may become permanent and can be passed on to Parental strand 3 Removal of primers and the next generation replacement with DNA where a 3 end is available These changes (mutations) are the source of the genetic variation 5 upon which natural selection operates 3 Second round of replication 5 New leading strand 3 New lagging strand 5 3 Further rounds of replication Shorter and shorter daughter molecules  Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called telomeres Concept 3: A chromosome consists of a DNA Telomeres do not prevent the shortening of DNA molecules, but they molecule packed together with proteins do postpone the erosion of genes near the ends of DNA molecules It has been proposed that the shortening of telomeres is connected to The bacterial chromosome is a double-stranded, circular DNA aging molecule associated with a small amount of protein If chromosomes of germ cells became shorter in every cell cycle, Eukaryotic chromosomes have linear DNA molecules associated with a essential genes would eventually be missing from the gametes they large amount of protein produce In a bacterium, the DNA is “supercoiled” and found in a region of the An enzyme called telomerase catalyzes the lengthening of telomeres cell called the nucleoid in germ cells Chromatin, a complex of DNA and protein, is found in the nucleus of The shortening of telomeres might protect cells from cancerous eukaryotic cells growth by limiting the number of cell divisions Chromosomes fit into the nucleus through an elaborate, multilevel There is evidence of telomerase activity in cancer cells, which may system of packing allow cancer cells to persist Nucleosome (10 nm in diameter) DNA double helix (2 nm in diameter) H1 Histone Histones tail Nucleosomes, or “beads on 1 m DNA, the double helix Histones a string” (10-nm fiber) Basic Principles of Transcription and Translation Nuclear envelope RNA is the bridge between genes and the proteins for which they code Transcription is the synthesis of RNA under the direction of DNA From Gene to Protein Transcription produces messenger RNA (mRNA) TRANSCRIPTION DNA Transcription & Translation Concept 1: Genes specify proteins via Translation is the synthesis of a polypeptide, using information in the Pre-mRNA transcription and translation mRNA RNA PROCESSING Ribosomes are the sites of translation mRNA DNA Presented by Dr Ghada Khawaja TRANSCRIPTION mRNA In prokaryotes, translation of mRNA can begin before transcription has Ribosome TRANSLATION Ribosome TRANSLATION finished In a eukaryotic cell, the nuclear envelope separates transcription from Polypeptide Polypeptide translation Eukaryotic RNA transcripts are modified through RNA processing to (a) Bacterial cell (b) Eukaryotic cell yield finished mRNA Overview: The Flow of Genetic Information The Products of Gene Expression: A Developing Story The information content of DNA is in the form of specific sequences of A primary transcript is the initial RNA transcript from any gene nucleotides prior to processing DNA Some proteins aren’t enzymes TRANSCRIPTION The DNA inherited by an organism leads to specific traits by dictating The central dogma is the concept that cells are governed by a Many proteins are composed of several polypeptides, each of the synthesis of proteins cellular chain of command: DNA RNA protein which has its own gene mRNA Proteins are the links between genotype and phenotype one gene–one polypeptide Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation Note that it is common to refer to gene products as proteins rather than polypeptides DNA RNA Protein (a) Bacterial cell  Nuclear envelope The Genetic Code During transcription, one of the two DNA strands, called the template How are the instructions for assembling amino acids into proteins strand, provides a template for ordering the sequence of DNA encoded into DNA? DNA TRANSCRIPTION complementary nucleotides in an RNA transcript TRANSCRIPTION There are 20 amino acids, but there are only four nucleotide bases in The template strand is always the same strand for a given gene Pre-mRNA DNA RNA PROCESSING During translation, the mRNA base triplets, called codons, are read in mRNA How many nucleotides correspond to an amino acid? the 5 to 3 direction Ribosome mRNA TRANSLATION Codons along an mRNA molecule are read by translation machinery Codons: Triplets of Nucleotides in the 5 to 3 direction Each codon specifies the amino acid (one of 20) to be placed at the Polypeptide The flow of information from gene to protein is based on a triplet corresponding position along a polypeptide code: a series of nonoverlapping, three-nucleotide words The words of a gene are transcribed into complementary nonoverlaping three-nucleotide words of mRNA (a) Bacterial cell These words are then translated into a chain of amino acids, forming (b) Eukaryotic cell a polypeptide Nuclear Nuclear envelope envelope Cracking the Code DNA template 3 5 DNA strand A C C A A A C C G A G T molecule All 64 codons were deciphered by the mid-1960s DNA DNA TRANSCRIPTION TRANSCRIPTION Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” T G G T T T G G C T C A 5 3 Gene 1 signals to end translation Pre-mRNA Pre-mRNA RNA PROCESSING The genetic code is redundant (more than one codon may specify a TRANSCRIPTION particular amino acid) but not ambiguous; no codon specifies more Gene 2 than one amino acid mRNA U G G U U U G G C U C A mRNA 5 3 Codons must be read in the correct reading frame (correct Codon groupings) in order for the specified polypeptide to be produced TRANSLATION TRANSLATION Ribosome Protein Trp Phe Gly Ser Polypeptide Gene 3 Amino acid (b) Eukaryotic cell (b) Eukaryotic cell Second mRNA base Promoter Transcription unit U C A G UUU UCU UAU UGU U Synthesis of an RNA Transcript 5 3 3 5 Phe Tyr Cys DNA Start point UUC UCC UAC UGC C U Ser RNA polymerase The three stages of transcription 1 Initiation UUA UCA UAA Stop UGA Stop A Leu Third mRNA base (3 end of codon) First mRNA base (5 end of codon) UUG UCG UAG Stop UGG Trp G – Initiation Nontemplate strand of DNA 5 3 CUU CCU CAU His CGU U – Elongation 3 5 Template strand of DNA C CUC Leu CCC Pro CAC CGC Arg C – Termination Unwound RNA transcript CUA CCA CAA Gln CGA A Concept 2: Transcription is the DNA-directed DNA CUG CCG CAG CGG G AUU ACU AAU AGU U synthesis of RNA: a closer look Asn Ser AUC Ile ACC AAC AGC C A AUA ACA Thr AAA AGA A Transcription is the first stage of gene expression Lys Arg Met or AUG start ACG AAG AGG G GUU GCU GAU GGU U Asp GUC GCC GAC GGC C G Val Ala Gly GUA GCA GAA GGA A Glu GUG GCG GAG GGG G Promoter Transcription unit Promoter Transcription unit Evolution of the Genetic Code Molecular Components of Transcription 5 3 3 5 5 3 3 5 DNA DNA Start point Start point RNA polymerase RNA polymerase The genetic code is nearly universal, shared by the simplest bacteria RNA synthesis is catalyzed by RNA polymerase, which pries the DNA 1 Initiation to the most complex animals strands apart and hooks together the RNA nucleotides Nontemplate strand of DNA Genes can be transcribed and translated after being transplanted The RNA is complementary to the DNA template strand 5 3 3 5 from one species to another RNA synthesis follows the same base-pairing rules as DNA, except that