ASAM NUKLEAT

ASAM NUKLEATStruktur dan Sifat DNA dan RNA Sistem Informasi GenetikMetabolismeBahan Genetik (DNA)REPLIKASITRANSKRIPSITRANSLASIProteinStrukturalRegulatorBiokatalis (enzim)PROTEINDNARNAReplikasi DNAReplikasi RNATranskripsi balik(Reverse transcription)TranskripsiTranslasiDogma Biologi Modern (Central Dogma)1PengantarAsam nukleat adalah polimer nukleotidaAsam NukleatNukleotida sebagai monomer asam nukleatNukleotida terdiri dari gula, gugus fosfat, dan basa nitrogenGula dan fosfat membentuk tulang punggung asam nukleat2Penyusun asam nukleat (DNA & RNA)Analog dengan peranan asam amino pd proteinPembawa energi dalam metabolisme seluler (ATP: adenosine triphosphate)Intermediet komunikasi sel (cAMP: adenosine 3,5-cyclic monophosphate, ppGpp: guanosine tetraphosphate)Komponen struktural kofaktor enzim (NAD: nicotinamide adenine dinucleotide, FAD: Flavin adenin dinucleotide)Peran Nukleotida3Karakteristik Pentosa dan Basa NitrogenNukleotida4

Basa Purin dan PirimidinBig word, small ring

Ingat: Penomoran dan struktur umum cincinSmall word, big ring 56

Deoksiribonukleotida (DNA)7

Ribonukleotida (RNA)Ikatan Fosfodiester Menghubungkan Nukleotida8

Ikatan fosfodiester dalam polimer DNA & RNA Ikatan fosfodiester, khususnya pada RNA, dapat dihidrolisis secara nonenzimatik9

RNA cepat terhidrolisis dalam kondisi alkali, DNA sulit terhidrolisis seperti RNA; gugus 2-hidroksil pada RNA terlibat langsung dalam proses hidrolisisHidrolisis RNA dalam kondisi alkaliIkatan Fosfodiester Menghubungkan NukleotidaNotasi Asam Nukleat10A short nucleic acid is referred to as an oligonucleotide. Short is somewhat arbitrary, but polymers containing 50 or fewer. A longer nucleic acid is called a polynucleotide.PRB3251ATCGATCGPOH535 pApTpCpGpApTpCpG-OH 35 pATCGATCG-OH 3ATCGATCGInformasi Genetik11GENSekuen DNA dengan panjang minimum tertentu yang mengkode urutan lengkap asam amino suatu polipeptida, atau RNAPROMOTERGEN STRUKTURALTERMINATORATGSTOPArah transkripsiStruktur dasar gen12Informasi GenetikBahan Genetik SelKromosomEkstrakromosom Plasmid DNA organel Mitokondria KloroplasGenomes and GenomicsThe word genome, coined by German botanist Hans Winkler in 1920, was derived simply by combining gene and the final syllable of chromosome. If not specified, genome usually refers to the nuclear genome!An organisms genome is defined as the complete haploid genetic complement of a typical cell. The genetic content of the organelles in the cell, is not considered part of the nuclear genome. In diploid organisms, sequence variations exist between the two copies of each chromosome present in a cell. The genome is the ultimate source of information about an organism.

Genetic Material in the Living CellsIn a non-dividing cell the nucleus is filled with a thread-like material known as "chromatin".Chromatin is made up of DNA and proteins (mainly histones and some non-histone acidic proteins). Chromosome is a combination of two words, i.e., Chroma-means colour and Somes-means body.

Chromosomes are the nucleoprotein structures that carry the genetic information. In eukaryotes they are located in the cell nucleus." Genome" is all the DNA contained in an organism or a cell, which includes the chromosomes plus the DNA in mitochondria (and DNA in the chloroplasts of plant cells). ChromosomesThe eukaryotic genome is made up of DNA/protein complexes called chromosomes. Gene sequences embedded within chromosomes must still be available for transcription by RNA polymerases and all of the DNA must be capable of being copied by DNA polymerases.Chromosomes have two main functions:To ensure that the DNA is segregated equally to daughter nuclei at cell division, and to ensure that the integrity of the genome is maintained and accurately replicated in each cell cycle. The elements responsible for these functions are centromeres, telomeres and replication origins, respectively

Each chromosome carries a couple of thousand genes.Many of these are common to all human beings.So, 99.9% of your DNA is identical to everyone else's.The remaining 0.1% influences the differences between us. height, hair color and susceptibility to a particular disease.Environmental factors, such as lifestyle also influence the way we look and our susceptibility to disease

Chromosome number/size There are mainly two type: Somatic chromosome number (2n), it is the number of chromosome found in somatic, merismatic and tissues of species. Gametic chromosome (n), it is one half of the somatic number basically it is the haploid number.Chromosome size shows variation depending upon stage of cell division, it is from 1 to 30 in length and diameter from 0.2 to 2 .Longest and thinnest chromosome seen during interphase. Types of chromosomes

There are four types of chromosomes based upon the position of the centromere.

Metacentric: the centromere occurs in the centre and all the four chromatids are of equal length.2) Submetacentric: the centromere is a little away from the centre and therefore chromatids of one side are slightly longer than the other side.3) Acrocentric: the centromere is located closer to one end of chromatid therefore the chromatids on opposite side are very long. 4) Telocentric: the centromere is placed at one end of the chromatid and hence only one arm. Such telocentric chromosomes are not seen in human cells.Prokaryotic and Eukaryotic CellsChromosomal differencesProkaryotes

The genome of E.coli contains amount of 4X106 base pairs> 90% of DNA encode proteinLacks a membrane-bound nucleus. Circular DNA and supercoiled domainHistones not present

Prokaryotic genomes generally contain one large circular piece of DNA referred to as a "chromosome" (not a true chromosome in the eukaryotic sense). Some bacteria have linear "chromosomes". Many bacteria have small circular DNA structures called plasmids which can be swapped between neighbors and across bacterial species. Continue

The term plasmid was first introduced by the American molecular biologist Joshua Lederberg in 1952.A plasmid is separate from, and can replicate independently of, the chromosomal DNA.Plasmid size varies from 1 to over 1,000 (kbp). Plasmid

ContinueEukaryotes

The genome of yeast cells contains 1.35x107 base pairsA small fraction of the total DNA encodes protein.Many repeats of non-coding sequencesAll chromosomes are contained in a membrane bound nucleusDNA is divided between two or more chromosomesA set of five histones DNA packaging and gene expression regulation

Eukaryotic GenomeNuclearMitochondrialPlasmids (in yeast and plant chloroplasts)

Number of genes in the human genomeNumber of genes at least 100,000.HOWEVER, the number of proteinencoding genes is only ~20,000 to 25,000.

How can we explain this?

Lecture no. 5279

Mitochondrial DNA

Mitochondrial DNA is a single double stranded circular molecule.There are several copies in each mitochondrion and there are many mitochondria in each of your cells. Mitochondrial DNA is similar to prokaryotic DNA. There are no histones or any other protein associated with mt DNA. The genes contain no introns. Maternal inheritance.Because it is in a highly oxidizing environment it has a much higher rate of mutations than nuclear DNA. The genes in mt DNA code for mitochondrial ribosomes and transfer RNAs. Some genes code for polypeptide subunits of the electron transport chain common to all mitochondria. 21DNA Molecules Have Distinctive Base CompositionsA most important clue to the structure of DNA came from the work of Erwin Chargaff and his colleagues in the late 1940s.The base composition of DNA generally varies from one species to another.DNA specimens isolated from different tissues of the same species have the same base composition.The base composition of DNA in a given species does not change with an organisms age, nutritional state, or changing environment.In all cellular DNAs, regardless of the species, the number of adenosine residues is equal to the number of thymidine residues (that is, A = T), and the number of guanosine residues is equal to the number of cytidine residues (G = C). From these relationships it follows that the sum of the purine residues equals the sum of the pyrimidine residues; that is, A + G = T + C.

Erwin ChargafDNA Is a Double Helix22

Rosalind Franklin and Maurice Wilkins used the powerful method of x-ray diffraction (1950).

DNA molecules are helical with two periodicities along their long axis, a primary one of 3.4 and a secondary one of 34 .In 1953 Watson and Crick postulated a three dimensional model of DNA structure that accounted for all the available data. Based on: X-ray data and Chargaf rule.

DNA StructureDNA consists of two helical chains wound around the same axis in a right-handed fashion aligned in an antiparallel fashion.There are 10.5 base pairs, or 36 , per turn of the helix. Alternating deoxyribose and phosphate groups on the backbone form the outside of the helix.The planar purine and pyrimidine bases of both strands are stacked inside the helix.

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ABZMajor grooveMinor groove29Comparison of A, B, and Z forms of DNAMost stable structurePyrimidines alternate with purines, alternating C and G.To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformationFavored in many solutions that are relatively devoid of water30

Comparison of A, B, and Z forms of DNAEnzymes in DNA replicationHelicase unwinds parental double helixBinding proteinsstabilize separatestrandsDNA polymerase binds nucleotides to form new strandsLigase joins Okazaki fragments and seals other nicks in sugar-phosphate backbonePrimase adds short primer to template strandExonuclease removesRNA primer and inserts the correct bases47

48Binding proteins prevent single strands from rewinding.ReplicationHelicase protein binds to DNA sequences called origins and unwinds DNA strands.

5 3 5 3Primase protein makes a short segment of RNA complementary to the DNA, a primer. 3 5 5 349ReplicationOverall directionof replication 5 35 3 5 3 3 5DNA polymerase enzyme adds DNA nucleotides to the RNA primer.50Replication 5 5 35 3 3 5 3Overall directionof replicationLeading strand synthesis continues in a 5 to 3 direction.51Replication 3 5 5 5 35 3 3 5 3Overall directionof replicationOkazaki fragmentLeading strand synthesis continues in a 5 to 3 direction.Discontinuous synthesis produces 5 to 3 DNA segments called Okazaki fragments. 52 5Replication 5 5 35 3 3 5 3Overall directionof replication 3Leading strand synthesis continues in a 5 to 3 direction.Discontinuous synthesis produces 5 to 3 DNA segments called Okazaki fragments. Okazaki fragment53Replication 5 5 3 5 3 35 3 3 5 5 3Leading strand synthesis continues in a 5 to 3 direction.Discontinuous synthesis produces 5 to 3 DNA segments called Okazaki fragments. 54Replication 3 5 3 5 5 35 3 3 5 5 3Leading strand synthesis continues in a 5 to 3 direction.Discontinuous synthesis produces 5 to 3 DNA segments called Okazaki fragments. 55Replication 5 5 3 3 5 3 5 35 3 3 5Exonuclease enzymes remove RNA primers.56ReplicationExonuclease enzymes remove RNA primers.Ligase forms bonds between sugar-phosphate backbone. 3 5 3 5 35 3 3 557