Dna and rna


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Dna and rna

  1. 1. 9/29/2011 DNA structure & function • DNA is able to accomplish 2 very important things DNA and RNA for an organism. – DNA is used to pass genetic information on to the next generation of organism. The Molecular Basis of Heredity – Determine an organism’s characteristic by controlling the synthesis of the protein. Thus….to understand both of above process…we need to know its chemical structure!DNA structure Hydrogen bond • DNA is a polymer. • The monomer units of DNA are nucleotides, and the polymer is known as a "polynucleotide.“ • Each nucleotide is composed of: - sugar molecule DNA nucleotide - a phosphate group - nitrogenous bases (Adenine, A; Guanine, G; Cytosine, C; and Thymine, T) DNA helix 3 hypothesis of DNA replication • Conservative - old strand acts as a template. - One daughter strand is the original template while the other strand is composed entirely out of new nucleotides. • Dispersive Model - Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA parts 1
  2. 2. 9/29/2011 • Semiconservative - old strand splits apart and acts as a template. -Both daughter strands are composed of one of the old strands and one comprised out of new nucleotides - Watson & CrickBut, how DNA replication works? Ingredients to make a copy of DNA • In DNA replication process…it involve 3 process • Template strand - The DNA serves as a template to guide the 1- Initiation incoming nucleotides. 2- Elongation 3- Termination • DNA polymerase - The enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. - "reads" an intact DNA strand as a template and http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replic uses it to synthesize the new strand. ation/index.html • Free 3’ hydrocyl (Primer) • DNA ligase - DNA polymerase can add a nucleotide onto only - It can catalyze the formation of a a preexisting 3-OH group, and, therefore, needs phosphodiester bond given an unattached but a primer at which it can add the first nucleotide. adjacent 3OH and 5phosphate. • Helicase • Single-stranded binding proteins - accomplishes unwinding of the original double - important to maintain the stability of the strand, once supercoiling has been eliminated by replication fork. the topoisomerase. • Ribonuclease H  removes RNA primers. 2
  3. 3. 9/29/2011 What happen during initiation process? • An enzyme, helicase bind (breaking of hydrogen bonds between bases of the two antiparallel strands. ) to the DNA and separate the 2 strands of DNA. Topoisomerase helps helicase! • The initiation point where the splitting starts is called "origin of replication“ which create replication fork!. • In prokaryotes, DNA replication begins at a single, fixed location in this molecule, the replication origin. • The splitting happens in places of the chains which are rich in A-T. Why? • That is because there are only two hydrogen bonds between Adenine and Thymine (there are three hydrogen bonds between Cytosine and Guanine). • Single-stranded DNA binding protein (SSB) attached to each strand  prevent re-annealing.How can entire chromosome be Now…the elongation process…replicated during S phase? DNA replication begins at many • One of the most important steps of DNA specific sites –replication bubbles! Replication is the binding of RNA Primase in the Parental strand Origin of replication Daughter strand the initiation point of the 3-5 parent chain. • RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3-5 strand due to the hydrogen bonds between the bases. • RNA primase build Primer which is strand of nucleic acid that serves as a starting point for Two daughter DNA molecules DNA synthesis. 3
  4. 4. 9/29/2011 • 5’-3’Template: The 5-3 template cannot be • The elongation process is different for the 5-3 "read" by DNA Polymerase. Why? and 3-5 template. • DNA polymerase can add free nucleotides to only • 3-5 Template: The 5-3 proceeding daughter the 3 end of the newly forming strand strand -that uses a 3-5 template- is called leading strand because DNA Polymerase can "read" the template and continuously adds • The replication of this template is complicated nucleotides (complementary to the nucleotides of and the new strand is called lagging strand. the template, for example Adenine opposite to Thymine etc). • In the lagging strand the RNA Primase adds more RNA Primers. Why we need primer? • It then create a short molecule of single-stranded • DNA polymerase can only extend a nucleic acid DNA at lagging strand  Okazaki fragment. chain but cannot start one from scratch. • To give the DNA polymerase a place to start, an RNA polymerase called primase first copies a short stretch of the DNA strand. • This creates a complementary RNA segment, up to 60 nucleotides long that is called a primer.What is DNA polymerase? • DNA polymerases are a family of enzymes that carry out all forms of DNA replication. • DNA polymerase then synthesizes a new strand of DNA by extending the 3 end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds. • DNA polymerases are extremely accurate, making less than one mistake for every 107 nucleotides added. 4
  5. 5. 9/29/2011 At the end of the process…termination! • In the lagging strand the DNA Pol I - • The RNA Primers are necessary for DNA exonuclease- reads the fragments and removes Polymerase to bind nucleotides to the 3 end of the RNA Primers. them. • Rnase H removes the RNA fragments used to • The daughter strand is elongated with the binding initiate replication by DNA Polymerase, and of more DNA nucleotides. another DNA Polymerase enters to fill the gaps. • The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone). • The DNA replication process is completed when the ligase enzyme joins the short DNA pieces together into one continuous strand.Summary of DNA replication • Helicase unwind the DNA, producing a replication • RNA primase initiate the DNA replication at origin fork. of replication with short RNA nucleotides called Primer. • Single-stranded binding protein (SSB) prevent the single stranded of DNA from recombining. • DNA polymerase attached to the RNA primer and begin elongation (adding the nucleotides to the • Topoisomerase removes twist and knots in the DNA complement strand) double stranded template as a result of the unwinding induced by helicase. • The leading complementary strand is assembled continuously. 5
  6. 6. 9/29/2011 RNA structure and function • The lagging complementary strand is assembled in short Okazaki fragment, which are subsequently joined by DNA ligase. • The RNA primer are replaced by DNA nucleotide.• Cells use DNA and RNA differently.• DNA is the original source for information to make proteins. • These various type of RNA all participate in making protein, but their role are different.• But, RNA is made by enzymes that read the protein-coding information in DNA.• RNA is single-stranded.• Different type of RNA molecules are classified by the way in which it used.• RNA can be classified as mRNA, tRNA and rRNAmRNA - messenger RNA - carries information from DNA of the structural gene to the ribosomewhere the protein is made rRNA - ribosomal RNA - major structural component of the ribosome where protein synthesis occurs tRNA - transfer RNA - carries amino acids to mRNA at the ribosome to assembly the protein being made 6
  7. 7. 9/29/2011Protein synthesis Process of protein synthesis DNA replication • DNA and RNA are both important part of making protein. Transcription • DNA ---> RNA ---> Protein Nucleus • beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA, which is then used as input for translation. Translation cytoplasm http://highered.mcgraw- hill.com/sites/0072507470/student_view0/chapter3/animation__mrna_synthesi s__transcription___quiz_1_.html DNA to mRNA (transcription) • Component needed are: • DNA Template - strand of DNA providing directions for transcription of mRNA. • RNA Polymerase - enzyme that helps to pull apart DNA strands and link new mRNA nucleotides. • Promoter - sequence of DNA that signals where (and on which strand) transcription should begin Transcription of mRNA • Termination Signal - sequence of DNA that Initiation causes RNA Polymerase to detach with the newly transcribed mRNA strand. Elongation Termination 7
  8. 8. 9/29/2011Transcription of mRNA: initiation Transcription of mRNA: Elongation • In eukaryotes, RNA polymerase, and therefore • As transcription proceeds, RNA polymerase the initiation of transcription, requires the traverses the template strand and uses base presence of a promoter sequence in the DNA. pairing complementarily with the DNA template to create an RNA copy. • Promoters are regions of DNA that promote transcription. RNA polymerase uses to find a • Unlike DNA replication, mRNA transcription can protein-coding region of DNA and to identify involve multiple RNA polymerases on a single which of the two DNA strand is the coding strand. DNA template and multiple rounds of transcription (amplification of particular mRNA), so many • Without these promoter sequence, RNA mRNA molecules can be rapidly produced from a polymerase will note transcribe the gene. single copy of a gene.Proofread… Transcription of mRNA: Termination • Elongation also involves a proofreading • When the RNA polymerase reaches the mechanism that can replace incorrectly termination sequence, the sequence cause the incorporated bases. mRNA to fold back on itself. • In eukaryotes, this may correspond with short • This prevent transcription from continuing and pauses during transcription that allow appropriate both the RNA polymerase and mRNA strand fall RNA editing factors to bind. off the DNA strand. • http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.htmlRemember!!! Summary of RNA transcription • The entire molecule of DNA is not expressed in • Initiation: RNA polymerase attached to the transcription. RNAs are synthesized only for promoter region on the DNA & begin to same selected regions of DNA. unzip/unwind the DNA into 2 strand. • RNA polymerase differs from DNA polymerase in • Elongation: RNA polymerase unzips/unwinds the two aspects. No primer is required for RNA DNA & assembles RNA nucleotides using one polymerase and , further this enzyme does not strand of the DNA template. possess end or exonuclease activity. Due to lack - Elongation occur in 5’  3’ direction. of the latter function, RNA polymerase has no - Only 1 DNA strand is transcribed. ability to repair the mistake in the RNA synthesized. 8
  9. 9. 9/29/2011 RNA processing • Termination: when RNA polymerase reaches a • Transcribed mRNA must first be processed special sequence of nucleotides that serves as before it can leave the nucleus for the cytoplasm. termination point (termination sequences). • Steps of mRNA Processing: - In eukaryotes: termination sequence always at DNA sequence AAAAAAA. - Guanine Cap - Several Guanine nucleotides are added to the front end of the mRNA strand in order to bind to the ribosome more effectively. - Poly-Adenine Tail - Several Adenine nucleotides are added to the tail end of the mRNA strand to prevent destruction by RNases (enzymes which break down RNA). - Splicing - Introns are removed and Exons are joined together - Intron - segment of mRNA which does NOT code for protein; therefore, it is removed. - Exon - segment of mRNA which does code for protein; therefore, it remains for expression in proteinProtein, here we come …vocabulary • Genetic code  “Genetic Alphabet” • Triplet Code - three nucleotides code for one amino acid • Genetic "Alphabets" - there are three alphabets involved in the entire process of protein synthesis: - Codon - three nucleotides of mRNA determining which amino acid is added to a protein 1) DNA - A, C, G and T 2) RNA - A, C, G and U - Sample Genetic Code 3) Protein - Twenty different amino acids • Example 1) mRNA Codon = AUG 2) Amino Acid = Methionine 9
  10. 10. 9/29/2011 Code characteristics • It is described in terms of the mRNA codons. STOP codons - UAA, UAG, UGA - all three of these codons signal the end of a polypeptide chain Universal - The genetic code is the same in all living organisms, from bacteria to humans. Degenerate - More than one codon is assigned to each amino acid. This allows for possible mutations to be less damaging. AAA - Lysine AAG - Lysine UAA - Lysine mRNA translation to protein • Initiation• Third Base is usually less specific than the first two. This is also known as the "Wobble - begin when the small ribosomal subunit Hypothesis" because often the third base can attaches to a special region near the 5’ end of the change, but the amino acid remains the same. mRNA. - A tRNA (with anticodon UAC) carrying the amino acid methionine attaches to the mRNA with the hydrogen bond (start codon is AUG). - large ribosomal subunit attaches to the mRNA, forming a complete with the tRNA occupying at P site. - The remaining tRNA moves from the A side to• Elongation the P site. Now the A side is unoccupied and a new codon is exposed. This is anologous to the - begin when next tRNA bind to the A site of the ribsome moving over one codon. ribosome. The methionine is removed from the first tRNA & attached to the amino acid on the - A new tRNA carrying a new amino acid enter newly arrived tRNA. the A side. The 2 amino acid on the tRNA in the P site are transferred to the new amino acid, - the first tRNA, which no longer carries an amino forming a chain of three amino acid. acid, is released. After its released, the tRNA can again bind with its specific amino acid, allowing - the tRNA in a P site is released, the process is repeated deliveries to the mRNA during repeated, polypeptide chain still growing. translation. 10
  11. 11. 9/29/2011 • Termination • Once the polyeptide is completeed, interaction among the amino acids give its secondary & - occurs when the ribosome encounters one of tertiary structure. the three “stop” codon. • Subsequent processing by the endoplasmic - At termination, the complete polypeptide, the reticulum or a Golgi apparatus may make final last tRNA, and the two ribosomal subunits are modifications before the protein functions as released. structural element or as an enzyme. - The ribosomal subunits can now attach to the same or another mRNA and repeat the process. Summary of protein synthesis!!!Applied Biotechnology • Polymerase Chain Reaction!! 11