Chapter 4 and Chapter 6
Chapter 4 and Chapter 6 BCM 475 - M001
Popular in Biochemistry I
Popular in Biochemistry
BCM 475 - M001
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This 7 page Class Notes was uploaded by Tiffany Liao on Monday November 9, 2015. The Class Notes belongs to BCM 475 - M001 at Syracuse University taught by M. Braiman, R. Welch in Fall 2015. Since its upload, it has received 173 views. For similar materials see Biochemistry I in Biochemistry at Syracuse University.
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Date Created: 11/09/15
Chapter 4 [Pg. 109134] DNA, RNA, and the Flow of Genetic Information DNA Transcription RNA Translation Protein DNA RNA mRNA = (Transcription) Gene expression Codon introns and exons = (Translation) A Nucleic Acid Consists of 4 Kinds of bases linked to a sugar- phosphate backbone DNA & RNA are linear polymers DNA & RNA Differs in the Sugar Component and One of the Bases DNA – Deoxyribose ( 2’ Carbon of the sugar lacks oxygen atom) RNA – Ribose ( 2’ Carbon of the sugar has oxygen atom) Backbone of DNA and RNA 3’-5’ phosphodiester linkages Purines: Adenine, Guanine Pyrimidines: Cytosine, Uracil, Thymine DNA has U instead of T Nucleotides are the monomeric Units of Nucleic Acids N-9 of purine, N-1 of pyrimidinse is attached to C-1’ of sugar by N-Glycosidic linkage Beta-Glycosidic linkage (base lies above the plane of sugar) 5’- ATP 3’- dGMP- differs from ATP; contains guanine rather than adenine, contains deoxyribose rather than ribose; one phosphate group at the 3’ DNA base sequence is 5’-3’ direction A pair of Nucleic Acid Chains with Complementary Sequences can form a Double-Helical Structure X-ray diffraction shows DNA, which the stack of nucleotide bases are 3.4 Å apart The Double Helix is Stabilized by Hydrogen Bonds and Van Der Waals Interactions Maurice Wilkins and Rosalind Franklin x-ray diffraction of DNA fibers Watson & Crick- Structural model for DNA Features: 1) 2 helical polynucleotide chains are coiled around a common axis with a right-handed screw sense. The chains are antiparallel- opposite polarity 2) Sugar-phosphate backbones are on the outside and the purine and pyrimidine bases lie on the inside 3) Bases are nearly perpendicular to the helix axis; adjacent bases are separated by 3.4 Å. The helical structure repeats every 34 Å, 10 bases. Each base rotated 36 degree form one below (360 degree/ full turn/ 10 bases per turn) 4) Diameter of the helix is 20 Å G-C [3 H-Bonds] / A-T [2 H-Bonds] - Stabilize by hydrogen bonds - Van der Waals stacking force Most DNA is in the B-form. Right handed, C-3’ endo- lies out of plane A-form DNA wider and shorter than B-form, base pairs is tilted rather than perpendicular. Also right handed, C-2’ endo-lie in approx. plane Z-from- left handed double helix in which backbone phosphate zigzag Alexander Rich Structure of CGCGCG- Anti-parallel strands held together by W-C base-pairing - Left- handed and has zigzagged backbone (Z-DNA) Different forms show DNA is flexible Some DNA Molecules are Circular and Supercoils Human DNA is linear Bacteria and archae are circular - Can be supercoiled into super helix - Relaxed molecule- not super coiled Supercoiling is important: - Supercoiling DNA is more compact than its relaxed counterpart - Supercoiling may hinder or favor the capacity of the double helix to unwind and affect the interaction btw. DNA and other molecules Single-Stranded Nucleic Acids Can Adopt Elaborate Structures Stem-loop- from single strand DNA/RNA RNA can have more complex structure that can be stabilized by 2+) metal ions such as (Mg The Double Helix Facilitates the Accurate Transmission of Hereditary Info. The sequence of bases of one strand of the double helix precisely determines the sequence of the other strand Semiconservative replication Differences in DNA Density Established the Validity of the Semiconservative – Replication Hypothesis Matthew Meselson and Franklin Stahl Semiconservation 15plicati14 test N and N labeled DNA revealed by density- gradient equilibrium sedimentation -Absence of 15N DNA indicated that parental DNA was not preserved as an intact unit after replication. Absence of 1N DNA indicated that all the dDNA derived some of their form from the parent DNA -RESULT: contains 14N DNA The Double Helix Can be Reversibly Melted DNA comes apart when H-bonds are disrupted Tm (melting temp.)- Temp at which half of the helical structure is lost (In cell)- Proteins “helicases” use chemical energy from ATP to disrupt the helix Hypochromism-stacked base in nucleic acids absorb less ultraviolet light than do un-stacked bases -Melting of nucleic acid can be monitored by measuring their absorption of light at 260nm Annealing- renature process of complementary strands (reannel- hybridize) DNA is Replicated by Polymerases that Take Instructions from Templates Arthur Kornberg isolated DNA polymerase from E.Coli DNA polymerase catalyzes phosphodiester- bridge formation: -DNA polymerase catalyzes step-by-step addition of deoxyribonucleotide units to a DNA chain (DNA)n + dNTP <-> (DNA)n+1 + PPi DNA synthesis characteristics: 1) Requires 4 activated precursors: the deoxynucl2+side 5’- triphosphates dATP, dGTP, dCTP, TTP, and Mg ion 2) The new DNA chain is assembled directly on a preexisting DNA template -DNA polymerase is a template-directed enzyme -Chai-Elongation Reaction- DNA polymerase catalyze the formation of a phosphodiester bridge 3) DNA polymerase require a primer to begin synthesis - A primer strand having free 3’-OH group must be already bound to the template - Chain-elongation reaction- a nucleophilic attack by the 3’-OH terminus of the growing chain on the innermost phosphorus atom of the deoxynucleoside triphosphate - A phosphodiester bridge is formed and pyrophosphate is released - 5’-3’ direction 4) DNA polymerases are able to correct mistakes in DNA by removing mismatched nucleotides DNA Polymerases are Able to Correct Mistakes in DNA by Removing Mismatched Nucleotides RNA template: RNA-directed RNA polymerase Retroviruses- genetic info flow from RNA DNA - On entering cell, RNA is copied into DNA through reverse transcriptase: Synthesis of the RNA, digestion of RNA, subsequent synthesis of DNA strand Gene expression is the transformation of DNA info into functional molecules Different kinds of RNAs: 1) mRNA- the template for protein synthesis, or translation 2) tRNA (Transfer)- Carries amino acids in an activated form to the ribosome for peptide-bond formation 3) rRNA- Major component of ribosomes- catalyst for protein synthesis- most abundant 4) SnRNA- participate in splicing of exons 5) Small RNA- essential component of the signal- recognition particle; helps guide newly synthesized proteins to intracellular or extracellular destinations 6) miRNA (micro)- a class of small noncoding RNAs that bind to complementary mRNA and inhibit their translation 7) SiRNA (Small interfering)- a class of small RNA molecules that bind to mRNA and facilitates its degradation 8) RNA is a component of telomerase maintains the telomeres ends of chromosomes during DNA replication All Cellular RNA is Synthesized by RNA Polymerase (RNA)n+ ribonucleoside triphosphate <-> (RNA)n+1 + ppi RNA polymerase requires: 1) Template: Double-stranded or single-stranded DNA 2) Activated precursors- ATP, GTP, UTP, CTP 2+ 2+ 3) A divalent metal ion, Mg or Mn - Similar to DNA synthesis except RNA polymerase don’t need a primer and the ability to correct mistakes is not as extensive RNA Polymerases take instructions from DNA Templates Complementarity btw. mRNA and DNA Transcription Begins Near Promoter Sites and Ends at Terminator Sites DNA templates contain regions: promoter sites that bind RNA polymerase and determine the starting site Eukaryotic have promoter sites with TATAAA -> TATA box or ”Hogness box” Some have CAAT box- GGNCAATCT Pribnow box- TATAAT RNA synthesis can be terminated by rho Start and stop signals for transcription are encoded in DNA template In Eukaryotes: modification of mRNA 5’Cap --- Coding region--- Poly A tail 3’ Transfer RNAs are the Adaptor Molecules in Protein Synthesis tRNA contains an amino acid attachment site and a template- recognition site the amino acid is esterified to the 3’-hydroxyl group of the terminal adenylate of tRNA Anticodon is the template recognition site Clover leaf structure Anticodon recognizes condon on mRNA Amino Acids are Encoded by Groups of 3 Bases Starting From a Fixed Point Genetic code: 1) 3 nucleotides encode an amino acid (codon) 2) The code is nonoverlapping 3) The code has no punctuation; the sequence of bases is read sequentially from a fixed starting point 4) Genetic code is degenerate Major Features of the Genetic Code Only Try and Met are encoded by just one triplet each (special) - Leu, Arg, Ser 6 condons each Number of Codons correlates with its frequency of occurrence in proteins Synonyms- condons that specify the same amino acid Degeneracy minimizes the deleterious effects of mutations mRNA Contains Start and Stop Signals for Protein Synthesis mRNA is translated into protein on ribosomes (Bacteria)- start with a modified amino-acid fMet recognizes AUG or GUG -Initiate codon is preceded away by a purine-rich sequence Shine Dalgarno Sequence - UAA, UAG, UGA Chain termination, read by release factors (NOT tRNA) The Genetic Code is Nearly Universal (to against mutation) Mitochondria encodes a distinct set of tRNA - AGA and AGG Stop Most Eukaryotic Genes are Mosaic of Introns and Exons RNA processing generates mature RNA Coding sequences are linked by a splicing enzyme to form the mature mRNA -Removed (introns) -Retained (exons) Spliceosomes- Splice introns out - Intron begins with GU and end with an AG that is preceded by a pyrimidine-rich tract - 5’—GU—Pyrimidine tract—AG—3’ Many Exons Encode Protein Domains Introns were present in ancestral genes and were lost in the evolution of organisms that have become optimized for very rapid growth, such as prokaryotes, Advantages of split genes: - Many exons encode discreet structural and functional units of proteins - New proteins arose in evolution by the rearrangement of exons encoding discrete structural elements, binding sites, and catalytic sites= (exon shuffling)- no deleterious effect on encoded proteins - Potential for generating a series of related proteins by splicing a nascent RNA transcript in different ways (alternative splicing)