Structure and roles of DNA, RNA 1 nucleotide = Pentose + nitrogenous base + phosphoric acid 1) 5 carbon sugar, RNA ribose

e (OH), DNA deoxyribose (H)

cytosine pairs guanine => 3 H bonds --- complimentary base pairing RNA - single stranded (except genomes of some viruses) - mRNA, tRNA, rRNA = involved in protein synthesis DNA is packed in chromosomes. Each DNA associates with proteins called histones. DNA is slightly negative in electronegativity. Histones are positively charged. Thus DNA and histones associate via ionic attractions. Most DNA is wound around outside of groups of 8 histones to form nucleosomes. Remaining is linker DNA, joining adjacent chromosomes. Nucleosomes and linkers constitute the chromatin fibre. Chromatin fibre coils around itself to form solenoid, 6 nucleosomes per turn of the helix in a solenoid. Further coiling chromosome Describe Process of DNA replication, evidence for semi-conservative replication Semi-conservative replication: Both strands of DNA separate and each act as a template for the synthesis of a new complementary strand. Each DNA formed Is a hybrid consisting of one old and one new strand (semi-conserved) Conservative replication: parental double-helix acts as template for synthesis of a new DNA double helix, Parental DNA remains intact and goes into one daughter cell while newly synthesized DNA goes into other daughter cell. Dispersive: Parental strand fragmented and dispersed to daughter strands. Each strand of both daughter molecules contains mixture of old and newly synthesized parts. Results of Meselson-Stahl experiment 1 generation cells: DNA bands in caesium chloride were located between pure 15N -DNA and pure 14 N -DNA. Thus, DNA of first generation cells was a hybrid (1 14 N strand, 1 15N strand)
st

no conservative replication (no hybrids 2nd generation cells: Half the cells had hybrid DNA, while the other half had pure 14 N-DNA Excludes dispersive replication (no pure 14 N DNA obtained) Semi- Conservative Replication - occurs during S-phase of eukaryotic cell cycle - Before start of DNA replication: free nucleotides are manufactured in cytoplasm, transported into nucleoplasm via nuclear pores Start of DNA Replication 1. replication begins at origins of replication (specific sequence of nucleotides) specific enzymes (helicases, topoisomerase) and other proteins initiate replication. They bind to each origin of replication on parental DNA molecule. Helicase/topoosomerase disrupts H bonds between complementary base pairs. Ensures 2 parental strands of double helix unwind and separate, replication forks form and spread in both directions creating replication bubble. Once a primer is in place, the enzyme DNA polymerase catalyses the elongation and synthesis of the complementary daughter strand. The end of the RNA primer provides free 3 OH which is required for DNA polymerase to initiate DNA synthesis. DNA polymerase recognizes the bases, selects free deoxyribonucleotides to be aligned in a sequence complementary to parental strand. DNA polymerase catalyses formation of phosphodiester bonds between adjacent deoxyribonucleotides of the newly formed daughter strand. As DNA polymerase moves along template, part of enzyme proof-reads (check if proper base pairing is made, swiftly

2)
3) a. b.

phosphoric acid (h3PO4), when dissociated, it gives nucleic acids its acidic character. nitrogenous bases- purines/ pyramidines purines double ring- adenine, guanine pyramidines single ring cytosine, thymine (uracil in RNA) Nucleotide Formation = Condensation rxns nitrogenous base attaches to 1C of sugar phosphoric acid attaches to 5C of sugar two water molecules are removed Nucleic Acid Formation = Condensation rxn nucleic acids formed by combining nucleotides (condensation btw phosphate group of one with sugar of other) covalent bond linking adjacent nucleotides called phosphodiester bond long polynucleotide chain has backbone of alternating sugar and phosphate groups with bases projected sideways frm sugar sugar-phosphate backbone Anti-parallel 5: phosphate group attached to sugar 5C 3: hydroxyl group to sugar 3C polynucleotide has 5 to 3 orientation Chargaffs Rules 1) ratio of A:T = 1: ration of G:C =1 2) ratio of (A+G): (C+T) = 1 width btw 2 sugar phosphate backbones = o.2nm = combined width of a pyramidine + purine 1 complete turn of the double helix has 10 base pairs, 3.4nm 2 strands held in position by weak hydrogen bonds forming btw nitrogenous bases of opposite strands Adenine pairs thymine => 2 H bonds

2. 3.

4.
5. 6.

7.
8.

remove incorrect deoxyribonucleotide, replace with correct one) 9. DNA polymerase links deoxyribonucleotides to growing daughter strand frm 5 to 3. 10. a different DNA polymerase removes RNA primer, replacing it with DNA

Replication is carried out by DNA polymerase in nucleolus Transcription carried out by RNA polymerase in Nucleolus Translation performed on ribosomes in cytoplasm

1.

Since parental strands are anti-parallel, 2 daughter strands synthesized in opposite directions. Leading strand is synthesized continuously in 5 to 3 direction, Lagging strand also same direction, but in shorter segments of 100 to 300 nucleotides. Fragments produced by this discontinuous synthesis are called Okazaki fragments. Each okazaki fragment initiated by RNA primer before addin deoxyribonucleotides Okazaki fragments extend in 5 to 3 direction and eventually join up with other fragments forming continuous DNA strand. continuous DNA strand when DNA polymerase excises RNA primer and replace it with DNA a linking enzyme ligase joins 3 of each new DNA fragment to 5 of growing chain by forming phosphodiester bond.

DNA code mRNA Sequence of bases on mRNA molecule complementary to that on DNA template it was derived from. Triplet bases in mRNA called codons. Code is degenerate, non overlapping, not punctuated, bordered by start [(AUG) and stop (UAG/UAA/UGA) codons, universal. Starts/stops polypeptide chain synthesis during translation Protein Synthesis Ribosomes interact with mRNA and amino-acidcarrying transfer RNA molecules, to translate info in mRNA molecule into polypeptide. mRNA (3-5%) of total RNA in cell, single-stranded RN formed from DNA template during transcription rRNA (80%), combines with protein to form large and small ribosomal subunits, existing via nuclear pores. In cytoplasm, subunits combine to form functional ribosomes. (synthesized in nucleolus) tRNA (15%)folded back upon itself, held in shape by H bonding between There is anticodon region made of specific triplet base sequence located at specific region on folded tRNA molecule complimentary to codon foud on mRNA 3 end of tRNA always ends with CCA, where amino acid specific to tRNA binds. 1. TRANSCRIPTION

DNA sequence of a gene is used as template to make complementary base sequence of mRNA. Transcription factors bind to promoter region, forming transcription factor-DNA complex. Complex recognized by RNA polymerase, binds to promoter region. RNA polymerase unwinds DNA doble helix at initiation site. DNA has 2 exposed strands, sense strand is transcribed (template) for mRNA production Free ribonucleotides from nucleoplasm matched with DNA template by complementary base pairing (A-U) RNA polymerase catalyses joining of adjacent ribonucleotides through formation for phosphodiester bonds. SO RNA Polymerase moves from 3 to 5 mRNA synthesized in 5 to 3 direction. When RNA polymerase reaches end of gene, polymerase dissociates and newly formed RNA released. Common termination sequence AATAAA. Pre-mRNA processed before leaving via nuclear pores. Splicing = excision of introns (non-coding regions), join exons.

2.

The sequence of nucleotides in the DNA molecule determines order in which amino acids are joined together to form proteins. Gene = specific sequence of nucleotides along DNA molecule, coding for specific sequence of amino acids in a polypeptide chain Central Dogma = flow of genetic info from DNA to protein 1. 2. 3. 4. genetic info stored as DNA in all cells, in many viruses too. Replication of genetic info involves DNA synthesis genetic info expressed in cell, flowing directionally from DNA to RNA RNA to protein (translation) reverse transcription possible (RNA to DNA)

Lets talk about RIBOSOMES. aggregates of protein and rRNA. Eukaryotes [40s small subunit, 60S large subunit = 80S ribosome] P site = peptidyl tRNA site A site = aminoacyl-tRNA site E site = exit site TRANSLATION is mRNA amino acid sequence Amino Acid activation Amino acid attached to specific tRNA. Reaction erquires ATP, catalysed by group of enzymes called aminoacyl-tRNA synthetases tRNA + amino acid = aminoacyl-tRNA complex. -

Binding of mRNA to ribosome Small subunit attaches to 5 end of mRNA. Slightly downstream from 5 end is AUG. Initiation of polypeptide chain Initiator aminoacyl-tRNA binds to AUG start codon MRNA, aminoacyl-tRNA, small ribosomal subunit is joined by large ribosomal subunit. Initiator aminoacyl tRNA positioned in P site of large ribosomal unit. GTP provides energy for assembly of this complex. 2nd level of specificity matching of specific anticodon to codon. Chain elongation Codon Recognition anticodon of 2nd aminoacyl-tRNA complex forms H bonds with second codon on mRNA through complementary base pairing. This is held at A site of ribosome. Hydrolysis of 2 molecules of GTP provides energy for this step. Peptide bond formation peptide bond formed between 1st and 2nd amino acid (catalysed by peptidyl transferase, present in large ribosomal subunit first a.a. dissociates from tRNA. Translocation ribosome shifts one codon down in 5 to 3 direction. 2nd aminoacyl-tRNA complex now from A site to P site. 2nd now exit site 1st tRNA is now released to cytoplasm for recycling. A site ready to receive 3rd aminoacyl-tRNA comlex with anticodon complementary to third codon along mRNA. So. P site holds the tRNA carrying growing polypeptide chain, while A site holds tRNA carrying next amino acid. Chain termination Specific proteins called release factors enter A site instead, causing hydrolysis of bond between polypeptide chain and tRNA in P site. Polypeptide is released from ribosome, to complete folding to assume secondary/tertiary structure.

Ribosome disassembles into subunits.