BASIC MOLECULAR GENETIC MECHANISMS Introduction:

Transcription

1 BASIC MOLECULAR GENETIC MECHANISMS Introduction: nucleic acids. (1) contain the information for determining the amino acid sequence & the structure and function of proteins (1) part of the cellular structures: -select & align amino acids in the correct order ( polypeptide chain) (3) catalyze chemical reactions e.g formation of peptide bonds between amino acids during protein synthesis.

2 Electron micrograph of DNA (green arrow) being transcribed into RNA (red arrow). [O. L. Miller, Jr., and Barbara R. Beatty, Oak Ridge National Laboratory.]

3 DNA: Contains information required to build the cells, tissues -exact replication of DNA assures genetic continuity from generation to Generation. - information stored in DNA arranged in hereditary units= genes, -Transcription:DNA into RNA RNA: Three distinct roles in protein synthesis. -Messenger RNA (mrna) carries the instructions from DNA that specify the correct order of amino acids

4 -Assembly of amino acids into proteins by translation -The information in mrna is interpreted by trna with the aid of rrna -Correct amino acids brought into sequence by trnas, linked by peptide bonds. central dogma of molecular biology

5 FIGURE 4-1 Overview of four basic molecular genetic processes.

6 Sourse: Text2: P Objectives: N.A structure -N.A : Linear Polymer with End-to-End Directionality - Native DNA a Double Helix of Complementary Antiparallel Strands -DNA Can Undergo Reversible Strand Separation - Many DNA Molecules Are Circular -Different Types of RNA Exhibit Various Conformations Related to Their Functions

7 KEY CONCEPTS DNA &RNA are long, unbranched polymers of nucleotides, consist of a phosphorylated pentose linked to organic base a purine or pyrimidine. Adjacent nucleotides in a polynucleotide linked by phosphodiester bonds.

8 The entire strand has a chemical directionality: 3 end with a free OH or phosphate group (5 end) Natural DNA (B DNA) contains two complementary antiparallel polynucleotide strands - wound together into a regular right-handed double helix with the bases in-side and sugar-phosphate backbones outside. Base pairing between strands and hydrophobic interactions between adjacent bases in same strand stabilize native structure.

9 bases in NA interact via hydrogen bonds. standard Watson-Crick base pairs G C, A T (in DNA), and A U (in RNA). Base pairing stabilizes the native threedimensional structures of DNA & RNA. Binding of protein to DNA can deform helical structure, causing local bending or unwinding of DNA molecule.( dense packing of DNA in chromatin)

10 FIGURE 4-2 Alternative representations of a N.A strand illustrating chemical directionality.

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12 FIGURE 4-3 The DNA double helix. Model of B DNA, the most common form of DNA in cells.

13 Alternative Forms of DNA: B form: Most DNA in cells is a right-handed helix: The x-ray diffraction the stacked bases : 0.36 nm apart helix makes complete turn/ 3.6 nm 10.5 pairs per turns Strands form two helical grooves major groove& minor groove - base within these grooves accessible for DNA binding proteins Low humidity:, e crystallographic B DNA changes to A form; RNA DNA & RNA-RNA helices in cells/ in vitro. Z form: Short DNA composed of alternating purine pyrimidine ( Gs and Cs) adopt left-handed helix.

14 evidence suggests t Z DNA may occur in cells(function unknown) Ttriple-stranded DNA: -formed when synthetic polymers of poly(a)&(u) mixed in the test tube. OR stretches C and T residues in one strand& A and G residues in the other form a triple-stranded -do not occur naturally in cells(useful as therapeutic agents).

15 FIGURE 4-4 Models of various known DNA structures.

16 FIGURE 4-5 Bending of DNA resulting from protein binding.

17 DNA Can Undergo Reversible Strand Separati: Concepts: Heat causes DNA strands to separate (denature). melting temperature Tm of DNA increases with percentage of G C base pairs. separated complementary nucleic acid strands renature.

18 Uunwinding & separation of DNA strands= denaturation, or melting, (in vitro) Increasing temperature---- increase molecular motion breaks hydrogen bonds & forces stabilize double helix strands separate, driven apart by repulsion of Negatively deoxyribose-phosphate. Near denaturation temperature, a small increase in temperature causes loss of weak interactions holding strands together along the entire length of the DNA molecules change in the absorption of ultraviolet (UV) light

19 melting temperature Tm at which DNA strands separate, factors : 1 Molecules contain a greater proportion of G C pairs require higher temperatures to denature? these base pairs more stable than A T pairs? 2- ion concentration decrease--- Tm decrease, negatively charged phosphate groups covered by positive ions,----decrease ions------increase repulsive force

20 Agents destabilize hydrogen bonds e.g formamide or urea lower Tm. extremes of ph denature DNA at low temperature. At low (acid) ph, bases become protonated positively charged----repelling each other. At high (alkaline) ph bases lose protons negatively charged----repelling. Lowering temperature, increasing ion concentration or neutralizing the ph causes the two complementary strands to reassociate into a perfect double helix---= renaturation dependent: time,dna concentration, and concentration.. Denaturation and renaturation of DNA basis of hybridization

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23 Many DNA Molecules Are Circular Prokaryotic DNAs, viral DNAs, mitochondria& chloroplasts,= : circular. two strands in circular DNA forms closed structure without free ends ! Uunwinding of circular DNA during replication DNA twists back on itself(overwound) forming supercoils Bacterial and eukaryotic contain topoisomerase I,= relieve OVERWOUND in DNA during replication

24 topoisomerase I binds to DNA at random sites & breaks phosphodiester bond in one strand = a nick broken end winds around the uncut strand to loss of supercoils same enzyme ligates two ends of broken strand topoisomerase II= breaks in both strands of ds DNA -----topoisomerase II relieve overwound & link two circular DNA Eeukaryotic DNA is linear: long loops of DNA fixed within chromosomes, supercoils could occur during replication topoisomerase I in eukaryotic Relieves overwound in DNA.

25 EXPERIMENTAL FIGURE 4-7 DNA supercoils can be removed by cleavage of one strand.

26 Different Types of RNA Exhibit Various Conformations Related to Their Functions RNA structure similar to DNA except:? hydroxyl group on C2 of ribose: 1--RNA more chemically labile than DNA 2- provides a chemically reactive group---- takes part in RNA-mediated catalysis RNA is cleaved into mononucleotides by alkaline solution but DNA not. Most RNAs SS and exhibit conformations permit RNA carry out specific functions in cell.

27 Simplest secondary structures in SS RNAs formed by pairing of complementary bases. Hairpins formed by pairing of bases within 5 10 nucleotides of each other & stem-loops by pairing of bases separated by >10 to several hundred nucleotides.

28 FIGURE 4-8 RNA secondary and tertiary structures.

29 These simple folds cooperate form complicated tertiary structures = pseudoknot., trna molecules adopt three-dimensional architecture in solution----protein synthesis rrna have three-dimensional structures & with flexible links in between. Secondary and tertiary structures recognized near ends of mrna Some RNAs have catalytic activity = ribozymes Ribozymes stabilized via association with proteins. Some ribozymes catalyze splicing! Where? Some RNAs carry out self-splicing.