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.
Electron micrograph of DNA (green arrow) being transcribed into RNA (red arrow). [O. L. Miller, Jr., and Barbara R. Beatty, Oak Ridge National Laboratory.]
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
-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
FIGURE 4-1 Overview of four basic molecular genetic processes.
Sourse: Text2: P.101-108 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
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.
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.
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)
FIGURE 4-2 Alternative representations of a N.A strand illustrating chemical directionality.
FIGURE 4-3 The DNA double helix. Model of B DNA, the most common form of DNA in cells.
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.
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).
FIGURE 4-4 Models of various known DNA structures.
FIGURE 4-5 Bending of DNA resulting from protein binding.
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.
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
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
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
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
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.
EXPERIMENTAL FIGURE 4-7 DNA supercoils can be removed by cleavage of one strand.
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.
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.
FIGURE 4-8 RNA secondary and tertiary structures.
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.