BASIC MOLECULAR GENETIC MECHANISMSIntroduction:

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 duringprotein synthesis.

Electron micrograph of DNA (green arrow) being transcribedinto 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 toGeneration. - 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 tRNAwith 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 geneticprocesses.

Sourse: Text2: P.101-108Objectives:

N.A structure -N.A : Linear Polymer with End-to-End Directionality

- Native DNA a Double Helix of ComplementaryAntiparallel 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 byphosphodiester 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 three-dimensional 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 proteinbinding.

DNA Can Undergo ReversibleStrand 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----- repellingeach other. At high (alkaline) pH ------bases lose protons ------negatively charged----- repelling.Lowering temperature, increasing ion concentration or neutralizing the pH causes the two complementarystrands 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 DNAsupercoils can be removed by cleavageof 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 secondaryand 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.