Fine Structure of Gene-

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Fine Structure of Gene : 

Fine Structure of Gene V.Parthasarathy, Associate Professor in Zoology, Vivekananda College, Tiruvedakam - West Madurai District - 625 214

Genetic material of cells… : 

Genetic material of cells… GENES – units of genetic material that CODES FOR A SPECIFIC TRAIT Called NUCLEIC ACIDS DNA is made up of repeating molecules called NUCLEOTIDES

Discoveries: The Chemical Nature of DNA : 

Discoveries: The Chemical Nature of DNA 1869—Fredrich Miescher named the chemical nuclei contained nuclein. Other chemists discovered it was acidic and named it nucleic acid. It was soon realized that there were two types of nucleic acids: DNA and RNA. Early in the 20th century, 4 types of nucleotides were discovered.

The Search for Genetic Material Leads to DNA : 

Once Morgan showed that genes are located on chromosomes, proteins and DNA were the candidates for the genetic material. Until the 1940s, the specificity of function of proteins seemed to indicate that they were the genetic material. However, this was not consistent with experiments with microorganisms, like bacteria and viruses. The Search for Genetic Material Leads to DNA

Slide 5: 

Frederick Griffith (1928) studied Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals. The R strain was harmless. The S strain was pathogenic. Griffith mixed heat-killed S strain with live R strain bacteria and injected this into a mouse. The mouse died and he recovered the pathogenic strain from the mouse’s blood. Griffith called this transformation, a change in genotype and phenotype due to the assimilation of a foreign substance by a cell.

A HISTORY OF DNA : 

A HISTORY OF DNA Discovery of the DNA double helix A. Frederick Griffith – Discovers that a factor in diseased bacteria can transform harmless bacteria into deadly bacteria (1928) B. Rosalind Franklin - X-ray photo of DNA. (1952) C. Watson and Crick - described the DNA molecule from Franklin’s X-ray. (1953)

Watson & Crick proposed… : 

Watson & Crick proposed… DNA had specific pairing between the nitrogen bases: ADENINE – THYMINE CYTOSINE - GUANINE DNA was made of 2 long stands of nucleotides arranged in a specific way called the “Complementary Rule”

DNA Double Helix : 

DNA Double Helix

DNA Double Helix : 

DNA Double Helix

Nitrogenous Bases : 

Nitrogenous Bases PURINES 1. Adenine (A) 2. Guanine (G) PYRIMIDINES 3. Thymine (T) 4. Cytosine (C)

Chargaff’s Rule : 

Chargaff’s Rule Adenine must pair with Thymine Guanine must pair with Cytosine Their amounts in a given DNA molecule will be about the same.

BASE-PAIRINGS : 

BASE-PAIRINGS

DNA GEOMETRY : 

DNA GEOMETRY A POLYMER OF DEOXYRIBONUCLEOTIDES DOUBLE-STRANDED INDIVIDUAL deoxyNUCLEOSIDE TRIPHOSPHATES ARE COUPLED BY PHOSPHODIESTER BONDS ESTERIFICATION LINK 3’ CARBON OF ONE RIBOSE WITH 5’ C OF ANOTHER TERMINAL ENDS : 5’ AND 3’ A “DOUBLE HELICAL” STRUCTURE COMMON AXIS FOR BOTH HELICES “HANDEDNESS” OF HELICES ANTIPARALLEL RELATIONSHIP BETWEEN 2 DNA STRANDS

DNA GEOMETRY : 

DNA GEOMETRY PERIPHERY OF DNA SUGAR-PHOSPHATE CHAINS CORE OF DNA BASES ARE STACKED IN PARALLEL FASHION CHARGAFF’S RULES A = T G = C “COMPLEMENTARY” BASE-PAIRING

TAUTOMERIC FORMS OF BASES : 

TAUTOMERIC FORMS OF BASES TWO POSSIBILITIES KETO (LACTAM) ENOL (LACTIM) PROTON SHIFTS BETWEEN TWO FORMS IMPORTANT IN ORDER TO SPECIFY HYDROGEN BONDING RELATIONSHIPS THE KETO FORM PREDOMINATES

MAJOR AND MINOR GROOVES : 

MAJOR AND MINOR GROOVES MINOR EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND MAJOR EXPOSES OPPOSITE EDGE OF BASE PAIR THE PATTERN OF H-BOND POSSIBILITIES IS MORE SPECIFIC AND MORE DISCRIMINATING IN THE MAJOR GROOVE

STRUCTURE OF THE DOUBLE HELIX : 

STRUCTURE OF THE DOUBLE HELIX THREE MAJOR FORMS A-DNA B-DNA Z-DNA B-DNA IS BIOLOGICALLY THE MOST COMMON RIGHT-HANDED (20 ANGSTROM (A) DIAMETER) COMPLEMENTARY BASE-PAIRING (WATSON-CRICK) A-T G-C EACH BASE PAIR HAS ~ THE SAME WIDTH 10.85 A FROM C1’ TO C1’ A-T AND G-C PAIRS ARE INTERCHANGEABLE

GEOMETRY OF B-DNA : 

GEOMETRY OF B-DNA IDEAL B-DNA HAS 10 BASE PAIRS PER TURN BASE THICKNESS AROMATIC RINGS WITH 3.4 A THICKNESS TO RINGS PITCH = 10 X 3.4 = 34 A PER COMPLETE TURN AXIS PASSES THROUGH MIDDLE OF EACH BP MINOR GROOVE IS NARROW MAJOR GROOVE IS WIDE

A-DNA : 

A-DNA RIGHT-HANDED HELIX WIDER AND FLATTER THAN B-DNA 11.6 BP PER TURN PITCH OF 34 A  AN AXIAL HOLE BASE PLANES ARE TILTED 20 DEGREES WITH RESPECT TO HELICAL AXIS HELIX AXIS PASSES “ABOVE” MAJOR GROOVE  DEEP MAJOR AND SHALLOW MINOR GROOVE

A-DNA : 

A-DNA WHEN RELATIVE HUMIDITY IS ~ 75% B-DNA  A-DNA (REVERSIBLE) MOST SELF-COMPLEMENTARY OLIGONUCLEO-IDES OF < 10 bp CRYSTALLIZE IN A-DNA CONF. A-DNA HAS BEEN OBSERVED IN 2 CONTEXTS: AT ACTIVE SITE OF DNA POLYMERASE (~ 3 bp ) GRAM (+) BACTERIA UNDERGOING SPORULATION

Z-DNA : 

Z-DNA A LEFT-HANDED HELIX SEEN IN CONDITIONS OF HIGH SALT CONCENTRATIONS REDUCES REPULSIONS BETWEEN CLOSEST PHOSPHATE GROUPS ON OPPOSITE STRANDS (8 A VS 12 A IN B-DNA) IN COMPLEMENTARY POLYNUCLEOTIDES WITH ALTERNATING PURINES AND PYRIMIDINES POLY d(GC) · POLY d(GC) POLY d(AC)  POLY d(GT)

Z-DNA : 

Z-DNA 12 W-C BASE PAIRS PER TURN A PITCH OF 44 DEGREES A DEEP MINOR GROOVE NO DISCERNIBLE MAJOR GROOVE REVERSIBLE CHANGE FROM B-DNA TO Z-DNA IN LOCALIZED REGIONS MAY ACT AS A “SWITCH” TO REGULATE GENE EXPRESSION ? TRANSIENT FORMATION BEHIND ACTIVELY TRAN- SCRIBING RNA POLYMERASE

FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES : 

FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES SUGAR-PHOSPHATE CHAIN CONFORMATIONS BASE PAIRING BASE-STACKING,HYDROPHOBIC IONIC INTERACTIONS

SUGAR-PHOSPHATE CHAIN IS FLEXIBLE TO AN EXTENT : 

SUGAR-PHOSPHATE CHAIN IS FLEXIBLE TO AN EXTENT CONFORMATIONAL FLEXIBILITY IS CONSTRAINED BY: SIX TORSION ANGLES OF SUGAR-PHOSPHATE BACKBONE TORSION ANGLES AROUND N-GLYCOSIDIC BOND RIBOSE RING PUCKER

IONIC INTERACTIONS : 

IONIC INTERACTIONS THE DOUBLE HELIX IS ANIONIC MULTIPLE PHOSPHATE GROUPS DOUBLE-STRANDED DNA HAS HIGHER ANIONIC CHARGE DENSITY THAT SS-DNA THERE IS AN EQUILIBRIUM BETWEEN SS-DNA AND DS-DNA IN AQUEOUS SOLUTION: DS-DNA == SS-DNA QUESTION: WHAT HAPPENS TO THE Tm OF DS-DNA AS [CATION] INCREASES? WHY?

IONIC INTERACTIONS : 

IONIC INTERACTIONS DIVALENT CATIONS ARE GOOD SHIELDING AGENTS MONOVALENT CATIONS INTERACT NON-SPECIFICALLY FOR EXAMPLE, IN AFFECTING Tm DIVALENT INTERACT SPECIFICALLY BIND TO PHOSPHATE GROUPS MAGNESIUM (2+) ION STABILIZES DNA AND RNA STRUCTURES ENZYMES THAT ARE INVOLVED IN RXNS’ WITH NUCLEIC ACID USUALLY REQUIRE Mg(2+) IONS FOR ACTIVITY

BASE STACKING : 

BASE STACKING PARTIAL OVERLAP OF PURINE AND PYRIMIDINE BASES IN SOLID-STATE (CRYSTAL) VANDERWAALS FORCES IN AQUEOUS SOLUTION MOSTLY HYDROPHOBIC FORCES ENTHALPICALLY-DRIVEN ENTROPICALLY-OPPOSED OPPOSITE TO THAT OF PROTEINS

BASE-PAIRING : 

BASE-PAIRING WATSON-CRICK GEOMETRY THE A-T PAIRS USE ADENINE’S N1 AS THE H-BOND ACCEPTOR HOOGSTEEN GEOMETRY N7 IS THE ACCEPTOR SEEN IN CRYSTALS OF MONOMERIC A-T BASE PAIRS IN DOUBLE HELICES, W-C IS MORE STABLE ALTHOUGH HOOGSTEIN IS MORE STABLE FOR A-T PAIRS, W-C IS MORE STABLE IN DOUBLE HELICES CO-CRYSTALLIZED MONOMERIC G-C PAIRS ALWAYS FOLLOW W-C GEOMETRY THREE H-BONDS

HYDROGEN BONDING : 

HYDROGEN BONDING REQUIRED FOR SPECIFICITY OF BASE PAIRING NOT VERY IMPORTANT IN DNA STABILIZATION HYDROPHOBIC FORCES ARE THE MOST IMPT.’

THE TOPOLOGY OF DNA : 

THE TOPOLOGY OF DNA “SUPERCOILING” : DNA’S “TERTIARY STRUCTURE L = “LINKING NUMBER” A TOPOLOGIC INVARIANT THE # OF TIMES ONE DNA STRAND WINDS AROUND THE OTHER L = T + W T IS THE “TWIST THE # OF COMPLETE REVOLUTIONS THAT ONE DNA STRAND MAKES AROUND THE DUPLEX AXIS W IS THE “WRITHE” THE # OF TIMES THE DUPLEX AXIS TURNS AROUND THE SUPERHELICAL AXIS

DNA TOPOLOGY : 

DNA TOPOLOGY THE TOPOLOGICAL PROPERTIES OF DNA HELP US TO EXPLAIN DNA COMPACTING IN THE NUCLEUS UNWINDING OF DNA AT THE REPLICATION FORK FORMATION AND MAINTENANCE OF THE TRANSCRIPTION BUBBLE MANAGING THE SUPERCOILING IN THE ADVANCING TRANSCRIPTION BUBBLE

Thanking You All : 

Thanking You All It is your time You can Rocket the questions If Not Now Later To zoopartha@yahoo.co.in