Lecture 5 The Chemical Basis of Heredity

Molecular Structure of DNA Watson and Crick

Transduction Experiments on Salmonella typhimurium Joshua Lederberg
Repetition of Griffith’s work Avery, MacLeod, MacCarty
Transformation using Diplococcus pneumoniae Frederick Griffith
DNA as Genetic Material Hermann Joseph Muller
Quantitative geneticist, 2 viewpoints Ronald A. Fisher
A virus infecting bacterium where DNA is enclosed by protein coat Bacteriophage
Provided evidence that when bacteriophage infects bacterial cell Alfred Hershey, Martha Chase
Chemical Composition of DNA
Basic unit of DNA nucleotides
Composition of nucleotide Phosphate group, Nucleoside
Composition of nucleoside 2-deoxy-D ribose, nitrogen bases
2 classes of nitrogen bases Purine and pyrimidine
What are the purines? Adenine, guanine
What are the pyrimidines? Thymine, cytosine
Molecular Structure of DNA
Linkage of DNA polymer 3’-5’ phosphodiester bonds
What is the Chargaff’s rule? A=T, G=C or Purines=Pyrimidines
Proposed double helix structure of DNA Watson and Crick
Characteristic of DNA molecule 2-stranded, anti-parallel
Distance between base pairs 3.4 A0
Angle of each base pair 360
Diameter of double helix 20 A0
Bond between a purine and a pyrimidine Hydrogen bond
Diameter and length of E. coli circular DNA 20 A0 in diameter, 107 in length
Organization of DNA in Chromosomes
Nucleoid is present in Prokaryotes
Prokaryotic chromosome nucleoid
Condensed state of DNA nucleoid
Formed by having the DNA molecule folded in loops held by RNA molecule nucleoid
Basic structural unit of eukaryotic chromosome nucleosome
Composition of nucleosome Octamer, DNA
Stabilizes association of nucleosome to form solenoid H1 histone
 Replication or Synthesis of DNA
Modes of DNA replication Conservative, dispersive, semi-conservative
[mode of replication] parental molecule is fully conserved; daughter molecules are newly synthesized Conservative mode
Parental molecule is degraded into nucleotides; nucleotides become part of newly synthesized Dispersive mode
Daughter molecule is composed of 1 strand from parent, another strand newly synthesized Semi-conservative
Semi-conservative mode of replication experiment Matthew Meselson, Franklin Stahl
E. coli chromosome isolation, labeled with radioactive (3H) thymidine John Cairns
Process of DNA Replication
Functions as master copy of upon synthesis of daughter DNA molecule occurs Parental or template DNA
Functions as substrates Deoxyribonucleic triphosphates
Responsible for unwinding of parent strands to create 2 template strands DNA helicase (Helix-unwinding protein)
Prevents separate paternal strands from reannealing Single-stranded DNA binding protein
Function in relaxing tension of supercoiled twists created in unwinding of parental strand DNA topoisomerase, DNA gyrase
Catalyzes synthesis of daughter DNA DNA polymerase III or DNA replicase
Initiates synthesis of RNA primer strands Primase
Cleaves RNA primer from elongating DNA strand DNA polymerase I
Joining enzyme catalyzing the formation of a covalent phosphodiester bond between adjacent DNA ligase
nucleotide
Absence of a covalent bond between 3’-OH end and a 5’-PO4 end Nick
DNA Replication Process
Unwinding of DNA molecule forms a replication fork
Facilitates unwinding of helix to create template strands Helicase
Prevents reannealing of separated strands SS [DNA] BP
Relaxes tension of supercoiling due to unwinding without rotation DNA gyrase
Addition of nucleotide is at the ___ direction 5’ to 3’ direction
Strand that is synthesized continuously Leading strand
Antiparallel strand synthesized discontinuously Lagging strand
As soon as DNA synthesis is primed, RNA primer is cleaved by a ___ 5’ -> 3’ exonuclease activity
Absence of a phosphodiester bond nick
Simultaneous synthesis of leading and lagging strand
Also called replication fork Replisome
Composition of replisome Holoenzyme DNA polymerase III and primosome
Conformations of DNA replication
Done by formation of replication bubbles Linear DNA replication
Initiated by formation of replication bubble, replication proceeds towards both direction Circular DNA: Theta conformation
Model for replication of single stranded DNA viruses Circular DNA: Rolling circle conformation
 Biosynthesis of Primer Molecules
Catalyzes RNA priming of phage fd DNA synthesis RNA polymerase
Catalyzes oligonucleotide priming of phage G4 and St-1 DNA synthesis dna G protein
The “proofreading” function of the DNA polymerases
Repair Mechanisms
Hydrolyzes bond linking a damaged base to the deoxyribose in the backbone of DNA strand N-glycosidase

Lecture 6 Gene Functions: Proteins and Enzymes

Genetic Control of Proteins

First suggested specific connection between genes and enzymes Archibald Garrod
Causes arthritis and production of urine turns black upon exposure of air Alcaptonuria
Examples of Inborn Errors of Metabolism because of loss of enzymatic activities
Thyroid malfunction, mental retardation Cretinism
Liver enlargement, galactose in urine and blood, cataracts Galactosemia
Progressive mental retardation Huntington’s chorea
Presence of bile in various tissues Jaundice
Mental retardation, self mutilation, spasticity, increased uric acid production Lesch-Nyhan Syndrome
Excretion of phenylalanine Phenylketonuria
Mental and motor retardation; death by 2-4 years old Tay-Sachs disease
One gene-One enzyme hypothesis
Formulated one gene-one enzyme hypothesis George Beadle, Edward Tatum
States that every gene controls an enzyme One gene-one enzyme hypothesis
Protein Structure
Refers to number and sequence of amino acids that constitute it Primary structure
Configuration imposed upon the protein by peptide linkages Secondary structure
Consequence of primary and secondary structures produces new configuration Tertiary structure
Protein consists of 2 or more polypeptides, referred as oligomeric Quaternary structure
Colinearity of DNA
A genetic map of nucleotide changes should correspond with a mutational map of amino acid changes Colinearity
Provided proof of colinearity Charles Yanofsky
Protein Synthesis
Central Dogma of Molecular Biology F.H.C. Crick
Central Dogma of Molecular Biology
DNA makes DNA and RNA Replication and transcription
RNA makes protein Translation
 RNA makes RNA and DNA Reverse transcription
General Transfers
Transcription process where the transfer of information is from DNA to RNA RNA synthesis
RNA is polymerized from ribonucleic triphosphate by enzyme ___ RNA polymerase
Transcription initiation site or promoter in prokaryotes PRIBNOW box
Transcription initiation site in eukaryotes TATA box or Hogness-Golberg box
Single stranded molecule that code the sequence of amino acids in protein synthesis mRNA
Has a clover leaf tertiary structure tRNA
Single stranded irregular structure of cell cytoplasm rRNA or ribosome
Where translation takes place cytoplasm
Catalyzes the formation of peptide bond between carboxyl group of amino acid residue on the tRNA Peptidyl transferase
A 1-strand of mRNA is seen associated with many ribosomes forming a cluster called polyribosome
Cyclic of ribosomal subunits occurs during Translation
Special Transfers
RNA to RNA RNA Replication
RNA to DNA Reverse Transcription
DNA to Protein DNA Translation
Interrupted Genes
Regions represented in the mRNA Exons
Missing from the mRNA or intervening sequences Introns
Composed of snRNA and proteins that remove introns Spliceosomes
Attachment of 5’ guanine with methyl to 5’ end by enzyme guananyl transferase 5’ capping
Triplet Codes
T4 phase mutant Crick, Barnett, Brenner, and Watts-Tobin
Experimented with artificial messenger, poly-uridylic acid Nirenberg, Matthaei
Stop codons UAA, UAG, UGA