• DNA= key element
• Replication necessary to duplicate chromosome
• Gene expression = protein expression= transcription and translation

• DNA= key element
  • serves as code for RNA, and all proteins
  • information w/in DNA can be transferred from 1 cell to another=heredity

Central Dogma 2

• Replication necessary to duplicate chromosome

• Gene expression = protein expression= transcription and translation
  • Regulation occurs at both levels

• Griffith's experiments with pneunococci and mice

• Strain S: virulent, smooth colonies and had capsule
• Strain R: nonvirulent, rough colonies, no capsule
• Hypothesis: Genetic Material can be transfered from 1 strain to the next

• Serves as control
• R: Mouse lives; R re-isolated
• S: mouse dies, S is re-isolated

• DNA from dead virulent cells can be transformed into live nonvirulent strain in some cases and expected some mice to die.
• Re-isolate both R and S (R= newly transformed)

• Took Griffith's experiments further to define material possible for inheritance

individually extracted and purified bichem components of S strain and examined each independently

• Polysaccharide
• Protein
• RNA
• DNA

• Added each ind. component in with nonvirulent R strain and then looked at colonial morphology change to indicate capsule formation

• Only observed transformation to smooth (virulent form) when DNA from strain S present
• IF DNA from strain S treated with DNAse, no transformation occured
• Proved DNA is genetic material

• Borrelia burgdoferi: linear chromosome
• Rhodobacter sp. have multiple chromosomes

• Twisted into supercoiled form
• Histone-like protiens are complexed w/ DNA for structural support

• Extrachromosomal DNA; much smaller in size than chromosome

• Contains non-essential genes but ones that would be advantageous under certain conditions

• Often includes genes for adding virulence, antibiotic resistance, and genes for using add. carbon for energy sources

• extrachromosomal DNA
• Much smaller than chromosome
• circular dsDNA supercioled with histone-like proteins
• Contains non-essential yet advantageous genes at certain times
• Includes genes that add: virulence, antibiotic resistance, and genes for using add. carbon and energy sources

• Nitrogenous base
• Deoxyribose
• Phosphate group

• Purines: Adenine or Guanine
• Pyrimidines: Cytosine or Thymine

• Nucleotides join by althernating position of sugar and phosphate group in the backbone of DNA molecule
• dsDNA contains 2 complementary and anti-parallel strands (5-3 and 3-5)

• Complementary strands of dsDNA held together via H bonds of paired nitrogenous bases

• Breaking
• It beigins at specific location on a chromosome called an origin (locus ori C)

• DnaA proteins bind to oriC and hydrolyzes ATP (breaks bonds)
• Creates initial replication fork

• DNA bends around DnaA proteins and stresses H bonds between strands until bonds break

• Unwinds short stretches of DNA ahead of replication forks, allowing replication fork to move up the DNA strands
• Hydrolyzes ATP

• specific helicase that removes supertwists incorporated in DNA as its unwound in 1 area and tightened in others

Step 3 DNA replication

•  Prevent reformation of H-bonds between complemntary base pairs b/c of physical distance

•  
  • ie: structural roadblock betwn DNA strands too far apart to re-form hydrogen bonds.

• short RNA primer sequence synthesized by RNA primase using nucleotides complementary to DNA template sequence.

• Protiens important to RNA primer synthesis
  • Together with RNA primase form a primosome
• One primer synthesized on each strand of partental DNA

• Stereochemistry of DNA molecule
• Specific direction of synthesis

• Contains core subunits which do the following
  • Catalyze DNA synthesis
  • Proofreading for fidelity
  • Invovled in Step 5

• Subunit of DNA polymerase
• Breaks hydrogen bonds between parental strands

• DNA polymerase subunit
• Tethers to DNA
• continually resynthesized on LAGGING strand

• Used in step 6
• removes RNA primer
• fills in gaps using complementray DNA as template (able to hook to leadig strand 5'-3')

Discontinous replication (Okazaki) fragments and DNA nucleotides replaces RNA primers must be joined to one antoher to produce continous DNA

DNA ligase involved in this step

• 2 replication forks develop at origins

Much like DNA but with exceptions:

• Single-stranded
• contains ribose instead of de-oxyribose
• contains uracil instead of thymine

• mRNA
• tRNA
• rRNA

• Genes may overlap on rare occasion and differentiated by organization of these to produce different proteins

• The template strand

• Upstream of the gene to be transcribed

• -35 consensus sequence
• 5'TTGACA3'

• - 10 consensus sequence (pribnow box)
• 5'TATAAT3'

The Shine-Delgarno sequence: 5'AGGA3'

Actual squence of DNA which will eventually be translated to protein

Does not include trailer or terminator sequences

• Found in DNA
• Causes transcription to mRNA to cease= not transcribed
• Uses complementary base pairing w/in mRNA to create stem/loop or hairpin structures

• section of mRNA not translated
• Past coding region of gene (including stop codon)
• regulates cessation of translation

• mRNA synthesis performed by RNA polymerase

• It helps recognize the start of the encoded genes (-35 consensus sequence in promoter)
• Unwinds DNA double helix and forms transcription bubble.
• Transcription starts 6-7 bp away from end of promoter sequence
• After first few nucs transcribed, sigma factor dissociates and core RNA polymerase continues transcription

• self-complementation forms stem-loop structures (hairpins) in mRNA as it is transcribed

• 6 U residues following hairpin structure
  • the AU bonds between DNA and mRNA are very very week!
• RNA polymerase dissociates from DNA by itself

• Hair-pin structure is formed, lacks the poly-U sequence in mRNA

• The unwinding of mRNA/ DNA complex= RNA: DNA helicase activity

• Occurs in prokaryotes but not eukaryotes... Why is this possible?

• Transcription occurs within the bounds of the nuclear membrane
• Translation occurs w/in the ribosomes (in the cytoplasm)

• Transcription and translation are not physically separated by a membrane
• As mRNA is transcribed, ribosomes can attache and begin translation.

• Single RNA polymerase for mRNA, tRNA, and rRNA
• Promoters: -35 consensus and -10 consensus
• No introns present
• No post-transcriptional modifications

• RNA pol I for rRNA
• RNA pol II for mRNA
• RNA pol III for tRNA

• -90 GC box
• -75 CAAT box
• -30 TATA box

• DNA has introns which are transcribed into mRNA; must be removed before translation