HMB201H1 Lecture 2 study guide: Genes and
Genomes
Slides 12-14 Griffith experiment
- Demonstrated Transformation + Evidence that DNA is the Inherited Genetic Material
- Smooth strain (S cells) causing infectious disease and harmless rough strain (R cells)
- Heat-killed S-cell = mouse survived / Heat-killed S cells mixed w R cells = mouse dies
- Living S cells are found in dead mice = Transformation of R cells 줍줍 S’s DNA
- Found that extracts from killed S cells treated with DNase mixed with living R cells did not
transform → Provided evidence that DNA is genetic material
Slide 16 Hershey-chase experiment: Protein or DNA is the genetic material?
- Used T2 bacteriophage, which consists of a protein coat and DNA inside.
- Infected bacteria (E. coli) with these labeled (DNA or Protein) viruses.
- ³²P (DNA) was found inside the bacteria, meaning DNA entered the cells.
- ³⁵S (Protein) remained outside the bacteria, meaning proteins did not enter
- DNA is the genetic material because only DNA entered the bacterial cells and directed viral
reproduction.
Slide 23-26 Complementary base pairing
- Base pairs = hydrogen bonds (weak electrostatic)
- Purine (A,G) - Pyrimidine (T,C)
- 2 DNA strains are antiparallel, polarity is reversed
- Main features of the genetic code: universal & degenerate
Slide 27- Synthetic biology = added synthesized “alien DNA” (X,Y)
- increase the variety, create proteins that do not exist naturally
Slides 29-30 Process of DNA replication (enzymes names + functions)
- Semiconservative replication
- Lagging strand / Leading strand
- Helicase: Unwinding DNA
- DNA Polymerase: Copying DNA (5’ → 3’)
, - DNA Primase:
- DNA-Ligase:
- RNA Primer: Priming
- Topoisomerase:
Slide 34 Microproteome
Slides 36-37 Chromosome Structure
- 2x Chromatin ~ 1/3 DNA, 1/3 histones, 1/3 nonhistone proteins
Slide 45 Different levels of regulation of gene expression
- Transcriptional regulation
- RNA processing, stability, localization
- Translational regulation
- Post translational regulation
- Trafficking
- Localization
- Degradation
Slides 47-49 Lac operon regulation (Used by bacteria)
- Organization of bacterial genes:
• Clusters of several related genes located together and controlled by a single promoter
• Operator – region within promoter
- Lac Operon:
Slides 51-57 Causes of mutations / consequences
- Mutation = change in the nucleotide sequence of DNA
- Spontaneous (background rate = 1-4x10^-8 mutations per gene / gamete
- Induced (Mutagen / Geneticist (=mutagenesis))
- Consequences
- Silent
- Missense
- Nonsense
- Indel mutations
, - Frameshift
- Mutations in promoter / termination signal sites
- Mutations in splice donor/acceptor site = incorrect retention/excision of intron
- Large additions/deletions => cause frameshifts
Slide 58 Difference between germline and somatic mutations
- Inherited mutations (germ cell)
- Acquired mutations (somatic cell)
Slide 64 Regulatory RNAs (siRNA, miRNA)
- Short interfering RNA (siRNA) –
- 22 nucleotide double stranded non-coding RNA. Target specific!
- Micro RNA (miRNA) single stranded (stem & loop)
- can potentially regulate the expression of many different genes
Slides 66 RNAi
- Can treat diseases that result from the accumulation of aberrant protein products
- Patisiran & vutrisiran have the same mechanism of action and similar efficacy, however
Patisiran is given intravenously every three weeks, while vutrisiran is given subcutaneously
every three months
Slide 68 RNA Approaches for Gene therapy (what is the outcome of each?)
- RNA interference (RNAi):
- Splice-Switching oligonucleotides (SSO):
Slides 70 - 77 SSO mode of action for treatment:
- Spinal Muscular Atrophy (SMA):
- Duchenne muscular dystrophy (DMD):
, HMB201H1 Lecture 3 study guide: Genetic
Engineering Genomics & Bioinformatics
Slide 9 Recombinant DNA
- Insert + Vector = DNA construct
Slide 13 purpose of each of the selection methods
- Antibiotic Selction:
- X-gal Blue-White selection:
- sacB or ccdB selection:
- sacB encodes levansucrase which turns sucrose into levan → a toxic substance to
bacteria
- ccdB encodes a DNA gyrase poison ultimately causing cell death
Slide 15-19 Advantages and disadvantages of the different vector types
Vector Type Insert size
Bacterial plasmid 6~12 kb
vectors (circular)
Bacteriophage vectors ~25 kb
(linear)
Cosmid (circular) ~35 kb
Bacterial artificial ~300 kb
chromosome (BAC,
circular)
Yeast artificial 200~2000
chromosome (YAC, kb
circular)
Ti vector Varies
Genomes
Slides 12-14 Griffith experiment
- Demonstrated Transformation + Evidence that DNA is the Inherited Genetic Material
- Smooth strain (S cells) causing infectious disease and harmless rough strain (R cells)
- Heat-killed S-cell = mouse survived / Heat-killed S cells mixed w R cells = mouse dies
- Living S cells are found in dead mice = Transformation of R cells 줍줍 S’s DNA
- Found that extracts from killed S cells treated with DNase mixed with living R cells did not
transform → Provided evidence that DNA is genetic material
Slide 16 Hershey-chase experiment: Protein or DNA is the genetic material?
- Used T2 bacteriophage, which consists of a protein coat and DNA inside.
- Infected bacteria (E. coli) with these labeled (DNA or Protein) viruses.
- ³²P (DNA) was found inside the bacteria, meaning DNA entered the cells.
- ³⁵S (Protein) remained outside the bacteria, meaning proteins did not enter
- DNA is the genetic material because only DNA entered the bacterial cells and directed viral
reproduction.
Slide 23-26 Complementary base pairing
- Base pairs = hydrogen bonds (weak electrostatic)
- Purine (A,G) - Pyrimidine (T,C)
- 2 DNA strains are antiparallel, polarity is reversed
- Main features of the genetic code: universal & degenerate
Slide 27- Synthetic biology = added synthesized “alien DNA” (X,Y)
- increase the variety, create proteins that do not exist naturally
Slides 29-30 Process of DNA replication (enzymes names + functions)
- Semiconservative replication
- Lagging strand / Leading strand
- Helicase: Unwinding DNA
- DNA Polymerase: Copying DNA (5’ → 3’)
, - DNA Primase:
- DNA-Ligase:
- RNA Primer: Priming
- Topoisomerase:
Slide 34 Microproteome
Slides 36-37 Chromosome Structure
- 2x Chromatin ~ 1/3 DNA, 1/3 histones, 1/3 nonhistone proteins
Slide 45 Different levels of regulation of gene expression
- Transcriptional regulation
- RNA processing, stability, localization
- Translational regulation
- Post translational regulation
- Trafficking
- Localization
- Degradation
Slides 47-49 Lac operon regulation (Used by bacteria)
- Organization of bacterial genes:
• Clusters of several related genes located together and controlled by a single promoter
• Operator – region within promoter
- Lac Operon:
Slides 51-57 Causes of mutations / consequences
- Mutation = change in the nucleotide sequence of DNA
- Spontaneous (background rate = 1-4x10^-8 mutations per gene / gamete
- Induced (Mutagen / Geneticist (=mutagenesis))
- Consequences
- Silent
- Missense
- Nonsense
- Indel mutations
, - Frameshift
- Mutations in promoter / termination signal sites
- Mutations in splice donor/acceptor site = incorrect retention/excision of intron
- Large additions/deletions => cause frameshifts
Slide 58 Difference between germline and somatic mutations
- Inherited mutations (germ cell)
- Acquired mutations (somatic cell)
Slide 64 Regulatory RNAs (siRNA, miRNA)
- Short interfering RNA (siRNA) –
- 22 nucleotide double stranded non-coding RNA. Target specific!
- Micro RNA (miRNA) single stranded (stem & loop)
- can potentially regulate the expression of many different genes
Slides 66 RNAi
- Can treat diseases that result from the accumulation of aberrant protein products
- Patisiran & vutrisiran have the same mechanism of action and similar efficacy, however
Patisiran is given intravenously every three weeks, while vutrisiran is given subcutaneously
every three months
Slide 68 RNA Approaches for Gene therapy (what is the outcome of each?)
- RNA interference (RNAi):
- Splice-Switching oligonucleotides (SSO):
Slides 70 - 77 SSO mode of action for treatment:
- Spinal Muscular Atrophy (SMA):
- Duchenne muscular dystrophy (DMD):
, HMB201H1 Lecture 3 study guide: Genetic
Engineering Genomics & Bioinformatics
Slide 9 Recombinant DNA
- Insert + Vector = DNA construct
Slide 13 purpose of each of the selection methods
- Antibiotic Selction:
- X-gal Blue-White selection:
- sacB or ccdB selection:
- sacB encodes levansucrase which turns sucrose into levan → a toxic substance to
bacteria
- ccdB encodes a DNA gyrase poison ultimately causing cell death
Slide 15-19 Advantages and disadvantages of the different vector types
Vector Type Insert size
Bacterial plasmid 6~12 kb
vectors (circular)
Bacteriophage vectors ~25 kb
(linear)
Cosmid (circular) ~35 kb
Bacterial artificial ~300 kb
chromosome (BAC,
circular)
Yeast artificial 200~2000
chromosome (YAC, kb
circular)
Ti vector Varies
