Genetics HC1 – 31/08/2020
Chapter 9: molecular structure of DNA and RNA
- DNA central role in medical sciences
o Genetic diseases
o Cancer
o Diagnostics
o Genetic therapies
o Understanding DNA damage
o Research in many areas
- Genetec material two jobs: duplicate itself and control the development of the rest of the cell in a
specific way (Francis Crick)
- Genetic material criteria:
o 1. Information
o 2. Transmission
o 3. Replication
o 4. Variation
- Friedrich Miescher discovered DNA
- Griffith’s experiment with mice DNA is the transforming principle allowing R bacteria to make a
smooth coat and allow infection
- Hershey and Chase experiment
o Viruses that infect bacteria
o Consist of protein and DNA
o Inject their hereditary (erfelijk) material into bacteria, as we now know
o The protein of the virus doesn’t change the bacterium, the DNA does
- Not all viruses have a DNA genome, also RNA can function as the genetic material, e.g. in the
case of viruses (coronavirus, influenza, flue)
Chapter 12: Gene transcription and RNA modification (processing)
- Decoding the genetic information
o DNA replication
o Transcription
o Translation
- DNA RNA protein
- Misconception about the ‘Central Dogma’ of genetics (Crick)
- RNA DNA = reverse transcription
- Inability from a protein to make DNA/RNA
12.1: Overview of transcription
- A key concept is that DNA bse sequences define the beginning and end of a gene and determine
to a great extent the regulate RNA synthesis
- Gene expression is the overall process by which the information within a gene results in the
production of a functional product, DNA/protein, causing a particular trait, in conjunction with the
environment.
- Introns = non-coding DNA
- DNA
o Regulatory sequences: site for the binding of regulatory proteins; the role of regulatory
proteins is to influence the rate of transcription. Regulatory sequences can be found in a
variety of locations
o Promoter: site for RNA polymerase binding: signals the beginning of transcription
o Terminator : signals the end of transcription
- mRNA
1
, o ribosomal binding side: site for ribosome binding, translation begins near this site in the
mRNA
o start code: specifies the first amino acid in a polypeptide sequence, usually a
formylmethionine (bacteria) or a methionine = Uaa uga uag
o Codons: 3-nucleotide sequences within the Mrna that specify particular amino acids
o Stop codon: specifies the end of polypeptide synthesis = aug
o Bacterial mrna may be polycistronic, which means it encodes two or more polypeptides
- Template strand
- Coding stand/sense strand
- Transcription factors
- Ribosomal-binding side
- The stages of transcription
o Initiation
o Elongation
o Termination
- These steps involve protein-DNA interactions
o Proteins, such as RNA polymerase, interact with DNA sequences
o Transcription factors
- RNA transcripts have different function
- The RNA transcripts from non-structural genes are not translated: non-coding RNA
o Do have various important cellular functions
o Can still confer traits
o Of many ncRNAs the function is unknown
o In some cases, the RNA transcript becomes part of a complex that contains protein
subunits
Ribosomes, spliceosomes
- TSS transcription start side
12.2: Transcription in bacteria
- Our molecular understanding of gene transcription came from studies involving bacteria and
bacteriophages
- Promotors
o Are DNA sequences that promote gene expression: molecular events occurs at this piece
of DNA that are needed to initiate RNA synthesis/transcription
o promoters are typically located just upstream of the transcription site
- Conventional numbering system of promoters
o Bases preceding this (transcription site) are numbered in a negative direction
o Bases to the right are numbered in a positive direction
o Most of the promoter region is labelled with negative numbers
- Sequence elements that play a key role in transcription
- Pribnow box
- Every gene has a particular name
- Tata box
- Initiation of bacterial transcription
o RNA polymerase is the enzyme that catalyses the synthesis of RNA = holoenzyme:
Core enzyme, five subunits
Sigma factor, one subunit
o These subunits play distinct functional roles
- A typical way of a transcription factor to bind DNA: Major Groove
o Amino acids within the a helices hydrogen bond with bases in the promoter sequence
elements
2
,- On average, the rate of RNA synthesis is about 43 nucleotides per second
- Helicase opens up the DNA, so that there is space for RNA
- DNA/RNA synthesis always 5’ 3’ (molecule that is synthesized)
- The template is used to make RNA, not the coding one!
- Upstream/downstream
- Bacterial genes are closely packed, and can be transcribed in opposite directions
- Genes in eukaryotes are much more spread along the DNA of a chromosome and can be
transcribed in opposite directions
- Operons?
- Termination is the end of RNA synthesis
o Occurs when the short RNA-DNA hybrid of the open complex is forced to separate
This releases the newly made RNA as well as the RNA polymerase
- Rho protein, p-dependent termination
- Rho-independent termination is facilitated by two sequences in the RNA
o A uracil-rich sequence located at the 3’ end of the RNA
o A stem-loop structure upstream of the U stretch
3
, 12.3: transcription in eukaryotes
- Many of the basic features of gene transcription are very similar in bacteria and eukaryotes
- However, gene transcription in eukaryotes is much more complex
o Larger organisms and cells
o …
- Several RNA types
- Eukaryotic RNA polymerase
o Nuclear DNA is transcribed by three different RNA polymerases
RNA pol I – transcribes all rRNA genes (except 5S-rRNA)
RNA pol II – transcribes all structural genes, some snRNA genes
RNA pol III – transcribes all tRNA genes
- The core promoter is relatively short
o Several contain a TATA box
Important in determining the precise start point for transcription
o The core promoter by itself produces a very low level of transcription
This is termed basal transcription
- III affect the binding of RNA polymerase tot the core promotor
o Regulatory elements relatively close to TSS
o Enhancers stimulate transcription strongly
o Silencers inhibit transcription
- Sequences of eukaryotic genes and interacting proteins
o Factors that control gene expression can be divided into two types, based on their
location
Cis-acting elements
Trans-acting elements
- RNA polymerase II and its transcription
4
Chapter 9: molecular structure of DNA and RNA
- DNA central role in medical sciences
o Genetic diseases
o Cancer
o Diagnostics
o Genetic therapies
o Understanding DNA damage
o Research in many areas
- Genetec material two jobs: duplicate itself and control the development of the rest of the cell in a
specific way (Francis Crick)
- Genetic material criteria:
o 1. Information
o 2. Transmission
o 3. Replication
o 4. Variation
- Friedrich Miescher discovered DNA
- Griffith’s experiment with mice DNA is the transforming principle allowing R bacteria to make a
smooth coat and allow infection
- Hershey and Chase experiment
o Viruses that infect bacteria
o Consist of protein and DNA
o Inject their hereditary (erfelijk) material into bacteria, as we now know
o The protein of the virus doesn’t change the bacterium, the DNA does
- Not all viruses have a DNA genome, also RNA can function as the genetic material, e.g. in the
case of viruses (coronavirus, influenza, flue)
Chapter 12: Gene transcription and RNA modification (processing)
- Decoding the genetic information
o DNA replication
o Transcription
o Translation
- DNA RNA protein
- Misconception about the ‘Central Dogma’ of genetics (Crick)
- RNA DNA = reverse transcription
- Inability from a protein to make DNA/RNA
12.1: Overview of transcription
- A key concept is that DNA bse sequences define the beginning and end of a gene and determine
to a great extent the regulate RNA synthesis
- Gene expression is the overall process by which the information within a gene results in the
production of a functional product, DNA/protein, causing a particular trait, in conjunction with the
environment.
- Introns = non-coding DNA
- DNA
o Regulatory sequences: site for the binding of regulatory proteins; the role of regulatory
proteins is to influence the rate of transcription. Regulatory sequences can be found in a
variety of locations
o Promoter: site for RNA polymerase binding: signals the beginning of transcription
o Terminator : signals the end of transcription
- mRNA
1
, o ribosomal binding side: site for ribosome binding, translation begins near this site in the
mRNA
o start code: specifies the first amino acid in a polypeptide sequence, usually a
formylmethionine (bacteria) or a methionine = Uaa uga uag
o Codons: 3-nucleotide sequences within the Mrna that specify particular amino acids
o Stop codon: specifies the end of polypeptide synthesis = aug
o Bacterial mrna may be polycistronic, which means it encodes two or more polypeptides
- Template strand
- Coding stand/sense strand
- Transcription factors
- Ribosomal-binding side
- The stages of transcription
o Initiation
o Elongation
o Termination
- These steps involve protein-DNA interactions
o Proteins, such as RNA polymerase, interact with DNA sequences
o Transcription factors
- RNA transcripts have different function
- The RNA transcripts from non-structural genes are not translated: non-coding RNA
o Do have various important cellular functions
o Can still confer traits
o Of many ncRNAs the function is unknown
o In some cases, the RNA transcript becomes part of a complex that contains protein
subunits
Ribosomes, spliceosomes
- TSS transcription start side
12.2: Transcription in bacteria
- Our molecular understanding of gene transcription came from studies involving bacteria and
bacteriophages
- Promotors
o Are DNA sequences that promote gene expression: molecular events occurs at this piece
of DNA that are needed to initiate RNA synthesis/transcription
o promoters are typically located just upstream of the transcription site
- Conventional numbering system of promoters
o Bases preceding this (transcription site) are numbered in a negative direction
o Bases to the right are numbered in a positive direction
o Most of the promoter region is labelled with negative numbers
- Sequence elements that play a key role in transcription
- Pribnow box
- Every gene has a particular name
- Tata box
- Initiation of bacterial transcription
o RNA polymerase is the enzyme that catalyses the synthesis of RNA = holoenzyme:
Core enzyme, five subunits
Sigma factor, one subunit
o These subunits play distinct functional roles
- A typical way of a transcription factor to bind DNA: Major Groove
o Amino acids within the a helices hydrogen bond with bases in the promoter sequence
elements
2
,- On average, the rate of RNA synthesis is about 43 nucleotides per second
- Helicase opens up the DNA, so that there is space for RNA
- DNA/RNA synthesis always 5’ 3’ (molecule that is synthesized)
- The template is used to make RNA, not the coding one!
- Upstream/downstream
- Bacterial genes are closely packed, and can be transcribed in opposite directions
- Genes in eukaryotes are much more spread along the DNA of a chromosome and can be
transcribed in opposite directions
- Operons?
- Termination is the end of RNA synthesis
o Occurs when the short RNA-DNA hybrid of the open complex is forced to separate
This releases the newly made RNA as well as the RNA polymerase
- Rho protein, p-dependent termination
- Rho-independent termination is facilitated by two sequences in the RNA
o A uracil-rich sequence located at the 3’ end of the RNA
o A stem-loop structure upstream of the U stretch
3
, 12.3: transcription in eukaryotes
- Many of the basic features of gene transcription are very similar in bacteria and eukaryotes
- However, gene transcription in eukaryotes is much more complex
o Larger organisms and cells
o …
- Several RNA types
- Eukaryotic RNA polymerase
o Nuclear DNA is transcribed by three different RNA polymerases
RNA pol I – transcribes all rRNA genes (except 5S-rRNA)
RNA pol II – transcribes all structural genes, some snRNA genes
RNA pol III – transcribes all tRNA genes
- The core promoter is relatively short
o Several contain a TATA box
Important in determining the precise start point for transcription
o The core promoter by itself produces a very low level of transcription
This is termed basal transcription
- III affect the binding of RNA polymerase tot the core promotor
o Regulatory elements relatively close to TSS
o Enhancers stimulate transcription strongly
o Silencers inhibit transcription
- Sequences of eukaryotic genes and interacting proteins
o Factors that control gene expression can be divided into two types, based on their
location
Cis-acting elements
Trans-acting elements
- RNA polymerase II and its transcription
4
