Tutorials, lectures and acquired reading
Period 2 - Tutorials GEN 11806
Week 1 - chapter 1 - the genetic revolution
of life sciences
Blending theory of inheritance
Gregor Mendel: (1856)
1. genes behave like particles and do not
blend together.
2. one allele is dominant to the other.
He found particles, known as genes, and those
genes have variants called alleles.
key concepts:
- Genetic discoveries made in a model organism are often
true of related
species and may even apply to all forms of life.
- Progress in genetics has both produced and been
catalyzed by the development
of molecular and mathematical tools for the analysis of
single genes and whole genomes.
- The integration of classical genetics and genomic
technologies allows the
causes of inherited diseases to be readily identified and
appropriate therapies applied.
- Evolutionary genetics provides the tools to document how
gene variants that provide
beneficial effect can rise in frequency in a population and
make individuals better adapted to the environment in
which they live.
- Genes reside on chromosomes and are made of DNA.
Genes encode proteins that conduct the basic enzymatic
work within cells.
• Somatic cells: cells of the body.
• Gametes: egg and sperm cells.
• Dominant: if present in allele, always in phenotype.
• Recessive: only present in phenotype when there is no dominant allele.
Thomas H. Morgan (1910) → Chromosome theory, place where genes are.
Fisher (1918) → The multifactorial hypothesis states that continuously variable traits are each
controlled by multiple Mendelian genes.
, Tutorials, lectures and acquired reading
DNA
Double helix – two stranded
The ladder is made of sugar and phosphate
groups of bases/ nucleotides:
1. Adenine
2. Thymine
3. Guanine
4. Cytosine
( A-T 2 hydrogen bonds, C-G 3 hydrogen bonds.
• Codon: 3 nucleotides in a row in mRNA.
• Codon: 3 nucleotides in a row in mRNA.
Regulatory elements(specific DNA
sequences to which a regulatory protein
binds and acts as either an activator or
repressor) control gene- expression
(whether a gene is turned on or off.)
• Central dogma:
From DNA → RNA → protein
Genetic information is saved in the base
sequence of DNA, transcribed into RNA.
The sequence of bases in mRNA dictates
the coupling of amino acid residues to
form a protein.
• Genomics: The
study of the
structure and
function of entire
genomes.
• DNA polymerases can make a copy of a single DNA strand by synthesizing a matching
strand with the complementary sequence of A’s, C’s, G’s, and T’s.
• Nucleases can cut DNA molecules in specific locations or degrade an entire DNA
molecule into single nucleotides.
• Ligases can join two DNA molecules together end-to-end.
, Tutorials, lectures and acquired reading
Mutation is a random process that occurs during DNA
replication.
• SNPs, single nucleotide polymorphisms: variation
in DNA. Difference in nucleotide base. Generally, a
segment of a chromosome will have several
differences in the sequence of A’s, C’s, G’s, and T’s
between the copy we inherited from our mother
and the one we inherited from our father.
SNPs are created by point mutations: changes of one
letter in the DNA code to another.
Week 1 - chapter 8 - the life cycle of RNA - cell
1. DNA Replication: DNA is copied to
produce identical DNA molecules during
cell division. This ensures that each new
cell receives a complete set of genetic
instructions.
2. Transcription: The information encoded
in DNA is transcribed into messenger RNA
(mRNA). During this process, a segment
of DNA is used as a template to produce
an RNA molecule, which carries the
genetic code from the DNA in the nucleus
to the ribosomes in the cytoplasm. 3
stages of transcription are called
initiation, elongation, and termination,
3. Translation: The mRNA is used as a
template to synthesize proteins.
Ribosomes read the mRNA sequence and
use transfer RNA (tRNA) to bring the
appropriate amino acids, linking them
together to form a protein based on the
sequence of codons in the mRNA.
, Tutorials, lectures and acquired reading
There are more proteins than genes, because one gene can have make multiple proteins
because of splicing.
• Capping: The 5’ end of a eukaryotic mRNA is modified to prevent decay and to serve as a
binding site for factors that mediate mRNA processing (e.g. splicing) and export. The 5′ end
of a eukaryotic mRNA is modified to prevent decay and to serve as a binding site for factors
that mediate mRNA processing and export. Capping of mRNAs is programmed to occur
early in transcription through the association of capping enzymes with phosphorylated
serine 5 on the CTD of RNA polymerase II.
Splicing: introns are removed and exons are joined
together. The sequence of an mRNA is not always
identical to its gene sequence introns are removed and
exons that remain are joined together (splicing). two-
step reaction: first cleavage at the 5′ splice, and
second is cleavage at the 3′ splice site
Alternative splicing: Greatly expands the number of
proteins encoded in the eukaryotic genomes. Creates
variety.
➔ Protein isoforms can be produced in
particular cells at different stages of
development by cell type-specific
alternative splicing.
➔ Post translational modifications (protein)
➔ Function: stability
➔ Examples: phosphorylation, glycosylation
Constitutive splicing is the process of intron removal
and exon ligation in the order in which they appear in a
gene. Alternative splicing is a deviation from this
preferred sequence where certain exons are skipped
resulting in various forms of mature mRNA. snRNAs
facilitate splicing by base pairing with conserved
sequences in the pre-mRNA.
• Decay: carried out by ribonucleases.
1. After removal of the poly(A) tail, mRNA
decay occurs in both the 5′-to-3′ and 3′-
to-5′
directions.
2. Small interfering RNAs (siRNAs), RNA is
produced but not translated into a
protein.
➔ Protects the genome from foreign DNA
(or silence expression of foreign genes)
➔ Specific and targets mRNA.
The first step of decay in bacteria is carried out by
an endonuclease, which cuts an RNA into two
pieces, and the next step is carried out by
exonucleases, which digest the RNA pieces into
single nucleotides starting at their 3′ end
Period 2 - Tutorials GEN 11806
Week 1 - chapter 1 - the genetic revolution
of life sciences
Blending theory of inheritance
Gregor Mendel: (1856)
1. genes behave like particles and do not
blend together.
2. one allele is dominant to the other.
He found particles, known as genes, and those
genes have variants called alleles.
key concepts:
- Genetic discoveries made in a model organism are often
true of related
species and may even apply to all forms of life.
- Progress in genetics has both produced and been
catalyzed by the development
of molecular and mathematical tools for the analysis of
single genes and whole genomes.
- The integration of classical genetics and genomic
technologies allows the
causes of inherited diseases to be readily identified and
appropriate therapies applied.
- Evolutionary genetics provides the tools to document how
gene variants that provide
beneficial effect can rise in frequency in a population and
make individuals better adapted to the environment in
which they live.
- Genes reside on chromosomes and are made of DNA.
Genes encode proteins that conduct the basic enzymatic
work within cells.
• Somatic cells: cells of the body.
• Gametes: egg and sperm cells.
• Dominant: if present in allele, always in phenotype.
• Recessive: only present in phenotype when there is no dominant allele.
Thomas H. Morgan (1910) → Chromosome theory, place where genes are.
Fisher (1918) → The multifactorial hypothesis states that continuously variable traits are each
controlled by multiple Mendelian genes.
, Tutorials, lectures and acquired reading
DNA
Double helix – two stranded
The ladder is made of sugar and phosphate
groups of bases/ nucleotides:
1. Adenine
2. Thymine
3. Guanine
4. Cytosine
( A-T 2 hydrogen bonds, C-G 3 hydrogen bonds.
• Codon: 3 nucleotides in a row in mRNA.
• Codon: 3 nucleotides in a row in mRNA.
Regulatory elements(specific DNA
sequences to which a regulatory protein
binds and acts as either an activator or
repressor) control gene- expression
(whether a gene is turned on or off.)
• Central dogma:
From DNA → RNA → protein
Genetic information is saved in the base
sequence of DNA, transcribed into RNA.
The sequence of bases in mRNA dictates
the coupling of amino acid residues to
form a protein.
• Genomics: The
study of the
structure and
function of entire
genomes.
• DNA polymerases can make a copy of a single DNA strand by synthesizing a matching
strand with the complementary sequence of A’s, C’s, G’s, and T’s.
• Nucleases can cut DNA molecules in specific locations or degrade an entire DNA
molecule into single nucleotides.
• Ligases can join two DNA molecules together end-to-end.
, Tutorials, lectures and acquired reading
Mutation is a random process that occurs during DNA
replication.
• SNPs, single nucleotide polymorphisms: variation
in DNA. Difference in nucleotide base. Generally, a
segment of a chromosome will have several
differences in the sequence of A’s, C’s, G’s, and T’s
between the copy we inherited from our mother
and the one we inherited from our father.
SNPs are created by point mutations: changes of one
letter in the DNA code to another.
Week 1 - chapter 8 - the life cycle of RNA - cell
1. DNA Replication: DNA is copied to
produce identical DNA molecules during
cell division. This ensures that each new
cell receives a complete set of genetic
instructions.
2. Transcription: The information encoded
in DNA is transcribed into messenger RNA
(mRNA). During this process, a segment
of DNA is used as a template to produce
an RNA molecule, which carries the
genetic code from the DNA in the nucleus
to the ribosomes in the cytoplasm. 3
stages of transcription are called
initiation, elongation, and termination,
3. Translation: The mRNA is used as a
template to synthesize proteins.
Ribosomes read the mRNA sequence and
use transfer RNA (tRNA) to bring the
appropriate amino acids, linking them
together to form a protein based on the
sequence of codons in the mRNA.
, Tutorials, lectures and acquired reading
There are more proteins than genes, because one gene can have make multiple proteins
because of splicing.
• Capping: The 5’ end of a eukaryotic mRNA is modified to prevent decay and to serve as a
binding site for factors that mediate mRNA processing (e.g. splicing) and export. The 5′ end
of a eukaryotic mRNA is modified to prevent decay and to serve as a binding site for factors
that mediate mRNA processing and export. Capping of mRNAs is programmed to occur
early in transcription through the association of capping enzymes with phosphorylated
serine 5 on the CTD of RNA polymerase II.
Splicing: introns are removed and exons are joined
together. The sequence of an mRNA is not always
identical to its gene sequence introns are removed and
exons that remain are joined together (splicing). two-
step reaction: first cleavage at the 5′ splice, and
second is cleavage at the 3′ splice site
Alternative splicing: Greatly expands the number of
proteins encoded in the eukaryotic genomes. Creates
variety.
➔ Protein isoforms can be produced in
particular cells at different stages of
development by cell type-specific
alternative splicing.
➔ Post translational modifications (protein)
➔ Function: stability
➔ Examples: phosphorylation, glycosylation
Constitutive splicing is the process of intron removal
and exon ligation in the order in which they appear in a
gene. Alternative splicing is a deviation from this
preferred sequence where certain exons are skipped
resulting in various forms of mature mRNA. snRNAs
facilitate splicing by base pairing with conserved
sequences in the pre-mRNA.
• Decay: carried out by ribonucleases.
1. After removal of the poly(A) tail, mRNA
decay occurs in both the 5′-to-3′ and 3′-
to-5′
directions.
2. Small interfering RNAs (siRNAs), RNA is
produced but not translated into a
protein.
➔ Protects the genome from foreign DNA
(or silence expression of foreign genes)
➔ Specific and targets mRNA.
The first step of decay in bacteria is carried out by
an endonuclease, which cuts an RNA into two
pieces, and the next step is carried out by
exonucleases, which digest the RNA pieces into
single nucleotides starting at their 3′ end
