1
AB_1022 Evolutionary Genetics
Learning goals
The student is able to
- is able to describe and explain the dynamic nature of genomes and the underlying molecular mechanisms in
relation to molecular evolution;
- can describe the regular mechanisms of transcriptional and post-transcriptional gene regulation and how
genetic variation can affect these processes in relation to new traits an adaptation;
- can describe how natural selection, genetic drift, mutation, and migration influence the genetic structure of
populations and speciation;
- is able to explain the various selection mechanisms;
- is able to explain the basic concepts of population genetics and apply those mathematically;
- can interpret and determine phylogenetic relationships and is able to use computer programs for the
construction of phylogenetic trees;
- is able to describe current hypotheses of ‘the origin of life’ and to discuss the evidence.
Course goals
- Develop a strong ‘intuition’ for evolutionary thinking and be able to explain life histories and genomic
evolution in molecular terms, become familiar with evolutionary mechanisms, and with some of the
mathematics applied in population genetics.
Content of the classes
- Causes and mechanisms of genetic variation at nucleotide, gene, and chromosomal level in pro- and
eukaryotes;
- Horizontal DNA transfer;
- Evolutionary consequences of genome evolution and sex;
- Causes of Speciation;
- Molecular evolution of viral and bacterial pathogens;
- ‘Origin of life’ models;
- The use of bioinformatics and comparative genomics;
- Population genetics: allele frequencies in relation to selection and genetic drift;
- Use of genetic variation to examine stochastic and deterministic processes;
- Selection mechanisms;
- Application of simple mathematical rules to examine the behaviour of alleles of one and two loci in ideal
populations, and for genes with a quantitative effect;
- Reconstruction of phylogenetic trees using DNA sequences and cladistic computer programs;
- Evolution - Development (Evo-Devo).
, 2
Intro to Evolutionary Genetics and Recap Essentials
Class content:
- Recap of basic molecular genetics and mechanics.
- What is a gene?
- Mutations.
- Origin of genes.
- Prokaryotes versus eukaryotes.
- Structure of genes and more.
DNA
- DNA (Deoxyribonucleic Acid): the molecule that carries the genetic instructions
for all living organisms and some viruses. It is often referred to as the ‘blueprint
of life’ because it contains the information necessary for the growth,
development, functioning, and reproduction of all cells.
Structure of DNA
- Double helix: DNA is shaped like a twisted ladder or spiral staircase.
- Nucleotides: DNA is made up of smaller units called nucleotides.
Each nucleotide consists of
- A sugar (deoxyribose).
- A phosphate group.
- A nitrogenous base (Adenine (A), Thymine (T), Cytosine (C), and Guanine (G)).
The bases pair in a specific way
- Base pair: the pairs of nucleotides that form the ‘rungs’ of the DNA double helix, connecting the two
strands of DNA. Each base pair consist of two nitrogenous bases held together by hydrogen bonds.
- Adenine (A) pairs with Thymine (T).
- In RNA, Adenine (A) pairs with Uracil (U).
- Cytosine (C) pairs with Guanine (G).
- This pairing creates the ‘rungs’ of the DNA ladder.
Why are base pairs important
- Base pairs allows DNA to store genetic information a stable, double-stranded structure.
- During replication, the base pairs separate, and each strand serves as a template for making a new
complementary strand.
- Base pairs also determine the sequence of codons in mRNA, which is translated into proteins during
gene expression.
Example of base paring
- If the DNA sequence is A-T-G-C, the complementary sequence is T-A-C-G.
- Each pair (like A-T) is referred to as 1 base pair (bp). The length of DNA is often measured in base
pairs (for example, 1000 bp = 1 kilobase (kb)).
What does DNA do
- Storing genetic information: DNA stores instructions for making all the proteins needed by an organism.
These instructions are coded in sequences of nucleotides, similar to letters in a sentence.
- Sequence: the specific order of subunits that make up a biological molecule, such as DNA (nucleotide
order of A, T, C, G), RNA (nucleotide order of A, U, C, G), or protein (order of amino acids). These subunits
encode information essential for the structure, function, and regulation of an organism.
- Transmitting genetic information: DNA is passed from one generation to the next during reproduction,
ensuring that offspring inherit traits from their parents.
- Directing protein synthesis: proteins perform most of the functions in a cell, and DNA controls the
production of proteins through two main processes (transcription and translation).
, 3
How DNA works
Step 1. Transcription (DNA to RNA)
- Inside the nucleus of a cell, a segment of DNA is ‘copied’ into messenger RNA (mRNA).
- Messenger RNA (mRNA): carries genetic instructions from DNA to the ribosome, acts as ‘template’.
- The DNA stays safe in the nucleus, but the mRNA can leave and carry the genetic information to other
parts of the cell.
Step 2. Translation (RNA to protein)
- In the cytoplasm, the mRNA binds to a ribosome, which reads the instructions and assembles a protein
by linking amino acids together.
What is a ribosome
- Ribosome: a cellular machine responsible for assembling proteins. It acts like a factory that reads
the instructions from messenger RNA (mRNA) and joins amino acids together to form a protein.
Location
- In prokaryotic cells (like bacteria), ribosomes float freely in the cytoplasm.
- In eukaryotic cells (like human cells), ribosomes are found in two places, namely floating freely
in the cytoplasm, and attached to the endoplasmic reticulum (forming the ‘rough ER’).
Composition
- Ribosomes are made of ribosomal RNA (rRNA) and proteins.
Function
- Ribosomes read the genetic code in mRNA and ‘translate’ it into a protein by linking amino
acids into the correct order.
What is a protein
- Protein: a large, complex molecule made up of chains of amino acids. Proteins perform most
of the important functions in living cells.
- Types of proteins are antibodies, enzymes, hormonal proteins, structural proteins, storage
proteins, and transport proteins.
Examples of protein functions
- Enzymes: speed up chemical reactions (for example, breaking down food).
- Structural proteins: build and support cell structures (e.g., collagen in skin, keratin in hair).
- Transport proteins: move substances around (e.g., haemoglobin carries oxygen in the blood).
- Hormonal proteins: send signals throughout the body (e.g., insulin regulates blood sugar).
What is an amino acid
- Amino acid: a small molecule that serves as the building block of proteins. There are 20 different
amino acids that combine in different sequences to create proteins.
Structure of an amino acid that each has
- A central carbon atom (C).
- An amino group (NH2).
- A carboxyl group (COOH).
- A side chain, also called the R group. The R group is different for each amino acid and
determines its properties (for example, size, charge, hydrophobicity).
Types of amino acids
- Essential amino acids: must come from food (the body cannot produce them).
- Non-essential amino acids: the body can produce these on its own.
, 4
How ribosomes, proteins and amino acids work together
- The ribosome reads the mRNA code three nucleotides at a time (called a codon).
- Each codon corresponds to one specific amino acid.
- Transfer RNA (tRNA) brings the correct amino acid to the ribosome based on the codon sequence.
- The ribosome links the amino acids together into a polypeptide chain, which folds into a functional
protein.
Analogy
- DNA is like the recipe.
- mRNA is a copy of the recipe that leaves the kitchen (nucleus).
- Ribosomes are like the chefs that read the recipe and put the ingredients together.
- Amino acids are the ingredients.
- Proteins are the final dish.
Why proteins matter
- Proteins are responsible for almost everything in the cell, including building structures (for example,
muscle fibres), speeding up chemical reactions (enzymes), and sending signals (hormones).
What is a gene
- Gene: a sequence of DNA that contains the necessary information to produce RNA. This RNA can then be
used to create proteins (coding RNA) or play regulatory and structural roles (non-coding RNA).
What is RNA
- RNA (Ribonucleic Acid): a single-stranded molecule that plays a crucial role in
the process of translating genetic information from DNA into proteins. RNA is
also involved in regulating gene expression and can even have enzymatic
functions in some cases.
Structure of RNA
- RNA is made up from nucleotides, similar to DNA, but with key differences.
- Sugar: RNA contains ribose instead of deoxyribose (found in DNA). Ribose
has an extra oxygen atom.
- Nitrogenous bases: RNA contains Adenine (A), Cytosine (C), Guanine (G),
and Uracil (U). Uracil (U) replaces Thymine (T) found in DNA.
- Single-stranded: RNA is typically single-stranded, unlike the double-
stranded helix of DNA.
Genes as DNA segments
- Coding genes: genes that produce
messenger RNA (mRNA) are used to
create proteins. In humans, around
20.000 genes encode proteins.
- Non-coding genes: these genes produce RNA molecules that are not translated into proteins but have
essential regulatory or structural functions. Examples include ribosomal RNA (rRNA) and long-non-coding
RNA (lncRNA). Humans have around 18.000 non-coding RNA genes.
From gene to protein
1. Transcription (DNA to pre-mRNA)
- Location: nucleus (a membrane-bound organelle found in eukaryotic cells. It serves as the control
centre of the cell, containing the cell’s genetic material (DNA) and directing cellular activities such as
growth, metabolism, and reproduction).
- Purpose: copy the DNA sequence of a gene into a temporary RNA copy (pre-mRNA).
AB_1022 Evolutionary Genetics
Learning goals
The student is able to
- is able to describe and explain the dynamic nature of genomes and the underlying molecular mechanisms in
relation to molecular evolution;
- can describe the regular mechanisms of transcriptional and post-transcriptional gene regulation and how
genetic variation can affect these processes in relation to new traits an adaptation;
- can describe how natural selection, genetic drift, mutation, and migration influence the genetic structure of
populations and speciation;
- is able to explain the various selection mechanisms;
- is able to explain the basic concepts of population genetics and apply those mathematically;
- can interpret and determine phylogenetic relationships and is able to use computer programs for the
construction of phylogenetic trees;
- is able to describe current hypotheses of ‘the origin of life’ and to discuss the evidence.
Course goals
- Develop a strong ‘intuition’ for evolutionary thinking and be able to explain life histories and genomic
evolution in molecular terms, become familiar with evolutionary mechanisms, and with some of the
mathematics applied in population genetics.
Content of the classes
- Causes and mechanisms of genetic variation at nucleotide, gene, and chromosomal level in pro- and
eukaryotes;
- Horizontal DNA transfer;
- Evolutionary consequences of genome evolution and sex;
- Causes of Speciation;
- Molecular evolution of viral and bacterial pathogens;
- ‘Origin of life’ models;
- The use of bioinformatics and comparative genomics;
- Population genetics: allele frequencies in relation to selection and genetic drift;
- Use of genetic variation to examine stochastic and deterministic processes;
- Selection mechanisms;
- Application of simple mathematical rules to examine the behaviour of alleles of one and two loci in ideal
populations, and for genes with a quantitative effect;
- Reconstruction of phylogenetic trees using DNA sequences and cladistic computer programs;
- Evolution - Development (Evo-Devo).
, 2
Intro to Evolutionary Genetics and Recap Essentials
Class content:
- Recap of basic molecular genetics and mechanics.
- What is a gene?
- Mutations.
- Origin of genes.
- Prokaryotes versus eukaryotes.
- Structure of genes and more.
DNA
- DNA (Deoxyribonucleic Acid): the molecule that carries the genetic instructions
for all living organisms and some viruses. It is often referred to as the ‘blueprint
of life’ because it contains the information necessary for the growth,
development, functioning, and reproduction of all cells.
Structure of DNA
- Double helix: DNA is shaped like a twisted ladder or spiral staircase.
- Nucleotides: DNA is made up of smaller units called nucleotides.
Each nucleotide consists of
- A sugar (deoxyribose).
- A phosphate group.
- A nitrogenous base (Adenine (A), Thymine (T), Cytosine (C), and Guanine (G)).
The bases pair in a specific way
- Base pair: the pairs of nucleotides that form the ‘rungs’ of the DNA double helix, connecting the two
strands of DNA. Each base pair consist of two nitrogenous bases held together by hydrogen bonds.
- Adenine (A) pairs with Thymine (T).
- In RNA, Adenine (A) pairs with Uracil (U).
- Cytosine (C) pairs with Guanine (G).
- This pairing creates the ‘rungs’ of the DNA ladder.
Why are base pairs important
- Base pairs allows DNA to store genetic information a stable, double-stranded structure.
- During replication, the base pairs separate, and each strand serves as a template for making a new
complementary strand.
- Base pairs also determine the sequence of codons in mRNA, which is translated into proteins during
gene expression.
Example of base paring
- If the DNA sequence is A-T-G-C, the complementary sequence is T-A-C-G.
- Each pair (like A-T) is referred to as 1 base pair (bp). The length of DNA is often measured in base
pairs (for example, 1000 bp = 1 kilobase (kb)).
What does DNA do
- Storing genetic information: DNA stores instructions for making all the proteins needed by an organism.
These instructions are coded in sequences of nucleotides, similar to letters in a sentence.
- Sequence: the specific order of subunits that make up a biological molecule, such as DNA (nucleotide
order of A, T, C, G), RNA (nucleotide order of A, U, C, G), or protein (order of amino acids). These subunits
encode information essential for the structure, function, and regulation of an organism.
- Transmitting genetic information: DNA is passed from one generation to the next during reproduction,
ensuring that offspring inherit traits from their parents.
- Directing protein synthesis: proteins perform most of the functions in a cell, and DNA controls the
production of proteins through two main processes (transcription and translation).
, 3
How DNA works
Step 1. Transcription (DNA to RNA)
- Inside the nucleus of a cell, a segment of DNA is ‘copied’ into messenger RNA (mRNA).
- Messenger RNA (mRNA): carries genetic instructions from DNA to the ribosome, acts as ‘template’.
- The DNA stays safe in the nucleus, but the mRNA can leave and carry the genetic information to other
parts of the cell.
Step 2. Translation (RNA to protein)
- In the cytoplasm, the mRNA binds to a ribosome, which reads the instructions and assembles a protein
by linking amino acids together.
What is a ribosome
- Ribosome: a cellular machine responsible for assembling proteins. It acts like a factory that reads
the instructions from messenger RNA (mRNA) and joins amino acids together to form a protein.
Location
- In prokaryotic cells (like bacteria), ribosomes float freely in the cytoplasm.
- In eukaryotic cells (like human cells), ribosomes are found in two places, namely floating freely
in the cytoplasm, and attached to the endoplasmic reticulum (forming the ‘rough ER’).
Composition
- Ribosomes are made of ribosomal RNA (rRNA) and proteins.
Function
- Ribosomes read the genetic code in mRNA and ‘translate’ it into a protein by linking amino
acids into the correct order.
What is a protein
- Protein: a large, complex molecule made up of chains of amino acids. Proteins perform most
of the important functions in living cells.
- Types of proteins are antibodies, enzymes, hormonal proteins, structural proteins, storage
proteins, and transport proteins.
Examples of protein functions
- Enzymes: speed up chemical reactions (for example, breaking down food).
- Structural proteins: build and support cell structures (e.g., collagen in skin, keratin in hair).
- Transport proteins: move substances around (e.g., haemoglobin carries oxygen in the blood).
- Hormonal proteins: send signals throughout the body (e.g., insulin regulates blood sugar).
What is an amino acid
- Amino acid: a small molecule that serves as the building block of proteins. There are 20 different
amino acids that combine in different sequences to create proteins.
Structure of an amino acid that each has
- A central carbon atom (C).
- An amino group (NH2).
- A carboxyl group (COOH).
- A side chain, also called the R group. The R group is different for each amino acid and
determines its properties (for example, size, charge, hydrophobicity).
Types of amino acids
- Essential amino acids: must come from food (the body cannot produce them).
- Non-essential amino acids: the body can produce these on its own.
, 4
How ribosomes, proteins and amino acids work together
- The ribosome reads the mRNA code three nucleotides at a time (called a codon).
- Each codon corresponds to one specific amino acid.
- Transfer RNA (tRNA) brings the correct amino acid to the ribosome based on the codon sequence.
- The ribosome links the amino acids together into a polypeptide chain, which folds into a functional
protein.
Analogy
- DNA is like the recipe.
- mRNA is a copy of the recipe that leaves the kitchen (nucleus).
- Ribosomes are like the chefs that read the recipe and put the ingredients together.
- Amino acids are the ingredients.
- Proteins are the final dish.
Why proteins matter
- Proteins are responsible for almost everything in the cell, including building structures (for example,
muscle fibres), speeding up chemical reactions (enzymes), and sending signals (hormones).
What is a gene
- Gene: a sequence of DNA that contains the necessary information to produce RNA. This RNA can then be
used to create proteins (coding RNA) or play regulatory and structural roles (non-coding RNA).
What is RNA
- RNA (Ribonucleic Acid): a single-stranded molecule that plays a crucial role in
the process of translating genetic information from DNA into proteins. RNA is
also involved in regulating gene expression and can even have enzymatic
functions in some cases.
Structure of RNA
- RNA is made up from nucleotides, similar to DNA, but with key differences.
- Sugar: RNA contains ribose instead of deoxyribose (found in DNA). Ribose
has an extra oxygen atom.
- Nitrogenous bases: RNA contains Adenine (A), Cytosine (C), Guanine (G),
and Uracil (U). Uracil (U) replaces Thymine (T) found in DNA.
- Single-stranded: RNA is typically single-stranded, unlike the double-
stranded helix of DNA.
Genes as DNA segments
- Coding genes: genes that produce
messenger RNA (mRNA) are used to
create proteins. In humans, around
20.000 genes encode proteins.
- Non-coding genes: these genes produce RNA molecules that are not translated into proteins but have
essential regulatory or structural functions. Examples include ribosomal RNA (rRNA) and long-non-coding
RNA (lncRNA). Humans have around 18.000 non-coding RNA genes.
From gene to protein
1. Transcription (DNA to pre-mRNA)
- Location: nucleus (a membrane-bound organelle found in eukaryotic cells. It serves as the control
centre of the cell, containing the cell’s genetic material (DNA) and directing cellular activities such as
growth, metabolism, and reproduction).
- Purpose: copy the DNA sequence of a gene into a temporary RNA copy (pre-mRNA).
