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Exam summary for Evolutionary Genetics

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Evolutionary Genetics

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Vrije Universiteit Amsterdam (VU)

Exam summary for the Evolutionary Genetics course for the Pre-Master Evolutionary Biology and Ecology. This summary covers all subjects of the 2023 Course

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Aantal pagina's 70
Geschreven in 2022/2023
Type Samenvatting

evolutionary genetics
genetic analysis
ecology
hiv
genome contents
genome variation
transposable elements
phylogenetic tree
horizontal gene transfer
rna world
mutations
population genetics

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Summary Evolutionary genetics
Contents
Quick exam summary:............................................................................................................................2
Terminology........................................................................................................................................2
HIV......................................................................................................................................................8
Genome contents and variations......................................................................................................12
Transposable elements.....................................................................................................................22
Phylogenetic trees A&B....................................................................................................................29
Horizontal gene Transfer & RNA world.............................................................................................37
Summary of Yumi’s lectures.............................................................................................................46
Mutation causes/frequencies.......................................................................................................46
Population genetics......................................................................................................................48
Quantitative genetics....................................................................................................................48
Sexual selection............................................................................................................................51
Evolution of sex............................................................................................................................53
Practice exam questions 2023..............................................................................................................55
Practice exam questions 2022..............................................................................................................62

,Quick exam summary:
Terminology
Nucleotide: Is the basic building block of nucleic acids (RNA and DNA). Consists of a nitrogen
containing base (adenine, guanine or cytosine in DNA, adenine, guanine, uracil or cytosine in RNA), a
phosphate group, and a sugar (deoxyribose in DNA, ribose in RNA).

Chromatin: Chromatin refers to a mixture of DNA and proteins that form the chromosomes found in
the cells of humans and other higher organisms. Many of the proteins namely, histones, package the
massive amount of DNA in a genome into a highly compact form that can fit in the cell nucleus.

Chromosome: Chromosomes are threadlike structures made of protein and a single molecule of DNA
that serve to carry the genomic information.

Ploidy: The number of sets of chromosomes in a cell or an organism. For example, haploid means
one set and diploid means two sets. For example, humans are diploid (they have 46 chromosomes
meaning that they have two sets of 23 chromosomes).

Amino acids: An amino acid is the fundamental molecule that serves as the building block for
proteins. There are 20 different amino acids.

Genes: Pieces of DNA that can produce RNA.

Allele: A version of a gene. There might be many versions of a single gene expressing a protein that
has an altered function.

Monoallelic expression: Transcription occurs from just one of the alleles.

Gene family: A collection of genes that share a common ancestor.

Genomic locus / Loci: Piece of DNA in a chromosome that can be transcribed (produces a protein).

Exons and introns: Exon is any part of the gene that will form a part of the final mature RNA
produced by that gene after introns have been removed by RNA splicing.

Promotor: DNA region in front of the gene which consist of TF binding sites. These TF binding sites
(and factors) together change the 3D structure of chromatin that allows transcription to happen or
prevents transcription from happening.

Splicing: Is the process where a newly-made precursor messenger RNA transcript is transformed into
a mature messenger RNA. It works by removing all the introns and splicing back together exons.

Alternative splicing: Is a cellular process in which exons from the same gene are joined in different
combinations, leading to different, but related, mRNA transcripts. These mRNAs can be translated to
produce different proteins with distinct structures and functions, all from a single gene.

Ligation: Is the joining of two nucleic acid fragments through the action of an enzyme.

Operon: A genetic regulatory system found in bacteria and their viruses in which genes coding for
functionally related proteins are clustered along the DNA.

Open Reading Frame (ORF):On a genomic scale, translated regions are identified as open reading
frames (ORFs) that are longer (typically >100 amino acids) than expected by chance, given sequence
composition.

,Transcribing Factor (FR): A transcription factor is a protein with DNA binding activity that controls
the rate of transcription of genetic information from DNA to messenger RNA, by binging to a specific
DNA sequence.

TF binding sites (TFBSs): Regions where the TFs are binding at.

TATA box: In molecular biology, the TATA box is a sequence of DNA found in the core promoter
region of genes in archaea and eukaryotes which specifies to other molecules where transcription
begins. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter
consensus sequence. The TATA box is considered a non-coding DNA sequence.

RNA polymerase: Is an enzyme that synthesizes RNA from a DNA template.

Mutations: Is a change in the DNA sequence of an organism. Mutations can result from errors in DNA
replication during cell division, exposure to mutagens or a viral infection.

Point mutation: A point mutation occurs in a genome when a single base pair is added, deleted or
changed.

Missense: A genetic alteration in which a single base pair substitution alters the genetic code in a
way that produces an amino acid that is different from the usual amino acid at that position.

Silent (Synonymous): A genetic alteration in which a single base pair substitution that does not alter
the original amino acid.

Nonsense: Occurs in DNA when a single base pair substitution gives rise to a stop codon rather than
a codon specifying an amino acid.

Insertion: Is a type of mutation that involves the addition of one or more nucleotides into a segment
of DNA.

Deletion: Is a type of mutation that involves the deletion of one or more nucleotides into a segment
of DNA.

Transcription: Is the process of copying a segment of DNA into RNA.

Translation: Is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize
proteins after the process of transcription of DNA to RNA in the cell’s nucleus.

Ribosome: Ribosomes are macromolecular machines, found within all cells, that perform biological
protein synthesis. Ribosomes link amino acids together in the order specified by the codons of
messenger RNA molecules to form polypeptide chains. Ribosomes consist of two major components:
the small and large ribosomal subunits.

Codons: A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of
genomic information encoding a particular amino acid.

Genetic code: The genetic code is the set of rules used by living cells to translate information
encoded within genetic material (DNA or RNA sequences of nucleotide triplets, or codons) into
proteins.

UTR: Untranslated region

3’UTR: Very important region, outside of the ORF, responsible for regulation the production of the
protein/ half-life of mRNA (which is the time that mRNA remains in the cell). It is related to small

, ncRNA (microRNAs). A possible mutation at the 3’UTR could cause problems with the linkage of the
small ncRNA binding and the RNA might remain in the cell longer (increased half-life) and that could
lead to ever expression of a particular protein (with possible negative or positive effects).

Epigenetic: All the events that occur on the DNA that are involved in regulation of gene expression
and the maintenance of the genome.

DNA Binding Domain (DBD): Is an independently folded protein domain that contains at least on
structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA
sequence (a recognition sequence) or have a general affinity to DNA.

Pseudogene: A piece of DNA that has the characteristics of a gene (containing an ORF), but it does
not produce a protein. Either not getting an RNA or the mRNA does not produce a functioning
protein.

Nucleosomes: A nucleosome is a section of DNA that is wrapped around a core of proteins
(histones). Inside the nucleus, DNA forma a complex with proteins called chromatin, which allows the
DNA to be condensed into a smaller volume. Very important for epigenetics.

Monophyletic group: descendants from a common ancestor

Polyphyletic group: lacks a direct common ancestor, characters called homoplasy’s > due to
convergent evolution

Paraphyletic group: consists of the group’s last common ancestor and all descendants of that
ancestor excluding a few—typically only one or two—monophyletic subgroups.

Homoplasy: analogous structures/traits originating from convergent evolution; independent
evolutionary events.

Autapomorphy: a trait that is unique to a particular taxon.

Synapomorphy (cladistics): a derived trait that is shared by two or more taxa of shared ancestry.

Plesiomorphic character: a primitive ancestral character

Symplesiomorphic character: shared ancestral character (a shared pleiomorphic), shared by two or
more taxa, but also with other taxa linked earlier in the clade.

Homologue: One of a pair of chromosomes that segregate from one another during the first meiotic
division. A gene related to a second gene by descent from a common ancestral DNA sequence.

Homologues alignment: If two regions are homologous, they could be aligned to underline their
evolutionary history. Let's call an alignment in which aligned positions have a common origin an
evolutionary alignment. The evolutionary alignment does not have to be the optimal alignment with
respect to any given scoring function.

UPGMA: is an algorithm that provides a rooted tree. (fast and dirty method that doesn’t account for
the rate of mutation that occurs in different branches)

Neighbour joining: The NJ (neighbour joining) algorithm is a widely used method for constructing
phylogenetic trees, based on the distance between species. NJ is a greedy algorithm, which
endeavours to minimize the sum of all the branch lengths of the resulting tree.

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