Was ist der maximale ENC-Wert (Maximale Effective Number of Codons), den ein Gen haben kann?
61, 1, 20, 64, 32
Maximaler ENC-Wert: 61
Dies bedeutet, dass alle Synonyme Codons gleich häufig genutzt werden – also keine Codon-Bias vorliegt.
Wie lautet die korrekte Reihenfolge der Genomgrößen dieser Drosophila-Arten?
Lau, Dros, Pod
Pod > Lau > Drosophila melanogaster
Pod steht für Drosophila pseudoobscura, Lau für D. willistoni (Lauana)
Welcher Organismus hat die meisten Gene?
C. elegans
Arabidopsis
Bakterium mit 4000 Genen
yeast
Drosophila
Arabidopsis > C. elegans > Drosophila > yeast > Bakterium mit 4000 Genen
Wie viele Gene hatte das erste „Minimal Core Genome“?
Das erste minimale Core Set (Mycoplasma genitalium) hatte 256 Gene
(Es handelt sich um Gene, die für das Überleben in einer kontrollierten Umgebung notwendig sind)
Was ist das kleinste bekannte freie (free-living) Bakterium?
Mycoplasma genitalium, mit einem Genom von ca. 580 kb und ca. 480–500 Genen.
Wie viel % Gene kann Bacillus subtilis durch Knockout verlieren und trotzdem überleben?
In Experimenten konnte Bacillus subtilis etwa 30–40 % seiner Gene verlieren und war dennoch lebensfähig (in künstlicher Umgebung).
Warum ist das Genom vom Grashüpfer so groß?
Sehr viele Transposons (mobile Elemente)
Große Mengen nicht-kodierender DNA
Kein direkter Zusammenhang mit Komplexität (C-Wert-Paradoxon)
Was passiert bei einer Mnt4-Mutation?
Ein Transposon wird in ein funktionelles Gen eingefügt, was zur Inaktivierung oder veränderten Expression führen kann.
Was schaust du dir für einen phylogenetischen Baum an?
homolog: Gene, die einen gemeinsamen evolutionären Ursprung haben. (-> Oberbegriff für orthologe und paraloge Gene.)
ortholog: Homologe Gene in verschiedenen Spezies, die durch eine Artaufspaltung (Speziation) entstanden sind, Sie erfüllen meist ähnliche Funktionen in beiden Organismen. (Hox Gen in Maus und Menschen)
paraloge: Homologe Gene innerhalb derselben Spezies (oder nach Genduplikation), die durch eine Duplikation eines Gens entstanden sind, Können sich funktionell unterscheiden. (Hämoglobin α- und β-Ketten im Menschen.)
analog: Gene oder Strukturen mit ähnlicher Funktion, aber unterschiedlichem evolutionärem Ursprung. Entstanden durch konvergente Evolution, nicht durch Vererbung von einem gemeinsamen Vorfahren. (Flügel von Vögeln und Insekten)
Für phylogenetische Bäume sind Orthologe am besten geeignet.
Unterschied Tuberculosis vs. Leprae?
M. leprae hat viel mehr Pseudogene als M. tuberculosis → Genom-Reduktion und Degradierung
Welches Chromosom ist zwischen Mensch und Schimpanse am ähnlichsten/unterschiedlichsten?
Größter Unterschied: Chromosom 2 is a single large chromosome in humans but 2 smaller chromosoms un chimpansea (2A and 2B, common in great apes)
Nucleotice divergence is gratest in the Y-chromosome but smallest in the X chromosome (higher mutation rate in males)
In welchem Gen gibt es den größten Unterschied zwischen Mensch und Schimpanse?
FOXP2 – 2 nicht-synonyme Mutationen, mit möglichem Zusammenhang zu Sprache
Weitere Unterschiede auch im SRGAP2, das mit neuronaler Entwicklung assoziiert ist.
RNA-seq vs. Microarrays – wofür werden sie verwendet?
Beides dient zur Genexpressionsanalyse.
RNA-seq ist moderner, sensitiver, quantitativer, erkennt neue Transkripte
Microarrays sind günstiger, aber auf bekannte Sequenzen limitiert.
Welche Methoden existieren zur Identifikation sex-biased Gene?
RNA-seq
Microarrays / Microchips
Analyse erfolgt oft über differentiellen Genexpressionsvergleich (♂ vs. ♀)
Was bedeutet „Large X effect“ und „Fast X evolution“?
Large X: X-Chromosom trägt überproportional viele geschlechtsgebundene Gene.
Fast X: Das X-Chromosom akkumuliert schneller adaptive Mutationen (v.a. bei sex-biased expression oder bei Selektion auf rezessive Allele).
Was bedeutet dN/dS-Wert für „no selection“ oder „purifying selection“?
dN/dS ≈ 1 → Neutral evolution (no selection)
dN/dS < 1 → Purifying selection (funktionell wichtige Gene)
dN/dS > 1 → Positive selection (adaptive Veränderungen)
dN
Rate der nicht-synonymen Mutationen → ändern die Aminosäure
dS
Rate der synonymen Mutationen → ändern nicht die Aminosäure
dN/dS = Verhältnis aus funktional veränderten Mutationen zu stillen Mutationen
Welche GO-Kategorien gibt es?
Molecular Function, Cellular component, biological process, genomic location
Molecular Function – z. B. ATP-Bindung
Biological Process – z. B. Zellzyklus
Cellular Component – z. B. Mitochondrion
Genomic location ist kein offizieller GO-Term
Welcher davon ist ein GO-Term?
z. B. „ATP binding“ (Molecular Function)
„cytoplasm“ (Cellular Component)
„translation“ (Biological Process)
Wofür wird BLAST verwendet?
Zum Vergleich von Sequenzen (DNA oder Protein)
Identifikation von Homologen, Funktion, Genfamilien
Suche nach ähnlichen Sequenzen in Datenbanken
Was ist bezeichnend für pathogene Genome?
Häufig größere Genome durch Transposons, Virulenzfaktoren, TEs
hohen Transposon-Anteil (TEs)
oft hohen AT-Gehalt
viele Pseudogene
Welches Gen ist für DDT-Resistenz verantwortlich?
Cytochrom P450 – Enzymgruppe, die Insektizide abbaut
Besonders: Cyp6g1
DDT-Resistenz bezeichnet die Fähigkeit von Insekten, das Insektizid DDT (Dichlordiphenyltrichlorethan) unschädlich zu machen oder seine Wirkung zu umgehen, sodass sie nicht mehr daran sterben.
Welches Lebewesen lebt bei über 100 °C?
Hyperthermophile Archaeen, z. B. Pyrolobus fumarii (Wachstum bis 113 °C)
Was ist einzigartig für Hyperthermophile?
Stabilisierung der Proteine und DNA, z. B. durch reverse DNA gyrase, spezielle Lipide, Hitze-stabile Enzyme
Ursprungskontinent von Drosophila?
Afrika, insbesondere D. melanogaster stammt ursprünglich aus dem afrikanischen Raum
Was ist die Größte Genfamilie im Menschen?
Olfactory Receptor Genes (Riechrezeptoren), >800 Gene
Welcher Organismus die höchste Anzahl an gleichen Krankheitsgenen wie der Mensch hat
Drosophila hat eine hohe Anzahl orthologer Gene zu Menschen.
Allerdings keine direkte Zuordnung zu einem bestimmten Chromosom – eher auf konservierte Gene achten.
Maus? Maus (Mus musculus)
Welcher Zelltyp ist dem Menschen am ähnlichsten?
Frage zielt vermutlich auf Vergleich Organe/Tissue bei Tiermodellen → z. B. Maus-Herz vs. Menschliches Herz
Oder: Niere vs. Leber – je nach Expressionsprofil
Welche Aussage beschreibt den Unterschied zwischen ENC (Effective Number of Codons) und FOP (Frequency of Optimal Codons) am besten?
A) ENC misst die Häufigkeit optimaler Codons, während FOP die Genexpression quantifiziert
B) ENC und FOP sind identisch, beide geben die durchschnittliche Länge eines Gens an
C) ENC beschreibt, wie gleichmäßig alle Codons verwendet werden, FOP misst den Anteil optimal genutzter Codons
D) FOP gibt an, wie oft RNA-seq Reads auf ein Gen fallen, ENC misst Genlänge
E) Beide Methoden werden zur Identifikation von sex-biased Genen verwendet
C)
ENC (Effective Number of Codons):
→ Gibt an, wie gleichmäßig alle Synonyme Codons in einem Gen verwendet werden
→ Wertebereich: 20 (starker Bias, nur 1 Codon pro Aminosäure) bis 61 (kein Bias, alle Codons gleich genutzt)
FOP (Frequency of Optimal Codons):
→ Misst den Anteil der optimalen Codons in einem Gen (Codons, die effizient und schnell übersetzt werden)
bevorzugte codons:
werden häufiger verwendet in stark exprimierten Genen
passen besser zur häufig vorkommenden tRNA → dadurch schnellere und effizientere Translation
führen zu höherer Proteinproduktionsrate und oft besserer Faltung des Proteins
In welchem Zelltyp ist das Gen Cytochrom P450 aktiv?“
Leberzellen (Mensch) oder Entgiftungsgewebe bei Insekten (z. B. Fettkörper)
→ Möglicherweise war die Antwortoption „Liver“ oder „Hepatic“
→ Wenn es um Drosophila ging, dann eher: Malpighische Gefäße, Fettkörper
Auf welchem Chromosom liegt das Gen Cytochrom P450?“
In Drosophila z. B. liegt Cyp6g1 auf dem 2R-Arm des Chromosoms 2
→ In Menschen sind viele Cytochrom P450-Gene auf Chromosom 1, 7, 10, 19 verteilt (z. B. CYP3A4 auf Chromosom 7)
Was ist der DDT resistance auslöser?
Insertion eines Transposons (z. B. Accord) vor dem Gen Cyp6g1 → Überexpression des Gens & Das Insekt baut DDT schneller ab → es wirkt nicht mehr tödlich.
A) Verwendung ungesättigter Fettsäuren in Membranen
B) DNA mit besonders niedriger GC-Rate
C) Hitzestabile Proteine mit verstärkten ionischen Bindungen
D) Verwendung von RNA anstelle von DNA als Erbmaterial
C) Hitzestabile Proteine mit verstärkten ionischen Bindungen ✅
Erklärung: Hyperthermophile (z. B. Pyrococcus furiosus) haben besonders stabile Proteine und Membranstrukturen, um Temperaturen über 100 °C zu überleben.
Welche Organismen besitzen keine heavy isochores?
Isochores sind große Abschnitte im Genom mit homogener GC-Zusammensetzung. Heavy isochores = GC-reich
→ z. B. typisch für Säuger, nicht für Drosophila oder Bakterien
Antwortmöglichkeiten:
A) Mensch
B) Hund
C) Drosophila melanogaster
D) Maus
C) Drosophila melanogaster ✅
Erklärung: Drosophila hat eine vergleichsweise gleichmäßige GC-Verteilung, keine starken Isochore-Strukturierungen wie bei Säugetieren.
Define Homologs/ homologues
general term for genes/proteins that have similar sequence and are derived from a common ancestral sequence
Define Orthologs/ orthologues
homologs derived through speciation
human alpha-globin and chimpanzee alpha-globin are orthologs
Define Paralogs/ paralogues
homologs derived through gene duplication
Define Analogs
genes with similar sequence due to convergent evolution (not common ancestry). This is
very rare at the sequence level, but there can be functional analogs: proteins that have non-
homologous sequences but perform the same molecular function.
What protein is specific to hyperthermophiles
reverse gyrase, a large protein (>1000 a.a.) that contains two protein domains,
helicase and topoisomerase. It introduces twists into double-stranded circular DNA and may help
prevent unwinding of DNA at high temperatures (DNA is normally denatured at high temp.).
What does a BLAST E-value of 1e-6 indicate?
A. There is a 1 in 6 chance that the match is significant.
B. The sequences are guaranteed to be orthologs.
C. There is a 1 in a million chance of obtaining such a match by chance.
D. The sequences are identical.
Correct: C
Which tool is commonly used for faster genome searches in genome browsers like UCSC?
A. BWA
B. Stampy
C. BLAST
D. BLAT
Correct: D
What is a key difference between BLAST and short-read alignment tools like Bowtie or BWA?
A. BLAST is used only for protein sequences.
B. Bowtie aligns complete sequences and expects high similarity.
C. BLAST always finds one-to-one orthologs.
D. Bowtie can find convergent evolution events.
Correct: B
What defines reciprocal best hits in BLAST-based orthology detection?
A. Each gene matches a pseudogene in the other species.
B. The same gene is the top hit when BLASTing in both directions.
C. Genes share more than 80% sequence identity.
D. Genes are duplicated in both species.
What is the likely cause of extensive gene loss in Mycobacterium leprae?
A. Selective advantage for faster replication
B. Mutation pressure due to lack of selection
C. Increase in intergenic DNA
D. Errors in genome sequencing
Which feature is typical of obligate intracellular symbionts like Buchnera or Carsonella?
A. Large genome size and high GC content
B. Complete independence from the host for survival
C. Genome reduction and high AT content
D. Capability to synthesize all amino acids and vitamins
Which of the following best explains why some bacteria retain many pseudogenes?
A. Pseudogenes are beneficial for thermal adaptation.
B. Pseudogenes enhance replication efficiency.
C. There is no selective pressure to delete them.
D. Pseudogenes are required for horizontal gene transfer.
Which of the following groups is known for having the smallest genomes among free-living bacteria?
A. Mycobacterium tuberculosis
B. Mycoplasma genitalium
C. Escherichia coli
D. Rickettsia rickettsii
Which gene is specifically associated with hyperthermophiles according to comparative genomics studies?
A. Topoisomerase I
B. Reverse gyrase
C. DNA polymerase
D. Ribosomal RNA
Which of the following is NOT a correct consideration when identifying temperature-specific genes?
A. Phylogenetic relationships must be ignored entirely.
B. The presence of a gene should correlate with growth temperature.
C. Some bacteria can also grow at high temperatures.
D. Some Archaea are mesophiles.
Correct: A
What is a unique feature of reverse gyrase?
A. It is only found in mesophiles.
B. It is made up of ribosomal and polymerase domains.
C. It combines helicase and topoisomerase domains.
D. It functions only in eukaryotic cells.
What is the main goal of minimal genome projects?
A. To identify the fastest replicating bacterial species
B. To determine the fewest number of genes needed for life
C. To build the largest known genome
D. To create antibiotic-resistant bacteria
Correct: B to find the essential genes
In the 1996 study by Mushegian and Koonin, how many genes were identified as the minimal core set?
A. 91
B. 256
C. 480
D. 359
Which of the following is a limitation of the early bioinformatic approach to identifying minimal genomes?
A. It excluded eukaryotic genomes entirely
B. It assumed all bacterial genes are non-essential
C. Orthologs are difficult to detect among distantly related species
D. It used experimental gene knockouts in yeast
What is Non-Orthologous gene Displacement (NOD)?
A. A method to delete essential genes in bacteria
B. The process by which a gene is horizontally transferred
C. The replacement of a gene by a non-homologous gene with similar function
D. The disruption of gene clusters during recombination
Non-Orthologous Gene Displacement (NOD) refers to the phenomenon where a gene in one species performs the same function as a gene in another species, but the two genes are not orthologs (i.e., they did not arise from a common ancestor through a speciation event). Instead, the function has been taken over by a gene that is either a paralog (a gene duplicated within the same species) or a completely unrelated gene in the second species.
According to a more recent analysis of the COG database, how many genes are shared by all domains of life (Archaea, Bacteria, Eukaryotes)?
A. 217
B. 91
C. 63
D. 480
91 genes are common to Archaea and Bacteria
217 genes are common to Bacteria
Which species did Craig Venter and colleagues use in their 1999 minimal genome study?
A. E. coli and Bacillus subtilis
B. Mycoplasma genitalium and Mycoplasma pneumoniae
C. H. influenzae and Thermus thermophilus
D. Salmonella and Pseudomonas aeruginosa
What technique did Venter’s team use to knock out genes?
A. CRISPR-Cas9
B. Site-directed mutagenesis
C. Transposable element insertion
D. RNA interference
In the Venter study, how many genes in M. genitalium were found to be non-essential based on TE insertions?
A. 93
B. 150
C. 121
D. 197
Why is the estimate of essential genes from the Venter experiment likely an overestimate?
A. The genome was not fully sequenced
B. They used only eukaryotic cells for validation
C. The experiment was not a saturation screen
D. The bacteria were grown under extreme conditions
What was the final estimated range for the number of essential genes in M. genitalium according to Venter’s group?
A. 256–300
B. 387–480
C. 265–350
D. 100–200
Q3.1
What are synthetic lethals in the context of minimal genome experiments?
A. Genes that are only lethal when mutated in synthetic organisms
B. Gene pairs where individual knockouts are viable, but double knockouts are lethal
C. Essential genes that function only in synthetic media
D. Genes that are overexpressed in minimal media
Why might some of the 111 undisrupted genes in M. genitalium still be essential?
A. They have been recently duplicated
B. They may be ribosomal RNA genes
C. They were not disrupted simply by chance
D. They are involved in DNA replication
What bacterium did Kobayashi et al. study in their 2003 experiment?
A. M. genitalium
B. E. coli
C. Bacillus subtilis
D. Thermotoga maritima
How many genes were found to be essential in Bacillus subtilis under laboratory conditions?
A. 359
B. 271
Which function was most common among essential B. subtilis genes?
A. Cell wall biosynthesis
B. Motility
C. Protein synthesis and DNA/RNA metabolism
D. Carbohydrate metabolism
What percentage of B. subtilis essential genes were conserved across 54 bacterial species?
A. 100%
B. 80%
C. ~30%
D. ~5%
What general trend has been observed between total genome size and percentage of essential genes?
A. No correlation exists
B. Larger genomes have a higher percentage of essential genes
C. Smaller genomes have a lower percentage of essential genes
D. Smaller genomes have a higher percentage of essential genes
What is the smallest synthetic genome successfully created, as of Hutchison et al. 2016?
A. 359 genes
B. 473 genes
C. 271 genes
D. 217 genes
Which technique enabled the creation of synthetic organisms by transplanting entire genomes?
A. DNA microarrays
B. RNA sequencing
C. Genome transplantation
D. Tn5 mutagenesis
What are the two major goals of comparative genomics?
A) To identify pseudogenes and sequence errors
B) To compare prokaryotic and eukaryotic expression
C) To find out what is conserved and what is unique across species
D) To compare genetic drift and mutation rates
When the Drosophila genome was completed in 2000, it allowed researchers to:
A) Predict protein folding structures
B) Compare gene conservation across eukaryotic model organisms
C) Analyze mammalian centromeres
D) Generate synthetic fly chromosomes
Which model organism shares the highest proportion of genes with mammals?
A) Yeast (S. cerevisiae)
B) Nematode (C. elegans)
C) Fly (D. melanogaster)
D) Arabidopsis thaliana
What proportion of fly genes had a significant match to mammalian genes?
A) 20%
B) 35%
C) 50%
D) 80%
Correct: C (significant BLAST (E < 10-10))
According to OMIM-based searches, how many human disease genes had hits in Drosophila?
A) 100
B) 120
C) 212
D) 230
What was concluded from Drosophila species genome comparisons (2007)?
A) Drosophila species lack core gene sets
B) 7,000 genes are single-copy orthologs across all 12 species
C) All Drosophila genes are unique to their lineage
D) Most genes contain transposable elements
What is a major evolutionary feature of the Arabidopsis genome?
A) Genome reduction
B) Chromosomal fusions
C) Extensive horizontal gene transfer
D) High proportion of paralogs
How many genes does Arabidopsis have approximately?
A) 10,000
B) 14,000
C) 25,000
D) 50,000
Which of the following is TRUE about Arabidopsis and rice gene conservation?
A) All rice genes are present in Arabidopsis
B) 80-85% of Arabidopsis genes have homologs in rice
C) Rice shares fewer genes with Arabidopsis than with yeast
D) Arabidopsis and rice genomes are nearly identical
What question is raised about the Arabidopsis genome in comparison to rice?
A) Does Arabidopsis represent a plant minimal genome?
B) Is rice evolutionarily older than Arabidopsis?
C) Has Arabidopsis undergone polyploidization recently?
D) Are Arabidopsis genes bacterial in origin?
In 2001, why did some researchers believe the human genome might contain bacterial genes?
A) They observed bacterial DNA contamination
B) Many human genes matched only to bacterial proteins
C) Human DNA has more GC-rich regions
D) All eukaryotic genes matched prokaryotic genes
What is the most likely possible explanation for bacterial-like genes in humans?
A) Gene transfer from humans to bacteria
B) Contamination in sequencing
C) Independent gene loss in other eukaryotes
What happened to the number of suspected bacterial genes in the human genome as more data became available?
A) Increased
B) Remained the same
C) Dropped below 40
D) Was confirmed as evidence for horizontal gene transfer
What did comparison of human and mouse genomes reveal?
A) Only 50% of mouse genes have human homologs
B) Strong synteny and conserved gene order
C) Mouse genome is more compact
D) Human genome lacks large-scale rearrangements
What does “synteny” mean in this context?
A) Genes are expressed at the same time
B) Genes are in the same order on the same chromosome
C) Genes share sequence similarity
D) Genes are derived from horizontal gene transfer
1. Humans and chimpanzees have over 98% identity in their DNA sequences. What does this imply?
A. They are phenotypically identical
B. They have similar mutation rates
C. Small genetic differences can lead to significant phenotypic differences
D. They evolved at the same rate
Which of the following is NOT a proposed explanation for phenotypic differences between humans and chimps?
A. Differences in gene regulation
B. Amino acid replacements
C. Presence of mitochondria
D. Species-specific genes
What is the estimated proportion of fixed nucleotide differences between human and chimp genomes?
A. 5%
B. 1%
C. 0.1%
D. 10%
What is a likely explanation for the high divergence observed on the Y chromosome?
A. It has more exons
B. It is shorter
C. It accumulates mutations faster in males
D. It undergoes recombination frequently
What proportion of human olfactory receptor (OR) genes are pseudogenes?
A. 10%
B. 30%
C. 60%
D. 90%
There are over 1,000 OR genes in the human genome, but only 40% have an intact
open reading frame (ORF). The other 60% are pseudogenes.
Which of the following is a hypothesis for the rapid loss of OR genes in humans?
A. Climate change
B. Lack of predators
C. Use of fire and cooking
D. Agricultural diet
A Ka/Ks ratio greater than 1 suggests:
A. Negative selection
B. Positive selection
C. Neutral evolution
D. Genetic drift
Ka/Ks<1 negative Selection
Which gene categories often show signs of positive selection in humans and chimps?
(Select all that apply)
A. Testis-expressed genes
B. Housekeeping genes
C. Immune defense genes
D. Genes expressed in brain
Correct: A & C
Mutations in the FOXP2 gene affect:
A. Muscle strength
B. Immune response
C. Vision
D. Speech and language
What do the microcephalin and ASPM genes have in common?
A. They are involved in olfaction
B. They regulate the immune system
C. They affect brain size
D. They are pseudogenes in humans
According to Enard et al. (2002), the brain transcriptome:
A. Evolved slowly
B. Showed the greatest change in humans
C. Was similar across all primates
D. Had fewer expressed genes than the liver
Which technique was used to compare human and chimp proteomes?
A. Western blot
B. Microarray
C. qPCR
D. 2D-PAGE
Later studies using more genes found:
A. No differences in expression between brain and liver
B. Human brain expression diverged the slowest
C. Chimp brains evolved faster
D. Expression changes were random
What does increased linkage disequilibrium (LD) around a gene suggest?
A. High mutation rate
B. Neutral evolution
C. Selective sweep
D. Recombination hotspot
This is consistent with “selective sweeps”, where
positive selection reduces variation and increases LD in regions of the genome containing a
target of selection.
What tissue showed the greatest metabolomic change on the human lineage?
A. Brain
B. Liver
C. Muscle
D. Heart
What is the proposed trade-off for the high energy requirements of the human brain?
A. Reduced fertility
B. Slower growth
C. Weaker muscles
D. Shorter lifespan
Which of the following statements is true?
A. All OR genes in humans are functional
B. Humans and chimps have identical proteins in all cases
C. Some disease-associated human variants are fixed in chimps without negative effects
D. Chimpanzees have more gene expression changes in the brain than humans
If Ka/Ks < 1 for a gene, this indicates:
A. The gene is positively selected
B. The gene is under purifying selection
C. The gene is not expressed
D. There are no mutations in the gene
negative/ purifying selestion
Why is an outgroup species such as macaque important in selection studies?
A. It increases the genome size
B. It improves protein alignment
C. It helps identify the lineage where selection occurred
D. It helps normalize gene expression
What is the C-value paradox?
A. Genome size is consistent across all species
B. Genome size always increases with gene number
C. Genome size does not correlate strongly with organism complexity
D. All DNA in the genome is coding DNA
How much of the human genome is protein-coding?
A. 2%
B. 10%
C. 20%
D. 50%
Which of the following best explains most of the variation in eukaryotic genome sizes?
A. Differences in gene number
B. Variation in non-coding DNA content
C. Differences in GC content
D. RNA editing efficiency
Microsatellites are:
A. Long repetitive elements found in centromeres
B. Tandem repeats of 1–5 base pairs dispersed throughout the genome
C. Non-repetitive coding regions
D. Only found in mitochondrial DNA
Microsatellites (SRS “short repetitive sequences”, STR “short tandem repeats”, SSR
“simple sequence repeats”) – very short sequences of 1-5 bp repeated 10–100 times.
Which disease is associated with expansion of a trinucleotide repeat?
A. Cystic fibrosis
B. Huntington’s disease
C. Alzheimer’s disease
D. Type 2 diabetes
What makes microsatellites useful for population genetics?
A. They are highly conserved
B. They are only found in coding regions
C. They have high mutation rates
D. They occur only once per genome
Where is satellite DNA typically found?
A. Within exons
B. In subtelomeric regions
C. In coding regions of genes
D. Around centromeres and heterochromatic regions
Which mechanism increases transposable element copy number via an RNA intermediate?
A. Conservative transposition
B. Replicative transposition
C. Retrotransposition
D. Recombination
Retrotransposition – the TE is transcribed into RNA, then reverse transcribed into
cDNA, then inserts into new chromosomal location. The copy number increases.
These elements are typically the most abundant in a genome. (“copy-and-paste”).
A non-autonomous transposon:
A. Can transpose on its own
B. Lacks transposase but can transpose with a helper element
C. Lacks terminal repeats
D. Cannot move under any condition
What portion of the human genome is estimated to be derived from transposable elements?
B. 15%
C. 50%
What defines a “dead-on-arrival” retrotransposon?
A. Lacks terminal repeats
B. Cannot be reverse transcribed
C. Has lost its promoter and cannot be transcribed
D. Is eliminated from the genome
What is a key feature of processed pseudogenes?
A. Presence of introns
B. Poly(A) tail and lack of promoter
C. Adjacent to the parent gene
D. Transposase activity
Key features:
- Does not have introns present in the “parental” gene
- If recent, may have a poly(A) sequence at 3’ end
- Usually lacks promoter sequences (thus “Dead on arrival” = not expressed)
Which of the following is true about unprocessed pseudogenes?
A. They arise through RNA processing
B. They are often found in centromeric regions
C. They arise from tandem duplication and are usually adjacent to the parent gene
D. They are transcribed into proteins
NUMTs (nuclear mitochondrial sequences) are:
A. Functional nuclear genes
B. Mitochondrial genes targeted to the nucleus
C. Non-functional nuclear copies of mitochondrial genes
D. Genes expressed only in muscles
What is one hypothesis explaining genome size variation across taxa?
A. All DNA must be expressed
B. Larger genomes are more efficient
C. Most non-coding DNA is functional and adaptive
D. Variation in DNA deletion rates among species
According to Petrov et al., what species has the fastest rate of spontaneous DNA deletion?
A. Laupala
B. Podisma
C. Drosophila
D. Grasshoppers
Which of the following is not a reason why NUMTs are non-functional?
A. They use a different genetic code
B. They contain stop codons
C. They lack a signal sequence
D. They often lack promoters
In eukaryotes, the relationship between genome size and gene number is:
A. Directly proportional
B. Highly variable and weak
C. Constant across species
D. Strongest in plants
What do transposons and retrotransposons have in common?
A. They move via RNA intermediates
B. They both rely on reverse transcriptase
C. They are repetitive elements capable of increasing copy number
D. They do not affect genome size
What is the trend relating genome size to DNA deletion rates across Drosophila, Laupala, and Podisma?
A. Drosophila has the largest genome and highest deletion rate
B. Genome size increases as DNA deletion rate decreases
C. All three have similar deletion rates
D. Laupala has the lowest genome size and highest mutation rate
Deletion rate: Dros > Lau > Pod
Deletion size: Dros > Lau > Pod
Genome size: Pod > Lau > Dros
What is meant by the term “%GC”?
A. Percent of genes coding for cytosine
B. Percent of guanine and cytosine nucleotides in DNA
C. GC to AT transition mutation rate
D. Number of guanine bases per kilobase
Which of the following shows the least variation in %GC across species?
A. Bacteria
B. Invertebrates
C. Vertebrates
D. Plants
What is an isochore?
A. A codon usage bias region
B. A chromatin remodeling domain
C. A long region of the genome with uniform GC content
D. A repetitive sequence cluster
In the traditional human isochore model, what is the GC range for the H3 isochore?
A. <37%
B. 37–42%
C. 47–52%
D. >52%
Which types of organisms tend to have heavy isochores?
A. Bacteria and archaea
B. Plants and fungi
C. Cold-blooded vertebrates
D. Warm-blooded vertebrates
According to the selectionist hypothesis, why might GC-rich regions be favored?
A. They bind more transcription factors
B. GC base pairs are more stable at higher temperatures
C. GC regions replicate more slowly
D. GC codons prevent mutations
According to the mutationist hypothesis, GC-rich regions arise because:
A. Transposons insert more frequently into GC-rich sites
B. GC nucleotides mutate less
C. Early-replicating regions have more GC nucleotides available
D. GC content is regulated by mRNA stability
Mutationist hypothesis – The pool of available nucleotides changes over replication
(which takes 8 or more hours for mammals). There is more GC available early in
replication, so mutations will be biased towards G or C. Over time, regions of the
genome that replicate early become GC-rich. In general, GC-rich regions have been
observed to replicate early.
What does the mutationist hypothesis predict about DNA replication?
A. Late-replicating regions will be GC-rich
B. GC nucleotides are randomly distributed
C. GC bias results from changes in the nucleotide pool during replication
D. GC nucleotides prevent recombination
According to Cohen et al. (2005), how much of the human genome is covered by isochores?
B. 25%
C. 41%
Cohen et al. concluded that the isochore theory is:
A. Strongly supported by new data
B. Useful only for plant genomes
C. Likely obsolete as a model for genome structure
D. Only applicable to prokaryotes
By doing a sliding window analysis of the human genome DNA sequence and defining
isochores as segments >300 kb with distinct %GC and low heterogeneity, the authors found
that isochores covered 41% of the human genome, and most had low %GC. They suggest a
four-family model with mean GC contents of 35%, 38%, 41%, and 48% and conclude:
“These findings undermine the utility of the isochore theory and seem to indicate that the
theory may have reached the limits of its usefulness as a description of genomic
compositional structures”
Which part of a gene generally has the highest GC content?
A. Coding region
B. Intron
C. 3’ flanking region
D. 5’ flanking region
Which statement about GC content across different gene regions is true?
A. GC content is consistent in all gene regions
B. There is a strong correlation of %GC among all regions of a gene
C. GC content is highest in introns
D. The 5’ flanking region always has the lowest GC content
What is codon bias?
A. Unequal use of synonymous codons for the same amino acid
B. The preference for certain amino acids in genes
C. Random use of all codons equally
D. Differences in codon usage between prokaryotes and eukaryotes only
Which of the following is a likely reason for codon bias?
A. All codons are recognized equally well by tRNAs
B. Codon usage is solely determined by GC content
C. Some codons are translated more efficiently than others
D. Codon bias only occurs in vertebrates
The preferred codons correspond
to the most abundant tRNA in each species, suggesting that selection favors the use of codons
that increase the level of gene expression. Note that the preferred codons may differ from
species to species.
Which of the following factors does NOT contribute to codon bias?
A. tRNA abundance
B. Replication timing
C. Translation efficiency
D. Selection for translational accuracy
In a genome with high GC content, which type of codon is likely to be more frequent?
A. Codons ending in A or T
B. Codons with intermediate GC content
C. Codons rich in G or C at the third position
D. Only non-degenerate codons
In highly expressed genes, codon bias is generally:
A. Weak or absent
B. Stronger than in lowly expressed genes
C. Randomized
D. Driven entirely by mutation
Why might codon bias evolve in certain genes?
A. To make protein folding slower
B. To enhance mRNA degradation
C. To match abundant tRNAs and improve translation efficiency
D. To minimize GC content in isochores
Which of the following best describes the relationship between isochores and genes?
A. All isochores lack genes
B. Heavy isochores tend to be gene-rich
C. Light isochores are found only in mitochondria
D. Isochores are unrelated to gene distribution
Which of the following statements best summarizes the differences between the selectionist and mutationist hypotheses for isochores?
A. Selectionist involves transcription, mutationist involves replication
B. Selectionist focuses on temperature adaptation; mutationist on replication timing
C. Mutationist is supported by vertebrate genomes only
D. Both theories reject the existence of isochores
Which of the following best describes a male-biased gene (MBG)?
A. A gene expressed only in males
B. A gene with expression level at least twice as high in males as in females
C. A gene located exclusively on the Y chromosome
D. A gene with a higher mutation rate in males than in females
Correct answer: B
Which mechanism best explains the under-representation of MBG on the X chromosome in Drosophila?
A. MBGs evolve too slowly to be retained on the X chromosome
B. Dosage compensation increases MBG expression in females
C. The X chromosome is hyperactive in male germline tissues
D. MBGs are enriched on the X due to female preference
What does the McDonald-Kreitman (MK) test compare?
A. The recombination rates of X-linked vs. autosomal genes
B. Expression levels of sex-biased genes across tissues
C. The ratio of nonsynonymous to synonymous divergence vs. polymorphism
D. The fold change in gene expression between males and females
Correct answer: C
Which of the following would best support the hypothesis that MBGs evolve rapidly due to positive selection?
A. High levels of nonsynonymous polymorphism within species
B. A negative correlation between divergence and recombination rate
C. A (Dn/Ds)/(Pn/Ps) ratio significantly greater than 1
D. Uniform gene expression in male and female tissues
What is the “fast-X” effect?
A. Faster accumulation of mutations on the X chromosome due to replication errors
B. Faster evolution of X-linked genes due to positive selection acting on recessive alleles in hemizygous males
C. Faster expression of X-linked genes in somatic tissues
D. A phenomenon where X-linked genes are more likely to undergo duplication
In Drosophila, which of the following is not a proposed explanation for the under-representation of MBGs on the X chromosome?
A. X inactivation in the male germline
B. Dosage imbalance between males and females
C. Increased recombination rates on the X chromosome
D. Sexual conflict affecting gene retention
According to the 2-fold expression cutoff in Drosophila, what is the average male-to-female expression ratio for MBGs?
A. 11
B. 2.5
C. 6
D. 3
Which pattern is observed regarding MBGs and chromosomal location in Drosophila?
A. MBGs are enriched on the X chromosome
B. MBGs are under-represented on the X chromosome
C. MBGs are exclusively found on autosomes
D. MBGs are equally distributed between the X chromosome and autosomes
What trend is observed for the evolutionary rate of MBGs compared to FBGs and UBGs?
A. MBGs evolve faster, especially at nonsynonymous sites
B. MBGs evolve more slowly
C. FBGs evolve faster than MBGs
D. MBGs evolve at the same rate
Correct answer: A
What does the “large-X effect” refer to?
A. The X chromosome is more prone to deletions during meiosis
B. Male-biased expression is enhanced in somatic X-linked genes
C. X-linked loci contribute disproportionately to hybrid incompatibilities and male sterility
D. X-linked genes are expressed at higher levels than autosomal genes
What distinguishes a cis-regulatory change from a trans-regulatory change?
A. A cis change affects translation efficiency, while a trans change alters splicing.
B. A cis change is located in a distant chromosome, while a trans change is linked to the gene.
C. A cis change affects expression of many genes, while a trans change affects only one.
D. A cis change occurs in the regulatory sequence near the gene, while a trans change affects expression through an unlinked factor.
Correct answer: D
In the hybrid expression experiment by Wittkopp et al. (2004), what would indicate trans-regulatory divergence?
A. Equal expression of both alleles in the hybrid
B. A large difference in total expression between the parents
C. Allele-specific expression in the hybrid
D. A greater number of SNPs near the gene in one species
What was the main conclusion from Wittkopp et al. (2004) regarding the cause of expression differences between D. melanogaster and D. simulans?
A. Most expression divergence is due to trans-regulatory changes
B. Cis-regulatory divergence accounts for the majority of differences
C. Gene duplication is the dominant mechanism
D. Post-transcriptional mechanisms are more important than regulatory sequence changes
What genetic change causes DDT resistance in Drosophila melanogaster?
A. A mutation in a protein-coding region of the Cyp6g1 gene
B. A deletion in the coding region of a detoxification enzyme
C. A transposable element insertion near the promoter of Cyp6g1
D. Overexpression of an unrelated transcription factor
What is the likely function of the MtnA gene in Drosophila?
A. Circadian rhythm regulation
B. Oxidative stress tolerance and heavy metal detoxification
C. Growth hormone synthesis
D. Regulation of reproductive behavior
What type of sequence change is associated with increased MtnA expression in non-African populations?
A. A coding-region duplication
B. An indel in the 5’ UTR
C. A deletion of a microRNA binding site in the 3’ UTR
D. A transposon insertion within the gene
What pattern supports the idea that the MtnA deletion is adaptive?
A. The deletion is found at high frequency in sub-Saharan Africa only
B. The deletion shows a clinal frequency pattern increasing with distance from the equator
C. The deletion is present in both parents of a hybrid cross
D. The deletion affects coding sequence and increases protein activity
What does a “reporter gene” experiment demonstrate in the CG9509 (fezzik) study?
A. Whether gene knockouts affect viability
B. Whether cis-regulatory differences affect gene expression
C. Whether protein function is conserved across populations
D. Whether microRNAs regulate gene expression
What observation suggests balancing selection may be acting on the CG9509 regulatory region?
A. The SNP associated with expression difference is fixed in all populations
B. The SNP is absent in cosmopolitan populations
C. The SNP shows intermediate frequency in non-African populations
D. There is complete loss of polymorphism in the CG9509 gene region globally
Which gene is associated with increased expression in non-African Drosophila populations and affects stress tolerance and body size?
A. MtnA
B. lacZ
C. fezzik (CG9509)
D. Cyp6g1
What distinguishes population transcriptomics from traditional population genetics?
A. It focuses solely on coding regions
B. It uses protein data to infer gene function
C. It combines expression-level measurements with genotype variation
D. It avoids using RNA-based methods
In studies comparing Swedish and Zambian Drosophila, what was the major source of expression variation?
A. Environmental exposure to metals
B. cis-regulatory sequence divergence
C. Differences in protein degradation rates
D. trans-acting factors
Which of the following is true about cis-variation in cytochrome P450 genes?
A. It is mainly due to changes in coding regions.
B. It is rare and limited to African populations.
C. It is enriched and often located within 2 kb upstream of the gene.
D. It does not influence gene expression.
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