Which organism has the most genes?
• A. thaliana
• C. elegans
• S. cerevisiae
• D. melanogaster
• H. sapiens
A. thaliana
Which organism has the largest genome size?
H. sapiens
What do you look at for constructing a phylogenetic tree?
• Homolog
• Paralog
• Ortholog
• Analog
Ortholog
What is the definition of a paralog?
• A sequence that is homologous due to gene duplication
• A sequence that is similar due to shared ancestry
• A sequence that is homologous due to speciation
• A sequence that evolved in parapatry
What is the primary purpose of BLAST (Basic Local Alignment Search Tool)?
• To design primers for PCR
• To align entire genomes globally
• To identify homologous sequences by finding regions of local similarity
• To visualize genes in a genome browser
• To predict protein 3D structures
Which BLAST program uses a protein query sequence to search a nucleotide
database translated in all six frames?
• blastn
• blastp
• blastx
• tblastn
• tblastx
• tblastn: Protein query sequence, Nucleotide database translated in all six frames
• blastn: Nucleotide query sequence, Nucleotide database
• blastp: Protein query sequence, Protein database
• blastx: Nucleotide query sequence translated in all six frames, Protein database
• tblastx: Nucleotide query sequence translated in all six frames, Nucleotide database
translated in all six frames
What does a low E-value in a BLAST search indicate?
• The sequences are likely unrelated
• The match is likely due to random chance
• There is high confidence that the sequences are homologous
• The sequences have different biochemical properties
• The alignment length is too short to interpret
Which of the following correctly distinguishes BLAST from BLAT?
• BLAT is slower and more accurate than BLAST
• BLAST is used for full-genome alignments; BLAT is for protein structures
• BLAT uses a faster algorithm and is based on k-mer matching
• BLAST uses E-values; BLAT uses only bit scores
• BLAT aligns sequences globally, while BLAST aligns them locally
How big is the genome of Mycoplasma genitalium?
• 180 Kb
• 280 Kb
• 380 Kb
• 480 Kb
• 580 Kb
How many protein-coding genes does Mycoplasma genitalium have?
• 180
• 280
• 380
• 480
• 580
Which statement about Mycobacterium leprae and Mycobacterium tuberculosis is
true?
• M. leprae has fewer pseudogenes than M. tuberculosis.
• M. leprae has lost function in about half of its genes and cannot be cultured in the lab.
• M. tuberculosis has the longest doubling time of any known bacterium.
• M. leprae has more coding genes than M. tuberculosis.
What is the main difference between Mycobacterium leprae and Mycobacterium
tuberculosis?
• The number of protein-coding genes in M. tuberculosis is less than half that in M.
leprae.
• M. leprae affects humans while M. tuberculosis does not
• The number of protein-coding genes in M. leprae is less than half that in M. tuberculosis.
• They are descended from different ancestors
Which organisms live at 100°C?
• Hyperthermophiles: mostly Archaea, some bacteria
• Hyperthermophiles: mostly bacteria, some Archaea
• Thermophiles: mostly Archaea, some bacteria
• Thermophiles: mostly bacteria, some Archaea
• Mesophiles: mostly Archaea, some bacteria
• Mesophiles: mostly bacteria, some Archaea
Which protein has been identified as specific to hyperthermophiles and is thought to
help stabilize DNA at high temperatures?
• DNA polymerase delta
• Histone H1
• Reverse gyrase
• Heat shock protein 70 (Hsp70)
• RNA helicase
Which organism has the highest number of disease-related genes in common with
humans?
• E. coli
How man genes did the first minimal core set contain (bioinformatics approach)?
• 1056
• 256
• 5656
• 56
• 456
What percentage of genes in Bacillus subtilis can be knocked out without affecting
survival under optimal laboratory conditions?
• 6%
• 25%
• 50%
• 75%
• 94%
Which gene family is the largest in the human genome?
• Zinc finger transcription factors
• Immunoglobulin genes
• Homeobox genes
• Olfactory receptor (OR) genes
• Cytochrome P450 genes
Which chromosome shows the greatest sequence divergence between humans and
chimpanzees?
• Chromosome 1
• Chromosome 21
• X chromosome
• Y chromosome
• Mitochondrial DNA
Which chromosome is the most similar (least divergent) between humans and
What is the approximate total genomic divergence between humans and chimpanzees
when small indels (1–15 bp) are included?
• 0.1%
• 1%
• 1.23%
• 3%
• 5%
On average, how many amino acid differences are found per protein between humans
and chimpanzees?
• 0
• 1
• 2
• 10
• 20
What percentage of proteins are identical between humans and chimpanzees?
• 10%
• 20%
• 30%
• 70%
How many amino acid differences exist in the FOXP2 gene between humans and
• 5
2
Mutations in which of the following genes are associated with primary microcephaly
(significantly reduced brain size) in humans?
• FOXP2 and BRCA1
• ASPM and microcephalin
• FOXP2 and microcephalin
• SRY and ASPM
• HOX and microcephalin
What evidence supports the idea that microcephalin and ASPM may have played a
role in recent human brain evolution?
• Both genes are identical in humans and chimps
• Both genes were lost in extinct human lineages
• They show evidence of accelerated amino acid evolution in the human lineage
• These genes are only expressed in non-human primates
• They are unrelated to brain development
What is the approximate brain volume of a human with a microcephalin mutation?
• 200 cm³
• 400 cm³
• 800 cm³
• 1,200 cm³
• 1,400 cm³
What is the approximate normal human brain volume?
• 1,000 cm³
In a comparison of gene evolution across different tissues (brain, heart, liver, kidney,
and testis), which tissue shows the fastest evolution in both gene expression and
protein sequence?
• Brain
• Heart
• Liver
• Kidney
• Testis
Which tissue shows the slowest rate of evolution in both gene expression and protein
sequence?
Which of the following would suggest positive selection?
• Ka/Ks > 1
• Ka/Ks = 0
• Ka/Ks < 0
• Ka/Ks < 1
• Ka/Ks = 1
Which of the following is expected for a pseudogene?
Which Ka/Ks (dN/dS) value indicates no selection (neutral evolution) on a gene?
• Ka/Ks < 0.1
Which Ka/Ks (dN/dS) value indicates that a gene is under purifying (negative)
selection?
• Ka/Ks >> 1
The ratio dN/dS is also sometimes referred to as:
• Omega
• Kappa
• Tao
• Alpha
• Delta
Omega
The fact that genome length is not correlated with organismic complexity is known
as:
• Haldane's rule
• C-value paradox
• G-value paradox
• Genomic paradox
What is the correct order of genome size?
• Lau > Dros > Pod
• Pod > Dros > Lau
• Pod > Lau > Dros
• Dros > Pod > Lau
• Dros > Lau > Pod
What is the correct order of deletion rate?
What is the correct order of deletion size?
Why is the genome of the grasshopper so large?
Very low rate of spontaneous DNA deletion, allowing non-functional DNA like
pseudogenes and transposable elements to accumulate over time.
Which of the following statements about NUMTs (nuclear copies of mitochondrial
genes) is not correct? NUMTs are non-functional because …
• The genetic code is different between mitochondria and nucleus
• They often lack a promoter
• NUMTs contain functional introns that disrupt coding regions
• They do not have a signal sequence to target them to mitochondria
NUMTs contain functional introns that disrupt coding regions
What is a key characteristic of NUMTs in the genome of organisms like grasshoppers
that makes them useful for evolutionary studies?
• They provide essential energy through oxidative phosphorylation
• They can be used to estimate mutation and deletion rates
• They regulate mitochondrial gene expression from the nucleus
• They are actively translated into mitochondrial proteins
• They serve as backup copies of functional mitochondrial genes
What are isochores?
• Small RNA segments that regulate gene expression
• Short repetitive elements found in all eukaryotic genomes
• Chromosomal regions defined by histone density
• DNA sequences associated with RNA polymerase binding sites
• Long stretches (100s of kb) of DNA with uniform %GC
What characterizes heavy isochores in the genome?
• High frequency of A and T nucleotides
• High GC content
• Low GC content
• High mutation rates in cold-blooded vertebrates
• Low gene density
In which type of organisms are heavy isochores typically found?
• All bacteria and plants
• Cold-blooded vertebrates like fish
• Warm-blooded vertebrates like mammals and birds
• Only invertebrates
• All vertebrates equally
Which of the following correctly ranks regions of a gene by average GC content, from
highest to lowest?
• Coding > introns > 5’ flanking > 3’ flanking
• 5’ flanking > coding > 3’ flanking > introns
• Introns > coding > 3’ flanking > 5’ flanking
• 3’ flanking > 5’ flanking > coding > introns
• Coding = introns = flanking regions
Which bacterial genus has the lowest known GC content, with approximately 18% GC
(i.e., over 80% of its genome is composed of A and T)?
• Mycoplasma
• Bacillus
• Escherichia
• Carsonella
• Rickettsia
What is the maximal value for ENC (effective number of codons)?
• 61
• 64
• 32
What does a low ENC (effective number of codons) value indicate about a gene?
• The gene uses all codons equally.
• The gene has high codon bias.
• The gene is not expressed.
• The gene is rich in stop codons.
• The gene uses only rare codons.
What is required to calculate the Fop (frequency of optimal codons) for a given
species?
• Only the gene's codon sequence
• Information on ribosomal binding sites
• Knowledge of protein structure
• Identification of optimal codons, which requires codon usage data from many genes and their expression levels
• Chromosomal location of the gene
What does a sex-biased gene primarily refer to?
• A gene that differs in sequence between sexes
• A gene expressed at different levels in males vs. females
• A gene that determines the sex of an individual
• A gene located only on the sex chromosome
Which methods are used to determine sex-biased genes?
• RNA-seq & male vs. female microarrays
• Shotgun sequencing and primer walking
• RAD-seq and mass spectrometry
• CRISPR-Cas and RNAi
• Microsequencing and cDNA-probing
The "Fast-X effect" is expected when beneficial mutations are:
• Recessive
• Common
• Overdominant
• Rare
• Dominant
• Recessive → answer because: recessive beneficial mutations can be fixed faster in males (only one X Chromosome)
What is the "Fast-X effect"?
• Suppression of X expression in the male germline
• An enrichment in loci that cause hybrid incompatibilities on the X chromosome
• An expected increase in the rate of adaptive evolution on the X chromosome due to the fixation of recessive, beneficial mutations in hemizygous males
• Upregulation of the single X chromosome in male somatic tissue approximately two-
fold
An expected increase in the rate of adaptive evolution on the X chromosome due to the fixation of recessive, beneficial mutations in hemizygous males
What is the "large-X effect"?
• An increase in the rate of adaptive evolution on the X chromosome
An enrichment in loci that cause hybrid incompatibilities on the X chromosome
What is the following result in a MK (McDonald-Kreitman) test indicative of?
Balancing selection
• Neutral protein evolution
• Weak purifying selection
• Positive selection for amino-acid changes
• Balancing selection
Suppression of the X chromosome occurs:
• in males and females
• in females, in the ovaries
• in males, throughout the entire body
• in males, in the testes
In Drosophila, sex chromosome dosage compensation involves:
• Upregulation of the male X
• Downregulation of the female autosomes
• Inactivation of one female X
• Downregulation of the male autosomes
• Downregulation of both female X’s
What is the purpose of dosage compensation?
• Equalize expression levels of sex-linked genes between sexes
• Suppress expression of autosomal genes in females
• Silence genes on both sex chromosomes in males
• Eliminate expression differences between all gene classes
Equalize expression levels of sex-linked genes between sexes
In which tissue is X-chromosome expression not upregulated in male Drosophila?
• Somatic cells
• Eye
In the male germline of Drosophila melanogaster:
• The X chromosome is completely inactivated
• The X chromosome is enriched with male-biased genes relative to the autosomes
• X-chromosomal gene expression is up-regulated approximately two-fold
• Expression of the X chromosome is suppressed relative to the autosomes
• X-chromosomal gene expression is up-regulated approximately four-fold
Expression of the X chromosome is suppressed relative to the autosomes
→ in germline it is completely inactivated, in somatic cells it is 2-fold
Which type of sex-biased genes are often found to be underrepresented on the X
chromosome in Drosophila?
• Female-biased genes
• Male-biased genes
• Unbiased genes
• Testis-expressed genes only
Male-biased genes
Ovary-specific genes are:
• over-represented on the X chromosome
• up-regulated in the female germline
• under-represented on the X chromosome
• only present on the X chromosome
What mechanism has likely facilitated the accumulation of male-biased genes on
autosomes?
• X chromosome duplication
• Retroposition from the X to autosomes
• Deletion of female-biased genes
• Silencing of X-linked enhancers
The defining feature of a cis-regulatory variant is that it:
• Alters the tissue in which a gene is expressed
• Only has an effect in heterozygotes
• Affects expression differently in males and females
• Is genetically linked to the gene it regulates
• Leads to the creation of a new splicing site
Which of the following best defines a trans-regulatory change affecting gene
expression?
• A mutation in the promoter of a gene that alters its own expression
• A change in the coding sequence that modifies protein function
• A mutation in a different, unlinked gene (e.g., a transcription factor) that alters expression of a target gene
• A duplication of the target gene leading to increased expression
Which gene has been identified as responsible for DDT resistance in Drosophila
melanogaster?
• Cyp3a4
• Cyp6g1
• DdtR1
• Gst1
• P450b1
What molecular change is associated with DDT resistance in Drosophila
• A gene deletion in Cyp6g1
• A missense mutation in a ribosomal protein gene
• Duplication of the DDT-binding receptor gene
• A transposable element insertion near the 5’ end of the Cyp6g1 gene
• Increased translation of detoxification enzymes due to mitochondrial mutation
A transposable element insertion near the 5’ end of the Cyp6g1 gene
What is the ancestral geographic origin of Drosophila melanogaster?
• South America
• Southeast Asia
• Sub-Saharan Africa
• Europe
• North America
Sub-Saharan Africa
What is the primary molecular cause of the expression difference of the gene CG9509
(fezzik) between African and European Drosophila populations?
• A coding mutation that changes enzyme activity
• A transposable element insertion within the gene
• Sequence divergence in the upstream regulatory region
• RNA splicing differences caused by intron variation
• A duplication of the CG9509 gene in European flies
Sequence divergence in the upstream regulatory region
In which tissue is the Drosophila gene CG9509 (fezzik) specifically expressed?
• Malpighian tubules
• Fat body
• Muscle tissue
• Gonads
What causes the expression difference of the MtnA gene between African and
European Drosophila melanogaster populations?
• A coding mutation in the MtnA gene
• A transposable element in the promoter
• A deletion of a negative regulatory element in the MtnA 3' UTR
• Duplication of the MtnA gene
A deletion of a negative regulatory element in the MtnA 3' UTR
What is the observed geographic pattern of the MtnA 3' UTR deletion?
• It is exclusive to tropical regions
• It is fixed globally in all populations
• It is only found in African populations
• It increases in frequency with distance from the equator
What type of selection likely maintains the polymorphism at the MtnA locus?
• Directional selection
• Stabilizing selection
• Purifying selection
What physiological function is associated with higher MtnA expression?
• Improved reproduction rate
• Better flight performance
• Enhanced vision in low light
• Increased oxidative stress tolerance
Which is not one of the main categories used in Gene Ontology (GO) to classify gene
functions?
• Molecular function
• Cellular component
• Genomic location
• Biological process
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