Genomics Quiz Questions for the Exam

What is the primary function of DNA in a cell?

Storing genetic information

Which enzyme is responsible for synthesizing a new DNA strand during replication?

DNA polymerase

Which nitrogenous bases pair with each other

DNA: Thymine to Adenine, Cytosine to Guanine

RNA: Uracil to Adenine, Cytosine to Guanine

What is the main product of transcription?

RNA

What is the main product of translation?

protein

During translation, ribosomes use ____ as a template to synthesize proteins.

mRNA

Which organelle is the primary site of protein synthesis?

ribosome

A mutation that changes one nucleotide in a DNA sequence is called a:

point mutation

What is the role of helicase during DNA replication?

Unwinding the DNA double helix

Which statement correctly desccribes the relationship between DNA, RNA, and protein?

DNA is transcribed into RNA, which is translated into protein

Which type of RNA carries amino acids to the ribosome during translation?

tRNA

Which method defines Sanger sequencing?

Chain-terminating dideoxynucleotides with capillary electrophoresis

A hallmark step of Illumina sequencing is:

bridge amplification forming clonal clusters on a flow cell

Oxford Nanopore primarily detects bases via:

Changes in ionic current as nucleic acids traverse a pore

PacBio sequencing is best described as:

Single-molecule fluorescence of nucleotide incorporations with laser detection

Shotgun genome sequencing most directly depends on:

De novo assembly of overlapping reads into contigs and scaffolds

In a genome assembly N50 is:

The shortest contig length needed to cover 50% of the entire genome assembly

In a whole-genome project, you sequenced a 3.2 Gb genome and obtained 400 million reads, each of which was 150bp long. What is the approximate average coverage (depth) of the genome?

19

Which statement correctly distinguishes contigs and scaffolds?

Scaffolds are ordered/oriented sets of contigs and may include gap Ns

Synteny between two species refers to

Conservation of gene order across chromosomal regions

Lineage-specific alternative splicing primarily leads to:

Proteome diversification enabling lineage or tissue specific functions

Which chromatin features indicate active promoters/enhancers?

DNase 1 hypersensitivity and histone acetylation (ex: H3K27ac)

Standard human DNA profiling primarily relies on:

Short tandem repeat (ex. microsatellite) length polymorphisms

Which statement correctly contrasts transposition and retrotransposition?

DNA transposons typically cut-and-paste: retrotransposons use a copy-and-paste mechanism

In human genetics, what is a “trait”?

Any measurable characteristic or phenotype of an individual

What is the primary goal of a genome-wide association study (GWAS)?

To find variants associated with a trait across the genome

Which best defines a single nucleotide polymorphism (SNP)?

A single base change at a specific genomic position common in a population

In GWAS results, “effect size” typically refers to:

Measurement of the statistical association between a specific genetic variant (ex. SNP) and a trait

The increasing allele for a quantitative trait is:

The allele that raises the measured value of the trait per copy

If you test 1,000,000 independent SNPs which Bonferroni-corrected significance threshold is closest to standard practice?

5×10^-8

In statistics, variability in a trait refers to:

The spread or dispersion of trait values across individuals

In GWAS, heritability is best described as:

The percent differences of a trait between individuals due to DNA differences

A polygenic score is:

A weighted sum of trait-increasing alleles across many loci

In a case-control GWAS, an odds ratio of 1.5 for allele indicates:

The allele increases odds of disease by 50% per copy

A haplotype is best defined as:

A set of alleles at multiple loci that tend to be inherited together on the same chromosome

Which scenario best illustrates confounding in a GWAS?

Population stratification leads to allele frequency differences correlated with both ancestry and the trait

If two SNPs are in strong LD (r²=0.9) which is most likely true?

One can often “tag” the other for association purposesMolecular evolution is best described

Molecular evolution is best described as:

The study of changes in DNA, RNA, and protein sequences over evolutionary time

Two genes are considered homologs if they:

Share a common evolutionary ancestor

Orthologs are genes that:

Arise by speciation and are usually found in different species

Paralogs are genes that

Result from gene duplication events

Conserved regions in proteins are often important because they

Often contain amino acids essential for structure or function

Apoptosis refers to

Programmed cell death

A proto-oncogene is:

A normal gene that can promote cell growth or division

An oncogene is usually formed when

A proto-oncogene becomes abnormally activated or overexpressed

Tumor suppressor genes normally function to

Prevent or regulate cell growth and division

Speciation is the process by which

One species splits into two or more distinct species

Natural selection occurs when

Individuals with advantageous heritable traits leave more offspring

A synonymous mutation is one that

Does not change the encoded amino acid

Which example best describes a.chromosomal inversion

A chromosome segment is reversed in orientation within the same chromosome

Exon shuffling supports the modular nature of proteins because it

Allows protein domains encoded by exons to be recombined into new gene arrangements

In sequence alignment identity refers to

The percentage or fraction of positions with exactly the same residue or nucleotide

In sequence analysis similarity is uaually broader than identity because similarity

Includes exact matches as well as conservative substitutions with similar biochemical properties

A global alignment is designed to

Align two sequences from beginning to end across their full lengths

A local alignment is most useful when

Only a region or domain within two sequences is similar

A dot matrix or dot plot is used to

visualize regions of similarity between two sequences

A scoring matrix in sequence alignment is used to

Determine how favorable or unfavorable residue substitutions are

BLOSUM62 is commonly used to

Score amino acid substitutions in protein sequence alignments

BLAST is best described as a tool that

searches sequence databases for regions similar to a query sequence

BLASTP is used to compare

A protein query sequence against a protein sequence database

BLASTN is used to compare

Nucleotide sequences against nucleotide databases

In BLAST the E-value represents

the expected number of alignments with a similar score that could occur by chance in a database search

A lower E-value generally indicates that a BLAST hit is

more likely to be biologically meaningful and less likely due to chance

A gap penalty is used in sequence alignment to

penalize the introduction or extension of gaps in an alignment

The raw score of an alignment is

The alignment score is calculated directly from matches, mismatches, substitutions, and gaps

Protein primary structure refers to

the linear sequence of amino acids in a polypeptide chain

protein secondary structure mainly includes

alpha helices and beta sheets stabilized by backbone hydrogen bonds

protein tertiary structure describes

the three-dimensional shape of a single polypeptide chain

X-ray crystallography determines protein structures by

measuring how protein crystals diffract X-rays

NMR spectroscopy is especially useful because it can

study proteins in solution and provide information about structure and dynamics

Cyrogenic electiron microscopy or Cryo-EM is commonly used to

image frozen biological molecules or complexes using elctron microscopy

In protein structure predication “ab initio” methods attempt to

predict structure from basic physical principles and sequence information, often without using a close template

Statistical and knowledge-based protein prediction methods generally rely on

patterns learned from known protein structures and sequence structure realtionships

Neural networks are useful in protein structure prediction because they can

learn complex patterns from large datasets of protein sequences and structures

AlphaFold2 is best known for

predicting protein three-dimensional structures from amino acid sequences with high accuracy for many proteins

Intrinsically disordered proteins (LDPs) are best described as

proteins that lack a single stable three-dimensional structure under physiological conditions

Intrinsically disordered regions (IDRs) are

flexible regions within proteins that do not adopt one fixed structure

Post-translational modification refers to

Chemical modification made to proteins after they are synthesized

The transcriptome is

the complete set of RNA transcripts produced by a cell or organism under specific conditions

The proteome is

the complete set of proteins expressed by cell,tissue, or organism under specific condition

A response element is

a DNA sequence that binds regulatory proteins and helps control gene expression

A microarray is commonly used to

measure the expression levels of many genes simultaneously using hybridization to probes

RNA seq is used to

measure and analyze RNA transcripts using high throughput sequencing

2D gel electrophoresis separates proteins mainly by

Isoelectric point and molecular weight

LC-MS is commonly used to

Identify and quantify proteins or peptides using liquid chromatography and mass spectrometry

A phylogeny is best described as

A hypothesis about the evolutionary relationships among organisms or genes

A molecular clock is base on the idea that

mutations or sequence changes may accumulate at an approximately regular rate over time

Divergence time refers to

The time when two lingeages last shared a common ancestor

Evolutionary distance generally measures

the amount of evolutionary change separating two sequences or taxa

A distance matrix is used in phylogenetics to

store pairwise evolutionary distances between sequences of taxa

A rooted tree differs from an unrooted tree because a rooted tree

shows the direction of evolutionary time from a common ancestor

An unrooted tree shows

evolutionary relationships without specifying the common ancestory or direction of time

In phylogenetic analysis, an outgroup is used to

Help root a tree by providing a reference lineage outside the group of interest

UPGMA assumes that

Evolutionary rates are equal across all lineages

Neighbor Joining is a method that

Builds a phylogenetic tree from a distance matrix without requiring a strict molecular clock