Genetics Exam 3 (Ch. 14-17)

Recombination

(1) in general, any process in a diploid or partly diploid cell that generates new gene or chromosomal combinations not previously found in that cell or in its progenitors (2) at meiosis, the process that generates a haploid product of meiosis whose genotype is different from either of the two haploid genotypes that constituted the meiotic diploid

Scaffolds

(1) the central framework of a chromosome to which the DNA solenoid is attached as loops; composed largely of topoisomerase (2) in genome projects, an ordered set of contigs in which there may be unsequenced gaps connected by paired-end sequence reads - (aka supercontigs)

Mutations

(1) the process that produces a gene or a chromosome set differing from that of the wild type (2) the gene or chromosome set that results from such a process

B. Nucleotide; translated amino acid

A BLAST sequence can be submitted as a _______ sequence or as a _____ sequence A. EST; nucleotide B. Nucleotide; translated amino acid C. Query; EST D. Query; translated amino acid

Expressed sequence tags (ESTs)

A cDNA clone for which only the 5' or the 3' ends or both have been sequenced; used to identify transcript ends in genomic analysis

Synonymous mutations (silent mutations)

A change to the sequence of a codon that does not change the encoded amino acid

A. Short sequences called adaptors are added to the center of the DNA fragments

A few different systems have been developed that, while they differ in their sequencing chemistry and machine design, each employs three strategies that have dramatically increased throughput. Which of these is NOT one of those strategies? A. Short sequences called adaptors are added to the center of the DNA fragments B. DNA molecules are prepared for sequencing in cell-free reactions, without cloning in microbial hosts C. Millions of individual DNA fragments are isolated and sequenced in parallel during each machine run D. Advanced fluid-handling technologies, cameras, and software make it possible to detect the products of sequencing reactions in extremely small reaction volumes

Sequence contigs

A group of overlapping cloned segments

D. Finished

A large research group has produced a sequence of the giraffe genome. This genome sequence is missing two small portions of giraffe chromosomes 16 and 18, but is otherwise intact (and appears correct). This research group has created a _____ sequence of the giraffe genome. A. Draft B. Mutant C. Complete D. Finished

Genome projects

A large-scale, often multilaboratory effort required to sequence a complex genome

Two-hybrid test

A method for detecting protein-protein interactions, typically performed in yeast

RNA sequencing (RNA-seq)

A method used to determine the transcribed regions of a genome within some specific cell population, tissue sample, or organism

Somatic mutations

A mutation in a cell that can be passed on to daughter cells in the course of cell division

Germ—line mutations

A mutation in the DNA of germ cells, sperm, or oocyte

Base insertion

A mutation in which a base pair in added to a DNA sequence

Base deletion

A mutation in which a base pair is removed from a DNA sequence

Indel mutations

A mutation in which one or more nucleotide pairs is added or deleted

Point mutation

A mutation that alters a single base position in a DNA molecule by converting it to a different base or by the insertion/deletion of a single base in a DNA molecule

Base substitutions

A mutation that exchanges one base pair for another in a DNA sequence

Pseudogenes

A mutationally inactive gene for which no functional counterpart exists in wild-type populations

DNA damage

A physical or chemical abnormality in the structure of DNA

Processed pseudogenes

A pseudogene that arose by the reverse transcription of a mature mRNA and its integration into the genome

C. It is also a globular protein

A researcher has performed a BLASTp search for a protein of interest. He identifies a globular protein that shares 35% of its amino acid sequence (and positioning) with his target protein. What can he conclude about the shape of his protein of interest. A. It is a fibrous protein B. It only has a primary structure C. It is also a globular protein D. It only demonstrates pleated sheets as part of its structure

C. These genomes will be approximately 50% identical.

A researcher is comparing the genomes of two humans. Which of these statements is FLASE regarding these two genomes? A. These genomes may demonstrate different numbers of copies of genes B. Differences in these genomes could determine what diseases these humans will get C. These genomes will be approximately 50% identical D. These genomes will differ by approximately 3 million base pairs

A. Orthologs

A researcher is comparing two different genes (at the same locus) - one in goats and the other in sheep. She determines that these goat and sheep genes are nearly identical in sequence and encode very similar proteins. These genes are most likely _____. A. Orthologs B. Paralogs C. Syntenlogs D. Phylologs

DNA sequencing library

A set of DNA fragments that will be used for sequencing

Synteny

A situation in which genes are arranged in similar blocks in different species

Whole-genome shotgun (WGS) sequencing

A strategy for obtaining the sequence of a genome by sequencing and assembling many short segments of genomic DNA

Open reading frames (ORFs)

A stretch of nucleotide sequence that is not interrupted by a stop codon in a given reading frame

RNA interference (RNAi)

A system in some eukaryotes to control the expression of genes through the action of siRNAs

Transition

A type of nucleotide-pair substitution in which a purine replaces another purine or in which a pyrimidine replaces another pyrimidine - for example, G-C to A-T

Transversion

A type of nucleotide-pair substitution in which a pyrimidine replaces a purine or vice versa - for example, G-C to T-A

ChIP-seq

A variation of the ChIP procedure in which all of the DNA binding sites of a regulatory protein in a genome are identified by sequencing

C. Introns

Alignment of a cDNA sequence with its corresponding genomic DNA is useful in identifying which of these? A. The open reading frame B. The location of a stop codon C. Introns D. BLAST

Reverse genetics

An experimental procedure that begins with a cloned segment of DNA or a protein sequence and uses it (through directed mutagenesis) to introduce programmed mutations back into the genome to investigate function

Comparative genomics

Analysis of the relations of the genome sequences of two or more species

D. Homologous

Bat wings and bear arms have similar features and are used in similar ways. Bats and bears therefore share a certain amount of genetic information. Some of the genes that encode bat wings and bear arms must be: A. Orthologous B. Paralogous C. Ultraconserved D. Homologous

D. Clone

Because each recombinant molecule is amplified from an individual cell, each cell is a distinct _____. A. Shotgun library B. Vector C. Sequence contig D. Clone

B. Break the genome into small random fragments

Because of restrictions on the number of base pairs that can be read from a single sequencing reaction, a scientist must do what to the full-length genome before running a sequencing reaction? A. Run a PCR reaction B. Break the genome into small random fragments C. Isolate RNA from the species of interest D. Purify the DNA from each chromosome individually

B. Orthologous

Both humans and dogs have the genes for the protein hemoglobin. Evolutionary biologists believe that this indicates that hemoglobin evolved before the last common ancestor of humans and dogs. This would make the genes that encode hemoglobin in the two species an example of ______ genes. A. Ultraconserved B. Orthologous C. Homologous D. Paralogous

Phylogenetic inference

Determining the state of a character or the direction of change in a character based on the distribution of that character within a phylogeny of organisms

C. To determine which genes are active or inactive under typical conditions compared to experimental conditions

For what is RNA-seq useful? A. To determine expression levels of mRNA in active genes in two different organisms B. To determine the sequence of a transcriptome C. To determine which genes are active or inactive under typical conditions compared to experimental conditions D. To determine if DNA has been transcribed E. To determine the sequence of cDNA libraries

Orthologs

Genes in different species that evolved from a common ancestral gene by speciation

Paralogs

Genes that are related by gene duplication in a genome

Homologous genes

Genes that share a common ancestor - can be paralogs or orthologs

B. 100-300 cycles

How many cycles are used during Illumina sequencing by synthesis? A. At most 100 B. 100-300 cycles C. At least 150 D. At least 300 E. 50-100 cycles

B. RNA-seq

If a researcher wanted to study the transcriptome, which technique would be utilized? A. Whole genome sequencing B. RNA-seq C. ChIP D. Two yeast hybrid

C. Tryptophan and leucine; tryptophan, leucine, and histidine

If two proteins do not interact, yeast cells will grow in medium lacking _______, but not in medium lacking _____. A. Leucine and histidine; tryptophan, leucine, and histidine B. Tryptophan and histidine; tryptophan, leucine, and histidine C. Tryptophan and leucine; tryptophan, leucine, and histidine D. Tryptophan, leucine, and histidine; leucine and histidine E. Tryptophan, leucine, and histidine; tryptophan and leucine

C. In the pellet

In ChIP, after precipitation by centrifugation, where are the complexes of interest found? A. In the supernatant B. Bound to proteins C. In the pellet D. In the solution

A. Years

In the 1980s, sequencing an entire genome could take _____ to complete and a large number of researchers A. Years B. Minutes C. Days D. Months

D. Vector

In traditional whole-genome shotgun sequencing, DNA fragments are sequenced from each end using primers that are complementary to _____ DNA. A. Donor B. Expressed tag C. Supercontig D. Vector

Paired-end reads

In whole-genome shotgun sequence assembly, the DNA sequences corresponding to both ends of a genomic DNA insert in a recombinant core

A. Synteny

Large portions of the mouse and human genomes show conserved _______ and the same gene order A. Synteny B. CNV C. Phylogeny D. Parsimony

D. She cannot determine anything (because the amino acid identity is less than 35%, nothing can be concluded about the shape of the protein of interest)

Myrna has performed a BLASTp search on a protein found in the arctic tern. She identifies a fibrous protein that shares 25% of its amino acid sequence (and positioning) with a target protein. What can she conclude about the shape of her protein of interest? A. It is a fibrous protein B. It demonstrates pleated sheets only as part of its structure C. It is also a globular protein D. She cannot determine anything

Missense mutations

Nucleotide-pair substitution within a protein-encoding region that leads to the replacement of one amino acid by another amino acid

A. The 3' poly A tail of mRNA

Oligo dT primers are complementary to A. The 3' poly A tail of mRNA B. Random hexamers C. The 5' poly A tail of mRNA D. cDNA E. 3' poly A tails of DNA

D. Query sequences

Predictions of mRNA and polypeptide structure from genomic DNA sequence depend on the integration of information from all of these EXCEPT: A. Codon bias B. Binding-site predictions C. Polypeptide similarities D. Query sequences

B. Binding several promoter regions

Regulatory proteins activate transcription of many genes simultaneously by A. Unraveling histones B. Binding several promoter regions C. Binding one promoter region D. Binding to reader proteins

A. Enhancers

Regulatory sequences such as ______ are not identifiable by mere inspection of DNA sequences. A. Enhancers B. Gene promoters C. 5' and 3' untranslated sequences D. Introns

D. Stop codons within genomic DNA

Statistical "gene-finding" computer programs search for all of these EXCEPT: A. For 3' and 5' splice sites B. For transcription start sites C. The predicted sequences of the various binding sites used for promoters D. Stop codons within genomic DNA

Outgroup

Taxa outside of a group of organisms among which evolutionary relationships are being determined

Personal genomics

The analysis of the genome of an individual to better understand his or her ancestry or the genetic basis of phenotypic traits such as his or her risk of developing a disease

Forward genetics

The classical approach to genetic analysis, in which genes are first identified by mutant alleles and mutant phenotypes and later cloned and subjected to molecular analysis

Genomics

The cloning and molecular characterization of entire genomes

Sequence assembly

The compilation of thousands or millions of independent DNA sequence reads into a set of contigs and scaffolds

Proteome

The complete set of proteins expressed in a cell, tissue, or organism

Interactome

The entire set of molecular interactions within cells, including in particular protein-protein interactions

Phylogeny

The evolutionary history of a group

Annotation

The identification of all the functional elements of a particular genome

B. Types of species sequenced

The methods of automated sequencing now available vary in all of these ways EXCEPT for: A. Raw accuracy B. Types of species sequenced C. The length of DNA sequence obtained D. The bases determined per second

C. DNA wrapped around histones

The nucleosome contains A. Reader proteins wrapped around histones B. DNA intertwined with reader proteins and histones C. DNA wrapped around histones D. Histones wrapped around DNA

Consensus sequence

The nucleotide or amino acid sequence of a nucleic acid or protein, respectively, that is derived by aligning similar sequences (either from the same or different organisms) and determining the most common nucleotide or amino acid at each position

B. Transcriptome

The sequence and expression patterns of all RNA transcripts in a particular cell type or population of cells is known as the A. cDNA library B. Transcriptome C. RNA library D. Illumina sequence

Exome

The sequence of all of the exons in a genome

Transcriptome

The set of RNAs expressed in cells, tissues, or organisms

Functional genomics

The study of the patterns of transcript and protein expression and of molecular interactions at a genome-wide level

C. Systems

The study of the way in which all gene products interact to produce the physiology of an organism is know as ____ biology A. Functional B. Comparative C. Systems D. Plant

D. Degenerate

The triplet code for amino acids is: A. Similar B. Complementary C. Predicted D. Degenerate

Chromatin immunoprecipitation (ChIP)

The use of antibodies to isolate specific regions of chromatin and to identify the regions of DNA to which regulatory proteins are bound

Parsimony

To favor the simplest explanation involving the smallest number of evolutionary changes

C. The adapter sequences of the DNA fragments

To what sequence are oligonucleotides on the flow cell complementary? A. The contig sequences B. The cluster bridge sequences C. The adapter sequences of the DNA fragments D. The overlap sequences on the DNA fragments

Copy number variations (CNVs)

Variation for a large DNA segment among homologous chromosomes caused by differences in the numbers of tandem copies of a single or multiple genes

C. DNA and its associated proteins

What can researchers analyze by utilizing ChIP (chromatin immunoprecipitation)? A. Functional genome elements B. Tandem repetitive elements C. DNA and its associated proteins D. Protein interactions

E. Uniform sizes of double stranded DNA fragments

What does a DNA sequencing library contain? A. Complete sequences of genes B. Uniform sizes of DNA contigs C. Uniform sizes of single stranded DNA fragments D. Double stranded DNA fragments of varying sizes E. Uniform sizes of double stranded DNA fragments

B. The change in species' genomes over time

What information can be inferred from phylogeny? A. Paired-end reads for high-throughput sequencing B. The change in species' genomes over time C. Genes that can be mutated for reverse genetics D. The various functional elements within the genome

D. Consumers may be able to find relatives they did not previously know

What is not a concern regarding direct to consumer testing? A. Consumers may stop taking preventative measures based on test results B. Consumers may not fully understand their personal genetic risks C. Consumers' test results may not be secured and protected from misuse D. Consumers may be able to find relatives they did not previously know

D. Dispersed repetitive elements

What is not a functional element of the genome? A. Sequences that encode proteins B. RNAs that regulate gene expression C. Binding sites for proteins D. Dispersed repetitive elements

1. Cross-link proteins to DNA 2. Break chromatin into small pieces 3. Add antibody to target protein and purify 4. Reverse cross-links to separate DNA and protein

What is the correct order of steps in ChIP? *Hint: 4 steps

1. Cut many genome copies into random fragments 2. Sequence each fragment 3. Overlap sequence reads 4. Overlap contigs for complete sequence

What is the correct order of steps in Next Generation WGS Sequencing? *Hint: 4 steps

1. Cross-link proteins to DNA 2. Break the chromatin into small pieces 3. Add antibody to target protein and purify 4. Reverse cross-links to separate DNA and protein

What is the correct order of steps in a chromatin immunoprecipitation assay (ChIP)? *Hint: 4 steps

A. Forward genetics focuses on phenotype, whereas reverse genetics focuses on genotypes

What is the difference between forward genetics and reverse genetics? A. Forward genetics focuses on phenotype, whereas reverse genetics focuses on genotypes B. Forward genetics focuses on functional genomics, whereas reverse genetics focuses on comparative genomics C. Forward genetics focuses on genotypes, whereas reverse genetics focuses on phenotypes D. Forward genetics focuses on comparative genomics, whereas reverse genetics focuses on functional genomics

1. mRNA fragmentation 2. cDNA synthesis 3. Illumina sequencing 4. Mapping to genes

What is the order of steps during RNA sequencing? *Hint: 4 steps

C. To obtain a large number of overlapping sequence reads

What is the purpose of next-generation whole-genome sequencing? A. To circumvent the problem of repetitive sequences and gaps B. To understand gene and protein function in biological processes C. To obtain a large number of overlapping sequence reads D. To consider the genomes of closely and distantly related species

B. Random hexamers are used as primers

What is used to reverse transcribe fragmented mRNA into cDNA? A. Poly A tails are used to identify targets for sequencing B. Random hexamers are used as primers C. Oligo dTs are used as a primer D. A ligase is used to join the fragments

D. Evolutionary conservation of sequences

Which aspect of a sequence indicates biological function? A. Tandem repetitive elements B. Open reading frames C. Functional elements within genomes D. Evolutionary conservation of sequences

D. GAL4 BD and GAL4 AD

Which domains of GAL4 need to be in close proximity to form an active transcription factor? A. Trp1+ and Leu2+ B. GAL4 BD and Leu2+ C. GAL4 BD and His+ D. GAL4 BD and GAL4 AD E. GAL4 AD and Trp1+

D. They cause the wrong sequences to be aligned together

Why do dispersed repetitive elements create a challenge for genome assembly? A. They create large gaps in the assembly of an entire genome B. They make it difficult for DNA fragments to be cut appropriately C. They cause loops to form during replication and sequencing D. They cause the wrong sequences to be aligned together

B. To considerably reduce target mRNA levels

Why do researchers utilize RNA interference (RNAi)? A. To create sequences with overlapping reads B. To considerably reduce target mRNA levels C. To cut DNA into small fragments D. To remove dispersed repetitive elements

D. A consensus sequence

_______ is a sequence for which there is consensus (or agreement) that it is an authentic representation of the sequence for each of the DNA molecules in that genome. A. An individual sequencing reaction B. A whole-genome shotgun sequence C. A sequence assembly D. A consensus sequence

A. Fish; bait

cDNAs are cloned next to the GAL4 AD forming ______ protein fusions that may interact with the GAL4 BD ______ fusion proteins. A. Fish; bait B. Bait; fish C. Bait; target D. Fish; fish E. Bait; bait