genetics test 3 short answer and essay questions

question

Suppose that you have been able to partially sequence a significant number of cDNA clones from an as yet unsequenced insect genome. These clones are useful as what sequences that can help annotation?
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ESTs
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A researcher has produced groups of contigs that are linked via paired-end sequences, although these include some sequence gaps. What are these groups called?
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scaffolds
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In 2000, when then-President Clinton along with Francis Collins of the Human Genome Project and Craig Venter of Celera announced the completion of a “draft” of the human genome, the event did not, in fact, represent true completion because most of what type of sequences were not included?
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repetitive
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Often, in the absence of experimental data, computerized algorithms are used to predict gene structures from large sequences. What is this approach known as?
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bioinformatics
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Suppose that you use the sequence of the lacI gene, whose function you know is to encode a transcription factor, to find similar sequences in another bacterial strain. Are you more likely to find similar operons or similar transcription factors?
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transcription factors
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In humans, a large number of genes associated with immune function share sequence similarity and are evolutionarily related. These would be known as what kind of group?
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a gene family
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In a simple bioinformatics exercise, students are asked to locate the beginning of an ORF among the six possible reading frames for a hypothetical DNA molecule. The first step in their process should involve looking for what sequence?
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ATG
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If a gene product is not a protein but a noncoding RNA, the sequence might be initially hypothesized from comparative genomics but must be confirmed how?
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by experimenting or experimentally
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Very many related genes can be recognized by conserved protein domains. To what gene structures do these domains correlate?
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exons
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Species whose ancestors might once have been free living may now be present as parasites. Would their genomes now tend to be larger, smaller, or approximately the same in size and complexity?
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smaller
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The BLAST program from NIH enables a researcher to look for homologous genes. It does so in general by searching for identity in what property?
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nucleotide sequence
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Interspecific genome studies show us conserved sequences, but intraspecific comparisons identify what?
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(sequence) differences or polymorphisms
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Suppose a geneticist sequences a specific gene region in two species, A and B, previously known to be closely related. He specifically wants to see which of the two species is closer to an ancestral species. The sequence comparison showed that this region in species B has an extra intron, unlike other near relatives, but that otherwise A and B are virtually the same for this region. Based on this data alone, he could reason that which species was more likely ancestral?
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A
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An Alu sequence is a kind of retrotransposon, and approximately 1.4 million of them are found in the human genome. As they move about in the genome, they generate mutation by what mechanism?
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insertion (into intron/exon)
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An inherited human disorder, familial dysautonomia, results from a nucleotide mutation in the gene IKAP that is expressed in the nervous system. The decreased IKAP protein leads to abnormal development, and the resulting disease is usually fatal by age 30. The nucleotide change alters splicing. If this change affects only the nervous system and not the immune system, in which the gene is also expressed, what feature must be found in this gene?
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alternative splicing
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A gene in a sheep-like species has been found to differ from that in related species by the inclusion of a variable number of tandem repeats of a short sequence. These repeats or duplications arise from what process?
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unequal crossing over
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Mammalian genomes all have a number of genes for globin polypeptides. Several of these genes are functional, but several are never expressed. What are the nonfunctional ones known as?
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pseudogenes
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Conserved noncoding sequences (CNGs) are usually sequences involved in what kinds of functions?
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regulatory or regulation
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The karyotypes of several primate species, such as chimpanzee and gorilla, show two nearly telocentric chromosomes as opposed to the single large metacentric chromosome 2 in humans. Does this demonstrate chromosome breakage or fusion at the time of lineage divergence?
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fusion
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The set of transcripts present in a cell or organism is called the _____.
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transcriptome
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Genome-wide expression patterns can be studied using _____.
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microarrays
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If an entire genome is fragmented and then a large number of pieces are sequenced, the approach is known as the ________ approach.
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shotgun
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The whole-genome shotgun approach (WGS) was first used on which eukaryotic model organism?
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Drosophila
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A genome sequence is considered to be complete when all its ________ sequences are included, as well as reasonable amounts of repetitive sequences.
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euchromatic
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Sequencing of DNA from a community of organisms rather than from a single individual is known as ________.
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metagenomics
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The process of finding the location of genes and functional (e.g., regulatory) sequences and their functions within a genome sequence is called ________.
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annotation
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The use of computational approaches to understand DNA sequence information is called _____.
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bioinformatics
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The movement of genes from one species into the genome of another is referred to as _____.
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lateral gene transfer
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Among the discoveries that Correns and Bauer (1908) made in plants was that, sometimes, reciprocal crosses resulted in what phenotype only?
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maternal
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When a cell divides, chloroplasts are randomly distributed. What is this called?
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replicative segregation
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Variation in numbers of mutated chloroplast genomes can give rise to green, white, or variegated leaves. What color leaves do you expect in offspring of pollen from a white-leafed plant and ovules from a green-leafed plant?
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green
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What is the name of the area of the organelle in which organelle DNA is packaged?
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nucleoid
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Which factor in organelle replication immediately precedes “organelle division”?
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Nucleoid division
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In mammals, the number of mitochondria per cell is highly variable. Which of the following would have the largest number: skin cells, red blood cells, or skeletal muscle cells?
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skeletal muscle (cells)
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In any mammal, the phenotype for a mitochondrial trait is based on what maternal characteristic?
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genotype
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Is the rate of mutation in mitochondrial DNA of mammals greater or less than that of the species’ nuclear DNA?
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greater than
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Allan Wilson showed that the mtDNA of Africans is more diverse than that of other human populations. Does this finding provide evidence for the multiregional (MRE) model or the recent African origin (RAO) model?
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RAO
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Three of the four modes of inheritance of organelle genes are • maternal inheritance as in mammals, • paternal inheritance as in gymnosperms, and • selective degradation of one source during mating. What is the fourth?
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biparental inheritance
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Mating in Chlamydomonas occurs between haploid mt+ and mt- individuals. The mt- chloroplast genome is selectively degraded 95% of the time. In one such mating, the mt+ genome is strR and mt- is strS. Will offspring live or die if they are exposed to streptomycin?
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live
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Mitochondrial genome transcription, translation, and replication occur where?
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in the (mitochondrial) matrix
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In one or two words, give two characteristics of mitochondrial genomes.
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Any two of the following: circular no histones/chromatin anchored (to the mitochondrial membrane) variable in size
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What name is given to the alteration of an RNA sequence after transcription?
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RNA editing
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The protein-coding genes of chloroplasts are involved in what part of photosynthesis?
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oxidative phosphorylation
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Do the protein-coding parts of organelle genes more closely resemble those of Bacteria (Eubacteria) or Archaea?
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Bacteria
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What are the closest “relatives” of chloroplasts still found as free-living organisms today?
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cyanobacteria
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Sequencing of genomes of eukaryotes, both mitochondrial and nuclear, have revealed evidence of sequence transfer from one to the other. Are such transfers ancient, recent, or both?
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both
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If a chloroplast coding sequence has been transferred to the nuclear genome, but the protein product is needed in the chloroplast, what must be added to the original polypeptide sequence?
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signal sequence
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DNA transfer has occurred many times between organelle and nuclear genomes. Two pairs of sequences are analyzed. Pair A has more similarities than pair B. Which of these is the most ancient transfer?
answer

Pair B
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Any form of inheritance that does not follow Mendelian patterns and that involves most of the cytoplasm being contributed to the embryo by one of the parents is called ________.
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extrachromosomal (inheritance)
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The organelles involved in organelle heredity are ________ and ________.
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chloroplast; mitochondria (the reverse order is also correct)
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If a cell includes a mixture of variable numbers of wild-type and mutant organelles, this condition is known as ________.
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heteroplasmy
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In the 1950s, mitochondrial genomes were discovered by differential staining for ________.
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DNA
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Mitochondrial mutations in mammals are passed to the offspring by the ________ parent.
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female or maternal
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Transcriptional regulation of mitochondrial genes closely resembles regulation of _______ operons.
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bacterial
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The chloroplast is derived from a precursor organelle called a _____.
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plastid
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Chloroplast RNA undergoes _______, which is the alteration of the RNA sequence after transcription.
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RNA editing
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An embryonic stem cell has the potential to differentiate into any cell or tissue type. Is it differentiated, pluripotent, or totipotent?
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totipotent
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What term describes the process by which a cell acquires a certain fate from its neighboring cell?
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induction
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What substance, in different concentrations, directs developmental fates?
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morphogen
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Which of the groups of early developmental genes in Drosophila act across segment boundaries to produce parasegments?
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pair rule (genes)
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Cell autonomous genes affect only those cells in which they are expressed. Which group of early developmental genes are not cell autonomous?
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segment polarity (genes)
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Homeotic genes in virtually all animals are said to show colinearity between the spatial arrangement of the tissues they act on as well as what other feature?
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gene location
question

The establishment of the axes of the body plan occurs during which stage of Drosophila development?
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embryo or embryonic
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If a cell from the blastoderm of the Drosophila embryo is committed to form part of an abdominal segment of the adult, such as the sixth one, and this cell is transplanted into the thorax-committed region of another embryo, will it develop properties of a thoracic or an abdominal segment?
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abdominal
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Certain mutations in non-Hox genes actually produce homeotic mutants due to a failure to modulate chromatin acetylation appropriately. This influence on cellular “memory” is called what?
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epigenetic
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A highly conserved protein domain of 60 amino acids is found in a large number of animals. This domain allows the proteins in question to bind to what?
answer

regulatory DNA (sequences)
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The maternal effect bicoid protein is a transcription factor that binds to the promoter of a zygotic gene to activate its expression. What is this second gene?
answer

hunchback
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Which group of genes in Drosophila embryos must be mutated if the result is elimination of a significantly sized, contiguous region of segmentation?
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gap genes
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The Antennapedia complex and the bithorax complex of genes all encode transcription factors that have a 180-bp DNA-binding domain. What is this domain called?
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homeobox
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What characteristic of a cellular blastoderm in Drosophila embryogenesis distinguishes it from the syncytial blastoderm?
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cell membranes or cell compartmentalization
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In the development of C. elegans, an embryo of 1090 cells then loses 131 cells. This is an example of what process?
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apoptosis
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Cell signaling during much of C. elegans development occurs along concentration gradients. What kind of signaling does this represent?
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inductive or induction
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During the evolution of development in animals, it is found that many regulatory genes have been co-opted for the development of different structures, such as limbs or digits. This is an example of what current area of research?
answer

evo-devo
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In Arabidopsis thaliana, a model organism in plant genetics, there are three classes of genes that control the development of floral structures: A, B, and C. Mutations of these genes cause organs to form in inappropriate places. What category of genes are they?
answer

homeotic
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In Drosophila and other animals, Hox genes encode transcription factors that control development; but in Arabidopsis, a different family of transcription factors is produced with a different set of conserved amino acids. These are encoded by what group of genes?
answer

MADS (box genes)
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Which structure in plants acts most like embryonic stem cells in animals?
answer

meristem
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Certain species of lilies, if eaten by pregnant ewes, can cause the ewes to produce lambs with severe birth defects because the plants’ cyclopamine can block embryonic response to Shh. This type of birth defect is a phenocopy of mutations in which genes?
answer

Shh
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Mouse eye genes can be inserted into Drosophila and can regulate the flies’ eye formation. Differences in size and shape of a zebra are controlled by a gene also found in zebrafish. What do these examples illustrate?
answer

conserved genes or conservation (of genes)
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A mutation in a fly causes an antenna to develop where a leg should be. This is an example of a ________ mutation.
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homeotic
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Molecules whose concentration and position in an embryo determine some aspect of development are called ________.
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morphogens
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The process by which the presence and activity of neighboring cells determine an aspect of development is called ________.
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induction
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If a cell is no longer able to differentiate into any type of tissue, it has become _______.
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differentiated
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Most of the genes controlling development encode either signal molecules or ________.
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transcription factors
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Coordinate genes in an organism such as Drosophila determine the ________ of the early embryo.
answer

polarity
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In limb-positioning in tetrapods, the _______ acts as an organizer to promote digit formation at the distal ends of limb buds.
answer

ZPA (zone of polarizing activity)

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