Genetics Final Exam

Gene regulatory networks may dominate developmental evolution -Sea urchin and sea star gene regulatory network. Sea urchins and sea stars diverged about ____ ____ years ago. Subnetwork of the gene regulatory networks governing __________ development in the sea urchin and sea star. Note that the red lines shown with Krox, FoxA, and GataE represent the only interactions that have not been ____ _____. -_____ in DNA are the basis of evolution; their effects may be deleterious, neutral, or favorable. Major _____ changes appear to result from mutations that affect ______ ______ ______. Many of these basic networks have been _____ throughout evolution.

500 million, mesoendodermal, highly conserved, mutations, phenotypic, developmental regulatory networks, conserved

How insulators work -Insulators bind a protein called ______ (______-____ ____) that facilitates the formation of DNA loops. -Insulators organize genomic DNA into _____, while enhancers activate transcription only from promoters within the ____ loop. The insulator-binding protein CTCF facilitates loop formation by interacting with other ____.

CTCF, CCCTC-binding factor, loops, same, proteins

The action of the Sxl protein in females -Sxl expression only in XX Drosophila. Later in development, transcriptional activators produced equally in XX and XY animals activate Sxl transcription from the ____ _______. When the Sxl protein is present (in females), it binds the Sxl ______ _____ to make a spliced mRNA that can be translated into more Sxl protein. The result is a _____ ____ that maintains Sxl protein in females but not in ____. (The early and late Sxl proteins differ slightly in their N-terminal amino acids.)

Pm promoter, primary transcript, feedback loop, males

16.5 A Comprehensive Example: Sex Determination in Drosophila essential concepts -The ____ gene is the master regulator of sex determination in Drosophila. Transcription of Sxl depends on ______ proteins encoded by genes on the ___ chromosome; only in cells with ___ X chromosomes is the concentration of activators high enough for Sxl transcription. -In females, the Sxl protein initiates a _____ _____ ____ that culminates in the synthesis of a ____ mRNA that encodes Dsx-F protein. In males without Sxl protein, alternative splicing results in a dsx mRNA that makes Dsx-M. -The Dsx-F and Dsx-M proteins are transcription factors that have ______ effects on the expression of genes whose products influence female- and male-specific _______ and behaviors.

Sxl, activator, X, 2, splicing factor cascade, dsx, opposite, morphologies

The cancer landscape and future horizons -Analysis of 178 lung squamous cell carcinomas. 81% have mutations in the ______ gene encoding ____.

TP53, p53

Prenatal Genetic Diagnosis -The most frequently used method for acquiring these cells is ______. -Obtaining ___ cells by amniocentesis. A physician guides the insertion of the needle into the ___ ___ (aided by ultrasound imaging) and extracts ___ __ containing fetal cells into the syringe.

amniocentesis, fetal, amniotic sac, amniotic fluid

Anaphase: Sister chromatids move to opposite spindle poles -The nearly simultaneous severing of the centromeric connection between the sister chromatids of all chromosomes indicates that _____ (from the Greek ana- meaning "up" as in "up toward the poles") is underway.

anaphase

Genes Can Also Be Regulated by Antisense RNAs -These regulatory RNAs are called ____ ___; the mRNAs they regulate are ___ ____. -Antisense RNAs ____ gene expression. Antisense transcripts that overlap ___ or ____ of the sequence of some sense mRNAs are transcribed from nearby ____ _____.

antisense RNAs, sense RNAs, inhibit, all, part, antisense promoters

Ras -A cell carrying a constitutively active Ras oncogene generates its own ______ signals to divide whether or not a growth factor is present. -Examples of oncogenic mutations. Certain _____ mutations in the Ras gene encode an altered Ras protein locked in the _____-activated form.

autocrine, point, GTP

Nature of the operator sequences -Gel electrophoresis and _________ (exposure of the gel to radiation-sensitive film) reveal bands at positions corresponding to the cleavage between each base, except in the region where bound protein protected the DNA. -_____ ____ show where proteins bind to DNA. A piece of DNA is labeled at one end with _______. ____ digestion with DNase-I produces a series of fragments. The enzyme cannot digest the DNA at sites covered by a ____ ____. Gel electrophoresis of the digested DNA shows which fragments were not generated and thus indicates where the ____ binds.

autoradiography, DNase footprints, radioactivity, Partial, bound protein, protein

Scope of heterochromatin effects -Research has identified _____ _____ which block the spread of heterochromatin.

barrier insulators

Proteins Act in trans to Control Transcription Initiation -Different types of proteins bind to each of the cis-acting regulatory regions: ____ ____ bind to the promoter, while _______ and _____ bind to the enhancers. -In this book, we use the term _____ ____ to describe all sequence-specific DNA binding proteins that influence transcription (whether they are basal factors, activators, or repressors).

basal factors, activators, repressors, transcription factor

Solved Problems II. What difficulties would arise if you tried to derive a molecular clock rate using a noncoding sequence in some species and a coding sequence in other species? Answer To answer this question, you need to think about how molecular clocks are derived and the constraints on ___ ____ in coding and noncoding sequences. The evolution of coding sequences is ____ by the fact that the gene sequence needs to be maintained for the gene product to _____. The sequence of noncoding regions generally can tolerate many ____ _____ without ____ acting on these sequences. Therefore, you would expect ___ substitutions in the noncoding sequence. The result would be an inconsistency in your clock rate if you are using a coding region in some species and noncoding DNA in other species. III. If the chromosomes diagrammed below misalign by the pairing of repeated sequences (shown as solid blocks) and crossing-over occurs, what will be the products? Answer This question requires an understanding of crossing-over via _____. When you align the homologous ___ ___ out of register, one of the resulting products will have a _____ of the region between the _____ and three copies of the _____ sequence and the other product will be ____ for the DNA ____ the repeats and contain only ___ repeated sequence.

base substitutions, restricted, function, base substitutions, selection, more, homology, repeated sequences, duplication, repeats, repeated, deleted, one

Cancer Involves the Proliferation of a Clone of Cells -Evidence for the _____ origin of tumors. Because of X chromosome _____, each cell in a female expresses only one allele of a polymorphic ___-___ gene. A patch of normal tissue will usually contain some cells that express one allele, and others that express the other allele. All the cells of a tumor express the ____ one allele, demonstrating that the tumor arose from a _____ cell. Electrophoresis distinguishes the two allelic forms of the gene's _____ product.

clonal, inactivation, X-linked, same, single, protein

19.1 Characteristics of Cancer Cells essential concepts -Cancer cells do not respond to _____ that limit the _____ of normal cells, such as contact inhibition, apoptosis signals, or the ______ of growth factors. -Because of telomerase expression, many caner cells can divide _____. -Many cancer cells exhibit high genomic instability, leading to increased accumulation of ___ ______ and ______ _____. -Advanced tumors can stimulate the local growth of ____ ____, evade the body's normal _____ defenses, and _______ to other tissues.

controls, division, absence, indefinitely, new mutations, chromosomal abnormalities, blood vessels, immune, metastasize

Coordinate expression of the lacZYA genes as a single polycistronic mRNA -The clustering of genes with similar functions into operons is a simple and efficient way to achieve _____ ____ ____.

coordinate gene expression

The Punnett square -The Punnett square: Visual summary of a _____. This Punnett square illustrates the combinations that can arise when an F1 hybrid undergoes gamete formation and self-fertilization. The F2 generation should have a ____ ratio of yellow to green peas. -Next, to visualize when the Yy hybrids self-fertilize, we set up a ____ ____ (named after British mathematician Reginald Punnett, who introduced it in 1906).

cross, 3:1, Punnett square

In Meiosis, the Chromosomes Replication Once but the Nucleus Divides Twice -Unlike mitosis, meiosis consists of two successive nuclear divisions, logically named ____ ___ __ ____ and ____ ___ ___ ___, or simply ___ __ and ____ __. -An overview of meiosis: The chromosomes replicate ___, while the nuclei divide ____. Note that the chromosomes duplicate before ____ __, but they do not duplicate between meiosis I and meiosis II.

division of meiosis I, division of meiosis II, meiosis I, meiosis II, once, twice, meiosis I

Reappearance of the recessive trait -He called the trait that appeared in all the F1 hybrids - in this case, yellow seeds- _____ and the "antagonistic" green-pea trait that remained hidden in the F1 hybrids but reappeared in the F2 generation _______.

dominant, recessive

1.1 DNA: The Fundamental Information Molecule of Life essential concepts -DNA, a ____-stranded macromolecule composed of four nucleotides, is the repository of _____ _____. -DNA is organized into ____ (of ____ different types in humans) that collectively constitute and organism's ____. -The human genome contains about _______ genes, most of which encode _____.

double, genetic information, chromosomes, 24, genome, 25,000, proteins

Genes: Discrete units of inheritance -Today, we call these units of inheritance _____. -Today we call the alternative forms of a single gene _____. -Individuals having two different alleles for a single trait are ______.

genes, alleles, heterozygotes

Cancer Is Generally a Disease of Old Age -Incidence of cancer with age. The incidence of most cancers shows a dramatic ____ with age, consistent with the _____ of mutations in _____ cells. The slope of the log-log plot of these data suggests that ____-____ somatic mutations in key ____ must accumulate for a cell to become cancerous. This estimate relies on several complex assumptions that are not discussed.

increase, accumulation, somatic, 6-10, genes

Meiosis Contributes to Genetic Diversity -How meiosis contributes to genetic diversity. The variation resulting from the ____ ____ of ______ chromosomes increases with the ____ of chromosomes in the genome. -_____-___ between ____ chromosomes ensures that each gamete is ____.

independent assortment, non homologous, number, crossing-over, homologous, different

1.5 Modern Genetic Techniques essential concepts -Mutation of _____ genes in ___ ___ reveals gene function. -Modern techniques such as automated ______ and computer analysis have made possible the rapid determination of ___ _____ in genomes. -Individual genome sequences may pinpoint the genetic basis of many _____ diseases.

individual, model organisms, sequencing, DNA sequences, inherited

Genetic exchange between related DNA elements -The genome contains many places where a flow of genetic information appears to have occurred from one DNA element to other related, but non allelic elements, located nearby or on different chromosomes. Such information flow between related DNA sequences occurs through an alternative outcome of the process responsible for unequal crossing-over. This alternative is known as _____ ___ _____. -Intergenic gene conversion. In intergenic gene conversion: one gene is changed, the other is ___. -Increasing the number of alleles. How gene conversion events from ____-class I genes could increase the _______ in ____ MHC class I genes in mice.

intergenic gene conversion, not, pseudogene, polymorphism, functional

Superrepressor (lacI^s) mutations -Superrepressor mutant ___. In superrepressor mutants, LacI^s binds to the operator but cannot bind to the _____, so the repressor cannot be removed from the operator and genes are continually _____.

lacI^s, inducer, repressed

Some Chemotherapies Target Cells Without Functional Tumor-Suppressor Genes -The reason is that cancerous cells ____ both functional copies of one or more tumor-suppressor genes and are thus missing factors needed for DNA repair or mitotic checkpoints. -For example, _____ _____ block the action of an enzyme called poly ADP ribose polymerase (PARP).

lack, PARP inhibitors

E. coli's Utilization of Lactose Provides a Model System of Gene Regulation -One of these is ____, a complex sugar composed of two monosaccharides glucose and galactose. -Lactose utilization in an E. coli cell. Lactose passes through the membranes of the cell via an opening formed by the ___ ____ protein. Inside the cell, ___-______ splits lactose into ________ and ______.

lactose, Lac permease, Beta-galactosidase, glucose, galactose

16.1 Overview of Eukaryotic Gene Regulation essential concepts -Control of eukaryotic gene expression occurs at many _____; these include transcription ______, transcript _________, mRNA ________, mRNA _______, protein ________, and protein ________. -The mechanisms of gene regulation in eukaryotes are more ______ than those in prokaryotes because eukaryotes have _______, eukaryotic transcripts require more _______, and transcripts are _______ from the nucleus to the cytoplasm for translation. In multicellular eukaryotes, complex gene regulation directs development of numerous ____ _____.

levels, initiation, processing, stability, translation, modifications, stability, complex, chromatin, processing, exported, cell types

20.4 A Comprehensive Example: Rapid Evolution in the Immune Response and in HIV -The immune response. Diverse receptors on _____ recognize different molecular structures from invading _____. T cells employ ___-___ ____; B cells employ ____. _____ B cells secrete antibodies that ____ or _____ antigens. Expanded numbers of _____ T cells and B cells allow ____ response to an antigen encountered a second time. -When the multiple copies of that one type of receptor in a cell's membrane encounter complementary foreign structures (called _____ ______), interaction between the immune receptors and the antigenic determinants triggers that lymphocyte to divide and differentiate.

lymphocytes, pathogens, T-cell receptors, antibodies, destroy, neutralize, memory, rapid, antigenic determinants

16.5 A Comprehensive Example: Sex Determination in Drosophila -Drosophila Mutations that Affect the Two Sexes Differently. Mutation in fruitless (fru) ; Phenotype of XY: ___ with aberrant ____ behavior ; Phenotype of XX: _____

male, courtship, female

Mediator -Transcription of many eukaryotic genes requires a multi-subunit complex called ______ that contains more than 20 proteins. -What transcriptional activators do. Activators associated with _____ DNA bind basal factors (in some cases, indirectly through _____) to stabilize the interaction of _____ __ with promoter DNA.

mediator, enhancer, mediators, pol II

Metaphase I: Paired homologs attach to spindle fibers from opposite poles -During ____ ___, it is the kinetochores of homologous chromosomes that attach to microtubules from opposite spindle poles.

metaphase I

Metaphase II: Chromosomes align at the metaphase plate -There are nonetheless two significant features of ____ ___ that distinguish it from mitosis.

metaphase II

Metaphase: Chromosomes align at the cell's equator -During _____ ("middle stage"), the connection of sister chromatids to opposite spindle poles sets in motion a series of jostling movements that cause the chromosomes to move toward an imaginary equator halfway between the two poles. -The imaginary midline is called the ____ ____.

metaphase, metaphase plate

Complex cells and multicellular organisms -The multicellular animals are often referred to as ______.

metazoans

Mistakes in Meiosis Produce Defective Gametes -If, for example, the homologs of a chromosome pair do not segregate during meiosis I (a mistake known as _______), they may travel together to the same pole and eventually become part of the same gamete.

nondisjunction

Centromeres and telomeres contain many repeat sequences -Much of the genome consists of "_____" DNA, including the _____ and ______ families of repeated elements. In contrast, ____ and ____ contain highly repetitive noncoding sequences that presumably have benefitted the function of these elements in _____ ______.

nonfunctional, LINE, SINE, centromeres, telomeres, chromosome replication

chapter 1 Genetics: The Study of Biological Information -Information can be stored in many ways, including the patterns of letters and words in books and the sequence of _____ in DNA molecules. -The biological information in ___ generates an enormous _____ of living organisms.

nucleotides, DNA, diversity

4.4 Meiosis: Cell Divisions that Halve Chromosome Number essential concepts -In meiosis, chromosomes replicate ___ (before meiosis I), but the nucleus divides twice (meiosis __ and __). -During metaphase of the first meiotic division, homologous chromosomes connect to opposite spindle poles. The ____ ____ of each pair of homologs ensures the _____ ____ of genes carried on different chromosomes. -Crossing-over during the first meiotic division maintains the connection between homologous chromosomes until ____ ___ and contributes to the ____ ___ of gametes. -Sister chromatids separate from each other during meiosis II so that gametes have only ___ copy of each chromosome. -Fertilization-the union of egg and sperm-restores the ___ number of chromosomes (__) to the zygote. -Errors during meiosis may produce gametes with missing or extra chromosomes, which often is ___ to offspring.

once, I, II, independent alignment, independent assortment, anaphase I, genetic diversity, one, diploid, 2n, lethal

Missing intermediates -Life may have begun when certain ____ ______ became ____-______. Some arguments suggest ____ as the original replicator; however, many questions remain unanswered about how life may have progressed from ______ _____ to ____.

organic molecules, self-replicating, RNA, replicator molecules, cells

chapter 19 The Genetics of Cancer -Percentages of cancers in the United States that occur at different sites in the body. Cancers affecting the same tissue may have very different _____ and ____; for example, breast cancers in different patients often have unique properties. -The insights of the new science of _____ ___ ____ are thus increasingly guiding researchers to treatments tailored for individual cancers.

origins, effects, personalized cancer genetics

Overlap of Operator and Promoter -Regulatory protein binding sites _____. The Lac repressor bound to the operator prevents ____ ____ from binding to the promoter. The binding sites for RNA polymerase and repressor (determined by ____ _____ experiments) show that there is overlap between the operator and promoter. Note the ____ ____ of nucleotide sequences in the operator and also in the binding site for ___-____.

overlap, RNA polymerase, DNase digestion, rotational symmetry , CRP-cAMP

Transcription factor modifications -One of the most important of these modifications is _______, the addition of a phosphate group to a protein by action of an enzyme called a ______.

phosphorylation, kinase

1.6 Human Genetics and Society essential concepts -Genome sequences may identify not only genes that always cause disease but also genes that _____ an individual to a disease. -Personal genome data can lead to methods to ____ or ____ at least some diseases. -As a society, we must ensure that genetic knowledge is properly interpreted and that individuals' ____ is protected.

predispose, prevent, cure, privacy

chapter 2 Mendel's Principles of Heredity -Although Mendel's laws can predict the _____ that an individual will have a particular genetic makeup, the ___ meeting of particular male and female gametes determines an individual's actual genetic fate. -A family portrait. The extended family shown here includes members of four generations. -The answers lie in our _____, the basic units of biological information, and in _____, the way genes transmit physiological, anatomical, and behavioral traits from parents to offspring. -_____, the science of heredity, pursues a precise explanation of the biological structures and mechanisms that determine inheritance. -Gregor Mendel. Photographed around 1862 holding one of his experimental plants. -Like begets ___ and ___. A Labrador retriever with her litter of pups.

probability, random, genes, heredity, genetics, like, unlike

1.2 Proteins: The Functional Molecules of Life Processes essential concepts -____ are responsible for most biological functions of cells and organisms. -A protein is a _______ consisting of ___ ___ linked in a linear sequence. -The sequence of amino acids in proteins are encoded by ____ within the DNA.

proteins, macromolecule, amino acids, genes

Development of pseudogenes -When a duplicated region that includes a functional gene survives for hundreds or thousands of generations, random mutations in the gene may turn it into a related gene with a different function, or into a nonfunctional ________.

pseudogene

Further Crosses Verify the Law of Segregation -Yellow F2 peas are of two types: ____ ____ and _____. The distribution of a pair of contrasting alleles (Y and y) after two generations of self-fertilization. The homozygous individuals of each generation breed ____, whereas the ___ do not.

pure breeding, hybrid, true, hybrids

15.5 A Comprehensive Example: Control of Bioluminescence by Quorum Sensing -The mechanism by which bioluminescence is controlled in V. fischeri was the first characterized example of _____ ____, a communication mechanism now known to be used universally by bacteria to regulate gene expression in response to population density.

quorum sensing

Duplications resulting from transposition -Duplication by transposition. Transposition may occur by excising and _______ the DNA segment; making an ____ copy, which is then converted to a DNA copy for insertion; or making a DNA copy for ______. In (b) and (c), the transposon is ______. -Transposition through direct movement of a DNA sequence. A DNA sequence may transpose from one chromosome to a _____ chromosome in a ____ cell. In subsequent generations, the transposed element may become _____.

reinserting, RNA, integration, duplicated, second, sex, fixed

Desirable Traits Sometimes Disappear and Reappear -Mendel's garden and microscope. Gregor Mendel's garden was part of his monastery's property in Brunn. Mendel used this microscope to examine plant ____ ___ and to pursue his interests in natural history.

reproductive organs

The "RNA world" -RNA molecules that can act as enzymes to catalyze specific chemical reactions are called ______. -Ribozyme. Some RNA molecules have _____ functions. Shown is a region of a hammerhead RNA found in many plant virsues. This RNA can ___ itself at the site indicated. -The hypothetical primordial world in which this RNA became the first replicator has been termed the ____ ____.

ribozymes, enzymatic, cleave, RNA world

Therapies attempt to tip the balance -The immune system response involves ____ for T and B cells that can bind a foreign antigen and their subsequent ____ ______. HIV evolves ______ because of the very high _____ ____ associated with its ____ ____; this evolution keeps it ahead of the immune system's response. Treatments attempt to target the ____ ____ and other virus-specific elements.

selection, rapid proliferation, rapidly, mutation rate, reverse transcriptase, reverse transcriptase

The fossil record allows inferences about later evolution -This confidence arises not just from what Darwin's theory says ____ happen but from the possibility of seeing the critical intermediate stages of biological complexity, all the way up the ladder from single cells to sponges, to worms, to fish, to reptiles, to mammals, to primates and humans.

should

Structures of Repressors -A _____ transcription factor can be both an activator and a _______. The Drosophila _____ protein acts as an activator of gene 1. At gene 2, another transcription factor bound to ______ 2 causes Dorsal to act as a ________ by helping it recruit a _______ called _______.

single, repressor, Dorsal, enhancer, repressor, corepressor, Groucho

Telophase: Identical sets of chromosomes are enclosed in two nuclei -The final transformation of chromosomes and the nucleus during mitosis happens at ____ (from the Greek telo- meaning "end").

telophase

The SINE family -Creation of SINE gene family. SINE elements can be ____, and because they form ___ ____ ___, they can be copied into _____ by _____-encoded _____ ____. These cDNA copies then _____ into the genome.

transcribed, 3' hairpin loops, cDNAs, LINE, reverse transcriptase, integrate

Transgenic Mice Prove that SRY is the Maleness Factor -A _____ mouse is one whose genome contains copies of a gene that came from another individual-or even from another species. -Such genes are called _____. -Next, the sperm or egg nucleus (called a _____ in the zygote) is injected with hundreds of copies of the SRY gene DNA. -Using ____ injection to generate mice transgenic for the SRY gene. -An XX mouse transformed with SRY is phenotypically ___. Both the transformed XX mouse and its normal XY littermate have normal ____ _____. Arrows point to the penis.

transgenic, transgenes, pronucleus, pronuclear, male, male genitalia

Feedback Between Cell Proliferation and Genomic Instability Underlies Tumor Progression -Thus, the phenomenon of _____ _____: Over time, tumors tend to grow faster and become more invasive of other tissues.

tumor progression

4.3 Mitosis: Cell Division That Preserves Chromosome Number essential concepts -Through mitosis, diploid cells produce ____ ___ ___ cells. -At metaphase, the ___ ___ are being pulled at their ____ toward ___ spindle poles; these poleward forces are balanced because the chromatids are connected at the _____. -At the beginning of anaphase, the ____ is severed so sister chromatids separate and move to opposite ____ ___. -Cell cycle checkpoints help ensure correct _____ and _____ of chromosomes.

two identical daughter, sister chromatids, kinetochores, opposite, centromere, centromere, spindle poles, replication, segregation

Dihybrid Crosses Reveal the Law of Independent Assortment -He asked how two pairs of alleles would segregate in a _____ individual, that is, in a plant that is heterozygous for two genes at the same time. -A dihybrid cross produces ______ types and ______ types. In this dihybrid cross, pure-breeding parents (P) produce a genetically ____ generation of F1 dihybrids. Self-pollination or cross-pollination of the F1 plants yields the characteristic F2 phenotypic ratio of __:___:__:__. -Would all the F2 progeny be ____ ___ that looked like either the original yellow round parent or the green wrinkled parent? -New phenotypic combinations like these are called _____ _____.

dihybrid, parental, recombinant, identical, 9:3:3:1, parental types, recombinant types

In Humans, the SRY Gene Determines Maleness -For example, rare humans with two X and one Y chromosome (XXY) are males displaying certain abnormalities collectively called ____ ____. -In contrast, humans carrying an X and no second sex chromosome (XO) are females with ___ ____. -In 1990, researchers discovered that it is not the entire Y chromosome, but rather a single Y-chromosome-specific gene called ____ (sex determining region of Y) that is the primary determinant of maleness. -The evidence implicating SRY came from so-called ___ ___: the existence of XX males and XY females. -Sex reversal. Sex-reversed XX males have a part of the Y including the ____ gene on one of their X chromosomes. Sex-reversed XY females lack ____ on their Y chromosome either because it has been replaced by part of the ___ chromosome, or because it has been inactivated by ____. -The two ends of the Y chromosome are called the ______ ____ (___), because homologous regions are present at the ends of the X chromosome. -Human sex chromosomes have both shared and ___ genes. _____ and ____ are homologous regions of the X and Y chromosomes that together contain about ___ genes. The ___ region is Y-specific and contains at least ___ genes needed for maleness itself (__) and for male ____.

Klinefelter syndrome, Turner syndrome, SRY, sex-reversal, SRY, SRY, X, mutation, psuedoautosomal regions (PAR), unique, PAR1, PAR2, 30, MSY, 78, SRY, fertility

Mendel's Genius Was Unappreciated Before 1900 -The science of genetics begins with the rediscovery of ____. Working independently near the beginning of the ____ century, Correns, de Vries, and von Tschermak each came to the same conclusions as those Mendel summarized in his laws.

Mendel, 20th

Changes in regulatory circuits -_____ life-forms diversified tremendously, although many lineages disappeared in ____ ____ ____. Humans ____ from a primate ancestor about 6 million years ago. What makes humans different from our closest relative, the _____, many not be the _____ that our genes encode but rather ___, ____, and at what ___ those proteins are expressed during ____ through evolutionary changes to _____ ______ ______.

Multicellular, mass extinction events, diverged, chimpanzee, proteins, when, where, level, development, master regulatory genes

Histone tail modifications -The ____-terminal tails of the core histone proteins extend _____ from the nucleosome. Various amino acids in these tails are targets for modifications such as _______ and _______ that can alter chromatin structure. -Such modifications of these _______ _____ can influence the packing of nucleosomes, and the modified tails can also serve as platforms to which chromatin modifier proteins can bind. -Histone tail modifications alter chromatin structure. In the heterochromatin, ____-_______ (M) nucleosomes are bound by ______ protein, which attracts _______ enzymes that methylate adjacent nucleosomes and thus spread the ____ "closed" state. In euchromatic regions, ____ enzymes _____ (Ac) core histones, resulting in "open" chromatin with nucleosomes sufficiently far apart so as to be accessible for transcription. ____ _____ that block the spread of heterochromatin are likely DNA sequences that attract _____ enzymes as shown, and/or ______ enzymes that reverse K9 methylation. -Lysine acetylation, accomplished by a family of enzymes called ______ ____ _____ (___), "opens" chromatin by preventing the close packing of nucleosomes. -_____ ____ enzymes that remove the acetyl groups reverse the process, resulting in "closed" chromatin and repressed transcription. -The enzymes that methylate histone tail amino acids are _____ ______ (_______), and enzymes that reverse histone methylation are called _______ ________.

N, outwards, methylation, acetylation, histone tails, K9-methylated, HP1, HMTase, inactive, HAT, acetylate, Barrier insulators, HAT, demethylase, histone acetyl transferases, HATs, Histone deacetylase, histone methyltransferases, HMTases, histone demethylases

The earliest cells -____ kingdoms. The distinct branches represent different _____ in each kingdom. The length of the branches is proportional to the _____ of species _______.

Three, organisms, time, divergence

Duplications resulting from unequal crossing-over -_____ ______-___, also referred to as ______ _______, occurs between nonequivalent loci. -So-called ______ _____ _____-____ also occurs, although much less often than homologous crossing-over. -______ arise from unequal crossing-over. The crossover shown involved dispersed _____ elements. In the crossover event, this originally unique gene is _____ in one chromosome and _____ in the other. -Repeat duplications _____ genome size. ______ moves a copy of a sequence from one chromosomal site to another; unequal crossing-over results in duplication of one region, and deletion of the same region in the ______ _______.

Unequal crossing-over, illegitimate recombination, non homologous unequal crossing-over, duplications, repeat, deleted, duplicated, increase, Transposition, reciprocal chromosome

Species Vary Enormously in Sex Determining Mechanisms -Sex Determination in Fruit Flies and Humans. Humans can tolerate extra __ chromosomes (e.g., XXX) better than can Drosophila because in humans all but one X chromosome becomes a ___ ___. Complete absence of an ____ chromosome is lethal to both fruit flies and humans. Additional Y chromosomes have ____ effect in either species. Although the Y chromosome in Drosophila does not determine whether a fly looks like a male, it is necessary for male ____; ___ flies are thus sterile males. -The gender having two different sex chromosomes is termed the ______ ____ because it gives rise to two different types of gametes. -Mechanisms of Sex Determination Sex is determined by sex chromosomes. The others have identical chromosomes in the two sexes, and sex is determined instead by _____ or other factors. Anemone fish undergo a ___ ___ from male to female as they age.

X, Barr body, A, little, fertility, X0, heterogametic sex, environmental, sex change

Counting of X chromosomes by the Sxl Promoter -Sxl expression only in ___ Drosophila. In the early ____-but not the male-Drosophila embryo, transcriptional _____ encoded by ___-linked genes are present in concentrations sufficient to initiate transcription from the ____ promoter of ___ to produce an mRNA that encodes the ___ ____.

XX, female, factors, X, Pe, Sxl, Sxl protein

Operator mutants -Operator mutants. The repressor cannot recognize the ____ ____ ____ in the lacO^c mutant site, so it ____ bind and repress the operon. -When mutations change the nucleotide sequence of the operator, the repressor is unable to recognize and bind to the site; the resulting phenotype is the ______ ______ of the lactose-utilization proteins. -They call the constitutive operator DNA alterations ___ mutations.

altered DNA sequence, cannot, constitutive synthesis, o^c

Anaphase I: Homologs move to opposite spindle poles -At the onset of ____ __, the chiasmata joining homologous chromosomes dissolve, which allows the maternal and paternal homologs to begin to move toward opposite spindle poles.

anaphase I

Anaphase II: Sister chromatids move to opposite spindle poles -Just as in mitosis, severing of the centomeric connection between sister chromatids allows them to move toward opposite spindle poles during ____ ____.

anaphase II

The immune system's response evolves according to the antigen present -Among the cells in each expanded clone are ____ ____, which may live as long as 40 years, and _____ ____, which actually carry out (or effect) the immune reactions that help dispose of the microorganisms. -The altered receptors with the closest fit to the antigenic determinants bind the determinants more tightly, and this high-affinity binding drives the amplification of the lymphocytes that carry the altered receptors - a process called _____ ______.

memory cells, effector cells, selective amplification

The duplication and shuffling of exons -Domains in antibody proteins. The antibody molecule is composed of ____ identical pairs of ____ (inner) and ____ (outer) chains. The variable regions of each chain are shown in tan; the constant regions in lavendar. The variable regions of a light and heavy chain form a ____ domain. Likewise, the pairs of ____, _____, and ____ regions generate the CH1, CH2, and CH3 domains, respectively. Each domain carries out _____ functions. -Entirely new genes may arise from _____ _____: the exchange of exons among different genes. -Duplication and shuffling of exons. The _____ ______ _____ (___) gene has evolved by the shuffling of exons from the genes for plasminogen, fibronectin, and epidermal growth factor.

two, light, heavy, V, CH1, CH2, CH3, separate, exon shuffling, tissue plasminogen activator (TPA)

Cooperativity in binding -Lac repressor tetramer binds to ____ sites. The Lac repressor is a _____. In reality, two identical LacI subunits bind to each _____ _____. Two of the subunits bind as a ___ to the sequence in one operator site (__), and the other two subunits bind to a second operator (either ___ or ___). -Mutations in ____ o2 or o3 thus have very little effect on repression. -By contrast, mutations in ___ o2 ___ o3 make repression 50 times less effective.

two, tetramer, operator site, dimer, o1, o2, o3, either, both, and

Imprinting and human disease -Genomic imprinting and human disease. A typical pedigree for a disease associated with deletion of a paternally imprinted autosomal gene. Fathers can pass the deletion to their sons or daughters who are ________; mothers can pass the deletion and the ______ to their children. A typical pedigree for a disease associated with deletion of a maternally imprinted gene. Here, it is the ______ who can pass the deletion to their sons and daughters without effect; ______ can pass the deletion and the disease to their sons and daughters who will be affected. Both pedigrees also apply for inheritance of a _______ _____-____-____ mutation of the imprinted gene instead of a deletion.

unaffected, disease, mother, fathers, recessive, loss-of-function

Basic components of genes -The basic structure of a gene. A typical eukaryotic protein-coding gene. The light green boxes represent the 5' and 3' _____ mRNA sequences. The small pink boxes represent regulatory sequences where _____ _____ bind.

untranslated, transcription factors

Proteins act in trans, DNA sites act in cis -Genotype: I-o+Z+Y-/F' (I+o+Z-Y+) ; lacZ Activity: Without inducer __ With inducer ____ ; lacY activity: Without inducer ___ With inducer ____ ; Conclusions: __ is dominant to ____ ; repressor acts in ____ -Genotype: I+o+Z+Y-/F' (I^so+Z-Y+) ; lacZ Activity: Without inducer __ With inducer ____ ; lacY activity: Without inducer ___ With inducer ____ ; Conclusions:___ is dominant to ___ ; superrepressor acts in ____ -Genotype: I+o^cZ+Y-/F' (I+o+Z-Y+) ; lacZ Activity: Without inducer __ With inducer ____ ; lacY activity: Without inducer ___ With inducer ____ ; Conclusions: o+ and o^c act in ____ -Elements that act in ___ can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell. -Elements that act in ___ can influence only the expression of adjacent genes on the same DNA molecule. -Studies of ________ (partial diploids) in which a second copy of the lac genes was introduced helped distinguish mutations in the operator site (o^c), which act in ____, from mutations in lacI, which encodes a protein that acts in ____.

-, +, -, +, I+, I-, trans, -, -, -, -, I^s, I^+, trans, +, +, -, +, cis, trans, cis, merodiploids, cis, trans

siRNAs -The idea is to introduce dsRNA corresponding to a particular gene into the cell or organism to shut off or knock down the expression of the endogenous gene in the genome; this technique is called _____ ______. -A complex similar to RISC called the ______-_____ ______ ____ (RITS) complex incorporates one strand of these duplexes, and uses this siRNA as a guide to bind its complement in a nascent transcript being transcribed from the DNA destined to become heterochromatin.

RNA interference, RNA-induced transcriptional silencing

o^c and o+: action in cis -o^c and o+ act in ___. The o^c _____ mutation and the o+ wild-type operator each affect only the operon of which they are a part. In this cell, only the chromosomal copy of the cell will be transcribed constitutively.

cis, constitutive

What Repressors Do -Eukaryotic repressors generally recruit ______ proteins to enhancers. -Repressor proteins bind DNA at enhancers and recruit corepressors. Some corepressor proteins directly prevent the ____ ___ ___ ____ from binding the _____. Other corepressors are _____-modifying enzymes that close the ______ at the _____ and prevent transcription.

corepressor, basal pol II complex, promoter, histone, chromatin, promoter

How the inducer triggers enzyme synthesis -In this sequence of events, the inducer is an ____ molecule that releases repression without itself binding to the DNA.

effector

Identifying transcription factors -Activators bind to an enhancer ______ to a ____ _____ and enable transcription, detected as _____ expression. A _____ in a gene encoding an activator can reduce transcription of the _____, leading to ___ of GFP expression.

fused, reporter gene, GFP, mutation, reporter, loss

15.1 The Elements of Prokaryotic Gene Expression -We saw in Chapter 8 that ____ _____ is the production of RNAs and proteins according to instructions encoded in DNA.

gene expression

Sex-Specific DNA Methylation is Responsible for Genomic Imprinting -The unusual phenomenon in which the expression of an allele depends on the parent that transmits it is known as ______ _______. -The term ______ signifies that whatever silences the maternal or paternal copy of an imprinted gene is not a change in the nucleotide sequence of DNA. -Instead, as you will see later in this section, the "whatever" is sex-specific methylation of certain DNA sequences called ______ _____ ____ (____). -About half of these 100 are ______ ______ ____, meaning that the allele inherited from the father is not expressed, while the allele from the mother is transcribed. -For _____ _____ _____, the allele inherited from the mother is not transcribed, and all of the mRNA for this gene is made from the paternal allele. -It may be easier for you to track this nomenclature by equating the term _______ with ______.

genomic imprinting, imprinting, imprinting control regions (ICRs), paternally imprinted genes, maternally imprinted genes, imprinted, silenced

Enhancers Integrate Cellular Information to Control Gene Transcription -Enhancers govern ____- and ____-specific gene expression. A hypothetical gene includes enhancers for expression in eyes or skin. Sequences in the enhancers are recognized by transcriptional activators or repressors that may be present in some _____ but not others. Certain transcription factors can be regulated ______ (for example, by hormone binding) or __________ (for example, by phosphorylation). The enhancer integrates information from the binding of ___ the transcription factors to determine whether the target gene should be transcribed, and if so, at what ____ and at what ____ ___ stage.

tissue, temporal, tissues, allosterically, posttranslationally, all, level, cell cycle

lacI+: dominant to lacI- in trans -LacI+ protein acts in ____. ____ protein, made from the lacI+ gene on the ____, can diffuse in the cytoplasm and bind to the _____ on the chromosome as well as to the operator on the _____.

trans, repressor, plasmid, operator, plasmid

11.3 Chromosomal Packaging and Gene Expression essential concepts -Remodeling complexes use the energy from ____ ______ to change the position of ______, exposing _____ and allowing gene transcription. -In heterochromatic regions, the promoters of genes are tightly wrapped in _______, preventing transcription and thus _____ the genes. -Position-effect variegation occurs when a _______ _______ places a gene next to the ________ region near the centromere. If the heterochromatin spreads into the gene ,then the gene will be silenced. -Methylation of a specific _____ (____) in histone _____ is a feature of silenced regions. In contrast, ______ of lysine in histone tails opens chromatin and allows gene expression. -The Xist gene is responsible for X inactivation. The Xist noncoding RNA (ncRNA) coats the ___ ____ that produces it and recruits histone modifying enzymes to inactivate the chromosome, which becomes a Barr body.

ATP hydrolysis, nucleosomes, promoters, nucleosomes, silencing, chromosomal rearrangement, heterochromatic, lysine, K9, H3, acetylation, X chromosome

Heterochromatin Formation Inactivates an X Chromosome in Cells of Female Mammals -The inactive X chromosomes, or ____ ___, are examples of facultative heterochromatin: An entire X chromosome becomes nearly completely heterochromatic in some cells, while other copies of this same X chromosome remain euchromatic in other cells. -Human X chromosomes contain a 450 kb region of DNA called the ___ _______ ___ (___) that mediates dosage compensation. -The Xist gene product is an unusually long (~17 kb) ______ ____ (____) that, unlike most transcripts, never leaves the nucleus and is never translated into a protein. -X chromosome inactivation. One of the genes in the X inactivation center (XIC) is ____, whose product is a non translated ncRNA. Xist is transcribed stably only from the ____ X chromosome. The Xist ncRNA binds to many sites on this chromosome; the Xist ncRNA then attracts _____ modifying proteins that _____ the DNA. Cells from an ___ female mouse showing binding of Xist ncRNA to the ________ X chromosome (the ___ ___) but not the active X chromosome.

Barr bodies, X inactivation center, XIC, noncoding RNA, ncRNA, Xist, inactive, histone, silence, XX, inactive, Barr body

Growth factors -_____ ____ in the form of steroids, peptides, and proteins act over long or short distances are collectively known as ______. -_____-____ _____, such as the histocompatibility proteins that distinguish an individual's cells from all foreign cells and molecules, require direct contact between cells for signal transmission. -Extracellular signals can _____ from one cell to another or be delivered by cell-to-cell contact. The _____ ___ produces thyroid-stimulating hormone (TSH) that moves through the _____ to the _____ ____. Cells in the thyroid produce another hormone, ______, that acts on many cells throughout the body. A ____ ____ ____ recognizes its virus-infected target cell by direct cell-to-cell contact. _____ on the T cell bind to complexes made between viral ______ and _______ _____ on the surface of the infected cell.

Extracellular signals, hormones, cell-bound signals, diffuse, pituitary gland, circulation, thyroid gland,Thyroxine, killer T cell, Receptors, antigens, histocompatibility proteins

The Operon Theory Explains How a Single Substance Can Regulate Several Clustered Genes -____ ____ played a key role in discovering the principles of gene regulation. -Results from many genetic studies led Monod and his close collaborator François Jacob to propose a model of gene regulation known as the _____ ____, which suggested that a single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process. -Clusters of genes regulated in this way are called _____. -The Lactose Operon in E. coli ; The Players: The coordination of various elements enables bacteria to utilize lactose in an _____-_____ way. These elements include: A closely linked cluster of three structural genes - ___, ___, and ____ - that encode the enzymes active in splitting lactose into glucose and galactose. The promoter acts in ____, affecting the expression of only downstream structural ___ genes on the same DNA molecule. A ___-acting DNA operator site lying very near the ___ operon promoter on the same DNA molecule. The three structural genes together with the promoter and the operator constitute the ___ ___. A ___-acting repressor that can bind to the operator. The repressor is encoded by the ____ gene, which is separate from the operon and is unregulated. -As shown, three so-called structural genes (lacZ, lacY, and lacA) encoding proteins needed for lactose utilization, together with two regulatory elements - the promoter (P) and the operator (o) - make up the ___ ____: a single DNA unit enabling the simultaneous regulation of the three structural genes in response to environmental changes. -Molecules that interact with the operon include the ______, which binds to the operon's operator, and the _____ (allolactose), which when present, binds to the repressor and prevents it from binding to the operator. -The repressor is an ______ ____ - a protein that undergoes a reversible change in conformation when bound to another molecule (in this case, allolactose).

Jacques Monod, operon theory, operons, energy-efficient, lacZ, lacY, lacA, cis, lac, cis, lac, lac operon, trans, lacI, lac operon, repressor, inducer, allosteric protein

Diverse RNA Leader Devices Act in cis to Regulate Gene Expression -All bacterial mRNAs begin with an untranslated region called the 5' UTR, or ____ _____ ____. -Through complementary base-pairing, many RNA leaders form secondary structures called ____ ____ (or ____ ___).

RNA leader sequence, stem loops, hairpin loops

Identification of new regulatory RNAs -Computerized analysis of the mRNA encoding the alternative sigma factor sigma^32 revealed the existence of a specialized kind of RNA leader mechanism called an ____ _____, which can be regarded as a rudimentary riboswitch. -An RNA thermometer. Some bacterial mRNAs contain leader sequences that regulate ______ in response to _______. ___-___ structures that occlude the ____ ___ ___ form at low temperatures. At ____ temperatures, the stem-loop unzips.

RNA thermometer, translation, temperature, stem-loop, ribosome binding site, high

Sequence-Specific RNA Binding Proteins Can Regulate RNA Splicing -One of the ways cells can generate more than one type of protein from a single gene is through ______ _____: that is, the splicing of primary transcripts into distinct mRNAs that produce different proteins. -____-____ splicing of the primary fru transcript. Splicing of fru RNA in the absence of ____ protein (in males) produces an mRNA that is translated into ____-___ protein. In females, Tra protein (with Tra2) blocks the use of one _____, causing the fru transcript to be spliced so as to encode Fru-F.

alternative splicing, sex-specific, Tra, Fru-M, exon

Dsx-F and Dsx-M Proteins Control Development of Somatic Sexual Characteristics -Male- and female-specific forms of Dsx protein. At the yp1 gene _____, Dsx-F acts as a transcriptional _____, whereas Dsx-M acts as a transcription ______.

enhancer, activator, repressor

Imprinting as an epigenetic phenomenon -As mentioned earlier, modifications to genes that alter gene expression without changing the base pair sequence and that are inherited directly through cell divisions are called _______ _____. -Genomic imprints are reset during _______. In ____-____ cells, somatic cell imprints are _____, and new ____-_____ imprints are established.

epigenetic changes, meiosis, germ-line, erased, sex-specific

chapter 16 Gene Regulation in Eukaryotes -In this chapter, we see that _______ ___ _____ - the control of gene expression in the cells of eukaryotes - depends on an array of interacting regulatory elements that turn genes on and off in the right places at the right times.

eukaryotic gene regulation

Sxl Protein Triggers a Cascade of Splicing -A cascade of alternate splicing. Sxl protein alters the splicing of tra RNA; female transcripts produce ______ Tra protein, while male transcripts cannot. Tra protein, in turn, alters the _____ pattern of dsx RNA; a different Dsx product results in males (Dsx-M) and in females (Dsx-F).

functional, splicing

Growth Factors Initiate Cell Division Through Signal Transduction Cascades -The molecular signals that influence cell proliferation and division are called ____ ____. -We focus in this chapter on _____: growth factors that stimulate cell proliferation. -When growth factors come into contact with proteins called ____ ____ ____ found on the surface of a cell, a series of biochemical reactions - a so-called ____ _____ ____- occurs within that cell. -The signal transduction cascade eventually reaches the nucleus, where it activates genes that encode ____ ____.

growth factors, mitogens, growth factor receptors, signal transduction cascade, transcription factors

Helix-turn-helix proteins -This _____-_____-____ (___) ____ in the protein fits well into the major groove of DNA. -Helix-turn-helix motifs recognize specific DNA sequences. A protein motif that has the shape of a helix-turn-helix fits into the ____ ____ of the DNA helix. Specific ____ ___ within the helical regions of the protein recognize a particular ____ sequence in the DNA.

helix-turn-helix (HTH) motif, major groove, amino acids, base

11.3 Chromosomal Packaging and Gene Expression -We then discuss a novel type of chromatin structure called _________ associated with chromosomal regions that are not transcribed.

heterochromatin

Most Genes in Heterochromatin Regions Are Silenced -Geneticists call these darker regions _________; they refer to the contrasting lighter regions as ________. -Nucleosome packaging and gene expression. DNA in heterochromatin is so tightly packaged that it is _______ _____. -Constitutive heterochromatin. Human ______ chromosomes were stained by a special technique that darkens the ______ _____, most of which is in regions surrounding the _______. -Chromosomal regions that remain condensed in heterochromatin at most times in all cells are known as _______ ______. -Heterochromatic regions are also repositories for many _______ _____-segments of DNA that move around the genome.

heterochromatin, euchromatin, transcriptionally inactive, metaphase, constitutive heterochromatin, centromeres, constitutive heterochromatin, transposable elements

Induction of coordinated gene expression by lactose -The process by which a specific molecule stimulates synthesis of a given protein is known as _____. -The molecule responsible for stimulating production of the protein is called the _______. -In the regulatory system under consideration, lactose modified to a derivative known as _____ is the inducer of the genes for lactose utilization.

induction, inducer, allolactose

Insulators Organize DNA to Control Enhancer/Promoter Interactions -The answer is that DNA elements called ______ organize chromatin so that enhancers have access only to particular promoters.

insulators

15.4 Discovering and Manipulating Bacterial Gene Regulatory Mechanisms essential concepts -Reporter genes constructed with ____ coding sequences allow the detection of ______ via production of ____-_____. Insertion of lacZ without regulatory sequences into random genomic positions can pinpoint ____ active under specific conditions. -____ ____ that combine the lac regulatory region with other genes' coding sequences allow the production of ______ useful protein products in bacteria. -RNA-Seq is a procedure for sequencing _______ and determining the relative levels of the transcription of all genes under different ______ conditions. -Computerized analysis has been applied to the discovery of _____, identification of _______ ______ and their ______ sites, and finding _______ ______.

lacZ, transcription, beta-galactosidase, promoters, gene fusions, medically, transcriptomes, environmental, operons, transcription factors, binding, regulatory RNAs

Domains of the Lac repressor protein -Domains of repressor protein. X-ray crystallographic data enable the construction of a model of repressor structure that shows a region to which ____ ____ binds and another region to which ____ binds. A third domain near the ____ terminus allows subunits to _______ into ______ and ______.

operator DNA, inducer, C, multimerize, dimers, tetramers

Why imprinting? -This so-called _____ ____ ____ imagines that because a fetus growing in the womb uses tremendous maternal resources, it is in the mother's interest for her baby to be small so as to balance her own needs with those of the child; conversely, the father's only interest is for his babies to be large and therefore more robust.

parental conflict hypothesis

piRNAs -piRNAs are generated by cleavage of long RNAs transcribed from _____ gene clusters located throughout the genome, each of which encodes between 10 and 1000 piRNAs.

piRNA

RNA Polymerase Is the Key Enzyme for Transcription -When bound to the core enzyme, the sigma subunit recognizes and binds specific DNA sequences at the ______. -When bound to the promoter, the complete ____ _______ ______ - core enzyme plus sigma - functions as a complex that both initiates transcription by unwinding the DNA and begins polymerization of bases complementary to the DNA template strand. -In Rho-independent termination, a sequence of bases in the RNA forms a secondary structure, known as a _____ _____, that serves as a signal for the release of RNA polymerase from the completed RNA.

promoter, RNA polymerase holoenzyme, hairpin loop

Promoters and Enhancers Are the Major cis-Acting Regulatory Elements -The first of these is the ______, which is always very close to the gene's protein-coding region. -Promoters usually contain a _____ ___ (or _____ ____), consisting of roughly seven nucleotides of the sequence T-A-T-A-(A or T)-A-(A or T), located just upstream of the transcription initiation site. -Binding of RNA polymerase to the TATA box allows a low, so-called ___ ____ of transcription. -The second type of DNA sequence element important for transcription is called an ______: a regulatory site that can be quite distant-up to tens of thousands of nucleotides away-from the promoter. -cis-acting elements of a gene. cis-acting regulatory elements are regions of DNA sequence located on the ____ DNA molecule as the gene they control. ____ ____ are typically adjacent to the start of transcription. ____ that regulate expression can sometimes lie thousands of base pairs away from a gene, either upstream of the promoter, or downstream of the promoter. Enhancers may even reside in one of the gene's _____. -This recombinant DNA is then used to generate a ______ _____ whose genome harbors the fusion. -Identifying enhancers with _____ ____. An enhancer, such as the eye-specific one shown here, can be found by fusing different fragments of DNA surrounding the _____ part of a gene to an "enhancer less" _______ ____ for jellyfish ____ ___ __ (___). When introduced into an organism's genome, only reporters fused to the ______ will produce large amounts of ____ in the correct _____. A mouse containing a GFP _____ ____ with a mouse ______ and an eye-specific ____ gene enhancer.

promoter, TATA box, initiation box, basal level, enhancer, same, TATA boxes, enhancers, introns, transgenic organism, GFP reporters, coding, reporter gene, Green Fluorescent Protein, GFP, enhancer, GFP, tissue, reporter gene, promoter, mouse

chapter 15 Gene Regulation in Prokaryotes -Bacteria use a communication system called ____ ____ to adjust their behavior according to their population density. -_____ bacteria protect squid from predators. Vibrio fischeri bacteria generate ___. These bacteria inhabit the ____ ____ of Hawaiian bobtail squid. -The coordinated control of gene expression in V. fischeri is an example of _____ ___ ___, the subject of this chapter. -____ ____ ___ binds to specific sites in the DNA to turn off expression of the lac operon in E. coli. Lac repressor is a ______ with two subunits binding to each of two operator sites, causing a ____ to form in the DNA. Each operator site exhibits ______ _____, so the two subunits forming a dimer are _____ oriented on the chromosome. This model also shows where the CRP protein binds to ___ DNA.

quorum sensing, luminescent, light, light organ, prokaryotic gene regulation, lac repressor protein, tetramer, loop, rotational symmetry, oppositely, lac

Recombinant Vibrio fischeri Bioluminescence Genes Confer Luminescence to E. coli -____ ___ controls Vibrio fischeri bioluminescence. ___ transcripts, one for luxR and the other for the _____ luxICDABE, are required for V. fischeri to generate light. The genes luxR and luxI encode the ____-____ proteins (____ and ____). The other lux genes encode the _____ proteins, including the subunits of ______, LuxA and LuxB. -The genes luxA and luxB encode subunits of the enzyme ______, which catalyzes light production.

quorum sensing, two, operon, quorum-sensing, receptor, synthase, bioluminescence, luciferase, luciferase

How insulators are identified -An enhancer placed between the promoters of two ____ ___ will activate transcription of both unless an _____ sequence is located between the enhancer and ___ promoter to ___ transcription from that promoter.

reporter genes, insulator, one, prevent

Repressors -Eukaryotic transcription factors that bind specific DNA sites near a gene, such as enhancers, and prevent the initiation of transcription of the gene are called ______.

repressors

Translation in Prokaryotes Begins Before Transcription Ends -Ribosomes bind to special initiation sites at the 5' end of the reading frame (the ____ ____ ___) while transcription of downstream regions of the RNA is still in progress. -Because prokaryotic mRNAs are _______ (that is, they contain open reading frames for several different proteins), ribosomes can initiate translation at several positions along a single mRNA molecule.

ribosome binding site, polycistronic

Riboswitches -One wide-spread mechanism involves _____: allosteric RNA leaders that bind small molecule effectors to control gene expression. -Whereas in attenuation the level of an amino acid like tryptophan governs the conformation of the leader indirectly (through participation of tRNAs and ribosomes), leaders that act as riboswitches have a region called the _______ that binds a particular effector directly. -Riboswitches also have a second region, called the ____ ____, which controls gene expression by altering its stem-loop structures in response to the aptamer configuration. -Riboswitches. The leader in the mRNA of many bacterial genes and operons forms into a ______ that controls expression in response to an effector molecule. A riboswitch contains an _____ that binds to an effector, altering conformation, and an _____ ____ that responds to the conformational change.

riboswitches, aptamer, expression platform, riboswitch, aptamer, expression platform

Structures of Activators -Two structural domains within the activator protein-the ____-____ ____ and the _____ _____-mediate these two biochemical functions. -Two well-characterized DNA-binding structures are ____-___-____ domains and _____ _____. -Activator protein families. Two common DNA-binding motifs found in activators are the helix-turn-helix and the zinc finger. -Many activator polypeptides also have a third domain- the ________ _____ -that enables them to interact with other transcription factor subunits to form multimeric proteins, as was the case for several regulatory proteins in bacteria such as the Lac repressor. -One structural motif in many dimerization domains is a _____ ____, a helix with leucines at regular intervals. -Most leucine zipper proteins also have a characteristic DNA-binding domain, called a _____ _____. -Jun can form dimers either with itself, making Jun-Jun _____, or with another protein called Fos, making Jun-Fos ______. -Jun-Jun and Jun-Fos dimers. Homodimers contain two _____ polypeptides, whereas heterodimers contain two _____ polypeptides. The leucine zipper motifs in two subunits interact ____ with each other, allowing ________ to occur. So-called "basic" DNA-binding domains are characteristic of most leucine-zipper containing ______ _____.

DNA-binding domain, activation domain, helix-turn-helix, Zinc fingers, dimerization domain, leucine zipper, basic domain, homodimers, heterodimers. identical, different, tightly, dimerization, transcription factors

Basal factors -The key component of the basal factor complex that forms on most promoters is the ____ ___-____ ___, or ___. -This protein recruits other proteins called ____-_______ ____, or _____, to the promoter in an ordered pathway of assembly.

TATA box-binding protein, TBP, TBP-associated factors, TAFs

Catabolic and Anabolic Pathways Require Different Types of Regulation -Many of these pathways are ______ _____ in which complicated molecules are broken down for the use of the cell; examples of catabolic pathways are those that break down sugars to provide cells with energy and carbon atoms. -Other pathways in the cell are _____ _____ that allow cells to construct end product molecules they need, such as amino acids and nucleotides, from simpler constituents. -Catabolic pathways demand ____ _______: This means the pathway should be turned on - that is, induced - only when the complex molecules to be broken down (_____) are present in the cell's environment. -In contrast, anabolic pathways require ________ ____: This means the pathway should be turned on only when the cell does not have enough of the needed _____ ___.

catholic pathways, anabolic pathways, inducible regulation, catabolites, repressible regulation, end product

Evidence for a repressor protein: the effect of lacI- mutations -Mutations in a gene called lacI, located near but not within the lac operon, produce _______ ____ that synthesize B-galactosidase and Lac permease even in the absence of lactose. -The existence of these constitutive mutants suggested that lacI encodes a negative regulator, or ________. -The _____ experiment. DNA carrying lacI+ and lacZ+ genes was introduced (by _____) into a lacI- lacZ- cell. In the recipient, B-galactosidase ____ synthesized from the introduced _____ gene initially, but as repressor (made from the introduced ____ copy of the gene) _____, the synthesis of B-galactosidase _____. If _____ is added, the synthesis of B-galactosidase resumes. -On the basis of these experiments, Monod and company proposed that the repressor protein prevents further transcription of lacY and lacZ by binding to a hypothetical ______ ____: a DNA sequence near the promoter of the lactose-utilization genes. -Repressor mutant (____). In some lacI- mutants, the repressor cannot ____ to the operator site and therefore cannot repress the operon. Other lacI- mutants are ____ mutants that make no protein.

constitutive mutants, repressor, PaJaMo, conjugation, was lacZ+, lacI+, accumulates, stops, inducer, operator site, lacI-, bind, null

RNA-Seq Is a General Tool for Characterizing Transcriptomes and Their Regulation -A ______ is the base sequence of every transcript that a cell produces under a particular set of conditions. -Transcriptome sequencing requires the production of a cDNA library and subsequent sequencing of many of these cDNAs; the entire procedure is called ____-____ or sometimes ___ ____ _____. -Construction of a directional cDNA library for RNA-Seq. Bacterial RNAs are fragmented with ____, and the resultant 5' ends are ___________ enzymatically. ____ ____ is then used to ligate a short synthetic single-stranded RNA sequence (_____ __) specifically to the ___ ends. (The adapter cannot attach to the ___ ends of the RNA fragments because no ___ group is present there.) After ____________ of the 5' ends with a _____ enzyme, a second ____ with a ____ base sequence (Adapter B) is ligated specifically to the phosphorylated ____ ends of the RNA fragments. On the _____ synthesized from these templates, the two adapter sequences mark the 5' and 3' ends of the original RNAs, respectively. -A cDNA library constructed in a manner that preserves this information, such as that shown, is called a ______ ____ ____. -RNA-Seq results. At bottom is a map of part of the ____: Numbers indicate base pairs and genes are shown pointing in the direction of _____. At top, the RNA-Seq data are plotted. Shows the number of times each ___ in the genomic sequence below was "read" in a cDNA sequence made from an RNA transcribed from both directions. -RNA-Seq has found that high temperatures specifically induce the transcription of a suite of genes encoding specialized ___-___ ___ that allow cells to survive. -Some of the induced heat-shock proteins recognize and degrade aberrant proteins, while other heat-shock proteins act as so-called _____ ____ which help refold other proteins and also prevent their aggregation.

transcriptome, RNA-Seq, cDNA deep sequencing, RNase, dephosphorylated, RNA ligase, Adapter A, 3', 5', phosphate, rephosphorylation, kinase, adapter, different, 5', cDNAs, directional cDNA library, genome, transcription, base, heat-shock proteins, molecular chaperones

Mendel Devised a New Experimental Approach -The homunculus: A misconception. Well into the ____ century, many prominent microscopists believed they saw a fully formed, miniature ___ crouched within the head of a sperm. -Another deceptive notion was the concept of ____ ____, the idea that parental traits become mixed and forever changed in the offspring, as when blue and yellow pigments merge to green on a painter's palette. -In ____-_____ (or ____), both egg and pollen come from the same plant. -The particular anatomy of pea flowers, however, makes it easy to prevent self-fertilization and instead to ____-___ (or ___) two individuals by brushing pollen from one plant onto a female organ of another plant. -Mendel's experimental organism: The ___ ___. Pea plants with white flowers. Pollen is produced in the ___. Mature pollen lands on the ____, which is connected to the ___ (which becomes the pea pod). After landing, the pollen grows a tube that extends through the stigma to one of the ____ (immature seeds), allowing fertilization to take place. To prevent self-fertilization, breeders remove the ____ from the female parents before the plant produces mature pollen. Pollen is then transferred with a paintbrush from the anthers of the ___ parent to the stigma of the female parent. Each fertilized ovule becomes an individual ___ (mature seed) that can grow into a new pea plant. All of the peas produced from one flower are encased in the same ___ __, but these peas form from ____ pollen grains and ovules. -The opposite of these so-called ____ ___ are ____ ____, such as height and skin color in humans. -Matings within such ___-____ (or ____-___) ___ produce offspring carrying specific parental traits that remain constant from generation to generation. -These lines are also called ____ because they have been mated only to each other for many generations. -The mating of parents with ______ traits produces hybrids. Note that each of the hybrids for the seven antagonistic traits studied by Mendel resembles only ____ of the parents. The parental trait that shows up in the hybrid is known as the "____" trait. -In his experiments, he not only perpetuated pure-breeding stocks for each member of a pair, but he also cross-fertilized pairs of plants to produce ____, offspring of genetically dissimilar parents, for each pair of antagonistic traits. -Not only did this allow him to carry out controlled breedings of selected traits, but he could also make _____ _____.

19th, fetus, blended inheritance, self-fertilization, selfing, cross-fertilize, cross, garden pea, anthers, stigma, ovary, ovules, anthers, pea, pea pod, different, discrete traits, continuous traits, pure-breeding, true-breeding, lines, inbred, antagonistic, one, dominant, hybrids, reciprocal crosses

The G1-to-S checkpoint -How CDK-cyclin complexes mediate the G1-to-S phase transition. In human cells, ______ complexed to _____, and CDK2 complexed to cyclinE, phosphorylate the ____ protein, causing it to dissociate from, and thus activate, the ____ transcription factor. E2F stimulates the transcription of many genes needed for ____ _____, including that for ______. At the transition into S phase, cyclinD is ____, while _____-_____ complexes are formed and then activate DNA replication. -The p53 pathway is part of the ___-__-__ ____. DNA damage activates the p53 transcription factor, which in turn induces expression of the _____ gene. The p21 protein inhibits the activity of ____-____ complexes, resulting in a G1 phase ____. Activated p53 protein also induces the expression of many ___ ____ and ______ genes. -In mammals, cells exposed to ionizing radiation or UV light during G1 delay entry into S phase by activating the _____ _____.

CDK4, cyclinD, Rb, E2F, DNA replication, cyclinA, destroyed, CDK2-cyclinA, G1-to-S checkpoint, p21, CDK-cyclin, arrest, DNA repair, apoptosis, p53 pathway

chapter 20 Evolution at the Molecular Level -____ ____ spent 5 years circling the globe collecting specimens. The material acquired on this grand tour provided the basis for his comparative analysis in ___ ___ ___ ___, published some 23 years after he returned to England. -In this chapter, we examine in detail the basic components of evolution at the molecular level: _____ into many variants, followed by _____ of one or a few variants for amplification (that is, differential reproduction) in a population over many generations.

Charles Darwin, The Origin of Species, diversification, selection

DNA Methylation at CpG Islands Silences Gene Expression -____ _____ are DNA sequences that may be a few hundred or a few thousand bp long, and within which the frequency of CpG dinucleotides is much higher than that of the rest of the genome. -DNA methylation and CpG islands. Transcription of some genes is controlled by ____ ___ (sequences rich in CpG residues), which contain binding sites for ______. Bound activators _____ methylation of the C residues. If activators are no longer present, the CpG island becomes methylated; repressors called _____-____ ____ ___ (____) bind methylated sites and _____ the chromatin. -The gene cannot be transcribed because repressors called _____-____-_____ ___ (______) bind to methylated CpG islands and close the chromatin structure. -Repression of genes by DNA methylation is often long-term because the methylation pattern is maintained through numerous cell divisions; long-term repression through DNA methylation is called ________. -Cytosine methylation is perpetuated during ____ ____. A dedicated ______ ______ (____) functions at the DNA replication _____; the pattern of cytosine methylation on the template strand is replicated on the _____ _____ strand of DNA.

CpG islands, CpG islands, activators, prevent, methyl-CpG binding proteins (MeCPs), silencing, DNA replication, DNA methyltransferase (DNMT), fork, newly synthesized

16.3 Epigenetics: Control of Transcription Initiation Through DNA Methylation -A second method by which cells can regulate transcription initiation is through the control of _____ _____:a biochemical modification of DNA itself in which a methyl (-CH3) group is added to the fifth carbon of the cytosine base in a 5' CpG 3' dinucleotide pair on one strand of the double helix. -DNA methylation and ____ ____. Chemical structure of a CpG dinucleotide where the ___ is methylated. -Enzymes called ____ _____ ____ (_____) catalyze the methylation of cytosines in CpG dinucleotides. -You will see that because DNA methylation affects gene transcription, and methylation patterns are copied during DNA replication, DNA methylation can alter gene expression heritably without changing the base sequence of DNA - and thus constitutes a so-called _______ ______. -Methylation is key to an epigenetic phenomenon seen in mammals (including humans) that is called _____ _____.

DNA methylation, CpG islands, C, DNA methyl transferases (DNMTs), epigenetic phenomenon, genomic imprinting

Transcription Requires Changes in Chromatin Structure and Nucleosome Position -When a previously inactive gene prepares for transcription during a later step of cellular differentiation, the promoter region is observed to change from a DNase resistant site to a _______ ________ ___. -The reason is that transcription regulatory proteins (_____ ____) bind DNA at nearby enhancers and recruit proteins that reorganize the chromatin in the vicinity. -One type of chromatin modulator consists of multi subunit _______ ______ that use the energy of ATP hydrolysis to alter nucleosome positioning. -Nucleosome packaging and gene expression. Gene _______ wrapped around ______ ____ are not accessible to RNA polymerase and other transcription factors. Chromatin remodeling complexes can expose promoters by placing them in _________-free regions that are hypersensitive to _______.

DNase hypersensitive site, transcription factors, remodeling complexes, promoters, nucleosome cores, nucleosome, DNase

The evolution of humans -Humans diverged from an ancestor shared with ______ about _ ____ years ago. Representatives of ____ alive today: orangutan, gorilla, chimpanzee, and human.

chimpanzees, 6 million, primates

2.2 Genetic Analysis According to Mendel Monohybrid Crosses Reveal Units of inheritance and the Law of Segregation -Analyzing a monohybrid cross. Cross-pollination of pure-breeding parental plants produces ___ ____, all of which resemble one of the parents. Self-pollination of F1 plants gives rise to an ___ generation with a ___:___ ratio of individuals resembling the two original parental types. -Early in the spring of 1854, for example, Mendel planted pure-breeding green peas and pure-breeding yellow peas and allowed them to grow into the ____ (___) _____. -These yellow peas, progeny of the P generation, were the beginning of what we now call the ___ ____ (___) _____. -Such experiments involving hybrids for a single trait are often called ______ _____. -He then harvested and counted the peas of the resulting ____ ___ (___) _____, progeny of the F1 generation.

F1 hybrids, F2, 3:1, parental (P) generation, first filial (F1) generation, monohybrid crosses, second filial (F2) generation

During Interphase, Cells Grow and Replicate Their Chromosomes -Interphase consists of three parts: gap 1 (__), synthesis (__), and gap 2 (___). -The microtubules radiate out into the cytoplasm from a single organizing center known as the _____, usually located near the nuclear envelope. -In animal cells, the discernible core of each centrosome is a pair of small, darkly staining bodies called ______.

G1, S, G2, centrosome, centrioles

Monoclonal antibodies to growth factor receptors: Herceptin -Herceptin: Possible modes of action. This drug is a monoclonal antibody that binds to the _____ protein on the surfaces of certain cancer cells. Binding of Herceptin to Her2 prevents receptor subunits from _____, thus blocking the growth-factor-initiated _____ ____. Binding of Herceptin to Her2 also directs ____ ___ ____ to the cancer cells.

Her2, dimerization, signaling cascade, killer T cells

15.1 The Elements of Prokaryotic Gene Expression essential concepts -____ ____ is the crucial enzyme for prokaryotic transcription. ___ ___ allows the enzyme to recognize promoters, while ___ (___) protein terminates the transcription of some genes. -No _____ encloses the bacterial chromosome, so translation of mRNA into a polypeptide can begin while _____ is taking place. -Many bacterial mRNAs are ______; each ____ ____ ___ in the transcript has its own ribosomal binding site. -Regulation of prokaryotic gene expression can occur at many different _____: transcription _____, _____, or ______ ; _____ stability; _____ initiation; or _____ stability or activity.

RNA polymerase, sigma factor, Rho (p), membrane, transcription, polycistronic, open reading frame, levels, initiation, elongation, termination, mRNA, translation, protein

1.3 Molecular Similarities of All Life-Forms -____ is an intermediary in the conversion of DNA information into protein via the ____ ____. The linear bases of DNA are copied through molecular ______ into the linear bases of RNA. The bases of RNA are read ____ at a time (that is, as _____) to encode the amino acid subunits of proteins. The genetic code dictionary specifies the relationship between ___ ___ and the amino acid subunits of proteins. -Comparisons of gene products in different species provide evidence for the ____ of living organisms. This chart shows the amino acid sequence for equivalent portions of the cytochrome C protein in six species: Saccharomyces cerisaie (yeast), Arabidopsis thaliana (a reedlike flowering plant), Caenorhabditis elegant (a nematode), Drosophila melanogaster (the fruit fly), Mus musculus (the house mouse), and Homo sapiens (humans). -The eyes of insects and humans have a ___ ___. A fly eye and human eye. -Biologists had long assumed that the evolution of eyes occurred independently, and in many evolution textbooks, eyes were used as an example of ____ ___, in which structurally unrelated but functionally analogous organs emerge in different species as a result of natural selection. -It means that in many cases, the experimental manipulation of organisms known as ___ ____ can shed light on gene functions in humans.

RNA, genetic code, complementarity, three, triplets, RNA triplets, relatedness, common ancestor, convergent evolution, model organisms

The LINE family: "Selfish DNA" -Creation of a LINE gene family. A complete LINE sequence can be copied into ____. It encodes a ____ ____ that can make ____ copies from the RNA. These copies may be complete or _______ and may _____ into other sites on any _____.

RNA, reverse transcriptase, cDNA, truncated, integrate, chromosome

Mitosis and Meiosis: A Comparison -Mitosis: -Occurs in somatic cells, Haploid and diploid cells can undergo mitosis, One round of division, Mitosis is preceded by ___ phase (chromosome duplication), Homologous chromosomes do ___ pair, Genetic exchange between homologous chromosomes is very ___, Sister chromatids attach to spindle fibers from opposite poles during metaphase, The ____ splits at the beginning of anaphase, Mitosis produces ___ new daughter cells, identical to each other and the original cell. Mitosis is thus genetically ____. -Meiosis: -Occurs in germ cells as part of the sexual cycle, Two rounds of division, meiosis I and meiosis II, Only diploid cells undergo meiosis, Chromosomes ____ prior to meiosis but not before meiosis II, During prophase of meiosis I, homologous chromosomes pair (____) along their length, ___-___ occurs between homologous chromosomes during prophase of meiosis I, Homologs chromosomes (not sister chromatids) attach to spindle fibers from opposite poles during metaphase I, The ___ does not split during meiosis I, Sister chromatids attach to spindle fibers from opposite poles during metaphase II, The ____ splits at the beginning of anaphase II, Meiosis produces four haploid cells, one (___) or all (___) of which can become gametes. None of these is ___ to each other or to the original cell, because meiosis results in ______ _____

S, not, rare, centromere, two, conservative, replicate, synapse, crossing-over, centromere, centromere, egg, sperm, identical, combinatorial change

Some Changes Alter a Tumor's Interactions with the Body -Some tumors evade this potential restriction to their growth by secreting substances that cause blood vessels to grow toward them. This phenomenon is called ______. -Changes that enable a tumor to grow and to invade distant tissues. _______. Tumor cells secrete substances that cause blood vessels to grow toward them, providing new supplies of nutrients for the tumor. ____. Some cancerous cells can break through membranes that define particular tissues and then travel through the bloodstream to colonize distant tissues. -The cancerous cells can then travel through the bloodstream to colonize distant tissues in a process called ________. -A different way in which cancerous cells influence their interactions with the body is that they can evade _____ ________.

angiogenesis, angiogenesis, metastasis, metastasis, immune surveillance

2.1 Background: The Historical Puzzle of Inheritance essential concepts -People practiced _____ ____ of crop plants and domestic animals for thousands of years without understanding how _____ works. -Mendel established pure-breeding lines of peas in which a specific characteristic would remain ____ from one generation to the next. -When Mendel crossed pure-breeding lines with alternative traits, the ____ progeny always had the characteristics of ___ parent. -In Mendel's experiments, the hybrid progeny produced by ____ ____-____ had the same characteristics; it did not matter which parent was male and which was female.

artificial selection, heredity, constant, F1, one, reciprocal cross-fertilzation

2.1 Background: The Historical Puzzle of Inheritance Artificial Selection Was the First Applied Genetic Technique -As a result of this ____ ___ - purposeful control over mating by choice of parents for the next generation-the domestic dog (Canis lupus familiaris) slowly arose from ancestral wolves (Canis lupus). -The earliest known record of applied genetics. In this 2800-year-old Assyrian relief from the Northwest Palace of Assurnasirpal II (883-859 B.C.), priests wearing bird masks artificially ____ flowers of female date palms.

artificial selection, pollinating

Attenuation -In analyzing why some mRNAs terminate before they can transcribe the structural trp genes, while others do not, the researchers discovered _____: control of gene-expression by RNA leader-mediated premature termination of transcription. -The 3-4 stem-loop configuration is called a _____ because when it forms in the trp operon transcript, RNA polymerase contacts it and stops transcription, producing a short, "attenuated" RNA. -The alternative RNA structure, called the _________, forms by base pairing between regions 2 and 3. -An attenuator in the tryptophan operon of E. coli. ___ ___ form by complementary base pairing in the trp ___ ___. ___ different conformations are possible: One of these includes a ___ that signals RNA polymerase to stop polymerization, while the other is an ______ that allows transcription of the operon's structural genes. The leader also contains a small ___ ___ __ with ___ codons for tryptophan. When tryptophan is present, the ribosome follows ___ along the transcript, and the ____ forms. If tryptophan is absent, the ribosome ___ at the trp codons, allowing formation of the _______.

attenuation, terminator, antiterminator, stem loops, leader RNA, two, terminator, antiterminator, open reading frame, two, quickly, terminator, stalls, antiterminator

Oncogenic protein inactivation: Gleevec -Gleevec: Mechanism of action. The product of the ____/____ fusion gene is a ____ ____ ____ that transfers a phosphate group from _____ to many substrate proteins. Gleevec binds tightly to the enzyme's ____ binding site, preventing the kinase function.

bcr/c-abl, protein tyrosine kinase, ATP, ATP

Binding of growth factors to receptors -Binding of growth factors to _____ initiates ___ ___ ___. A growth factor binds to the ______ domain of a specific receptor embedded in the cell membrane.

receptors, signal transduction cascades, extracellular

New Methods Provide Global Views of cis- and trans-Acting Transcriptional Regulators -The recent emergence of ________-a field of science in which biology, computer science, and information technology merge to form a single discipline- promises to facilitate the understanding of complex transcriptional programs. -_____ ___________-_____ (____-___) is a powerful new technology for finding all the target genes of a particular transcription factor within the entire genome of a particular type of cell. -ChIP-Seq. An ______ against a specific transcription factor is used to ____ the protein bound to its target gene DNA sites (by attaching the antibody to ______ _____). Sequencing of the DNA fragments within the purified protein-DNA complexes identifies the genes the transcription factor regulates. -Purification, through antibody binding, of specific proteins bound to other proteins or nucleic acids is called __________.

bioinformatics, chromatin immunoprecipitation-sequencing, ChIP-Seq, antibody, purify, microscopic beads, immunoprecipitation

The drama of metazoan evolution -Burgess Shale organisms. Although all these life-forms are now extinct, fossils have revealed the enormous diversity of their ____ ___. The Pikaia contains a ______, which makes it an ancestor to modern-day ______. -This rapid evolution is an example of ______ ______: the tendency of evolution to proceed through long periods of stasis (lack of change) followed by short periods of explosive change.

body plans, notochord, vertebrates, punctuated equilibrium

Branched-line diagrams -A convenient way to keep track of the probabilities of each potential outcome in a genetic cross is to construct a _____-___ ____, which shows all the possibilities for each gene in a sequence of columns. -Following crosses with branched-line diagrams. A branched line diagram, which uses a series of columns to track every gene in a cross, provides an organized overview of all ____ outcomes. This branched-line diagram of a dihybrid cross generate the same ______ ratios as the Punnett square, showing that the two methods are ______.

branched-line diagram, possible, phenotypic, equivalent

Analysis of Cell-Cycle Mutants in Yeast -A cell-cycle mutant of yeast grown at permissive temperature. These cells display ____ of all sizes, including some with small buds and some with large buds. -A cell-cycle mutant of yeast grown at restrictive temperature. These cells have all _____ with a large bud. (Other cell-cycle mutants may arrest with buds of different ____ or ___ bud at all.) Cells that were early in the cell cycle (with small buds) at the time of the temperature shift arrest in the first cell cycle. Cells that were later in the cell cycle at the time of the shift finish the first cell cycle and arrest in the second, producing clumps with two large-budded cells.

buds, arrested, sizes, no

CRP protein and the response to glucose -Inside bacterial cells, the small nucleotide known as ____ (___ ____ ______) binds to a protein called _____ ____ ____, or ___. -_____ regulation of the lac operon. High-level expression of the lac operon requires that a positive regulator, the ____-____ complex, be bound to a site near the ____. The complex is a ____, and the site to which it is bound contains ______ _______ DNA sequences. The CRP-cAMP complex contacts ______ _____ directly to help in transcription _____. -CRP thus functions as a positive regulator that enhances the transcriptional activity of RNA polymerase at the lac promoter, while cAMP is an _____ whose binding to CRP enables CRP to bind to DNA near the promoter and carry out its regulatory function. -An inducer such as allolactose is, like cAMP, an effector that activates gene expression; we will shortly look at other effectors called ______ that turn down gene expression at other operons.) -Glucose controls the amount of cAMP in the cell indirectly by decreasing the activity of _____ ____, the enzyme that converts ATP into cAMP. -Catabolite repression. ____ controls the activity of the enzyme adenyl cyclase that synthesizes ____. When glucose is high, adenyl cyclase activity and thus cAMP levels are ____, so the positive regulator CRP does ___ bind to the lac operon. As a result, transcription of the lac operon is ___ when glucose is available to the cell. -The overall effect of glucose in preventing lac gene transcription is known as _____ ____, because the presence of a preferred catabolite (glucose) represses transcription of the operon.

cAMP, cyclic adenosine monophosphate, cAMP receptor protein, CRP, positive, CRP-cAMP, promoter, dimer, rotationally symmetrical, RNA polymerase, initiation, effector, corepressors, adenyl cyclase, glucose, cAMP, low, not, low, catabolite repression

Finding oncogenes through association with tumor viruses -Oncogenes and retroviruses. Rarely, double-stranded viral _____ integrates adjacent to a ____-_____ in the host genome. Powerful _____ in the cDNA can lead to ______ of the proto-oncogene. Examples of highly oncogenic retroviruses. Occasionally, an adjacent proto-oncogene can become "captured" - that is, incorporated into the ____ ____ so as to become an ______.

cDNA, proto-oncogene, promoters, over expression, viral genome, oncogene

Environmental Mutagens Increase the Likelihood of Cancer -______ effects of smoking. Lung cancer death rates in the United States began increasing rapidly for men in the 1940s and for women in the 1960s. This difference reflects the fact that smoking became prevalent among men about 20 years before it did among women.

carcinogenic

15.2 Regulation of Transcription Initiation via DNA-Binding Proteins essential concepts -____ ____ are induced when the molecule to be broken down is present; _____ ___ are repressed when the molecule that is the end product is present. -In the lac operon, binding of the Lac repressor to the DNA operator ___ transcription. The inducer ______ binds to the repressor, ____ it from the operator and allowing transcription. -Mutations affecting regulatory proteins act in ____, while mutations in DNA-binding sites act in cis. -Lac repressor protein has a ____-___-___ ____-___ domain, an ____-____ domain, and a domain that allows ______; in this way the repressor can recognize and bind tightly to clustered ____. -The cAMP regulatory protein (CRP) can bind to the lac _____ region to allow ______ transcription only in the absence of ____, when cAMP levels are ____. -____ regulators like the Lac repressor inhibit RNA polymerase from binding to the ____; positive regulators like ___-____ physically contact RNA polymerase and encourage its binding to the promoter. -In _____ (biosynthetic) operons, repressor proteins bind to operators only in the presence of a ______, which is usually the ____ ____ of the pathway.

catabolic pathways, anabolic pathways, prevents, allolactose, releasing, trans, helix-turn-helix DNA-binding, inducer-binding, multimerization, operators, promoter, maximum, glucose, high, negative, promoter, CRP-cAMP, anabolic, corepressor, end product

Different CDK-cyclin complexes for different cell-cycle transitions -Different CDK-cyclin complexes govern different cell-cycle transitions. Complexes made of various cyclin-dependent kinases and the cyclins with which they associate appear during specific stages of the ____ ___ and prompt the cell to ____ to the next stage. The regular appearance and disappearance of these complexes is due to the synthesis of particular cyclins at particular _____, as well as the ____ of cyclins when they are no longer needed.

cell cycle, progress, times, destruction

Cell-Cycle Checkpoints Ensure Genomic Stability -These additional controls are called ______ because they check for the integrity of the genome before allowing the cell to continue to the next phase of the cell cycle. -In this section, we focus on the molecular mechanism of a different system, the _____-___-___ ______, which ensures that cells will not perform the G1-to-S transition if they have damaged DNA.

checkpoints, G1-to-S checkpoint

Regulatory Checkpoints Ensure Correct Chromosome Separation -A number of _____-moments at which the cell evaluates the results of previous steps-allow the sequential coordination of cell-cycle events. -Checkpoints help regulate the cell cycle. Cellular checkpoints ensure that important events in the cell cycle occur in the proper _____. At each checkpoint, the cell determines whether prior events have been completed before it can proceed to the next step of the cell cycle.

checkpoints, sequence

19.5 Personalized Cancer Treatment -Prostate cancer detected by X-ray tomography in a 2000-year old mummy. -In the 1940s, medical scientists began to explore _______; that is, treating patients with drugs that kill cancer cells.

chemotherapy

4.3 Mitosis: Cell Division That Preserves Chromosome Number -If you were to peer through a microscope and follow the history of one cell through time, you would see that for much of your observation, the chromosomes resemble a mass of extremely fine tangled string - called _____ -surrounded by the ____ ____. -You would also be able to distinguish one or two darker areas of chromatin called _____ (singular, ____, literally "small nucleus")' nucleoli play a key role in the manufacture of ribosomes, organelles that function in protein synthesis. -Each rod in a duo is called a _____; as described earlier, it is an exact duplicate of the other sister chromatid to which it is connected. -The two cells, known as ____ ___, are thus genetically identical.. -The repeating pattern of cell growth (an increase in size) followed by division (the splitting of one cell into two) is called the ___ ___. -The cell cycle: An alternation between _____ and mitosis. Chromosomes replicate to form sister chromatids during ___ (__ phase); the sister chromatids segregate to daughter cells during _____ (___ phase). The gaps between the S and M phases during which most cell growth takes place, are called the ____ and ___ phases. In multicellular organisms, some _____ _____ cells stop dividing and arrest in a "__" stage. ___ consists of the G1, S, and G2 phases together. -Only a small part of the cell cycle is spent in division (or ___ __); the period between divisions is called ____.

chromatin, nuclear membrane, nucleoli, nucleolus, chromatid, daughter cells, cell cycle, interphase, synthesis (S), G1, G2, terminally differentiated, G0, interphase, M phase, interphase

4.1 Chromosomes: The Carriers of Genes Genes Reside in the Nucleus Genes Reside in Chromosomes -In the 1880s, for example, a newly discovered combination of organic and inorganic dyes revealed the existence of the long, brightly staining, threadlike bodies within the nucleus that we call _____ (literally "colored bodies"). -The kind of nuclear division followed by cell division that results in two daughter cells containing the same number and type of chromosomes as the original parent cells is called _____ (from the Greek mitos meaning "thread" and -osis meaning "formation" or "increase"). -The kind of nuclear division that generates egg or sperm cells containing half the number of chromosomes found in other cells within the same organism is called ____ (from the Greek word for "diminution").

chromosomes, mitosis, meiosis

15.3 RNA-Mediated Mechanisms of Gene Regulation essential concepts -Prokaryotic mRNA leaders can act in ___ as regulators of transcription or translation by folding into ____ ___ ___ in response to ______ ____. -Small RNAs (sRNAs) regulate the ____ of mRNAs in ___ through complementary base pairing that can ___ or ____ the ____ ____ ___. -Antisense RNAs, transcribed from the ____ DNA strand, can regulate some genes by inhibiting sense mRNA ______ or _____.

cis, alternate stem loops, environmental conditions, translation, trans, hide, expose, ribosome binding site, opposite, translation, transcription

What Activators Do -Activators recruit ____; these are proteins that open local chromatin structure to allow gene transcription. -Activator proteins can also recruit _______ ____ - for example, enzymes that modify ____ ____ so as to clear the _______ DNA of _______. If the enhancer and promoter are far apart, _____ _____ is required for either mechanism of _____ function.

coactivators, coactivator proteins, histone tails, promoter, nucleosomes, DNA looping, activator

1.1 DNA: The Fundamental Information Molecular of Life -____ ___ ___ are a key feature of the DNA molecule. A single strand of DNA is composed of nucleotide subunits each consisting of a _____ ____, a ____, and one of ___ ____ ___ - adenine, _____, cytosine, or _____. ___ ____ enable A to associate tightly with ___, and C to associate tightly with ____. Thus the two strands are _____ to each other. The arrows labeled 5' to 3' show that the strands have ______ orientation. -The DNA regions that encode proteins are called _____. -Within the cells of an organism, DNA molecules carrying the genes are assembled into _____: organized structures containing DNA and proteins that package and manage the storage, duplication, expression, and evolution of DNA. -A human chromosome. Each chromosome contains hundreds to _____ of genes. -The DNA within the entire collection of chromosomes in each cell of an organism is its _____. -The amount of information that can be encoded in this size genome is equivalent to 6 million pages of text containing 250 words per page, with each letter corresponding to one ___ ___, or pair of nucleotides.

complementary base pairs, deoxyribose sugar, phosphate, four nitrogenous bases, thymine, guanine, hydrogen bonds, T, G, complementary, opposite, exons, chromosomes, thousands, genome, base pair

Concerted evolution and multigene homogeneity -There appears to be an ongoing process of _____ _____, which allows changes in single genetic elements to spread across a complete set of genes in a particular family. -Concerted evolution can lead to _____ _______. ____ cycles of ______ _____ events or ___ _____ cause the duplicated genes on each chromosome to become progressively more homogenized. -A gene family results from ____ ______ of a single gene and _____ among the copies. A few gene families have maintained ________ among members through concerted evolution, which occurs through ___ processes: _____ that acts to keep the ___ of the gene family within an optimal range; and intergenic gene conversion that _____ homogeneity among members.

concerted evolution, gene homogeneity, repeated, unequal crossover, gene conversion, repeated duplication, diversification, homogeneity, two, selection, size, increases

Cancerous Cells Evade Normal Controls on Cell Growth -In another example, most cells will stop dividing when they come into physical contact with other cells; this property is called _____ ______. -In particular, most cells are instructed to die through a process called ______ (or ____ ____ ____) that is activated when the genomic DNA becomes too damaged. -Phenotypic changes causing uncontrolled growth of cancer cells. _____ ____: Many tumor cells can divide in the absence of external growth signals required for the proliferation of normal cells. ___ __ ____ ____: Normal cells stop growing when they contact each other; as a result, they form a monolayer one cell thick when grown in culture. Tumor cells lose this contact inhibition and climb over each other to form piles many cells thick called ______ _____. ____ __ ____. When normal cells are damaged, they die by a process called ____ ___ ___, or _____. Many cancer cells fail to die when damaged to the same extent. -Some cancer cells make their own division-stimulating signals (_____ ____), or they can lose contact inhibition.

contact inhibition, apoptosis, programmed cell death, autocrine stimulation, Loss of contact inhibition, transformed foci, loss of apoptosis, programmed cell death, apoptosis, autocrine stimulation

Repressor/Corepressor Interaction Enables Repressible Regulation of Transcription Initiation -Tryptophan acts as a ______. When tryptophan is available, it binds to the _____ repressor, causing the molecule to change ___ so that the repressor can bind to the operator of the ___ operon and repress transcription. When tryptophan is not available, the repressor ____ bind to the operator, and the tryptophan biosynthetic genes are ____. -In contrast to allolactose, which functions as an inducer that prevents the Lac repressor from binding to the operator, tryptophan functions as a _______ for the TrpR repressor protein. -The difference is simple but essential: In the presence of the inducer allolactose, the Lac repressor _____ bind to the lac operator; while the TrpR repressor ___ bind to the operator only when the corepressor tryptophan is present.

corepressor, TrpR, shape, trp, cannot, expressed, corepressor, cannot, can

Cyclins and Cyclin-Dependent Kinases Are the Essential Drivers of Cell-Cycle Events -A family of protein kinases, called ____-____ ___ (____), are central controlling elements that guide the transitions from one cell-cycle stage to the next. -As the name implies, CDKs function only after associating with proteins called _____. -As an example, consider the action of one CDK-cyclin complex on the ______ _____, proteins that underlie the inner surface of the nuclear membrane and provide structural support for the nucleus. -Cyclin-dependent kinases (CDKs) control the cell cycle by ______ other proteins. A CDK combines with a cyclin and acquires the capacity to phosphorylate other proteins. Phosphorylation of a protein can either ______ or activate it. CDK phosphorylation of nuclear structure proteins called lamins is responsible for ______ of the nuclear membrane at _______ of mitosis.

cyclin-dependent kinases (CDKs), cyclins, nuclear lamins, phosphorylating, inactivate, dissolution, prometaphase

Transcriptional regulation of cell-cycle genes Important classes of cell-cycle genes activated transcriptionally in response to growth factors are the _____ and _____-____ ____ described in the next section.

cyclins, cyclin-dependent kinases

Cytokinesis: The cytoplasm divides -This final stage of division is called ____ (literally "cell movement"). -In animal cells, cytoplasmic division depends on a _____ ___ that pinches the cell into two approximately equal halves, similar to the way the pulling of a string closes the opening of a bag of marbles. -In plants, whose cells are surrounded by a rigid cell wall, a membrane-enclosed disk, known as the ___ __, forms inside the cell near the equator and then grows rapidly outward, thereby dividing the cell in two. -Cytokinesis: The cytoplasm ___, producing ___ ___ cells. In this dividing frog zygote, the contractile ring at the cell's _____ has contracted to form a ____ ___ that will eventually pinch the cell in two. In this dividing onion root cell, a cell plate that begins forming near the ____ of the cell expands to the periphery, separating the two daughter cells. -An animal cell with two or more nuclei is known as ______. -If ______ does not follow mitosis, one cell may contain many ____. In fertilized Drosophila eggs, 13 rounds of ____ take place without cytokinesis. The result is a ___-celled ____ embryo that contains several thousand nuclei. The photograph shows part of an embryo in which the nuclei are all dividing. ____ eventually grow around these nuclei, dividing the embryo into ___. -A multi-nucleate plant tissue is called a ______; coconut milk is a nutrient-rich food composed of coenocytes. -Mitosis ____ the chromosome number of the parent cell in the two daughter nuclei. In the photomicrographs of new lung cells...

cytokinesis, contractile ring, cell plate, divides, two daughter, periphery, cleavage furrow, equator, syncytium, cytokinesis, nuclei, mitosis, single, syncytial, membranes, cells, coenocyte, maintains

Mutations can be classified according to effect -Different mutations can be ______, _____, or ____ to the organisms that inherit them. -Genetic changes that are truly neutral are unaffected by the agents of selection. They survive or disappear from a population through ____ ____, which is the result of chance reproductive events. -Some mutations (such as those that cause sickle-cell anemia) are deleterious to homozygotes for the mutation but advantageous to heterozygotes. Because of this _____ ____, selection retains these mutations in a population at a low equilibrium level. -Ultimately, the allele that began as a mutation is present in nearly every member of the population on both chromosomes. At this stage, the allele has become _____ in the population.

deleterious, neutral, favorable, genetic drift, heterozygous advantage, fixed

16.2 Control of Transcription Initiation Through Enhancers essential concepts -Enhancers are DNA sequences which may be ____ from a gene's promoter and act in particular ___ ___ to increase or decrease the amount of transcription relative to a ____ ___. -Transcription factors are ____-acting proteins that include ____ ____ that bind the promoter, and activators and repressors that bind enhancers. Once bound to DNA, transcription factors can recruit other _____ to the gene. -Enhancers can have binding sites for _____ _____ activators and repressors; this property of enhancers enables them to impart _______ and ____ ____ specificity to gene transcription. -Insulators are DNA elements that organize ______ into loops; an enhancer and a _____ can interact only if they are in the ____ loop. -Bioinformatics enables _____-wide searches for new _______ ______ and their ____ ___. ChIP-Seq uses specific antibodies to identify genes regulated by transcription factors of interest.

distant, cell types, basal level, trans, basal factors, proteins, many different, temporal, cell type, chromatin, promoter, same, genome, transcription factors, binding sites

The retinoic acid receptor (RAR) is a transcription factor that is similar to steroid hormone receptors. The substance (ligand) that binds to this receptor is retinoic acid. One of the genes whose transcription is activated by retinoic acid binding to the receptor is myoD. The diagram at the end of this problem shows a schematic of the RAR protein produced by a gene into which one of two different 12-base double-stranded oligonucleotides had been inserted in the ORF. The insertion site (a-m) associated with each mutant protein is indicated with the appropriate letter on the polypeptide map below. For constructs encoding a-e, oligonucleotide 1 (5' TTAATTAATTAA 3' read off either strand) was inserted into the RAR gene. For constructs encoding f-m, oligonucleotide 2 (5' CCGGCCGGCCGG 3') was inserted into the gene. Each mutant protein was tested for its ability to bind retinoic acid, bind to DNA, and activate transcription of the moD gene. Results are tabulated as follows: a. What is the effect of inserting oligonucleotide 1 anywhere in the protein? b.What are the possible effects of inserting oligonucleotide 2 anywhere in the protein? c. Indicate the three protein domains of RAR on a copy of the preceding drawing. Answer This question involves the concept of _____ within proteins and the use of the genetic code to understand the effects of oligonucleotide ______. a. Oligonucleotide 1 contains a ___ ____ in any of its ____ reading frames. This means it will cause ______ of ______ of the protein in either _______ wherever it is inserted. b. Oligonucleotide 2 does ___ contain any stop codons, and so it will just ____ amino acids to the protein. Because there are 12 bases in the oligonucleotide, it will ____ change the ____ ____ of the protein. Insertion of the oligonucleotide can ____ the function of a site in which it inserts, although this will ___ necessarily be the case. c. Looking at the data overall, notice that all mutants that are defective in DNA binding are also defective in ______ ____, as would be expected for a transcription factor that binds to DNA. The mutants that will be informative about the transcriptional activation domain are those that do ___ have a DNA-binding defect. Inserts a, b, and c using oligonucleotide 1, which ______ the protein at the site of insertion, are defective in all three activities. DNA binding and transcription activation are both seen in mutant ___, so these two activities must lie closer to the ____ terminus than d. Truncation at d is negative for retinoic acid binding, but the truncation at e does bind to retinoic acid. The retinoic acid-binding activity must lie _____ e. Using the oligonucleotide 2 set of insertions, transcriptional activation was disrupted by insertions at sites g and h, indicating that this region in part of the _________ _____; I and j insertions disputed the DNA binding, and k and l insertions disrupted the retinoic acid binding. The ______ endpoints of the domains of RAR as determined from these data are summarized in the following schematic.

domains, insertions, stop codon, three, termination, translation, orientation, not, add, not, reading frame, disrupt, not, transcriptional activation, not, truncates, d, N, before, transcriptional domain, minimal

1.4 The Modular Construction of Genomes essential concepts -Gene _____ followed by the _____ of copies is one explanation for how new _____ evolve. -The reshuffling of _____ in eukaryotes provides another mechanism for the rapid ______ of genomes. -Changes in DNA that affect ____ ______-where, when, and to what degree genes are expressed-also generate evolutionary change.

duplication, divergence, functions, exons, diversification, gene regulation

During Meiosis I, Homologs Pair, Exchange Parts and Then Segregate -Meiosis: One Diploid Cell Produces ___ ___ Cells Homologus chromosomes enter _____. The ____ ____ forms. ____-___, genetic exchange between non sister chromatids of a homologs pair, occurs. A ____ of four chromatids is visible. Crossover points appear as ____, holding non sister chromatids together. Tetrads line up along the ___ ___. This is similar to interphase with one important exception: ___ ___ ____ takes place.

four haploid, synapsis, synaptonemal complex, crossing-over, tetrad, chiasmata, metaphase plate, no chromosomal duplication

The law of segregation -_____ are the specialized cells-eggs within the ovules of the female parent and sperm cells within the pollen grains-that carry genes between generations. -He imagined that during the formation of pollen and eggs, the two copies of each gene in the parent separate (or ______) so that each gamete receives only one allele for each trait. -At fertilization, pollen with one or the other allele unites at random with an egg carrying one or the other allele, restoring the two copies of the gene for each trait in the fertilized egg, or _______. -The law of segregation. The two identical alleles of pure-breeding plants separate (segregate) during _____ formation. As a result, each pollen grain or egg carries only ____ of each pair of parental alleles. Cross-pollination and fertilization between pure-breeding parents with antagonistic traits result in F1 hybrid zygotes with ___ _____ alleles. For the seed color gene, a ____ hybrid zygote will develop into a yellow pea. -Mendel's ____ ___ ____ encapsulates this general principle of heredity: The ___ alleles for each trait separate (segregate) during ____ formation, and then ____ at random, one from each parent, at fertilization. -Throughout this book, the term ______ refers to such equal segregation in which one allele, and only one allele, of each gene goes to each gamete.

gametes, segregate, zygote, gamete, one, two different, Yy, law of segregation, two, gamete, meet, segregation

c-Abl -The c-Abl part of the protein is a _____ _____ ___, which adds phosphate groups to tyrosine amino acids in other proteins.

protein tyrosine kinase

The necessity of checkpoints -Another manifestation of chromosome instability in cells with a defective G1-to-S checkpoint is a propensity for _____ ____: an increase from the normal two copies to hundreds of copies of a gene. -This amplification is often visible under the microscope, appearing either as an enlarged area within a chromosome known as a ______ _____ ____ (____) that contains many tandem repeats of a gene, or as small chromosome-like bodies (called ____ ____ because of their small size) that lack centromeres and telomeres. -Gene amplification in cells with defective G1-to-S checkpoints. ____ cells with defective checkpoints often exhibit amplified regions of DNA. These can appear as homogeneously staining regions (HSRs) containing many ___ ___ of one or more genes; or as double minutes, which are small pieces of _______ DNA.

gene amplification, homogeneously staining region (HSR), double minutes, Tumor, tandem repeats, extrachromosomal

1.4 The Modular Construction of Genomes -The information obtained reveals that ___ ___ have arisen by duplication of a primordial gene; after duplication, mutations and rearrangements may cause the two copies to diverge from each other. -How genes arise by duplication and ______. Ancestral gene A contains exons separated by ____. Gene A is duplicated to create two copies that are originally ____, but ______ in either or both cause the copies to diverge. Additional rounds of duplication and divergence create a family of _____ genes. -The protein-coding region of most genes is subdivided into as many as 10 or more small pieces (called _____), separated by DNA that does not code for protein (called _____). -Fossil evidence for Some Major Stages in the Evolution of Life. ___ ____ years ago: Primaevifilum amoenum, an early ______ ; ___ ___ years ago: First ____-___ eukaryotes ; ___-___ ___ years ago: Early _____ eukaryotes ; ____ explosion ; ____-____ ____ years ago: Ancestors of many present-day plants and animals -_____ cells such as bacteria, which do not have a membrane-bounded nucleus, evolved about 3.7 billion years ago; _____ cells such as algae, which have a membrane-bounded nucleus, emerged around 2 billion years ago; and multicellular eukaryotic organisms appeared 7--600 million years ago. -Exons are arranged into genes; genes duplicate and diverge to generate multigene families; and multigene families sometimes rapidly expand to ____ _____ containing hundreds of related genes. -Two-winged and four-winged flies. Geneticists converted a contemporary normal two-winged fly to a four-winged insect resembling the fly's _______ antecedent. They accomplished this by _____ a key element in the fly's ______ network. Note the club-shaped _______ behind the wings of the fly at the top.

gene families, divergence, introns, identical, mutations, related, exons, introns, 3.7 billion, prokaryote, 2 billion, single-cell, 700-600 million, multicellular, Cambrian, 570-560 million, prokaryotic, eukaryotic, gene superfamilies, evolutionary, mutating, regulatory, halteres

The evolution of gene superfamilies -Molecular geneticists use the phrase ____ _______ to describe a large set of related genes that is divisible into smaller sets, or families, with the genes in each family being more closely related to each other than to other members of the larger superfamily. -Evolution of the mouse globin superfamily. _____ gene _____ by various mechanisms gave rise to the globin supergene family in mice, with ___ multigene families (___ and ____) and one single gene (_____). The alpha family has both ______ arrayed and ____ gene members. -Pseudogenes existing in isolation from their parental families are called _____. -Evolution of the Hox gene superfamily of mouse and Drosophila. This gene superfamily arose by a series of ____ _____. ____ multigene families are present in the mouse and ____ in Drosophila. -A gene superfamily is a collection of ____ _____ families found at _____ chromosomal locations. One example is the _____ superfamily that contains the myoglobin gene as well as different hemoglobin genes; another is the ____ gene superfamily that contains genes involved in ____ of gene expression.

gene superfamilies, repeated, duplication, 2, alpha, beta, myoglobin, tenderly, dispersed, orphons, gene duplications, four, related multigene, different, globin, Hox, regulation

2.2 Genetic Analysis According to Mendel essential concepts -Discrete units called ____ control the appearance of inherited traits; genes come in alternative forms called _____. -A sexually reproducing organism's body cells contain ___ alleles for every gene. These alleles may be the ___ (in a homozygote) or _____ (in a heterozygote).. -Genotype refers to the ____ an individual possesses; phenotype refers to the ____ the individual exhibits. -The ____ allele controls the phenotype of a trait in heterozygotes; the other allele in the heterozygote is recessive. In monohybrid crosses between heterozygotes, the dominant and recessive phenotypes will appear in the progeny in a ratio of ___:___. -Alleles segregate during the formation of gametes, which thus contain only one allele of each gene. Male and female gametes unite at random at fertilization. Mendel described the operation of these processes as the ___ __ ______. -The segregation of alleles of any one gene is independent of the segregation of the alleles of other genes. Mendel termed this principle the ____ __ ____ ___. According to this law, crosses between Aa Bb dihybrids will generate progeny with a phenotypic ratio of __ (A-B-) : __ (A-bb) : ___ (aaB-): __ (aa bb). -The most common explanation for why one allele of a particular gene is dominant and an alternative allele is recessive is that the dominant allele encodes a _____ product (a protein), while the recessive allele determines either a ____ functional or _____ version of the protein, or ___ protein at all.

genes, alleles, two, same, different, alleles, traits, dominant, 3:1, law of segregation, law of independent assortment, 9:3:3:1, functional, less, nonfunctional, no

Most Cancer Cells Have Unstable Genomes -Another manifestation of ______ _______ is that many cancer cells have major chromosomal aberrations. -Genomic instability in cancer cells. In many cancer cells, enzymatic systems for repairing ____ ____ are disrupted. As a result, the cells have enormously increased rates of _____. Cancer cells often have karyotypes showing abnormal _____ of chromosomes and many ______ _____ such as translocations. These karyotypic changes result from defective DNA damage and _____ ____ mechanisms.

genomic instability, DNA damage, mutation, numbers, chromosomal rearrangements, chromosome segregation

p53 -Loss of p53 function leads to _____ _____. In cells without the p53 _____ ____ that also sustain single-stranded breaks in their DNA: (1) ____ is not induced, so the cells progress to __ ___. (2) Genes for ____ ____ are not transcribed. Thus, upon DNA replication, the single-stranded nicks are converted to _____-____ ___, which in turn cause ______ and chromosomal _____. (3) Apoptotic genes are not induced, so the cells with DNA damage do not die as they should.

genomic instability, transcription factor, p21, S phase, DNA repair, double-strand breaks, mutations, instability

1.6 Human Genetics and Society -Many Social Issues Need to be Addressed -To many people, the most frightening potential of the new genetics is the development of technology that can alter or add to genes present within the ___ ___ (reproductive cell precursors) of human embryos.

germ line

4.5 Gametogenesis -In all sexually reproducing animals, the embryonic germ cells (collectively know as the ___ __) undergo a series of mitotic divisions that yield a collection of specialized diploid cells, which subsequently divide by meiosis to produce haploid cells. -Gamete formation, or _____, thus gives rise to haploid gametes marked not only by the events of meiosis per se but also by cellular events that precede and follow meiosis.

germ line, gametogenesis

19.4 How Mutations Cause Cancer Phenotypes essential concepts -Proto-oncogenes usually encode proteins that participate in _____-_____-dependent _____ ____ ____. Oncogenic mutations are dominant, gain-of-function mutations in proto-oncogenes that result in activation of these pathways even in the ____ of the growth factor. -The normal alleles of tumor-suppressor genes encode proteins that act as ____ on the cell cycle or that maintain _____ stability. Loss-of-function mutations in tumor-suppressor genes are recessive at the level of the ___ because both normal copies must be lost to promote cancer. Individuals with a mutant copy of a tumor-suppressor gene have a dominantly inherited ______ to cancer because of the high probability that the remaining wild-type copy of the tumor-suppressor gene will be lost in at least ___ cell.

growth-factor, signal transduction pathways, absence, brakes, genomic, cell, predisposition, one

Allosteric interactions -Steroid _____ receptors. The ____-____ domains of steroid hormone receptors are in an _____ conformation until _____ changes caused by the binding of a steroid hormone molecule to another domain within the activator protein allow the DNA-binding domain to recognize sequences within the _____.

hormone, DNA-binding, inactive, allosteric, enhancer

Finding oncogenes through cell transformation assays -Finding oncogenes in tumor cell DNA. DNA isolated from some ____ ___ changes normal mouse cells into cancer cells that lose _____ ____ and form _____ ___. Human oncogenes can be identified in DNA from the transformed cells by looking for human-specific ____ sequences adjacent to oncogenes.

human cancers, contact inhibition, transformed foci, Alu

chapter 4 The Chromosome Theory of Inheritance -Each of these three human chromosomes carries ____ of genes. -Down syndrome: One extra chromosome ___ has widespread phenotypic consequences. ____ ___ usually causes changes in physical appearance as well as in the potential for _____. Many children with Down syndrome, such as the fifth grader at the center of the photograph, can participate fully in regular activities. -In this chapter, we describe how geneticists concluded that chromosomes are the carriers of genes, an idea that became known as the _____ ____ ___ ______. -First, direct microscopic observation of chromosomes during gamete formation led early twentieth-century investigators to recognize that chromosome movements parallel the behavior of _____ _____, so chromosomes are likely to carry the _____ ____.

hundreds, 21, Trisomy 21, learning, chromosome theory of inheritance, Mendel's genes, genetic information

Duplications have created multigene families and gene superfamilies -Duplications ____ genome size. Genome size increases through duplication of _____, ____, ____ _____, and finally of entire ______.

increase, exons, genes, gene families, genomes

The law of independent assortment -From the observed ratios, Mendel inferred the biological mechanism of shuffling-the ____ ____ of gene pairs during gamete formation. -The preceding analysis became the basis of Mendel's second general genetic principle, the ___ ___ ____ _____: During gamete formation, different pairs of _____ segregate _____ of each other. -The law of independent assortment. In a dihybrid cross, each pair of alleles assorts independently during gamete formation. In the gametes, Y is equally likely to be found with ___ or ___ (that is, Y R = Y r); the same is true for ___ (that is, y R = y r). As a result, all four possible types of gametes (Y R, Y r, y R, y r) are produced in ____ ____ among a large population.

independent assortment, law of independent assortment, alleles, independently, R, r, y, equal frequencies

Testcrosses with dihybrids -Testcrosses on dihybrids. Testcrosses involving two pairs of ______ ____ alleles yield different, predictable results depending on the tested individual's ____ for the two genes in question.

independently assorting, genotype

Indirect repression -Many regulatory proteins-called _____ ___-prevent transcription initiation indirectly, not by recruiting corepressors, but instead by interfering with the function of activators. -In another form of indirect repression called _____, a protein can bind the activation domain of an activator bound to an enhancer and thereby prevent the activator from functioning. -A repressor may act ____ directly and indirectly by sharing with an activator a _____ or ______ binding site within an _____; the repressor can ___-____ the activator for enhancer binding. An indirect repressor can bind an activator and hide its _____ ____. An activator can be _______ in the ______ when bound to an indirect repressor. Formation of _______ indirect repressor/activator _____ can prevent the formation of functional activator ______.

indirect repressors, quenching, both, single, overlapping, enhancer, out-compete, activation domain, sequestered, cytoplasm, nonfunctional, heterodimers, homodimers

Insulator Mechanism -Genomic imprinting mechanisms. Maternal imprinting of Igf2 is controlled by methylation of an ________ located between the Igf2 _____ and promoter. On the maternal homolog, the insulator is __________ and therefore functional (binds _____); on the paternal homolog, the insulator is methylated and does ____ function.

insulator, enhancer, unmethylated, CTCF, not

Small RNAs Regulate mRNA Stability and Translation -Small RNAs in Eukaryotes. miRNAs (micro-RNAs); Targets: ____ ; Effects: Block mRNA _____, _______ mRNAs ; siRNAs (small interfering RNAs); mRNAs, _____ transcripts of chromosomal regions destined to become ________ ; Block translation/Destabilize mRNAs, Recruit _______-modifying enzymes to DNA, resulting in _______ formation ; piRNAs (Piwi-interacting RNAs) ; _____ _____ transcripts, Transposable element ______ ; _______ of transposable element mRNA, Facilitate _____ modifications that inhibit transposable element transcription -Three classes of small regulatory RNAs have now been identified: ____-____ (_____), ____ _____ ____ (_____), and _____-_____ ____ )____).

mRNA, translation, destabilize, nascent, heterochromatin, histone, heterochromatin, transposable element, promoters, degradation, histone, micro-RNAs, miRNAs, small interfering RNAs, siRNAs, Piwi-interacting RNAs, piRNAs

1.2 Proteins: The Functional Molecules of Life Processes -The chemical and physical reactions that carry out these conversions are known as _______. -Most properties of living organisms ultimately arise from the class of molecules known as _____-large polymers composed of hundreds to thousands of amino acid subunits strung together in long chains. -Proteins are polymers of amino acids that fold in ____ dimensions. The specific sequence of amino acids in a chain determines the precise three-dimensional ____ of the molecule. Structural formulas for two amino acids: alanine and tyrosine. All amino acids have a ____ ____ group (-NH) at one end and an ____ ____ group (-COOH) at the other. The specific ___ ____ determines the amino acid's chemical properties. A comparison of equivalent segments in the chains of two digestive proteins, chymotrypsin and elastase. The red lines connect sites in the two sequences that carry ____ amino acids; the two chains differ at the other sites shown. Schematic drawings of the hemoglobin B chain and lactate dehydrogenase show the different three-dimensional shapes determined by different ____ ___ sequences.

metabolism, proteins, three, shape, basic amino, acidic carboxyl, side chain, identical, amino acid

Noncoding RNA (ncRNA) Mechanism -Genomic imprinting mechanisms. Paternal imprinting of Igfr2 depends on _______ of a ______ _____ that controls transcription of the Air _____; when Air is transcribed, Igfr2 is ____ expressed. The CpG island on the maternal homolog is ________, _______ Air transcription and ______ Igfr2 expression; the paternal Igfr2 allele is ______ because the CpG island is _________ and ____ is transcribed.

methylation, CpG island, ncRNA, not, methylated, silencing, allowing, silenced, unmethylated, Air

16.2 Control of Transcription Initiation Through Enhancers -We focus first on mechanisms for regulation of genes transcribed in a cell-type-specific manner; later in the chapter, we will address a mechanism (______ and ______ of ____ ___) that is key for the constitutive transcription of housekeeping genes and is also of importance for regulation of certain cell-type-specific genes.

methylation, demethylation, CpG islands

4.5 Gametogenesis essential concepts -Diploid germ cell precursors proliferate by ____ and then undergo meiosis to produce ___ gametes. -Human females are born with ___ arrested in prophase of meiosis I. Meiosis resumes at _____ but is not completed until _____. -Spermatogenesis begins at ____ and continues through the lifetimes of human males. -The two meiotic divisions of oogenesis are _____, so that a primary oocyte results in a single egg. The two meiotic divisions of spermatogenesis are ____, so that a primary spermatocyte results in four sperm. -All human oocytes contain a single __ chromosome; sperm contain either an X or a Y.

mitosis, haploid, oocytes, ovulation, fertilization, puberty, asymmetrical, symmetrical, X

19.2 The Genetic Basis of Cancers essential concepts -Cancers result from the accumulation of mutations in certain critical genes in a ______ dividing ___ of ____ cells. -Support for this model of cancer genetics comes from observations that cancer rates are increased by exposure to ______, by advancing ____ of the patient, and by rare ____ mutations. -Increased cell _______ promotes genomic _____; some of the resulting mutations can in turn lead to more ______ and the acquisition of additional cancer-______ properties.

mitotically, clone, somatic, mutagens, age, inherited, proliferation, instability, proliferation, promoting

1.5 Modern Genetic Techniques -Seven ___ ____ whose genomes were sequenced as part of the ___ ___ ___. The chart indicates genome size in millions of base pairs, or _____ (___). The bottom row shows the approximate number of genes for each organism. -The inheritance pattern observed for microcephaly indicated that it is a so-called ____ disease, meaning that diseased people inherit two mutant gene copies, one from each normal parent. -A _____ gene for microcephaly identified by ____ sequencing. Magnetic resonance images of normal and microcephalic brains. Sequence analysis of normal and mutant copies of the WDR62 gene. The mutation is a _____ of the four nucleotides TGCC that causes a major change in the ___ ___ sequence of the protein product of the gene. The letters above each triplet sequence identify the encoded amino acid. Five different mutations in the WDR62 gene in five different families are shown. Four of the mutations affect the identity of a ___ amino acid in the protein encoded by the gene. For example, W224S means that the ______ amino acid is normally W (______) but is changed to S (____) by the mutation. The arrow indicates the position of the TGCC deletion mutation shown.

model organisms, Human Genome Project, Megabases (Mb) recessive, causal, exome, deletion, amino acid, single, 224th, tryptophan, serine

16.4 Regulation After Transcription essential concepts -In eukaryotes, alternative splicing can produce different _____ from a single transcript. Sequence-specific _____-_____ ___ can inhibit or promote the use of particular _____-_____ sequences. -___ classes of small RNAs regulate mRNA stability, translation, or transcription through _______ ____ _____: miRNA, siRNAs, and piRNAs. These small RNAs act as guides to bring ____ ____ to particular target mRNAs (leading to mRNA ______ or preventing _____) or to DNA sequences near _____ (blocking transcription or promoting _________).

proteins, RNA-binding proteins, splice-junction, three, complementary base pairing, protein complexes, degradation, translation, promoters, heterochromatization

Molecular clocks allow inference of phylogenetic relationships -Then, in the 1950s, Linus Pauling and Emile Zuckerkandl analyzed hemoglobin and cytochrome C protein sequences from different species and noted that the rates of amino acid substitution in each type of protein are similar for various mammalian lineages. On the basis of this observation, they postulated that for a given protein, the rate of evolution is constant across all lineages. They called this idea of a constant rate of change for each type of molecule a _______ ______. -Scientists use molecular data in various ways to construct _______ _____ that illustrate the relatedness of homologous genes or proteins. -A phylogenetic tree consists of _____ and ______. -A phylogenetic tree. This phylogenetic tree diagrams the evolutionary history of human hemoglobin genes. The ____ ____ denotes a pseudogene linkage. Only one of the two a-hemoglobin genes is shown because their date of divergence is so ____. -Individual proteins have been found to mutate at a ____ ____ across lineages. Biologists can use these molecular clocks to estimate times of _______ and to construct ______ based phylogenetic trees. The genes of some proteins evolve more _____ than others, allowing analysis of _____ divergences or more ____ speciation.

molecular clock, phylogenetic trees, nodes, branches, broken line, recent, constant rate, divergence, molecularly, quickly, distant, recent

1.3 Molecular Similarities of All Life-Forms essential concepts -Living organisms exhibit marked similarities at the _____ level in the ways they use ____ and ____ to make proteins. -Certain genes have persisted through the evolution of widely _____ species.

molecular, DNA, RNA, divergent

Creation of a multigene family -A _______ ____ is a set of genes descended by duplication and diversification from one ancestral gene. -Multigene families. _____ and ____ multigene families on segments of the indicated chromosomes. -Evolution via ______ within families. A schematic illustration of how a crossover can ______ and _____ gene numbers in a multigene family.

multigene family, tandem, dispersed, crossovers, expand, contract

Geneticists use Mendel's Laws to Calculate Probabilities and Make Predictions -Mendel performed several sets of dihybrid crosses and also carried out _______ ____: matings between the F1 progeny of pure-breeding parents that differed in three or more unrelated traits.

multihybrid crosses

19.5 Personalized Cancer Treatment essential concepts -Several anticancer drugs target proteins encoded by _____ _______. -Other drugs exploit the fact that many cancerous cells are particularly sensitive to ___ ____ because of the absence of _____ or ____ ____ proteins. -___-___ _____ of cancer cells helps pinpoint potential treatments directed against the particular set of mutations in individual tumors.

mutant oncogenes, DNA damage, checkpoints, DNA repair, whole-genome sequencing

Diversification leading to new functionality -In many cases, ______ turn a _____ gene into a non-functional pseudogene. In other cases, mutations may confer a _____ ____ on a duplicated gene on which ______ can act. If the new function provides a selective advantage, the newly functional gene will be ______.

mutations, duplicated, new function, selection, retained

19.4 How Mutations Cause Cancer Phenotypes -Mutant alleles that act in a dominant fashion to promote cancer are called ______; in a diploid cell, one mutant oncogenic allele is sufficient to help cause a cancer-related phenotype. -Mutant alleles that act recessively to promot cancer are mutations in _____-_____ ____; in a diploid cell, both copies of a tumor-suppressor gene must be mutant to make the cell abnormal. -Two kinds of cancer-producing mutations. Proto-oncogenes often encode proteins that promote ____ ______. A dominant ___-__-___ mutation in a wild-type proto-oncogene generates a cancer-causing oncogene. Mutant oncogenic alleles are _______ or ______ that produce either proteins with abnormal _____ or _____ amounts of normal protein. Wild-type tumor-suppressor genes encode proteins that _____ cell proliferation or ____ ___ proteins that guard against ____ instability. Recessive ___-__-___ mutations in tumor-suppressor genes (_____ or ______) exhibit no phenotype in ______ cells that also have a wild-type allele. However, when a ____ mutation inactivates the wild-type allele, the cell _____ out of control or rapidly accumulates ______. -The normal, non mutant allele of an oncogene is called a ____-______, and it often encodes a protein needed for cell-cycle progression.

oncogenes, tumor-suppressor genes, cell proliferation, gain-of-function, hypermorphs, neomorphs, activity, excessive, restrict, DNA repair, genome, loss-of-function, hypomorphs, amorphs, heterozygous, second, proliferates, mutations, proto-oncogene

Her2 -Examples of _____ mutations. In breast cancer cells but not in normal cells, the Her2 gene is ____ on multiple _____-___ chromosomes.

oncogenic, amplified, double-minute

15.5 A Comprehensive Example: Control of Bioluminescence by Quorum Sensing essential concepts -The genes for bioluminescence and ____ ____ were identified by transforming E. coli cells with V. fischeri ____ and looking for colonies that _____. -V. fischeri uses quorum sensing so that cells make light only when their population is _____. The basis of quorum sensing is that only ___ groups of cells accumulate levels of _____ sufficient to activate _____ of the bioluminescence ____ to high levels. -Quorum-sensing _____ may be excellent targets for future _________ _____ because immunity would provide no _____ _____ to individual cells.

quorum sensing, DNA, glowed, dense, large, autoinducer, transcription, operon, proteins, antimicrobial drugs, selective advantage

I. In the galactose operon of E. coli, a repressor, encoded by the galR gene, binds to an operator site, galo, to regulate the expression of three structural genes, galF, galT, and galK. Expression is induced by the presence of galactose in the media. For each of the strains listed, would the cell show constitutive, inducible, or no expression of each of the structural genes? (Assume that galR- is a loss-of-function mutation). a. galR-galo+galE+galT+galK+ b. galR+galo^cgalE+galT+galK+ c.galR-galo+galE+galT+galK-/galR+galo+galE-galT+galK+ d. galR-galo^cgalE+galT+galK-/galR+galo+galE-galT+galK+ Answer: This problem requires an understanding of how regulatory sites and the proteins that bind to these sites behave. To predict expression in the four strains, look at each copy of the ____ individually, and then assess what effect alleles present in the other copy of the operon could have on the expression. After doing that for each copy of the operon, combine the results. a. The galR gene encodes a ____, so the lack of GalR protein would lead to ______ ____ of the galE, T, and K genes. -The galo^c mutation is an ______ ___ mutation. By analogy with the lac operon, the designation galo^c indicates that _____ cannot bind, so ____ ____ of galE, T, and K would result. c. The first copy of the operon listed has a galR- mutation, but the other copy is wild type for the galR gene. The wild type allele produces a repressor that can act in ____ on both copies of the operon, overriding the effect of the _____ mutation. Overall, there will be ______ ___ of the three gal genes. The GalE protein will be made from the ___ copy of the operon, the GalK protein from the ____, and the GalT protein from ___ copies. d. The first copy of the operon contains a galo^c mutation, leading to ____ synthesis of ____ and ____. The other copy has a wild-type operator, so it is ____, but neither operator has effects on the ____ copy of the operon. The net result is _____ galE and galT expression and _____ galK expression.

operon, repressor, constitutive expression, operator site, repressor, constitutive expression, trans, galR-, inducible expression, first, second, both, constitutive, galE, galT, inducible, other, constitutive, inducible

Oogenesis in Humans Produces One Ovum from Each Primary Ooctye -The end product of egg formation in humans in a large, nutrient-rich ____ whose stored resources can sustain the early embryo. -The process, known as ____, begins when diploid germ cells in the ovary, called _____ (singular ,oogonium), multiply rapidly by mitosis and produce a large number of ____ ____, which then undergo meiosis. -In humans, egg formation begins in the ___ __ and arrests during the ___ of meiosis _. Fetal ovaries contain about _____ primary oocytes arrested in the diplotene substage of meiosis I. IF the egg released during a ____ ___ is fertilized, ___ is completed. Only ___ of the three cells produced by meiosis serves as the functional gamete, or ___. -The larger of these cells, the ____ ____, receives over 95% of the cytoplasm. -The other small sister cell is known as the first ____ ___. -During meiosis II, the secondary oocyte undergoes another asymmetrical division to produce a large haploid ____ and a small, haploid second polar body.

ovum, oogenesis, oogonia, primary oocytes, fetal ovaries, prophase, I, 500,000, menstrual cycle, meiosis, 1, ovum, secondary oocyte, polar body, ovum

Testcrosses: A way to establish genotype -An observable characteristic, such as yellow or green pea pods is a _____, while the actual pair of alleles present in an individual is its ______. -A YY or a yy genotype is called ______, because the two copies of the gene that determine the particular trait in question are the same. -In contrast, a genotype with two different alleles for a trait is _______; in other words, it is a hybrid for that trait. -Genotype versus phenotype in homozygotes and heterozygotes. The relationship between genotype and phenotype with a pair of contrasting allele where one allele (Y) shows ___ ____ over the other (y). -An individual with a homozygous genotype is a _____; one with a heterozygous genotype is a ______. -This method, called the ______, is a mating in which an individual showing the dominant phenotype, for instance, a Y- plant grown from a yellow pea, is crossed with an individual expressing the recessive phenotype, in this case a yy plant grown from a green pea. -How a testcross reveals _____. An individual of unknown genotype, but ____ phenotype, is crossed with a _____ ____. If the unknown genotype is homozygous, all progeny will exhibit the ____ phenotype. If the unknown genotype is heterozygous, ___ the progeny will exhibit the dominant trait, ___ the recessive trait.

phenotype, genotype, homozygous, heterozygous, complete dominance, homozygote, heterozygote, testcross, genotype, dominant, recessive homozygote, dominant, half, half

16.1 Overview of Eukaryotic Gene Regulation -Gene expression in eukaryotes. Gene expression first involves transcription and mRNA processing in the nucleus. The mRNA is transported to the cytoplasm, where it is translated into a protein. _________ ______ such as phosphorylation (P) can affect the ______, stability, or ________ of the protein product.

posttranslational modifications, activity, localization

Binding of operator by purified Lac repressor -The Lac repressor binds to operator DNA. A ______ tag is attached to the Lac repressor protein so it can be followed in the experiment. When repressor protein from lacI+ cells was purified and mixed with DNA containing the lac operator (on a bacterial ____ ____), the protein _____ with the DNA. When wild-type repressor was mixed with DNA containing a mutant operator site, no _____ sedimented with the DNA.

radioactive, virus chromosome, cosedimented, radioactivity

LuxI and LuxR Are the Quorum-Sensing Proteins in Vibrio fischeri -LuxR protein is a type of transcriptional activator protein called a _____, and it is needed for transcription of luxICDABE mRNA. -LuxI protein is a _____ enzyme; synthase generates a molecule called an _______. -Quorum sensing controls Vibrio fischeri bioluminescence. LuxI generates a molecule called _______ that the cell releases into the environment and which can also ____ the cell. When its levels reach a ______, autoinducer binds ____ protein, which can then bind the promoter of the bioluminescence _____ and activate its transcription.

receptor, synthase, autoinducer, autoinducer, reenter, threshold, LuxR, operon

miRNAs -These genes are transcribed by RNA polymerase II into long primary transcripts called ___-_____ that contain one or more miRNA sequences in the form of mostly double-stranded stem loops. -micro-RNA-containing genes. Primary miRNA transcripts (pri-miRNAs) can contain one or _____ miRNAs. Some of these primary transcripts do ____ encode proteins, but in other cases miRNAs can be processed from the ______ of protein-coding transcripts. -This multistep process is aided by two ribonuclease enzymes called _____ and ______. -miRNA processing. Immediately after transcription, pri-miRNAs are recognized by the nuclear enzyme _____, which crops out pre-miRNA ____-____ structures from the larger RNA. The pre-miRNAs undergo active transport from the nucleus into the _______, where they are recognized by the enzyme _____. Dicer reduces the pre-miRNA into a short-lived _____*:______ duplex, which is released and picked up by a _____. The RISC becomes a functional and highly specific ______ by eliminating the _____ strand that is partially complementary to the miRNA that will serve as the ____ in the miRSC. -Furthermore, the miRNAs become incorporated into ribonucleoprotein complexes called ______-_____ ______ _____ (_____); each miRISC contains a particular member of the Argonaute protein family. -The ribonucleoprotein complexes (miRISCs) containing miRNAs mediate diverse functions depending on the particular Argonaute protein they possess, and on the extent of sequence complementarity between the miRNA in the complex (called the ____) and the target sequences in mRNA 3' UTRs. -How miRISCs interfere with gene expression. The miRISC can ____-regulate target genes in two different ways. If the miRNA and its target mRNA contain _____ complementary sequences, miRISC ____ the mRNA. The two cleavage products are no longer protected from ______ and are rapidly ______. If the miRNA and its target mRNA have only partial complementarity, _____ of the mRNA is inhibited by an unknown mechanism.

pri-miRNAs, several, not, introns, Drosha, Dicer, Drosha, stem-loop, cytoplasm, Dicer, miRNA*:miRNA, RISC, miRISC, miRNA*, guide, miRNA-induced silencing complexes (miRISC), guide, down, perfectly, cleaves, RNase, degraded, translation

The product rule -The _____ ____ states that the probability of two or more _____ _____ occurring together is the _____ of the probabilities that each event will occur by itself. -With independent events: Probability of event 1 ____ event 2 = Probability of event 1 ___ probability of event 2 -It is important to realize that each box in the Punnett square represents an equally likely outcome of the cross (an equally likely fertilization event) ____ ____ each of the two types of pollen and eggs (Y and y) are produced at equal frequencies.

product rule, independent events, product, and, x, only because

Mendel's Results Reflect Basic Rules of Probability -Though you may not have realized it, the Punnett square illustrates two simple rules of probability - the ____ ___ and the ____ ____- that are central to the analysis of genetic crosses.

product rule, sum rule

The p53 pathway and apoptosis -If the DNA damage is great enough, wild-type cells producing functional p53 not only arrest in G1, but they also "commit suicide" in a process known as _____ ____ _____, or ______. -Apoptosis. If a normal cell's DNA is too highly damage for repair, the cell will undergo programmed cell death (apoptosis). The DNA is _____, the nucleus ______, and the damaged cells emit signals attracting ______ cells to "eat up" the dying cell. Many apoptotic proteins are expressed only when the ____ transcription factor is active.

programmed cell death, apoptosis, degraded, condenses, phagocytic, p53

Prometaphase: The spindle forms -_____ ("before middle stage") begins with the breakdown of the nuclear envelope, which allows microtubules extending from the two centrosomes to invade the nucleus. -Chromosomes attach to these microtubules through the ______, a structure in the centromere region of each chromatid that is specialized for conveyance. -During prometaphase, three different types of microtubule fibers together form the ____ ____; all of these microtubules originate from the centrosomes, which function as the two "poles" of the spindle apparatus. -Microtubules that extend between a centrosome and the kinetochore of a chromatid are called ______ _____, or ______ _____. -Microtubules from each centrosome that are directed toward the middle of the cell are _____ ______; polar microtubules originating in opposite centrosomes interdigitate near the cell's equator. -Finally, there are short ____ ____ that extend out from the centrosome toward the cell's periphery.

prometaphase, kinetochore, mitotic spindle, kinetochore microtubules, centromeric fibers, polar microtubules, astral microtubules

Prophase I: Homologs condense and pair, and crossing-over occurs -Among the critical events of ____ ___ are the condensation of chromatin, the pairing of homologous chromosomes, and the reciprocal exchange of genetic information between these paired homologs. -____ (from the Greek for "thin" and "delicate") is the first definable substage of prophase I, the time when the long, thin chromosomes begin to thicken. -______ (from the Greek for "conjugation") begins as each chromosome seeks out its homologs partner and the matching chromosomes become zipped together in a process known as _____. -The "zipper" itself is an elaborate protein structure called the ____ ____ that aligns the homologs with remarkable precision, juxtaposing the corresponding genetic regions of the chromosome pair. -_____ (from the Greek for "thick" or "fat") begins at the completion of synapsis when homologous chromosomes are united along their length. -Each synapsed chromosome pair is known as a _____ (because it encompasses two chromosomes), or a ____ (because it contains four chromatids). -During pachytene, structures called _____ _____ begin to appear along the synaptonemal complex, and an exchange of parts between non sister (that is, between maternal and paternal) chromatids occurs at these nodules. -Such an exchange is known as ____-___; it results in the _____ of genetic material. -_____ (from the Greek for "twofold" or "double") is signaled by the gradual dissolution of the synaptonemal zipper complex and a slight separation of regions of the homologous chromosomes. -The aligned homologous chromosomes of each bivalent nonetheless remain very tightly merged at intervals along their length called ____ (singular, chiasma), which represent the sites where crossing-over occurred. -_____ (from the Greek for "double movement") is accompanied by further condensation of the chromatids.

prophase I, leptotene, zygotene, synapsis, synaptonemal complex, pachytene, bivalent, tetrad, recombination nodules, crossing-over, recombination, diplotene, chiasmata, diakinesis

During Meiosis II, Sister Chromatids Separate to Produce Haploid Gametes Prophase II: The chromosomes condense -If the chromosomes decondensed during the preceding interphase, they recondense during ____ ____.

prophase II

During Mitosis, Sister Chromatids Separate and Two Daughter Nuclei Form Prophase: Chromosomes condense -At _____ (from the Greek pro- meaning "before"), the gradual emergence, or _____, of individual chromosomes from the undifferentiated mass of chromatin marks the beginning of mitosis.

prophase, condensation

Finding tumor-suppressor genes through analysis of pedigrees and genomes -Mutations in tumor-suppressor genes are _____ at the cellular level but _____ at the organism level. A child with a retinoblastoma tumor in one eye. A pedigree indicating that inheritance of a single RB- allele _____ predisposes an individual to retinoblastoma. In an RB+/RB- person, loss of the remaining RB+ from the genome of a single retinal cell can lead to a retinoblastoma. Such "second hits" are rare, but the retina contains so many cells that such an event likely will occur in one or more of them. -Many different kinds of rare events can occur to knock out the remaining RB+ allele in a heterozygous cell; all of these events produce a ____-__-______ because they change an RB-/RB+ cell into one that is RB-/RB-. -Events causing loss-of-heterozygosity in somatic cells of RB+/RB- individuals. RB- is inherited through the ___ ___ as an autosomal _____ mutation. Subsequent changes to the RB+ allele during ____ divisions generate a clone of cells homozygous or ______ for the nonfunctional RB- allele. _______ ______ means that the two copies of a chromosome in a cell were obtained from one parent. Two events are needed to produce a cell with uniparental disomy; for example, the first event could be loss of one _____, and the second event could be _______ of the remaining chromosome.

recessive, dominant, dominantly, loss-of-heterozygosity, germ line, recessive, mitotic, hemizygous, uniparental disomy, chromosome, duplication

lac Operon Regulatory Sequences Help Produce Protein Drugs in Bacteria -Making E. coli into a factory for protein production. The lac ______ _____ can be fused to gene X to control the expression of genes. In this example, a cDNA encoding human growth hormone is ____ next to the lac control region and ____ into E. coli. Conditions that ___ lac expression will cause expression of ____ ____ that can be purified from the cells.

regulatory region, cloned, transformed, induce, growth hormone

lacZ Reporter Genes Help Reveal the Regulation of Other Genes -Because it is so easy to measure B-galactosidase levels, the lacZ gene that encodes it can serve as a ______ ____ to detect the amount of transcription that occurs in response to any specific regulatory element. -In cells with this ____ ____, conditions that normally induce the expression of gene X will generate B-galactosidase. -lacZ as a reporter gene. The lacZ ____ sequences can be fused to a ______ ____ of gene x. Expression of B-galactosidase will depend on signals in the regulatory region to which lacZ is ____. -Using a _______ lacZ gene. _____ of the lacZ gene without its promoter creates a collection of E. coli cells with insertions at ____ chromosomal positions. If lacZ integrates within a gene in the _____ of transcription, lacZ expression will be controlled by that gene's _____ region. Researchers screen the _____ of clones to identify insertions in genes regulated by a ____ signal.

reporter gene, fusion gene, coding, regulatory region, fused, promoterless, transposition, random, orientation, regulatory, library, common

16.3 Epigenetics: Control of Transcription Initiation Through DNA Methylation essential concepts -Certain _______ bind methylated CpG islands, blocking transcription ______; this repression is maintained through generations of cells because CpG methylation patterns are copied during ____ _____. -The expression patterns of about _____ human genes depend on whether they were inherited from the ____ or ____ parent. Paternally imprinted genes are silenced when inherited from the ______, while maternally imprinted genes are silenced when inherited from the ______. -Epigenetic phenomena, such as imprinting, are caused by changes in _____ that alter gene expression without changing ____-____ sequence and that are ______ during cell division. -Genomic imprinting results from _____-_____ DNA methylation of ___-acting elements (____) that control the expression of particular genes. During ______, the old imprints are erased and new sex-specific methylation patterns are established.

repressors, activators, DNA replication, 100, female, male, male, female, DNA, base-pair, heritable, sex-specific, cis, ICRs, meiosis

Rotational Symmetry of the Operator -The lac operator sequences revealed by DNA foot printing experiments using Lac repressor protein display the interesting property of _____ _____.

rotational symmetry

Regulatory Small RNAs Act in trans to Regulate the Translation of mRNAs -Bacterial genomes encode many small RNA molecules, or _____, that regulate translation in ___ by base pairing with mRNAs. -Regulation by ___-acting sRNAs. Base-pairing of an sRNA with the leader sequence can inhibit. translation of an mRNA by hiding the _____ ____ ____. An sRNA can facilitate mRNA translation through base pairing interactions with the leader that prevent the formation of a ___ ___ that occludes the ____ ____ ___. -This generalization means that sRNAs often act as intermediaries in ____ ____ in which one regulator influences the expression of a different regulator.

sRNAs, trans, trans, ribosome binding site, stem loop, ribosome binding site, regulatory cascades

4.2 Sex Chromosomes and Sex Determination -The great lubber grasshopper. In this mating pair, the smaller male is astride the female. -Several researchers studying other organisms soon verified that in many sexually reproducing species, two distinct chromosomes - known as the ___ ___ - provide the basis of sex determination. -The ___ and __ chromosomes determine sex in humans. This colorize micrograph shows the human X chromosome and the human Y. Children can receive only an __ chromosome from their mother, but they can inherit either an __ or a ___ from their father.

sex chromosomes, X, Y, X, X, Y

Fertilization: The union of haploid gametes to produce diploid zygotes -The corresponding maternal and paternal chromosomes appear alike in size and shape, forming pairs (with one exception - the ____ ____ - which we discuss in a later section). -Gametes and other cells that carry only a single set of chromosomes are called _____ (from the Greek word for "single"). -Zygotes and other cells carrying two matching sets are _____ (from the Greek word for "double"). -The number of chromosomes in a normal haploid cell is designated by the shorthand symbol __; the number of chromosomes in a normal diploid cell is then ____. -Diploid versus haploid: 2n versus n. Most body cells are ____: They carry a maternal and _____ copy of each chromosome. Meiosis generates ____ gametes with only one copy of each chromosome. In Drosophila, diploid cells have eight chromosomes (___ __ __), while gametes have four chromosomes (__ __ __). Note that the chromosomes in this diagram are pictured before their replication. The X and Y chromosomes determine the ___ of the individual.

sex chromosomes, haploid, diploid, n, 2n, 2n, paternal, n, 2n = 8, n=4, sex

4.2 Sex chromosomes and Sex Determination essential concepts -Many sexually reproducing organisms have chromosomes that are ___-specific and that determine ____. -In humans, ___ sex determination is triggered by a ___-linked gene called ____; female sex determination occurs in ___ embryos by default. -Mechanisms of sex determination ___ remarkably; in some species sex is determined by environmental factors rather than by specific chromosomes.

sex, gender, male, Y, SRY, XX, vary

Discovery of transcription factors and their binding sites -Sigma factor recognition sequences. The promoters of "housekeeping" genes expressed at normal temperatures are recognized by ____. The promoters of genes encoding heat-shock proteins have sequences that are recognized by the ___-___ sigma factor ____.

sigma^70, heat-resistant, sigma^32

Signal transduction cascades -The cytoplasmic proteins responsible for relaying the signal inside the cell are known as ______ _______. -Binding of growth factors to receptors initiates signal transduction cascades. This binding transmits a signal to the ______ domain of the receptor protein, which in turn interacts with other signaling molecules in the cell. At the end of the signal transduction cascade initiated by a ______ is a _____ ____ that can turn on the expression of genes whose protein products stimulate ____ ____. -Next, Ras-GTP activates a series of three enzymes called ______ ______ that can add phosphate groups to other proteins. -The trio turned on by Ras-GTP is known as _____ (_____-______ ____) ____ ____. -A Ras-mediated signal transduction cascade. The ___ protein is an intracellular signaling molecule that is induced to exchange a bound _____ (inactive) for a bound ____ (____) when a growth factor binds to the cellular receptor with which Ras interacts.

signal transducers, intracellular, mitogen, transcription factor, cell division, MAP (mitogen-activated protein) kinase cascade, Was, GDP, GTP

19.3 How Cell Division is Normally Controlled essential concepts -Cell division is initiated by the binding of growth factors to receptor proteins on the cell surface. This binding initiates ____ transduction cascades that activate transcription factors controlling the expression of cell-cycle genes. -The formation and subsequent _____ of different CDK-cyclin complexes drive ______ between cell-cycle stages. -The G1-to-S checkpoint prevents cells from replicating their chromosomes if the DNA is _____. The ____ protein is a key component of this checkpoint.

signal, degradation, transitions, damaged, p53

chapter 20 Evolution at the Molecular Level essential concepts -All forms of life on earth are descendants of a ____ ____ - a common ancestor that existed approximately ____ ___ years ago. -____ ____ explained how biological evolution occurs through a process of _____ _____, which operates on ____ forms of _____ traits. The variant that provides the highest degree of _____ ____ is selected over many generations to become the predominant form in the entire population. -____ _____ provide a continuous source of variation. Mutations with no effect on fitness are considered neutral. Neutral mutations are not acted on by selection and are subject instead to _____ _____. Selection operates against mutation with a deleterious effect, and operates in favor of the extremely ___ mutations that have a positive effect on fitness. Selection can operate simultaneously at hundreds or thousands of ____ ___ within a population. -____ can carry genetic information as well as catalyze chemical reactions. These two properties have led scientists to speculate that RNA may have pre-dated the cell as the original ____ ____, or ____-____-___. -The ___ ____ as well as living organisms of all levels of complexity provide scientists with a detailed picture of the evolution of ____ life from the first cell to human beings. -Preliminary studies on the evolution of ____ _____ ____ suggest that it can account for the evolution of biological complexity. -The evolution of organismal complexity generally correlates with an increase in ____ ___, which occurs through ____ ____. Some duplications result from ______, while others arise from ____ ____-____. -Mutations rendering genes nonfunctional turn many duplicated genes into ______ that over time ____ into random DNA sequences. However, rare advantageous mutations can turn a second copy of a gene into a new functional unit able to survive and spread through ____ ____. -Sequence comparisons make it possible to construct ____ ___ illustrating the relatedness of species, populations, individuals, or _____. -The mammalian genome contains genes, multi-gene families, gene superfamilies, genome-wide ____ ____; ___ ___ ___; and repetitive elements in _____ and telomeres. -Complex genomes arose from ___ levels of duplication followed by _____ and ___: ___ duplication to create larger, more complex genes; gene duplication to create multigene families; multi-gene family duplication to create gene _____; and the duplication of entire genomes. -Genetic exchange between related DNA elements by intergenic gene conversion most often increases the _____ among members of a multigene family. Sometimes, however, it can contribute to concerted evolution, which creates a family of ____ ____ genes. -The human immune system is capable of a response that evolves on the ____ level through ______ of T and B cells that match an antigen. ____ can undergo rapid evolution due to the high ____ ___ of its reverse transcriptase. Therapies aim to slow the _____ of HIV by targeting reverse transcriptase and other viral enzymes.

single cell, 3.7 billion, Charles Darwin, natural selection, variant, inherited, reproductive fitness, new mutations, genetic drift, rare, variant loci, RNA, independent replicator, proto-life-form, fossil record, complex, gene regulatory networks, genome size, repeated duplications, transpositions, unequal crossing-over, pseudogenes, diverge, positive selection, phylogenetic trees, molecules, repetitive elements, simple sequence repeats, centromeres, four, diversification, selection, exon, superfamilies, variation, nearly identical, molecular, cloning, HIV, mutation rate, proliferation

Species variation in the number and shape of chromosomes -Each chromosomes now consists of two identical halves known as ____ ___ attached to each other at a specific location called the _____. -____ chromosomes can be classified by centromere position. Before cell division, each chromosome ____ into two sister chromatids connected to a centromere. In highly ____ metaphase chromosomes, the centromere can appear near the middle (a _____ chromosome), very near an end (an _____ chromosome), or anywhere in between. In a diploid cell, one ____ chromosome in each pair is from the mother and the other is from the father. -In _____ chromosomes, the centromere is more or less in the middle; in ____ chromosomes, the centromere is very close to one end. -Chromosomes that match in size, shape, and banding are called ______ ____, or _____. -______ ____, which carry completely unrelated sets of genetic information, appear in different colors. -To study the chromosomes of a single organism, geneticists arrange micrographs of the stained chromosomes in homologous pairs of decreasing size to produce a _____. -Karyotype of a human male. Photos of ____ human chromosomes are paired and arranged in order of _____ size. In a normal human male karyotype, there are ____ pairs of autosomes, as well as an X and a Y (___ __ ___). Homologous chromosomes share the same characteristic pattern of dark and light ___. -The 44 chromosomes in matching pairs are known as _____. -The two unmatched chromosomes in this male karyotype are called ____ ___, because they determine the sex of the individual. -Physicians use karyotype analysis and a technique called _______ to diagnose Down syndrome prenatally, roughly three months after a fetus is conceived.

sister chromatids, centromere, metaphase, replicates, condensed, metacentric, acrocentric, homologous, metacentric, acrocentric, homologous chromosomes, homologs, nonhomologous chromosomes, karyotype, metaphase, decreasing, 22, 2n=46, bands, autosomes, sex chromosomes, amnicentesis

4.4 Meiosis: Cell Divisions That Halve Chromosome Number -These mitotically dividing and G0-arrested cells are the so-called ____ ___ whose descendants continue to make up the vast majority of each organism's tissues throughout the lifetime of the individual. -These are ___ __: cells destined for a specialized role in the production of gametes.

somatic cells, germ cells

lacI^s: dominant to lacI+ in trans -LacI^s protein acts in ___. The _____ encoded by lacI^s on the plasmid diffuses and binds to _____ on both the plasmid and the chromosome to repress the lac operon, even if the ____ is present.

trans, superrepressor, operators, inducer

Spermatogenesis in Humans Produces Four Sperm from Each Primary Spermatocyte -The production of sperm, or ______, begins in the male testes in germ cells known as _______. -Human sperm form ____ in the tests after puberty. Spermatogonia are located near the ___ of ____ ___ in a human testis. Once they divide to produce the primary spermatocytes, the subsequent stages of spermatogenesis - meiotic divisions in the spermatocytes and maturation of spermatids into sperm - occur successively closer to the ____ of the tubule. Mature sperm are released into the ___ ___ of the tubule for ejaculation. -Mitotic divisions of the spermatogonia produce many diploid cells, the ____ ____. -Unlike primary oocytes, primary spermatocytes undergo a symmetrical meiosis I, producing two ____ _____, each of which undergoes a symmetrical meiosis II. -At the conclusion of meiosis, each original primary spermatocyte thus yields four equivalent haploid ____. -These spermatids then mature by developing a characteristic whiplike tail and by concentrating all their chromosomal material in a head, thereby becoming functional _____. -A human sperm, much smaller than the ovum it will fertilize, contains 22 autosomes and ___ an X __ a Y sex chromosome.

spermatogenesis, spermatogonia, continually, exterior, seminiferous tubules, middle, central lumen, primary spermatocytes, secondary spermatocytes, spermatids, sperm, either, or

The Dominance or Recessiveness of Mendel's Alleles Reflects the Influence of Molecules on Phenotype -Molecular explanations of Mendel's pea shape and pea color genes. The R allele of the pea shape gene specifies the enzyme Sbe1, which converts unbranched _____ to _____ starch. The r allele does ___ encode ____. The buildup of unbranched starch in rr peas ultimately causes seed ________. The Y allele of the pea color gene specifies the enzyme Sgr, which functions in the pathway to break down ______ during pea maturation, resulting in _____ peas. The y allele does not produce ____. _____ is not broken down in yy peas, and they remain _____.

starch, branched, not, Sbe1, wrinkling, chlorophyll, yellow, Sgr, chlorophyll, green

Cancer Cells Often Acquire a Potential for Immortality -Many cancer cells are "immortal." Most normal somatic cells (except for rare ____ ____) spontaneously stop growing after a specific number of cell divisions. Tumor cells, by contrast, can divide ______. One reason for this difference is that cancer cells often express the enzyme ______, while normal cells do not. -One reason for tumor cells' "immortality" has to do with expression of the enzyme ______.

stem cells, indefinitely, telomerase, telomerase

4.1 Chromosomes: The Carriers of Genes essential concepts -Chromosomes are cellular structures specialized for the ____ and _____ of genetic material. -____ are located on chromosomes and travel with them during ___ ___ and ___ formation. -____ ___ carry a precise number of homologous pairs of chromosomes, which is characteristic of the ___. -In diploid organisms, one homolog of a pair is of ____ origin, and the other paternal.

storage, expression, genes, cell division, gamete, somatic cells, species, maternal

19.2 The Genetic Basis of Cancers -A model for the genetic basis of cancer. Cancer is thought to arise by _____ ____ to ___ ___ within a _____ of ______ cells.

successive mutations, key genes, clone, proliferating

The sum rule -A second rule of probability, the ____ ____, states that the probability of either of two such _____ _____ ____ occurring is the ____ of their individual probabilities. -With mutually exclusive events: Probability of event 1 ___ event 2 = Probability of event 1 ____ probability of event 2

sum rule, mutually exclusive events, sum, or, +

DNA alterations form the basis of genomic evolution -Substitutions occurring in a coding region are silent, or _______, when they have no effect on the amino acid encoded; by contrast, they are ________ when the change in nucleotide determines a change in an amino acid or creates a premature termination codon, leading to a truncated gene product.

synonymous, nonsynonymous

Telophase I: Nuclear envelopes re-form -The telophase of the first meiotic division, or ____ ___, takes place when nuclear membranes begin to form around the chromosomes that have moved to the poles. -Because the number of chromosome is reduced to one-half the normal diploid number, meiosis I is often called the _____ ____. -The relatively brief interphase between meiosis I and meiosis II is known as ______.

telophase I, reductional division, interkinesis

Telophase II: Nuclear membranes re-form, and cytokinesis follows -Membranes form around each of four daughter nuclei in ____ ___, and cytokinesis places each nucleus in a separate cell. -For this reason, meiosis II is termed an _____ ____.

telophase II, equational division

Heterochromatin Can Spread Along a Chromosome and Silence Nearby Euchromatic Genes -Position-effect variegation in Drosophila. When the ____ eye color gene is brought near an area of heterochromatin by chromosomal ______, the eyes of the fly become _______, with some ___ cells and some white cells. A model for position-effect variegation of the w+ and roughest (rst+) genes postulates that heterochromatin can spread ________ from its normal location surrounding the _______ to nearby genes, causing their ______. -Such rearrangements silence w+ gene expression in some cells and not others, producing _______-_____ ______ (____). -The phenomenon of position-effect variegation thus reflects the existence of ________ ________: regions of chromosomes (or even whole chromosomes) that are heterochromatic in some cells and euchromatic in other cells of the same organism.

w+, inversion, variegated, red, linearly, centromere, inactivation, position-effect variegation (PEV), facultative heterochromatin