Chapter 28 Regulation of Gene Expression

Multiple Choice Questions

1. Principles of gene regulation Page: 1082 Difficult : 2 !ns: " Housekeeping genes in bacteria are commonly expressed constitutively, but not all of these genes are expressed at the same level (the same number of molecules per cell). The primary mechanism responsible for variations in the level of constitutive en ymes from different genes is that! ") $) ') () )) all constitutive en ymes are synthesi ed at the same rate, but are not degraded e#ually. their promoters have different affinities for %&" polymerase holoen yme. some constitutively expressed genes are more inducible than others. some constitutively expressed genes are more repressible than others. the same number of m%&" copies are made from each gene, but are translated at different rates.

2. Principles of gene regulation Pages: 1082#108$ Difficult : 2 !ns: D *hich of the follo+ing statements correctly describes promoters in E. coli, ") $) ') () " promoter may be present on either side of a gene or in the middle of it. "ll promoters have the same se#uence that is recogni ed by %&" polymerase holoen yme. )very promoter has a different se#uence, +ith little or no resemblance to other promoters. -any promoters are similar and resemble a consensus se#uence, +hich has the highest affinity for %&" polymerase holoen yme. )) .romoters are not essential for gene transcription, but can increase its rate by t+o/ to three/fold. $. Principles of gene regulation Pages: 108$#108% Difficult : 2 !ns: D The operator region normally can be bound by! ") $) ') () )) attenuator. inducer. m%&". repressor. suppressor t%&".

%. Principles of gene regulation Pages: 108$#108% Difficult : 2 !ns: C 0mall signal molecules that regulate transcription are not kno+n to! ") cause activator proteins to bind (&" sites. $) cause repressor proteins to bind (&" sites. ') directly bind to (&" sites. () prevent activator proteins from binding to (&" sites. )) release repressor proteins from (&" sites.

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Chapter 28 Regulation of Gene Expression

&. Principles of gene regulation Pages: 108$#108& Difficult : 2 !ns: E The diagram belo+ represents a hypothetical operon in the bacterium E. coli. The operon consists of t+o structural genes (" and $), +hich code for the en ymes "/ase and $/ase, respectively, and also includes . (promoter) and 1 (operator) regions as sho+n.

*hen a certain compound (2) is added to the gro+th medium of E. coli, the separate en ymes "/ase and $/ase are both synthesi ed at a 34/fold higher rate than in the absence of 2. (2 has a molecular +eight of about 544.) *hich of the follo+ing statements is true of the operon decribed above, ") "ll four genes (", $, 1, and .) +ill be transcribed into an m%&" that +ill then be translated into four different proteins. $) The 6' end of the m%&" from the operon +ill correspond to the left end of the operon as dra+n. ') The 3' end of the messenger from this operon +ill correspond to the right end of the operon as dra+n. () The repressor for this operon binds 7ust to the right of ". )) *hen %&" polymerase makes m%&" from this operon, it begins %&" synthesis 7ust to the left of gene ". '. Principles of gene regulation Pages: 108$#108& Difficult : 2 !ns: ! The diagram belo+ represents a hypothetical operon in the bacterium E. coli. The operon consists of t+o structural genes (" and $) that code for the en ymes "/ase and $/ase, respectively, and also includes . (promoter) and 1 (operator) regions as sho+n.

*hen a certain compound (2) is added to the gro+th medium of E. coli, the separate en ymes "/ase and $/ase are both synthesi ed at a 34/fold higher rate than in the absence of 2 (+hich has a molecular +eight of about 544). *hich one of the follo+ing statements is true of such an operon, ") $) ') () "dding 2 to the gro+th medium causes a repressor protein to be released from the 1 region. "dding 2 to the gro+th medium causes a repressor protein to bind tightly to the 1 region. 0ynthesis of the m%&" from this operon is not changed by the addition of compound 2. The m%&" copied from this operon +ill be covalently linked to a short piece of (&" at the 3 ' end. )) T+o m%&" molecules are made from this operon, one from gene " the other from gene $. (. Principles of gene regulation Pages: 108&#108( Difficult : 2 !ns: " Transcription of the lactose operon in E. coli is stimulated by! ") $) ') () )) a mutation in the repressor gene that strengthens the affinity of the repressor for the operator. a mutation in the repressor gene that +eakens the affinity of the repressor for the operator. a mutation in the repressor gene that +eakens the affinity of the repressor for the inducer. binding of the repressor to the operator. the presence of glucose in the gro+th medium.

Chapter 28 Regulation of Gene Expression

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8. Principles of gene regulation Page: 1088 Difficult : $ !ns: D .rotein amino acid side chains can hydrogen bond in the ma7or groove of (&", and discriminate bet+een each of the four possible base pairs. 8n +hich one of the follo+ing groups of amino acids can all three members potentially be used in such (&"/protein recognition, ") $) ') () )) "la, "sn, 9lu "rg, 9ln, :eu "sn, 9ln, Trp "sn, 9lu, :ys 9lu, :ys, .ro

). Principles of gene regulation Pages: 1088#108) Difficult : 2 !ns: ! The (&" binding motif for many prokaryotic regulatory proteins, such as the lac repressor, is! ") $) ') () )) helix/turn/helix. homeobox. homeodomain. leucine ipper. inc finger.

10. Principles of gene regulation Pages: 1088#10)1 Difficult : 2 !ns: D .rotein structural motifs often have general functions in common. *hich one of the follo+ing motifs is kno+n to be involved in protein dimer formation, but not in direct protein/(&" interactions, A) $) ') () )) /barrel helix/turn/helix homeodomain leucine ipper inc finger

11. Regulation of gene expression in pro*ar otes Pages: 10)$#10)% Difficult : 2 !ns: ! *hich of the follo+ing statements about regulation of the lac operon is true, ") $) ') () )) 9lucose in the gro+th medium decreases the inducibility by lactose. 9lucose in the gro+th medium does not affect the inducibility by lactose. 9lucose in the gro+th medium increases the inducibility by lactose. 8ts expression is regulated mainly at the level of translation. The lac operon is fully induced +henever lactose is present.

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Chapter 28 Regulation of Gene Expression

12. Regulation of gene expression in pro*ar otes Page: 10)$ Difficult : 2 !ns: ! The binding of '%. (c"-. receptor protein of E. coli) to (&" in the lac operon! ") $) ') () )) assists %&" polymerase binding to the lac promoter. is inhibited by a high level of c"-.. occurs in the lac repressor region. occurs only +hen glucose is present in the gro+th medium. prevents repressor from binding to the lac operator.

1$. Regulation of gene expression in pro*ar otes Page: 10)$ Difficult : 2 !ns: C 'onsider the lac operon of E. coli. *hen there is neither glucose nor lactose in the gro+th medium! ") $) ') () )) '%. protein binds to the lac operator. '%. protein displaces the :ac repressor from the lac promoter. repressor is bound to the lac operator. %&" polymerase binds lac promoter and transcribes the lac operon. the operon is fully induced.

1%. Regulation of gene expression in pro*ar otes Page: 10)% Difficult : 1 !ns: " " regulon is a(n)! ") $) ') () )) group of related triplet codons. net+ork of operons +ith a common regulator. operon that is sub7ect to regulation. protein that regulates gene expression. ribosomal protein that regulates translation.

1&. Regulation of gene expression in pro*ar otes Pages: 10)%#10)& Difficult : 2 !ns: C The tryptophan operon of E. coli is repressed by tryptophan added to the gro+th medium. The tryptophan repressor probably! ") $) ') () )) binds to %&" polymerase +hen tryptophan is present. binds to the trp operator in the absence of tryptophan. binds to the trp operator in the presence of tryptophan. is a (&" se#uence. is an attenuator.

1'. Regulation of gene expression in pro*ar otes Pages: 10)%#10)( Difficult : 2 !ns: ! *hich one of the follo+ing statements about the transcription attenuation mechanism is true, ") $) ') () )) 8n some operons (e.g., the his operon), attenuation may be the only regulatory mechanism. 0e#uences of the trp operon leader %&" resemble an operator. The leader peptide acts by a mechanism that is similar to that of a repressor protein. The leader peptide gene of the trp operon includes no Trp codons. The leader peptide is an en yme that cataly es transcription attenuation.

Chapter 28 Regulation of Gene Expression

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1(. Regulation of gene expression in pro*ar otes Pages: 10)%#10)( Difficult : 2 !ns: D *hich of the follo+ing statements is true of the attenuation mechanism used to regulate the tryptophan biosynthetic operon in E. coli, ") "ttenuation is the only mechanism used to regulate the trp operon. $) 1ne of the en ymes in the Trp biosynthetic path+ay binds to the m%&" and blocks translation +hen tryptophan levels are high. ') The leader peptide plays a direct role in causing %&" polymerase to attenuate transcription. () Trp codons in the leader peptide gene allo+ the system to respond to tryptophan levels in the cell. )) *hen tryptophan levels are lo+, the trp operon transcripts are attenuated (halted) before the operon;s structural genes are transcribed. 18. Regulation of gene expression in pro*ar otes Pages: 10)%#10)( Difficult : $ !ns: " "ttenuation in the trp operon of E. coli: ") $) ') () )) can ad7ust transcription of the structural genes up+ards +hen tryptophan is present. can fine/tune the transcription of the operon in response to small changes in Trp availability. is a mechanism for inhibiting translation of existing (complete) trp m%&"s. results from the binding of the Trp repressor to the operator. results from the presence of short leader peptides at the 3 ' end of each structural gene.

1). Regulation of gene expression in pro*ar otes Pages: 10)(#10)8 Difficult : 2 !ns: D %ec" protein provides the functional link bet+een (&" damage and the 010 response by displacing the :ex" protein from its operator sites on the 010 genes. %ec" does so by! ") $) ') () )) associating +ith polymerase holoen yme to help it remove :ex" from operator. bending :ex" operator (&" to force dissociation of :ex" repressor. binding to :ex" protein to +eaken directly its affinity for operator sites. causing self/cleavage of :ex", thus inactivating its binding to operator. competitively binding to :ex" operators and serving as an activator.

20. Regulation of gene expression in pro*ar otes Pages: 10)8#10)) Difficult : 2 !ns: D "n example of coordinate control is the do+n/regulation of ribosomal %&" synthesis in response to amino acid starvation, +hich +ill cause synthesis of ribosomal proteins to be limited. *hat is the correct order of the follo+ing events that participate in the signaling process, <. $inding of stringent factor to the ribosome. 5. =ormation of the unusual nucleotide pp9pp. 6. =ormation of the unusual nucleotide ppp9pp. >. ?ncharged t%&" binds in the ribosomal "/site. ") $) ') () <, >, 5, 6 <, >, 6, 5 >, <, 5, 6 >, <, 6, 5

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Chapter 28 Regulation of Gene Expression

)) >, 5, <, 6 21. Regulation of gene expression in eu*ar otes Page: 110$#110% Difficult : 2 !ns: " *hich one of the follo+ing statements about eukaryotic gene regulation is correct, ") $) ') () )) :arge polycistronic transcripts are common. -ost regulation is positive, involving activators rather than repressors. Transcription and translation are mechanistically coupled. Transcription does not involve promoters. Transcription occurs +ithout ma7or changes in chromosomal organi ation.

22. Regulation of gene expression in eu*ar otes Page: 110% Difficult : 1 !ns: C *hich of the follo+ing is a (&" se#uence, ") $) ') () )) 'oactivator 'orepressor )nhancer 8nducer Transactivator

2$. Regulation of gene expression in eu*ar otes Page: 110% Difficult : 2 !ns: E *hich one of the follo+ing types of eukaryotic regulatory proteins interact +ith enhancers, ") $) ') () )) $asal transcription factors 'oactivators %epressors T"T"/binding proteins Transactivators

2%. Regulation of gene expression in eu*ar otes Page: 1108 Difficult : 2 !ns: ! *hich one of the follo+ing is not involved in steroid hormone action, ") $) ') () )) 'ell surface receptors Hormone/receptor complexes 0pecific (&" se#uences Transcription activation and repression @inc fingers

2&. Regulation of gene expression in eu*ar otes Page: 1112 Difficult : 2 !ns: C *hich one of the follo+ing classes is expressed in the unfertili ed egg and is involved in directing the spatial organi ation of the Drosophila embryo early in development, ") $) ') () 9ap genes Homeotic genes -aternal genes 0egment polarity genes

Chapter 28 Regulation of Gene Expression

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)) 0egmentation genes 2'. Regulation of gene expression in eu*ar otes Pages: 1112+ 111' Difficult : 2 !ns: " *hich one of the follo+ing classes of genes is involved in specifying the locali ation of organs in the Drosophila embryo, ") $) ') () )) 9ap genes Homeotic genes -aternal genes 0egment polarity genes 0egmentation genes

2(. Regulation of gene expression in eu*ar otes Pages: 1112+ 111' Difficult : 2 !ns: C 8n the development of the fly Drosophila, homeotic genes! ") $) ') () )) are transcribed during egg productionA their m%&"s lie dormant in the egg until it is fertili ed. determine the number of body segments that +ill form. are expressed late and determine the detailed structure of each body segment. generally have no introns. are not translated into proteins.

,hort !ns-er Questions

28. Principles of gene regulation Page: 108$ Difficult : 2 ?sually, a mutation in the promoter region of an operon causes reduced levels of synthesis of the proteins encoded by that operon. 1ccasionally, a mutation in the promoter region actually causes increased levels of synthesis. 'an you suggest (briefly) a plausible explanation, !ns: 8t is possible for a mutation to result in a promoter +ith higher/than/normal affinity for %&" polymerase (i.e., a promoter that more closely matches the promoter consensus se#uence), resulting in increased expression in the mutant of the genes in this operon. 2). Principles of gene regulation Page: 108% Difficult : 2 (escribe and contrast positive regulation and negative regulation of gene expression. !ns: .ositive regulation involves an activator protein that, +hen bound in the vicinity of the regulated gene, facilitates the binding of %&" polymerase to its promoter. The affinity of the activator for the (&" may be either increased or decreased by a signal molecule. &egative regulation involves a repressor protein that, +hen bound near the regulated gene, hinders access of %&" polymerase to its promoter or inhibits its activity. %epressor affinity for its binding site (the operator) may be increased or decreased by a signal molecule. (0ee =ig. 5B/>, p. <4B>.) $0. Principles of gene regulation Pages: 108& Difficult : 2 (efine operon and polycistronic m%&".

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Chapter 28 Regulation of Gene Expression

!ns: "n operon is several contiguous structural genes that are coordinately regulated by promoter and operator regions, as depicted in =ig. 5B/3, p. <4B3. "ll of the genes in an operon are transcribed in a polycistronic m%&"Ca single m%&" molecule encoding more than one structural gene. &ote! operons are not found in eukaryotic organisms. $1. Principles of gene regulation Pages: 1088#10)1 Difficult : 2 -atch the protein or structural feature on the left +ith one appropriate description on the right. DDDD activator DDDD helix/turn/helix DDDD leucine ipper DDDD repressor DDDD inc finger (a) a positive regulator (b) a negative regulator (c) facilitates transcription only +hen bound to a signal molecule (d) a (&"/binding structural motif found in many prokaryotic regulatory proteins (e) a structural feature involved in protein/protein interactions bet+een some regulatory protein monomers (f) a protein that dissociates from (&" +hen bound to a signal molecule (g) a (&"/binding structural motif found in many eukaryotic regulatory proteins

!ns: aA dA eA bA g $2. Regulation of gene expression in pro*ar otes Pages: 108&#108'+ 10)$#10)% Difficult : 2 E. coli cells are placed in a gro+th medium containing lactose. 8ndicate ho+ the follo+ing circumstances +ould affect the expression of the lactose operon (increaseEdecreaseEno change). (a) "ddition of high levels of glucose (b) " :ac repressor mutation that prevents dissociation of :ac repressor from the operator (c) " mutation that inactivates /galactosidase (d) " mutation that inactivates galactoside permease (e) " mutation that prevents binding of '%. to its binding site near the lac promoter !ns: (a) decreaseA (b) decreaseA (c) decrease (this en yme converts lactose into allolactose, the inducer)A (d) decrease (because external lactose +ould not enter the cell, and allolactose +ould not be present to induce the operon)A (e) decrease $$. Regulation of gene expression in pro*ar otes Pages: 108'+ 10)$#10)% Difficult : 2 (ra+ a simple map of the lactose operon indicating the relative positions of promoter, operator, '%./ binding site, repressor gene (8), and the structural genes of the operon (", F, @). 8ndicate +here the '%. protein binds +ithin this operon. *hen it is bound to this site, does the '%. protein have a positive or negative effect on gene expression in this system, !ns: $ound '%. stimulates (has a positive effect on) transcription of this operon. (0ee =ig. 5B/G, p. <4BH, and =ig. 5B/<G, p. <4I6.) $%. Regulation of gene expression in pro*ar otes Pages: 10)$#10)% Difficult : 2 $riefly explain (a) +hy there is a lag in cell gro+th +hen bacteria are s+itched from a medium containing glucose to one containing lactose. (b) *hen the gro+th medium contains both lactose and

Chapter 28 Regulation of Gene Expression

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glucose, +hat proteins +ill be bound to the lac operon regulatory region, (c) 8f only lactose is in the gro+th medium, +hat proteins +ill be bound to the lac operon regulatory region, !ns: (a) The lag represents the time re#uired for lactose to enter the cell, be converted into the inducer allolactose, and turn on the synthesis of the genes of the lac operon that are essential for gro+th on lactose. (b) *hen both glucose and lactose are present, neither :ac repressor nor '%. +ill be bound. (c) 8f only lactose is present, '%. +ill be bound. (0ee =ig. 5B/<B, p.<4I>.) $&. Regulation of gene expression in pro*ar otes Pages: 10)%#10)( Difficutl : $ 8n prokaryotes such as E. coli, many operons that encode en ymes involved in amino acid biosynthesis begin +ith a se#uence coding for a leader peptide. This peptide has no kno+n en ymatic function and is rich in the amino acid that is synthesi ed by the en ymes coded for in the operon. *hat is the function of this leader peptide, !ns: The leader peptide is integral to the regulatory mechanism called transcription attenuation. 8n prokaryotes, transcription and translation are closely coupled. The ability to translate the leader peptide signals that the relevant amino acid is readily available in the cell and that transcription of the operon is undesirable at this time. Translation through the leader peptide (+hen the amino acid is abundant) allo+s the formation of a hairpin attenuator structure do+nstream in the nascent %&" chain. This attenuator acts as a transcription terminator, causing dissociation of the %&" polymerase. *hen the relevant amino acid is in short supply, the ribosome stalls trying to synthesi e the leader peptide. " different secondary structure forms in the nascent %&", preventing formation of the terminator and allo+ing continued transcription of the operon. (0ee =ig. 5B/5<, p.<4IH.) $'. Regulation of gene expression in pro*ar otes Page: 10)(#10)8 Difficult : $ The 010 response in E. coli is triggered by extensive damage to the cell;s (&" and increases the capacity for repairing such (&". *hat molecular events bring about expression of the 010 genes, !ns: The 010 genes are located in several operons, all under the regulation of the :ex" repressor, +hich normally represses these operons. *hen (&" is damaged extensively, %ec" protein binds to single/stranded (&" at the damaged sites, and bound %ec" activates specific proteolysis of the :ex" protein, relieving the repression of the 010 operons. (0ee =ig. 5B/55, p. <4IG.) $(. Regulation of gene expression in pro*ar otes Pages: 10)8#10)) Difficult : $ )xplain ho+ synthesis of ribosomal proteins in E. coli is regulated at the level of translation. !ns: %ibosomal proteins are encoded in several operons. 1ne protein encoded in each operon, +hen not part of an assembled ribosome, binds tightly to that operon;s m%&", preventing its translation. Thus, +hen an excess of that protein is present, it slo+s its o+n translation. (0ee =ig. 5B/56, p. <4II.) $8. Regulation of gene expression in eu*ar otes Pages: 1102#110$ Difficult : 2 (escribe briefly the relationship bet+een chromatin structure and transcription in eukaryotes. !ns: Heterochromatin is highly condensed and transcriptionally inert because the chromatin proteins make promoters inaccessible. The less condensed euchromatin has undergone alteration of its structure (remodeling), allo+ing some regions to be transcribed. These alterations include covalent modification (such as acetylation) of histones and displacement of nucleosomes, creating exposed regions of (&" (hypersensitive sites) that are probably binding sites for regulatory proteins.

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Chapter 28 Regulation of Gene Expression

$). Regulation of gene expression in eu*ar otes Pages: 1102#110% Difficult : 2 (efine each in about t+o sentences! (a) hypersensitive sites in eukaryotic chromosomesA (b) enhancers (upstream activator se#uences)A (c) chromatin remodeling. !ns: (a) " hypersensitive site is a region of eukaryotic (&" that is being associated +ith actively transcribed (&" and is unusually sensitive to degradation by nucleases. (b) )nhancers are (&" se#uences that regulate the transcription of certain genes by allo+ing binding of specific transactivator proteins. These se#uences may occur thousands of base pairs a+ay from the gene +hose transcription they regulate. (c) 'hromatin remodeling reflects structural changes resulting from en ymes that covalently modify the core histone complex in nucleosomes (such as histone acetyltransferases) and those that move or displace nucleosomes using the energy of "T. hdyrolysis. (0ee Table 5B/5, p. <<46.) %0. Regulation of gene expression in eu*ar otes Page: 110% Difficult : 1 (escribe in one or t+o sentences the role of each of the follo+ing types of proteins in the regulation of gene expression in eukaryotes! (a) basal transcription factorsA (b) transactivatorsA (c) coactivators. !ns: (a) $asal transcription factors interact +ith specific (&" se#uences andEor each other andEor +ith %&" polymerase to form a complex at promoters. (b) Transactivators interact +ith both target sites on (&" and +ith other regulatory proteins such as coactivators to activate transcription. (c) 'oactivators interact +ith transactivators and proteins at the promoters to activate transcription. %1. Regulation of gene expression in eu*ar otes Pages: 110'#1108 Difficult : 2 (&"/binding transactivating proteins often possess a domain separate from their (&"/binding domains that serves as a docking site for interactions +ith the transcription complex, coactivators, corepressors, or even chromatin remodeling proteins, to regulate gene transcription. (escribe three kno+n kinds of such domains, and provide an example of each. !ns: (<) 9al>p (in yeast) has an acidic activation domain rich in aspartic and glutamic acid, (5) 0p< in higher eukaryotes has t+o activation domains comprised of about 53J glutamine, and (6) 'T=< has a proline/rich (K54J) activation domain. %2. Regulation of gene expression in eu*ar otes Pages: 1108#110) Difficult : 2 (escribe briefly the process by +hich steroid hormones affect gene expression. !ns: 0teroid hormones usually enter a cell by diffusion and then bind to a nuclear receptor protein. The binding changes the conformation of the receptor protein such that the hormone/receptor complex can bind to specific (&" se#uences (hormone response elements). This binding can either activate or repress the expression of ad7acent genes. %$. Regulation of gene expression in eu*ar otes Page: 1110 Difficult : 1 *hat are three mechanisms of translational repression that are kno+n to exist in eukaryotes, !ns: (a) inactivation of initiation factors usually by phosphorylationA (b) binding of repressor proteins

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to the m%&", thereby interfering +ith initiation factors or the ribosomeA (c) interference +ith elongation by the binding of proteins to elongation factors. %%. Regulation of gene expression in eu*ar otes Pages: 1110#1111 Difficult : 2 :arge numbers of micro/%&"s (mi%&"s), also kno+n as small temporal %&"s (st%&"s) have no+ been discovered in higher eukaryotes. (escribe their characteristics and general function. !ns: Their primary transcripts are about G4 nucleotides, +ith self/complementary internal se#uences that can form hairpin structures. These are cleaved into 54/53 nt partial duplexes, one strand of +hich can bind to complementary stretches in cellular m%&"s. This can then inhibit gene expression by blocking translation of the target m%&" or facilitating its degradation. %&. Regulation of gene expression in eu*ar otes Pages: 1112#111' Difficult : 1 (escribe briefly the general role of the protein products of each of the follo+ing types of genes in the embryonic development of the Drosophila: (a) maternal genesA (b) segmentation genesA (c) homeotic genes. !ns: (a) " maternal gene in Drosophila is a gene that is expressed in the unfertili ed egg (see =ig. 5B/6H, p. <<<>). These genes are involved in directing the spatial organi ation of the Drosophila embryo early in development. (b) 0egmentation genes direct the formation of the correct number of body segments, and include the gap genes, pair/rule genes, and segment polarity genes as subclasses. (c) Homeotic genes help specific locali ation of organs and appendages in the segments of the embryo. They regulate their target genes by highly conserved (&"/binding homeodomains, depicted in =ig. 5B/<6, p. <4I4.