Chapter 15, 17, 18, 19 Flashcards
A model proposed by Jacob and Monod whereby a group of genes is regulated and expressed together as a unit.
Operon model
How does lacI gene regulate the transcription of the structural genes?
By producing a repressor molecule, and that the repressor is allosteric, meaning that it reversibly interacts with another molecule, causing both a conformational change in the repressor’s three-dimensional shape and a change in its chemical activity.
Because transcription occurs only when the
repressor fails to bind to the operator region, regulation is said to be under?
negative control
If a regulator gene needs to be located adjacent to the gene it regulates, it is said to be?
cis-acting factor (example: O region in lac operon)
If a regulator gene does not need to be located adjacent to the gene it regulates, it is said to be?
trans-acting factor (example: I gene in lac operon)
A molecule called the catabolite-activating protein (CAP) helps activate expression of the lac operon but is able to inhibit expression when glucose is present. This inhibition is called?
catabolite repression
True or False. For maximal transcription of the structural genes, the repressor must be bound by lactose (so as not to repress lac operon transcription), and CAP must be bound to the CAP-binding site.
True
This enzyme catalyzes the conversion of ATP to cyclic adenosine monophosphate.
adenyl cyclase
What is the role of glucose in catabolite expression?
inhibits the activity of adenyl cyclase
When both RNA polymerase and cAMP-CAP complex are together in the presence of the lac promoter DNA, a tightly bound complex is formed. This is an example of a phenomenon called?
cooperative binding
Tryptophan is referred to as ____ because is participates in the repression of genes coding tryptophan synthesizing enzymes.
corepressor
When tryptophan is present and the trp operon is repressed, initiation of transcription still occurs at a low level but is subsequently terminated at a point
about 140 nucleotides along the transcript. This process is called?
Attenuation
The site involved in attenuation is located 115 to 140 nucleotides into the leader sequence and is referred to as?
Attenuator region
The initial DNA sequence that is transcribed gives rise to an mRNA sequence that has the potential to fold into two mutually exclusive stem-loop structures referred to as?
hairpins
In the presence of excess tryptophan, the mRNA hairpin that is formed behave as a ____ structure, and transcription is almost always terminated prematurely, just beyond the attenuator.
terminator hairpin
If tryptophan is scarce, an alternative mRNA
hairpin referred to as the ______ is formed.
antiterminator hairpin
Biosynthesis of which amino acids uses attenuation as regulatory mechanism?
- tryptophan
- threonine
- histidine
- leucine
- phenylalanine
Are mRNA sequences (or elements) present in the
5’-untranslated region (5’-UTR) upstream from the coding sequences. These elements are capable of binding with small molecule ligands, such as metabolites, whose synthesis or activity is controlled by the genes encoded by the mRNA.
riboswitches
It is the ligand binding site within a riboswitch.
aptamer
It one of the domains of a riboswitch capable of forming the terminator structure.
expression platform
True of False. Eukaryotic gene expression is influenced by chromatin modification.
True
In the interphase nucleus, each chromosome occupies a discrete domain called a _______ and stays separate from other chromosomes.
chromosome territory
Channels between chromosomes contain little or no DNA and are called ____?
interchromosomal domains.
Are nuclear sites at which most RNA polymerase II transcription occurs. These sites also contain the majority of active RNA polymerase and other transcription factors.
transcription factory
True or False. The tight association of DNA with nucleosomes and other chromatin-binding proteins inhibits access of the DNA to the proteins involved in many functions, including transcription.
True
True or False. Acetylation decreases the positive charge on histones, resulting in a reduced affinity of the histone for DNA. In turn, this may assist the formation of open chromatin conformations, which would allow the binding of transcription regulatory proteins to DNA.
True
Histone acetylation is catalyzed by which enzyme? They are recruited to genes by the presence of certain transcription activator proteins that bind to transcription regulatory regions.
histone acetyltransferase enzymes (HATs).
This enzymes reverses the action of HAT by removing acetyl groups from histone tails. They are recruited to genes by the presence of certain repressor proteins on regulatory regions.
histone deacetylases
HDACs
Are large multi-subunit complexes that use the energy of ATP hydrolysis to move and rearrange nucleosomes along the DNA.
Chromatin remodeling complexes
True or False. Repositioned nucleosomes make regions of the chromosome accessible to transcription regulatory proteins, such as transcription activators and RNA polymerase II.
True
Addition or removal of methyl groups to or from bases in DNA. Cytosine is most often involved.
DNA methylation
True or False. A direct relationship exists between the degree of methylation and the degree of expression.
False. Inverse
True or False. Methylation patterns are tissue specific and, once established, are heritable for all cells of that tissue.
True
True or False. Data from in vitro studies suggest that methylation can repress transcription by inhibiting the binding of transcription factors to DNA. Methylated DNA may also recruit repressive chromatin remodeling complexes to gene-regulatory regions.
True
It is a region of DNA that binds one or more proteins that regulate transcription initiation. It is located immediately adjacent to the genes they regulate.
Promoter
Are short nucleotide sequences located within promoters that bind specific regulatory factors.
Promoter elements
A eukaryotic promoter element that determines the accurate initiation of transcription by RNA polymerase II.
core promoter
A eukaryotic promoter element that modulates
the efficiency of basal levels of transcription.
proximal promoter elements
Type of core promoter that specifies transcription initiation at a single specific nucleotide (the transcription start site).
Focused promoters
Type of core promoter that direct initiation from
a number of weak transcription start sites located over a 50- to 100-nucleotide region.
dispersed promoters
True or False. Focused promoters are usually associated with genes whose transcription levels are highly regulated, whereas dispersed promoters are associated with genes that are transcribed constitutively.
True
True or False. Focused promoters are usually found within CG-rich regions, suggesting that chromatin modifications may influence initiation from these promoters.
False. Dispersed promoters
What are the components of focused promoters?
- BRE (TFIIB recognition site)
- TATA (TATA Box)
- Inr (initiator element)
- MTE (motif ten element)
- DPE (downstream promoter element)
True or False. Core-promoter elements are usually located between -40 and +40 nucleotides, relative to the transcription start site, indicated as +1. None of these elements is universal, and a core promoter may contain only one, or several, of these elements.
True
This core promoter element encompasses the transcription start site, from approximately nucleotides -2 to +4, relative to the start site.
Inr element
What is the Inr consensus sequence?
YYANA/TYY where Y is any pyrimidine and N indicates any nucleotide.
Located at approximately -30 relative to the transcription start site and has the consensus sequence TATAA/TAAR (where R indicates any purine nucleotide).
TATA box
Core promoter element usually found in some core promoters at positions either immediately upstream or downstream from the TATA box.
BRE
Is a common proximal-promoter element located about 70 to 80 base pairs upstream from the start site. Mutations on either side of this element have no effect on transcription, whereas mutations within the CAAT sequence dramatically lower the rate of transcription.
CAAT box (consensus sequence: CAAT or CCAAT)
A proximal-promoter element often found in proximal promoter regions and has the consensus sequence GGGCGG. It is located, in one or more copies, at about position -110.
GC Box
A type of cis-acting transcription regulatory element that acts upon eukaryotic genes to repress the level of transcription initiation. They are short DNA sequence elements that affect the rate of transcription initiated from an associated promoter. They often act in tissue- or temporal-specific ways to control gene expression.
silencers
Transcription factors that increase the levels of transcription initiation and are known as?
Activators
Transcription factors that reduce the levels of transcription initiation and are known as?
Repressors
The product of this gene is a protein that binds
to heavy metals such as zinc and cadmium, thereby protecting cells from the toxic effects of high levels of these metals.
The human metallothionein IIA gene (hMTIIA)
General transcription factors assemble at the promoter region in a specific order, forming a structure called?
transcriptional pre initiation complex (PIC); provides a platform for RNA polymerase to recognize and bind to the promoter.
The first step in the formation of a pre-initiation complex is the binding of ____ to the TATA box of the core promoter. It is a multi-subunit complex that contains TBP (TATA Binding Protein) and approximately 13 proteins called TAFs (TBP Associated Factors).
Transcription Factor II D (TFIID)
In this model on how transcription activators and repressors bring about changes to RNA polymerase II transcription, enhancer and silencer elements act as donors that increase the concentrations of important regulatory proteins at gene promoters. By enhancing the rate of PIC assembly or stability, or by accelerating the release of RNA polymerase II from a promoter, transcription activators bound at enhancers may stimulate the rate of transcription initiation.
Recruitment model
In recruitment model, to make contact with promoter-bound factors, activators are thought to interact with other proteins called coactivators to form a complex known as an ______.
Enhanceosomes
This model of transcription activation and repression states that enhancer or repressor looping may relocate a target gene to a nuclear region that is favorable or inhibitory to transcription.
Nuclear relocation model
Modifications of eukaryotic nuclear RNA transcripts prior to translation are called?
posttranscriptional regulation
Regulatory modifications of eukaryotic nuclear RNA transcripts prior to translation are called?
posttranscriptional regulation
Posttranscriptional regulation includes what processes?
- removal of noncoding introns
- precise splicing together of the remaining exons
- the addition of a cap at the mRNA’s 5’ end and a poly-A tail at its 3’-end.
This splicing mechanism can generate different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins with similar or different functions.
Alternative splicing
True or Fasle. In thyroid cells, the calcitonin/calcitonin gene-related peptide (CT/CGRP) gene primary transcript is spliced in such a way that the mature mRNA contains the first four exons
only.
True
Refers to the proteins that an organism can make.
proteome
It is caused by the expansion of the trinucleotide
repeat CTG in the 3’-untranslated region of the DMPK gene. In unaffected individuals, the DMPK gene contains between 5 and 35 copies of the CTG repeat sequence, whereas in individuals affected by this disease, the gene contains between 150 and 2000 copies. The severity of the symptoms is directly related to the number of copies of the repeat sequence.
myotonic dystrophy 1
It is caused by an expansion of the repeat sequence CCTG within the first intron of the ZNF9 gene. Affected individuals may have up to 11,000 copies of the repeat sequence in the ZNF9 intron. The
severity of symptoms is not related to the number of repeats.
myotonic dystrophy 2
Defects in the regulation of RNA splicing.
spliceopathies
The ______ of an mRNA is its amount in the cell as determined by a combination of the rate at which the gene is transcribed and the rate at which the mRNA is degraded.
steady-state level
True or False. Most mRNA molecules become unstable in cells that are treated with translation inhibitors.
False. stable
The presence of premature stop codons in the body of an mRNA, as well as premature translation termination, causes rapid degradation of mRNAs.
True
True or False. Many of the ribonucleases and mRNA-binding proteins that affect mRNA stability associate with ribosomes.
True
Are a stretch of ribonucleotides that consist of A and U ribonucleotides. These are usually located in the 3’-untranslated regions of mRNAs that have short, regulated half-lives.
Adenosine-uracil rich elements
True or False. In cells that are not growing or require low levels of gene expression, specific complexes bind to the ARE elements of these mRNA molecules, bringing about shortening of the poly-A tail and rapid mRNA degradation.
True
True or False. Under normal conditions, the levels of p53 protein are extremely high in cells, and the p53 that is present is inactive. When cells suffer DNA damage or metabolic stress, the amount of p53 protein increases dramatically, and p53 becomes an active transcription factor.
False. In normal circumstances levels of p53 protein are extremely low.
Are small protein that tags other proteins for degradation by proteolytic enzymes.
Ubiquitin
In unstressed cells, p53 is bound by another protein called ____.
Mdm2
True of False. When cells are stressed, Mdm2 and p53 become modified by phosphorylation and acetylation, resulting in the release of Mdm2 from p53. As a consequence, p53 proteins become stable, the levels of p53 increase, and the protein is able to act as a transcription factor.
True
First discovered in plants, they are now known to regulate gene expression in the cytoplasm of plants, animals, and fungi by repressing translation and triggering the degradation of mRNAs.
small noncoding RNA (sncRNAs)
First discovered in plants, sncRNAs are now known to regulate gene expression in the cytoplasm of plants, animals, and fungi by repressing translation and triggering the degradation of mRNAs. This form of sequence-specific posttranscriptional regulation is known as _____.
RNA interference (RNAi)
The sncRNAs have been shown to act in the nucleus to alter chromatin structure and bring about repression of transcription. This phenomenon is known as
RNA-induced gene silencing
Methods used to copy or clone DNA are called ____ and often known as “gene splicing”.
Recombinant DNA technology
Are produced by bacteria as a defense mechanism against infection by bacteriophage. They restrict or prevent viral infection by degrading the DNA of invading viruses.
Restriction enzyme
A restriction enzyme recognizes and binds to DNA at a specific nucleotide sequence called a?
recognition sequence or restriction site
A form of symmetry where the nucleotide sequence reads the same on both strands of the DNA when read in the 5’ to 3’ direction.
Palindrome
Enzymes such as EcoRI and HindIII make offset cuts in the DNA strands, thus producing fragments with single-stranded overhanging ends called?
cohesive ends (or “sticky” ends)
AluI and BalI cut both strands at the same nucleotide pair, producing DNA fragments with double-stranded ends called?
blunt-end fragments
It is a DNA molecules that accept DNA fragments and replicate these fragments when vectors are introduced into host cells.
Cloning vectors
To distinguish host cells that have taken up vectors from host cells that have not, the vector contains a _____ (usually an antibiotic resistance gene or a gene that encodes a protein which produces a visible product, such as color or fluorescent light).
selectable marker gene
It is the process by which plasmid cloning vector are introduced to the host cell.
transformation
This transformation technique uses a brief, but high-intensity, pulse of electricity to move DNA into bacterial cells.
electroporation
Plasmid vectors have also been genetically engineered to contain a number of restriction sites for commonly used restriction enzymes
in a region called?
multiple cloning sites
Process of selecting and identifying bacteria containing recombinant plasmids.
“blue-white” screening
Phage vectors are recombinant versions of what bacteriophage?
bacteriophage lambda
These vectors are designed to ensure mRNA expression of a cloned gene with the purpose of producing many copies of the gene’s encoded protein in a host cell.
expression vectors
This bacterium is commonly utilized to introduce genes into plant cells. It infects plant cells and produces tumors called crown galls.
Rhizobium radiobacter
Represent a collection of cloned DNA.
DNA libraries
Consists of many overlapping fragments of the genome, with at least one copy of every DNA sequence in an organism’s genome, which in summary span the entire genome.
Genomic libraries
Contains DNA copies which are made from mRNA molecules isolated from cultured cells or a tissue sample. Thus, it contains only expressed genes.
Complementary DNA (cDNA) libraries
Methods that allow for sorting through a library and isolate specific genes of interest,
library screening
Is any DNA or RNA sequence that is complementary to some part of a cloned sequence present in the library—the target gene or sequence to be identified.
Probe
One complete polymerase chain reaction is called?
cycle
The double-stranded DNA to be amplified is denatured into single strands by heating to 92−95°C for about 1 minute. This process is called?
Denaturation
The temperature of the reaction is lowered to a temperature between 45°C and 65°C, which causes primer binding to the denatured, single-stranded DNA. This process is called
Hybridization or Annealing
Polymerase chain reaction is automated by instruments called ____ or simply PCR machines, that can be programmed to carry out a predetermined number of cycles.
thermocyclers
This enzyme is capable of tolerating extreme temperature changes and was the first thermostable polymerase used for PCR.
Taq polymerase (derived from Thermus aquaticus)
Applications of PCR:
- to synthesize allele-specific probes for genetic testing;
- a key diagnostic methodology for detecting bacteria and viruses (such as hepatitis or HIV) in humans, and pathogenic bacteria such as E. coli and Staphylococcus aureus in contaminated food
A powerful methodology for studying gene expression, that is, mRNA production by cells or tissues.
Reverse transcription PCR (RT-PCR)
This approach makes it possible to determine the amount of PCR product made during an experiment, which enables researchers to quantify amplification reactions as they occur in “real time” without having to run a gel.
quantitative real-time PCR (qPCR)
It establishes the number of, order of, and distances between restriction-enzyme cleavage sites along a cloned segment of DNA, thus providing information about the length of the cloned insert and the location of restriction-enzyme cleavage sites within the clone.
Restriction mapping
This method can be used to identify which clones in a library contain a given DNA sequence and to characterize the size of the fragments. This can also be used to identify fragments carrying specific genes in genomic DNA digested with a restriction enzyme.
Southern blot
Two steps of Southern blotting:
- gel electrophoresis and hybridization (to characterize the number of fragments produced by restriction digestion of relatively small pieces of DNA and to estimate their molecular weights)
- and hybridization of the fragments using labeled probes (identification of specific fragments)
RNA blotting was subsequently called?
Northern blotting
Blotting technique involving blotting is called?
Western blotting
Provides information about the expression of specific genes and are used to study patterns of gene expression in embryonic tissues, cancer, and genetic disorders.
Northern blotting
True or False. Northern blots also detect alternatively spliced mRNAs (multiple types of transcripts derived from a single gene) and can be used to derive other information about transcribed mRNAs such as the size of a gene’s mRNA transcripts, measuring band density and the amount of mRNA expressed by a gene.
True
A powerful tool that involves hybridizing a probe directly to a chromosome or RNA without blotting.
fluorescence in situ hybridization or FISH
Variations of the FISH technique are also used to produce ____ in which individual chromosomes can be detected using probes labeled with dyes that will fluoresce at different wavelengths.
spectral karyotypes
The most commonly used method of DNA sequencing was developed by Fred Sanger and his colleagues and is known as _____.
dideoxynucleotide chain-termination sequencing or simply Sanger sequencing.
Groups of genes that share similar but not identical DNA sequences through duplication and descent from a single ancestral gene. Their gene products frequently have similar functions, and the genes are often, but not always, found at a single chromosomal locus.
multigene families
Bacteria also adapt to their environment, producing certain enzymes only when specific chemical substrates are present. These enzymes are referred to as?
inducible enzyme
Bacteria also adapt to their environment, producing certain enzymes only when specific chemical substrates are present. These chemical substrates are considered to be the?
Inducers
Enzymes that are produced continuously, regardless of the chemical makeup of the environment, are called?
Constitutive enzyme
Tryptophan expression is said to be_____ because a high level of tryptophan in the environment inhibits the genes coding for the necessary biomolecules for tryptophan synthesis.
Repressible
Under ____ control, gene expression occurs unless it is shut off by some form of a regulator molecule.
negative
Under _____ control, transcription occurs only if a regulator molecule directly stimulates RNA production.
positive
Genes coding for the primary structure of the
enzymes are called?
Structural genes
What are the three structural genes in the lac operon?
- lacZ
- lacY
- lacA
The gene lacZ, one of the structural genes in the lac operon codes for _____, an enzyme whose role is to convert the disaccharide lactose to the monosaccharides glucose and galactose
B-galactosidase
The gene lacY one of the structural genes in the lac operon codes for _____, an enzyme that facilitates the entry of lactose into the bacterial cell.
Permease
The gene lacA one of the structural genes in the lac operon codes for ____, which is involved in the removal of toxic by-products of lactose digestion from the cell.
Transacetylase
Mutant cells that fail to produce active b-galactosidase (lacZ-) or permease (lacY-) are unable to use lactose as an energy source and are collectively known as?
lac^- mutant
True or False. All three genes in the lac operon region are transcribed as a single unit, resulting in a polycistronic mRNA. This results in the coordinated regulation of all three genes, since a single messenger RNA is simultaneously translated into all three gene products.
True
These are chemical analogs of lactose. Examples include sulfur analog isopropylthiogalactoside. They behave like natural inducers, but they do not serve as substrates for the enzymes that are subsequently synthesized.
gratuitous inducers
At the cellular level, development is marked by three important events, namely:
- Specification
- Determination
- Differentiation
This stage of development occurs when the first cues confer spatial identity.
Specification
This stage of development occurs when a specific developmental fate for a cell becomes fixed.
Determination
The process by which a cell achieves its final adult form and function.
Differentiation
Laid the foundation for our understanding of developmental events at the molecular and cellular levels, which contribute to the continually changing phenotype of the newly formed organism.
developmental genetics
The attainment of a differentiated state by all the cells of an organism
development
True or False. Development involves progressive
activation of different groups of gene sets in different cells of the embryo. Development depends on patterns of differential gene expression.
True
The idea that differentiation is accomplished by activating and inactivating genes at different times and in different cell types is called the?
variable gene activity hypothesis
Underlying assumptions of variable gene activity
hypothesis:
- each cell contains an entire genome
2. differential transcription of selected genes controls the development and differentiation of each cell.
True or False. In multicellular organisms, the genes involved with development have been conserved throughout evolution, along with the patterns of differential transcription, and the ensuing developmental mechanisms.
True
True or False. Genetic analysis of development across a wide range of organisms has shown that the size and shape of all animal bodies are controlled by different sets of genes and developmental mechanisms.
False. Common sets of genes and developmental mechanisms.
Most of the differences in anatomical structures between organisms as diverse as zebras and zebrafish result from different patterns of expression in a single gene set, called the?
Homeotic (Hox) gene
Studies comparing developmental processes in different organisms:
evolutionary developmental biology
True or False. Although many developmental mechanisms are common to all animals, over evolutionary time, several new and unique ways of transforming a zygote into an adult have appeared.
True
Cells with multiple nuclei are called?
syncytium
True or False. In the development of D. melanogaster, germ cells, which in the adult, are destined to undergo meiosis and produce gametes, form at the anterior pole of the embryo
False. Posterior
In the development of D. melanogaster, nuclei in other regions of the embryo normally form somatic cells.
True
True or False. Transcriptional programs activated by cytoplasmic components in somatic (non–germ-cell) nuclei form the embryo’s anterior–posterior (front to back) and dorsal– ventral (upper to lower) axes of symmetry, leading to the formation of a segmented embryo
True
Two different gene sets control embryonic development in Drosophila:
- maternal-effect gene
2. zygotic genes
In the development of D. melanogaster, products of gene set are placed in the cytoplasm of the
developing egg.
maternal-effect gene
True or False. Female flies homozygous for deleterious recessive mutations of maternal-effect genes are sterile. None of their embryos receive wild-type maternal gene products, so all of the embryos develop abnormally and die.
True
In the development of D. melanogaster, the products of this gene set are those transcribed in the embryonic nuclei formed after fertilization.
Zygotic gene
True or False. In the development of D. melanogaster, products of zygotic genes are differentially transcribed in specific regions of the embryo in response to the distribution of maternal-effect proteins.
True
Segmentation genes group into three namely:
gap, pair-rule, and segment polarity genes
Wieschaus proposed a model in which embryonic development is initiated by gradients of maternal-effect gene products. Then, the positional information laid down by these gradients is interpreted by two sets of zygotic (embryonic) genes namely,
- segmentation genes
2. homeotic selector (Hox) gene
This set of zygotic gene divide the embryo into a series of stripes or segments and define the number, size, and polarity of each segment.
segmentation genes
This set of zygotic gene specifies the developmental fate of cells within each segment as well as the adult structures that will be formed from each segment.
homeotic genes
In the development of D. melanogaster, many maternal genes products encode transcription factors that activate _____, whose expression divides the embryo into regions corresponding to the head, thorax, and abdomen of the
adult
gap genes
In the development of D. melanogaster, the activated gap genes encode other transcription factors that activate ___, whose products divide the embryo into smaller regions about two segments wide.
pair-rule genes
In the development of D. melanogaster, expression of the ____ activates the segment polarity genes, which divide each segment into anterior and posterior regions
pair-rule genes
In the development of D. melanogaster, the collective action of the maternal genes and the segmentation genes define the anterior-posterior axis, which is the field of action for the
homeotic (Hox) genes
True
True or False. In D. melanogaster, mutations in gap genes delete a group of adjacent segments, causing gaps in the normal body plan of the embryo,
True
True or False. In D. melanogaster, mutations in pair-rule genes affect every other segment and eliminate a specific part of each affected segment.
True
True or False. In D. melanogaster, mutations in segment polarity genes cause defects in portions of each segment.
True
This mutation in the gap genes lose head and thorax structures.
Hunchback mutants
This mutation in the gap genes lose most abdominal structures..
knirps mutants
This mutation in the gap genes lose thoracic and abdominal structures.
Krüppel mutants
True or False. Gap genes encode transcription factors that bind to enhancer regions that control the expression of pair-rule genes.
True
These genes expressed in a series of seven narrow bands or stripes of nuclei extending around the circumference of the embryo.
Pair-rule genes
Expression of pair-rule genes does two things namely,
- establishes the boundaries of segments
- programs the developmental fate of the cells within each segment by controlling expression of the segment polarity genes.
Expression of segment polarity genes is controlled by transcription factors encoded by ____.
pair-rule genes.
The products of the ____ control the cellular identity within each of them and establish the anterior–posterior pattern (the polarity) within each segment.
segment polarity genes
This is one of the pair-rule genes in Drosophila. Later in development, it controls aspects of sex determination and the formation of the nervous system. The gene encodes a protein that regulates the transcription of its target genes.
runt gene
Runt contains a 128-amino-acid DNA-binding region, called the ____ that is highly conserved in Drosophila, mouse, and human proteins.
runt domain
True or False. Although the target gene sets controlled by runt are different in Drosophila and the mouse, in both organisms, expression of runt specifies the fate of uncommitted cells in the embryo by regulating transcription of target genes.
True
This is the human homolog of runt. Mutations in this gene causes cleidocranial dysplasia (CCD), an autosomal dominantly inherited trait.
RUNX2
Those affected with CCD have a hole in the top of their skull because bone does not form in the membranous gap known as the ____.
fontanel
Expression of _____ determines which adult structures will be formed by each body segment.
homeotic selector genes
Wild-type allele of the homeotic selector gene ___ specifies formation of a leg on the second segment of the thorax.
Antennapedia (Antp)
Mutations in Hox selector genes are called?
homeotic mutations
This cluster in the Drosophila homeotic selector gene (chromosome 3) contains five genes that specify structures in the head and first two segments of the thorax.
Antennapedia (ANT-C) cluster
This cluster in the Drosophila homeotic selector gene (chromosome 3) contains three genes that specify structures in the second and third segments of the thorax, and the abdominal segments.
bithorax (BX-C) complex
Two properties of Hox genes common in winde range of species:
- each contains a highly conserved 180-bp nucleotide sequence known as a homeobox
- In most species, expression of Hox genes is colinear with the anterior to posterior organization of the body.
A highly conserved 180-bp nucleotide sequence in Hox genes.
homeobox
Homeobox encodes a DNA-binding region of 60 amino acids known as?
homeodomain
This is caused by mutations in the human Hox gene, HOXD13, a malformation characterized by extra fingers and toes, and abnormalities in bones of the hands and feet
synpolydactyly (SPD)
Hox genes that program a cell to follow one of the two developmental pathways. These genes, which encode transcription factors, are defined by their ability to initiate complete development of an organ or a tissue type and are part of gene-regulatory networks (GRNs) and subnetworks that program transcription of gene sets at specific times and specific stages of tissue and organ formation.
binary switch genes
Hox genes that program a cell to follow one of the two developmental pathways. These genes, which encode transcription factors, are defined by their ability to initiate complete development of an organ or a tissue type and are part of gene-regulatory networks (GRNs) and subnetworks that program transcription of gene sets at specific times and specific stages of tissue and organ formation.
binary switch genes
A cluster of undifferentiated cells, called the _____, gives rise to flowers
floral meristem
What class of genes acts to specify sepals in plants?
class A
Which class/es of genes acts to specify petals in plants?
class A and B
Which class/es of genes acts to specify stamen formation in plants?
class B and C
Which class/es of genes acts to specify carpels in plants?
class C
True or False. During flower development class A genes are active in whorls 1 and 2 (sepals and petals), class B genes are expressed in whorls 2 and 3 (petals and stamens), and class C genes are expressed in whorls 3 and 4 (stamens and carpels).
True
Mutation in this plant homeotic selector gene causes abnormal arrangements of the flower parts wherein the order of organs is carpel, stamen, stamen, and carpel instead of the normal order, sepal, petal, stamen, and carpel.
APETALA2 mutants (ap2)
Mutations in these class B plant homeotic selector genes causes petals to become sepals, and stamens are transformed into carpels, and the order of organs becomes sepal, sepal, carpel, carpel.
class B loss-of-function mutants (ap3, pi)
Plants carrying a mutation for the
Class 3 gene _____ will have petals in whorl 3 (instead of stamens) and sepals in whorl 4 (instead of carpels), and the order of organs will be sepal, petal, petal, and sepal.
AGAMOUS
This signaling pathway works through direct cell–cell contact to control the developmental fate of interacting cells.
Notch signaling pathway
This gene encodes a receptor protein embedded in the plasma membrane.
Notch gene
The signal specific for membrane protein receptor encoded by the notch gene is encoded by which gene?
Delta gene
True or False. Because both the signal and receptor are membrane proteins, the Notch signal system
works only when adjacent cells come into physical contact.
True
When the Delta protein from one cell binds to the Notch receptor protein on a neighboring cell, the cytoplasmic tail of the Notch protein is cleaved off and binds to a cytoplasmic protein encoded by the ____.
Su(H) (suppressor of Hairless) gene
Which signaling pathway is used for the: Dorsalization of body, Female reproductive development, Dorsal–ventral differences?
Wnt Pathway
Which signaling pathway is used for the: Mesoderm induction, Left–right asymmetry, Bone development?
TGF-B Pathway
Which signaling pathway is used for the: Notochord induction, Somitogenesis, Gut/visceral mesoderm
Hedgehog Pathway
Which signaling pathway is used for the: Mesoderm maintenance
Receptor Tyrosine Kinase Pathway
Adults sexes in C. elegans include:
- XX self-fertilizing hermaphrodites
2. XO males
Adult C. elegans hermaphrodites lay eggs through the ___, an opening near the middle of the body
vulva
In C. elegans, interaction between two neighboring cells, _____, determines which will become the gonadal anchor cell (from which the vulva forms) and which will become a precursor to the uterus.
Z1.ppp and Z4.aaa
In vulvu development in C. elegans, the determination of which cell becomes which occurs during the second larval stage (L2) and is controlled by?
Notch receptor gene, lin-12
True or False. In recessive lin-12(0) mutants (a loss-of-function mutant), no functional receptor protein is present, and both cells become anchor cells.
True
True or False. The dominant mutation lin-12(d) (a gain-of-function mutation) causes both to become uterine precursors.
True
True or False. Expression of lin-12 directs selection of the uterine pathway because in the absence of the LIN-12 (Notch) receptor, both cells become anchor cells.
True
Once the gonadal anchor cell has been determined, a second round of cell–cell interaction leads to formation of the vulva. This interaction involves the anchor cell (located in the gonad) and six neighboring cells (called precursor cells) located in the skin. The precursor cells, named P3.p to P8.p, are called
Pn.p cells
True or False. The developmental fate
of each Pn.p cell is specified by its position relative to the anchor cell.
True
During vulval development, the _____ is synthesized by the anchor cell; this signal is received and processed by three adjacent Pn.p precursor cells (Pn.p 5–7).
LIN-3 signal protein
True or False. During vulval development, the cell closest to the anchor cell (usually Pn.p 6) becomes the primary vulval precursor cell, and the adjacent cells (Pn.p 5 and 7) become secondary precursor cells.
True
Describes what happens to allele and genotype frequencies in an “ideal” population that is infinitely large and randomly mating, and that is not subject to any evolutionary forces such as mutation, migration, or selection.
Hardy–Weinberg law
Genes in the population gene pool that are not not being operated on by the forces of evolution.
neutral genes
Changes in allele frequencies in a population that do not directly result in species formation are examples of ____.
microevolution
What are the two predictions of the Hardy-Weinberg Law
- Allele frequencies in our population do not change from one generation to the next
- After one generation of random mating, genotype frequencies can be predicted from the allele frequencies.
This gene encodes a protein called C-C chemokine receptor-5 which is utilized by HIV 1 to gain entry into the cells. Individuals having a homozygous mutant genotype of this gene are immune to HIV1 infection due to 32-bp deletion, making the encoded protein shorter and nonfunctional.
CCR5 gene
Assumptions of the Hardy-Weinberg equilibrium:
- Individuals of all genotypes have equal rates of survival and equal reproductive success—that is, there is no selection.
- No new alleles are created or converted from one allele into another by mutation.
- Individuals do not migrate into or out of the population.
- The population is infinitely large, which in practical terms means that the population is large enough that
sampling errors and other random effects are negligible. - Individuals in the population mate randomly.
True or False. Weinberg assumptions are not evolving because allele frequencies (for the generations tested) are not changing. However, a population may be in Hardy–Weinberg equilibrium for the alleles being tested, but other genes may not be in equilibrium.
True
True or False. In natural selection, Traits that promote differential survival and reproduction will become more common, and traits that confer a lowered ability for survival and reproduction will become less common.
True
Is the principal force that shifts allele frequencies within large populations by promoting differential survival and reproduction. It is one of the most important factors in evolutionary change.
Natural selection
An individual organism’s genetic contribution to future generations is called its ___?
Fitness
In this type of natural selection, traits at one end of a spectrum of phenotypes present in the population become selected for or against, usually as a result of changes in the environment.
Directional selection
This type of natural selection selects for intermediate phenotypes, with those at both extremes being selected against.
Stabilizing selection
This type of natural selection, selects against intermediate phenotypes and selection for phenotypes at both extremes.
Disruptive selection
In small populations, significant random fluctuations in allele frequencies are possible by chance alone, a situation known as ___.
Genetic drift
In addition to small population size, genetic drift can arise through the ____ which occurs when a population originates from a small number of individuals.
founder effect
Drift can also arise via a ____. This develops when a large population undergoes a drastic but temporary reduction in numbers.
genetic bottleneck
In this non-random mating, similar genotypes are more likely to mate than dissimilar ones.
Positive Assortive mating
This non-random mating occurs when dissimilar genotypes are more likely to mate.
Negative Assortive mating
The form of nonrandom mating most commonly found to affect genotype frequencies in population genetics is ____. It is briefly defined as mating among relatives as it occurs when mating individuals are more closely related that any two individuals drawn from the population at random.
Inbreeding
True or False. In inbreeding, for a given allele, inbreeding increases the proportion of homozygotes and decreases the proportion of heterozygotes in the population.
True
This coefficient quantifies the probability that the two alleles of a given gene present in an individual are identical because they are descended from the same single copy of the allele in an ancestor.
coefficient of inbreeding (F)
It can be defined as a group of actually or potentially interbreeding organisms that is reproductively isolated in nature from all other such groups.
Species
The biological barriers that prevent or reduce interbreeding between populations are called ____. These mechanisms may be ecological, behavioral, seasonal, mechanical, or physiological.
reproductive isolating mechanisms
This type of reproductive isolating mechanism prevent individuals from mating in the first place. Individuals from different populations may not find each other at the right time, may not recognize each other as suitable mates, or may try to mate but find that they are unable to do so because of differences in mating behavior.
Prezygotic isolating mechanisms
This type of reproductive isolating mechanism creates reproductive isolation even when the members of two populations are willing and able to mate with each other. For example,
mating may take place, and hybrid zygotes may be formed, but all or most of them may be inviable. Alternatively, the hybrids may be viable, but be sterile or suffer from reduced fertility.
Postzygotic isolating mechanisms
