A chromosome (from ancient Greek: χρωμόσωμα, chromosoma, chroma means color, soma means body) is a DNA molecule with part or all of the genetic material (genome) of an organism. Most eukaryotic chromosomes include packaging proteins which, aided by chaperone proteins, bind to and condense the DNA molecule to prevent it from becoming an unmanageable tangle.
Chromosomes are normally visible under a light microscope only when the cell is undergoing the metaphase of cell division (where all chromosomes are aligned in the center of the cell in their condensed form). Before this happens, every chromosome is copied once (S phase), and the copy is joined to the original by a centromere, resulting either in an X-shaped structure (pictured to the right) if the centromere is located in the middle of the chromosome or a two-arm structure if the centromere is located near one of the ends. The original chromosome and the copy are now called sister chromatids. During metaphase the X-shape structure is called a metaphase chromosome. In this highly condensed form chromosomes are easiest to distinguish and study. In animal cells, chromosomes reach their highest compaction level in anaphase during segregation.
Chromosomal recombination during meiosis and subsequent sexual reproduction play a significant role in genetic diversity. If these structures are manipulated incorrectly, through processes known as chromosomal instability and translocation, the cell may undergo mitotic catastrophe and die. Mutations in the cell can allow it to inappropriately evade apoptosis and lead to the progression of cancer.
Some use the term chromosome in a wider sense, to refer to the individualized portions of chromatin in cells, either visible or not under light microscopy. However, others use the concept in a narrower sense, to refer to the individualized portions of chromatin during cell division, visible under light microscopy due to high condensation.
The word chromosome () comes from the Greekχρῶμα (chroma, "colour") and σῶμα (soma, "body"), describing their strong staining by particular dyes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, which was introduced by Walther Flemming.
Emilio Battaglia (1917-2011) points out that over time many of the most familiar caryological terms have become inadequate or illogical or, in some cases, etymologically incorrect so that they should be replaced by more adequate alternatives suggested by the present scientific progress. The author has been particularly disappointed by the illogicality of the present chromosomal (chromatin-chromosome) terminology based on, or inferred by, two terms, Chromatin (Flemming 1880) and Chromosom (Waldeyer 1888), both inappropriately ascribed to a basically non coloured state.
History of discovery
Schleiden,Virchow and Bütschli were among the first scientists who recognized the structures now familiar as chromosomes.
In a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes.[further explanation needed] It is the second of these principles that was so original.Wilhelm Roux suggested that each chromosome carries a different genetic load. Boveri was able to test and confirm this hypothesis. Aided by the rediscovery at the start of the 1900s of Gregor Mendel's earlier work, Boveri was able to point out the connection between the rules of inheritance and the behaviour of the chromosomes. Boveri influenced two generations of American cytologists: Edmund Beecher Wilson, Nettie Stevens, Walter Sutton and Theophilus Painter were all influenced by Boveri (Wilson, Stevens, and Painter actually worked with him).
In his famous textbook The Cell in Development and Heredity, Wilson linked together the independent work of Boveri and Sutton (both around 1902) by naming the chromosome theory of inheritance the Boveri–Sutton chromosome theory (the names are sometimes reversed).Ernst Mayr remarks that the theory was hotly contested by some famous geneticists: William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic turn of mind. Eventually, complete proof came from chromosome maps in Morgan's own lab.
The number of human chromosomes was published in 1923 by Theophilus Painter. By inspection through the microscope, he counted 24 pairs, which would mean 48 chromosomes. His error was copied by others and it was not until 1956 that the true number, 46, was determined by Indonesia-born cytogeneticist Joe Hin Tjio.
The prokaryotes – bacteria and archaea – typically have a single circular chromosome, but many variations exist. The chromosomes of most bacteria, which some authors prefer to call genophores, can range in size from only 130,000 base pairs in the endosymbiotic bacteria Candidatus Hodgkinia cicadicola and Candidatus Tremblaya princeps, to more than 14,000,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum.Spirochaetes of the genusBorrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.
Structure in sequences
Prokaryotic chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a one-point (the origin of replication) from which replication starts, whereas some archaea contain multiple replication origins. The genes in prokaryotes are often organized in operons, and do not usually contain introns, unlike eukaryotes.
Prokaryotes do not possess nuclei. Instead, their DNA is organized into a structure called the nucleoid. The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes.
Certain bacteria also contain plasmids or other extrachromosomal DNA. These are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. In prokaryotes (see nucleoids) and viruses, the DNA is often densely packed and organized; in the case of archaea, by homology to eukaryotic histones, and in the case of bacteria, by histone-like proteins.
Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).
Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for transcription, regulation, and replication.
See also: Eukaryotic chromosome fine structure
Chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes (histone octamers with part of a DNA strand attached to and wrapped around it). Chromatin fibers are packaged by proteins into a condensed structure called chromatin. Chromatin contains the vast majority of DNA and a small amount inherited maternally, can be found in the mitochondria. Chromatin is present in most cells, with a few exceptions, for example, red blood cells.
Chromatin allows the very long DNA molecules to fit into the cell nucleus. During cell division chromatin condenses further to form microscopically visible chromosomes. The structure of chromosomes varies through the cell cycle. During cellular division chromosomes are replicated, divided, and passed successfully to their daughter cells so as to ensure the genetic diversity and survival of their progeny. Chromosomes may exist as either duplicated or unduplicated. Unduplicated chromosomes are single double helixes, whereas duplicated chromosomes contain two identical copies (called chromatids or sister chromatids) joined by a centromere.
Eukaryotes (cells with nuclei such as those found in plants, fungi, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although, under most circumstances, these arms are not visible as such. In addition, most eukaryotes have a small circular mitochondrialgenome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.
In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.
During interphase (the period of the cell cycle where the cell is not dividing), two types of chromatin can be distinguished:
- Euchromatin, which consists of DNA that is active, e.g., being expressed as protein.
- Heterochromatin, which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
- Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
- Facultative heterochromatin, which is sometimes expressed.
Structure of Eukaryotic chromosome
- Each chromosome is made up of two chromatids(chromosomal arms) which are joined to each other at a small constricted region called the centromere.(Primary constriction). These sister chromatids are conjoined twins the result of DNA replication.
- The centromere helps the chromatids attach to the spindle fibres during cell division, it is also concerned with the anaphase movement of the chromosomes, by which the spindle fibers pull the chromatids to the two opposite poles by their contraction during anaphase.
- Besides the primary constriction, in certain chromosomes there is a secondary constriction as well. Because a small portion is pinched off from the chromosomal body; this portion is called a 'satellite' and the chromosome is called an SAT chromosome.
- The two chromatids are made up of very thin chromatin fibres which are made up of 40% DNA and 60% histone proteins
- Each chromatin fibre consists of one DNA helix coiled around eight histone molecules like a loop; such a complex is called nucleosome and resembles a bead on a string. These nucleosomes pack tighter, during condensation required to get to metaphase.
- The primary constriction cannot take up most stains, so during cell division this region is a gap in staining.
- Within the primary constriction there is a clear zone called Centromere.
- The centromere with the DNA and histone proteins bound to them form a disc shaped structure called kinetochore.
- the chromonemata is a word that means a chromatid in the early stage of condensation.
Metaphase chromatin and division
See also: mitosis and meiosis
In the early stages of mitosis or meiosis (cell division), the chromatin double helix become more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. This compact form makes the individual chromosomes visible, and they form the classic four arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the Frenchpetit, small) and the longer arms are called q arms (q follows p in the Latin alphabet; q-g "grande"; alternatively it is sometimes said q is short for queue meaning tail in French). This is the only natural context in which individual chromosomes are visible with an optical microscope.
Mitotic metaphase chromosomes are best described by a linearly organized longitudinally compressed array of consecutive chromatin loops.
During mitosis, microtubules grow from centrosomes located at opposite ends of the cell and also attach to the centromere at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region. The microtubules then pull the chromatids apart toward the centrosomes, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and DNA can again be transcribed. In spite of their appearance, chromosomes are structurally highly condensed, which enables these giant DNA structures to be contained within a cell nucleus.
Chromosomes in humans can be divided into two types: autosomes (body chromosome(s)) and allosome (sex chromosome(s)). Certain genetic traits are linked to a person's sex and are passed on through the sex chromosomes. The autosomes contain the rest of the genetic hereditary information. All act in the same way during cell division. Human cells have 23 pairs of chromosomes (22 pairs of autosomes and one pair of sex chromosomes), giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. Number of genes is an estimate, as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.
|Chromosome||Genes||Total base pairs||% of bases||Sequenced base pairs|
|X (sex chromosome)||800||154,913,754||5.0||151,058,754|
|Y (sex chromosome)||50||57,741,652||1.9||25,121,652|
Number in various organisms
Main article: List of organisms by chromosome count
These tables give the total number of chromosomes (including sex chromosomes) in a cell nucleus. For example, most eukaryotes are diploid, like humans who have 22 different types of autosomes, each present as two homologous pairs, and two sex chromosomes. This gives 46 chromosomes in total. Other organisms have more than two copies of their chromosome types, such as bread wheat, which is hexaploid and has six copies of seven different chromosome types – 42 chromosomes in total.
Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes (see the table). Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell.
Asexually reproducing species have one set of chromosomes that are the same in all body cells. However, asexual species can be either haploid or diploid.
Sexually reproducing species have somatic cells (body cells), which are diploid [2n] having two sets of chromosomes (23 pairs in humans with one set of 23 chromosomes from each parent), one set from the mother and one from the father. Gametes, reproductive cells, are haploid [n]: They have one set of chromosomes. Gametes are produced by meiosis of a diploid germ line cell. During meiosis, the matching chromosomes of father and mother can exchange small parts of themselves (crossover), and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge (fertilization), a new diploid organism is formed.
Some animal and plant species are polyploid [Xn]: They have more than two sets of homologous chromosomes. Plants important in agriculture such as tobacco or wheat are often polyploid, compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more-common pasta and bread wheat types are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes, compared to the 14 (diploid) chromosomes in the wild wheat.
Prokaryotespecies generally have one copy of each major chromosome, but most cells can easily survive with multiple copies. For example, Buchnera, a symbiont of aphids has multiple copies of its chromosome, ranging from 10–400 copies per cell. However, in some large bacteria, such as Epulopiscium fishelsoni up to 100,000 copies of the chromosome can be present. Plasmids and plasmid-like small chromosomes are, as in eukaryotes, highly variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid – fast division causes high copy number.
Main article: Karyotype
In general, the karyotype is the characteristic chromosome complement of a eukaryotespecies. The preparation and study of karyotypes is part of cytogenetics.
Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases, there is significant variation within species. Often there is:
- 1. variation between the two sexes
- 2. variation between the germ-line and soma (between gametes and the rest of the body)
- 3. variation between members of a population, due to balanced genetic polymorphism
- 4. geographical variation between races
- 5. mosaics or otherwise abnormal individuals.
Also, variation in karyotype may occur during development from the fertilized egg.
The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed, and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here X/Y) at the end.
Like many sexually reproducing species, humans have special gonosomes (sex chromosomes, in contrast to autosomes). These are XX in females and XY in males.
Investigation into the human karyotype took many years to settle the most basic question: How many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XOsex determination mechanism.Painter in 1922 was not certain whether the diploid number of man is 46 or 48, at first favouring 46. He revised his opinion later from 46 to 48, and he correctly insisted on humans having an XX/XY system.
New techniques were needed to definitively solve the problem:
- Using cells in culture
- Arresting mitosis in metaphase by a solution of colchicine
- Pretreating cells in a hypotonic solution 0.075 M KCl, which swells them and spreads the chromosomes
- Squashing the preparation on the slide forcing the chromosomes into a single plane
- Cutting up a photomicrograph and arranging the result into an indisputable karyogram.
It took until 1954 before the human diploid number was confirmed as 46. Considering the techniques of Winiwarter and Painter, their results were quite remarkable.Chimpanzees, the closest living relatives to modern humans, have 48 chromosomes as do the other great apes: in humans two chromosomes fused to form chromosome 2.
(See Also: Argument from authority#Inaccurate chromosome number)
Chromosomal aberrations are disruptions in the normal chromosomal content of a cell and are a major cause of genetic conditions in humans, such as Down syndrome, although most aberrations have little to no effect. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of bearing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, called aneuploidy, may be lethal or may give rise to genetic disorders.Genetic counseling is offered for families that may carry a chromosome rearrangement.
The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:
- Cri du chat, which is caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French; the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, moderate to severe mental health problems, and are very short.
- Down syndrome, the most common trisomy, usually caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes and mild to moderate developmental disability.
- Edwards syndrome, or trisomy-18, the second most common trisomy. Symptoms include motor retardation, developmental disability and numerous congenital anomalies causing serious health problems. Ninety percent of those affected die in infancy. They have characteristic clenched hands and overlapping fingers.
- Isodicentric 15, also called idic(15), partial tetrasomy 15q, or inverted duplication 15 (inv dup 15).
- Jacobsen syndrome, which is very rare. It is also called the terminal 11q deletion disorder. Those affected have normal intelligence or mild developmental disability, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome.
- Klinefelter syndrome (XXY). Men with Klinefelter syndrome are usually sterile and tend to be taller and have longer arms and legs than their peers. Boys with the syndrome are often shy and quiet and have a higher incidence of speech delay and dyslexia. Without testosterone treatment, some may develop gynecomastia during puberty.
- Patau Syndrome, also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, without the characteristic folded hand.
- Small supernumerary marker chromosome. This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister–Killian syndrome.
- Triple-X syndrome (XXX). XXX girls tend to be tall and thin and have a higher incidence of dyslexia.
- Turner syndrome (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. Females with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development and a "caved-in" appearance to the chest.
- Wolf–Hirschhorn syndrome, which is caused by partial deletion of the short arm of chromosome 4. It is characterized by growth retardation, delayed motor skills development, "Greek Helmet" facial features, and mild to profound mental health problems.
- XYY syndrome. XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are more likely to have learning difficulties.
Exposure of males to certain lifestyle, environmental and/or occupational hazards may increase the risk of aneuploid spermatozoa. In particular, risk of aneuploidy is increased by tobacco smoking, and occupational exposure to benzene, insecticides, and perfluorinated compounds. Increased aneuploidy is often associated with increased DNA damage in spermatozoa.
Notes and references
- ^Hammond, Colin M.; Strømme, Caroline B.; Huang, Hongda; Patel, Dinshaw J.; Groth, Anja (2017). "Histone chaperone networks shaping chromatin function". Nature Reviews Molecular Cell Biology. 18 (3): 141–158. doi:10.1038/nrm.2016.159. ISSN 1471-0072.
- ^Wilson, John (2002). Molecular biology of the cell : a problems approach. New York: Garland Science. ISBN 0-8153-3577-6.
- ^Alberts, Bruce; Bray, Dennis; Hopkin, Karen; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2014). Essential Cell Biology (Fourth ed.). New York, NY, USA: Garland Science. pp. 621–626. ISBN 978-0-8153-4454-4.
- ^ abcSchleyden, M. J. (1847). Microscopical researches into the accordance in the structure and growth of animals and plants.
- ^Wolfram, Antonin; Neumann, Heinz (2016). "Chromosome condensation and decondensation during mitosis". Current Opinion in Cell Biology. Elsevier Ltd. 40: 19. doi:10.1016/j.ceb.2016.01.013. Retrieved 2017-11-06.
- ^Jones, Daniel (2003) , Peter Roach, James Hartmann and Jane Setter, eds., English Pronouncing Dictionary, Cambridge: Cambridge University Press, ISBN 3-12-539683-2
- ^"Chromosome". Merriam-Webster Dictionary.
- ^Coxx, H. J. (1925). Biological Stains - A Handbook on the Nature and Uses of the Dyes Employed in the Biological Laboratory. Commission on Standardization of Biological Stains.
- ^Waldeyer-Hartz (1888). "Über Karyokinese und ihre Beziehungen zu den Befruchtungsvorgängen". Archiv für mikroskopische Anatomie und Entwicklungsmechanik. 32: 27.
- ^Garbari, Fabio; Bedini, Gianni; Peruzzi, Lorenzo (2012). "Chromosome numbers of the Italian flora. From the Caryologia foundation to present". Caryologia - International Journal of Cytology, Cytosystematics and Cytogenetics. Oxfordshire, England: Taylor & Francis. 65 (1): 65–66. doi:10.1080/00087114.2012.678090. Retrieved 2017-11-06.
- ^Peruzzi, L.; Garbari, F.; Bedini, G. (2012). "New trends in plant cytogenetics and cytoembryology: Dedicated to the memory of Emilio Battaglia". Plant Biosystems - An International Journal Dealing. Pisa, Italy: Taylor & Francis. 146 (3): 674–675. doi:10.1080/11263504.2012.712553. Retrieved 2017-11-06.
- ^Battaglia, Emilio (2009). "Caryoneme alternative to chromosome and a new caryological nomenclature"(PDF). Caryologia - International Journal of Cytology, Cytosystematics. Florence: Mozzon S.r.l. 62 (4): 1–80. Retrieved 2017-11-06.
- ^Fokin S.I. (2013). "Otto Bütschli (1848–1920) Where we will genuflect?"(PDF). Protistology. 8 (1): 22–35.
- ^Carlson, Elof A. (2004). Mendel's Legacy: The Origin of Classical Genetics(PDF). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. p. 88. ISBN 978-087969675-7.
- ^Wilson, E.B. (1925). The Cell in Development and Heredity, Ed. 3. Macmillan, New York. p. 923.
- ^Mayr, E. (1982). The growth of biological thought. Harvard. p. 749.
- ^Matthews, Robert. "The bizarre case of the chromosome that never was"(PDF). Archived from the original(PDF) on 15 December 2013. Retrieved 13 July 2013. [self-published source?]
- ^Thanbichler M; Shapiro L (2006). "Chromosome organization and segregation in bacteria". J. Struct. Biol. 156 (2): 292–303. doi:10.1016/j.jsb.2006.05.007. PMID 16860572.
- ^Van Leuven, JT; Meister, RC; Simon, C; McCutcheon, JP (11 September 2014). "Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one". Cell. 158 (6): 1270–80. doi:10.1016/j.cell.2014.07.047. PMID 25175626.
Estimated number of genes and base pairs (in mega base pairs) on each human chromosome
Practice Exam 2
Exam #2 Gene Expression MCB 201
When you have completed the examination, hand in:
1. Your answer sheet with your name on it.
2. Your bluebook with your name on it.
3. Your copy of the exam with your name on it.
Part I (Multiple choice) Each multiple choice question is designed to have one correct answer.
1. Negatively charged phosphate groups in the DNA backbone must be neutralized in order for folding of DNA to occur. In bacterial DNA, this charge neutralization is carried out by small positively charged molecules called polyamines. What proteins carry out this same function in eukaryotic cells?
A. Transcription factors
B. High mobility group proteins (HMG-1)
D. Scaffold proteins
2. There are five major types of histones in eukaryotic cells. One of these is not part of the structure of nucleosomes and is thought to participate in forming the 30-nm condensed chromatin fiber. Which histone is this?
B. H2A and B
3. When chromatin is extracted from nuclei and viewed in the electron microscope, its form depends upon the salt concentration to which it is exposed. What is the form of chromatin when it is isolated in isotonic buffers, i.e. same salt concentration as in cells (about 0.15 M KCl)?
A. Beads-on-a-string form
B. 30 nm condensed fibers
C. Loop structure
D. Condensed metaphase chromatin
4. In which phase of the eukaryotic cell cycle is the DNA in its most highly condensed form.
A. M phase
B. G1 phase
C. S phase
D. G2 phase
5. There is a growing body of evidence that acetylation of histone N-termini in specific chromosomal regions contributes to gene control by regulating the binding of histones to DNA and regulation of the folding state of chromatin. The extent of histone acetylation is correlated with the relative resistance of chromatin DNA to digestion by nucleases. Which combination of histone acetylation state and DNAse 1 resistance is characteristic of actively transcribed regions of chromatin?
A. Little or no histone acetylation, highly resistant to DNAse 1
B. Little or no histone acetylation, highly sensitive to DNAse 1
C. High level of histone acetylation, highly resistant to DNAse 1
D. High level of histone acetylation, highly sensitive to DNAse 1
6. The chromosomal karyotypes of two species of small deer, the Reeves muntjac and the Indian muntjac, are strikingly different despite the fact that the two genomes contain about the same amount of DNA. However, within a species, there are properties of chromosomes that are the same, i.e. species-specific. Select the answer that contains all of these species-specific properties of chromosomes at metaphase.
A. Chromosome number only
B. Chromosome number and size only
C. Chromosome number, size and shape only
D. none of the above
7. Select the answer that describes a region of DNA in which genes are likely to be located.
A. DNA loops in heterochromatin
B. DNA loops in euchromatin
C. Scaffold or matrix attachment regions in heterochromatin
D. Scaffold or matrix attachment regions in euchromatin
8. Select the answer that names the three functional elements that are required for replication and stable inheritance of chromosomes.
A. Origins for initiation of DNA replication, centromeres, telomeres
B. Scaffold attachment regions, origins for initiation of DNA replication, centromeres
C. Nucleosomes, origins for initiation of DNA replication, centromeres
D. Nucleosomes, centromeres, telomeres
9. The classic experiments showing that this step in gene expression is regulated were done by Jacob and Monod in the 1950's. Which step in gene expression was it?
C. Reverse transcription
10. Jacob and Monod deduced that protein-binding regulatory sequences exist in DNA segments associated with genes. Which response below correctly indicates the type(s) of cells to which this principle applies?
A. Bacteria only
B. Animal cells only
C. Yeast cells only
D. Bacterial, animal and yeast cells
11. Jacob and Monod deduced that transcription can be either activated or repressed by the binding of a regulatory protein to one of these sequences in DNA. Which response below correctly indicates the type(s) of cells to which this principle applies?
A. Bacteria only
B. Animal cells only
C. Yeast cells only
D. Bacterial, animal and yeast cells
12. Gene regulation can only be fully understood in the context of cellular physiology and/or development. The fact that the lactose operon is off when repressor protein is bound to the operator DNA sequence only takes on significance when we understand the effect that the disaccharide lactose has on this operon. When lactose is taken up by bacterial cells, it is converted to allolactose. How does allolactose activate the lactose operon?
A. Allolactose is converted to the very effective inducer IPTG which binds to repressor protein to inactivate it.
B. Allolactose is converted to the very effective inducer IPTG which binds to repressor protein to activate it.
C. Allolactose binds to repressor protein directly and inactivates the repressor.
D. Allolactose binds to repressor protein directly and activates the repressor.
13. Which of the following proteins is encoded in the LacI gene?
A. Repressor protein
D. Lactose permease
14. Select the response that correctly describes a property of an operon.
A. consist of multiple transcription units
B. are a cluster of genes that are transcribed into a single mRNA
C. are common in eukaryotes
D. are transcribed as monocistronic mRNAs
15. The DNA that encodes protein or RNA accounts for approximately what percentage of the total DNA in eukaryotic cells?
A. 0.01 percent
B. 0.1 percent
C. 5 percent
D. 50 percent
16. The mRNA produced from the lactose operon would not hybridize to
A. the lacY gene
B. the lacZ gene
C. the lac promoter
D. the lac operator
17. An enhancer element shows all of the following properties except
A. acts as a binding site for transcription factors
B. acts as a binding site for RNA polymerase
C. is functional when located upstream or downstream of the transcription initiation site
D. is functional when located in an intron
18. The figure below shows the assay part of a procedure involving construction and analysis of 5'-deletion mutants to locate transcription control (regulatory) sequences in DNA upstream of a eukaryotic gene. Based on the tabulated results of the reporter-gene expression assay, which plasmids are likely to carry an enhancer element?
A. Plasmids 1 and 2
B. Plasmid 3
C. Plasmid 4
D. Plasmid 5
19. Refer to the figure in Question 18 again.
Which plasmid(s) is(are) likely to have lost the
TATA box regulatory element?
A. Plasmids 1 and 2
B. Plasmid 3
C. Plasmid 4
D. Plasmid 5
20. Relative rates of animal cellular gene transcription can be measured using a method known as a nascent RNA chain run-on transcription assay. Which statement below regarding this assay is false?
A. The assay is carried out using isolated nuclei.
B. Radioactively labeled ribonucleside triphosphates can be used to label the newly synthesized RNA.
C. New transcription initiation events frequently occur in the isolated nuclei.
D. This method can be used to study the differential expression of genes in different organs such as liver and kidney.
Answer Key for Part I, Multiple Choice
|1. C||6. C||11. D||16. C|
|2. A||7. B||12. C||17. B|
|3. B||8. A||13. A||18. A|
|4. A||9. D||14. B||19. D|
|5. D||10. D||15. C||20. C|
Part II: Amino acid names, structure and properties: Fill in the blank next to the name of the amino acid with the following descriptors: Identify each amino acid as either hydrophilic or hydrophobic; for amino acids that you identify as hydrophilic, further identify them according to the properties of their R groups (side chains) as either 1) acidic, 2) basic, 3) polar with uncharged R groups.
21. Lysine___________________, __________________________
22. Aspartic acid_________________, ______________________
23. Serine_________________, ____________________
24. Leucine________________, __________________
25. Tyrosine__________________, ______________________
Match the name of the amino acid above with its structure (questions 26-30):
Part III : Answer one short essay question in the blue book provided (You may choose which one to answer)
1. The DNA of eukaryotic cells is tightly associated with protein, forming a complex called chromatin, which can exist in an extended and condensed form. Describe how eukaryotic chromatin is organized within chromosomes so that the genome can fit within a nucleus. Illustrate your anwer with drawings of the various folding stages of chromatin.
2. Altering the spacing between promoter-proximal DNA elements or enhancers and the TATA box has little effect on transcription from some eukaryotic promoters. Explain this finding in terms of the structure of transcription factors and the location of cis-acting control regions. Why is such leeway not observed for most prokaryotic genes? Illustrate your answer with a drawing showing a representative bacterial gene and a representative eukaryotic regulatory region.
Part IV: Problem Solving. Solve one problem and write the solution in the blue book provided.
Two problems will be given.