Chapter 10 The Nature of the Gene and the Genome PDF

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10.1 The Concept of a Gene as a Unit of Inheritance Introduction This activity is based on Chapter 10, Sections 10.1, 10.2, 10.3, 10.4, 10.5, and 10.7. It will prepare you to recognize the structure and function of a gene. Textbook Readings 10.1 “The Concept of a Gene as a Unit of Inheritance” while considering the following points:

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An overview of the most important early discoveries on the nature of the gene is illustrated in Figure 10.1

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We learn which regions of our genome have been duplicated We can learn which have been lost since our split with a common ancestor Which nucleotides have undergone change and which have remained constant

Gregor Mendel -

Early studies thought that genes were discrete factors retained throughout life and passed on Hereditary factors where shown to reside on chromosomes and consists of DNA o DNA  macromolecule with extraordinary proteins

Genome: collective body of genetic information that is present in a species -

Genome consists of all the genes required to build a particular organism

The past decade – laboratories collaborate to complete nucleotide sequences of many different genomes for human species and chimps -

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We can compare the genome and specific locations of the genome to related organisms

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1860 and the science of genetics was began by Gregor Mendel Plan was to cross a pea plant with another that has different inheritable characteristics Wanted to determine the pattern the characteristics are received by the offspring Focused on 7 traits and crossbreed for sever years and concluded Be familiar with Gregor Mendel’s conclusions:

Genes govern the characteristics of an organism -

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The distinct factors of inheritance = genes An individual plant had two copies of each gene that controlled the development of each trait o One maternal and on paternal copy of the gene Allels: the alternate forms of a gene o in each trait there is a dominant allele over the other other o when both alleles are present in the gene one takes dominance

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the dominant masks the recessive

Each gamete (reproductive cell) contains only one copy of the gene -

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A gamete could have either a recessive or dominant allele for a given trait but could not have both Each plant arose from the union of a trait inherited from the allele of the female and the other allele from the male parent

The “Law of Segregation” -

A pair of alleles that governed a trait stayed together throughout the life of a mother or parent they separate from one another to form gametes

The “Law of Independent Assortment” -

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The segregation of the pair of alleles for one trait had no effect on the segregation of alleles for another trait One gamete can receive a paternal gene for seed colour and a maternal gene for seed shape

required to build and maintain plans an animals had to fit inside a cell Fleming -

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Process of fertilization was observed -

The roles of two gametes (sperm egg) were described Sperm was known to be equally important as the egg despite being a much smaller cell

What did they have in common? -

The chromosomes Nucleus

Polyspermy: -

Review questions: What is an allele and what is its relationship to a gene?

Revealed the contents of the cytoplasm were shuttled into a daughter cell The cell divided in half at the furrow The cells worked hard to split the contents equally During cell division the material inside the nucleus (genome) became organized into coloured bodies meaning chromosomes – that are organized by visible threads

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the fertilization of one egg by two sperm having two sperm fertilize the egg results in the death of an embryo the second sperm donates a second set of chromosome and an extra centriole

Allele alternate form of genes, can be identical or non-identical – one allele is dominant over the other one

Centriole: two barrels of microtubule structures that arrange themselves perpendicular to form a centrosome

Gene the response for distinct alleles = each gene slightly different characteristics

Centriole pair: made up of two centrioles – also known as a centromere

10.2 The Discovery of Chromosomes -

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The physical basis for heredity The biologist were not aware of Mendels work at this time but knew that whatever it was that made inherited characteristic would have to be passed form generation (cell to cell) to the next This was a very important realization: that all the genetic information

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leads to abnormal cell division

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father) that have perfectly correlated alleles for the same trait

the daughter cell receives variable number of

Centrosome

chromosomes Bivalen

Boveri concluded: orderly process of normal development is “dependent upon a particular combination of chromosomes” -

Meaning that individual chromosomes must posses different qualities

Meiosis and Weismann’s “reduction division”

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Noticed that a cell of worm had 4 chromosomes After feralization – before two nuclei fuse together – the male and female nuclei had two chromosomes each

Reduction division: Weismann proposed the meiosis included a reduction division – the chromosome number was reduced by half prior to the formation of the gametes -

Without this the union of two gametes at reduced, would double the number of gametes

10.3 Chromosomes as the Carriers of Genetic Information

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Chromosomes are the physical carriers of genetic information

Look a-like pairs: the similarity between the shapes and sizes of the chromosomes in the grasshopper suggested that there was 11 pairs of chromosomes that were similar and 1 accessory chromosome Homologous chromosomes: a pair of chromosomes (one chromatin from the mother and one chromatin from the

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You should know what is meant by homologous chromosomes, which are illustrated in Figure 10.3.

The reduction division was supportive of Mendel’s findings -

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Gametes could contain only one version (allele) of each gene The number of gametes containing one allele was equal to the number containing the other allele Fertilization would produce an individual with two alleles for each trait

How are the genes organized within chromosomes? Could the location of the specific genes be determined? -

If genes are packaged together on chromosomes then genes should be passed in packages to the next generation

Linkage group: groups of genes that reside on the same chromosome causing nonindependent segregation of traits controlled by these genes -

If two traits are linked, then they reside on the same chromosome

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The number of linkage groups is equal to the number of homologous chromosome pairs a species has

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Lead to explain the unexpected combination of genetic traits – see 10.7

10.4 Genetic Analysis in Drosphila Mutant: an individual having a inheritable trait that differs from the normal -

Mutations occurred randomly which alter the trait permanently as passed from generation to generation

Linked to origin of variation in evolution -

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The variants of genes could arise spontaneously Therefore isolated populations could become genetically different o Could give rise to new species Not all mutations assort independently – they belong to linkage groups

Crossing Over and Recombination -

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Alleles of two different genes that were originally presenting together on the same chromosome did not always remain together during the production of gametes Maternal and paternal characteristics that were inherited by an individual on separate homologous chromosomes  could be reshuffled so that they end up on the same chromosome of a gamete Conversely: two characteristics that were inherited together on the same chromosome could become separated from one another and end up on separate gametes

Bivalents: a pair of two homologous chromosomes “breakdown” in linkages: homologous chromosomes within bivalents become wrapped around each other and the interaction during meiosis suggested breaking and exchanging of some pieces Crossing over: shuffling of the genes on chromosomes (which disrupts the linkage groups), that occurs during meiosis as a result of the breakage and reunion of segments of homologous chromosomes

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Analysis of the offspring found -

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Percentage of recombination between a given pair of genes on a chromosome (eye colour, wing length) was essentially constant from one experiment to another The percentage of recombination between different pairs of genes (such as wing length and eye colour vs eye colour and body colour) could be very different

Loci: the position of gene on a chromosome

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Analyses of giant polytene chromosomes, such as the one illustrated in the scanning electron micrograph in Figure 10.8, can provide direct visualization of gene expression.

Polytene chromosomes: giant chromosomes of insects that contain perfectly aligned duplicated DNA strands,

with as many as 1,024 times the number of DNA strands of a normal chromosome -

Unusual and rich in detail Chromosomes puff state then is actively transcribing The dark stained bands are the loci of particular genes Stained = more tightly combined DNA By comparing the giant insect chromosomes to other polytene chromosomes of different species shows evolutionary change on the chromosomal level

10.5 The Structure of DNA – Watson and Crick – 1953 Nucleotide: the basic building block (monomers) combined into a large polymer of DNA made up of three parts -

A phosphate group A five carbon sugar – deoxyribose And a nitrogenous base

concept in Activity 1.2B. Be able to distinguish between purines and pyrimidines. Two flavours of Nitrogenous bases Purines: two rings – remember Purina is a dog food brand and its always better to have two pets -

Guanine Adenine

Pyrimidines: single ring -

Thymine Cytosine

Good Couple; Always Together -

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Adenine binds with Thymine and Guanine binds with Cytosine Be able to explain the rules of DNA base composition as discovered by Chargaff.

Numerical relationship -

The number of adenines always equaled the number of thymine’s and the number of guanine’s always equaled the number of cytosines [A]=[T], [G]=[C], but [A] +[T]  [G]+[C] Be able to recognize the components of the structure of DNA as illustrated in the double helix in Figure 10.11. Watson and Crick received the Nobel Prize in 1962 for discovering the three-dimensional structure of DNA.

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The bond between the phosphate backbone and the sugar is esterified on the 5th position of the carbon ring The nucleotides are covalently bonded to one another to form a linear polymer The backbone alters between sugar and phosphate groups joined by 3’5’ phosphodiester bonds Nucleotide is polarized o The phosphate end is 5’ end (PHOS sounds like FFFFIve) The chemical structure of DNA is illustrated in Figure 10.10. Remember that we studied this

The Structure of DNA -

Two strands of nucleotides Spiral into a right hand helix (looking down it appears to be going away from the observer)

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The two nucleotide strands run antiparallel The sugar phosphate sugar phosphate backbone of each strand is located on the outside o the molecule with two sets of bases projecting toward the center The bases occupy planes that are approximatly perpenduclar to the long axis of the molecule and therefore stacked one on top of the other like a pile of plates o Hydrophobic interactions and van der Waals forced between the base pairs give the DNA stability o The helical turns and planar base pairs cause the molecule to resemble a spiral staircase Two strands are held together by hydrogen bonds between each base of one strand and the associated base on the other stand o Hydrogen bond are weak and therefore sometimes DNA strands can become separated during various activities o The strength of hydrogen bonds are additive so the more there are the stronger the stands hold together The width of a double helix is 2nm A pyrimidine is always paired with a purine to keep the width of the DNA molecule the same all the way along Ketone and amino forms only which means the only possible pairs are AT and GC The space between adjacent turns of the helix form two grooves o Minor groove o Major grove They spiral around the outer surface of the double helix The double helix makes one complete turn every 10 residues (3.4nm) The two chains are complementary to one another o A is complementary to T,

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5’-AGC-3’ is complementary to 3’-TCG-5’ Very important in the activities and mechanisms the nucleic acids are involved in

Figure 10.12 illustrates the three functions required of the genetic material. Be able to describe these functions. a) DNA must contain the information the encodes inheritable traits b) DNA must contain the information that directs it own duplication c) DNA must contain the information that directs the assembly of specific proteins

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Relaxed – the same as tertiary structure – no folding over of itself – normal Can still be in relaxed state in a circle as long as the two ends are not twisted and fuse together

If the strands were twisted in opposite direction than the duplex the molecule tends to unwind Underwound DNA: greater than average number of base bair per turn of the helix -

Review Q: What does it mean that DNA strand has polarity?

The molecule is most stable with 10 bases per turn o Because of this the molecule will try to resist by twisting upon itself to a supercoiled formation

Negatively supercoiled : underwound Positively supercoiled: overwound -

What is the relationship between Chargaff’s analysis of DNA base composition and the structure of the double helix?

Circular DNA found in nature is negatively underwound

Because AT CG are the only pairs it makes the 2nm wide structure DNA can be either positively supercoiled (overwound) or negatively supercoiled (underwound). Topoisomerases change the state and degree of supercoiling. DNA supercoiling is important for the compaction necessary for packaging large amounts of DNA into cells.

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10.7 DNA Supercoiling -

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Twisting on itself = smaller and more compact shape Telephone cord = x; a tangled telephone cord = 0.5X – it gets smaller and more compact o Occupies less volume and move more rapidly in response to  Centrifugal force  Electrical force

Supercoiling in linear DNA -

Eukaryotic DNA Supercoiling plays an important role in making DNA fit inside a cell nucleus Because negatively supercoiled DNA is underwound the force helps separate the two strands of the helix which is required o Replication (DNA synthesis) o Transcription (RNA synthesis)

Topoisomerase: enzymes found in both prokaryotic and eukaryotic cells that are able to change the supercoiled state of the DNA duplex -

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They are essential in the processes such as DNA replication, transcription that require DNA duplex to unwind Transient break Dramatic conformational changes

Key Learning 1.

How do polytene chromosomes of an insect differ from normal chromosomes?

Thicker and larger, several more 2. 1.

What is meant by saying that a DNA strand has polarity?

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Explain the meaning of the term antiparallel DNA strands.

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Describe the major and a minor groove of a DNA molecule.

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Explain how DNA strands can be complementary to one another.

b. What are the three functions required of the genetic material?

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