GENERAL PATHOLOGY
Introduction :
DNA Structure
DNA is found in the nucleus of every human cell. The information in
DNA guides the cell (along with RNA) in making new proteins that determine all of our biological traits, and gets passed (copied) from one generation to the next
The key to all of these functions is found in the molecular structure of
DNA, Although it may look complicated, the DNA in a cell is really just a pattern made up of four different parts called nucleotides. Imagine a set of blocks that has only four shapes, or an alphabet that has only four letters. DNA is a long string of these blocks or letters. Each nucleotide consists of a sugar (deoxyribose) bound on one side to a phosphate group and bound on the other side to a nitrogenous base .
The nucleotide is the basic building block of nucleic acids.
There are two classes of nitrogen bases called purines (double-ringed structures) and pyrimidines (single-ringed structures). The four bases in
DNA's alphabet are : adenine (A) - a purine cytosine(C) - a pyrimidine guanine (G) - a purine thymine (T) - a pyrimidine
Strands of DNA are made of the sugar and phosphate portions of the nucleotides, while the middle parts are made of the nitrogenous bases.
The nitrogenous bases on the two strands of DNA pair up, purine with pyrimidine (A with T, G with C), and are held together by weak hydrogen bonds.
Watson and Crick discovered that DNA had two sides, or strands, and that these strands were twisted together like a twisted ladder -- the double helix.
The sides of the ladder comprise the sugar-phosphate portions of adjacent nucleotides bonded together. The phosphate of one nucleotide is covalently bound (a bond in which one or more pairs of electrons are shared by two atoms) to the sugar of the next nucleotide. The hydrogen bonds between phosphates cause the DNA strand to twist. Each base pair is formed from two complementary nucleotides (purine with pyrimidine) bound together by hydrogen bonds. The base pairs in DNA are adenine with thymine and cytosine with guanine .

Normal karyotype
As is well known, human somatic cells contain 46 chromosomes; these comprise 22 homologous pairs of autosomes and two sex chromosomes,
XX in the female and XY in the male. The study of chromosomes-karyotyping--is the basic tool of the cytogeneticist. The usual procedure of producing a chromosome spread is to arrest mitosis in dividing cells in metaphase by the use of colchicine and then to stain the chromosomes. In a metaphase spread, the individual chromosomes take the form of two chromatids connected at the centromere. A karyotype is a standard arrangement of a photographed or imaged stained metaphase spread in which chromosome pairs are arranged in order of decreasing length.
A variety of staining methods that allow identification of each individual chromosome on the basis of a distinctive and reliable pattern of alternating light and dark bands along the length of the chromosome have been developed. The one most commonly employed uses a Giemsa stain and is hence called G banding.
Karyotypes are usually described using a shorthand system of notations.
In general, the following order is used: Total number of chromosomes is given first, followed by the sex chromosome complement, and finally the description of any abnormality. For example, a male with trisomy 21 is designated 47,XY,+ 21. Some of the notations denoting structural alterations of chromosomes are described along with the abnormalities in a later section. Here we should mention that the short arm of a chromosome is designated p (for petit), and the long arm is referred to as q . In a banded karyotype, each arm of the chromosome is divided into two or more regions by prominent bands. The regions are numbered 1, 2,
3) from the centromere outward. Each region is further subdivided into bands and sub-bands, and these are ordered numerically . Thus, the notation Xp21.2 refers to a chromosomal segment located on the short arm of the X chromosome, in region 2, band 1, and sub-band 2.
Fluorescence In Situ Hybridization.
Fluorescence in situ hybridization (FISH) has become an important adjunct to routine karyotyping and has greatly expanded the power of cytogenetic analysis. A major limitation of karyotyping is that it is applicable only to cells that are dividing or can be induced to divide in vitro. This problem can be overcome with DNA probes that recognize chromosome-specific sequences. Such probes are labeled with fluorescent dyes and applied to nuclei. The probe binds to its complementary sequence on the chromosome and thus labels the specific chromosome that can then be visualized under a fluorescent microscope . Thus, FISH can be used to enumerate chromosomes in interphase nuclei. The application of FISH is not limited to interphase nuclei, however. By using
DNA probes that are specific for defined regions of the chromosomes,

FISH can be used to demonstrate subtle microdeletions and complex translocations not readily detectable by routine karyotyping .
Mutation:
Mutation is a permanent change in the DNA.
Mutations that affect germ cells are transmitted to the progenitor cells and give rise to inherited disorders (diseases), while the mutations that affect somatic cells do not cause hereditary diseases but are important in the genesis of cancers and congenital malformations.
Mutations can be divided into the following types:
1- genome mutation (numerical mutation): it represent loss or gain of whole chromosome and give rise to monosomy and trisomy.
The number of human chromosomes are 23 pairs (46 chromosomes), 22 pairs are somatic and the last pair represent the sex chromosomes.
The causes of numerical chromosomal defects is the non-disjunction of homologus pair at first meiotic division, or failure of sister chromosomes to separate during second meiotic division.
Monosomy = n – 1 like XO (Turner's syndrome).
Trisomy = n + 1 like trisomy 21 (Down's syndrome).
2- structural mutations: a- chromosomal mutations: result from rearrangements of genetic material and give rise to visible structural changes in the chromosomes, usually they result from chromosomal breakage followed by loss or rearrangement of genetic materials, many types of such mutations seen as followings:
Deletion : its refers to loss of a portion of chromosome.
It may be terminal or interstitial. Terminal deletions result from a single break in the arm of a chromosome, producing a fragment with no centromere, which is then lost at the next cell division. One can specify in which region and at what band the break and deletion has occurred, as, for example, 46,XY,del(16)(p14), meaning a break point in region 1 band
4 of the short arm of chromosome 16. Interstitial deletions occur when there are two breaks in the chromosome followed by loss of the region between the breaks.
A ring chromosome : is a special form of deletion. It is produced when a deletion occurs at both ends of a chromosome with fusion of the damaged ends . If significant genetic material is lost, phenotypic abnormalities result. This might be expressed as 46,XY,r(14). Ring chromosomes do not behave normally in meiosis or mitosis and usually result in serious consequences.
Inversion : refers to a rearrangement that involves two breaks within a single chromosome with inverted reincorporation of the segment . Such an inversion involving only one arm of the chromosome is known as paracentric. If the breaks are on opposite sides of the centromere, it is

known as pericentric. Inversions are perfectly compatible with normal development.
Isochromosome formation : results when one arm of a chromosome is lost and the remaining arm is duplicated, resulting in a chromosome consisting of two short arms only or of two long arms . An isochromosome has genetic information that is morphologically identical in both arms. The most common isochromosome present in live births involves the long arm of the X and is designated i(X)(q10).
Translocation : a segment of one chromosome is transferred to another .
In one form, called balanced reciprocal translocation, there are single breaks in each of two chromosomes, with exchange of material. Such a translocation might not be disclosed without banding techniques. A balanced reciprocal translocation between the long arm of chromosome 2 and the short arm of chromosome 5 would be written
46,XX,t(2;5)(q31;p14). This individual has 46 chromosomes with altered morphology of one of the chromosomes 2 and one of the chromosomes 5.
Because there has been no loss of genetic material, the individual is phenotypically normal. A balanced translocation carrier, however, is at increased risk for producing abnormal gametes, resulting in spontaneous abortion or birth of a malformed child. The other important pattern of translocation is called a robertsonian translocation (or centric fusion), a translocation between two acrocentric chromosomes. Typically the breaks occur close to the centromeres of each chromosome. Transfer of the segments then leads to one very large chromosome and one extremely small one. Usually the small product is lost ; however, it carries so little genetic information that this loss is compatible with a normal phenotype, and robertsonian translocation between two chromosomes is encountered in 1 in 1000 apparently normal individuals.
It is estimated that approximately 7.5% of all conceptions have a chromosomal abnormality, most of which are not compatible with survival or live birth. Thus, chromosome abnormalities are identified in
50% of early spontaneous abortuses and in 5% of stillbirths and infants who die in the immediate postnatal period. Even in live-born infants, the frequency is approximately 0.5 to 1.0%. b- gene mutations : result from deletion of a gene or more, often affect a single base; as for example a single nucleotide base can be substituted by a different base result in 'point mutation', less common two bases or more may be inserted into or deleted from DNA, leading to alteration in the reading frame of DNA strand, hence these are referred to as frame shift mutation.
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Point mutation within coding sequence :

Replacement of one amino acid by another in the gene production, the best example is sickle cell anemia affecting B- globulin chain of hemoglobin.
CTC – those code for glutamic acid
GAG
CAC—those code for valine.
GUG
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Mutation within non-coding sequence (intron):
Lead to interference with normal processing of the initial mRNA transcription like some types of hemolytic anemia.
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Deletion or insertion of nucleotide bases lead to DNA frame shift mutation.
How the mutation represent their effects:
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Enzyme defects cause substrates to accumulate (i.e., the storage diseases, alkaptonuria), and/or prevent formation of a good end product (albinism, red hair, other white people) perhaps even with accumulation of unwholesome precursors (Lesch-Nyhan), and/or fail to inactivate something bad (i.e., α1-protease inhibitor deficiency)

Defects in receptors and transport systems produce various malabsorption syndromes, urinary wasting syndromes, unresponsiveness to hormones, problems mobilizing lipoproteins, and so forth.

Altered non-enzyme proteins include altered structure and function
(hemoglobinopathies, collagen problems), and abnormal quantities
(the prime example is the thalassemia family)
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Altered responses to drugs you'll study in "Pharm". If you lack
G6PD, you get hemolytic anemia from various oxidizing drugs, fava beans, and so forth. Some people are "slow acetylators" of certain drugs, etc., etc .
Transmission pattern of single gene mutation:
1.Autosomal dominant.
2.Autosomal Recessive.
3.x-linked
1-Autosomal dominant disorders:
-disorders manifested in heterozygous states
-male and female affected equally
-if affected parson married unaffected one ,50%of their offspring
Will be affected.

-some patient develop disease but they don’t have affected parents
,this result from new mutation.
-in many condition the age at onset is delayed sign and symptom delayed till adult hood.
Mechanism: most mutation lead to reduced production of agene products or give rise to an inactive protein.
If mutation affects an enzyme protein the heterozygous is usually normal because 50% loss of enzyme actively can be compensated for mutation.
Heterozygous defect of structural protein produce defect or disease.
Ex : familial polyposis coli, spherocytosis, and polycyctic kidney.
2-autosomal recessive mutation:
Disorder develop only when both alleles are involved :
-both parent carry the trait but can give affect siblings.
-siblings have 25%chance to develop the disorder.
-onset is early in life.
-complete penetrance is common.
-male &female are affected equally.
Ex: sickle cell anemia, thalassemia , and cyctic fibrosis.
3- X-linked disorder:

Most x-linked disorder are x-linked recessive characterized by:
1)they are transmitted by heterozygous female carrier to sons ; who of course are hemizygous for x chromosome.
2)an affected male does not transmit the disorder to sons ; but all daughter are carrier.
Sons of heterozygous women have one chance in two "50%" of receiving the mutated gene. ex: hemophilia A & B, and G6PD.
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X- linked dominant mutations:
50 % of sons and daughter of heterozygous affected female are affected, while male can not carry the disease to the sons but all daughters are affected.
Although Down's syndrome is very common, we don't understand the reason that the extra chromosome 21 causes so many problems.
It affects around 1 child in 700. Advanced maternal age is important risk factor. May be 1 in 25 live births to mothers over 45 have Down's synrome. In only 20% of cases is the extra chromosome of paternal origin.
Pediatricians look for several signs. Don't expect to see them all:

1.
flattened face
2.
open mouth, big tongue.
3.
slanting palpebral fissures and epicanthic folds ("mongolism")
4.
mental retardation
5.
lack of muscle tone at birth ("floppy baby")
6.
low-set ears
7.
single palmar crease ("simian crease")
8.
heart defects (40%, notably endocardial cushion defects)
9.
conductive hearing loss
10.
bad respiratory infections
11.
various leukemias .
Klinefelter's syndrome
This occurs when a man has more than one X chromosome (i.e.,
47,XXY, 48,XXXY, etc.). 1 man in about 850 person is affected. The etiology is unknown, but advanced maternal age contributes.
At puberty, the typical features generally appear. They include small testes, long arms and legs, often smallish penis. Klinefelter patients generally are not very hairy, and rarely go bald.
Because the Leydig cells do not function well, serum gonadotropins are high, Leydig cells are hyperplastic, plasma testosterone is low, and estrogens are high, with about half getting gynecomastia. The seminiferous tubules are always underdeveloped to some degree.
In any case, almost all of these men are sterile, and Klinefelter's syndrome is a consideration whenever a couple is having difficulty having a child.
Turner's syndrome
This is the result of monosomy for the short arm of the X chromosome. About 1 out of every 2000 women are affected. Of these, around half are XO, and the remainder either have an isochromosome of the long arm of X, or have partial deletion of the short arm of X.
The major problem is failure of feminization at adolescence.
Patients have "webbed neck", "shield-shaped chest", and "cubitus valgus" (elbows turned out). However, most patients are not diagnosed until the teens (if then).
They fail to menstruate (i.e. "primary amenorrhea" -- Turner's is the most common identifiable cause) or develop secondary sex characteristics.
Rarely, lymph channels fail to form properly, and lymphedema of the hands and feet makes the diagnosis apparent at birth. Or an alert clinician notes the "webbed neck" or "shield-shaped chest" of the patient.