Pedigree Analysis

Basic principles
If more than one individual in a family is afflicted with a disease, it is a clue that the disease may be inherited. A doctor needs to look at the family history to determine whether the disease is indeed inherited and, if it is, to establish the mode of inheritance. This information can then be used to predict recurrence risk in future generations.

A basic method for determining the pattern of inheritance of any trait (which may be a physical attribute like eye color or a serious disease like Marfan syndrome) is to look at its occurrence in several individuals within a family, spanning as many generations as possible. For a disease trait, a doctor has to examine existing family members to determine who is affected and who is not. The same information may be difficult to obtain about more distant relatives, and is often incomplete.

Once family history is determined, the doctor will draw up the information in the form of a special chart or family tree that uses a particular set of standardized symbols. This is referred to as a pedigree. In a pedigree, males are represented by squares  and females by circles . An individual who exhibits the trait in question, for example, someone who suffers from Marfan syndrome, is represented by a filled symbol  or . A horizontal line between two symbols represents a mating . The offspring are connected to each other by a horizontal line above the symbols and to the parents by vertical lines. Roman numerals (I, II, III, etc.) symbolize generations. Arabic numerals (1,2,3, etc.) symbolize birth order within each generation. In this way, any individual within the pedigree can be identified by the combination of two numbers (i.e., individual II3).

Dominant and recessive traits
Using genetic principles, the information presented in a pedigree can be analyzed to determine whether a given physical trait is inherited or not and what the pattern of inheritance is. In simple terms, traits can be either dominant or recessive. A dominant trait is passed on to a son or daughter from only one parent. Characteristics of a dominant pedigree are: 1) Every affected individual has at least one affected parent; 2) Affected individuals who mate with unaffected individuals have a 50% chance of transmitting the trait to each child; and 3) Two affected individuals may have unaffected children.

Recessive traits are passed on to children from both parents, although the parents may seem perfectly "normal." Characteristics of recessive pedigrees are: 1) An individual who is affected may have parents who are not affected; 2) All the children of two affected individuals are affected; and 3) In pedigrees involving rare traits, the unaffected parents of an affected individual may be related to each other.

The reason for the two distinct patterns of inheritance has to do with the genes that predispose an individual to a given disease. Genes exist in different forms known as alleles, usually distinguished one from the other by the traits they specify. Individuals carrying identical alleles of a given gene are said to be homozygous for the gene in question. Similarly, when two different alleles are present in a gene pair, the individual is said to be heterozygous. Dominant traits are expressed in the heterozygous condition (in other words, you only need to inherit one disease-causing allele from one parent to have the disease). Recessive traits are only expressed in the homozygous condition (in other words, you need to inherit the same disease-causing allele from both parents to have the disease).

Penetrance and expressivity
Penetrance is the probability that a disease will appear in an individual when a disease-allele is present. For example, if all the individuals who have the disease-causing allele for a dominant disorder have the disease, the allele is said to have 100% penetrance. If only a quarter of individuals carrying the disease-causing allele show symptoms of the disease, the penetrance is 25%. Expressivity, on the other hand, refers to the range of symptoms that are possible for a given disease. For example, an inherited disease like Marfan syndrome can have either severe or mild symptoms, making it difficult to diagnose.

Non-inherited traits
Not all diseases that occur in families are inherited. Other factors that can cause diseases to cluster within a family are viral infections or exposure to disease-causing agents (for example, asbestos). The first clue that a disease is not inherited is that it does not show a pattern of inheritance that is consistent with genetic principles (in other words, it does not look anything like a dominant or recessive pedigree).

Basic Karyotyping analysis

Karyotyping is a test that helps find genetic problems. It is usually carried out to examine abnormalities, genetic disorders or defects.

Ameeta had an unexpected miscarriage. She could hardly grasp the reality. Soon her doctor prescribed some test to be carried out. One of them was blood karyotyping. She was waiting for her reports to arrive. But at the back of her mind she had this tiny question popping, what is karyotyping?

There are many pre natal tests that doctors may suggest. Understanding these tests can lessen your anxieties, help you understand the problem better and let you make corrections as required. Once you know what your doctor is trying to do for you, you can co-operate better. Read on to understand karyotyping and be in sync with what you are doing.

What is Karyotyping? Karyotyping is one of the many techniques that help study the human genes for several genetic diseases. Karyotyping comes from the word karyotype. Karyotype is a complete profile of an individual's chromosomal set up. Any changes in the arrangement of a karyotype helps doctors study possiblegenetic disorders. In simpler terms, karyotyping is a close study of chromosomes.

What does a Karyotype Show?

A karyotype shows the details of the chromosomes. Karyotyping identifies and helps determine the sex of an unborn child. When doctors study a human karyotype they look for some significant features. Here are a few important ones.

• Check if the 46 chromosomes are present
• Check the presence of the two identical chromosomes and 2 sex chromosomes
• Check if there are any missing or rearranged chromosomes

What a Karyotype does not show?

While a karyotype provides significant in-depth insight into the chromosomes there are some things it will not show. They are:

• Presence and location of small mutations. So if diseases are caused by small mutations they cannot be predicted
• Individual DNA strands or genes
• The number of genes in any given area of a chromosome

How is blood karyotyping performed?

There are usually no special requirements before performing the test. It is performed on a sample of blood, bone marrow, the amniotic fluid or the tissue from the placenta. Blood is drawn from the body if it requires blood sample. Amniocentesis is carried out to test amniotic fluid. A bone marrow test would require a bone marrow biopsy. The given sample is placed on a tray and allowed to grow in the confines of a laboratory. The cells from the growing sample are then stained. The stained sample is closely examined to study the chromosome arrangement.

Predicting disorders with karyotyping A normal human being has 46 chromosomes, 22 autosomes and two sex chromosomes. When there is a disharmony between this set up, a genetic disorderoccurs. Too many chromosomes, missing chromosomes or mixed up bits of chromosomes show the presence of a problem. The state of the chromosomes helps predict any possible genetic disorder in an unborn child. Chromosomes carry information that is passed to the cell. Extra copies of the information, mixed information or missing information can inform about anyabnormalities or defects.

What makes blood karyotyping helpful?

Blood Karyotyping is a very helpful method of studying chromosomes and predicting genetic disorder. It counts the number of chromosomes and looks for any structural changes in chromosomes. It informs if the unborn babywill suffer from a genetic disorder or not. It is often used during pre-natal testing and diagnosing possible genetic diseases. It is extremely helpful for those who have suffered the loss of a childthrough a miscarriage. For couples coping with a miscarriage karyotyping can mean identifying and correcting problems to give birth to a healthy child.

Bioenergetics.

The free energy change (DG) of a reaction determines its spontaneity. The free energy change (DG), and its relation to equilibrium constant, are discussed on p. 57-59 of Biochemistry 3rd Edition by Voet & Voet. A reaction is spontaneous if DG is negative (if the free energy of the products is less than the free energy of the reactants).

DG = change in free energy, DGo' = standard free energy change (with 1 M reactants and products, at pH 7), R = gas constant, T = absolute temperature.

Note that the standard free energy change (DG^o') of a reaction may be positive, for example, and the actual free energy change (DG) negative, depending on cellular concentrations of reactants and products. Many reactions for which DG^o' is positive are spontaneous because other reactions cause depletion of products or maintenance of high substrate concentrations.

At equilibrium, DG equals zero. Solving for DGo' yields the relationship at left.K'eq, the ratio [C][D]/[A][B] at equilibrium, is called the equilibrium constant. An equilibrium constant greater than one (more products than reactants at equilibrium) indicates a spontaneous reaction (negative DG°').

The variation of equilibrium constant with DG^o' is shown in the table below.

Keq	DGo' (kJ/mol)	Starting with 1 M reactants and products, the reaction:
104	– 23	proceeds forward (spontaneous)
102	– 11	proceeds forward (spontaneous)
100 = 1	0	is at equilibrium
10–2	+ 11	proceeds in reverse
10–4	+ 23	proceeds in reverse

Energy coupling is discussed on p. 59-60 & 566-567.

• A spontaneous reaction may drive a non-spontaneous reaction.
• Free energy changes of coupled reactions are additive.

Examples of different types of coupling:
A. Some enzyme-catalyzed reactions are interpretable as two coupled half-reactions, one spontaneous and the other non-spontaneous. At the enzyme active site, the coupled reaction is kinetically facilitated, while the individual half-reactions are prevented. The free energy changes of the half-reactions may be summed, to yield the free energy of the coupled reaction.
For example, in the reaction catalyzed by the Glycolysis enzyme Hexokinase, the two half-reactions are:

• ATP + H₂O « ADP + P_i .................. DG^o' = -31 kJoules/mol
• P_i + glucose « glucose-6-P + H₂O ... DG^o' = +14 kJoules/mol

Coupled reaction: ATP + glucose « ADP + glucose-6-P .. DG^o' = -17 kJoules/mol
The structure of the enzyme active site, from which water is excluded, prevents the individual hydrolytic reactions, while favoring the coupled reaction. 
B. Two separate enzyme-catalyzed reactions occurring in the same cellular compartment, one spontaneous and the other non-spontaneous, may be coupled by a common intermediate (reactant or product).
A hypothetical, but typical, example involving pyrophosphate:

• enzyme 1: A + ATP « B + AMP + PP_i ....DG^o' = +15 kJ/mol
• enzyme 2: PP_i + H₂O « 2 P_i ....................DG^o' = –33 kJ/mol

Overall: A + ATP + H₂O « B + AMP  +  2P_i ... DG^o' = –18 kJ/mol
Pyrophosphate (PP_i) is often the product of a reaction that needs a driving force. Its spontaneous hydrolysis, catalyzed by Pyrophosphatase enzyme, drives the reaction for which PP_i is a product. For an example of such a reaction, see the discussion of cAMP formation below.

C. Ion transport may be coupled to a chemical reaction, e.g., hydrolysis or synthesis of ATP.In the diagram at right and below, water is not shown. It should be recalled that the ATP hydrolysis/synthesis reaction is ATP + H2O « ADP + Pi. Equivalent to equation 20-3 on p. 727, the free energy change (electrochemical potential difference) associated with transport of an ion S across a membrane from side 1 to side 2 is represented below.

R = gas constant, T = temperature, Z = charge on the ion, F = Faraday constant, and DY = voltage across the membrane.

Since free energy changes are additive, the spontaneous direction for the coupled reaction will depend on the relative magnitudes of:

• DG for the ion flux (DG varies with the ion gradient and voltage.)
• DG for the chemical reaction (DG^o' is negative in the direction of ATP hydrolysis. The magnitude of DG depends also on concentrations of ATP, ADP, and P_i .)

Two examples of such coupling are:1. Active transport. Spontaneous ATP hydrolysis (negative DG) is coupled to (drives) ion flux against a gradient (positive DG). For an example, see the discussion of SERCA.
2. ATP synthesis in mitochondria. Spontaneous H+ flux across a membrane (negative DG) is coupled to (drives) ATP synthesis (positive DG). See the discussion of the ATP Synthase.

"High Energy" Bonds
The structure of ATP is shown below at right (see also p. 566). Anhydride bonds (in red) link the terminal phosphates.

Phosphoanhydride bonds (formed by splitting out water between two phosphoric acids or between a carboxylic acid and a phosphoric acid) tend to have a large negative DG of hydrolysis, and are thus said to be "high energy" bonds. It is important to realize that the bond energy is not necessarily high, just the free energy of hydrolysis.

"High energy" bonds are often represented by the "~" symbol (squiggle), with ~P representing a phosphate group with a high free energy of hydrolysis.
Compounds with "high energy" bonds are said to have high group transfer potential. For example, P_i may be spontaneously removed from ATP for transfer to another compound (e.g., to a hydroxyl group on glucose).
Potentially two "high energy" bonds can be cleaved, as two phosphates are released by hydrolysis from ATP (adenosine triphosphate), yielding ADP (adenosine diphosphate), and ultimately AMP (adenosine monophosphate). This may be represented as follows (omitting waters of hydrolysis):

• AMP~P~P ® AMP~P + P_i   (ATP ® ADP + P_i)
• AMP~P ® AMP + P_i            (ADP  ® AMP + P_i)

Alternatively, as discussed above:

• AMP~P~P ® AMP + P~P_i    (ATP ® AMP + PP_i)
• P~P ® 2 P_i

ATP often serves as an energy source. Hydrolytic cleavage of one or both of the "high energy" bonds of ATP is coupled to an energy-requiring (non-spontaneous) reaction, as in the examples presented above.
AMP functions as an energy sensor and regulator of metabolism. When ATP production does not keep up with needs, a higher portion of a cell's adenine nucleotide pool is in the form of AMP. AMP then stimulatesmetabolic pathways that produce ATP.

• Some examples of this role involve direct allosteric activation of pathway enzymes by AMP. (E.g., activation of the Glycogen Phosphorylase enzyme by AMP will be discussed later.)
• Some regulatory effects of AMP are mediated by the enzyme AMP-Activated Protein Kinase. (For example the role of AMP-Activated Protein Kinase in stimulation of fatty acid catabolism by AMP will be discussed later.)

Artificial ATP analogs have been designed that are resistant to cleavage of the terminal phosphate by hydrolysis, e.g., AMPPNP, depicted at right.Such analogs have been used to study the dependence of coupled reactions on ATP hydrolysis. In addition, they have made it possible to crystallize an enzyme that catalyzes ATP hydrolysis with an ATP analog at the active site.

A reaction that is important for equilibrating ~P among adenine nucleotides within a cell is that catalyzed by Adenylate Kinase:

 ATP + AMP « 2 ADP

The Adenylate Kinase reaction is also important because the substrate for ATP synthesis, e.g., by the mitochondrial ATP Synthase, is ADP, while some cellular reactions dephosphorylate ATP all the way to AMP.
The enzyme Nucleoside Diphosphate Kinase (NuDiKi) equilibrates ~P among the various nucleotides that are needed, e.g., for synthesis of DNA and RNA. NuDiKi catalyzes reversible reactions such as:

ATP + GDP « ADP + GTP  ,   ATP + UDP « ADP + UTP  , etc.

Many organisms store energy as inorganic polyphosphate, a chain of many phosphate residues linked by phosphoanhydride bonds. It may be represented as: P~P~P~P~P... Hydrolysis of P_i residues from polyphosphate may be coupled to energy-dependent reactions. Depending on the organism or cell type, inorganic polyphosphate may have additional functions. For example, it may serve as a reservoir for P_i, a chelator of metal ions, a buffer, or a regulator.
Why do phosphoanhydride linkages have a high free energy of hydrolysis? Contributing factors for ATP and PP_i are thought to include:

• Resonance stabilization of the products of hydrolysis exceeds resonance stabilization of the compound itself. See Fig. 16-22 p. 568.
• Electrostatic repulsion between negatively charged phosphate oxygens favors separation of the phosphates.

Phosphocreatine (also called creatine phosphate), another compound with a "high energy" phosphate linkage, is used in nerve and muscle cells for storage of ~P bonds.Creatine Kinase catalyzes:   phosphocreatine + ADP « ATP + creatine This is a reversible reaction, though the equilibrium constant slightly favors phosphocreatine formation. Phosphocreatine is produced when ATP levels are high. When ATP is depleted during exercise in muscle, phosphate is transferred from phosphocreatine to ADP, to replenish ATP.

Phosphoenolpyruvate (PEP), involved in production of ATP in Glycolysis, has a larger negative DG of phosphate hydrolysis than ATP.Removal of phosphate from the ester linkage in PEP is spontaneous because the enol product spontaneously converts to a ketone.

The ester linkage in PEP is an exception. Generally phosphate esters, formed by splitting out water between a phosphoric acid and a hydroxyl group, have a low but negative DG of hydrolysis. Examples, shown below, include:

the linkage between the first phosphate and the ribose hydroxyl of ATP. the linkage between phosphate and a hydroxyl group in glucose-6-phosphate or glycerol-3-phosphate. the linkage between phosphate and the hydroxyl group of an amino acid residue in a protein (serine, threonine or tyrosine). Regulation of proteins by phosphorylation and dephosphorylation will be discussed later. An example mentioned above is AMP-Activated Protein Kinase.

ATP has special roles in energy coupling and phosphate transfer. The free energy of hydrolysis of phosphate from ATP is intermediate among the examples listed in the table below (more complete table p. 566). ATP can thus act as a phosphate donor, and ATP can be synthesized by transfer of phosphate from other compounds, such as phosphoenolpyruvate (PEP).

Phage Structure:

1) Most phage's occur in 1 of 2 structural forms, having either cubic or helical symmetry. In overall appearance, cubic phage's are regular solids or polyhedral helical phage's are rod-shaped.
2) polyhedral phage's are icosahedral in shape. This means that the capsid has 20 facets, each of which is equilateral triangle, these facts come together to form the 12 corners.
3) In the simplest capsid there is a capsomere at each of 12 vertices, this capsomeres which is surrounded by  5 other capsomere is termed as penton.
4) In larger and more complex capsid the triangular facets are subdivided into a progressively larger number of equivalent triangle. thus a capsid may be composed of hundreds of camsomeres but it is still based on simplest on the simplest icosahedron model.
5) The elongated head of some tailed phage's are the derivatives of the icosahedral.
6) Rod- shaped viruses have there capsomeres arrange helically and not in staked ring.
7) Some bacteriophage's such as teven coliphages have very complex structure including a head and a tail. They are said to have binal symmetry because each virion has has both an icosahedral head and a hallow helical tail.

STRUCTURE OF ICOSAHEDRAL CAPSID

STRUCTURE OF HELICAL SHAPED VIRUSES (Tobacco mosaic virus) 

Bacteriophage's Morphology

1) All phage's have a nucleic acid core covered by a protein coat or capsid. The capsid is made up of  morphology subunits called CAPSOMERES. The capsomeres consist of number of protein subunits or molecules called PROMOTERS.
2) Bacterial viruses may be grouped into 6 morphological types :-
  A: This most complex type has a hexagonal head, a rigid tail with a contractile sheath and tail fibres
  B: Similar to A, this type has a hexagonal head however it lacks a contractile sheath, its tail is flexibly and it may or may not have tail fibres.
  C: This type is characterized by a hexagonal head and a tail shorter than the head. The tail has no contractile sheath and may or may not have tail fibres.
  D: This type has a head made up of large capsomeres but has no tail.
  E: This type has a head made up of small capsomeres but has no tail.
  F: This type is failamentous.
 3) Type A,B and C show a morphological unique to bacteria phage's. The morphological types in group D and E are found in plants and animals.
The filamentous form of group F is found in some plant viruses.
 4) Pleomorphic viruses were recently discovered to have a lipid- containing envelop have no detectable capsid and posses double-Stranded DNA.

Viruses of bacteria. (Bacteriophage)

* INTRODUCTION OF VIRUSES:
   1) Viruses are obligate intracellular parasites whose genomes are a nucleic acid.
   2) Viruses are 10-100 times smaller than most bacteria. with approximate size range of  20 to 300nm.
   3) Viruses are incapable of independent growth in an artificial media, they can grow only in animal or plant  cell's or in micro-organisms
   4) Viruses lack metabolic machinery of there own to generate energy or to synthesize proteins they depend on the host cell's to carry out these vital functions.
   5) the viral genetic material is either DNA or RNA hence viruses doesn't have both.
   6) the nucleic acid is enclosed in highly specialized protein coat. the coat protects the genetic material when the virus is outside of any host cells and serves as a vehicle in order to enter another specific host cells.
  7) infectious virus is called as VIRION .

* BACTERIOPHAGE'S
  1) Bacteriophage's are the viruses that infect bacteria.
  2) Bacteriophage's like all viruses are composed of a nucleic acid core surrounded by a protein coat, bacterial virus appears in different shapes, although many have a tail through which they inoculate the host and cells with viral nucleic acid
  3) there are two main types of bacterial virus LYTIC and VIRULENT and TEMPERATE or A VIRULENT
  4) When lytic phage's infect cells, the cells respond by producing large number of new viruses . That is at the end of the incubation period the host cell burst or lysis , releasing new phage's to infect other host cells. This is called LYTIC cycle.
  5) In the temperature type of infection the results are not so readily apparent. The viral nucleic acid is carried and replicated in host bacterial cell from one generation to the another generation   without any cell lycis . However temperature phage's may spontaneously become virus lent at some subsequence generation and lyses the host.

What is RNA?

Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate.

RNA comes in a variety of different shapes. Double-stranded DNA is a staircase-like molecule. Image Credit: National Institute of General Medical Sciences

RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.

Ribonucleic acid (RNA) has the bases adenine (A), cytosine (C), guanine (G), and uracil (U). Image Credit: National Institute of General Medical Sciences

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of mostviruses.
RNA and DNA are both nucleic acids, but differ in three main ways. First, unlike DNAwhich is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Second, while DNA contains ''deoxyribose'', RNA contains ''ribose'' (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine. For instance, determination of the structure of the ribosome—an enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA.