Human genetics is the science which looks at the inherited variations in humans, a study of the mechanisms of evolution, and the process of change in gene frequency. Medical genetics is the application of these principles to health. Medicine is passing through a revolution in how diseases are diagnosed , classified and treated as a result of the advances in genetics. Equally, nutrition is significantly the science of health, the study of how food fortifies and sustains the normal individual. Many genetic differences relate to rare conditions. The challenges are the explanation of the causes of common conditions which are secondary to disease, causing mutations and the relationship between the genetic makeup of individuals and populations and the environment and diet of the individual.
Every individual has a specific potential for survival and reproduction which is dictated in part by genetically determined characteristics which influence metabolism, fecundity, birth, growth and death.
Vocabulary for Genetics —
The vocabulary of molecular biology is specialised but necessary to gain an understanding. Therefore vocabularies are given, even these vocabularies are technical and therefore it is recommended that they are referred to when reading the text.
The Human Chromosomes —
Humans have 22 pairs of autosomal chromosomes (autosomes in the diploid ie paired state), and the sexes are differentiated at this level by the additional pair of sex chromosomes of which the female has a pair of X chromosomes and the male has XY chromosomes. During cell division there is paired exchange between closely associated chromatids. A chromatid is one of the two similar strands of a duplicated chromosome. Centromere, is a compact region on a chromosome where sister chromatids join. The regions on either side of the centromere are arms and are of unequal lengths, long and short arms.
A chiasma is the site where chromatids are broken at corresponding points and which join in a crossover manner producing new chromatids. This process is called breakage and reunion and leads to recombination. Translocation occurs when part of one chromosome breaks and becomes attached to a different chromosome. Translocations can be balanced with no loss of chromosome material or unbalanced with loss of chromosome material. The balanced form usually has no phenotypic consequences whereas the unbalanced may have profound effects eg Downs syndrome. Recombination is the process by which DNA is exchanged between pairs of equivalent chromosomes during egg and sperm formation. In this process the chromosomes of the parent and offspring become different. Deletion is when a segment of a chromosome is missing as the result of two breaks and the loss of the intervening piece. Inversion occurs where there are two breaks in the chromosome with rotation of the intervening segment. Paracentric inversion if on the same side of the centromere and pericentric inversion if on the opposite side.
Each pair of chromosomes is numbered, from 1 to 22, and there are also the sex chromosomes. Loss or gain in chromosomes is shown by “+” or “-“ , after the chromosome number and arm designation eg 5p, “p” or “q” indicates the short or long arm respectively. Translocation by “t” and inversionby “inv” with the chromosome involved in the first bracket and the breakpoint in the second. The locus on the chromosome is identified by staining bands on the chromosome using cytological staining techniques, eg normal chromosome 9 normal band 22.
inv(9)(q22q34) means break and paracentric inversion in a single chromosomal arm ie long arm q of chromosome 9 between region 2 band 2 and region 3 band 4. The segment of chromosome between is reversed (inverted)
Principles of inheritance —
Mendel clarified the process of inheritance through his studies on peas. In the mating process, paired genes from each parent separate ( segregate ) into single units, pass to the next generation, as individuals, independently of each other, and are never present together in the next generation. This is Mendel’s first law .The second law is that pairs of genes pass to the next generation as though they were independent of one another. Mendel showed that when the newly paired genes from the parent generation are either both dominant or both recessive then the offspring will be homozygous for that gene. If there is a mix of dominant and recessive genes the resulting individual is heterozygous. Homozygous is when there are two identical genes at a single site or locus of a chromosome; heterozygous is when these two genes are different. A dominant gene determines a characteristic regardless of whether or not it is in a homozygous or heterozygous pairing. The recessive gene in the heterozygous situation does not express itself in the resultant individual. This means that in the next generation, when the paired genes are reshuffled, there will be offspring who are homozygous, and others who will be heterozygous for the dominant and recessive genes . The two parents each contribute to the total heritage of the offspring, four grandparents a fourth part and each great grandparent an eighth. The appearance of that contribution will be dependent upon whether it is dominant or recessive.. However, such characteristics do not appear equally in all offspring. A characteristic or phenotype from one parent may be dominant to the other parent’s recessive phenotypic contribution. Phenotypes conceal a great variety of recessive genotypes which may become apparent in subsequent generations.
All genes can be pleiotrophic, dominant in one aspect of their expression and recessive in another. A favoured gene will increase in frequency and expression and a favourable characteristic will eventually become dominant. However, when the circumstances change then that gene may become disadvantageous and loses that dominance. Major genes have defined functions which determine specific characteristics, as distinct from polygenes, which are a group of genes, functioning together , each of which have a small but additive effect on the phenotype. Major genes function at a single locus and may function in different allelomorphic states.
Alleles may be:
• completely dominant
• incompletely or partially dominant; the phenotype of the heterozygote is intermediate between that of the two homozygotes
• codominant and contribute equally to the phenotype
According to Mendel’s second law, in the second generation, alleles assort independently so that equal numbers of each of the four types of gamete are produced. Two general types of offspring are produced:
• two parental types
• a recombinant type where the dominant of one parent and the recessive of the other parent are combined
After conception, when two sets of chromosomes pair, the pairs of alleles determine the characteristics of the developing individual. Some inherited characteristics are probably dependent upon several alleles; that is, there is a cumulative influence of several genes. Genes close together on a chromosome tend to remain close to each other during cell division ( gamete production ). Population genetics vocabulary
A species consists of a set of individuals who can actually or potentially interbreed and may adapt but are reproductively separate from other species.
A population is an inter-breeding group of individuals.
The phenotypic variation of a characteristic in a population usually takes the form of a unimodal frequency distribution which can be described as a mean and variance.
Heterozygote is an individual with different alleles at a corresponding locus and homozygote have the same alleles at corresponding loci on the same chromosome. As fitness to survive in an environment increases so genetic variability is reduced; that is, inbreeding results in fewer heterozygotic and more homozygotic individuals
There are systematic effects in which the size and direction of change are determined including:
• immigration into and migration from a population; the effect will be dependent on the relative sizes of the immigrant and total populations
? evolution is a process of change in a population or species over the course of successive generations.
• unique mutations occur which may provide novel forms essential for evolution
A micro evolution is when there is a change in a population either to fit into a new environment or over time to meet the challenges of a changing environment. If a population is large and there are no migrations or selective mutations, mating is random, the gene pool is large, then the population will develop a genetic equilibrium after one or two generations. If a situation occurs in the environment wherein a rare allele is favoured, that allele increases in frequency slowly at a 5% increment until equilibrium is achieved.
Homology, which has two subclasses, parology- the relationship between genes which have originated by gene duplication; and orthology refers to genes which originated by species.
Mutations or changes in genotype may take place where new characteristics are needed in order to survive.
Any mutation must be consistent with the viability of the organism if it is not to be a lethal mutation.
A nonsense mutation in a gene is one which prevents the protein specific to the gene from being synthesised. Other mutations, called suppressers, may allow the nonsense mutation to be overcome so that the protein can be synthesised. Spontaneous mutations occur at a rate of between 1:105 to 10:107 per locus per generation.
Human genetics is a science that looks at the inherited variations in humans, the study of the mechanism of evolution and the process of change in gene frequency.
2. Evolution is when there is a change in a population either to fit into a new environment or over time to meet the challenges of a changing environment. Mutations or changes in genotype take place all the time in individuals. These mutations may or may not increase in the population dependent on whether new characteristics are favourable to survival.
3. A species consists of a set of individuals who may interbreed. Evolution is a process of adjustment by selection of existing genetic populations. Mutations may influence the viability of the organism and population. Immigration and movement within the population may affect the genetic pool.
4.The genetic makeup of an individual or population will be a significant factor in the ability to cope with the stresses imposed by the environment.
5. Inheritance is encoded in genes. Genes can be dominant or recessive. An allele is one of several forms of a gene occupying the same position or locus on a chromosome.
6. Humans have 22 pairs of autosomal chromosomes and one pair of sex chromosomes (X and Y) a total of 23 pairs. The chromosome contains the genes and divides during cell division. Recombination is the process whereby DNA is exchanged between pairs of equivalent chromosomes during egg and sperm formation, the chromosomes of the offspring become different from the parents.
The Genome vocabulary
A gene is the store of genetic information held in the form of deoxyribonucleic acid (DNA). The genome is the complete DNA sequence of an organism. The gene rich regions of a genome are the euchromatin. The gene poor regions of a genome and which contain simple sequence repeats are called heterochromatin. Proteome is the complete set of proteins encoded by the genome. Genes are found on chromosomes, structures which are composed of DNA and associated proteins eg histones. The gene, which may exist in several forms, is encoded for and determines the synthesis of proteins and hence the functioning of the cells, organs and organism. Autosomes are all the chromosomes except the sex chromosomes. A normal somatic cell is diploid, that is, it has two sets of paired chromosomes. A gene can exist in more than one format on the same point or locus on a chromosome, called an allele or allelomorph.. Different alleles of the same gene are called multiple alleles. Gene frequency in the population is the frequency of one kind of allele in the population.
Genes that are present in two quite distinct organism or species are said to be conserved. Such conservation requires similarity at the DNA, RNA or amino acid sequence in the encoded protein. Changes in the gene’s DNA are mutations. The total genetic constitution of an organism is the genotype, and this can also refer to the particular pair of alleles that an individual has at a given region of the genome. The haplotype is a particular combination of alleles or sequence variations which are close together, and hence likely to be inherited together on the same chromosome. The function and physical appearance of an individual is the phenotype. Polymorphism is a region of the genome that varies between individual members of a population, and is present in a significant number of individuals in the population.. Epistasis is when one gene eliminates the phenotypic effect or the expression of another gene at another locus. A gene is said to have a high penetrance if it has a high frequency of expression in individuals who are carriers of that gene A gene is said to be pleiotrophic if it is responsible for multiple, distinct, apparently unrelated phenotypic effects.
The cell, the ‘triumph of evolution’ is the basic unit of living organisms. The cell is divided into different structures and functions forming physical and biochemical compartments. Chemicals move between compartments by specific transport mechanisms. Cells interact with their environment through chemical signals at the external surface, transduction of these signals within the cell, and by secretion of synthetic products from the cell.
The cell compartments, include the nucleus, cytosol, mitochondria, endoplasmic reticulum (ER), Golgi apparatus, lysosomes and peroxisomes.
The compartments of the cell
Compartment Boundary Cell volume (%) Function Nucleus Nuclear envelope 5 Gene transcription Cytosol Plasma membrane 55 Protein synthesis Mitochondria Mitochondrial envelope 25 Energy production Endoplasmic reticulum Folded membrane 10 Protein modification Golgi apparatus Membrane stacks 5 Protein sorting Lysosome Closed membrane < 1 Protein degradation Peroxisome Closed membrane < 1 Oxidation reactions Nucleus
The nucleus contains the genes encoded for the synthesis of proteins. The DNA is complexed with protein and forms exceptionally long continuous strands the chromosomes, and in humans each diploid human cell contains 23 pairs of chromosomes. The nucleus is surrounded by a double membrane, the layers of which contain pores necessary for the transfer of material to the cytosol.
All of the DNA in the nucleus is replicated when cells divide. Exact copies of each chromosome are distributed between the two daughter cells of each division. Transcription is another form of DNA copying. Small sections of the genome are selectively copied and each segmental copy (transcript) is formed of ribonucleic acid (RNA) not DNA.
The interior of the cell (cytoplasm) has an aqueous phase (the cytosol) in which many of the enzymes catalysing metabolic reactions function. Some enzymes, however, are membrane-bound in the various organelles found within the cytoplasm.
These are self replicating organelles consisting of elongated cylinders ( diameter 0.5-1.0 mm) . Mitochondria may move within the cell and change shape according to the cell they are stationed in. There are about 1000 mitochondria in each cell involved in tissue respiration. The organelles are surrounded with a double lipid membrane, the inner membrane being convoluted into cristae, and this creates two separate compartments, the matrix and inter-membrane space. Many enzymes are bound to the mitochondrial membranes and function in transport and oxidative metabolism to produce energy that is stored in adenosine triphosphate (ATP).
The distribution of enzymes within a mitochondrion
Enzymes for oxidation of pyruvate, fatty acids, tricarboxylic acid cycle,
DNA and the associated genetic apparatus
Inner mitochondrial membrane:
ATP synthetase, respiratory chain enzymes and transport proteins.
cytochrome b5, fatty acid elongation processing, mono amine oxidase, transferases.
All mitochondrial DNA is inherited from the mother since the portion of the male sperm which enters the female ovum has no mitochondria. There is a well supported theory that mitochondria are descended from of aerobic bacteria which invaded and then coexisted in early cells.
These are membrane sheets of rough ( with associated ribosomes) and smooth endoplasmic reticulum and are so-called because of their electron micrograph appearance. They form tubular channels called cisternae.
The Rough endoplasmic reticulum
The attached ribosomes are the site of the translation of the messenger RNA to synthesise
proteins which are either retained in the cysternae, the lysosomes or exported from the cells,
glycoproteins are glycosylated within the cisternae.
The Smooth endosplasmic reticulum
receives proteins synthesised in the rough ER
proteins being transfered from the cell for export to the Golgi apparatus.
proteins returning to the rough ER
phosphorylation of lysosomal proteins
detoxification of lipid soluble drugs and chemicals.
These organelles are the site of protein synthesis, are 200 A in diameter, and form a large complex made of several ribosomal RNA (rRNA) molecules and more than 50 proteins organised into a large subunit and a small subunit. The two subunits, both contain rRNA and protein, and are classified on the basis of centrifugation characteristics as 40S and 60S. ( S indicating centrifugation properties in Svedberg units, after Svedberg, the designer of the centrifugation system).
The complex structure associates with a set of proteins physically to move along an mRNA molecule to catalyse the synthesis of amino acids into protein chains. They also bind tRNAs which are also involved in protein synthesis.
The rRNA is encoded by genes in the nucleus. The sequence of the rRNA genes is highly conserved within species and when differences are found between rRNA genes, this information can be used as a basis for taxonomic classification and for estimating how close different species are in the evolutionary process.
This is a stack of membrane cisternae, often found close to the nucleus, and involved in the sorting of protein from the endoplasmic reticulum for subsequent transport both within and outside the cell.. The Golgi apparatus is also involved in the modification of core oligosaccharides of glycoproteins, sorting proteins for transport to defined locations and the synthesis of glycosaminoglycans.
The strands of DNA are polymers of deoxyribonucleotides; and RNA of ribonucleotides. Each unit is composed of the sugar deoxyribose (DNA) or ribose (RNA), covalently linked to a triphosphate ester of a nitrogenous base. The bases are adenine and guanine (purines) and cytosine and thymine (DNA) or uracil (RNA) (pyrimidines) (Figure 7.8 ). The corresponding DNA nucleoside monophosphate 2¢-deoxy form is deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxycytidine monophosphate (dCMP) and deoxythymidine monophosphate (dTMP). For RNA the ribonucleotides are adenosine monophosphate (AMP), guanosine monophosphate (GMP), cytidine monophosphate (CMP) and uradine triphosphate (UMP).
The polymer consists of phosphodiester bonds linking the 3¢ carbon of one deoxyribose ring to the 5¢ carbon of the next.The polymer is helical in shape, with the base moieties protruding into the centre of the helix. Two single helices of DNA interact to form a duplex strand, the double helix . The size and shape of the bases in each helix determine the ability of the two strands to interact. Because of the constraints of the helical backbone and the space within the centre of the helix, the strands will only associate if adenine and guanine on one strand lie opposite and pair with thymine and cytosine on the other. Each of the associating strands is complementary to the other, the sequence of one strand determining the sequence of the other. The base pairs, the interacting purine-pyrimidine bases on opposite strands, are non-covalently linked by hydrogen bonding .This complementation is the basis for the replication of DNA and the transcription of RNA.
Whilst every cell within the body has the same genetic material the expression of this information must of necessity vary from organ to organ and during different stages of life. Genes are turned off and on through epigenetic mechanisms, an example of which is DNA methylation. The double helix has further structure and constraints imposed upon it. DNA molecules are made more compact by the coiling of the double helix around protein particularly histone proteins H2A, H2B, H3 and H4. to form nucleosomes. The histones ( mw 11,000 to 21,000 Da) are rich in lysine and arginine. The flexible tails of the histones protrude from the globular DNA wrapped nucleosomes. Histones may be acetylated, methylated, phosphorylated or ATP ribosylated, the additon or removal of these alters the charge and shape of the histone which has important consequences for the regulation of DNA transcription. Some gene silencing activities require the removal of acetyl groups from histones and the methylation of DNA or methylation and demethylation of both DNA and histones. Two proteins SUV39H1 and heterochromatin protein 1 mark, methylate and bind to histone tails. Eventually long tracts of bases and the gene are inactivated. Another consequence of the extensive acetylation of histone is to loosen the chromatin and to allow DNA repair systems to gain access to the genome and to seek out mutations that require repair.
The double helix DNA is further tightly folded in the nucleus in a super-coiled formation. This folding and unfolding is controlled by the enzymes topoisomerase I and II . This tight coiled, double-helical state makes the base sequences inside the helix inaccessible for transcription. During cell division, each DNA strand divides to produce two new DNA molecules formed from , an old and a new DNA strand. A new strand of DNA is synthesised in the 5′ to 3¢ direction with the 3¢ end extending. One DNA duplex strand acts as a template for a complementary second strand by the polymerisation of dATP, dGTP, dCTP and dTTP.
The functions of the cell depends significantly upon proteins. Cell function, growth, differentiation, and metabolism, depends on the synthesis of specific proteins acting at critical times in a concerted manner in the life cycle of the cell. The proteins SUV39H1 and heterochromatin protein 1 are involved in the regulation of specific cell-cycle genes and the progression of cells through the G1 and S-phase. The overall process is very tightly controlled, in part by methylation and removal of acetyl groups histones.
The Human gene system can be separated into two functions. The underlying system of cellular function which is common to all creatures across the kingdoms and those functions specifically required by a complex, mobile , aware human vertebrate.
Human gene and protein systems can be separated into two functions
1. general cellular function intra- and inter cellular signalling
control of gene transcription.
. 2. specific vertebrate systems neuronal complexity
acquired immune response
The transfer of information encoded on DNA into proteins requires the production of a single strand RNA molecule. Gene expression progresses from the initial transcription of a gene to the translation of mRNA in the cytoplasm. In the nucleus, the sequence of transcription, pre-mRNA splicing and 3¢ end formation begins with the recognition of either DNA or RNA of a multiprotein complex which provides a scaffold on which transcription, splicing and 3¢ end formation takes place. Only 1.1 to 1.4% of the DNA sequence encodes protein, which is 5% of the 28% of the total genome which can be transcribed into messenger RNA ( mRNA). The protein coding sections of the genomes are found in the exons , which are separated by non coding sequences called introns. Most of the increase in size of genes in humans compared to other species is due to extended introns. Half of the overall DNA consists of various repeated sequences which have no known function, these zones are a feature of the large vertebrate genome. This repetitive DNA is regarded by some biologists as junk. Whatever their function, these regions give considerable information about biological processes and their evolution. It is now possible to establish ancestral linkages or family trees for the various components of these genome repeat regions. Within the neutral non-protein encoded regions are regulatory regions which encode instructions for regulating gene expression. These instructions are deciphered by protein transcription factors , which recognise and enhance transcription through the recognition of DNA motifs. These switch genes on and off in specific spatial and temporal patterns during development. Many evolutionarily important changes are buried within these neutral regions or have no consequence functionally.
The discovery of a gene does not necessarily mean that this gene encodes a protein, the sequence may be a non-expressed pseudo-gene. Two apparently related genes may be expressed under differing circumstances for example at different sites in cells or at differing stages in development or maturity. Therefore the cellular position and control mechanisms on the gene and hence the mode of expression becomes very important.
Disordered gene transcription, or the synthesis of non-functional proteins because of DNA mutations can have disastrous consequences for the organism. Cells have many methods for DNA repair, but these are not discussed in this book. This might become an important topic if nutrients were shown to assist the protective processes involved if DNA is damaged.
Transcription is a highly regulated process, during polymerase binding, transcription initiation, and the elongation and termination stages, with each stage requiring specific regulatory proteins. Gene transcription begins with a transient unwinding of the DNA coil and separation of the strands of duplex DNA in the region of the transcribed gene. One strand of the DNA acts as a template for the synthesis of single strand RNA. The actual process of transcription requires an RNA polymerase binding to a DNA promoter sequence, which indicates the site of initiation of transcription, the amount of RNA produced and tissue specificity . TATA boxes are an example of a promotor. There are three RNA polymerases, the most important of which is RNA polymerase II which is involved in the synthesis of mRNA and some specialised RNAs.
During transcription, protein coding genes are transcribed by RNA polymerase II , which requires other proteins including general or basic transcription factors and transcriptional activators. The binding of proteins to sequences close to the promoter regulates gene expression, by activation or repression. These proteins assemble on the promoter to form a pre-initiation complex , which is initiated by interaction with the TATA box. Transcriptional activity is strongly stimulated by promoter specific activators which are sequence specific DNA binding proteins eg C2H2 zinc finger proteins. Specific sequences signal the completion or termination of the RNA synthesis and elongation. The RNA and DNA soon peel off and separate after replication has been completed.
The newly synthesised RNA molecule is a primary transcript, the direct and total copy or transcript of the information encoded in the gene and includes all the introns, and exons in the DNA. The primary transcript RNA has to be modified. Introns are removed dependent upon the particular protein being encoded by the messenger RNA ( mRNA) . The essential coding sequences , the exons are joined to produce the specific sequence required to encoded a protein. This means that the same RNA can be used to synthesise different proteins, a process called alternative splicing. The spliceosome and several other RNA enzymes require metal ions eg magnesium as essential cofactors. Pre-mRNA splicing takes place in the sliceosome, where 4 small nuclear ribonuclearprotein (snRNP) and other proteins interact with the pre-mRNA. A modified 5¢ cap of 7-methylguanosine is added at the 5¢ end. mRNAs have a 3¢poly(A) tail added after endonucleatic cleavage of the pre-mRNA. This addition of poly (A) is directed by a polyadenylation sequence just upstream from the polyadenylation site. The amount of mRNA available for translation regulates the stability and turnover of the mRNA and hence intracellular concentration. This mRNA may be translated into protein, or sequestrated in an untranslated form or degraded.
Humans have more examples of alternative splicing and complex regulatory networks than other species. This suggests that in humans there are many ways in which exons join together to create a particular functioning messenger RNA for translation into a protein. This process of splicing allows one gene to produce several mRNAs synthesising an extended range of proteins encoded by that gene, all of which requires complex regulation of the gene. By altering the pattern of introns the genetic diversity of the genome is increased without increasing the number of genes. This flexibility becomes of particular importance in specific developmental stages and different cell types. The calcitonin gene is capable of producing calcitonin or calcitonin-gene related peptide. These nascent RNAs then associate with several nuclear proteins. This RNA – protein complex synthesised in the nucleus must be transferred to the cell cytoplasm where protein synthesis takes place. The nuclear membrane pore complex allows fully processed mature mRNA to move out and proteins synthesised on the ribosomes and to move into the nucleus. mRNA contains linear encoding for a protein and also information giving an ability to pair with ribosomal RNA, and accessibility to the inside of ribosomes.
Protein synthesis and transcription
The proteome is the sum total of all the proteins in the body. The complexity of the proteome increases from the single celled yeast to the multicellular invertebrates, vertebrates and humans.
The human genome has a least 1300 protein families which are common to other species, animals, worms, insects and plants. These protein family groups are the conserved core proteins found throughout biology and which are responsible for the basic house keeping functions of the cell , metabolism, DNA replication and repair, and translation. Many are anabolic enzymes responsible for the respiratory chain and nucleotide synthesis. There are few catabolic enzymes in these groups. Humans have many proteins involved in cytoskeleton structure, defence and immunity and transcription and translation. Many human proteins function in more than one capacity. Families of human proteins present in increased numbers compared to other species eg the worm and fly include the families of immunoglobulins (IG); developmental proteins eg fibroblast growth factors and transforming growth factor and intermediate filament proteins. The vertebrate olfactory receptor genes are another large gene family with some 1000 genes and pseudogenes, reflecting the importance of the sense of smell to vertebrates. Following the success of the Human Genome project the next phase, the study of the proteins encoded by the genes described in the Human Genome project is to be lead by the Human Proteome Organisation ( HUPO), still in its preparatory phase. The project will have three key areas of development, protein expression, protein function and a database.
Functional categories of proteins in humans
(In order of frequency in the body)
- Intracellular signalling
- Cell-cell communication
- Defence and immunity
- Protein folding and degradation
- Cytoskeletal /structure
- DNA replication and modification
- Multifunctional proteins
- cellular processes
taken from http://www.geneontology.org
Translation the process of mRNA controlled protein synthesis..
There are three different types of RNA involved in protein synthesis or translation.
a. Messenger RNA (mRNA) carries the encoded message from DNA as a strand of three-base codons. These codons ( triple base sequences) specifically read either to record an amino acid in the resultant protein, or signal the start or end of the amino acid sequencing message ( start or stop codon). After leaving the nucleus, mRNA enters the cytoplasm and becomes available to act as template for the synthesis of protein.
b. Transfer RNA, ( t RNA), is the carrier system by which amino acids are bound and transferred to the extending end of the protein being synthesised according to the dictates of the mRNA. The specificity of the sytem occurs because of the recognition of each codon by a t RNA, specific for each amino acid.The attachment between the two is catalysed by a specific aminoacyl-tRNA synthetase. The two mRNA and t RNA function as bivalent adaptors , the tRNA contains a three-base sequence which pairs with its complementary codon in the mRNA, the anticodon,
c. Ribosomal RNA (rRNA) is associated with a set of proteins to form ribosomes. This complex moves along an mRNA molecule to catalyse protein synthesis. The complex also binds tRNA and other molecules necessary for protein synthesis.
These three RNA types and the associated proteins in the ribosome allow 20 different amino acids in varying sequences and amounts to be the template for the synthesis of specific proteins.
The sequence of three consecutive bases (a codon) in the RNA molecule encode an amino acid in the elongating polypeptide chain. After leaving the nucleus, mRNA enters the cytoplasm and forms a template for protein synthesis. The sequence of bases in RNA, triple base sequence or codon is translated into a linear sequence of amino acids which forms the structural units of protein. In order to act as template for protein synthesis, the mRNA must first bind to specific sites on the ribosome .This specificity relies on the recognition of each codon for each amino acid by a separate transfer RNA (tRNA). This allows a specific amino acid to bind to an attachment site at one end of the molecule, and recognising the codon for the amino acid by means of an ‘anticodon’ triplet of bases at the other end.
In the synthesis of protein from mRNA ,
1. a specific first codon , the initiation codon UAG, indicates the beginning of the reading frame, which then runs through the codons for the consecutive amino acids for the protein being synthesised until a termination codon is reached ( UAA, UAG or UGA) and the synthesis of that protein is complete.
2. There is activation of amino acids in the cytosol. Each of the 20 amino acids are covalently attached to their specific tRNA which utilises aminoacyl-tRNA synthetase .
3. The initiation complex comprises a triad. The mRNA encoding the protein being synthesised binds to the smaller ribosomal subunit and the initiating aminoacyl-tRNA, then the larger ribosomal subunit binds. The codon of the initiating aminoacyl-tRNA base pairs with the starter codon on the mRNA. This signals the beginning of protein synthesis, a process controlled by initiation factor proteins
4 Elongation is dictated by the codon sequence of the mRNA, the corresponding tRNA bringing the appropriate amino acid for protein synthesis.
5 Termination and release occurs when a termination codon indicates that the process is finished, Release factor proteins enable the new protein to be released
6 The new protein folds into its tertiary formation. To achieve this amino acids are removed from the amino acid terminus and methyl, acetyl, phosphoryl, carboxyl, and other groups may be conjugated to the protein which determines the charges along the protein and hence its shape.
7 Proteins that fail to fold properly or to form the correct quaternary structure are retained in the endoplasmic reticulum and are eventually degraded in the proteasomes. This is an endoplasmic reticulum quality control system.
Proteins are the most tightly packed of any form of organic matter. This provides a rigid core upon which the arrangement of functional groups can take place for example catalytic side chains for enzymes. The basic protein folds are predetermined by the physical properties of the protein chain. The protein folds are formed from a chain of some 80 to 200 amino acids, producing a number of natural forms, following definite rules for the construction of each. The total number of permissible folds is somewhere between 500 and 1000. The folds are very robust and fixed, and like a steel coil will revert to a constant shape after being straightened.
Protein sorting or trafficking
All cellular proteins are synthesised on the rough endoplasmic reticulum (ER). The 10,000 or more proteins in any one cell are directed to the site of use, otherwise if misplaced they are at the best ineffective and could be a hindrance. The directing of proteins to their site of optimal activity is called protein sorting or trafficking.
Some are secreted from the cell, others are selectively distributed to various organelles, and others remain within the cytosol. The mechanisms regulating protein sorting depends upon a short sequence of amino acids, the signal sequence, which is specific to the protein and its eventual location. Proteins intended for the ER have the signal sequence attached to the protein amino terminus. Once the newly synthesised protein is in the lumen of the ER the signal sequence is removed.
Precursor proteins transported from the cytosol to the mitochondria have amino terminal signal sequences attached and are accompanied by cytosolic chaperone proteins. These new precursor proteins are held in an unfolded, incomplete form by chaperones, cytosolic Hsc70 and mitochondrial-import stimulation factor. The passage of the protein through the mitochondrial membrane is facilitated by proteins and selective membrane receptors, utilising a channel dependent upon ATP or GTP hydrolysis or a transmembrane electrochemical potential difference. The signal sequence is then removed and the intact protein folds and settles in its directed site and to its appointed task.
Those proteins synthesised in mitochondrial ribosomes and needed locally, are added directly to the appropriate compartment.
The majority of proteins are transported by the secretory pathway for those proteins which are directed by a specific signal to the endosplasmic reticulum. Synthesis is completed by ribosomes on the rough endoplasmic reticulum, some proteins remain to function there. The majority move in vesicles onto the Golgi apparatus, fold into their mature form, are then sorted and dispatched onwards or remain locally. During this process oligosaccharide side chains are added to some proteins. Some soluble proteins (digestive enzymes, hormones and neurotransmitter) are held in vesicles to be released by suitable stimuli, the process of regulated secretion. Others proteins are held in transport vesicles to be released by continuous secretion, the process of exocytosis.
Most proteins undergo further transformations forming the mature protein before secretion.
Protein synthesis ®the rough ER lumen ®Golgi cysternae®secretory vesicles ®regulated
Other proteins are synthesised on cytosolic ribosomes and are thereafter directed by signalling sequences to their destination. Within the cell, small vesicles transport proteins from one organelle to another. The protein coat of the vesicles determines where the protein is deposited.
Coated vesicle transport routes
Clathrin vesicles ® plasma membrane and Golgi ® endosomes.
COP I vesicles ® Golgi cisternae ® rough endoplasmic reticulum
COPII vesicles ® rough endoplasmic reticulum ® Golgi
The coated vesicles also contain adapter proteins eg clathrin and AP1 and AP2
Cells can also transport proteins from outside the cell into their cytoplasm using clathrin coated pits and vesicles on the membrane surface, the process of endocytosis. A specific receptor on the cell surface may bind the extracellular macromolecule, the ligand, forming a transport vesicle, within the cell of the receptor-ligand complex. Low density lipoproteins (LDL), transferrin and insulin are good examples of such a transport system.. The ligands dissociate from the receptor and return to the surface.
During cell division the nucleus is emptied when the membrane is divided. The released proteins have to be moved back into the nucleus, a recycling process using proteins; importin a and b and a GTPase called Ran.
Human genetic variation
Within any species, populations and families there are biological variables. Differences in our genomes account for some of these differences. The amino acid sequence of each protein is determined primarily by the codon and subsequent splicing. The function of each cell protein, including of course enzymes, is determined by this amino acid sequence and the folding of the mature protein which may include enzymatic substitution of some of the amino acid residues after translation. The activity and amount of all proteins are controlled principally by regulation of gene transcription.
In the uterus the genes of the evolving foetus are derived from the mother and father. The environment is created by the mother. Which of these competing genes at each locus of the chromosome is active or not is decided by methylation or demethylation of the maternal or paternal equivalent gene, an imprinting gene.
Haemoglobin illustrates how a single point mutation within an exon can have significant effects on the function of an expressed protein. Haemoglobin is the oxygen-carrying protein of the blood. Transport of oxygen to tissue cells is a fundamental requirement for metabolism. The transport of water and fuel (food) is subsidiary only in the sense that cell death occurs more rapidly from deficiency of oxygen than from deficiency of water or fuel. Haemoglobin is an abundant protein, amongst the first to be studied and is one of the best characterised of human proteins.
Similar mutations occur in the genes encoding other proteins. Many severe diseases are caused by alterations or premature termination of the amino acid sequence of enzymes involved in metabolic pathways, leading to loss of catalytic function, eg phenylketonuria, galactosaemia and the ‘storage diseases’.
Thus, genetically based seemingly minor alterations in the DNA and subsequent synthesis and sequence of one protein may give rise to variably severe consequences. It is highly likely that such mechanisms underlie the differences between individuals in the way in which some nutrients are handled.
The uniqueness of the DNA sequences of individuals is shown by restriction fragment length polymorphism or ‘genetic finger-printing’, a technique with forensic applications.
Enzymes and isoenzymes
An important feature of an enzyme and indeed many other functional proteins are the domains, regions of the protein created by the local amino acids chain sequence and subsequent folding into stable globular units fashioning specific functions. In enzymes these are catalytic domains and in membrane proteins, transmembrane domains. There may be more than one domain in an enzyme for that enzyme’s function. The complexity of proteins and the number and combinations of domains increases with evolution. Nevertheless more than 90% of protein domains in humans are also present in other species from other kingdoms.
Adaptation to a changing environment is of paramount importance to all organisms. One such environmental change is the availability and type of nutrients and their subsequent processing by the metabolic system. Such an adaptation will depend upon a responsive regulatory system, which includes enzymatic activity and transport systems. The spectrum and activity of the enzymes and transport systems synthesised by the genome of the individual is unique to that person. Hence, the metabolic response in normal, abundant and deficient dietary intakes will be dictated by the enzyme types and transport systems and their cellular distribution and activity. Such differences in enzyme activity and response result from the isoenzymes or enzymes. An individual metabolic pathway consists of a sequence of enzymatically catalysed reactions, with different rates of activity according to the body’s enzymes or isoenzyme profile. An isoenzyme, sometimes called an isozyme, is a member of a group of enzymes which are structurally similar, and which catalyse the same reaction, but with differing rates of activity. These isoenzymes may differ by only an amino acid or by different aggregation of subunits of polypeptides.
Inter-individual differences in enzyme profile
An example is the enzymatic difference between Caucasians and Mongol races in the type and activity of the enzyme glyceraldehyde dehydrogenase. A deficiency or reduced enzyme activity as in Mongol races results in accumulation of blood glyceraldehyde folowing the ingestion of alcohol with resultant flushing.
Another enzymatic difference between individuals is the slow and fast acetylation of certain drugs. Acetylation of fat-soluble chemicals is a liver enzymatic activity which facilitates the biliary excretion of water-insoluble xenobiotic end products. Caffeine is eliminated in the urine after hepatic acetylation and hence becomes more soluble in water. Wakefulness after drinking coffee in the later part of the day may result from caffeine accumulation in the body due to slow clearance secondary to slow acetylator activity.
Before the discovery of isoenzymes, differences in metabolic activity between tissues and to a lesser extent between individuals were believed to be due to variations in the amounts of enzyme and substrate available, cell permeability, compartmentalisation and hormone effects. These are important, but equally important are the qualitative aspects of tissue enzymology.
Enzymes are, fundamentally catalysts of biochemical reactions. Their activity can be regulated by three mechanisms.
1. Enzyme molecule synthesis and degradation. In general, enzyme synthesis is constant, a zero-order reaction. Degradation is a first-order reaction, ie the degradation rate is a percentage of the available enzyme pool. A steady-state exists when synthesis and degradation rates are equal. Changes in steady-state results in changes in enzyme activity, dependent upon the half life of the enzyme
2. Conversion from an inactive to an active form. This is a rapid mechanism, eg by phosphorylation or dephosphorylation. Glycogen synthetase and pyruvic dehydrogenase are active in the dephosphorylated form, whereas phosphorylase, an enzyme involved in glycogen breakdown, is active only when phosphorylated. A single enzyme may be responsible for the initiation of a major metabolic change.
One enzyme initiates a major metabolic change
For example, a hormonal trigger for glycogen degradation activates adenylcyclase at the cellular membrane. Cyclic AMP is synthesised from ATP and stimulates kinase which catalyses the activation of phosphorylase kinase. Phosphorylase kinase catalyses the phosphorylation of phosphorylase b to the active a form. The active enzyme then acts on glycogen to form glucose-1-phosphate which then leads to the formation of glucose.
Some enzymes, especially proteases, are synthesized as the inactive ‘pro-’ forms zymogens eg trypsinogen, chymotrypsinogen and pepsinogen which are converted, when required to the active form by very specific proteolytic cleavage at a peptide bond. In the lumen of the duodenum trypsinogen is cleaved by enterokinase, a small intestinal brush border enzyme. Trypsin in turn activates the other pancreatic zymogens. Similar chain reactions occur in blood coagulation, fibrinolysis, hormone action and the complement system.
3. Changes in concentration of metabolic intermediates. Changes in concentrations of substrates, cofactors, activators and inhibitors provide the fine and immediate control of enzyme activity. Enzyme activity is related to substrate and cofactor concentration, according to the Michaelis-Menten equation.
Vm x [ S ]
V = —————————————
Km + [ S ]
where V is the velocity of the reaction and Vm is the maximal velocity, Km is the Michaelis constant, ie the concentration of substrate at which the velocity is half Vm, and [S] is the concentration of substrate or cofactor. The Michaelis constant indicates the physiological concentration at which the enzyme will function. This identifies the possibility of catalytic effectiveness at a tissue substrate concentration.
An alternative enzymatic relationship between velocity and substrate concentration is sigmoidal in type. This occurs as a result of a co-operative binding of substrate to enzymes formed of multiple sub-units. The first molecule attaches to a subunit and causes a change in the shape of the subunit, which in turn facilitates the binding of substrate to a second subunit, and so on. The best-known example of this allosteric interaction is the binding of oxygen by the subunits of haemoglobin. Activation and inhibition of enzyme activity are important. Activation may originate in the cell or be mediated from an extraneous source which activates a receptor. An inhibitor may compete with a substrate for the binding site. Alternatively, the inhibitor or activator may be attached at another site and elicit allosteric interactions either to reduce or augment enzyme activity. The effector may also alter the rate of release of product from the enzyme, thereby altering Km of the reaction.
Allosteric describes a protein, or more specifically an enzyme, with more than one distinct receptor sites. One site which binds the substrate is the active site, the other the allosteric site is separate from the active site and is affected by the same or another metabolite. The protein – allosteric effector complex reversibly alters the molecular structure of the protein and for an allosteric enzyme alters the shape of the protein and the properties of the active site (the allosteric effect). An allosteric enzyme is to be found at a branch point in a metabolic pathway. A ligand is any atom, ion or molecule that binds specifically to a larger one, in this case an enzyme. The ligand is chemically altered by the enzymatic reaction and the enzyme changes shape to allow these reactions to take place at several sites on the enzyme.
Rate limiting enzyme and step
This is the slowest step in a reaction sequence, the step which is catalysed by the enzyme with the slowest rate constant. Such a step is where the system is most readily saturated.
Isoenzyme and metabolic reversibility
The separation of metabolic pathways by physical compartmentalisation is an essential component of metabolism. Isoenzymes are separated into different cellular compartments. Metabolism is a series of discrete unidirectional chemical reactions catalysed by polyisoenzyme complexes. The same reaction may occur in different directions in different compartments of a cell, or in two different cells within the same organism. Each will be catalysed by a different isoenzyme, with different Km values and at least one will require the input of energy from a different reaction, or the efficient removal of the products of the thermodynamically unfavourable reaction.
Metabolic variables and the isoenzymes implicated Variable Isoenzyme Km Hexokinase Pyruvate kinase Glutaminase Creatine kinase Substrate and cofactor Aldolase Alcohol dehydrogenase Isocitrate dehydrogenase Allosteric properties Hexokinase Pyruvate kinase Aspartate kinase Glutaminase Fructose bisphosphatase Subcellular localization Isocitrate dehydrogenase Adenylate kinase Dietary and hormonal control Hexokinase Tyrosine aminotransferase Pyruvate kinase Arginase Isoenzyme compositions in tissues
The liver and muscle have different isoenzyme compositions. There are distinct muscle-type phosphofructokinase, aldolase, enolase and pyruvate kinase enzymes which are not present in liver and vice versa. Glycogen phosphorylase is an other example. Glucokinase is present in the liver and not present in the muscle. These differences reflect the different metabolic requirements of the tissues.
Of the 10 enzymes involved in the sequential metabolism of glucose to pyruvate nine have isoenzymes. Enzyme multiplicity may arise as a result of various factors.
Multiple alleles at a single genetic locus The heterozygous individual with two different allelic variants (one on the maternally derived chromosome and one on the paternally derived chromosome) will produce two different types of enzyme subunits. If the enzyme is composed of multiple subunits, an individual heterozygous for the genes of some or all of the subunits will be capable of assembling a greater variety of types.
Multiple genetic loci The organism may produce one protein with a given enzyme function in one tissue, and a different protein which catalyses the same reaction in a different tissue. Gene expression varies from tissue to tissue and at varying times in the overall development, from foetus to adult and even with ageing in the adult. Multiple gene loci produce differences in isoenzyme profile.
Secondary or post-translational alterations in isoenzymes
Enzyme subunits can be modified to produce a range of composite enzymes from the same gene complex. Only part of the enzyme subunit may be involved.
Aldolase is encoded at three genetic loci. In muscle, aldolase A has two subunits, A alpha and A beta. The transition from A alpha to A beta is by slow deamination of an asparagine residue near the carboxyl terminus. The post translational process may be tissue-specific, creating differences in tissue isoenzymes. For example, pyruvate kinase is a tetrameric enzyme. Its activity is inhibited when the enzyme is phosphorylated. The predominant isoform in the liver is designated L and its activity is modulated by phosphorylation. Two other isoforms are less susceptible to phosphorylation. In this way hormone action inhibits utilisation of glucose by the liver (by phosphorylation of the L isoenzyme) when the blood glucose level is low and the substrate is more urgently required by other tissues such as brain and muscle.
Artefacts or apparent isoenzymes from the same enzyme or proenzyme can be created under differing conditions of extraction and storage conditions. Only permanent forms are considered to be true isoenzymes.
Coenzymes and prosthetic groups
Many enzymes require coenzymes such as NAD/NADH or Coenzyme A (CoA), and the prosthetic groups, the metal ions , haem groups and vitamin derived cofactors. These extend the specificity of the enzymes. The covalent attachments of certain prosthetic groups allow the transfer of intermediates in a reaction between the active sites of multi-enzyme complexes, which is the swinging arm system.
1. Metabolism is in part dependent on the structure of the cell. Structure and functions are distributed between cells and chemicals move between compartments by specific transport mechanisms. The cell compartments include the nucleus, cytosol, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosome and peroxisome. The nucleus contains the genes for the synthesis of cellular proteins. Cytosol is an aqueous phase containing many of the enzymes catalysing metabolic reactions. The mitochondria include the enzymes which function to transport oxidatively metabolized nutrients. The endoplasmic reticulum is involved in protein synthesis.
2. The strands of DNA within the nucleus are polymers of deoxyribonucleotides; RNA polymers of ribonucleotides. Each unit consists of deoxyribose covalently linked to bases, adenine and guanine (purines) and cytosine and thymine (DNA); uracil (RNA) (pyrimidines). The reading of the code of the DNA and RNA is in triplets of any three of these bases, the codon. The order of any three of these bases determines the amino acid sequence of proteins produced by the DNA molecule.
3. Stretches of DNA in the chromosome are genes; much of the remainder of the sequences between genes appear as yet, to have no known function. Other sequences, while not transcribed to proteins, act as regulatory elements by facilitating the binding of functional proteins to the DNA strand.
4. The number of protein-encoding genes is between 26-31,000, the correct figure is probably 31,000; of these some 740 genes are non-protein- coding RNAs involved in cellular function.
5. The DNA sequence which is encoded for protein synthesis is initially transcribed into mRNA. mRNA may undergo splicing which enables one gene to encode for several proteins. The mRNA passes from the nucleus, enters the cytoplasm and becomes available to act as a template for the synthesis of protein. Amino acids required for protein synthesis are provided by specific transfer RNAs.
6. Proteins synthesised in the cell are subsequently sorted or trafficked to other parts of the cell or other organs
. 7. Isoenzymes (isozymes) are protein enzymes which are identical in all respects with the prime functioning enzyme but differ in functional efficiency by virtue of small but important amino acid variations from the other isoenzymes in that family. The range of enzymes provided by the genetic configuration is individual to each person. Hence, the metabolic pathways in normal, abundant and deficient dietary states will be dictated by the enzyme amounts and activity, in turn, dependent on the isoenzymes or enzyme separation in the individuals cell or organs.
8 Enzyme activity may be regulated by three mechanisms: enzyme synthesis and degradation; conversion from an inactive to an active form; and changes in concentration of metabolic intermediates. The activity of an enzyme is described by Michaelis-Menten equations.
As gene identification translates into gene function and the structure of gene products, there is much to be learnt about biochemical pathways and their regulation, which is of great relevance to nutrition. The metabolic process by which each nutrient is converted to energy or to structure and other functions will be individual and dependent upon the efficiency of the isoenzyme complexes in the metabolic pathways. This individual metabolic response will be genetically determined. Major nutrients ( glucose, fatty acids, amino acids ) and minor nutrients ( iron, vitamins ) are involved with hormones in the regulation of gene expression. All nutrients are involved in some manner in the control of gene expression and post translational events. In each section where the metabolism of nutrients is discussed the nutrient – gene interaction will be mentioned.
Variations in the genome structure and resultant protein allosteric variations will dictate the differences in an individual’s ability to metabolise individual nutrients, and this will in part dictate the well being of that individual. The effect of a single gene mutation on an individuals metabolic response to a nutrient may be obvious, though not always so. The effect of such mutations, increased when several genes are involved, may be considerable, in addition to which there are the complicating actions of secondary and tertiary modifiers and other coincidental nutritional factors. All contribute to a complicated interplay between the genome and diet where the impact of inheritance may be low and several dietary factors involved.
The enzyme and isoenzyme differences become important when there is an excess or deficiency of a nutrient when the important differences, and hence vulnerabilities, of individuals will be exposed. Starvation adversely affects individuals regardless of their genetic makeup. What is much more complicated is to understand the response of individuals and different populations to a sufficiency or excess of food. The population eating the food will be of different genetic constitution and the food eaten by different populations will be of differing constitution. Stark examples of populations being exposed to a radically new diet format are provided by the Aborigines of Australia, the Polynesian Islanders and the Native American changing from their accustomed traditional diet to a European type diet. It is recommended by some that we revert to hunter gatherer type diets from 40,000 years ago, yet our alleles may be more in accord with our current diet. The cultural element of taste has also to be taken into the equation.
Medical genetics has enabled the scientist and clinician to study the aetiology of non-infective disease at the cellular and molecular level. Many conditions are now recognised as belonging to a group of conditions, wherein changes in the genetic material are either entirely or partially responsible for the pathology.
The interpretation of human pedigree patterns is complex and beyond the scope of this book (see McKusick, 1998 for further details).
Mendelian disorders are caused by a mutation at a single genetic locus. Gene mapping precisely locates the disease loci on a chromosome and then searches for cloned sequences within the gene to identify how this differs from the advantageous gene.
Mutations in DNA sequences cause changes in phenotype. It may be quite difficult to identify the evolutionary relevant mutations. Many mutations have no noticeable impact on an organism, implying that the loss of an enzyme may not always have apparent consequences for function or survival Many evolutionary relevant mutations are outside the protein encoding regions. DNA regions that encode genes also contain long lengths of neutral variations which have no effect on the phenotype..
Phenotype variation is nevertheless a common feature of human disease as a result of a single gene mutation. The effect of such mutations are even greater in the relatively few conditions where several genes are involved.. There are also the actions of secondary and tertiary modifiers and of environmental factors. There is thus a complicated interplay between the genome and environment in multifactorial disorders where the impact of inheritance may be low and where several environmental agents are involved.
To identify a gene dependent condition the genetic markers are Mendelian characters or disorders which are used to follow a small section of chromosome through a pedigree. Ideally, a marker should have a known chromosomal location, be highly polymorphic, show codominant inheritance and be measurable by blood tests. Genetic heterogeneity implies a clinically similar condition produced by different genes or different mutations within in the same gene. In practice, a number of gene mechanisms may be involved.
More than 10,000 human genes have been catalogued in the Online Mendelian Inheritance in Man ( OMIM) which documents inherited human diseases and their causal gene mutations. There are approximately 1000 single genes associated with an increased susceptibility to a disease or a disorder
Disorders caused by mutation of genes encoding
Type of disorder dominant or recessive peak age of onset
enzyme primarily recessive first year of life
modifiers of protein function, recessive or dominant : early adulthood)
receptors: recessive or dominant first year of life and adulthood
Transcription factors) largely dominant in utero
Approximately half of the diseases of the first year of life are related to defects in genes encoding enzymes. The developing foetus is protected from this defect through access to the mother’s metabolic system through the placenta. The baby is normal at birth and the inborn errors of metabolism present only after the infant is totally dependent upon its own metabolism.
In mammals, genes found next to each other rarely share common function but often have a common evolutionary history. Segments of DNA which encode for a protein region that has a function, for example a domain are most likely to retain their sequence through the evolutionary process.Genes that are tightly linked, that is clustered in the same region of the chromosome in one species tend to be tightly linked in other species. The majority of sex related genes, which determine gender are found in the X-linked chromosome.
New mutations occur in the human population at a rate of 1-100 mutations each generation. Duplication has been a major reason for changes in genes during vertebrate evolution. Hundreds of human genes are direct inserts or transferred from bacteria. Sex chromosomes differ in their mutation pattern during the formation of eggs and sperm, mutations occur most frequently in males. Possibly because the female has two X chromosomes balancing each other, whereas in the male the single X and Y chromosome are unbalanced.
Mutation rates can be calculated from the rates at which identified genes are eliminated by natural selection and created by mutation. Most mutations for autosomal recessive conditions occur undetected in normal heterozygotes and may be transmitted by phenotypically normal carriers over many generations before appearing in an affected person.
The Human Genome Project allows rapid identification of candidate genes for many conditions and functions and makes it easier to study diseases of unknown biochemical malfunction. The identification programme first maps the chromosomal region containing the gene by linkage analysis in affected families and then searches for the gene itself. The sequencing of the genome has also allowed an understanding of the mechanisms wherein common chromosomal deletion syndromes occur. The Human Genome Project has identified and mapped some 1.4 million examples of single nucleotide polymorphism SNPs. SNPs reflect past singular event mutations., and follow a change in one base in the DNA. Individuals differ from each other by about one base pair per thousand SNPs . Individuals sharing a variant allele have a common evolutionary heritage. The variation in SNPs is least in the sex chromosomes. Every permutation of single nucleotide polymorphism will occur somewhere in the 3 billion base pairs of the human genome in the 6 billion individuals alive today.
It is easier to identify a population with a particular disadvantaged gene and disease expression than to study populations who are vulnerable or resistant to environmental factors such as a deficiency or excess of dietary constituents, tobacco smoking or alcohol. The tension between the gene and its outside environment is called an interaction. In many studies, whether case-control or cohort studies the environmental side of the gene-environment interaction can be incorrect. That is the wrong environmental factor is studied or the measurement is faulty. There is sometimes a subjective element to the choice of the environmental factor. The definition of interaction is seldom made. Statistically gene-environmental interaction occurs when the effect of the genotype on the disease only occurs when a particular environmental situation prevails, eg alcohol intake or the oral contraceptive. Some progress has been made in identifying factors determining an individual response to alcohol. Suffice to say these conditions are less marked or absent in life long abstainers. Venous thrombosis is rare in young women who don’t take the contraceptive pill, increased four fold in the entire population of women who use the oral contraceptive and increased eight fold in those women who take the oral contraceptive and also have the Arg506Gly ( Leiden ) mutation in the blood clotting factor V gene.
A genetic basis to a condition, physical attribute or disease may be determined by:
1. The DNA sequence. The delta-globin gene was discovered on chromosome 11 during DNA sequencing studies. The nucleotide sequence suggests that the transcripted protein is a member of the ?-globin family.
2. A definable protein abnormality. ?-1 antitrypsin was discovered as a serum protease inhibitor. Absence of this enzyme was shown to be associated with pulmonary emphysema and cirrhosis of the liver. This has been mapped to chromosome 14.
3. A disease entity. Cystic fibrosis has been shown by its familial occurrence pattern to be a genetic disease. Linkage analysis has implicated a gene on chromosome 7.
When there is a mutation or change in a gene or chromosome, which is associated with a disease or vulnerability or variation from the expected, that gene or chromosome is often called after that disease or vulnerability or variation. Implying that the gene or chromosome is the cause. This is not the case, it is only when there is a variation or mutation in the gene or chromosome from the healthy form that the association applies.
Some neurological diseases, Huntingdon’s chorea and fragile X syndrome have similar genetic abnormalities in that there is a lengthening of tracts of repeat DNA sequences. This ‘repeat instability’ may arise during the repair of damage to DNA
These single-gene defects or single-locus disorders result from a mutant allele or a pair of mutant alleles at a single locus. Such changes can be inherited or arise de novo through a mutation. When an allele is dominant or recessive, alleles may result in dominant or recessive conditions respectively. Modern geneticists suggest that these conditions are not attributable to dominant or recessive genes but rather that the consequent phenotypes are dominant or recessive. The inheritance is either autosomal dominant, autosomal recessive, autosomal codominant or X-linked inheritance dominant or recessive. Y-linked traits occur less commonly.
autosomal dominance. A dominant trait which is carried on the autosomal chromosomes
codominant. both alleles contribute to the phenotype , with either being dominant.
penetrance. The degree to which a genotype is expressed phenotypically in a population of gene carriers.
recessive allelle is hidden in the phenotype of a heterozygote by the presence of the dominant allele X-linked the trait is carried on the X- chromosome
Autosomal dominant conditions
In these disorders, usually:
• both homozygotes and heterozygotes manifest the condition
• affected individuals an affected parent
• the risk is 1 in 2 for each child of one affected and one unaffected parent
• both sexes are equally affected
• both sexes are equally likely to transmit the condition
Variable expression, non-penetrance or mutation may affect how mild or severe is the condition. Even a dominant disease may show variable expression. Non-penetrance may result in a person with no signs of the condition carrying the genes from an affected parent and producing an affected child.
Familial Diseases associated with gene changes. ( locus by chromosome number p short arm, q long: gene)
cystic fibrosis, a condition of abnormal mucous secretions in lungs and other organs resulting in chronic bronchial infection and gastrointestinal abnormalities due to an abnormal chloride channel. ( 7q:CFTR)
Duchenne muscular dystrophy, a muscular weakness, initially affecting the upper legs and arms , slowly becoming more general in distribution. Increased blood creatinine kinase concentrations are a feature. (Xp21: Dystrophin)
familial combined hyperlipidaemia, a common , familial condition associated with a raised blood cholesterol or triglycerides or both. Genetically heterogeneous, ( 1q; HYPLIP) or even (11p: HYLIP)
haemoglobinopathies, conditions associated with changes in the chemistry of haemoglobin which affects oxygen carriage or the life span of the red cell. Alpha 1 locus, ( 16p: HBA1) and beta locus (11p: HBB)
haemophilia A and B, a condition with abnormal blood coagulation, due to a failure to produce blood clotting Factor VIII or Factor IX ( Xq: Factor VIII), ( Xq: Factor IX)
Huntington’s disease, a neurological disease, declaring in middle age with chorea, (involuntary jerky movements), dementia and later seizures. (4p: Huntintin)
phenylketonuria, abnormal metabolism of phenylalanine, due to phenylalanine 4-monooxygenase deficiency . The affected babies are born with normal intellects , but as the concentrations of phenylpyruvate increase the intellect declines. ( 12q: Phenylal hydrox)
polyposis coli, multiple polyps in the colon which predispose to cancerous change ( 5q: APC0.
X-linked hypophosphataemic rickets, reduced blood phosphate concentrations, inherited through the X-chromosome leading to abnormal bone structure and other problems of calcium/phosphorous metabolism. ( Xp: PHEX)
Autosomal recessive conditions
These diseases are determined by a single autosomal locus. The condition is manifest only in people who are homozygous for the abnormal allele (aa). The parents of affected children are phenotypically normal carriers Aa. When the two parents are heterozygous for a particular phenotype, the offspring stand a 25% chance of being normal, 50% of being heterozygotes and 25 % will show clinical expression of the condition. Each child has a 1:4 risk of being affected. The distinctive features are:
• phenotypically normal parents may have one or more affected children
• unless an affected person mates with a carrier, all the children are unaffected
• both sexes are equally affected
• the condition may often be demonstrated biochemically, eg the haemoglobinopathies, cystic fibrosis, phenylketonuria or sickle cell anaemia. Other conditions eg Friederick’s ataxia. are not demonstrated biochemically.
This is the simplest form of Mendelian inheritance. The characteristics are determined by a single genetic locus with two alleles (alternative forms of a gene Aa) located on one of the autosomes (any chromosomes except the sex chromosome X or Y). In the heterozygote Aa, both alleles are expressed. The homozygote form is AA or aa, each of which shows a different phenotype. Many biochemical variants, eg isoenzymes (different types of the same enzyme) are codominant. Examples are:
• blood groups ABO, Rhesus
• red cell enzymes acid phosphatase, adenylate kinase
• cell surface antigens, human leukocyte antigen systems (HLA)
The inheritance pattern is one where the males are affected and the condition is carried on by the unaffected or very mildly affected females. If conception results in a male foetus, then the mother provides the X chromosome and the father the Y chromosome. If the conception results in a girl then the abnormal gene is carried on one X chromosome and the female will pass one of the X chromosomes to her daughter who will be heterozygous as her mother. The other normal gene will compensate for the abnormal gene. In the next generation, 50% of boys born of the heterozygous female will manifest the disease as they have no compensating X chromosome. An affected male will produce heterozygous daughters but normal sons who will only receive his normal Y chromosome. An example is glucose-6-phosphate dehydrogenase deficiency.
The specific features are:
- The disease affects mainly males.
- Affected males have unaffected parents but may have affected maternal uncles.
- The disease is transmitted by carrier women who are usually asymptomatic, half of the sons of a carrier are affected and half the daughters are carriers.
- The children of an affected male are unaffected but all of his daughters are carriers.
- The daughters of an unaffected man and a carrier woman have a 50% chance of being carriers, as did their mothers.
The variability of X-linked conditions may be the result of the suppression of one of the female X chromosomes, achieved, in part by methylation of a dinucleotide ( termed lyonized). Which X chromosome is inactivated is random but persists through the life of that cell line. Some genes in the tip of the short arm of the X chromosome may escape inactivation and are expressed , eg Duchenne muscular dystrophy, or haemophilia A and B.
X-linked dominant inheritance is not common. These include X-linked hypophosphataemic rickets which occurs only in females but is believed to be lethal in males.
Somatic genetic disorders
Mutations in somatic cells may occur in tumour cells with alterations in large groups of genes involved. A gene often observed to be affected in tumour formation is the p53 gene, a tumour suppressor gene found on the short arm of chromosome 17. A series of cancers have been found which have alterations in regions of the chromosomes within the malignant cell.
An extreme form of non-Mendelian inheritance occurs when the genotype of only one parent is inherited and the other is permanently lost. This contrasts with Mendelian genetics where the contribution of both parents is equally inherited. Usually it is the mother whose genotype is preferentially or solely inherited. This maternal inheritance occurs because the the genes of the mitochondria are inherited entirely through the ovum and not through the sperm. In mammals mitochondrial DNA appears to mutate more rapidly than nuclear DNA.
These disorders occur when a phenotypic characteristic is revealed in an individual with a genetic predisposition by a particular environmental situation. Such associations are demonstrated by twin, sibling or family studies. This genetic predisposition which results from the interaction of multiple genes is important in the understanding of conditions which are often attributed entirely to an outside influence, eg nutrition. A predisposition is highlighted by the interaction with an environmental precipitant, for example the response to alcohol by men and women in different racial groups. Following the drinking of alcohol Mongol races flush due to accumulation of blood acetaldehyde. Other examples are insulin-dependent diabetes, hypertension, colonic cancer and manic depressive disorders.
Locus heterogeneity. This term is applied when an apparently single clinical disease is caused by either of two or more separately located genes. An increased risk of breast cancer is an example, which is associated with the BRCA1 gene on chromosome 17p. However, only a proportion of breast cancers can be attributed to this mechanism.
Intra-locus heterogeneity. Different mutations or deletions within a single gene may cause different phenotypes.
Intra-family heterogeneity. This is a situation wherein the disease manifestations and clinical course are very variable even within a family with the same inherited gene defect. This variability may be due to the action of two or more modifying genes.
Anticipation. This refers to the severity of the disease increasing with successive generations.
Genomic imprinting. This is when a deletion on a chromosome results in a different clinical consequence in males and females.
Inter-family heterogeneity. Between families there is a great variation in disease phenotype, but the disease within families is remarkably constant. Any heterogeneity in such conditions is due to intra-locus differences rather than being due to two separate but closely linked genes.
It is likely that differential methylation which is sex-specific at the gamete level causes this variation in gene expression in genes on the X chromosome. . The Barr body is the inactivated X chromosome, and is inactivated by methylation.
Haplotypes and linkage disequilibrium. A disease mutation can occur when a particular cluster of individual genetic attributes occurs, eg female, blood group, HLA-A type. This would allow a prediction of what point on the chromosome the mutation has occurred.
These are much less common than allele based conditions, and are the result of the loss, gain or abnormal arrangement of one or more of the 23 pairs of chromosomes and are in general the result of a numerical or structural mutation in the parent’s germ cell. Polyploidy is when multiples of 23 chromosomes occur and is most frequently observed in spontaneously aborted infants, with triploidy 69 and tetraploidy 92 chromosomes. Where a single chromosome is lost or gained then this is called aneuploidy. This usually results when a chromosome fails to separate during cell division. The resulting child may have all aneuploid cells or have a mosaic of normal cells and some with an aneuploid chromosome complement. The consequence of the development of aneuploidy is either trisomy, an extra chromosome or monosomy, loss of a chromosome, eg:
• Down’s syndrome chromosome 21 trisomy
• Klinefelter’s syndrome sex chromosome 47, XXY
• Turner’s syndrome 45, X
If there is chromosomal breakage then translocation may occur with complex genetic consequences.Bernlohr DA, Simpson MA, Hertzel AV, Banaszak LJ.(1997) Intracellular lipid-binding proteins and their genes. Annu Rev Nutr. 17:277-303 Brenner S and Miller JF (2001), Encyclopedia of Genetics. Academic Press Clayton D, McKeigue PM (2001) Epidemiological methods for studying genes and environmental factors in complex diseases British Medical Journal 358, 1356-60 Connor, M. and Ferguson-Smith, M. (1997) Essential Medical Genetics, 5th edn, Blackwell Scientific Publications, Oxford. Emery, A.E.H and Rimoin, D.L. (1997) Principles and Practice of Medical Genetics, 3rd edn, Churchill Livingstone, Edinburgh. Girard J, Ferre and Foufelle F ( 1997 ) . Mechanism by which carbohydrates regulate expression of genes for glycolytic and lipogenic enzymes. Annu Rev Nutr. 17: 325-52 Horwitz M (2000 ) Basic Concepts in Medical Genetics , McGraw-Hill New York. Jimenez-Sanchez G, Childs B and Valle D . Human disease genes . Nature 409, 853-855, ( 2001) Jump DB and Clarke SD ( 1999 ) Regulation of gene expression by dietary fat. Annu Rev Nutr. 19:163-90. McKuisick VA (1998 ). Mendelian Inheritance in Man . Catalogues of Human Genes and Genetic Disorders. John Hopkins Univ. Press. Olson AL and Pessin JE ( 1996) Structure, function and regulation of the mammalian facilitative glucose transporter gene family. Annu Rev Nutr. 16: 235-56 Redei GP ( 2001) Genetics: An Encyclopedic Dictionary. Academic Press. Sanderson IR and Naik S (2000 ) Dietary regulation of gene expression . Annu Rev Nutr. 20, 5-52: 311-38 Sinden RR (2001) Origins of instability. Nature 411 757-8 Towle HC, Kaytor EN, Shih H-M ( 1997 ). Regulation of the expression of lipogenic enzyme genes by carbohydrates. Annu Rev Nutr. 17: 405-33
online Mendelian inheritance in man, listing and gene dependent human disease
online Mendelian inheritance in man, listing and gene dependent human disease
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