Teaching Purposes: Studying the human genome, definition and structure of gene include exon, intron, and promoter, flanking regions, types of promoter, DNA sequence, muti-gene family, gene super family, gene cluster, pseudo genes, regulation of gene expression, genetic imprinting, definition and types of gene mutation. 
Teaching Requirements:
a)	To be familiar with the definition of gene;
b)	To be master with the definition and structure of gene;
c)	To be familiar with the DNA sequence, muti-gene family, gene super family, gene cluster, pseudo genes, regulation of gene expression, genetic imprinting;
d)	To master with the definition and types of gene mutation.


● Gene 
● Mutation
 


Genes are situated in the chromosomes and are transmitted from parent to offspring and are considered the basic unit of inheritance. Gene is a structural unit of inheritance. A sequence of chromosome DNA is required for production of a functional product. It is estimated that there are about 23, 000 genes locating on 23 human chromosomes (as per Human Genome Project, 2001). The arrangement of the genes in the chromosome is linear, similar to the arrangement of strings on the beads.There are two different kinds of genes in the chromosomes, i.e. structural genes and control genes (regulatory genes). Structural genes: A piece of DNA that determines the structure of a certain protein molecule, the function of which is to transcribe the carried genetic information to mRNA (messenger ribonucleic acid) and then synthesize a protein with a specific amino acid sequence using mRNA as a template. Regulatory genes: a gene that regulates protein synthesis. It enables structural genes to be synthesized when an enzyme is needed, and stops when not needed. It regulates structural genes on different chromosomes.


3.1.Molecular Structure of a 
..Gene
Gene is composed of DNA chemically. A simple language can be used to define a structural gene as “a piece of DNA that determines the structure of a protein or RNA molecule”. Thus genes are nothing but instructions for making proteins.
Since the polypeptide chain is composed of a specific amino acid sequence, it is considered that there must be a continuous DNA sequence encoding these amino acids in the structural gene. However, not all of the structural genes are composed of coding sequences, but a coding sequence without a coding is inserted in the middle of the coding sequence, and such a gene is called split gene. In the split gene, the coding region gene is called an exon, and the non-coding region is called an intron.
The number of introns in various genes is variable and in many genes, the cumulative length of the introns makes up a far greater proportion of a gene’s total length than the exons do (Figure. 3.1). Though introns are transcribed but not included in mature mRNA. There is GT-AG law between the exon and intron, the means is the first two nucleotides of intron are always GT , and while the last two nucleotides of intron are always AG (Figure. 3.2). 
The structure of a structural gene not only contains the sequences of exon and introns but also possesses flanking regions at the ends. These flanking regions are important for regulation of gene (Figure. 3.2).
At the 5’ end, the flanking regions consist of DNA sequences that control transcription. This region is referred as the promoter region and contains the “TATA” box, while the presence of the TATA, CAAT and GC boxes is critical for transcription, as transcriptional regulation initiates translation (ATG) code through the binding of transcription factors to this region. At 3’end the flank region consists of translation termination codon (TAA), which is followed by poly (A) cap codon (refer transcription).


3.2.DNA Sequences
DNA is mainly found in the nucleus and mitochondria, and only a small fraction of the total DNA content of the chromosome acts as a protein-coding gene. It is currently estimated that there are approximately 23, 000 protein-coding genes in the human genome. The remaining large numbers of DNA sequences are not transcriptionally active, they do not function as protein-coding genes and are therefore referred as junk DNA. Junk DNA consists of repeated DNA sequences. The DNA, present in the nucleus, therefore can be grouped into two category i.e., genic DNA and extragenic DNA.
The genic DNA consists single or low copy number DNA sequences while extragentic DNA consists of highly repetitive DNA sequences. 


There are some foundings about genes. Most of the genes in the chromosome are usually present below telomere. Distribution of genes in different chromosomes also varies. For example, chromosomes 19 and 22 are rich in genes, chromosome 19 contains 1300-1700 genes, and the number of chromosome 22 contains 600-700 genes, but chromosomes 4 and 18 contain very few genes, and chromosome 18 is the lowest in all chromosome. Some genes are small (consisting of single exon) and others are very large (consisting up to 79 exons). A single exon may contain many nucleotide base pairs.
Most of human genes are single (single-copy genes). Genes coding for enzymes hormones, receptors and structural and regulatory protein are single-copy genes. In addition to single-copy genes, there are many genes with similar structures and functions For example many a-globin genes are present on chromosome number 16 and many .-globin genes are present in groups on chromosome number 11. Similarly, many copies of genes coding for the ribosomal RNAs are present on the short arms of various acrocentric chromosomes. Theses genes are known as multi-gene families and may arise through gene duplication and are closely related to the evolutionary origin.
A large number of DNA sequences are made up of highly repetitive DNA sequences that are not transcribed (non-genic or extragenic). Though these DNA sequences are known as junk DNA but some portion of it may play a role in the regulation of gene expression. There are two different types of repetitive DNA sequences, tandem repeats and scattered repeats.


A large number of DNA sequences are made up of repetitive DNA sequences that are not transcribed (non-genic or extragenic).Though these DNA sequences are known as junk DNA but some portion of lit may play a role in the regulation of gene expression. The repetitive DNA sequence are of two different types, tandemly repeated DNA sequences and interspersed repetitive DNA sequences.


The tandem repeat DNA sequence is mainly composed of a short sequence of non-coding DNA, which is end-to-end and consists of tandem repeats.These are divided as satellite DNA, minisatellite DNA and microsatellite DNA.The satellite DNA consists of short tandemly repeated DNA sequences and is present near centromere.
The minisatellite DNA mainly consists of telomeric DNA. Human telomeres are short, multi-repeat non-transcribed sequences consisting of tandem repeats of the TTAGGG sequence between 5 and 20 kb in length. Telomere is like a chromosomal hat that acts to maintain chromosome integrity (Figure. 3.3).
In addition to telomeric DNA microsatellites, tandem repeats are also present elsewhere in the chromosome. These minisatellites consist of highly variable DNA sequences (also called hypervariable minisatellite DNA). The high variability of these tandem repeats forms the basis of DNA fingerprinting.
The microsatellite DNA are tandem repeats of few (one to four) base pair sequences. These repeat base pair sequences are present throughout the genome.


Some repetitive DNA sequences are interspersed throughout the genome. They are either short interspersed nuclear elements (DNA sequences of approximately 300 bp) or long interspersed nuclear elements (DNA sequences of up to 6000 bp). 


The function of a large number of repetitive DNA sequences in the human genome is not fully understood yet. For example, although extragenic DNA is considered to be junk DNA, some of it may play a role in the regulation of gene expression. The high variability of small satellite DNA is the basis of fingerprints, and the stability of telomere small satellite DNA in chromosomes plays an important role.


3.3.Regulation of Gene 
.Expression
All cells in the body have the same genetic material, and they all contain exactly the same DNA sequence. But why do different human tissues synthesize different kinds of proteins? i.e. skin cells produce keratin, endocrine pancreas synthesize insulin and red blood cells produce hemoglobin, etc.? This is because most genes are transcribed in specific tissues only at specific time points. In most cells, only a small number of genes are active, while others are at rest, so there is a mechanism to control gene expression. 
In higher organisms, transcriptional regulation is more complex through the action of hormones or growth factors and is specific to certain tissues or cells. Regulation of transcription is achieved by binding of transcription factors to specific DN sequences in the promoter region. This region includes TATA, CAAT and GC boxes, etc. (Figure. 3.1). A DNA sequence that increases the level of gene transcription is referred as an “enhancer”. Similarly, there are also DNA sequences that inhibit gene transcription, called “silencers” .


3.4.Genetic Imprinting
Genetic Imprinting includes genomic imprinting and parental imprinting. Parental imprinting is the phenomenon whereby the degree to which a gene expresses itself depends upon the parent transmitting it. i.e. Huntington chorea: if transmitted by mother no genetic imprinting phenomia but if transmitted by father there will be (Figure 3.4).


3.5.Mutation
Mutations can be defined as stable, heritable changes in the genetic material of an individual. The term “genetic material” is used broadly and can refer to either the smallest unit of nucleotides of a gene or “a set of chromosomes”. Thus, mutations can occur in a single gene or in a chromosome.
If a gene undergoes a genetic change in its structure, it is called a genetic mutation or a point mutation. When the structure or number of chromosomes changes, it is called a chromosomal mutation. However, the term “mutation” is primarily used for genetic mutations. The number and structural abnormalities of chromosomes are described in Chapter 8. In this chapter, we will only deal with genetic mutations or point mutations.
Mutation is seen in all living organism. It is the ultimate source of all genetic variations. Mutation is essential for long term survival of any species. Without mutation a species cannot acquire new genes which are necessary for adaptation in changing environment. Thus, mutation provides raw material for evolution. However, most mutations are harmful. 


3.6.Somatic and Germline 
.Mutation
If a mutation occurs in a somatic cell or tissue, it is called a somatic mutation, and if it occurs in a germ cell (egg or sperm), it is called a germline mutation. Germline mutations will be passed on to the next generation, but somatic mutations will not be passed on to the offspring. Somatic mutations can cause local phenotypic changes in the individual, while germline mutations will have a general impact on the individual. Individuals with somatic mutations are mosaics (genically, they will have two different types of cells. In the case of germline mutations, since the mutation is transmitted through sperm or eggs, the offspring will not mosaic, as all of its cells will carry the mutation.


3.7.“Loss of Function 
.Mutation” and “Gain of 
.Function Mutation”
Mutations often result in loss of function of the gene. However, sometimes mutations may also lead to new functions or increased levels of gene expression.
If the mutation results in either the complete inactivation of gene (elimination of the function of gene) or decreased gene activity. then it is called as “loss of function mutation”. This is also known as “knockout” or “null” mutation. Most of the loss of function mutations is recessive.
The “gain of function mutation” may result in overexpression of the gene (gene product is over produced) or become active in tissue types where the gene is usually inactive. Most “ gain of function mutation “ are dominant. When these mutations occur in homozygous state they manifest as sever disorder, e.g. homozygous achondroplasia. Most mutations that cause gene overexpression are associated with cancer.


3.8.Molecular Basis of Gene 
.Mutation (Point Mutation)
Although the DNA replication process is very precise, sometimes the arrangement of nucleotides in the polynucleotide chain of a DNA molecule may change. These changes are not observed under the microscope, but have multiple phenotypic effects on the individual. These minimal changes may involve substitutions, deletions, and insertions of individual nucleotides in a DNA molecule, which are called genetic mutations or point mutations. Gene mutations (point mutations) have the following types: base substitution mutations and frameshift mutations (deletion or insertion mutations).
Substitution mutation: This is a relatively common type of mutation. In this mutation, one of the nitrogen-containing bases of the triplet code of the DNA (the codon consists of three base pairs) is replaced by another nitrogen-containing base, which changes the codons that can encode different amino acids (Figure 3.5). For example, in sickle cell anemia, in GAG triplet code of mRNA (which codes for glutamic acid) if base A is replaced by U, at the time of transcription, code GTG will produce valine amino acid instead of glutamic acid. This one different amino acid in a polypeptide chain will lead to the formation of altered protein. The defective βglobin polypeptide chain will form needle like crystals and will deform RBCs. The effect of deformed RBCs may be seen as many abnormalities throughout the body (Figure 3.6).
The substitution mutation may or may not be lethal. Since the substitution of only one amino acid in the polypeptide chain occurs, this substitution does not affect the activity of the corresponding protein and does not produce any significant changes. This mutation is called a silent mutation. However, on other hand, in sickle cell anemia, there occurs the substitution of single nucleotide which leads to serious disease. However, sometimes gene mutation may also be beneficial. For beneficial effects of sickle cell mutation, turn to chapter 9. 
Frame shift mutation: It refers that the number of nucleotides deleted or inserted in the gene coding region is not a multiple of 3, resulting in the movement of the reading frame, thereby changing the corresponding coding sequence of the gene (Figure. 3.7).
A frameshift mutation may involve an insertion or deletion of one, two or more nucleotides (not a multiple of 3 or 3, i.e. an inserted or deleted nucleotide is not equivalent to one or more triplet codes). The frameshift mutation causes a shift in the transcription of the triplet codon, and the protein properties are highly altered, usually a lethal mutation.
Dynamic mutation, i.e. Fra X syndrome and Huntington chorea.nucleotides selquence increase copies gradually wrongly.


3.9.Mutagens
Mutations can occur naturally where no cause can be detected. These kinds of mutations are called spontaneous mutations. Spontaneous mutations are usually caused by accidental errors in DNA replication, transcription, and repair. Mutations are also known to occur due to the exposure to environmental agents. These agents are known as mutagens. 
There are two types of mutagens:
1.	Chemical and physical mutagens: Many chemicals like mustard gas, formaldehyde, benzene, thalidomide and L.S.D. are considered as mutagenic in animals. Physical agent like high temperature is a known mutagenic agent in animals.
2.	Radiation: Both natural and artificial ionizing radiations are known to cause mutation. Natural radiations that come from cosmic rays of the sun (natural sunlight) and UV lamps are the source of mutations. The other source of natural radiation is the radioactive elements like thorium, radium and uranium presenting on earth. Artificial ionizing radiation includes X-rays, gamma rays, alpha and beta rays (particles) and neutrons. The effect of ionizing radiation on the chromosome is very serious. The direct effect is that the base of the deoxyribose is oxidized, or the chemical bond of the deoxyribose and the sugar-phosphate are broken. It can cause chromosomal aberrations, chromosome and chromatid cleavage, resulting in abnormal chromosome number and structural loss, translocation and inversion (Ch. 8).


Summary
Gene: The structural gene is defined as “a DNA fragment that determines the synthesis of a protein or RNA molecule structure”. Structural genes encode a large number of proteins with different functions.The control genes regulate the activity of structural genes.The DNA portion of a structural gene not only contains coding sequences for amino acids (exons) but also contains non-coding sequences (introns).
A structural gene also contains flanking regions at the ends which are important for regulation of gene.
Genetic code: Protein is made up of polypeptide chains which in turn are made up of amino acids. A sequence of three bases on DNA strands codes for one amino acid. Thus a portion of DNA strand that constitutes a structural gene contains the sequentially arranged codes for all the amino acids which forms a complete polypeptide chain.
Transcription: The process by which genetic information stored in the DNA of a gene (in the form of a triplet encoding) is passed to messenger RNA.
Since base pairing is performed according to the principle of base complementation, the information of the DNA strand is invariably transferred to the mRNA. 
Transcription factors: It refers to a protein that recognizes a promoter, enhancer or a specific DNA sequence and forms a dynamic transcription complex with RNA polymerase activity, thereby controlling the expression of the gene at a specific time and space with a specific intensity. It plays an important role in the transcription process.
Translation: It is the process of synthesizing a polypeptide chain according to the order of bases on the mRNA. Translation is mainly carried out in cytoplasmic ribosomes. During translation, mRNA is attached to ribosomes, small units of ribosomes read the code on mRNA, large units align consecutive tRNAs, and tRNAs are linked to specific amino acids, according to A codon on the mRNA that aligns these linked amino acids to extend the growing polypeptide chain.
Regulation of gene expression: Regulatory genes are genes that regulate and control the transcription process of structural genes. Control genes are of two different kinds, i.e. regulator gene and operator gene. The unit of operator gene and structural gene is called operon. regulatory gene is a gene that encodes a protein. In a negative control system, the product of a regulatory gene is a repressor. In a positive control system, the product of the regulatory gene is an activator protein. An operator is a binding site that regulates a gene product, also known as a manipulation region. When an active repressor binds to this site, transcription of the structural gene is prevented. In higher organisms, regulation of transcription is more complex.
Mutation: A stable, heritable change in an individual’s genetic material is defined as a mutation. Mutations may occur in genes (point mutations or gene mutations) or in chromosomes (mutations in chromosome number or structure). Point mutations include base substitution mutations and frameshift mutations (deletion or insertion mutations) due to the addition, deletion or substitution of a single nucleotide in a DNA molecule.
If a mutation occurs in a somatic cell, it is called a somatic mutation, and if it occurs in a germ cell, it is called a germline mutation. Environmental factors such as chemicals and radiation can also cause mutations. These agents are called mutagens.
Monogenic or Mendelian inheritance 
●	Autosomal dominant inheritance 
●	Autosomal recessive inheritance
●	Sex-linked inheritance
In order to accurately diagnose genetic diseases, understand the characteristics of genetic diseases, calculate the risk of genetic diseases in offspring and recommend methods to prevent genetic diseases are really important, inwhioh the most important thing is to understand the genetic model of genetic diseases (dominant inheritance, recessive inheritance, Sex-linked inheritance etc.). The inheritance of common traits or disorders follows following patterns: Monogenic (single gene) or Mendelian inheritance and Polygenic (multiple genes) inheritance/Multifactorial inheritance.


Exercises
Key Terms
1. Multigene family	2. Split gene
3. Codon		4. Gene
5. Mutation
Fill in the Blanks
1. Lyon hypothesis: (1) Inactivation occurs one of two 　　　　 chromosome. (2) Happened at an 
　　　　 stage of embryogenesis. (3) Happened on a 　　　　 basis and maintained in all descendant cells. 
2. Synapsis happened in 　　　　 stage.
3. Crossover occurred in 　　　　 stage.
4. Split gene: genes containing coding regions
 　　　　 that are interrupted by noncoding regions 　　　　 . 
5. Codon: the nucleotide 　　　　 in the mRNA that specifying a single amino acid during translation.
True or False
1. CAAT box is one kind of enhancer (　　).
2. TATA box is one kind of promoter (　　).
3. Pesudogene is an inactive gene within a gene family, derived by mutation of an ancestral active gene and frequently located within the same region of the chromosome as its functional counterpart (　　).
4. X chromosome determines the sex of the offspring (　　).
5. Multigene family is a set of genes descended by duplication and variation from some ancestral gene (　　).
6. During splicing, exons are removed and introns are joined (　　).
7. The phenomena on which more than one codons for the same amino acid was called translation (　　).
8. Globin genes belong to multigene family (　　).
9. Lyon hypothesis shows that X chromatin happened on a random basis and maintained in all descendant cells (　　).
10. Triplet repeats are a sequence of three base pairs that occur in varying numbers in front of, within or just after a gene (　　). 
MCQs
1. Coding part of eukaryotic gene is (　　).
A. exon		B. intron
C. promotor		D. enhancer
E. poly A
2. Structural gene includes (　　).
A. promoter		B. exon
C. enhancer		D. intron
E. all of them
3. Types of point mutation according the effect they cause Except (　　).
A. samesence mutation
B. nonesence mutation
C. missence mutation
D. termination codon mutation
E. frame shift mutation
4. Which of the following is NOT true of meiosis I? (　　)
A. leptotene--chromosome is elongated and thin
B. zygotene--homologous chromosomes, synapsis, bivalent
C. pachytene--chromosome becomes thin, tetrads, noncrossover
D. diplotene--chiasmata
E. diakinesis--chromosome thickens
5. Which type of mutation below does NOT belong to transition? (　　)
A. T→C		B. A→T
C. A→G		D. G→A
E. C→T
6. What happens during meiosis? (　　)
A. An egg cell fuses with a sperm cell.   
B. Haploid cells change into diploid cells.
C. Diploid cells change into haploid cells.   
D. A diploid set of chromosomes is reproduced.
E. A haploid set of chromosomes is reproduced.
7. Mutations can affect a gene (　　).
A. in noncoding regions of the gene
B. in coding regions of a gene, disrupting the coding sense
C. in coding regions of a gene, resulting in amino acid substitutions
D. in coding regions of a gene, resulting in no change in the protein
E. all of the above
8. Which of the following is NOT true of MITOSIS? (　　)
A. Each of the homologous chromosomes segregates intact to the daughter cells such that both chromatids are of maternal or paternal origin.
B. Nondisjunction of sister chromatids would result in two identical copies of either the maternal or paternal chromosome.
C. In anaphase, kinetochore microtubules shorten to pull the chromosomes towards the spindle pole.
D. In anaphase, polar microtubules elongate to push the spindle poles apart.
E. Each daughter cell contains 46 chromosomes (2N).
9. Why would you predict that half of the human babies born will be males and half will be females? (　　)
A. Because of the segregation of the X and Y chromosomes during male meiosis
B. Because of the segregation of the X chromosomes during female meiosis
C. Because all eggs contain an X chromosome
D. Because, on average, one-half of all eggs produce females
E. Because of the formation of the Barr body  occuring in early embryonic development
10. Sickle-cell disease is the result of a single nucleotide substitution that produces a single amino acid substitution. This is best described as a  (　　).
A. frameshift mutation	B. nonsense mutation
C. splice-site mutation	D. missense mutation
E. none of the above
11. Which base is NOT found in the DNA of most organisms? (　　)
A. adenine		B. guanine
C. cytosine		D. uracil
E. thymine
12. Which of the following is NOT involved in the processing of mRNA precursors in eukaryotic cells? (　　)
A. capping of the 5’ end	B. addition of poly A
C. excision of introns	D. splicing of exons
E. transport of the pre-mRNA to the cytoplasm
13. Mitosis proceeds in the order (　　).
A. cytokinesis, prophase, prometaphase, telophase, metaphase, and anaphase.
B. telophase, anaphase, prophase, prometaphase, metaphase, and cytokinesis.
C. prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis.
D. prophase, prometaphase, metaphase, cytokinesis, anaphase, and telophase.
E. prophase, prometaphase, cytokinesis, metaphase, anaphase, and telophase.
14. Paired chromatids separate and begin to move toward the spindle poles in mitotic (　　).
A. prophase		B. prometaphase
C. metaphase		D. anaphase
E. telophase
15. Meiosis differs from mitosis in that (　　).
A. The centrioles do not separate during the first meiotic division.
B. Meiotic divisions are always asymmetric.
C. Meiosis generates cells with half as much DNA as the progeny of mitotic division have.
D. Movement of chromosomes toward the spindles is slower.
E. all of the above.
16. Which of the following is NOT a function of the DNA molecule?
A .specification of amino acid sequence
B. assembly of amino acids into proteins
C. transcription of chemical coding onto RNA
D. self replication
E. storage of genetic information in most organisms
17. In which phase does cytokinesis occur?
A. the C phase	B. the S phase
C. the G3 phase	D. the M phase
E. the G1 phase
18. In which phase does synapsis occur?
A. leptotene		B. zygotene
C. pachytene		D. diplotene
E. diakinesis
19. What kind of DNA alteration below can cause frameshift mutation?
A. transition of one basepair
B. transversion of one basepair
C. insertion of three basepairs
D. inversion of one segment of DNA
E. insertion of one basepair
20. The occurrence mechanism of dynamic mutation is (　　).
A. gene deletion	B. gene mutation
C. gene duplication	D. gene replication
E. amplication of tandem trinucleotide repeats







医学遗传学 Medical Genetics

医学遗传学 Medical Genetics

The Bases of Genetics

Chapter .3  The Bases of Genetics

14

13

Chapter   3
The Bases of Genetics

Three


Figure 3.1　GT - AG law


Figure 3.2　Structure of a structural gene


Chromosome

Cell

C

C

C

T

A

A

Telomere

G

G

A

T

T

G

Telomere

Figure 3.3　The telomere
(From http://www.sohu.com)


Ⅰ

 (39)

Ⅱ

 (38)

Ⅲ

Ⅳ

 (23)

Figure 3.4　Pedigree of Huntington chorea


Figure 3.5.Triplet Condon



Figure 3.6　Point mutation
(http://www.doc88.com/p-7953888701890.html)

Figure 3.7　Frame shift mutation which leads to the change in the triplet genetic code.