Genetics and Molecular Biology strive to comprehend how the molecules that cells consist of discerns living things’ behavior. Biologists use molecular and genetic tools to explore the function of those molecules in the complex milieu of the living cell. To understand the complexity of genetic diversity, mechanism of gene and several functions of its nature and how their evolution gets affected by that.

Concepts of Genetics 

Genetics is the study of genes and heredity. How specific attributes or traits are handed down through generations as a consequence of changes in DNA sequence. The genome contains all of an organism’s genetic information, such as its genes and other variables supporting those genes to function. 

Introduction 

Genetics is the study of genes to understand the goal of understanding what they are and how they function. Living beings acquire features or qualities from their forefathers through genes. For example, children often look like their parents because they received their parents’ genes. 

Genes consist of DNA, a complex molecule that is replicated and down from generation to generation. Inside this lengthy molecule, DNA consists of simple components. These units line up in a certain order. Similar to how the sequence of letters on a page contains information, the arrangement of these units transmits genetic information. 

The genetic code acts like a software language that DNA uses to make organisms function accordingly. This code allows them to access the information stored in the genes. This data contains the instructions for building and running a live creature. Genetics aims to determine which qualities are inherited and how they are handed down from generation to generation.

 Information within a gene is not always the same from one creature to the next. Various copies of a gene do not always transmit the same instructions. An allele is a name given to each variant of a single gene. One allele of the hair color gene, for example, may tell the body to create a lot of pigment, resulting in black hair.

Mutations are unintentional alterations in genes that can result in the emergence of new alleles. Mutations can also result in the emergence of new characteristics, such as when an allele for black hair is mutated to form a new allele for white hair. In evolution, the introduction of new features is critical.

Linkage and Crossing Over

The process of splitting and recombining DNA fragments to form new allele combinations is known as recombination. This recombination mechanism generates genetic variation at the gene level by reflecting differences in DNA sequences within species.

The processes of linkage and recombination describe the inheritance of genes. A linkage is a condition in which two or more connected genes are always passed down in the same order for more than two generations.

During the meiosis phase of sexual reproduction, DNA sequences near together on a chromosome tend to be inherited together. When two genetic markers are physically close to one another. they are less likely to be divided into distinct chromatids during the chromosomal crossover. Therefore, considered to be more connected than markers that are far apart; in other words, the closer two genes are on a chromosome, the less likely they are to recombine, and the more probable they will be inherited together. Different chromosomal markers are completely unrelated.

Thomas Hunt Morgan’s work contributed to a better understanding of linkage. Morgan’s observation that the amount of crossover between related genes differs. This led to the concept that crossover frequency may measure the chromosomal distance between genes.

A centimorgan is a common unit of genetic linkage (cM). When two markers are separated by 1 cM, they are separated to different chromosomes on average once per 100 meiotic products or every 50 meiosis.

Crossing over, also known as a chromosomal crossover, is the exchange of genetic material between the non-sister chromatids of two homologous chromosomes, resulting in recombinant chromosomes. One of the final phases of genetic recombination happens during synapsis in the pachytene stage of meiosis’s prophase I. Synapsis begins before the synaptonemal complex formation and is not completed until late in prophase I. When matching sections on matching chromosomes split and rejoin to the opposite chromosome, this is known as crossover.

Genetic Mapping 

Genetic mapping, also known as linkage mapping, can prove that an illness passed down from one parent to offspring is connected to one or more genes. Mapping also reveals which chromosome the gene is found on and the precise location of the gene on that chromosome.

The method for determining a gene’s locus and the distances between genes is known as gene mapping. The distances between distinct places inside a gene can also be described via gene mapping.

Physical mapping and genetic linkage mapping are two types of genome mapping procedures in which distances are assessed in base pairs and recombination frequency, respectively.

Saliva is the most commonly utilized sample in gene mapping, particularly in personal genomic studies. Scientists then isolate DNA from the samples and study it closely, seeking patterns in the DNA of family members who do carry the disease that isn’t present in the DNA of those who don’t. These different molecular sequences in DNA are known as polymorphisms or markers.

Non-biologists may inaccurately refer to genome sequencing as “genome mapping.” The procedure of “shotgun sequencing” is similar to physical mapping in that it smashes the genome into minute pieces, characterizes each fragment, and then reassembles it.

Genes and Genomes: Structure and Function

A gene is a unit of genetic information that sits at a specific location (locus) on a chromosome. Genes exert their influence via controlling the production of proteins.

A gene is a unit of genetic information that sits at a specific location (locus) on a chromosome. Genes exert their influence via controlling the production of proteins.

A genome contains all the genetic information of an organism. It consists of nucleotide sequences present in DNA and RNA sequences. The genome contains both genes (coding sections) and noncoding DNA, along with mitochondrial and chloroplast DNA. Genomic science is the study of the genome.

Structure of Polynucleotide Chain: 

A nucleotide is composed of the following parts:

1. 5-carbon sugar is referred to as pentose sugar. This sugar is deoxyribose in the case of DNA and ribose in the case of RNA.

2. Phosphate family

3. Nitrogenous bases are classified into two types:

• Purines – Adenine and Guanine 
• Pyrimidines – Cytosine, Thymine, and Uracil. Thymine in DNA and Uracil in RNA.

4. A nucleoside is formed by combining a nitrogenous base with a pentose sugar (through an N-glycosidic bond).

Nucleotide = nucleoside + phosphate group (through phosphoester linkage).

Dinucleotide = Nucleotide + Nucleotide (through 3′-5′ phosphodiester linkage).

A polynucleotide is a group of nucleotides that have been joined together.

The free phosphate group at the 5′ end of a polynucleotide is called the 5′ end. Similarly, the sugar possesses a free 3′-OH group at the polynucleotide’s opposite end, known as the 3′ end. The backbone of a polynucleotide chain comprises pentose sugars and phosphate groups, from which nitrogenous bases extend.

Nucleotide chain and DNA double helix structure

The Salient Feature of DNA

• It comprises two polynucleotide chains, the backbone of which is made up of sugar and phosphate groups, and the nitrogenous bases project within the helix.
• The polarity of the two polynucleotide chains is anti-parallel, which means that if one strand has 5′ 3′ polarity, the other strand has 3′ 5′ polarity.
• Hydrogen bonds join the bases on opposing strands, generating base pairs (bp). Adenine always creates two hydrogen bonds with thymine from the opposing strand, and the reverse is true. Guanine makes three hydrogen bonds with the opposite strand’s cytosine and vice versa. As a result,  purine on one strand always couples with a pyrimidine on the other, resulting in a consistent distance between the two strands of the helix.
• The two strands are wound in a right-handed coil. Each helix of DNA turn is 3.4nm (or 34 Angstrom units) in length and contains 10 nucleotides. The distance between these nucleotides is 0.34nm (or 3.4 Angstrom units).
• Because of the base pairs that stack on top of one another and the hydrogen bonds that hold the bases together, the helix is stable.

Discovery of DNA as Genetic Material 

Frederick Griffith, a British bacteriologist, conducted a series of tests using Streptococcus pneumoniae bacterium and mice in 1928. Griffith’s goal was not to locate the genetic material but rather to create a vaccination against pneumonia. In his tests, Griffith utilized two similar strains of bacteria identified as R and S.

However, when harmless R bacteria were paired with harmless heat-killed S bacteria and put into a mouse, the trials took an unexpected turn. The mouse not only developed pneumonia and died, but when Griffith obtained a blood sample from the deceased mouse, he discovered that it contained live S bacteria!

Griffith gave the conclusion that the R-strain bacteria must have picked up a “transforming principle” from the injected killed S bacteria, allowing them to “transform” into smooth S strain bacteria and become virulent.

Later in 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty, three Canadian and American scholars, worked on Griffith’s “transforming principle.”

Avery and his colleagues were led to believe that the transformative principle may be DNA by several lines of evidence

• The refined material produced a negative result in chemical tests known to identify proteins. But a significantly positive result in a sample solution known to detect DNA.
• The purified transforming principle’s elemental makeup closely approximated DNA in terms of nitrogen and phosphorous ratio.
• Protein- & RNA-degrading enzymes had a minor impact on the transforming principle, whereas DNA-degrading enzymes destroyed the transforming action.

Because of this possibility, scientists debated the importance of DNA until 1952, while Alfred Hershey and Martha Chase utilized a different way to definitively establish DNA as the genetic material.

Hershey and Chase researched bacteriophages or viruses that kill bacteria in their now-legendary studies. They employed basic phages built of protein and DNA, with the outside structures made of protein and the inner core comprised of DNA.

Hershey and Chase created two batches of phage to determine whether the phage injected DNA or protein into host bacteria. The phage was created in the presence of a particular radioactive element. Each batch was integrated into the macromolecules (DNA and protein) that comprised the phage.

Hershey and Chase concluded that DNA, not protein, was transferred into host cells and formed the phage’s genetic material based on this and other tests.

DNA Replication

The process by which DNA duplicates itself during cell division is known as DNA replication. The purpose of DNA replication is to ‘unzip’ the DNA molecule’s double helix shape. This is accomplished by an enzyme known as helicase, which breaks the hydrogen bonds that keep the complementary bases of DNA together (A with T, C with G).

The separation of two single strands of DNA results in a ‘Y’ form known as a replication fork.’ The two split strands will serve as templates for creating new DNA strands.

The leading strand is one of the strands that is directed in the 3′ to 5′ orientation (towards the replication fork). The lagging strand is orientated in the 5′ to 3′ orientation (away from the replication fork). Because of this variation in the orientation, both the strands get copied differently. 

After all the bases have been matched (A with T, C with G), an enzyme called exonuclease removes the primer (s). The gaps left by the primer(s) are subsequently filled with extra complementary nucleotides.

The new strand is proofread to ensure that the new DNA sequence is error-free. Finally, an enzyme known as DNA ligase seals the DNA sequence into two continuous double strands.

The end outcome of DNA replication is two DNA molecules, one new and one old nucleotide chain. This is why DNA replication is referred to be semi-conservative; half of the chain is recycled from the original DNA molecule, while the other half is completely new. Following replication, the new DNA naturally forms a double helix.

Structure of the Genes

Genes are made up of the polynucleotide chain since they are DNA strands. 

The gene structure is compromises of two sorts of components: core elements and regulatory elements.

The core elements or sequences are involved in protein production. Whereas the regulatory elements keep gene expression going.

Exons are essential components. On the other hand, sequences such as promoters, enhancers, and silencers comprise regulatory elements of a gene.

Maintenance elements, the third type of element, include DNA repair, modification, and replication information. A gene’s functional or physical structure consists of introns, exons, promoters, enhancers, and UTRs.

Introns are noncoding sequences that are deleted from the final transcript. Exons are coding segments of a gene that are linked after splicing to form the final transcript.

Regulatory elements are found at the ends of genes.

Promotes are noncoding regions that assist the interaction of enzymes and transcriptional factors. TATA box and CCAAT sequences are used in the promoter to bind enzymes. The complete promoter region is positioned on the 5′ end and is composed of core and proximal promoter sequences.

TThe core promoter promotes the binding of RNA polymerase (and other proteins) to initiate transcription. The proximal promoter serves as a binding site for transcription factors.

The enhancer promotes transcription, whereas the silencer inhibits it. Enhancers and silencers, which are placed far away from the exon, work together to control gene expression. 

The 3′ untranslated regions are noncoding sections of the gene that aid in the transcription process’s termination and the final transcript’s formation. When the RNA polymerase reaches the untranslated region, it ceases RNA synthesis and separates off the strand.

More regulatory sequences are found in eukaryotic genes than in prokaryotic genes. Furthermore, the entire mechanism of transcription and translation differs between the two.

The operon notion of bacterial genes refers to a group of genes that perform similar activities. An operon does not contain introns.

In contrast, eukaryotic genes are made up of introns (noncoding DNA) that are spaced at regular intervals. Each gene has its promoter region to enhance transcription.

Transcription – The Basic Process

A part of the double-stranded Template DNA is converted into a single-stranded RNA molecule during transcription. 

Although DNA is double-stranded, only one strand functions as a transcription template at any one moment, the template strand is sometimes referred to as the Noncoding strand. Because its sequence is identical to that of the new RNA molecule, the non-template strand is also called the coding strand. In most species, the DNA strand that acts as the template for one gene may also function as the non-template strand for other genes on the same chromosome.

Step 1: Transcription Initiation

The first process of transcription is initiation. It starts its process when an enzyme RNA polymerase attaches to the promoter gene. This causes the DNA to unwind, allowing the enzyme to read the nucleotides in one of the DNA strands. RNA polymerase is now ready to make an mRNA strand with a complementary base sequence.

Step 2: Strand Elongation 

The extension of nucleotides to the mRNA strand is known as elongation. RNA polymerase reads the unfolded DNA strand and uses complementary base pairs to construct the mRNA molecule. The newly produced RNA is bonded to the unfolded DNA for a limited period during this process. During this step, an adenine (A) in the DNA bonds to uracil (U) in the RNA.

Step 3: Transcription Termination

The transcription termination occurs when RNA polymerase passes a stop (termination) sequence in the gene. The mRNA strand is completed and separates from the DNA.

Genetic Code

Cells decode mRNAs by reading them in three-nucleotide groups known as codons.

The majority of codons define an amino acid. The genetic code has 64 codons that result from the recombination and pairing of the four bases of nucleic acids.

Three “stop” codons mark a protein’s end. AUG is a “start” codon that both marks the beginning of a protein and encodes the amino acid methionine.

During translation, codons in an mRNA are read, beginning with a start codon and continuing until a stop codon is reached. The order of amino acids in a protein from the N-terminus (methionine) to the C-terminus is specified by mRNA codons, which are read from 5′ to 3′.

The start codon is the first codon of a messenger RNA (mRNA) transcript that a ribosome will translate. AUG is the most often used start codon (i.e., ATG in the corresponding DNA sequence). A 5′ untranslated region (5′ UTR) is frequently present before the start codon. This includes the ribosome binding site in prokaryotes.

There are three genetic STOP codons: UAG, UGA, and UAA. These stop codons do not code for an amino acid. Therefore, these codons are sometimes known as nonsense codons or termination codons. The three STOP codons are amber (UAG), ochre (UAA), and opal or umber (UGA). 

Reading frame 

Depending on where the translation begins, the genetic code can be translated in various ways. For instance, if the sequence of bases is GGGAAACCC, reading might begin with the first letter, G, and there will be three codons – GGG, AAA, and CCC. If you start reading from G in the second place, the string will have two codons: GGA and AAC. When reading begins at the third base G, two codons are produced – GAA and ACC.

Codon Table 

Translation

Translation, or protein synthesis, is the second stage in gene expression, and it involves a ribosome decoding an mRNA message into a polypeptide product.

In addition to the mRNA template, several substances and macromolecules are involved in the translation process. Translation necessitates using an mRNA template, ribosomes, tRNAs, and several enzyme components.

A ribosome is a complex macromolecule made up of catalytic rRNAs (known as ribozymes) and structural rRNAs, and a variety of polypeptides. Mature rRNAs account for almost half of each ribosome. Prokaryotic cells have 70S ribosomes, whereas eukaryotic cells have 80S ribosomes. When ribosomes are not generating proteins, they divide into big and tiny subunits. A polyribosome is an entire structure that includes an mRNA and many related ribosomes (or polysome). 

Many ribosomes translate each mRNA molecule simultaneously, all making protein in the same direction: reading the mRNA from 5′ to 3′ and synthesizing the polypeptide from the N terminus to the C terminus.

Transfer RNAs (tRNAs) are functional RNA molecules found in the cytoplasm in various forms depending on the species. Bacterial species are frequently divided into 60 to 90 distinct types. Each form of tRNA works as an adaptor, attaching to a specific codon on the mRNA template and adding the appropriate amino acid to the polypeptide chain. As a result, tRNAs are the molecules responsible for “translating” the RNA language into the protein language.

Mature tRNAs take on a three-dimensional structure when complementary bases are exposed in the single-stranded RNA molecule hydrogen bond with one other. Aminoacyl tRNA synthetases, ribosomes, and mRNA are the three components that interact with the tRNA molecule. The amino acid is activated initially by adding adenosine monophosphate (AMP) and then transported throughout the process.

The translation process is divided into three stages:

The ribosome begins to assemble around the target mRNA. The first tRNA is bound to the first codon.

Elongation: The amino acid carried by the final tRNA validated by the small ribosomal subunit (accommodation) is transferred to the large ribosomal subunit, which attaches it to one of the previously accepted tRNAs (transpeptidation). The ribosome subsequently proceeds to the next mRNA codon to complete the process (translocation), resulting in an amino acid chain formation.

Termination: When a stop codon is reached, the ribosome releases the polypeptide. The ribosomal complex is unaffected and continues to the next mRNA to be translated.

Mutations

A mutation is a change in our DNA sequence that arises as a consequence of errors during DNA replication or as a result of environmental influences such as UV radiation and cigarette smoke.

Our DNA can change or mutations in the sequence of bases, A, C, G, and T, during our lives. This causes alterations in the proteins that are produced. This may be both a good and a terrible thing.

Mutations can arise during DNA replication if mistakes occur and are not addressed promptly. Mutations can also develop as a result of external factors such as smoking, sunshine, and radiation exposure.

Cells can frequently detect and repair possibly mutation-causing damage before it becomes a permanent mutation.

Mutations can also be passed down across families, especially if they have a favorable effect.

The condition sickle cell anemia, for example, is caused by a mutation in the gene? That directs the formation of a protein called hemoglobin. As a result, the red blood cells take on an unnatural, hard, sickle form. In African people, however, harboring this mutation also protects against malaria.

On the other hand, mutation can disrupt normal gene function and result in disorders such as cancer.

Cancer is the most frequent genetic illness in humans, and mutations cause it in a variety of growth-controlling genes. Cancer-causing genes can present from birth in some cases, increasing a person’s risk of developing cancer.