28.2: Introduction - Biology

28.2: Introduction - Biology

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28.2: Introduction

What students will learn

By the time they finish this course, students will learn or be able to demonstrate an understanding of the fundamental principles of biology by systematically exploring the following characteristics of life:

  1. Life is organized into hierarchical levels.
  2. Life maintains internal stability through a process called homeostasis.
  3. Life requires energy.
  4. Life grows, develops, and reproduces.
  5. Life evolves.
  6. Life is interdependent.

28 Important Questions on Bioinformatics | Genetics

Ans: Human genome project was started in 1987.

Q.2. What is Bioinformatics?

Ans: Bioinformatics is an integrated field, which combines computational, mathematical and statical methods to manage and analyze the biological data or information.

Bioinformatics is the management and analysis of biological information’s contained in biological databases.

Bioinformatics is a new subject of genetic information collection, analysis, and dissemination to the research community.

Q.3. Which are the main sub-disciplines of bioinformatics?

Ans: There are three main sub-disciplines within bioinformatics:

a. To develop, new algorithms and statical methods which may be used to access the relationships among information’s present in large databases.

b. To analyze and interpret various types of information, which include nucleic acid and amino acid sequences with protein structures and protein domains.

c. To develop new computer tools that enable efficient access and management of different types of biological information.

Q.4. What is medical-informatics?

Ans: Medical-informatics is a new field, which is used by physicians to manage and analyze clinical information contained in hospital database.

Q.5. Which types of issues or problems related to biological data are dealt with the bioinformatics?

Ans: Mainly, bioinformatics deals with development of data analysis tools, molecular modelling of various biological macromolecules in two dimensional and three dimensional structures, metabolic pathways, in pharmaceutical industries to develop new drug molecules, peptide vaccines, proteins etc.

Q.6. What is the main role of a bioinformatician in present biological research and development area?

Ans: The main role a bioinformatician is to create a framework that can support the needs of information based R&D for biological research.

Q.7. Why do we move towards the use of bioinformatics?

Ans: There are many reasons, that provide support to the use of bioinformatics such as:

a. For handling the biological data and manage it in such a way to give more meaningful information with the help of highly sophisticated computers.

b. To communicate among people, projects, and institutions engaged in biological R&D and applications.

c. To organize, give access and retrieving facility of biological information, documents and literature.

d. To analyze and interpret biological data through the computational facilities.

Q.8. Which type of skills are required to be a good bioinformatician?

Ans: To be a good bioinformatician, it is necessary to have a sound knowledge of molecular biology, biochemistry, molecular biophysics, molecular modelling, computer, information technology, and biostatistics. Beside, a bioinformatics professional must understand the central dogma of molecular biology and bioinformatics software packages.

Q.9. Why dry lab term is used for defining bioinformatics?

Ans: The meaning of dry lab is related to work without any type of chemicals, solutions in laboratory conditions. Bioinformatics mainly relate to work with computer and internet to analyze the biological information that is present on internet servers in different databases, due to these specific requirements dry lab term is used for defining the bioinformatics.

Q.10. What is data mining?

Ans: Discovery and retrieving of required data from different databases is known as data mining.

Ans: Knowledge Discovery in Databases (KDD) is an emerging field combining the theoretical and practical issues of extracting high level information from volume of low level data.

Q.12. How the term bioinformaticist is different from bioinformatician?

Ans: A bioinformaticist is an expert who knows how to use bioinformatics tools as well as to write interface for effective use of the tools. While a bioinformatician is a trained individual who only knows to use bioinformatics tools without having the knowledge of its construction.

Q.13. What is integrative bioinformatics?

Ans: The study of informative processes in biotic systems is known as integrative bioinformatics. In other words the high throughput interpretation of biological pathways is known as integrative bioinformatics.

Q.14. Define term database.

Ans: Database is the combination of same type of information or files that are collectively called as database.

Ans: OMIM is a database that provides all the information about the human inheritance. The complete meaning of OMIM is Online Mendelian Inheritance in Man.

Q.16. Which type of databases are used in bioinformatics?

Ans: There are more than 200 databases which are used in bioinformatics but the main categories of database relate to annoyed database, curated database, federated databases, integrated databases, interoperability databases, non-redundant databases, proprietary databases, redundant databases, relational databases, in-depth flat files and indexed flat files.

Q.17. What is federated database?

Ans: Federated database is an integrated repository information of multiple data sources presented with consistent and coherent semantics.

Q.18. What is interoperability?

Ans: The ability of different platforms of computers, networks, operating systems and applications to work effectively, without prior communication in order to exchange the information in a useful and meaningful manner is known as interoperability.

Q.19. What is non-redundant database?

Ans: A database that has redundant entries present in merged condition. These entries are typically those that are 100% character by character identical.

Q.20. What is complementarity?

Ans: The sequence specific or shape specific recognition that occurs when two or more molecules binds together.

Q.21. What is consensus sequence?

Ans: The most commonly occurring amino acid or nucleotide at each position of an aligned series of proteins or polynucleotide is known as consensus sequence.

Q.22. Define the consensus map.

Ans: The location of all consensus sequences in a series of multiple aligned proteins or polynucleotide is called the consensus map.

Q.23. What do you understand by the term-conserved sequence?

Ans: Conserved sequence is a sequence present in DNA or Protein that is consistent across species or has remained unchanged within the species over its evolutionary changes.

Q.24. What are proprietary databases?

Ans: These are a charge subscription type database, which require fees to access those on commercial level, such as LifeSeq and Gene Logic’s.

Q.25. Define redundant databases.

Ans: In general, the primary type database is known as redundant databases or when sequences were first created in the database is called as redundant database.

Q.26. Define the following terms.

Ans: a. Allele: Different forms of a gene, which occupy the same position on the chromosome.

b. Amplification: The process of repeatedly making copies of the same piece of DNA.

c. BAC (Bacterial artificial chromosome): A long sequencing vector, which is created from a bacterial chromosome by splicing a DNA fragment of 100kb from another species.

d. Base pair: The complementary bases on opposite strands of DNA which are held together by hydrogen bonding.

e. Beauty : BEAUTY or BLAST enhanced alignment utility, a tool developed by Baylor College of Medicine which uses BLAST to search several custom databases and incorporates sequence family information, location of conserved domains and information about any annotated sited or domains directly into the BLAST query results.

f. Blocks: a database of un-gapped multiple alignments for protein or peptide families in PROSITE.

Q.27. What is search engine?

Ans: A search engine is a type of utility or tools, which provide facility to retrieve information from different databases. In general life we use many search engines such as Goggle, Rediff and Yahoo but for bioinformatics there are mainly two search engines BLAST and FASTA.

Ans: Basic local alignment searching tool, used to find out the queried sequence from different databases of protein, DNA, RNA etc..

In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents. [1] Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype. [2]

The complete set of observable traits of the structure and behavior of an organism is called its phenotype. These traits arise from the interaction of its genotype with the environment. [3] As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight [4] thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in their genotype: [5] a striking example is people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn. [6]

Heritable traits are known to be passed from one generation to the next via DNA, a molecule that encodes genetic information. [2] DNA is a long polymer that incorporates four types of bases, which are interchangeable. The Nucleic acid sequence (the sequence of bases along a particular DNA molecule) specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text. [7] Before a cell divides through mitosis, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. A portion of a DNA molecule that specifies a single functional unit is called a gene different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. Organisms inherit genetic material from their parents in the form of homologous chromosomes, containing a unique combination of DNA sequences that code for genes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a particular locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. [8]

However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes within and among organisms. [9] [10] Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in developmental plasticity and canalization. [11]

Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule. These phenomena are classed as epigenetic inheritance systems that are causally or independently evolving over genes. Research into modes and mechanisms of epigenetic inheritance is still in its scientific infancy, however, this area of research has attracted much recent activity as it broadens the scope of heritability and evolutionary biology in general. [12] DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference, and the three dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level. [13] [14] Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. [15] Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits, group heritability, and symbiogenesis. [16] [17] [18] These examples of heritability that operate above the gene are covered broadly under the title of multilevel or hierarchical selection, which has been a subject of intense debate in the history of evolutionary science. [17] [19]

When Charles Darwin proposed his theory of evolution in 1859, one of its major problems was the lack of an underlying mechanism for heredity. [20] Darwin believed in a mix of blending inheritance and the inheritance of acquired traits (pangenesis). Blending inheritance would lead to uniformity across populations in only a few generations and then would remove variation from a population on which natural selection could act. [21] This led to Darwin adopting some Lamarckian ideas in later editions of On the Origin of Species and his later biological works. [22] Darwin's primary approach to heredity was to outline how it appeared to work (noticing that traits that were not expressed explicitly in the parent at the time of reproduction could be inherited, that certain traits could be sex-linked, etc.) rather than suggesting mechanisms.

Darwin's initial model of heredity was adopted by, and then heavily modified by, his cousin Francis Galton, who laid the framework for the biometric school of heredity. [23] Galton found no evidence to support the aspects of Darwin's pangenesis model, which relied on acquired traits. [24]

The inheritance of acquired traits was shown to have little basis in the 1880s when August Weismann cut the tails off many generations of mice and found that their offspring continued to develop tails. [25]

Scientists in Antiquity had a variety of ideas about heredity: Theophrastus proposed that male flowers caused female flowers to ripen [26] Hippocrates speculated that "seeds" were produced by various body parts and transmitted to offspring at the time of conception [27] and Aristotle thought that male and female fluids mixed at conception. [28] Aeschylus, in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sown within her". [29]

Ancient understandings of heredity transitioned to two debated doctrines in the 18th century. The Doctrine of Epigenesis and the Doctrine of Preformation were two distinct views of the understanding of heredity. The Doctrine of Epigenesis, originated by Aristotle, claimed that an embryo continually develops. The modifications of the parent's traits are passed off to an embryo during its lifetime. The foundation of this doctrine was based on the theory of inheritance of acquired traits. In direct opposition, the Doctrine of Preformation claimed that "like generates like" where the germ would evolve to yield offspring similar to the parents. The Preformationist view believed procreation was an act of revealing what had been created long before. However, this was disputed by the creation of the cell theory in the 19th century, where the fundamental unit of life is the cell, and not some preformed parts of an organism. Various hereditary mechanisms, including blending inheritance were also envisaged without being properly tested or quantified, and were later disputed. Nevertheless, people were able to develop domestic breeds of animals as well as crops through artificial selection. The inheritance of acquired traits also formed a part of early Lamarckian ideas on evolution.

During the 18th century, Dutch microscopist Antonie van Leeuwenhoek (1632–1723) discovered "animalcules" in the sperm of humans and other animals. [30] Some scientists speculated they saw a "little man" (homunculus) inside each sperm. These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. [31] An opposing school of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception. [32]

An early research initiative emerged in 1878 when Alpheus Hyatt led an investigation to study the laws of heredity through compiling data on family phenotypes (nose size, ear shape, etc.) and expression of pathological conditions and abnormal characteristics, particularly with respect to the age of appearance. One of the projects aims was to tabulate data to better understand why certain traits are consistently expressed while others are highly irregular. [33]

Gregor Mendel: father of genetics Edit

The idea of particulate inheritance of genes can be attributed to the Moravian [34] monk Gregor Mendel who published his work on pea plants in 1865. However, his work was not widely known and was rediscovered in 1901. It was initially assumed that Mendelian inheritance only accounted for large (qualitative) differences, such as those seen by Mendel in his pea plants – and the idea of additive effect of (quantitative) genes was not realised until R.A. Fisher's (1918) paper, "The Correlation Between Relatives on the Supposition of Mendelian Inheritance" Mendel's overall contribution gave scientists a useful overview that traits were inheritable. His pea plant demonstration became the foundation of the study of Mendelian Traits. These traits can be traced on a single locus. [35]

Modern development of genetics and heredity Edit

In the 1930s, work by Fisher and others resulted in a combination of Mendelian and biometric schools into the modern evolutionary synthesis. The modern synthesis bridged the gap between experimental geneticists and naturalists and between both and palaeontologists, stating that: [36] [37]

  1. All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.
  2. Evolution is gradual: small genetic changes, recombination ordered by natural selection. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction (not saltation). is overwhelmingly the main mechanism of change even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment. The role of genetic drift is equivocal though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.
  3. The primacy of population thinking: the genetic diversity carried in natural populations is a key factor in evolution. The strength of natural selection in the wild was greater than expected the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.

The idea that speciation occurs after populations are reproductively isolated has been much debated. [38] In plants, polyploidy must be included in any view of speciation. Formulations such as 'evolution consists primarily of changes in the frequencies of alleles between one generation and another' were proposed rather later. The traditional view is that developmental biology ('evo-devo') played little part in the synthesis, but an account of Gavin de Beer's work by Stephen Jay Gould suggests he may be an exception. [39]

Almost all aspects of the synthesis have been challenged at times, with varying degrees of success. There is no doubt, however, that the synthesis was a great landmark in evolutionary biology. [40] It cleared up many confusions, and was directly responsible for stimulating a great deal of research in the post-World War II era.

Trofim Lysenko however caused a backlash of what is now called Lysenkoism in the Soviet Union when he emphasised Lamarckian ideas on the inheritance of acquired traits. This movement affected agricultural research and led to food shortages in the 1960s and seriously affected the USSR. [41]

There is growing evidence that there is transgenerational inheritance of epigenetic changes in humans [42] and other animals. [43]

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Basic Principles of Biology

The foundation of biology as it exists today is based on five basic principles. They are the cell theory, gene theory, evolution, homeostasis, and laws of thermodynamics.

    : all living organisms are composed of cells. The cell is the basic unit of life. : traits are inherited through gene transmission. Genes are located on chromosomes and consist of DNA. : any genetic change in a population that is inherited over several generations. These changes may be small or large, noticeable or not so noticeable. : ability to maintain a constant internal environment in response to environmental changes. : energy is constant and energy transformation is not completely efficient.

Subdiciplines of Biology
The field of biology is very broad in scope and can be divided into several disciplines. In the most general sense, these disciplines are categorized based on the type of organism studied. For example, zoology deals with animal studies, botany deals with plant studies, and microbiology is the study of microorganisms. These fields of study can be broken down further into several specialized sub-disciplines. Some of which include anatomy, cell biology, genetics, and physiology.

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The opening unit introduces students to the sciences, including the scientific method and the fundamental concepts of chemistry and physics that provide a framework within which learners comprehend biological processes.

  • Identify the shared characteristics of the natural sciences
  • Summarize the steps of the scientific method
  • Compare inductive reasoning with deductive reasoning
  • Describe the goals of basic science and applied science
  • Knowledge Check
  • Identify and describe the properties of life
  • Describe the levels of organization among living things
  • Recognize and interpret a phylogenetic tree
  • List examples of different subdisciplines in biology
  • Knowledge Check

The Study of Life - Final Assessment

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Watch the video: Chapter 28 The Nervous System (September 2022).