Chemistry of Life Essay

Differentiating living from non-living is an intuitive thing for all of us. With no ambiguity we can tell if a thing is alive from our observations and basic understanding of the ‘properties of life’. Science has defined life precisely based on a few traits and key characteristics common to all living organisms, of which, the basic 7 properties of life have been enlisted as:

1. Cellular organization: Life on earth began with a single cell. A cell is the fundamental unit of all living organisms. Organisms made of a single cell are called unicellular organisms which are microscopic i.e. invisible to the naked eye. With time these single cellular organisms started evolving into multicellular organisms wherein the multiple cells combined to form a tissue. Tissues in turn collaborated to form organs which work together forming organ systems, each system working discretely towards individual goals and in an organized manner forming an organization called the living body.

2. Response to stimuli: The living has the ability to respond to its vicinity. They have sensitivity to various stimuli. For example, the touch-me-not plant retrieves itself on touch, sunflowers moving in the direction of the sun, our reflexes to heat/cold. Even single celled organisms have sensitivity to chemicals (chemotaxis) e.g. sperm reaches the egg in the ovary by the virtue of chemotaxis.

3. Reproduction: The rudimentary property of living organisms is that they can reproduce their own like. Reproduction is the process where the genetic material of the species is passed on to its offsprings which ensures that the offspring has the same characteristic features such as shape and size as that of the parent species. Unicellular organisms like the bacteria reproduce asexually by duplicating their genetic material followed by cell division. Whereas, the multicellular organisms have a well organized system called the reproductive system consisting of specialized fertile sex cells and their corresponding reproductive organs. Multicellular organisms hence reproduce sexually.

4. Growth and development: Living organisms undergo regulated growth, become larger in size through cell division. Living organisms grow and develop in patterns determined by heredity, the traits passed to offspring by parents.

5. Regulation/Metabolism: The complexity of living organisms requires multiple regulatory mechanisms to maintain internal functions. These regulatory mechanisms are made up of enormous number of interlocking chemical reactions which gives the organisms the ability to do work like growing, reproducing etc. Metabolism is essentially a collection of such chemical reactions occurring within the body (or cell). Photosynthesis in plants, respiration and digestion of food in animals are some of the examples.

6. Homeostasis: It is inevitable for all the living organisms to maintain a steady internal environment for proper cell functioning. Homeostasis means ‘steady-state’. Important internal parameters such as body fluid pH, body temperature, blood sugar levels etc are required to be constantly maintained and regulated as the external environment changes.

7. Evolution:

Over the ages living organisms have been evolving per generation. The genetic makeup changes overtime as a consequence of changing environment and habitats of the living organisms. Evolution involves natural selection, in which a heritable trait, such as darker fur color or narrower beak shape, lets organisms survive and reproduce better in a particular environment.

v Chemistry of life

The fundamental unit of life on earth is the ‘cell’ which in turn is made up of four basic molecules namely proteins, carbohydrates, lipids and nucleic acids. These molecules are also called the ‘molecules of life’.

1. Proteins: Proteins are essentially the building blocks of life. They are the first molecules of life which has the ability to reproduce. In fact, a prion which is only a defective protein has an ability to induce the change in a normal protein and turn it into another prion (what is a prion, Scientific American, n.d.) — i.e. it has life in itself and can reproduce. Proteins are the most important component of a cell and are involved in a vast range of cell’s biochemistry. Structurally, proteins are made up of long chains of molecules called ‘amino acids’ (nitrogen based compounds). There are 20 essential amino acids that arrange themselves in a variety of combinations to form long chains which subsequently twists and turns to form unique structures of proteins. They are involved in muscle movement, storage of energy, digestion, immune defense and much more.

2. Carbohydrates:

If proteins are the building blocks of life then carbohydrates are the source of energy of life. Carbohydrates are composed of carbon, hydrogen and oxygen atoms. In common terms they are also called sugars. Single sugar unit is called a monosaccharide e.g. glucose, fructose and galactose. Whereas two sugar molecules linked together are called disaccharides e.g. sucrose, lactose etc. and when many sugar molecules are linked together they are called polysaccharides. Our bodies need all the three types of carbohydrates for their own reasons.

3. Lipids: A group of molecules like fats, oil, and certain steroids form lipids. Lipids constitute mainly of carbon and hydrogen atoms, forming chains called fatty acids. Lipids are important to living organisms for a number of reasons. One type of lipid, the triglycerides, is sequestered as fat in adipose cells, which serve as the energy-storage depot for organisms and also provide thermal insulation. Some lipids such as steroid hormones serve as chemical messengers between cells, tissues, and organs, and others communicate signals between biochemical systems within a single cell. The membranes of cells and organelles (structures within cells) are microscopically thin structures formed from two layers of phospholipid molecules (Lipids, Britannica, n.d.).

4. Nucleic acids: The unit molecules that form the genetic material inside a cell are nucleic acids. There are two main types of nucleic acids - DNA and RNA. Deoxyribonucleic acid (DNA) is the one that carries the genetic information important for the functioning and reproduction of living organisms. While the ribonucleic acid (RNA) plays a role in translation of the information stored in DNA involved in protein synthesis. Structurally nucleic acids are very complex. The base unit of nucleic acids is called ‘nucleotides’ which in turn are composed of 3 molecules – sugar, a base and a phosphate group. The two major differences between DNA and RNA are :

i. DNA has deoxyribose sugar while RNA has ribose sugar

ii. The basic groups in DNA are adenine (A), guanine (G), thymine (T) and cytosine (C). While in RNA thymine (T) is replaced by uracil (U). A and G are categorized as purines, and C, T, and U are collectively called pyrimidines (Nucleic acid, Britannica, n.d.).

v Cell – the biological unit of life

1. Cell theory: According to the ‘Cell theory’:

i. All known living things are composed of one or more cells.

ii. All new cells are created by pre-existing cells dividing in two.

iii. The cell is the most basic unit of structure and function in all living organisms.

2. Cell anatomy: A cell consists of three major components:

i. Cell membrane: It is a permeable membrane that envelops and protects the contents of the cell and its internal environment. The cell exchanges various nutrients and waste materials with its vicinity through the selective permeability of the cell membrane via active and passive transport. Processes like osmosis, diffusion and energy pumps (ATP) occur at the membrane.

ii.  Nucleus: It is the core of the cell and is the most important part as it contains the genetic material (DNA) consisting of all the information for the cellular functioning.  The DNA is tightly wound up tightly with the support of proteins and packaged to form chromosomes. Furthermore, the nucleus consists of a nucleolus (involved in protein synthesis with the help of RNA) and nuclear membrane.

iii. Cytoplasm: It fills up rest of the cell and contains the cellular organelles. A list of these cellular organelles along with their roles in cellular functioning has been tabulated as follows:

Mitochondria

Sites of cellular respiration which provides energy for the cell’s various activities

Endoplasmic reticulum

Network of membranes composed of both regions with ribosomes (rough ER involved in protein synthesis) and regions without ribosomes (smooth ER involved in carbohydrates and lipid synthesis)

Ribosomes

Consist of RNA and proteins; Responsible for protein production

Golgi apparatus

Made up of folded sacs, responsible for manufacturing certain cellular products

Lysosomes

Membranous sacs filled with enzymes that digest waste like bacteria and old cellular macromolecules

Cytoskeleton

Helps cells maintain their shape and internal organization; Provides mechanical support to the cells to carry out essential functions like division and movement

3. Cell types: Based on the cell components, broadly , there are two types of cells-

i. Prokaryotic cells: these are the most primitive type of cells which lack a proper cell membrane and a nucleus.

ii. Eukaryotic cells: they contain membrane bound organelles and a well defined nucleus. They are further classified into plant cells and animal cells.

4. Cell physiology: Cell physiology is the biological study that refers to all the normal functions that take place in a living organism. The study of cellular physiology is important as cell is the smallest unit capable of carrying out the processes associated with life such as respiration, photosynthesis and reproduction.

i. Respiration: The term cellular respiration refers to the complex biochemical pathway by which cells release energy from the chemical bonds of food molecules and provide that energy for the essential processes of life. Basically a glucose molecule is broken down into carbon dioxide and water consequently releasing energy. There are two types of cellular respiration-

a. Aerobic respiration: It occurs in the presence of oxygen. Eukaryotic cells undergo aerobic respiration which takes place in the mitochondria of the cell. The energy so produced is in the form of ATP (adenosinetriphosphate).

b. Anaerobic respiration: It occurs in the absence of oxygen. Prokaryotic cells undergo anaerobic respiration within the cytoplasm or on the inner surfaces of the cells.

The overall process, however, can be distilled into three main metabolic stages or steps: glycolysis, tricarboxylic acid cycle (TCA cycle) and oxidative phosphorylation (respiratory-chain phosphorylation).

ii. Photosynthesis: It is the process by which plants, some bacteria and some protistans use the energy from sunlight to produce glucose from carbon dioxide and water. This glucose can be converted into pyruvate which releases adenosine triphosphate (ATP) by cellular respiration. Oxygen is also formed.

Photosynthesis may be summarised by the word equation:

carbon dioxide + water

glucose + oxygen

The conversion of usable sunlight energy into chemical energy is associated with the action of the green pigment chlorophyll. Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants and other photosynthetic organisms. All photosynthetic organisms have chlorophyll a. Accessory pigments absorb energy that chlorophyll a does not absorb. Accessory pigments include chlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophyll a absorbs its energy from the violet-blue and reddish orange-red wavelengths, and little from the intermediate (green-yellow-orange) wavelengths (Photosynthesis, RSC, n.d.).

iii. Reproduction: A cell reproduces via the mode of cell division. In case of unicellular organisms cell division is the means of reproduction while in multicellular organisms cell division is required for tissue growth and maintenance. Cell division are of two types-

a. Mitosis: Each time a cell divides, it makes a copy of all of its chromosomes, which are tightly coiled strands of DNA, the genetic material that holds the instructions for all life, and sends an identical copy to the new cell that is created. This is a process called Mitosis which can be further subdivided into 5 phases-

Prophase- thickening and coiling of the chromosomes

Prometaphase- chromosomes attach to the spindle fibers

Metaphase- condensed chromosomes align at the equator or the middle of the cell

Anaphase- chromatid pairs separate into two identical chromosomes as they are pulled apart by the spindle fibres.

Telophase- a neuclear membrane is formed around the newly formed chromosome followed by the division of the cytoplasm giving rise to two daughter cells each containing the same number of chromosomes as that of the mother cell.

b. Meiosis: Meiosis is a type of cell division that reduces the number of chromosomes in the parent cell by half and produces four gamete cells. This process is required to produce egg and sperm cells for sexual reproduction. Meiosis has both similarities to and differences from mitosis. Meiosis begins following one round of DNA replication in cells in the male or female sex organs. The process is split into meiosis I and meiosis II, and both meiotic divisions have multiple phases. Meiosis I is a type of cell division unique to germ cells, while meiosis II is similar to mitosis (Meiosis, Nature education, 2014).

v Mendel’s laws of inheritance

Gregor Mendel, through his work on pea plants, discovered the fundamental laws of inheritance in the mid nineteenth century. He deduced that genes come in pairs and are inherited as distinct units, one from each parent. As mentioned earlier, in meiosis cell duplicates its DNA and divides twice to produce four gametes, or reproductive cells. Most cells in the body are diploid, meaning they have two copies of each chromosome. But because gametes have gone through meiosis, they have one copy of each chromosome and are haploid. During sexual reproduction two gametes, called the egg and sperm, join together and form a diploid cell that will eventually become an individual organism. This diploid cell, called a zygote, received one copy of each chromosome from each parent. Mendel tracked the segregation of parental genes and their appearance in the offspring as dominant or recessive traits. Mendel's Laws of Heredity (Johann Gregor Mendel, Retrieved from http://www.dnaftb.org/1/bio.html) are usually stated as:

1. The Law of Segregation: Each inherited trait is defined by a gene pair. Parental genes are randomly separated to the sex cells so that sex cells contain only one gene of the pair. Offspring therefore inherit one genetic allele from each parent when sex cells unite in fertilization.

2. The Law of Independent Assortment: Genes for different traits are sorted separately from one another so that the inheritance of one trait is not dependent on the inheritance of another.

3. The Law of Dominance: An organism with alternate forms of a gene will express the form that is dominant.

v DNA – structure and function

1. The double helix structure:

Early in 1940s biologists saw DNA as a long polymer consisting of chemically identical four subunits. In 1950s DNA was first examined by X-ray diffraction analysis and it was then observed that DNA was a double stranded complex molecule which gave rise to the widely accepted Watson-Crick model.

A DNA molecule consists of two long polynucleotide chains. Each of this polynucleotide chain is called a DNA strand and both these strands are held together by strong hydrogen bonds. A polynucleotide chain consists of four types of nucleotide subunits. As discussed earlier a nucleotide subunit is composed of a sugar moiety, a nitrogenous base and a phosphate group. In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “backbone” of alternating sugar-phosphate-sugar-phosphate with only the nitrogenous base differing in each of the four types of nucleotides.

The three-dimensional structure of DNA—the double helix—arises from the chemical and structural features of its two polynucleotide chains. Because these two chains are held to-gether by hydrogen bonding between the bases on the different strands, all the bases are on the inside of the double helix, and the sugar-phosphate backbones are on the outside. A always pairs with T, and G with C. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones an equal distance apart along the DNA molecule.

2. Function: DNA plays vital role in protein synthesis and passing on the genetic information/heredity. DNA encodes information through the order, or sequence, of the nucleotides along each strand. Each base—A, C, T, or G—can be considered as a letter in a four-letter alphabet that spells out biological messages in the chemical structure of the DNA. This information contained in the genes is encoded for producing proteins. This process is known as gene expression, through which a cell translates the nucleotide sequence of a gene into the amino acid sequence of a protein. The complete set of information in an organism's DNA is called its genome, and it carries the information for all the proteins the organism will ever synthesize. Since each strand of DNA contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand, each strand can act as a template, or mold, for the synthesis of a new complementary strand. The ability of each strand of a DNA molecule to act as a template for producing a complementary strand enables a cell to copy, or replicate, its genes before passing them on to its descendants (Alberts, 2002).

v Cancer and gene control

      The most important property of living organism is homeostasis that is proper regulation of the internal processes. Any untoward changes in the same can lead to severe diseases and cancer is one such deadly disease.

Cancer: Cancer is a genetic disease which is a multistep process that starts when a single cell acquires a series of mutations, usually one after another, that collectively change a once-normal cell into a cancerous cell that divides uncontrollably and may eventually spread throughout the body.

Genes: Genes are a part of the DNA that control how the cells work by making proteins. The proteins have specific functions and act as messengers for the cell. Each gene must have the correct instructions for making its protein. This allows the protein to perform the correct function for the cell.

Mutation: All cancers begin when one or more genes in a cell mutate. A mutation is a change. It creates an abnormal protein. Or it may prevent a protein’s formation.

Genes That Drive Cancer: Tumor Suppressor Genes and Proto-oncogenes: Mutations in two general types of genes lead to cancer: tumor suppressor genes, which normally act like "brakes" to inhibit cell growth and division, and proto-oncogenes, which normally act like "gas pedals" to accelerate cell growth and division. Mutations that inhibit the activity of tumor suppressor genes or that overactivate proto-oncogenes can drive cells to cancer; in either case, cells lose their brakes, hit the gas pedal, and accelerate uncontrollably toward a cancerous state.

Types of genetic mutations: There are 2 basic types of genetic mutations:

i. Acquired mutations- These are the most common cause of cancer. They occur from damage to genes in a particular cell during a person’s life. Acquired mutations are not found in every cell in the body and they are not passed from parent to child. Factors that cause these mutations include:

Tobacco

Ultraviolet (UV) radiation

Viruses

Age

ii. Germline mutations- These are less common. A germline mutation occurs in a sperm cell or egg cell. It passes directly from a parent to a child at the time of conception. As the embryo grows into a baby, the mutation from the initial sperm or egg cell is copied into every cell within the body. Because the mutation affects reproductive cells, it can pass from generation to generation.

      Genetic screening using blood samples can be used to identify germ-line mutations in individuals with a family history of cancer in order to assess cancer risk. In addition, genetic analysis of a tumor can be used to determine the somatic changes that have occurred. Knowledge of both germ-line mutations and tumor-associated somatic mutations can in turn be used to tailor cancer therapy in order to most effectively and specifically target tumor cells. Thus, although tremendous progress has been made since the "war" on cancer was declared in 1971, this war is still far from over (Chial, 2008).

v References

Alberts B, Johnson A, Lewis J, et al. 2002, Molecular Biology of the Cell. 4th edition. New York: Garland Science; The Structure and Function of DNA.

Retrieved from: https://www.ncbi.nlm.nih.gov/books/NBK26821/

Chial, H. (2008) Genetic regulation of cancer. Nature Education 1(1):67.

Retrieved from: https://www.nature.com/scitable/topicpage/genetic-regulation-of-cancer-891

Johann Gregor Mendel,

Retrieved from: http://www.dnaftb.org/1/bio.html

Lipids, Britannica, n.d.

Retrieved from: https://www.britannica.com/science/lipid

Meiosis, Nature education, 2014.

Retrieved from: https://www.nature.com/scitable/definition/meiosis-88

Nucleic acid, Britannica, n.d.

 Retrieved from: https://www.britannica.com/science/nucleic-acid

Photosynthesis, RSC, n.d.

Retrieved from: http://www.rsc.org/Education/Teachers/Resources/cfb/Photosynthesis.htm

What is a prion, Scientific American, n.d.

Retrieved from: https://www.scientificamerican.com/article/what-is-a-prion-specifica/