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Molecular Composition and Relationships Between Organisms

Biological Molecules

These are carbon-based compounds that are found in all living things. They include carbohydrates, proteins, lipids, and nucleic acids. They can all be broken down into single units called monomers.

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Its monomers are monosaccharides, which include glucose, fructose, and galactose. Glucose has two isomers, alpha, and beta glucose, both differentiated by the position of the hydroxyl bond. The larger unit, disaccharides are formed from the condensation of two monosaccharides. These include maltose (2 glucose molecules), sucrose (glucose and fructose), and lactose (glucose and galactose). Polysaccharides are formed from the condensation of numerous monosaccharides. Glycogen and starch are products of alpha glucose whereas cellulose is from beta glucose.

They can be further classified into reducing and non-reducing sugars. Reducing sugars are mainly monosaccharides as they contain the aldehyde group. They change the color of Benedict’s solution from a range of green to red. The constituents of polysaccharides can be analyzed using paper chromatography. The monosaccharides are identified based on the Rf value of the different units depending on the solvent used.

Glucose is integral to the body’s metabolism. All sugars such as starch have to be broken down into the simplest monosaccharide before the conversion to energy as ATP. The normal blood glucose is in a range of 70-110mg/dl. Derangements of this concentration can give you either hypoglycemia or hyperglycemia (diabetes mellitus).

Lipids

They consist of two major groups, phospholipids, and triglycerides. Triglycerides are the condensation products of one fatty acid and three glycerol molecules with the formation of ester bonds. Fatty acids can be further classified as saturated or unsaturated. The saturated type contains only single bonds in the R group whereas the unsaturated kind has at least one double bond. On the other hand, phospholipids are formed when one of the fatty acids in the triglyceride molecule is replaced by a phosphate-containing group. The emulsion test is used to identify lipids based on their dissolving in ethanol and immiscibility with water.

Proteins

The structural subunits of proteins are amino acids. These contain carboxyl and amine groups with an R side chain. The R group forms the basis of the differentiation of the 20 amino acids. A peptide bond is formed from the condensation of two amino acids to result in either dipeptide (2 amino acids) or polypeptides (more than two amino acids). Proteins perform various roles: structural, enzymatic, carriers or hormones. They can be organized into the primary, secondary, tertiary, or quaternary levels. The primary level is the amino acid sequence. The secondary structure is from the folding of the chains to form an alpha helix or beta-pleated sheets. The tertiary structure is the overall 3D form. The quaternary structure is formed from the combination of two or more polypeptides. Any changes in the shapes of these structures through varying temperatures or pH lead to loss of function. The biuret test checks for the presence of peptide bonds through a purplish change in the color of the solution. The main role of proteins is in their enzymatic function. Enzymes are specific for their substrates as evidenced by their unique substrate binding sites. The rate of the reactions is influenced by enzyme/ substrate concentration, inhibition (competitive or non-competitive), temperature, and pH.

Nucleic acids

They are information-carrying molecules (mainly the genetic code). They are divided into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA is mainly involved in the storage of genetic information whereas RNA has a role in its transfer. Their monomers are called nucleotides and consist of a phosphate group, a pentose sugar, and a nitrogen base. DNA and RNA differ in their pentose group, deoxyribose, and ribose sugars respectively. Nucleotides are linked by phosphodiester bonds whereas polynucleotide chains are held by hydrogen bonds in a DNA molecule. The base pairing is specific (adenine with thymine or cytosine and guanine). In DNA replication, the double helix strands are unwound by DNA helicase with the breakage of the hydrogen bonds. The complementary strand is replicated dependent on the base pairing and the template strand through the action of DNA polymerase.

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Other important molecules

ATP (Adenosine triphosphate) is a nucleotide derivative involved mainly in the body’s metabolism. It consists of adenine, ribose, and three phosphate groups. The hydrolysis of ATP to ADP is a high-energy yielding reaction. ADP is reconverted to ATP either during respiration or photosynthesis.

Water is integral to the human body. It acts as a solvent and heat buffer. It is a by-product of several reactions and also cools living things through vaporization. Inorganic ions perform different roles. The main ones include sodium, potassium, calcium, and chloride ions.

Cells

The basic living unit is a cell. They can replicate binary fission in prokaryotes or mitosis and meiosis in eukaryotes. They have cell membranes that may have embedded proteins. These proteins either act as receptors, channels, or antigens. Eukaryotic cells have membrane-bound organelles (nucleus, lysosomes, ribosomes, Golgi apparatus, and endoplasmic reticulum) unlike prokaryotes. The cell can be visualized using microscopes. Different parts of the cell can be stained to ensure easy visualization i.e. iodine staining of starch.

Eukaryotic cells replicate via the cell cycle. The stages include interphase, prophase, metaphase, anaphase, and telophase. These 5 stages summarize mitosis whose results include two identical daughter cells. Failure of regulation of mitosis may lead to uncontrolled replication which results in cancer and tumorigenesis. On the other hand, binary fission involves replication of the plasmids and circular DNA with the division of the cytoplasm to form two daughter cells.

Movement across cellular membranes is classified as simple diffusion, facilitated diffusion, osmosis, active transport, and co-transport. Located on the cell membranes, are unique identifiers that are mostly proteins. They allow the identification of the cells as foreign (pathogens or cells from other organisms of the same species or other species). These unique molecules are termed antigens. When a cell is detected as foreign by the immune system, different responses occur depending on the immune cell i.e. phagocytosis by macrophages, stimulation of cytotoxic cells by T lymphocytes, and antibody production by B lymphocytes. Active immunity involves the body producing its antibodies in response to a foreign antigen. Passive immunity involves the introduction of preformed antibodies from a different source. Vaccines perform their role based on their stimulation of either passive or active immunity. As a larger proportion of the population becomes immune to disease through vaccination, the unvaccinated population is protected as the disease transmission/ replication is prevented.

HIV has become one of the better-known epidemics of the 20th and 21st centuries. It contains antigens on its cell membranes that are detected by the immune cells as foreign. Once phagocytosed, it undergoes replication in the cell which eventually leads to cell death and release of the new virions with subsequent reinfection of other cells. This depletes the immune cells leading to immunosuppression.

Organisms exchange with their environment

For the survival of living organisms, there needs to be an exchange of substances across the cell membrane to provide the constituents of various important chemical reactions. This depends on the distance of the cell membrane from the substance necessitating the need for a mass transport system to aid the exchange. This exchange at the membrane can occur through the various processes of simple diffusion, facilitated diffusion, osmosis, active transport, and co-transport. The surface area to volume ratio acts as a major factor. A higher surface area to volume ratio increases the rate of exchange. Similarly, organisms with a higher ratio have a higher metabolism.

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Gas Exchange

In single-celled organisms, gas exchange occurs mainly via simple diffusion which is dependent on the concentration gradient. Plants have stomata which provide the entry of gases into the leaf its diffusion into the plant cells. Insects have spiracles on the side of their body which lead to the trachea and further subdivide to tracheoles. Mammals have complex respiratory systems with lungs. In fish, the gills are bathed with water and are highly vascularized. Oxygen diffuses into the fish as carbon dioxide is released. Blood in the gills flows in an opposite direction to the flow of water (counter-current principle). All these systems provide the moist environments with oxygen which is then utilized by the organism.

In the human body, the respiratory system consists of the nostrils, trachea, bronchi, bronchioles, and alveoli. The lung is made up of numerous alveoli and is supplied by a rich network of blood vessels. During inspiration, the lungs expand with the relaxation of the diaphragm creating negative intrapulmonary pressure, resulting in entry of air. With expiration, the diaphragm contracts increasing intrathoracic pressure forcing out air leading to exhalation.

Digestion and absorption

Digestion is the breakdown by enzymes of large food particles into the smallest subunits that can readily cross the cell membranes. The enzymes involved are amylases and disaccharidases (carbohydrates), lipases (lipids), and endopeptidases, exopeptidases, and dipeptidases (proteins). The mechanism of absorption is mainly via diffusion (simple or facilitated- sodium-glucose cotransporter.).

Mass transport

Due to the complex anatomical structure of mammals and other higher animals, nutrients and oxygen need to be transported for a distance from the point of entry/ absorption. Mammals perform this function through the circulatory system. These include the heart, arteries, veins, capillaries, arterioles, and blood. The heart contracts propelling oxygenated blood through arteries throughout the body. Capillaries are the endpoint and form the membrane for the diffusion of the nutrients as they are bound by a single-cell thick barrier. The veins carry deoxygenated blood back to the heart. Hemoglobin in the blood is the carrier of oxygen.

In plants, water and organic substances are transported via different mechanisms and structures. Water is dependent on the xylem through the cohesion-tension theory. This is aided by the continuous transpiration pull. Organic substances are dependent on the mass flow theory which is dependent on the functioning of the xylem.

Genetic information, variation, and relationships between organisms

The diversity in living things among the same or different species is accounted for by the difference in the genetic composition. Environmental influence also plays a major role in the manifestation of the differences. A gene is a segment of DNA found at a locus, a specific position of the DNA molecule. It contains genetic information that determines the amino acid sequence during protein synthesis. In the same species, differences can be accounted for by changes in the genetic material through chromosomal/ genetic mutations or reorganization during meiosis.

DNA, Genes, and Chromosomes

Prokaryotes have DNA that is short and circular. Eukaryotes have DNA that is associated with histone proteins to form chromosomes. Mitochondria and chloroplasts in eukaryotes have DNA that is similar in structure to prokaryotes. A gene is a base sequence that codes for the amino acid sequence of proteins or a functional RNA (transfer RNAs or ribosomal RNAs). A sequence of three DNA bases usually codes for a single amino acid. In the entire sequence, most of the multiple triple repeats do not code for protein i.e. introns. Exons are the sequences responsible for protein formation.

During protein formation, transcription of the DNA results in the formation of mRNA. The next process is translocation which involves the arrangement of amino acids as per the sequence of bases on the mRNA. The amino acids are placed on the chain by the tRNA. The process of protein formation is an energy-dependent process.

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Gene mutations are changes in the base pairs of the chromosomes. They can be spontaneous or induced. They mainly occur through the process of base substitution or deletion. Chromosomal mutations can occur during meiosis mainly due to non-disjunction. Mitosis results in daughter cells that are identical to the parent cell whereas meiosis results in different daughter cells. In meiosis, the daughter cells are haploid. Crossing over can take place during the separation of chromosomes resulting in further variation.

Genetic diversity is the number of different alleles of genes in a population. They can be either beneficial or harmful. The beneficial ones are inherited by subsequent generations as the carriers of the harmful ones are eliminated. This is mainly evidenced by the development of antibiotic resistance by bacteria.

A phylogenetic classification system has been developed for the arrangement of species based on evolutionary origins and relationships. Each group is called a taxon i.e. kingdom, phylum, class, order, family, genus, and species.

Species richness is the number of different species in a community. It is mainly assessed using the index of diversity.

d = N (N – 1)

∑ n (n – 1)

where N = total number of organisms of all species

and n = total number of organisms of each species.

The diversity can be further analyzed by comparison of the observable characteristics, the base sequences of DNA or mRNA, and amino acids encoded by the nucleotides.

Energy transfers in and between organisms

The main mechanisms of the production of energy in plants and animals are photosynthesis and respiration respectively. Both processes result in the production of ATP and are not 100 percent efficient.

Photosynthesis is a light-dependent reaction. Chlorophyll absorbs lights and is photoionized. Only some of the heat is utilized from the energy released to produce ATP and reduced NADP. Water is photolyzed to produce protons, electrons, and oxygen. The reduced NADP is used to form a simple sugar supplemented with the energy from the hydrolyzed ATP. The factors that affect photosynthesis include temperature, light intensity, and carbon dioxide concentration.

In respiration, ATP can be produced by both the aerobic and anaerobic types. The first stage in both types is glycolysis. At the end of glycolysis, pyruvate reduced NAD, and ATP is the product. In anaerobic respiration, the pyruvate is converted to ethanol or lactate. In aerobic respiration, the pyruvate enters the mitochondria to produce ATP, water, and carbon dioxide. Aerobic respiration produces more molecules of ATP.

Energy and ecosystems

The primary source of energy in any ecosystem is planted. The organic compounds are synthesized from carbon dioxide. They form the biomass of the plants. Gross primary production is the chemical energy stored in plant biomass in a given area. Net Primary Production is the chemical energy stored in the plant biomass after respiratory losses.

NPP = GPP R (Respiratory losses)

N (Net production of consumers) = I (Chemical energy in ingested food) – F (chemical energy lost in feces + R (Respiratory losses to the environment).

Nutrient cycles

The main ones are the phosphorous and nitrogen cycles. Microorganisms play a major role in ensuring the recycling of these elements.

Organisms respond to changes in their internal and external environments

Any change in the internal or external environment is called a stimulus. It is detected by a receptor with a coordinator formulating the response by an effector. In animals, these processes are mainly modulated by the nervous and hormonal systems. The only difference is in their speed with the neuronal response being more rapid.

In plants, there is a growth response to both light and gravity. These responses ensure that the plants acquire the maximal amount of ingredients needed for their growth. The experiment using indoleacetic acid best exemplified how plants grow in response to their environments.

Receptors in the human body are specific for particular stimuli. The Pacinian corpuscle in the skin is a mechanoreceptor that is linked to neurons. Stimulation of the receptor generates action potentials. With continuous stimulation, regeneration of the membrane potential is prolonged hence reducing the sensitivity of the receptors (habituation).

The heart’s activity is dependent on autonomic control of myocardial contraction. The synchronized activity of the cardiac muscle is dependent on the stimulation by the sinoatrial node, atrioventricular node, and Purkinje fibers. This system detects any changes in the body’s requirements and the heart’s activity is modified especially contractility.

any changes in the body's requirements and the heart's activity is modified especially contractility.

Neuronal activity is dependent on changes in the membrane potential. The resting membrane potential is determined by the balance of intracellular and extracellular sodium and potassium balance. Depolarization of the membrane results in the generation of an action potential which is transmitted down the axon. With myelination, the speed of conduction is increased. Other factors that affect it include axonal diameter, temperature, saltatory conduction due to the presence of nodes of Ranvier.

When a neuron transmits an impulse, it causes a release of neurotransmitters (excitatory or inhibitory) at the synapse (junction between the axon terminal and cell body). The released chemicals bind to receptors and cause a change in membrane potential. Excitatory neurotransmitters include glutamate, norepinephrine, and dopamine. Inhibitory ones include GABA and serotonin.

Some of the effectors include muscles that are excited by neuronal impulses. It is an energy-dependent process that requires ATP. The response of muscles is contraction by myofibrils through the coordination of actin and myosin.

Homeostasis

This is a process that aims to maintain the internal physiological environments within the set levels. It can be through a negative feedback system that detects a change in the different controls and causes a response that reverts it to the normal. One of the major homeostatic mechanisms is glucose control. It is under the control of different hormones. Insulin reduces blood glucose by increasing its entry into the cells. It also activates glycogenesis. Glucagon increases blood glucose by activating glycogenolysis and gluconeogenesis. Osmoregulation is the control of water in the body. It involves the actions of ADH on the nephrons in the kidney.

Genetics, populations, evolution, and ecosystems

In many environments, there is interaction between similar species and different species. The variability arises from genetics. Even among the same species, there exist differences due to alleles.

Genotype is the genetic constitution of an organism. The phenotype is the physical expression of this constitution and its interaction with the environment. Alleles can either be dominant or recessive. A population is a particular group of species living in a particular area at a certain point in time and can interbreed.

Hardy-Weinberg equation

p2 + 2pq + q2 = 1; where p is the frequency of one (usually the dominant) allele and q is the frequency of the other (usually recessive) allele of the gene.

The survival of a species is dependent on natural selection. This is guided by predation, disease, and competition. The organisms with advantageous phenotypes tend to survive and propagate their traits to subsequent generations.

An ecosystem is only able to support a specified number of organisms termed its carrying capacity. The size can be estimated using the quadrat method and mark-release-recapture method.

The control of gene expression

Transcription and translation of sequences are used to control the metabolic activities of cells. Changes in the sequence of bases can alter the structure of proteins especially if it affects the exons. These mutations occur through addition, deletion, substitution, inversion, duplication, and translocation of bases. They can be spontaneous or induced.

Totipotent cells can divide and produce any type of cell through changes in their DNA and are found only in the human embryo. Pluripotent cells are found in embryos and can differentiate to form a limited number of cells. Unipotent cells are limited to one cell type.

Transcription and translation can be regulated by hormones. These hormones produce second messengers which affect the transcription of DNA at the nucleus. Cell replication is a tightly controlled process that is also under the influence of tumor suppressor genes. Loss of function of these genes leads to uncontrolled replication e.g. tumors.

References

Cooper, G. (2000). The Cell: A Molecular Approach (2nd ed.). Sinauer Associates Inc.

Molnar, C. (2015). 2.3 Biological Molecules – Concepts of Biology – 1st Canadian Edition. Pressbooks. Web.

Nucleic acids (article). (2014). Khan Academy. Web.

The Biological Building Blocks. (2016). CancerQuest. Web.

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StudyCorgi. (2021, December 30). Molecular Composition and Relationships Between Organisms. Retrieved from https://studycorgi.com/molecular-composition-and-relationships-between-organisms/

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