The study of life reveals unifying themes

Properties of Life

1. Order 2. Evolutionary Adaptation 3. Regulation 4. Energy Processing 5. Growth and Development 6. Response to the Environment 7. Reproduction

5 Unifying Themes

1. Organization 2. Information 3. Energy and Matter 4. Interactions 5. Evolution

Eukaryotic Cell

A eukaryotic cell contains membrane-enclosed organelles. Some organelles, such as the DNA-containing nucleus, are found in the cells of all eukaryotes; other organelles are specific to particular cell types. For example, the chloroplast is an organelle found only in eukaryotic cells that carry out photosynthesis.

Living Organisms Use Energy for Activities

A fundamental characteristic of living organisms is their use of energy to carry out life's activities. Moving, growing, reproducing, and the various cellular activities of life are work, and work requires energy. The input of energy, primarily from the sun, and the transformation of energy from one form to another make life possible.

Molecules

A molecule is a chemical structure consisting of two or more units called atoms. --> chlorophyll is the pigment that makes a leaf green, and it absorbs sunlight during photosynthesis. Within each chloroplast, millions of chlorophyll molecules are organized into systems that convert light energy to the chemical energy in food.

Populations

A population consists of all the individuals of a spices living within the bounds of a specified area. A community is therefore the set of populations that inhabit a particular area. --> (meadow) a population of lupine and a population of mule deer.

Cells Share Certain Characteristics

All cells share certain characteristics. For instance, every cell is enclosed by a membrane that regulates the passage of materials between between the cell and its surroundings. Nevertheless, we distinguish two main forms of cells: prokaryotic and eukaryotic. The cells of two groups of single-celled microorganisms--bacteria (singular, bacterium) and archaea (singular, archaean)-- are prokaryotic. All other forms of life, including plants and animals, are composed of eukaryotic cells.

Biology

Although biologists know a great deal about life on Earth, many mysteries remain. Posing questions about the living world and seeking answers through scientific inquiry are the central activities of biology, the scientific study of life.

Example of Emergent Properties

Although photosynthesis occurs in an intact chloroplast, it will not take place in a disorganized test-tube mixture of chlorophyll and other chloroplast molecules. The coordinated processes of photosynthesis require a specific organization of these molecules in the chloroplast. Isolated components of living systems--the objects of study in a reductionist approach--lack a number of significant properties that emerge at higher levels of organization.

Ecosystems

An ecosystem consists of all the living things in a particular area, along with all the nonliving components of the environment with which life interacts, such as soil, water, atmospheric gases, and light. --> mountain meadow, tropical forests, grasslands, deserts, and coral reefs

Evolution

An organism's adaptations to its environment are the result of evolution, the process of change over time that has resulted in the astounding array of organisms found on Earth. Evolution is the fundamental principle of biology.

Extinction

As habitats deteriorate, hundreds of plant and animal species are shifting their ranges to more suitable locations--but for some, there is insufficient suitable habitat, or they may not be able to migrate quickly enough. As a result, the populations of many species are shrinking in size or even disappearing. This trend can result in extinction, the permanent loss of a species. The consequences of these changes for humans and other organisms may be profound.

Example of Feedback Regulation

As seen in the example of insulin signaling, after a meal the level of the sugar glucose in our blood rises, which stimulates cells of the pancreas to secrete insulin. Insulin, in turn, causes body cells to take up glucose and liver cells to store it, thus decreasing blood sugar levels. This eliminates the stimulus for insulin secretion, shutting off the pathway. Thus, the output of the process negatively regulates that process.

Interactions Between System Parts Allow for Whole Functionality

At any level of the biological hierarchy, interactions between the components of the system ensure smooth integration of all the parts, such that they function as a whole. This holds true equally well for molecules in a cell and the components of an ecosystem.

Correlation Between Structure & Function

At each level of the biological hierarchy, we find a correlation of structure and function. Consider a leaf. Its thin, flat shape maximized the capture of sunlight by chloroplasts. Because such correlations of structure and function are common in all forms of life, analyzing biological structure gives us clues about what it does and how it works. Conversely, knowing the function of something provides insight into its structures and organization.

Feedback is Crucial for a Smooth Operation

At lower levels of organization, the interactions between components that make up living organisms--organs, tissues, cells, and molecules--are crucial to their smooth operation. Consider the regulation of blood sugar levels, for instance. Cells in the body must match the supply of fuel (sugar) to demand, regulating the opposing processes of sugar breakdown and storage. The key is the ability of many biological processes to self-regulate by a mechanism called feedback.

Interactions Between Organisms (mutually or singularly beneficial)

At the ecosystem level, every organism interacts with other organisms. For instance, an acacia tree interacts with soil microorganisms associated with its roots, insects that live on it, and animals that eat its leaves and fruit. Interactions between organisms include those that are mutually beneficial (as when "cleaner fish" eat small parasites on a turtle), and those in which one species benefits and the other is harmed (as when a lion kills and eats a zebra).

What is Life?

At the most fundamental level, we may ask: What is life? Yet the phenomenon we call life defies a simple, one-sentence definition. We recognize life by what living things do.

Genes

Before a cell divides, the DNA is first replicated, or copied, and each of the two cellular offspring inherits a complete set of chromosomes, identical to that of the parent cell. Each chromosome contains one very long DNA molecule with hundreds or thousands of genes, each a section of the DNA of the chromosome. Transmitted from parents to offspring, genes are the units of inheritance. They encode the information necessary to build all of the molecules synthesized within a cell, which in turn establish the cell's identity and function.

Emergent Properties

Beginning at the molecular level and then zooming out, this allows us to see novel properties emerge at each level that are absent from the preceding one. These emergent properties are due to the arrangement and interactions of parts as complexity increases.

Biology Forms New Kinds of Questions

By examining and modeling the dynamic behavior of of an integrated network of components, systems biology enables us to pose new kinds of questions. For example, how do networks of molecular interactions in our bodies generate our 24-hour cycle of wakefulness and sleep? At a larger scale, how does a gradual increase in atmospheric carbon dioxide alter ecosystems and the entire biosphere? Systems biology can be used to study life at all levels.

Chemicals are Eventually Returned the Environment

Chemicals that a plant absorbs from the air or soil may be incorporated into the plant's body and then passed to an animal that eats the plant. Eventually, these chemicals will be returned to the environment by decomposers such as bacteria and fungi that break down waste products, leaf litter, and the bodies of dead organisms. The chemicals are then available to be taken up by plants again, thereby completing the cycle.

Organelles

Chloroplasts are examples of organelles, the various functional components present in cells.

Example of Climate Change Affecting Organisms

Climate change has already affected organisms and their habitats all over the planet. For example, polar bears have lost much of the ice platform from which they hunt, leading to food shortages and increased mortality rates.

Organisms and the Environment Affect Each Other

Each organism also interacts continuously with physical factors in its environment. The leaves of a tree, for example, absorb light from the sun, take in carbon dioxide from the air, and release oxygen to the air. The environment is also affected by organisms. For instance, in addition to taking up water and minerals from the soil, the roots of a plant break up the rocks as they grow, contributing to the formation of soil. On a global scale, plants and other photosynthetic organisms have generated all the oxygen in the atmosphere.

Emergent Properties Analogy to BIKES

Emergent properties are not unique to life. A box of bicycle parts won't transport you anywhere, but if they are arranged in a certain way, you can pedal to your chosen destination. Compared with such nonliving examples, however, biological systems are far more complex, making the emergent properties of life especially challenging to study.

The Biosphere

Even from space, we can see signs of Earth's life--in the green mosaic of the forests, for example. We can also see the entire biosphere, which consists of all life on Earth and all the places where life exists: most regions of land, most bodies of water, the atmosphere to an altitude of several kilometers, and even sediments far below the ocean floor.

Genes Provide Blueprints for Making Proteins

For many genes, the sequence provides the blueprint for making a protein. For instance, a given bacterial gene may specify a particular protein (an enzyme) required to break down a certain sugar molecule, while a human gene may denote a different protein (an antibody) that helps fight off infection. Overall, proteins are major players in building and maintaining the cell and carrying out its activities.

All Forms of Life Employ the Same Genetic Code

In carrying out gene expression, all forms of life employ essentially the same genetic code: A particular sequence of nucleotides says the same thing in one organism as it does in another. Differences between organisms reflect differences between their nucleotide sequences rather than between their genetic codes.

Prokaryotic Cell

In contrast to eukaryotic cells, a prokaryotic cell lacks a nucleus or other membrane-enclosed organelles. Furthermore, prokaryotic cells are generally smaller than eukaryotic cells.

Products of Cellular Functions

In fact, the actions of organisms are all based on the functioning of cells. For instance, the movement of your eyes as you read this sentence results from the activities of muscle and nerve cells. Even a process that occurs on a global scale, such as the recycling of carbon atoms, is the product of cellular functions, including the photosynthetic activity of chloroplasts in leaf cells.

Feedback Regulation

In feedback regulation, the output or product of a process regulates that very process. The most common form of regulation in living systems is negative feedback, a loop in which the response reduces the initial stimulus.

Cell Theory

In life's structural hierarchy, the cell is the smallest unit of organization that can perform all activities required for life. The so-called Cell Theory was first developed in the 1800s, based on the observations of many scientists. The theory states that all living organisms are made of cells, which are the basic unit of life.

Interactions Between Organisms (both are harmed)

In some interactions between species, both are harmed--for example, when two plants compete for a soil resource that is in short supply. Interactions among organisms help regulate the functioning of the ecosystem as a whole.

Organisms

Individual living things are called organisms. --> (meadow) each plant is an organism, and so is each animal, fungus, and bacterium.

(2nd Research Development) Bioinformatics

The second major development is bioinformatics, the use of computational tools to store, organize, and analyze the huge volume of data that results from high-throughput methods.

Human's Harmful Interaction with Environment

Like other organisms, we humans interact with our environment. Our interactions sometimes have dire consequences: For example, over the past 150 years, humans have greatly increased the burning of fossil fuels (coal, oil, and gas). This practice releases large amounts of carbon dioxide and other gases into the atmosphere, causing heat to be trapped close to the Earth's surface.

Example of Correlation Between Structure & Function

Many examples from the animal kingdom show a correlation between structure and function. The hummingbird's anatomy allows the wings to rotate at the shoulder, so hummingbirds have the ability, unique among birds, to fly backward or hover in place. While hovering, the birds can extend their long slender beaks into flowers and feed on nectar. The elegant match of form and function in the structures of life is explained by natural selection.

Gene Expression

Protein-encoding genes control protein production indirectly, using a related molecule called RNA as an intermediary. The sequence of nucleotides along a gene is transcribed into mRNA, which is then translated into a linked series of protein building blocks called amino acids. Once completed, the amino acid chain forms a specific protein with a unique shape and function. The entire process by which the information in a gene directs the manufacture of a cellular product is called gene expression.

Genes Specify all of the RNAs

Recently, scientists have discovered whole new classes of RNA that play other roles in the cells, such as regulating the functioning of protein-coding genes. Genes specify all of these RNAs as well, and their production is also referred to as gene expression. By carrying the instructions for making proteins and RNAs and by replicating with each cell division, DNA ensures faithful inheritance of genetic information from generation to generation.

Example of Reductionism

Reductionism is a powerful strategy in biology. For example, by studying the molecular structure of DNA that had been extracted from cells, James Watson and Francis Crick inferred the chemical basis of biological inheritance. Reductionism has propelled many major discoveries, but it provides a necessarily incomplete view of life on Earth.

Scientists Predict a Rise in the Planet Temperature

Scientists calculate that the carbon dioxide that human activities have added to the atmosphere has increased the average temperature of the planet by one degree C since 1900. At the current rates that carbon dioxide and other gases are being added to the atmosphere, global models predict an additional rise of at least 3 degrees C before the end of this century.

The Genome Sequence

Since the early 1900s, the pace at which researchers can determine the sequence of a genome has accelerated at an astounding rate, enabled by a revolution in technology. The genome sequence--the entire sequence of nucleotides for a representative member of a species--is now known for humans and many other animals, as well as numerous plants, fungi, bacteria, and archaea.

Communities

The array of organisms inhabiting a particular ecosystem is called a biological community. Each of these forms of life belongs to a species, a group whose members can only reproduce with other members of the group. --> (meadow ecosystem) includes many kinds of plants, various animals, mushrooms and other fungi, and enormous numbers of diverse microorganisms, such as bacteria that are too small to see without a microscope

Cells

The cell is life's fundamental unit of structure and function. Some organisms consist of a single cell, which performs all the functions of life. Other organisms are multicellular and feature a division of labor among specialized cells. Within these tiny cells are even smaller green structures called chloroplasts, which are responsible for photosynthesis.

Example of Positive Feedback

The clotting of your blood in response to an injury is an example. When a blood vessel is damaged, structures in the blood called platelets begin to aggregate at the site. Positive feedback occurs as chemicals released by platelets attract more platelets. The platelet pileup then initiates a complex process that seals the wound with a clot.

Genome

The entire "library" of genetic instructions that an organism inherits is called its genome. A typical human cell has two similar sets of chromosomes, and each set has approximately 3 billion nucleotide pairs of DNA. If the one-letter abbreviation for the nucleotides of a set were written in letters the size of those you are now reading, the genomic test would fill about 700 biology books.

Proteome

The entire set of proteins expressed by a given cell, tissue, or organism is called a proteome.

The mRNA Molecule

The mRNA molecule is translated into a protein, but other cellular RNAs function differently. For example, we have known for decades that some types of RNA are actually components of the cellular machinery that manufactures proteins.

Molecular Structure of DNA

The molecular structure of DNA accounts for its ability to store information. A DNA molecule is made up of two long chains, called strands, arranged in a double helix. Each chain is made up of four kinds of chemical building blocks called nucleotides, abbreviated A, T, C, and G. Specific sequences of these four nucleotides encode the information in genes.

Organs

The structural hierarchy of life continues to unfold as we explore the architecture of a complex organism. A leaf is an example of an organ, a body part that is made up of multiple tissues and has specific functions in the body. Leaves, stems, and roots are major organs of plants. Within an organ, each tissue has a distinct arrangement and contributes particular properties to organ function.

Biological Hierarchy

The study of life on Earth extends from the microscopic scale of the molecules and cells that make up organisms to the global scale of the entire living planet. As biologists, we can divide this enormous range into different levels of biological organization.

Proteomics

The term proteomics refers to the study of sets of proteins and their properties.

(3rd Research Development) Interdisciplinary Research Teams

The third development is the formation of interdisciplinary research teams--groups of diverse specialists that may include computer scientists, mathematicians, engineers, chemists, physicists, and, of course, biologists from a variety of fields. Researchers in such teams aim to learn how the activities of all the proteins and RNAs encoded by the DNA are coordinated in cells in and in whole organisms.

DNA and Alphabet Analogy

The way DNA encodes information is analogous to how we arrange the letters of the alphabet into words and phrases with specific meanings. The word rat, for example, evokes a rodent; the words tar and art, which contain the same letters, mean very different things. We can think of nucleotides as a four-letter alphabet.

Climate Change

This ongoing global warming is a major aspect of climate change, a directional change to the global climate that lasts for three decades or more (as opposed to short-term changes in the weather). But global warming is not the only way the climate is changing: Wind and precipitation patterns are also shifting, and extreme weather events such as storms and droughts are occurring more often.

All Life is Related

This universality of the genetic code is as strong piece of evidence that all life is related. Comparing the sequences in several species for a gene that codes for a particular protein can provide valuable information both about the protein and about the relationship of the species to each other.

Positive Feedback

Though less common than processes regulated by negative feedback, there are also many biological processes regulated by positive feedback, in which an end product speeds up its own production.

(1st Research Development) High-throughput Technology

Three important research developments have made the genomic and proteomic approaches possible. One is "high-throughput" technology, tools that can analyze many biological samples very rapidly.

Systems Biology

To fully explore emergent properties, biologists today complement reductionism with systems biology, the exploration of a biological system by analyzing the interactions among its parts. In this context, a single leaf cell can be considered a system, as can a frog, an ant colony, or a desert ecosystem.

Genomics

To make sense of the deluge of data from genome-sequencing projects and the growing catalog of known gene functions, scientists are applying a systems biology approach at the cellular and molecular levels. Rather than investigating a single gene at a time, researchers study whole sets of genes (or other DNA) in one or more species--an approach called genomics.

Inherited DNA Directs Development of an Organism

Transmitted from parents to offspring, genes are the units of inheritance. They encode the information necessary to build all of the molecules synthesized within a cell, which in turn establish the cell's identity and function. You began as a single cell stocked with DNA inherited from your parents. The replication of that DNA prior to each cell division transmitted copies of the DNA to what eventually became the trillions of cells of your body. As the cells grew and divided, the genetic information encoded by the DNA directed your development

Tissues

Viewing the tissues of a leaf requires a microscope. Each tissue is a group of cells that work together, performing a specialized function. --> The honeycombed tissue in the interior of the leaf is the main location of photosynthesis. The jigsaw puzzle-like "skin" on the surface of the leaf is a tissue called epidermis. The pores through the epidermis allow entry of the gas.

Photosynthesis

When a plant's leaves absorb sunlight, molecules within the leaves convert the energy of sunlight to the chemical energy of food, such as sugars, in the process of photosynthesis. The chemical energy in the food molecules is then passed along by plants and other photosynthetic organisms (producers) to consumers. Consumers are organisms, such as animals, that feed on other organisms or their remains.

Energy Flows Through and Cycles Within Ecosystems

When an organism uses chemical energy to perform work, such as muscle contraction or cell division, some of that energy is lost to the surroundings as heat. As a result, energy flows through an ecosystem in one direction, usually entering as light and exiting as heat. In contrast, chemicals cycle within an ecosystem, where they are used and then recycled.

Biology is an Ongoing Inquiry

When questions occur to you as you observe the natural world, you are thinking like a biologist. More than anything, biology is a quest, an ongoing inquiry about the nature of life.

DNA (deoxyribonucleic acid)

Within cells, structures called chromosomes contain genetic material in the form of DNA (deoxyribonucleic acid). In cells that are preparing to divide, the chromosomes may be made visible using a dye that appears blue when bound to the DNA.

Reductionism

Zooming in through the levels of the biological hierarchy at ever-finer resolution illustrates an approach called reductionism. This method is so names because it reduces the complex systems into simpler components that are more manageable to study.