Principles of Life A Chapter 1

Chapter 1 Principles of Life Key Concepts 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow 1.2 Life Depends on Organization and Energy 1.3 Genetic Systems Control the Flow, Exchange, Storage, and Use of Information

Chapter 1 Principles of Life 1.4 Evolution Explains the Diversity as Well as the Unity of Life 1.5 Science Is Based on Quantitative Observations, Experiments, and Reasoning

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Biology: the scientific study of living things or organisms. Living things are all descended from a single-celled ancestor (a single common ancestor). The characteristics shared by all organisms logically lead to the conclusion that all life has a common ancestry.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Characteristics shared by all living organisms: Composed of a common set of chemical components and similar structures (e.g., cells) Depend on interactions among structurally complex parts to maintain the living state Contain genetic information that uses a nearly universal code Convert molecules obtained from their environment into new biological molecules

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Extract energy from the environment and use it for life functions Replicate their genetic information in the same manner when reproducing Share structural similarities among a fundamental set of genes Evolve through gradual changes in genetic information

Earth formed between 4.6 and 4.5 billion years ago. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Earth formed between 4.6 and 4.5 billion years ago. The earliest life evolved about 600 million years later.

Figure 1.1 Life’s Calendar Figure 1.1 Life’s Calendar Depicting Earth’s history on the scale of a 30-day month provides a sense of the immensity of evolutionary time.

Critical step for evolution of life: Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Complex biological molecules possibly arose from random associations of chemicals in the early environment. Experiments that simulate conditions on early Earth show that this was possible. Critical step for evolution of life: Formation of nucleic acids that could reproduce themselves and contain the information to produce proteins.

Biological molecules were enclosed in a membranes, to form a cell. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow The next step: Biological molecules were enclosed in a membranes, to form a cell. Fatty acids, which form membrane-like films in water, were important in forming membranes. Membranes separate the cell from the surrounding environment.

For 2 billion years, organisms were unicellular prokaryotes. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow For 2 billion years, organisms were unicellular prokaryotes. Early prokaryotes were confined to oceans, where they were protected from UV light. There was little or no O2 in the atmosphere, and hence no protective ozone (O3) layer.

Figure 1.2 The Basic Unit of Life Is the Cell Figure 1.2 The Basic Unit of Life Is the Cell The concentration of reactions within the enclosing membrane of a cell allowed the evolution of integrated organisms. Today all organisms, even the largest and most complex, are made up of cells. Single-celled organisms such as this one, however, remain the most abundant living organisms (in absolute numbers) on Earth.

Photosynthesis evolved about 2.7 billion years ago. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Photosynthesis evolved about 2.7 billion years ago. The energy of sunlight is transformed into the chemical-bond energy of biological molecules. Earliest photosynthetic cells were probably similar to cyanobacteria. O2 was a by-product of photosynthesis, and it began to accumulate in the atmosphere.

Figure 1.3 Photosynthetic Organisms Changed Earth’s Atmosphere Figure 1.3 Photosynthetic Organisms Changed Earth’s Atmosphere Cyanobacteria were the first photosynthetic organisms on Earth. (A) Colonies of cyanobacteria called stromatolites are known from the ancient fossil record. (B) Living stromatolites are still found in suitable environments on Earth today. Stromalites

O2 was poisonous to many early prokaryotes. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow O2 was poisonous to many early prokaryotes. Organisms that could tolerate O2 evolved aerobic metabolism (energy production using O2), which is more efficient than anaerobic metabolism. Organisms were able to grow larger. Aerobic metabolism is used by most living organisms today.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow O2 also produced a layer of ozone (O3) in the upper atmosphere. This layer absorbs UV light, and its formation allowed organisms to move from the ocean to land.

The nucleus contains the genetic information. Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Some cells evolved membrane-enclosed compartments called organelles, where specialized functions can be performed. The nucleus contains the genetic information. These cells are called eukaryotes. Prokaryotes lack nuclei and other internal compartments.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Some organelles may have originated by endosymbiosis, when larger cells engulfed smaller ones. Mitochondria (sites of energy generation) probably evolved from engulfed prokaryotic organisms. Chloroplasts (sites of photosynthesis) probably evolved from engulfed photosynthetic prokaryotes.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Multicellular organisms arose about 1 billion years ago. Groups of eukaryote cells probably failed to separate after division. Cellular specialization—cells became specialized to perform certain functions. This allowed multicellular eukaryotes to become larger and adapt to specific environments.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Evolution of species: Mutations (changes) are introduced when a genome is replicated. Some mutations give rise to structural and functional changes in organisms, and new species arise.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Each species has a distinct scientific name, a binomial: • Genus name • Species name Example: Homo sapiens

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Evolutionary relationships of species can be determined by comparing genomes. Genome sequencing and other molecular techniques have added molecular evidence to knowledge from the fossil record. Phylogenetic trees document and diagram evolutionary relationships.

Figure 1.4 The Tree of Life Figure 1.4 The Tree of Life The classification system used in this book divides Earth’s organisms into three primary domains: Bacteria, Archaea, and Eukarya. The dark blue branches within Eukarya represent various groups of microbial protists (mostly unicellular eukaryotes). Animals, plants, and fungi (green and turquoise branches) are the most familiar groups of multicellular eukaryotes. In this book we adopt the convention that time flows from left to right, so this tree (and other trees in this book) lies on its side, with its root—the common ancestor—at the left.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Relationships in the tree of life are based on fossil evidence, structures, metabolic processes, behavior, and molecular analyses. Three domains of life: • Bacteria (prokaryotes) • Archaea (prokaryotes) • Eukarya (eukaryotes)

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow All organisms that are alive today descended from common ancestors in the past. Living species did not evolve from other species living today.

Concept 1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow Because all life is related, discoveries made using one type of organism can be extended to other types. Biologists use model organisms for research, such as the green alga Chlorella to study photosynthesis.

Concept 1.2 Life Depends on Organization and Energy The second law of thermodynamics states that, left to themselves, organized entities tend to become more random. Energy is required for cells to combat the tendency for their molecules, structures, and systems to lose organization. Energy is required by cells throughout their lives.

Concept 1.2 Life Depends on Organization and Energy Organization is apparent in a hierarchy of levels from molecules to ecosystems. Cells use energy to synthesize complex molecules by assembling atoms into new, highly organized configurations. Organization is essential for cells to function in a multicellular organism, which has many levels of organization.

Figure 1.5 Life Consists of Organized Systems at a Hierarchy of Scales (1) Figure 1.5 Life Consists of Organized Systems at a Hierarchy of Scales (A) The hierarchy of systems within a multicellular organism. DNA—a molecule—encodes the information for cells—a higher level of organization. Cells, in turn, are the components of still higher levels of organization: tissues, organs, and the organism itself. (B) Organisms interacting with their external environment form ecological systems on a hierarchy of scales. Individual organisms form the smallest ecological system. Individuals of a species form populations, which interact with other populations to form communities. Multiple communities in turn interact within landscapes at progressively larger scales until they include all the landscapes and organisms of Earth: the entire biosphere.

Concept 1.2 Life Depends on Organization and Energy Organisms also interact with their physical environment and with each other, resulting in hierarchy in the larger biological world.

Figure 1.5 Life Consists of Organized Systems at a Hierarchy of Scales (2) ECOSYSTEM Figure 1.5 Life Consists of Organized Systems at a Hierarchy of Scales (A) The hierarchy of systems within a multicellular organism. DNA—a molecule—encodes the information for cells—a higher level of organization. Cells, in turn, are the components of still higher levels of organization: tissues, organs, and the organism itself. (B) Organisms interacting with their external environment form ecological systems on a hierarchy of scales. Individual organisms form the smallest ecological system. Individuals of a species form populations, which interact with other populations to form communities. Multiple communities in turn interact within landscapes at progressively larger scales until they include all the landscapes and organisms of Earth: the entire biosphere.

Concept 1.2 Life Depends on Organization and Energy A system is a set of interacting parts (components) in which neither the parts nor the whole can be understood without taking into account the interactions (processes). Systems are found at every level of biological organization.

Figure 1.6 A Generalized System Figure 1.6 A Generalized System Systems in cells, whole organisms, and ecosystems can be represented with boxes and arrows.

Figure 1.7 Organized Systems Exist at Many Levels Figure 1.7 Organized Systems Exist at Many Levels (A) This cellular-level system synthesizes and breaks down a cell protein called Protein T. (B) This organismal-level system determines the amount (and thus the concentration) of sodium (Na+) in the blood plasma and other extracellular body fluids of a human. (C) This community-level system helps determine the number of meadow voles (Microtus pennsylvanicus) in a field in the spring.

Concept 1.2 Life Depends on Organization and Energy Biological systems are dynamic: Characterized by rapid flows of matter and energy. They constantly exchange energy and matter with their surroundings. But even though there is constant turnover of atoms, molecules, etc., the organization of the systems persist.

Concept 1.2 Life Depends on Organization and Energy Feedback: the amount of one component in a system affects the rate of an earlier process in the system. Positive feedback occurs when a product of the system speeds up an earlier process. Negative feedback occurs when a product of the system slows down an earlier process.

Figure 1.8 Feedback Can Be Positive or Negative Figure 1.8 Feedback Can Be Positive or Negative Positive feedback tends to destabilize a system, whereas negative feedback typically stabilizes a system.

Concept 1.2 Life Depends on Organization and Energy Positive feedback tends to destabilize a system (sometimes advantageous, provided it is ultimately brought under control). Negative feedback tends to stabilize systems and is very common in regulatory systems.

Concept 1.2 Life Depends on Organization and Energy Systems analysis is used to understand how biological systems function. The system components are identified, and processes by which the components interact are determined. Rates of interactions can be affected by feedback. Then we can analyze how the system will change through time.

Concept 1.2 Life Depends on Organization and Energy Mathematical equations express amounts of the different components and include processes and their rates, resulting in a computational model.

Concept 1.2 Life Depends on Organization and Energy If a computational model is well grounded in factual knowledge of the biological system, it will mimic the biological system. Computational models can be used for prediction, for instance, the future behavior of a system in a warming world. Parameters of the model are adjusted to take into account the expected increases in temperature.

DNA consists of repeating subunits called nucleotides. Concept 1.3 Genetic Systems Control the Flow, Exchange, Storage, and Use of Information The genome is the sum total of all the information encoded by an organism’s genes. DNA consists of repeating subunits called nucleotides. A gene is a specific segment of DNA that contains information for making one or more proteins. Proteins govern chemical reactions in cells and form much of an organism’s structure.

Figure 1.9 DNA Is Life’s Blueprint Figure 1.9 DNA Is Life’s Blueprint The instructions for life are contained in the sequences of nucleotides in DNA molecules. Specific DNA nucleotide sequences comprise genes. The average length of a single human gene is 27,000 nucleotides. The information in each gene provides the cell with the information it needs to manufacture molecules of a specific protein.

Concept 1.3 Genetic Systems Control the Flow, Exchange, Storage, and Use of Information All cells in a multicellular organism contain the same genome, but different cells have different functions. The different types of cells must express different parts of the genome. How cells control genome expression is a major focus of biological research.

Concept 1.3 Genetic Systems Control the Flow, Exchange, Storage, and Use of Information Mutations alter nucleotide sequences of a gene, and the protein is often altered as well. Mutations may occur during replication or be caused by chemicals and radiation. Most are harmful or have no effect, but some may improve the functioning of the organism. Mutations are the raw material of evolution.

Complete genome sequences have been determined for many organisms. Concept 1.3 Genetic Systems Control the Flow, Exchange, Storage, and Use of Information Complete genome sequences have been determined for many organisms. They are used to study the genetic basis of everything from physical structure to inherited diseases and evolutionary relationships. Bioinformatics is the field of study that developed to organize and process the immense amount of data resulting from genome sequencing.

A common set of evolutionary mechanisms applies to all organisms. Concept 1.4 Evolution Explains the Diversity as Well as the Unity of Life Evolution is a change in genetic makeup of biological populations through time—a major unifying principle of biology. A common set of evolutionary mechanisms applies to all organisms. The constant change that occurs among populations gives rise to all the diversity of life.

Concept 1.4 Evolution Explains the Diversity as Well as the Unity of Life Charles Darwin proposed that all living organisms are descended from a common ancestor by the mechanism of natural selection. Natural selection leads to adaptations—structural, physiological, or behavioral traits that enhance an organism’s chances of survival and reproduction.

Figure 1.10 Adaptations to the Environment Figure 1.10 Adaptations to the Environment The limbs of frogs show adaptations to the different environments of each species.

Concept 1.4 Evolution Explains the Diversity as Well as the Unity of Life Two kinds of explanations for adaptations: Proximate explanations—immediate genetic, physiological, neurological, and developmental processes that explain how an adaption works. Ultimate explanations—what processes led to the evolution of an adaptation.

Concept 1.4 Evolution Explains the Diversity as Well as the Unity of Life In science, a theory is a body of scientific work in which rigorously tested and well-established facts and principles are used to make predictions about the natural world. Evolutionary theory is: 1. A body of knowledge supported by facts 2. The resulting understanding of processes by which populations have changed and diversified over time, and continue to evolve

Concept 1.4 Evolution Explains the Diversity as Well as the Unity of Life Evolution can be observed and measured by: Changes in genetic composition of populations over short time frames The fossil record—population changes over very long time frames

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Scientific investigations are based on observation, experimentation, and reasoning. Understanding the natural history of organisms—how they get food, reproduce, behave, regulate functions, and interact with other organisms—facilitates observation and leads to questions.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Observation is enhanced by technology—microscopes, imaging, genome sequencing, satellites. Observations must be quantified by measurement and mathematical and statistical calculations.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments The scientific method (hypothesis–prediction method): Observations Questions Hypotheses Predictions Testing

Figure 1.11 Scientific Methodology Figure 1.11 Scientific Methodology The process of observation, speculation and questioning, hypothesis formation, prediction, and experimentation is a cornerstone of modern science, although scientists may initiate their research at any of several different points.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments To answer questions, biologists look at what is already known to form possible answers, or hypotheses. Predictions are made based on observations, and experiments are designed to test these predictions.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Controlled experiments manipulate the factor, or variable, that is predicted to be causing the phenomenon being investigated. A method is devised to manipulate only that variable in an “experimental” group, which is compared with an unmanipulated “control” group.

Figure 1.12 Controlled Experiments Manipulate a Variable (Part 1) Figure 1.12 Controlled Experiments Manipulate a Variable The Hayes laboratory created controlled environments that differed only in the concentrations of atrazine in the water. Eggs from leopard frogs (Rana pipiens) raised specifically for laboratory use were allowed to hatch and the tadpoles were separated into experimental tanks containing water with different concentrations of atrazine.a [a T. Hayes et al. 2003. Environmental Health Perspectives III: 568–575.]

Figure 1.12 Controlled Experiments Manipulate a Variable (Part 2) Figure 1.12 Controlled Experiments Manipulate a Variable The Hayes laboratory created controlled environments that differed only in the concentrations of atrazine in the water. Eggs from leopard frogs (Rana pipiens) raised specifically for laboratory use were allowed to hatch and the tadpoles were separated into experimental tanks containing water with different concentrations of atrazine.a [a T. Hayes et al. 2003. Environmental Health Perspectives III: 568–575.]

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Independent variable—the variable being manipulated Dependent variable—the response that is measured

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Comparative experiments look for differences between samples or groups. The variables cannot be controlled; data are gathered from different sample groups and compared.

Figure 1.13 Comparative Experiments Look for Differences among Groups (Part 1) Figure 1.13 Comparative Experiments Look for Differences among Groups To see whether the presence of atrazine correlates with testicular abnormalities in male frogs, the Hayes lab collected frogs and water samples from different locations around the U.S. The analysis that followed was “blind,” meaning that the frogs and water samples were coded so that experimenters working with each specimen did not know which site the specimen came from.a [a T. Hayes et al. 2002. Nature 419: 895–896.]

Figure 1.13 Comparative Experiments Look for Differences among Groups (Part 2) Figure 1.13 Comparative Experiments Look for Differences among Groups To see whether the presence of atrazine correlates with testicular abnormalities in male frogs, the Hayes lab collected frogs and water samples from different locations around the U.S. The analysis that followed was “blind,” meaning that the frogs and water samples were coded so that experimenters working with each specimen did not know which site the specimen came from.a [a T. Hayes et al. 2002. Nature 419: 895–896.]

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Statistical methods help scientists determine if differences between groups are significant. Statistical tests start with a null hypothesis—that no differences exists. Statistical methods eliminate the possibility that results are due to random variation.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Not all forms of inquiry into nature are scientific. Scientific hypotheses must be testable and have the potential of being rejected. Science depends on evidence that comes from reproducible and quantifiable observations.

Concept 1.5 Science Is Based on Quantifiable Observations and Experiments Religious or spiritual explanations of natural phenomena are not testable and therefore are not science. Science does not say that untestable religious beliefs are necessarily wrong, just that they cannot be addressed using scientific methods. Many advances in science raise ethical concerns. Science can not tell us how we should address these concerns.