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Lecture Notes

CHAPTER 1: Introduction: Themes in the study of Life

Evolution is the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today.

Biology is the scientific study of life.

Q. List seven Properties of Life, discuss these properties with examples

Answer:

1. Order. There is highly ordered structure that characterizes life. Example: sunflower2. Evolutionary adaptation. Adaptations evolve over many generations by the

reproductive success of those individuals with heritable traits that are best suited to their environments. Example: The pink appearance of pygmy sea horse camouflages the animal in its environment.

3. Response to the environment. Organisms respond to stimuli from their environment. Example: Venus flytrap closes its trap rapidly in response to the environmental stimulus of a damselfly landing on the open trap.

4. Regulation. Organisms regulate their internal environment to maintain a steady-state, even in the face of a fluctuating external environment. Example: The regulation of blood flow through the blood vessels of jackrabbit’s ears helps maintain a constant body temperature by adjusting heat exchange with the surrounding air.

5. Energy processing. Organisms take in and transform energy to do work, including the maintenance of their ordered state. The hummingbird obtains fuel in the form of nectar from flowers. The hummingbird will use chemical energy stored in its food to power flight and other work.

6. Reproduction. Organisms (living things) reproduce their own kind. Example: a baby giraffe.

7. Growth and development. Inherited information carried by genes controls the pattern of growth and development of organisms. Example: Nile crocodile.

Q. List Seven Themes of Life

Answer:

1. New Properties Emerge at Each Level in the Biological Hierarchy2. Organisms Interact with Other Organisms and the Physical Environment3. Life Requires Energy Transfer and Transformation4. Structure and Function Are Correlated at All Levels of Biological Organization5. The Cell Is an Organism’s Basic Unit of Structure and Function6. The Continuity of Life Is Based on Heritable Information in the Form of DNA7. Feedback Mechanisms Regulate Biological Systems

The core theme of Biology is evolution.

1Lecture Notes prepared by Dr. Syed Abdullah Gilani

Q. Explain Seven Themes of LifeAnswer:

1. New Properties Emerge at Each Level in the Biological Hierarchy

We need to explain the following topics for understanding how the new properties emerge at each level in the biological hierarchy.

a. Biological hierarchy (levels of biological organization)b. Emergent propertiesc. Reductionismd. Systems Biology

a. Biological hierarchy (levels of biological organization)

Biological hierarchy here mentioned is from higher to lower levels of biological organization.

1) The Biosphere

The biosphere consists of all life on Earth and all the places where life exists.

Examples: Earth and its continents and oceans, atmosphere, sediments below the ocean floor and rocks many kilometers below Earth’s surface.

2) 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. All of Earth’s ecosystems combined make up the biosphere.

Examples: Forest, grasslands, deserts, and the ocean’s coral reefs are other types of ecosystems.

3) Communities

The entire array of organisms inhabiting a particular ecosystem is called a biological community.

Examples: The community in forest ecosystem includes many kinds of plants, animals, and microorganisms.

4) Populations

A population consists of all the individuals of a species living within the bounds of a specified area.


Example:A population of sugar maple trees and a population of white-tailed deer in a forest.

5) Organisms

Individual living things are called organisms.

Examples:

Maple trees and other plants in the forest or deer, squirrel, frog, or beetle.

6) Organs and Organ Systems

The structural hierarchy of life continues to unfold as we explore the architecture of the more complex organisms. Organs consist of multiple tissues.

Examples:

Plants: A maple leaf, Stems and roots Animals: human organs are the brain, heart, and kidney, tongue, stomach, and intestines.

7) Tissues

Each tissue is made up of a group of cells that work together, performing a specialized function.

Examples:

The honeycombed tissue in the interior of the leaf is the main location of photosynthesis, the process that converts light energy to the chemical energy of sugar and other food.

8) Cells

The cell is life’s fundamental unit of structure and function.

Some organisms, such as amoebas and most bacteria, are single cells. Other organisms, including plants and animals, are multicellular.

Examples:

Chloroplast cells in plants for photosynthesis, Single-celled bacteria, muscle cells and nerve cells in animals or human

9) Organelles

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


10) Molecules

A molecule is a chemical structure consisting of two or more small chemical units called atoms.

Example:

Chlorophyll molecule.

Chlorophyll is the pigment molecule that makes a maple leaf green. It absorbs sunlight during the first step of photosynthesis. Within each chloroplast, millions of chlorophyll molecules, together with accessory molecules, are organized into the equipment that converts light energy to the chemical energy of food.

b. Emergent properties

Novel properties emerge at each step, properties that are not present at the preceding level. These emergent properties are due to the arrangement and interactions of parts as complexity increases. Examples:

a) Although photosynthesis occurs in an intact chloroplast, it will not take place in a disorganized test-tube mixture of chlorophyll and other chloroplast molecules. Photosynthesis requires a specific organization of these molecules in the chloroplast.

b) If a blow to the head disrupts the intricate architecture of a human brain, the mind may cease to function properly even though all of the brain tissues are still present. Our thoughts and memories are emergent properties of a complex network of nerve cells.

c) At a much higher level of biological organization—at the ecosystem level—the recycling of chemical elements essential to life, such as carbon, depends on a network of diverse organisms interacting

c. Reductionism

Reductionism is an approach of reducing complex systems to simpler components that are more manageable to study. It 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, in 1953, how this molecule could serve as the chemical basis of inheritance. The central role of DNA in cells and organisms became better understood, however, when scientists were able to study the interactions of DNA with other molecules. Biologists must balance the reductionist strategy with the larger-scale, holistic objective of understanding emergent properties—how the parts of cells, organisms, and higher levels of order, such as ecosystems, work together. This is the goal of an approach developed over the last 50 years called systems biology.


d. Systems Biology

Systems biology is an approach that attempts to model the dynamic behavior of whole biological systems based on a study of the interactions among the system’s parts.

Successful models enable biologists to predict how a change in one or more variables will affect other components and the whole system.

Examples:

1) How multiple organs coordinate processes such as the regulation of sugar concentration in the blood?

2) How might a drug that lowers blood pressure affect the functioning of organs throughout the human body?

3) How might increasing a crop’s water supply affect processes in the plants, such as the storage of molecules essential for human nutrition?

4) How might a gradual increase in atmospheric carbon dioxide alter ecosystems and the entire biosphere?

2. Organisms Interact with Other Organisms and the Physical Environment

Interaction of organism and environment is explained in the following figure


Due to the industrial Revolution, enormous amount of CO2 is released by burning fossil fuels (coal, oil, gas). The additional CO2 stays in atmosphere, acts like a glass layer that admits radiation that warms the earth and preventing release of heat to the space. This is causing global warming which is a major aspect of Global Climate Change.

3. Life Requires Energy Transfer and Transformation

In life, organisms transform one form of energy to another. Chlorophyll molecules within the tree’s leaves harness the energy of sunlight and use it to drive photosynthesis, converting carbon dioxide and water to sugar and oxygen. The chemical energy in sugar is then passed along by plants and other photosynthetic organisms (producers) to consumers. Consumers are organisms,such as animals, that feed on producers and other consumers.An animal’s muscle cells use sugar as fuel to power movements, converting chemical energy to kinetic energy, the energy of motion.

4. Structure and Function Are Correlated at All Levels of Biological Organization

The structure and functions are correlated to each other. Example: Strong but lightweight wing bone structure with honeycombed internal structure help the bird to fly.

The thin and flat shape of the leaf maximizes the amount of sunlight that can be captured by its chloroplasts.

5. The Cell is an Organism’s Basic Unit of Structure and Function

The Cell is the basic unit of structure and function of living organisms. It may be divided into two groups, prokaryotic cells and eukaryotics cells.

Q. Compare and Contrast between Prokaryotic and Eukaryotic Cells

Answer:


Similarities between all cells:

All cells have cell membrane and DNA. DNA transfer genetic information from parents to offsprings.

Differences:

Prokaryotic Cells Eukaryotic cellsmaller in size Larger in sizeSimple Complexlack membrane bound organelles Membrane bound orgenelles presentDNA is not separated from the cell DNA is enclosed in nucleus having nuclear

membrane

6. The Continuity of Life Is Based on Heritable Information in the Form of DNA

When the cells divide, the chromosomes also divide. The chromosomes contain all the genetic material known as DNA (Deoxyribonucleic acid). DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring.

Example:

The blood group (A, B, AB, or O), for example, is the result of certain genes that you inherited from your parents.

Q. Write a Note on DNA structure and Function

The chromosomes contain DNA, the DNA consists of hundreds or thousands of genes. The genes encode the information necessary to build other molecules in the cell, most notably proteins. Proteins play structural roles and are also responsible for carrying out cellular work. They thus establish a cell’s identity.

The DNA consists of several nucleotides. Each nucleotide is the combination of dexyribose sugar, phosphate group, and nitrogenous bases (adenine, Guanine, Cytosine, or Thyamine).

Gene Expression

The DNA is double stranded that synthesizes single stranded RNA (Ribonucleic acid) containing genes, which is then translated to protein synthesis, known as gene expression.

Q. Genomics: Large-Scale Analysis of DNA Sequences.

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 DNA totalling


about 3 billion nucleotide pairs. The human genome consists of 26,000 genes that encode 75,000 proteins. Genome sequence can be done by using Whole genome Sequence.

Genomics

Studying whole sets of genes of a species as well as comparing genomes between species—an approach called genomics.

Q. What are the three important research developments in genomics research?

1). high-throughput” technology, tools that can analyze biological materials very rapidlyand produce enormous amounts of data. The automatic DNA-sequencing machines that made the sequencing of the human genome possible are examples of high-throughputdevices. 2) Bioinformatics which is the use of computational tools to store, organize, and analyze the huge volume of data that result from high-throughput methods.

3) Formation of interdisciplinary research teams— that may include computer scientists, mathematicians, engineers, chemists, physicists, and, biologists from a variety of fields.

7. Feedback Mechanisms Regulate Biological Systems

Q. Differentiate between negative and positive feedback mechanisms. Give examples.

Answer:

Negative feedback

Accumulation of an end product of a process slows that process.

Examples

1) The cell’s breakdown of sugar generates chemical energy in the form of a substance called ATP. When a cell makes more ATP than it can use, the excess ATP “feeds back” and inhibits an enzyme near the beginning of the pathway.

2) When the body's blood glucose level rises, the pancreas secretes insulin and, as a result, the blood glucose level declines. When the blood glucose level is low, the pancreas secretes glucagon and, as a result, the blood glucose level rises.

Positive feedback

An end product speeds up its own production.

Examples

1) The clotting of blood in response to injury occurs. 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 the platelets attract more platelets. The platelet pileup then initiates a complex process that seals the wound with a clot.


2) The increasing labor contractions occur before childbirth. Once labor begins in childbirth, contractions increase in intensity and frequency until delivery.

Q. What theme or themes are exemplified by a) sharp spines of a porcupine b) cloning of a plant from a single cell c) hummingbird using sugar to power flight –

Answer:a) function and structure are correlated at all levels of biological organization b) Cells are an organism's basic units and continuity of life is based on the inheritable information in the form of DNA c) organism interacts with its environment exchanging matter and energy

Q. What are the three domains of life

There are four domains, bacteria, archaea, fungi and Eukarya. Bacteria and Archaea are all Prokaryotes.

1) Domain Bacteria are the most diverse and widespread prokaryotes and are now classified into multiple kingdoms.

2) Domain Archaea live in Earth’s extreme environments, such as salty lakes and boiling hot springs (often known as extremophiles, thermophiles etc.)

3) Domain Eukarya includes eukaryotes. It is divided into three kingdoms, Plantae, Animalia, and Protists.

a. Kingdom Plantae consists of plants that produce their own food through photosynthesis.

b. Kingdom Animalia consists of consists of multicellular eukaryotes that ingest other organisms.

c. Kingdom Fungi Fungi absorb dissolved nutrients from their surroundings; many decompose dead organisms and organic wastes (such as leaf litter and animal feces) and absorb nutrients from these sources.


d. Kingdom Protists are mostly unicellular eukaryotes and some relatively simple multicellular relatives.

Q. Explain Unity among living organism by giving examples.Answer:

Similarities (unity) between organisms are present at all levels of the biological hierarchy.

Example:

Cilia (singular, cilium) are extensions of cells that function in locomotion. They occur in eukaryotes as diverse as Paramecium and humans. Even organisms so different share a common architecture for their cilia, which have an elaborate system of tubules.

The cilia of the single-celled Paramecium propel the organism through pond water. The cells that line the human windpipe are equipped with cilia that help keep the lungs clean by sweeping a film of debris-trapping mucus upward.

Unity and diversity in the orchid family.

These three orchids are variations on a common floral theme; Each of these flowers has a liplike petal that helps attract pollinating insects and provides a landing platform for the pollinators.

Q. Explain the Theory of Natural Selection proposed by Charles Darwin

Answer:

The process of evolution illuminates both the similarities and differences among Earth′s life.

Charles Robert Darwin published the book “the Origin of Species by Means of Natural Selection”. Darwin’s book was an immediate bestseller and discussed widely.

Charles Darwin’s book emphasized on two points:

A. Descent with modification mentioning that contemporary species arose from a succession of ancestors.

B. Evolutionary mechanism i.e., natural selection.

He started with the following three observations from nature: i) Individuals in a population vary in their traits, many of which seem to be heritable

(passed on from parents to offspring). ii) A population can produce far more offspring than can survive to produce

offspring of their own. With more individuals than the environment is able to support, competition is inevitable.


iii) Species generally adapt to their environments. For instance, a common adaptation among birds with tough seeds as their major food source is that they have especially strong beaks.

Darwin made INFERENCES from these observations to arrive at his theory of evolution.

i) Unequal reproduction: Individuals with inherited traits that are best suited to the local environment are more likely to survive and reproduce than less suited individuals. Over many generations, a higher and higher proportion of individuals in a population will have the advantageous traits.

ii) Evolutionary adaptation: Evolution occurs as the unequal reproductive success of individuals ultimately leads to adaptation to their environment, as long as the environment remains the same. This mechanism is known as Natural Selection.

Examples:

Beetle population has colonized a locale where the soil has been blackened by a recent brush fire. Initially, the population varies extensively in the inherited coloration of the individuals, from very light gray to charcoal. For hungry birds that prey on the beetles, it is easiest to spot the beetles that are lightest in color.Bat’s forelimbs, though adapted for flight, actually have all the same bones, joints, nerves, and blood vessels found in other limbs as diverse as the human arm, the horse’s foreleg, and the whale’s flipper.

The “family tree” of 14 finches, found in Galapagos Island, illustrates a famous example of adaptive radiation of new species from a common ancestor.

Explain how Biologists use various forms of inquiry to explore life?

Answer:

At the heart of science is INQUIRY, a search for information and explanation, often focusing on specific questions. It is possible to distill certain characteristics that help to distinguish science from other ways of describing and explaining nature.

Biology blends two main processes of scientific inquiry: discovery science and hypothesis–based science. Discovery science is mostly about describing nature.Hypothesis–based science is mostly about explaining nature.

Discovery Science Discovery science describes natural structures and processes as accurately as possible through careful observation and analysis of data.

Types of Data

Induction in Discovery Science


Discovery science can lead to important conclusions based on a type of logic called induction, or inductive reasoning.

Through INDUCTION (INDUCTIVE REASONING), we derive generalizations based on a large number of specific observations (reasoning from a set of specific observations to reach a general conclusion).

• “The sun always rises in the east” is an example.• And so is “All organisms are made of cells.”

Hypothesis–Based Science

Hypothesis based science includes observations, hypotheses, predictions, and experiments. It is related to proposing and testing of hypothetical explanations, or hypotheses.

The observations and inductions of discovery science engage inquisitive minds to seek natural causes and explanations for those observations.

• What caused the diversification of finches on the Galápagos Islands?• What causes the roots of a plant seedling to grow downward and the leaf–bearing

shoot to grow upward?• What explains the generalization that the sun always rises in the east?

The Role of Hypotheses in Inquiry

A HYPOTHESIS is a tentative answer to a well–framed question—an explanation on trial. A scientific hypothesis makes predictions that can be tested by recording additional observations or by designing experiments.

An observation: flashlight fails during a camp–out. • The question: Why doesn′t the flashlight work?• Two reasonable hypotheses (based on past experience):(1) the batteries in the flashlight are dead or (2) the bulb is burnt out.

Each of these alternative hypotheses makes predictions you can test with experiments.

Q. What is deductive reasoning? How it would explain with if-then logic of hypothesis-based science.

Answer

In deductive reasoning, the logic flows from the general to the specific. Deductive reasoning is generally used after the hypothesis has been developed.

From general premises, we conclude to the specific results we should expect if the premises are true.

Example:


IF all organisms are made of cells (premise 1), and humans are organisms (premise 2), THEN humans are composed of cells.

Deduction usually takes the form of predictions about what outcomes of experiments (or observations) we should expect if a particular hypothesis (premise) is correct.

We then test the hypothesis by performing the experiment to see whether or not the results are as predicted.

The flashlight example: If the dead–battery hypothesis is correct, and you replace the batteries with new ones, then the flashlight should work.

Q. Explain scientific inquiry with the help of example of investigating mimicry in honey bee and snake populations.

Example 1:

A stinging honeybee and its nonstinging mimic, a flower fly.

Example 2: Snake population

The king snake mimics the warning coloration of the poisonous eastern coral snake. These two snake species cohabit many regions throughout North and South Carolina, but the geographic range of the king snake extends north and west of the range of the coral snake.

Avoiding snakes with warning coloration is an adaptation present only in predator populations that evolved in areas where the venomous coral snakes are present. Therefore, mimicry helps protecting kingsnakes from predators only in regions where coral snakes also live.


The mimicry hypothesis predicts that predators adapted to the warning coloration of coralsnakes will attack kingsnakes less frequently than will predators in areas where coral snakes are absent.

Q. Explain the mimicry hypothesis “that predators adapted to the warning coloration of coral snakes will attack kingsnakes less frequently than will predators in areas where coral snakes are absent” by explaining field experiments with Artificial Snakes

Answer:

To test the prediction, Harcombe made hundreds of artificial snakes out of wire covered with plasticine. He used two versions of fake snakes: an experimental group with the red, black,and white ring pattern of kingsnakes and a control group of plain brown artificial snakes as a basis of comparison. The researchers placed equal numbers of the two types of artificial snakes in field sites throughout North and South Carolina, including the region where coral snakes are absent.The results showed that compared to the brown artificial snakes, the ringed artificial snakes were attacked by predators less frequently only in field sites within the geographic range of the venomous coral snakes.In field sites where coral snakes are absent, most attacks were on artificial kingsnakes. Where coral snakes were present, most attacks were on brown artificial snakes.

Q. Define Controlled Experiment.

Controlled experiment means that scientists control the experimental environment to keep everything constant except the one variable being tested.

Controlled experiment is designed to compare an experimental group (the artificial kingsnakes) with a control group (the brown artificial snakes).


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