Science and Technology and Engineering: Biology (Review)

Subfields of Biology
There are a number of subfields of biology:

Zoology – The study of animals
Botany – The study of plants
Biophysics – The application of the laws of physics to the processes of organisms and the application of the facts about living things to human processes and inventions
Biochemistry – The study of the chemistry of living organisms, including diseases and the pharmaceutical drugs used to cure them
Cytology – The study of cells
Histology – The study of the tissues of plants and animals
Organology – The study of tissues organized into organs
Physiology – The study of the way organisms function, including metabolism, the exchange of matter and energy in nutrition, the senses, reproduction and development, and the work of the nervous system and brain
Genetics – The study of heredity as it relates to the transmission of genes
Ethology – The study of animal behavior
Ecology – The study of the relationship of living organisms to their environments

Classification of Life Forms
All living creatures can be classified into one of three domains and then into one of six kingdoms:

Domain Bacteria
- Kingdom Eubacteria—single celled prokaryotes with little internal complexity, contains peptidoglycan. Members have just one chromosome, reproduce asexually, may have flagella, and are very simple in form.

Domain Archaea
Archaebacteria—single celled prokaryotes with little internal complexity, does not contain peptidoglycan. Members have just one chromosome, reproduce asexually, may have flagella, and are very simple in form.

Domain Eukarya
- Kingdom Protista—single celled eukaryotes with greater internal complexity than Bacteria or Archaea. They have a true nucleus surrounded by a membrane that separates it from the cytoplasm. Most are one-celled and have no complex tissues like plants.
- Kingdom Fungi—single celled or multicellular with considerable variation and complexity. Members have no chlorophyll, so they don't make their own food like plants. They reproduce using spores. Fungi are made up of filaments called hyphae that, in larger fungi, can interlace to form a tissue called mycelium.

- Kingdom Plantae—multicellular with great variation and complexity, rigid cell walls. This group consists of organisms that have chlorophyll and make their own food. Plants have differentiated tissues and reproduce either sexually or asexually.
- Kingdom Animalia—multicellular with much variation and complexity, cell membrane. This group consists of organisms that move around and have to feed on existing organic material.

Characteristics of Invertebrates
Invertebrates are animals with no internal skeletons. They can be divided into three groups:
1. Marine Invertebrates – Members of this group live in oceans and seas. Marine invertebrates include sponges, corals, jellyfish, snails, clams, octopuses, squids, and crustaceans, none of which live on the surface.
2. Freshwater Invertebrates – Members of this group live in lakes and rivers. Freshwater invertebrates include worms on the bottom, microscopic crustaceans, and terrestrial insect larvae that live in the water column, but only where there is no strong current. Some live on the surface of the water.
3.  Terrestrial Invertebrates – Members of this group live on dry ground. Terrestrial invertebrates include insects, mollusks (snails, slugs), arachnids, and myriapods (centipedes and millipedes). Terrestrial invertebrates breathe through a series of tubes that penetrate into the body (trachea) and deliver oxygen into tissues. Underground terrestrial invertebrates are generally light-colored with atrophied eyes and no cuticle to protect them from desiccation. They include worms that live underground and in caves and rock crevices. This group also includes insects such as ants that create colonies underground.

Characteristics of Vertebrate Groups
The vertebrates, animals with an internal skeleton, are divided into four groups:
1. Fish – This group is the most primitive, but is also the group from which all other groups evolved. Fish live in water, breathe with gills, are cold-blooded, have fins and scales, and are typically oviparous, which means they lay eggs. Fish typically have either cartilaginous skeletons (such as rays and sharks) or bony skeletons.
2. Amphibians – The skin of animals in this group is delicate and permeable, so they need water to keep it moist. Amphibians are oviparous. The young start out in water with gills, but the adults use lungs.
3. Reptiles and birds – The skin of animals in this group has very hard, horn-like scales. Birds have exchanged scales for feathers. Reptiles and birds are oviparous, although birds care for their eggs and reptiles do not.
Members have a cloaca, an excretory and reproductive cavity that opens to the outside. Reptiles are cold-blooded, but birds are warm-blooded.
4.  Mammals – These are the most highly evolved vertebrates. Mammals have bodies covered with fur; are warm-blooded; are viviparous, meaning they give birth to live young which are fed with milk from female mammary glands; and are tetrapods
(four-legged). Most live on the ground (except whales and dolphins) and a few fly (bats).

Hunters and Prey Animals
The interaction between predators and their prey is important to controlling the balance of an ecosystem. Hunters are carnivorous animals at the top of the ecological pyramid that eat other animals. Hunters tend to be territorial, leaving signs to warn others to stay out or risk a fight. Hunters are equipped to capture with claws, curved beaks, spurs, fangs, etc. They try to use a minimum amount of energy for each capture, so they prey upon the more vulnerable (the old, ill, or very young) when given a choice.
Predators never kill more than they can eat. Some hunters have great speed, some stalk, and some hunt in groups. Prey animals are those that are captured by predators for food. They are usually herbivores further down the ecological pyramid. Prey animals have special characteristics to help them flee from predators. They may hide in nests or caves, become totally immobile to escape detection, have protective coloration or camouflage, have warning coloration to indicate being poisonous, or have shells or quills for protection.

Life Processes That All Living Things Have in Common
Living things share many processes that are necessary to survival, but the ways these processes and interactions occur are highly diverse. Processes include those related to:
Nutrition – the process of obtaining, ingesting, and digesting foods; excreting unused or excess substances; and extracting energy from the foods to maintain structure.
Transport (circulation) – the process of circulating essential materials such as nutrients, cells, hormones, and gases (oxygen and hydrogen) to the places they are needed by moving them through veins, arteries, and capillaries. Needed materials do not travel alone, but are 'piggybacked' on transporting molecules.
Respiration – the process of breathing, which is exchanging gases between the interior and exterior using gills, trachea
(insects), or lungs.
Regulation – the process of coordinating life activities through the nervous and endocrine systems.
Reproduction and growth – the process of producing more of one's own kind and growing from birth to adulthood. The more highly evolved an animal is, the longer its growth time is.
Locomotion (in animals) – the process of moving from place to place in the environment by using legs, flight, or body motions.

Organisms That Interfere with Cell Activity
Viruses, bacteria, fungi, and other parasites may infect plants and animals and interfere with normal life functions, create imbalances, or disrupt the operations of cells.
Viruses – These enter the body by inhalation (airborne) or through contact with contaminated food, water, or infected tissues. They affect the body by taking over the cell's protein synthesis mechanism to make more viruses. They kill the host cell and impact tissue and organ operations.
Examples of viruses include measles, rabies, pneumonia, and AIDS.
Bacteria – These enter the body through breaks in the skin or contaminated food or water, or by inhalation. They reproduce rapidly and produce toxins that kill healthy host tissues. Examples include diphtheria, bubonic plague, tuberculosis, and syphilis.
Fungi – These feed on healthy tissues of the body by sending rootlike tendrils into the tissues to digest them extracellularly.
Examples include athlete's foot and ringworm.
Parasites – These enter the body through the skin, via insect bites, or through contaminated food or water. Examples include tapeworms, malaria, or typhus.

Hydrocarbons and Carbohydrates
Carbon is an element found in all living things. Two types of carbon molecules that are essential to life are hydrocarbons and carbohydrates. Hydrocarbons, composed only of hydrogen and carbon, are the simplest organic molecules. The simplest of these is methane, which has one carbon atom and four hydrogen atoms. Methane is produced by the decomposition of animal or vegetable matter, and is part of petroleum and natural gas. Carbohydrates are compounds made of hydrogen, carbon, and oxygen. There are three types of these macromolecules (large molecules):
1.  Sugars are soluble in water and, although they have less energy than fats, provide energy more quickly.
2.  Starches, insoluble in water, are long chains of glucose that act as reserve substances.
Potatoes and cereals are valuable foods because they are rich in starch.
Animals retain glucose in their cells as glycogen, a special type of starch.
3.  Cellulose, composed of glucose chains, makes up the cells and tissues of plants. It is one of the most common organic materials.

Lipids, Proteins, and Nucleic Acids
Besides hydrocarbons and carbohydrates, there are three other types of carbon molecules that are essential to life: lipids, proteins, and nucleic acids. Lipids are compounds that are insoluble or only partially soluble in water. There are three main types: fats, which act as an energy reserve for organisms; phospholipids, which are one of the essential components of cell membranes; and steroids such as cholesterol and estrogen, which are very important to metabolism. Proteins are complex substances that make up almost half the dry weight of animal bodies. These molecules contain hydrogen, carbon, oxygen, and other elements, chiefly nitrogen and sulfur. Proteins make up muscle fibers and, as enzymes, act as catalysts. Nucleic acids are large molecules (polymers) composed of a large number of simpler molecules (nucleotides). Each one has a sugar containing five carbons (pentose), a phosphorous compound (phosphate group), and a nitrogen compound (nitrogenated base). Nucleic acids facilitate perpetuation of the species because they carry genetic information as DNA and RNA.

Cell
The cell is the basic organizational unit of all living things. Each piece within a cell has a function that helps organisms grow and survive. There are many different types of cells, but cells are unique to each type of organism. The one thing that all cells have in common is a membrane, which is comparable to a semi-permeable plastic bag. The membrane is composed of phospholipids. There are also some transport holes, which are proteins that help certain molecules and ions move in and out of the cell. The cell is filled with a fluid called cytoplasm or cytosol. Within the cell are a variety of organelles, groups of complex molecules that help a cell survive, each with its own unique membrane that has a different chemical makeup from the cell membrane. The larger the cell, the more organelles it will need to live.

Nucleus and Mitochondria in Eukaryotic Cells
Eukaryotic cells have a nucleus, a big dark spot floating somewhere in the center that acts like the brain of the cell by controlling eating, movement, and reproduction. A nuclear envelope surrounds the nucleus and its contents, but allows RNA and proteins to pass through. Chromatin, made up of DNA, RNA, and nuclear proteins, is present in the nucleus. The nucleus also contains a nucleolus made of RNA and protein. Mitochondria are very small organelles that take in nutrients, break them down, and create energy for the cell through a process called cellular respiration. There might be thousands of mitochondria depending on the cell's purpose. A muscle cell needs more energy for movement than a cell that transmits nerve impulses, for example. Mitochondria have two membranes: a cover and the inner cristae that folds over many times to increase the surface work area. The fluid inside the mitochondria, the matrix, is filled with water and enzymes that take food molecules and combine them with oxygen so they can be digested.

Chloroplasts of Plant Cells
Chloroplasts, which make plants green, are the food producers of a plant cell. They differ from an animal cell's mitochondria, which break down sugars and nutrients. Photosynthesis occurs when the energy from the sun hits a chloroplast and the chlorophyll uses that energy to combine carbon dioxide and water to make sugars and oxygen. The nutrition and oxygen obtained from plants makes them the basis of all life on earth. A chloroplast has two membranes to contain and protect the inner parts. The stroma is an area inside the chloroplast where reactions occur and starches are created. A thylakoid has chlorophyll molecules on its surface, and a stack of thylakoids is called a granum. The stacks of sacs are connected by stromal lamellae, which act like the skeleton of the chloroplast, keeping all the sacs a safe distance from each other and maximizing the efficiency of the organelle.

Passive and Active Transport
Passive transport within a cell does not require energy and work. For example, when there is a large concentration difference between the outside and the inside of a cell, the pressure of the greater concentration, not energy, will move molecules across the lipid bilayer into the cell. Another example of passive transport is osmosis, which is the movement of water across a membrane. Too much water in a cell can cause it to burst, so the cell moves ions in and out to help equalize the amount of water. Active transport is when a cell uses energy to move individual molecules across the cell membrane to maintain a proper balance. Proteins embedded in the lipid bilayer do most of the transport work. There are hundreds of different types of proteins because they are specific. For instance, a protein that moves glucose will not move calcium. The activity of these proteins can be stopped by inhibitors or poisons, which can destroy or plug up a protein.

Mitotic Cell Replication
Mitosis is the duplication of a cell and all its parts, including the DNA, into two identical daughter cells. There are five phases in the life cycle of a cell:

1.  Prophase – This is the process of duplicating everything in preparation for division.
2. Metaphase – The cell's different pieces align themselves for the split. The DNA lines up along a central axis and the centrioles send out specialized tubules that connect to the centromere. The centromere has two strands of a chromosome (condensed DNA) attached to it.
3. Anaphase – Half of the chromosomes go one way and half go another.
4. Telophase – When the chromosomes get to the side of the cell, the cell membrane closes in and splits the cell into two pieces. This results in two separate cells, each with half of the original DNA.
5.  Interphase – This is the normal state of the cell, or the resting stage between divisions.
During this stage, the cell duplicates nucleic acids in preparation for the next division.


Microbes
Microbes are the smallest, simplest, and most abundant organisms on earth. Their numbers are incalculable, and a microscope is required to see them. There is a huge variety of microbes, including bacteria, fungi, some algae, and protozoa. Microbes can be harmful or helpful.
Microbes can be heterotrophic (eat other things) or autotrophic (make food for themselves). They can be solitary or colonial, sexual or asexual. Examples include mold, a multi-cellular type of fungus, and yeasts, which are single-celled (but may live in colonies). A mushroom is a fungus that lives as a group of strands underground called hyphae that decompose leaves or bark on the ground. When it reproduces, it develops a mushroom whose cap contains spores. Mold is a type of zygote fungi that reproduces with a stalk, but releases zygospores. Good bacteria can be those that help plants absorb the nitrogen needed for growth or help grazing animals break down the cellulose in plants. Some bad bacteria are killed by the penicillin developed from a fungus.

Roots, Stems, and Leaves
Roots are structures designed to pull water and minerals from soil or water. In large plants such as trees, the roots usually go deep into the ground to not only reach the water, but also to support and stabilize the tree. There are some plant species that have roots above ground, and there are also plants called epiphytes that live in trees with their roots clinging to the branches. Some roots, like carrots and turnips, serve as food.
Roots are classified as primary and lateral (like a trunk and branches). The apical meristem is the tip of a root or shoot that helps the plant increase in length. Root hairs are fuzzy root extensions that help with the absorption of water and nutrients. The majority of the plant above ground is made up of the stems (trunk and branches) and leaves. Stems transport food and water and act as support structures. Leaves are the site for photosynthesis, and are connected to the rest of the plant by a vascular system.

Gymnosperms, Cycads, and Conifers
Gymnosperms are plants with vascular systems and seeds but no flowers (flowers are an evolutionary advancement). The function of the seed is to ensure offspring can be produced by the plant by providing a protective coating that lets the plant survive for long periods until it germinates. It also stores food for the new plant to use until it can make its own. Seeds can be spread over a wide area. Cycads are sturdy plants with big, waxy fronds that make them look like ferns or palms. They can survive in harsh conditions if there is warm weather. For reproduction, they have big cones located in the center of the plant. The female plant grows a fruit in the middle of the stem. Conifers are trees that thrive in northern latitudes and have cones. Examples of conifers are pine, cedar, redwood, and spruce.
Conifers are evergreens because they have needles that take full advantage of the sun year-round. They are also very tall and strong because of the chemical substance xylem in their systems.

Angiosperms
Angiosperms are plants that have flowers. This is advantageous because the plant's seeds and pollen can be spread not only by gravity and wind, but also by insects and animals. Flowers are able to attract organisms that can help pollinate the plant and distribute seeds. Some flowering plants also produce fruit. When an animal eats the fruit, the plant seeds within will be spread far and wide in the animal's excrement. There are two kinds of angiosperm seeds: monocotyledons (monocots) and dicotyledons (dicots). A cotyledon is the seed leaf or food package for the developing plant. Monocots are simple flowering plants such as grasses, corn, palm trees, and lilies. They always have three petals on their flowers, and their leaves are long strands (like a palm frond). A dicot has seeds with two cotyledons, or two seed leaves of food. Most everyday flowers are dicots with four or five petals and extremely complex leaves with veins.
Examples include roses, sunflowers, cacti, and cherry trees.

Arthropods
Arthropods have a number of unique characteristics:
They have an exoskeleton (outside instead of inside).
They molt. As the arthropod grows, it must shed its old shell and grow a new one.
They have several legs, which are jointed.
Their advanced nervous systems allow for hunting, moving around, finding a mate, and learning new behaviors for adaptation.
They develop through metamorphosis. As arthropods develop, they change body shape. There are two types of metamorphosis:

Complete – The entire body shape changes. An example is butterflies, which change from worm-like larvae to insects with wings.
Gradual – The arthropod starts off small with no wings, and then molts and grows wings. Example: Grasshoppers.
Arthropods include spiders, crustaceans, and the enormous insect species (26 orders) called uniramians.
Ranging from fleas to mosquitoes, beetles, dragonflies, aphids, bees, flies, and many more, uniramians have exoskeletons made of chitin, compound eyes, complex digestive systems, and usually six legs. This group is extremely diverse. Some can fly, some have toxins or antennae, and some can make wax, silk, or honey.

Reptiles
One group of vertebrates is the reptile. This group includes:
Crocodilia – This is a group of reptiles that can grow quite large, and includes alligators and crocodiles. Normally found near the water in warmer climates, Crocodilia might be more closely related to birds than other reptiles.
Squamata – This is the order of reptiles that includes snakes and lizards. Snakes are special because they have no legs and no ears.
They feel vibrations, smell with their tongues, have specialized scales, and can unhinge their jaws to swallow prey that is larger than they are. Like snakes, lizards have scales, but they differ in that they have legs, can dig, can climb trees, and can grab things.
Chelonia – This is the order of reptiles that includes turtles and tortoises. It is a special group because its members have shells.
Different varieties live in forests, water, and deserts, or anywhere the climate is warm enough. They also live a long time, up to hundreds of years.
Turtles are typically found near water and tortoises on land, even dry areas.

Reproduction in Mammals
When classified according to how they reproduce, there are three types of mammals:
1. Monotremes are rare mammals that lay eggs. These were the first mammals, and are more closely related to reptiles than other mammals. Examples include the duck-billed platypus and the spiny anteater.
2. Marsupials are special mammals. They give birth to live young, but the babies mature in pouches, where they are carried and can feed on milk.
Many are found in Australia. The isolation of this island continent prevented placental mammals from taking hold. Examples of marsupials include kangaroos, possums, and koalas.

3.  Placental mammals give birth from the females' placenta to live young. The young may be able to walk immediately, or they may need to be carried. They are still dependent on parental care for at least a short time. Placental mammals are the dominant form of mammals. Members of this group include cetaceans such as whales and dolphins, which are mammals that evolved but returned to the ocean.

Respiratory System
The respiratory system exchanges gases with the environment. Amphibians exchange gases through their moist skin, and fish use gills, but mammals, birds, and reptiles have lungs.
The human respiratory system is made up of the nose, mouth, pharynx, trachea, and two lungs. The purpose of the respiratory system is to bring oxygen into the body and expel carbon dioxide. The respiratory system can inhale viruses, bacteria, and dangerous chemicals, so it is vulnerable to toxins and diseases such as pneumonia, which causes the lungs to fill with fluid until they cannot take in enough oxygen to support the body. Emphysema, often caused by smoking tobacco, destroys the tissues in the lungs, which cannot be regenerated. The respiratory system interacts with the digestive system in that the mouth and pharynx are used to swallow food and drink, as well as to breathe. It interacts with the circulatory system in that it provides fresh oxygen through blood vessels that pass through the lungs. This oxygen is then carried by the circulatory system throughout the body.

Skeletal System
The human body has an endoskeleton, meaning it is inside the body. It is made up of bones instead of the hard plate of exoskeletons or fluids in tubes, which comprise the hydrostatic system of the starfish. The purpose of the skeleton is to support the body, provide a framework to which the muscles and organs can connect, and protect the inner organs. The skull protects the all-important brain and the ribs protect the internal organs from impact. The skeletal system interacts with the muscular system to help the body move, and softer cartilage works with the calcified bone to allow smooth movement of the body. The skeletal system also interacts with the circulatory system in that the marrow inside the bones helps produce both white and red blood cells.

Nervous System
The nervous system is divided into two parts: the central nervous system (brain and spinal cord) and the peripheral nervous system (a network of billions of neurons of different types throughout the entire body). The neurons are connected end to end, and transmit electrical impulses to each other. Efferent neurons send impulses from the central system to the limbs and organs. Afferent neurons receive sensory information and transmit it back to the central system. The nervous system is concerned with senses and action. In other words, it senses something and then acts upon it. An example is a predator sensing prey and attacking it. The nervous system also automatically senses activity inside the body and reacts to stimuli. For example, the first bite of a meal sets the whole digestive system into motion. The nervous system interacts with every other system in the body because all the tissues and organs need instruction, even when individuals are not aware of any activity occurring. For instance, the endocrine system is constantly working to produce hormones or adrenaline as needed.

Genetics, Genes, and Chromosomes
Genetics is the science devoted to the study of how characteristics are transmitted from one generation to another. In the 1800s, Gregor Mendel discovered the three laws of heredity that explain how genetics works. Genes are the hereditary units of material that are transmitted from one generation to the next. They are capable of undergoing mutations, can be recombined with other genes, and can determine the nature of an organism, including its color, shape, and size. Genotype is the genetic makeup of an individual based on one or more characteristics, while phenotype is the external manifestation of the genotype. For example, genotype determines hair color genes, whereas phenotype is the actual color of the hair observed. Chromosomes are the structures inside the nucleus of a cell made up primarily of deoxyribonucleic acid (DNA) and proteins. The chromosomes carry the genes. The numbers vary according to the species, but they are always the same for each species. For example, the human has 46 chromosomes, and the water lily has 112.

Mendel's Contributions to Genetics
Johann Gregor Mendel is known as the father of genetics.
Mendel was an Austrian monk who performed thousands of experiments involving the breeding of the common pea plant in the garden of his monastery. Mendel kept detailed records including seed color, pod color, seed type, flower color, and plant height for eight years and published his work in 1865. Unfortunately, his work was largely ignored until the early 1900s. Mendel's work showed that genes come in pairs and that dominant and recessive traits are inherited independently of each other. His work established the law of segregation, the law of independent assortment, and the law of dominance.

Darwin's Contributions to the Theory of Evolution
Charles Darwin's theory of evolution is the unifying concept in biology today. From 1831 to 1836, Darwin traveled as a naturalist on a five-year voyage on the H.M.S. Beagle around the tip of South America and to the Galápagos Islands. He studied finches, took copious amounts of meticulous notes, and collected thousands of plant and animal specimens. He collected 13 species of finches each with a unique bill for a distinct food source, which led him to believe, due to similarities between the finches, that the finches shared a common ancestor.
The similarities and differences of fossils of extinct rodents and modern mammal fossils led him to believe that the mammals had changed over time.
Darwin believed that these changes were the result of random genetic changes called mutations. He believed that mutations could be beneficial and eventually result in a different organism over time. In 1859, in his first book, On the Origin of Species, Darwin proposed that natural selection was the means by which adaptations would arise over time. He coined the term 'natural selection' and said that it is the mechanism of evolution. Because variety exists among individuals of a species, he stated that those individuals must compete for the same limited resources. Some would die, and others would survive. According to Darwin, evolution is a slow, gradual process. In 1871, Darwin published his second book, Descent of Man, and Selection in Relation to Sex, in which he discussed the evolution of man.

Contribution to Genetics Made by Alfred Hershey and Martha Chase
Alfred Hershey and Martha Chase did a series of experiments in 1952 known as the Hershey-Chase experiments. These experiments showed that deoxyribonucleic acid (DNA), not protein, is the genetic material that transfers information for inheritance. The Hershey-Chase experiments used a bacteriophage, a virus that infects bacteria, to infect the bacteria Escherichia coli. The bacteriophage T2 is basically a small piece of DNA enclosed in a protein coating. The DNA contains phosphorus, and the protein coating contains sulfur. In the first set of experiments, the T2 was marked with radioactive phosphorus-32. In the second set of experiments, the T2 was marked with radioactive sulfur-35. For both sets of experiments, after the E. coli was infected by the T2, the E. coli was isolated using a centrifuge. In the first set of experiments, the radioactive isotope (P-32) was found in the E. coli, showing that the genetic information was transferred by the DNA. In the second set of experiments, the radioactive isotope (S-35) was not found in the E. coli, showing that the genetic information was not transferred by the protein as was previously thought. Hershey and Chase conducted further experiments allowing the bacteria from the first set of experiments to reproduce, and the offspring was also found to contain the radioactive isotope (P-32) further confirming that the DNA transferred the genetic material.