General Science Review: Biology

Cells
The main difference between eukaryotic and prokaryotic cells is that eukaryotic cells have a nucleus and prokaryotic cells do not.

Eukaryotic cells are considered more complex, while prokaryotic cells are smaller and simpler. Eukaryotic cells have membrane-bound organelles that perform various functions and contribute to the complexity of these types of cells. Prokaryotic cells do not contain membrane-bound organelles.

In prokaryotic cells, the genetic material (DNA) is not contained within a membrane-bound nucleus.

Instead, it aggregates in the cytoplasm in a nucleoid. In eukaryotic cells, DNA is mostly contained in chromosomes in the nucleus, although there is some DNA in mitochondria and chloroplasts. Prokaryotic cells usually divide by binary fission and are haploid. Eukaryotic cells divide by mitosis and are diploid.

Prokaryotic structures include plasmids, ribosomes, cytoplasm, a cytoskeleton, granules of nutritional substances, a plasma membrane, flagella, and a few others. They are single-celled organisms. Bacteria are prokaryotic cells.



The functions of plant and animal cells vary greatly, and the functions of different cells within a single organism can also be vastly different. Animal and plant cells are similar in structure in that they are eukaryotic, which means they contain a nucleus. The nucleus is a round structure that controls the activities of the cell and contains chromosomes.

Both types of cells have cell membranes, cytoplasm, vacuoles, and other structures.

The main difference between the two is that plant cells have a cell wall made of cellulose that can handle high levels of pressure within the cell, which can occur when liquid enters a plant cell. Plant cells have chloroplasts that are used during the process of photosynthesis, which is the conversion of sunlight into food. Plant cells usually have one large vacuole, whereas animal cells can have many smaller ones. Plant cells have a regular shape, while the shapes of animal cell can vary.

Plant cells can be much larger than animal cells, ranging from 10 to 100 micrometers. Animal cells are 10 to 30 micrometers in size.

Plant cells can have much larger vacuoles that occupy a large portion of the cell. They also have cell walls, which are thick barriers consisting of protein and sugars. Animal cells lack cell walls.  Chloroplasts in plants that perform photosynthesis absorb sunlight and convert it into energy. Mitochondria produce energy from food in animal cells. Plant and animal cells are both eukaryotic, meaning they contain a nucleus. Both plant and animal cells duplicate genetic material, separate it, and then divide in half to reproduce. Plant cells build a cell plate between the two new cells, while animal cells make a cleavage furrow and pinch in half. Microtubules are components of the cytoskeleton in both plant and animal cells. Microtubule organizing centers (MTOCs) make microtubules in plant cells, while centrioles make microtubules in animal cells.

Photosynthesis is the conversion of sunlight into energy in plant cells, and also occurs in some types of bacteria and protists. Carbon dioxide and water are converted into glucose during photosynthesis, and light is required during this process. Cyanobacteria are thought to be the descendants of the first organisms to use photosynthesis about 3.5 billion years ago. Photosynthesis is a form of cellular respiration. It occurs in chloroplasts that use thylakoids, which are structures in the membrane that contain light reaction chemicals. Chlorophyll is a pigment that absorbs light.

During the process, water is used and oxygen is released. The equation for the chemical reaction that occurs during photosynthesis is 6H2O + 6CO2→ C6H12O6 + 6O2. During photosynthesis, six molecules of water and six molecules of carbon dioxide react to form one molecule of sugar and six molecules of oxygen.

The term cell cycle refers to the process by which a cell reproduces, which involves cell growth, the duplication of genetic material, and cell division. Complex organisms with many cells use the cell cycle to replace cells as they lose their functionality and wear out. The entire cell cycle in animal cells can take 24 hours. The time required varies among different cell types. Human skin cells, for example, are constantly reproducing. Some other cells only divide infrequently. Once neurons are mature, they do not grow or divide. The two ways that cells can reproduce are through meiosis and mitosis. When cells replicate through mitosis, the 'daughter cell' is an exact replica of the parent cell. When cells divide through meiosis, the daughter cells have different genetic coding than the parent cell. Meiosis only happens in specialized reproductive cells called gametes.

Mitosis is the process of cell reproduction in which a eukaryotic cell splits into two separate, but completely identical, cells.  This process is divided into a number of different phases.

Interphase: The cell prepares for division by replicating its genetic and cytoplasmic material. Interphase can be further divided into G1, S, and G2.

Prophase: The chromatin thickens into chromosomes and the nuclear membrane begins to disintegrate. Pairs of centrioles move to opposite sides of the cell and spindle fibers begin to form. The mitotic spindle, formed from cytoskeleton parts, moves chromosomes around within the cell.

Metaphase: The spindle moves to the center of the cell and chromosome pairs align along the center of the spindle structure.

Anaphase: The pairs of chromosomes, called sisters, begin to pull apart, and may bend. When they are separated, they are called daughter chromosomes. Grooves appear in the cell membrane.

Telophase: The spindle disintegrates, the nuclear membranes reform, and the chromosomes revert to chromatin. In animal cells, the membrane is pinched. In plant cells, a new cell wall begins to form.

Cytokinesis: This is the physical splitting of the cell (including the cytoplasm) into two cells. Some believe this occurs following telophase. Others say it occurs from anaphase, as the cell begins to furrow, through telophase, when the cell actually splits into two.

Meiosis is another process by which eukaryotic cells reproduce.  However, meiosis is used by more complex life forms such as plants and animals and results in four unique cells rather than two identical cells as in mitosis.  Meiosis has the same phases as mitosis, but they happen twice. In addition, different events occur during some phases of meiosis than mitosis.

The events that occur during the first phase of meiosis are interphase (I), prophase (I), metaphase (I), anaphase (I), telophase (I), and cytokinesis (I).

During this first phase of meiosis, chromosomes cross over, genetic material is exchanged, and tetrads of four chromatids are formed. The nuclear membrane dissolves. Homologous pairs of chromatids are separated and travel to different poles. At this point, there has been one cell division resulting in two cells.

Each cell goes through a second cell division, which consists of prophase (II), metaphase (II), anaphase (II), telophase (II), and cytokinesis (II). The result is four daughter cells with different sets of chromosomes. The daughter cells are haploid, which means they contain half the genetic material of the parent cell. The second phase of meiosis is similar to the process of mitosis. Meiosis encourages genetic diversity.



Genetics

Chromosomes consist of genes, which are single units of genetic information. Genes are made up of deoxyribonucleic acid (DNA). DNA is a nucleic acid located in the cell nucleus. There is also DNA in the mitochondria. DNA replicates to pass on genetic information. The DNA in almost all cells is the same. It is also involved in the biosynthesis of proteins. The model or structure of DNA is described as a double helix. A helix is a curve, and a double helix is two congruent curves connected by horizontal members. The model can be likened to a spiral staircase. It is right-handed. The British scientist Rosalind Elsie Franklin is credited with taking the x-ray diffraction image in 1952 that was used by Francis Crick and James Watson to formulate the double-helix model of DNA and speculate about its important role in carrying and transferring genetic information.

DNA has a double helix shape, resembles a twisted ladder, and is compact. It consists of nucleotides.

Nucleotides consist of a five-carbon sugar (pentose), a phosphate group, and a nitrogenous base. Two bases pair up to form the rungs of the ladder. The 'side rails' or backbone consists of the covalently bonded sugar and phosphate. The bases are attached to each other with hydrogen bonds, which are easily dismantled so replication can occur. Each base is attached to a phosphate and to a sugar. There are four types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). There are about 3 billion bases in human DNA. The bases are mostly the same in everybody, but their order is different.

It is the order of these bases that creates diversity in people. Adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).



A gene is a portion of DNA that identifies how traits are expressed and passed on in an organism. A gene is part of the genetic code.

Collectively, all genes form the genotype of an individual. The genotype includes genes that may not be expressed, such as recessive genes. The phenotype is the physical, visual manifestation of genes. It is determined by the basic genetic information and how genes have been affected by their environment. An allele is a variation of a gene. Also known as a trait, it determines the manifestation of a gene. This manifestation results in a specific physical appearance of some facet of an organism, such as eye color or height. For example, the genetic information for eye color is a gene. The gene variations responsible for blue, green, brown, or black eyes are called alleles. Locus (pl. loci) refers to the location of a gene or alleles.

Mendel's laws are the law of segregation (the first law) and the law of independent assortment (the second law). The law of segregation states that there are two alleles and that half of the total number of alleles are contributed by each parent organism. The law of independent assortment states that traits are passed on randomly and are not influenced by other traits. The exception to this is linked traits. A Punnett square can illustrate how alleles combine from the contributing genes to form various phenotypes. One set of a parent's genes are put in columns, while the genes from the other parent are placed in rows. The allele combinations are shown in each cell. When two different alleles are present in a pair, the dominant one is expressed. A Punnett square can be used to predict the outcome of crosses.



Gene traits are represented in pairs with an upper-case letter for the dominant trait (A) and a lower-case letter for the recessive trait (a). Genes occur in pairs (AA, Aa, or aa). There is one gene on each chromosome half supplied by each parent organism. Since half the genetic material is from each parent, the offspring's traits are represented as a combination of these. A dominant trait only requires one gene of a gene pair for it to be expressed in a phenotype, whereas a recessive requires both genes in order to be manifested. For example, if the mother's genotype is Dd and the father's is dd, the possible combinations are Dd and dd. The dominant trait will be manifested if the genotype is DD or Dd. The recessive trait will be manifested if the genotype is dd. Both DD and dd are homozygous pairs. Dd is heterozygous.



Evolution

Scientific evidence supporting the theory of evolution can be found in biogeography, comparative anatomy and embryology, the fossil record, and molecular evidence. Biogeography studies the geographical distribution of animals and plants. Evidence of evolution related to the area of biogeography includes species that are well suited for extreme environments.

The fossil record shows that species lived only for a short time period before becoming extinct. The fossil record can also show the succession of plants and animals. Living fossils are existing species that have not changed much morphologically and are very similar to ancient examples in the fossil record. Examples include the horseshoe crab and ginkgo. Comparative embryology studies how species are similar in the embryonic stage, but become increasingly specialized and diverse as they age. Vestigial organs are those that still exist, but become nonfunctional. Examples include the hind limbs of whales and the wings of birds that can no longer fly, such as ostriches.

The rate of evolution is affected by the variability of a population. Variability increases the likelihood of evolution. Variability in a population can be increased by mutations, immigration, sexual reproduction (as opposed to asexual reproduction), and size. Natural selection, emigration, and smaller populations can lead to decreased variability. Sexual selection affects evolution. If fewer genes are available, it will limit the number of genes passed on to subsequent generations. Some animal mating behaviors are not as successful as others. A male that does not attract a female because of a weak mating call or dull feathers, for example, will not pass on its genes. Mechanical isolation, which refers to sex organs that do not fit together very well, can also decrease successful mating.

Natural selection: This theory developed by Darwin states that traits that help give a species a survival advantage are passed on to subsequent generations. Members of a species that do not have the advantageous trait die before they reproduce. Darwin's four principles are: from generation to generation, there are various individuals within a species; genes determine variations; more individuals are born than survive to maturation; and specific genes enable an organism to better survive.

Gradualism: This can be contrasted with punctuationism. It is an idea that evolution proceeds at a steady pace and does not include sudden developments of new species or features from one generation to the next.

Punctuated Equilibrium: This can be contrasted with gradualism. It is the idea in evolutionary biology that states that evolution involves long time periods of no change (stasis) accompanied by relatively brief periods (hundreds of thousands of years) of rapid change.

Three types of evolution are divergent, convergent, and parallel. Divergent evolution refers to two species that become different over time. This can be caused by one of the species adapting to a different environment. Convergent evolution refers to two species that start out fairly different, but evolve to share many similar traits. Parallel evolution refers to species that are not similar and do not become more or less similar over time. Mechanisms of evolution include descent (the passing on of genetic information), mutation, migration, natural selection, and genetic variation and drift. The biological definition of species refers to a group of individuals that can mate and reproduce. Speciation refers to the evolution of a new biological species. The biological species concept (BSC) basically states that a species is a community of individuals that can reproduce and have a niche in nature.

One theory of how life originated on Earth is that life developed from nonliving materials. The first stage of this transformation happened when abiotic (nonliving) synthesis took place, which is the formation of monomers like amino acids and nucleotides. Next, monomers joined together to create polymers such as proteins and nucleic acids. These polymers are then believed to have formed into protobionts. The last stage was the development of the process of heredity. Supporters of this theory believe that RNA was the first genetic material. Another theory postulates that hereditary systems came about before the origination of nucleic acids. Another theory is that life, or the precursors for it, were transported to Earth from a meteorite or other object from space. There is no real evidence to support this theory.

A number of scientists have made significant contributions to the theory of evolution:

Cuvier (1744-1829): Cuvier was a French naturalist who used the fossil record (paleontology) to compare the anatomies of extinct species and existing species to make conclusions about extinction. He believed in the catastrophism theory more strongly than the theory of evolution.

Lamarck (1769-1832): Lamarck was a French naturalist who believed in the idea of evolution and thought it was a natural occurrence influenced by the environment. He studied medicine and botany. Lamarck put forth a theory of evolution by inheritance of acquired characteristics. He theorized that organisms became more complex by moving up a ladder of progress.

Lyell (1797-1875): Lyell was a British geologist who believed in geographical uniformitarianism, which can be contrasted with catastrophism.

Charles Robert Darwin (1809-1882): Darwin was an English naturalist known for his belief that evolution occurred by natural selection. He believed that species descend from common ancestors.

Alfred Russell Wallace (1823-1913): He was a British naturalist who independently developed a theory of evolution by natural selection. He believed in the transmutation of species (that one species develops into another).



Organism Classification

The most widely accepted system for taxonomy is the three-domain classification system; sometimes called the six-kingdom classification system. The three domains are Archaea, Bacteria, and Eukarya.

Both Archaea and Bacteria are made of prokaryotic cells, while Eukarya are made of eukaryotic cells. The domains of Bacteria and Archaea each have a single kingdom Eubacteria and Archaebacteria, respectively. The domain Eukarya has four kingdoms: Protista, Fungi, Plantae, and Animalia. Kingdom Protista includes about 250,000 species of unicellular protozoans and unicellular and multicellular algae. Kingdom Fungi includes about 100,000 species. Kingdom Plantae includes about 320,000 species. Kingdom Animalia is estimated to include more than 1,500,000 species. The groupings in this system, in descending order from broadest to most specific, are: domain, kingdom, phylum/division, class, order, family, genus, and species. A memory aid for this is: Dear King Philip Came Over For Good Soup. According to the three-domain classification system, humans are: domain Eukarya, kingdom Animalia, phylum Chordata, subphylum Vertebrata, class Mammalia, order Primate, family Hominidae, genus Homo, and species Sapiens. An organism is a living thing. A unicellular organism is an organism that has only one cell. Examples of unicellular organisms are bacteria and paramecium. A multicellular organism is one that consists of many cells.

Humans are a good example. By some estimates, the human body is made up of billions of cells. Others think the human body has more than 75 trillion cells.

The term microbe refers to small organisms that are only visible through a microscope. Examples include viruses, bacteria, fungi, and protozoa. Microbes are also referred to as microorganisms, and it is these that are studied by microbiologists. Bacteria can be rod shaped, round (cocci), or spiral (spirilla). These shapes are used to differentiate among types of bacteria.

Bacteria can be identified by staining them. This particular type of stain is called a gram stain. If bacteria are gram-positive, they absorb the stain and become purple. If bacteria are gram-negative, they do not absorb the stain and become a pinkish color.

Organisms in the Protista kingdom are classified according to their methods of locomotion, their methods of reproduction, and how they get their nutrients. Protists can move by the use of a flagellum, cilia, or pseudopod. Flagellates have flagellum, which are long tails or whip-like structures that are rotated to help the protist move. Ciliates use cilia, which are smaller hair-like structures on the exterior of a cell that wiggle to help move the surrounding matter. Amoeboids use pseudopodia to move. Bacteria reproduce either sexually or asexually. Binary fission is a form of asexual reproduction whereby bacteria divide in half to produce two new organisms that are clones of the parent. In sexual reproduction, genetic material is exchanged. When kingdom members are categorized according to how they obtain nutrients, the three types of protists are photosynthetic, consumers, and saprophytes. Photosynthetic protists convert sunlight into energy. Organisms that use photosynthesis are considered producers. Consumers, also known as heterotrophs, eat or consume other organisms. Saprophytes consume dead or decaying substances.

Mycology is the study of fungi. The Fungi kingdom includes about 100,000 species. They are further delineated as mushrooms, yeasts, molds, rusts, mildews, stinkhorns, puffballs, and truffles. Fungi are characterized by cell walls that have chitin, a long chain polymer carbohydrate. Fungi are different from species in the Plant kingdom, which have cell walls consisting of cellulose. Fungi are thought to have evolved from a single ancestor.

Although they are often thought of as a type of plant, they are more similar to animals than plants. Fungi are typically small and numerous, and have a diverse morphology among species. They can have bright red cups and be orange jellylike masses, and their shapes can resemble golf balls, bird nests with eggs, starfish, parasols, and male genitalia. Some members of the stinkhorn family emit odors similar to dog scat to attract flies that help transport spores that are involved in reproduction. Fungi of this family are also consumed by humans.

Chlorophyta are green algae. Bryophyta are nonvascular mosses and liverworts. They have root-like parts called rhizoids. Since they do not have the vascular structures to transport water, they live in moist environments. Lycophyta are club mosses. They are vascular plants. They use spores and need water to reproduce. Equisetopsida (sphenophyta) are horsetails.

Like lycophyta, they need water to reproduce with spores. They have rhizoids and needle-like leaves. The pteridophytes (filicopsida) are ferns. They have stems (rhizomes). Spermatopsida are the seed plants. Gymnosperms are a conifer, which means they have cones with seeds that are used in reproduction. Plants with seeds require less water. Cycadophyta are cone-bearing and look like palms. Gnetophyta are plants that live in the desert. Coniferophyta are pine trees, and have both cones and needles. Ginkgophyta are gingkos. Anthophyta is the division with the largest number of plant species, and includes flowering plants with true seeds.

Only plants in the division bryophyta (mosses and liverworts) are nonvascular, which means they do not have xylem to transport water. All of the plants in the remaining divisions are vascular, meaning they have true roots, stems, leaves, and xylem. Pteridophytes are plants that use spores and not seeds to reproduce. They include the following divisions:

Psilophyta (whisk fern), Lycophyta (club mosses), Sphenophyta (horsetails), and Pterophyta (ferns). Spermatophytes are plants that use seeds to reproduce.

Included in this category are gymnosperms, which are flowerless plants that use naked seeds, and angiosperms, which are flowering plants that contain seeds in or on a fruit. Gymnosperms include the following divisions: cycadophyta (cycads), ginkgophyta (maidenhair tree), gnetophyta (ephedra and welwitschia), and coniferophyta (which includes pinophyta conifers). Angiosperms comprise the division anthophyta (flowering plants).

Plants are autotrophs, which mean they make their own food.

In a sense, they are self-sufficient. Three major processes used by plants are photosynthesis, transpiration, and respiration. Photosynthesis involves using sunlight to make food for plants. Transpiration evaporates water out of plants.

Respiration is the utilization of food that was produced during photosynthesis.

Two major systems in plants are the shoot and the root system. The shoot system includes leaves, buds, and stems. It also includes the flowers and fruits in flowering plants. The shoot system is located above the ground. The root system is the component of the plant that is underground, and includes roots, tubers, and rhizomes. Meristems form plant cells by mitosis.

Cells then differentiate into cell types to form the three types of plant tissues, which are dermal, ground, and vascular. Dermal refers to tissues that form the covering or outer layer of a plant. Ground tissues consist of parenchyma, collenchyma, and/or sclerenchyma cells.

There are at least 230,000 species of flowering plants. They represent about 90 percent of all plants. Angiosperms have a sexual reproduction phase that includes flowering. When growing plants, one may think they develop in the following order: seeds, growth, flowers, and fruit. The reproductive cycle has the following order: flowers, fruit, and seeds. In other words, seeds are the products of successful reproduction. The colors and scents of flowers serve to attract pollinators. Flowers and other plants can also be pollinated by wind. When a pollen grain meets the ovule and is successfully fertilized, the ovule develops into a seed. A seed consists of three parts: the embryo, the endosperm, and a seed coat. The embryo is a small plant that has started to develop, but this development is paused. Germination is when the embryo starts to grow again. The endosperm consists of proteins, carbohydrates, or fats. It typically serves as a food source for the embryo. The seed coat provides protection from disease, insects, and water.

The animal kingdom is comprised of more than one million species in about 30 phyla (the plant kingdom sometimes uses the term division).

There about 800,000 species of insects alone, representing half of all animal species. The characteristics that distinguish members of the animal kingdom from members of other kingdoms are that they are multicellular, are heterotrophic, reproduce sexually (there are some exceptions), have cells that do not contain cell walls or photosynthetic pigments, can move at some stage of life, and can rapidly respond to the environment as a result of specialized tissues like nerve and muscle. Heterotrophic refers to the method of getting energy by eating food that has energy releasing substances. Plants, on the other hand, are autotrophs, which mean they make their own energy. During reproduction, animals have a diploid embryo in the blastula stage. This structure is unique to animals. The blastula resembles a fluid-filled ball.

The animal kingdom includes about one million species.

Metazoans are multicellular animals. Food is ingested and enters a mesoderm-lined coelom (body cavity). Phylum porifera and coelenterate are exceptions. The taxonomy of animals involves grouping them into phyla according to body symmetry and plan, as well as the presence of or lack of segmentation.

The more complex phyla that have a coelom and a digestive system are further classified as protostomes or deuterostomes according to blastula development.

In protostomes, the blastula's blastopore (opening) forms a mouth. In deuterostomes, the blastopore forms an anus. Taxonomy schemes vary, but there are about 36 phyla of animals. The corresponding term for plants at this level is division. The most notable phyla include chordata, mollusca, porifera, cnidaria, platyhelminthes, nematoda, annelida, arthropoda, and echinodermata, which account for about 96 percent of all animal species.

These four animal phyla lack a coelom or have a pseudocoelom.

Porifera: These are sponges. They lack a coelom and get food as water flows through them. They are usually found in marine and sometimes in freshwater environments. They are perforated and diploblastic, meaning there are two layers of cells.

Cnidaria: Members of this phylum are hydrozoa, jellyfish, and obelia. They have radial symmetry, sac-like bodies, and a polyp or medusa (jellyfish) body plan. They are diploblastic, possessing both an ectoderm and an endoderm. Food can get in through a cavity, but members of this phylum do not have an anus.

Platyhelminthes: These are also known as flatworms. 
Classes include turbellaria (planarian) and trematoda (which include lung, liver, and blood fluke parasites). They have organs and bilateral symmetry.

They have three layers of tissue: an ectoderm, a mesoderm, and an endoderm.

Nematoda: These are roundworms. Hookworms and many other parasites are members of this phylum. They have a pseudocoelom, which means the coelom is not completely enclosed within the mesoderm. They also have a digestive tract that runs directly from the mouth to the anus. They are nonsegmented.

Members of the protostomic phyla have mouths that are formed from blastopores.

Mollusca: Classes include bivalvia (organisms with two shells, such as clams, mussels, and oysters), gastropoda (snails and slugs), cephalopoda (octopus, squid, and chambered nautilus), scaphopoda, amphineura (chitons), and monoplacophora.

Annelida: This phylum includes the classes oligochaeta (earthworms), polychaeta (clam worms), and hirudinea (leeches).

They have true coeloms enclosed within the mesoderm. They are segmented, have repeating units, and have a nerve trunk.

Arthropoda: The phylum is diverse and populous.

Members can be found in all types of environments. They have external skeletons, jointed appendages, bilateral symmetry, and nerve cords. They also have open circulatory systems and sense organs. Subphyla include crustacea (lobster, barnacles, pill bugs, and daphnia), hexapoda (all insects, which have three body segments, six legs, and usual wings), myriapoda (centipedes and millipedes), and chelicerata (the horseshoe crab and arachnids). Pill bugs have gills. Bees, ants, and wasps belong to the order hymenoptera. Like several other insect orders, they undergo complete metamorphosis.

Members of the deuterostomic phyla have anuses that are formed from blastopores.

Echinodermata: Members of this phylum have radial symmetry, are marine organisms, and have a water vascular system. Classes include echinoidea (sea urchins and sand dollars), crinoidea (sea lilies), asteroidea

(starfish), ophiuroidea (brittle stars), and holothuroidea (sea cucumbers).

Chordata: This phylum includes humans and all other vertebrates, as well as a few invertebrates (urochordata and cephalochordata).

Members of this phylum include agnatha (lampreys and hagfish), gnathostomata, chondrichthyes (cartilaginous fish-like sharks, skates, and rays), osteichthyes (bony fishes, including ray-finned fish that humans eat), amphibians (frogs, salamander, and newts), reptiles (lizards, snakes, crocodiles, and dinosaurs), birds, and mammals.



Anatomy

Extrinsic refers to homeostatic systems that are controlled from outside the body. In higher animals, the nervous system and endocrine system help regulate body functions by responding to stimuli. Hormones in animals regulate many processes, including growth, metabolism, reproduction, and fluid balance. The names of hormones tend to end in "-one."

Endocrine hormones are proteins or steroids. Steroid hormones (anabolic steroids) help control the manufacture of protein in muscles and bones.

Invertebrates do not have a backbone, whereas vertebrates do. The great majority of animal species (an estimated 98 percent) are invertebrates, including worms, jellyfish, mollusks, slugs, insects, and spiders. They comprise 30 phyla in all. Vertebrates belong to the phylum chordata. The vertebrate body has two cavities. The thoracic cavity holds the heart and lungs and the abdominal cavity holds the digestive organs. Animals with exoskeletons have skeletons on the outside. Examples are crabs and turtles. Animals with endoskeletons have skeletons on the inside. Examples are humans, tigers, birds, and reptiles.

The 11 major organ systems are: skeletal, muscular, nervous, digestive, respiratory, circulatory, skin, excretory, immune, endocrine, and reproductive.

Skeletal: This consists of the bones and joints. The skeletal system provides support for the body through its rigid structure, provides protection for internal organs, and works to make organisms motile.

Growth hormone affects the rate of reproduction and the size of body cells, and also helps amino acids move through membranes.

Muscular: This includes the muscles. The muscular system allows the body to move and respond to its environment.

Nervous: This includes the brain, spinal cord, and nerves. The nervous system is a signaling system for intrabody communications among systems, responses to stimuli, and interaction within an environment. Signals are electrochemical. Conscious thoughts and memories and sense interpretation occur in the nervous system. It also controls involuntary muscles and functions, such as breathing and the beating of the heart.

Digestive: This includes the mouth, pharynx, esophagus, stomach, intestines, rectum, anal canal, teeth, salivary glands, tongue, liver, gallbladder, pancreas, and appendix. The system helps change food into a form that the body can process and use for energy and nutrients.

Food is eventually eliminated as solid waste. Digestive processes can be mechanical, such as chewing food and churning it in the stomach, and chemical, such as secreting hydrochloric acid to kill bacteria and converting protein to amino acids. The overall system converts large food particles into molecules so the body can use them. The small intestine transports the molecules to the circulatory system. The large intestine absorbs nutrients and prepares the unused portions of food for elimination.

Carbohydrates are the primary source of energy as they can be easily converted to glucose. Fats (oils or lipids) are usually not very water soluble, and vitamins A, D, E, and K are fat soluble. Fats are needed to help process these vitamins and can also store energy. Fats have the highest calorie value per gram (9,000 calories). Dietary fiber, or roughage, helps the excretory system. In humans, fiber can help regulate blood sugar levels, reduce heart disease, help food pass through the digestive system, and add bulk.

Dietary minerals are chemical elements that are involved with biochemical functions in the body. Proteins consist of amino acids. Proteins are broken down in the body into amino acids that are used for protein biosynthesis or fuel. Vitamins are compounds that are not made by the body, but obtained through the diet. Water is necessary to prevent dehydration since water is lost through the excretory system and perspiration.

Respiratory: This includes the nose, pharynx, larynx, trachea, bronchi, and lungs. It is involved in gas exchange, which occurs in the alveoli. Fish have gills instead of lungs.

Circulatory: This includes the heart, blood, and blood vessels, such as veins, arteries, and capillaries. Blood transports oxygen and nutrients to cells and carbon dioxide to the lungs.

Skin (integumentary): This includes skin, hair, nails, sense receptors, sweat glands, and oil glands. The skin is a sense organ, provides an exterior barrier against disease, regulates body temperature through perspiration, manufactures chemicals and hormones, and provides a place for nerves from the nervous system and parts of the circulation system to travel through. Skin has three layers: epidermis, dermis, and subcutaneous. The epidermis is the thin, outermost, waterproof layer. Basal cells are located in the epidermis. The dermis contains the sweat glands, oil glands, and hair follicles. The subcutaneous layer has connective tissue, and also contains adipose (fat) tissue, nerves, arteries, and veins.

Excretory: This includes the kidneys, ureters, bladder, and urethra. The excretory system helps maintain the amount of fluids in the body. Wastes from the blood system and excess water are removed in urine. The system also helps remove solid waste.

Immune: This includes the lymphatic system, lymph nodes, lymph vessels, thymus, and spleen. Lymph fluid is moved throughout the body by lymph vessels that provide protection against disease. This system protects the body from external intrusions, such as microscopic organisms and foreign substances. It can also protect against some cancerous cells.

Endocrine: This includes the pituitary gland, pineal gland, hypothalamus, thyroid gland, parathyroids, thymus, adrenals, pancreas, ovaries, and testes. It controls systems and processes by secreting hormones into the blood system. Exocrine glands are those that secrete fluid into ducts.

Endocrine glands secrete hormones directly into the blood stream without the use of ducts. Prostaglandin (tissue hormones) diffuses only a short distance from the tissue that created it, and influences nearby cells only. Adrenal glands are located above each kidney. The cortex secretes some sex hormones, as well as mineralocorticoids and glucocorticoids involved in immune suppression and stress response. The medulla secretes epinephrine and norepinephrine. Both elevate blood sugar, increase blood pressure, and accelerate heart rate.

Epinephrine also stimulates heart muscle. The islets of Langerhans are clumped within the pancreas and secrete glucagon and insulin, thereby regulating blood sugar levels. The four parathyroid glands at the rear of the thyroid secrete parathyroid hormone.

Reproductive: In the male, this system includes the testes, vas deferens, urethra, prostate, penis, and scrotum. In the female, this system includes the ovaries, fallopian tubes (oviduct and uterine tubes), cervix, uterus, vagina, vulva, and mammary glands. Sexual reproduction helps provide genetic diversity as gametes from each parent contribute half the DNA to the zygote offspring. The system provides a method of transporting the male gametes to the female. It also allows for the growth and development of the embryo. Hormones involved are testosterone, interstitial cell stimulating hormone (ICSH), luteinizing hormone (LH), follicle stimulating hormone (FSH), and estrogen. Estrogens secreted from the ovaries include estradiol, estrone, and estriol. They encourage growth, among other things. Progesterone helps prepare the endometrium for pregnancy.

Based on whether or not and when an organism uses meiosis or mitosis, the three possible cycles of reproduction are haplontic, diplontic, and haplodiplontic. Fungi, green algae, and protozoa are haplontic. Animals and some brown algae and fungi are diplontic. Plants and some fungi are haplodiplontic. Diplontic organisms, like multicelled animals, have a dominant diploid life cycle. The haploid generation is simply the egg and sperm.

Monoecious species are bisexual (hermaphroditic). In this case, the individual has both male and female organs: sperm-bearing testicles and egg-bearing ovaries. Hermaphroditic species can self-fertilize. Some worms are hermaphroditic. Cross fertilization is when individuals exchange genetic information. Most animal species are dioecious, meaning individuals are distinctly male or female.



Biological Relationships: As heterotrophs, animals can be further classified as carnivores, herbivores, omnivores, and parasites. Predation refers to a predator that feeds on another organism, which results in its death.

Detritivory refers to heterotrophs that consume organic dead matter. Carnivores are animals that are meat eaters. Herbivores are plant eaters, and omnivores eat both meat and plants. A parasite's food source is its host. A parasite lives off of a host, which does not benefit from the interaction. Nutrients can be classified as carbohydrates, fats, fiber, minerals, proteins, vitamins, and water. Each supply a specific substance required for various species to survive, grow, and reproduce. A calorie is a measurement of heat energy. It can be used to represent both how much energy a food can provide and how much energy an organism needs to live.

Biochemical cycles are how chemical elements, required by living organisms, cycle between living and nonliving organisms. Elements that are frequently required are phosphorus, sulfur, oxygen, carbon, gaseous nitrogen, and water. Elements can go through gas cycles, sedimentary cycles, or both. Elements circulate through the air in a gas cycle and from land to water in a sedimentary one.

A food chain is a linking of organisms in a community that is based on how they use each other as food sources. Each link in the chain consumes the link above it and is consumed by the link below it. The exceptions are the organism at the top of the food chain and the organism at the bottom.

Biomagnification

(bioamplification): This refers to an increase in concentration of a substance within a food chain. Examples are pesticides or mercury. Mercury is emitted from coal-fired power plants and gets into the water supply, where it is eaten by a fish. A larger fish eats smaller fish, and humans eat fish. The concentration of mercury in humans has now risen. Biomagnification is affected by the persistence of a chemical, whether it can be broken down and negated, food chain energetics, and whether organisms can reduce or negate the substance.



A food web consists of interconnected food chains in a community. The organisms can be linked to show the direction of energy flow. Energy flow in this sense is used to refer to the actual caloric flow through a system from trophic level to trophic level.

Trophic level refers to a link in a food chain or a level of nutrition. The 10% rule is that from trophic level to level, about 90% of the energy is lost (in the form of heat, for example). The lowest trophic level consists of primary producers (usually plants), then primary consumers, then secondary consumers, and finally tertiary consumers (large carnivores). The final link is decomposers, which break down the consumers at the top. Food chains usually do not contain more than six links. These links may also be referred to as ecological pyramids.



Ecosystem stability is a concept that states that a stable ecosystem is perfectly efficient. Seasonal changes or expected climate fluctuations are balanced by homeostasis. It also states that interspecies interactions are part of the balance of the system.

Four principles of ecosystem stability are that waste disposal and nutrient replenishment by recycling is complete, the system uses sunlight as an energy source, biodiversity remains, and populations are stable in that they do not over consume resources.  Ecologic succession is the concept that states that there is an orderly progression of change within a community. An example of primary succession is that over hundreds of years bare rock decomposes to sand, which eventually leads to soil formation, which eventually leads to the growth of grasses and trees. Secondary succession occurs after a disturbance or major event that greatly affects a community, such as a wild fire or construction of a dam.



Population is a measure of how many individuals exist in a specific area. It can be used to measure the size of human, plant, or animal groups. Population growth depends on many factors. Factors that can limit the number of individuals in a population include lack of resources such as food and water, space, habitat destruction, competition, disease, and predators.

Exponential growth refers to an unlimited rising growth rate. This kind of growth can be plotted on a chart in the shape of a J. Carrying capacity is the population size that can be sustained. The world's population is about 6.8 billion and growing. The human population has not yet reached its carrying capacity. Population dynamics refers to how a population changes over time and the factors that cause changes. An S-shaped curve shows that population growth has leveled off. Biotic potential refers to the maximum reproductive capacity of a population given ideal environmental conditions.


Biological concepts

Territoriality: This refers to members of a species protecting areas from other members of their species and from other species. Species members claim specific areas as their own.

Dominance: This refers to the species in a community that is the most populous.

Altruism: This is when a species or individual in a community exhibits behavior that benefit another individual at a cost to itself. In biology, altruism does not have to be a conscious sacrifice.

Threat display: This refers to behavior by an organism that is intended to intimidate or frighten away members of its own or another species.

The principle of competitive exclusion (Gause's Law) states that if there are limited or insufficient resources and species are competing for them, these species will not be able to co-exist. The result is that one of the species will become extinct or be forced to undergo a behavioral or evolutionary change. Another way to say this is that "complete competitors cannot coexist."

A community is any number of species interacting within a given area. A niche is the role of a species within a community. Species diversity refers to the number of species within a community and their populations.  A biome refers to an area in which species are associated because of climate. The six major biomes in North America are desert, tropical rain forest, grassland, coniferous forest, deciduous forest, and tundra.

Biotic: Biotic factors are the living factors, such as other organisms, that affect a community or population. Abiotic factors are nonliving factors that affect a community or population, such as facets of the environment.

Ecology: Ecology is the study of plants, animals, their environments, and how they interact.

Ecosystem: An ecosystem is a community of species and all of the environment factors that affect them.

Biomass: In ecology, biomass refers to the mass of one or all of the species (species biomass) in an ecosystem or area.

Predation, parasitism, commensalism, and mutualism are all types of species interactions that affect species populations. Intraspecific relationships are relationships among members of a species. Interspecific relationships are relationships between members of different species.

Predation: This is a relationship in which one individual feeds on another (the prey), causing the prey to die.   Mimicry is an adaptation developed as a response to predation. It refers to an organism that has a similar appearance to another species, which is meant to fool the predator into thinking the organism is more dangerous than it really is. Two examples are the drone fly and the io moth. The fly looks like a bee, but cannot sting. The io moth has markings on its wings that make it look like an owl. The moth can startle predators and gain time to escape. Predators can also use mimicry to lure their prey.

Commensalism: This refers to interspecific relationships in which one of the organisms benefits.  Mutualism, competition, and parasitism are all types of commensalism.

Mutualism: This is a relationship in which both organisms benefit from an interaction.

Competition: This is a relationship in which both organisms are harmed.

Parasitism: This is a relationship in which one organism benefits and the other is harmed.