Biology 40S Unit 1: Classifying and Understanding Life

1. Biology 40SUnit 1: Classifying and Understanding Life Developed by Trevor Boehm Hutterian Interactive TV Prairie Rose School Division

2. Major Topics in Unit 1 • Definition of Life • Linnean system of classifying life • The five kingdoms (Monera, Protista, Fungi, Plantae, and Animalia) • Prokaryotic (bacteria / archaea) and eukaryotic (fungi / animal / plant) cells • Domains of life (bacteria / archaea / eukaryotic) • Cell theory • Components of cells and their functions • Differences between plant, animal, and bacterial cells • Structure of DNA • Nucleotide bases • DNA replication • Life processes: • Cellular respiration • Cell division (mitosis) and the cell cycle • Protein synthesis

3. What is “Life”? • What a silly question, right? • I dare you to answer it without using words like “alive” or “living”. • And no trying to explain it with examples, either! • Not so easy, eh?

4. Life Comes in All Shapes and Sizes • There are currently 2 million recognized species of living organisms on earth… maybe a lot more. • Some are so small they can’t be seen with a microscope. Some are larger than a truck! • Some live for hundreds of years. Some live for a few hours. • Some walk around. Some swim. Some fly. Some don’t seem like they’re moving at all. • All of the images on the left of this PowerPoint are alive, and they look nothing alike! • Obviously, we can’t use shape or size (what it looks like) to tell if something is alive or not.

5. Characteristics of Life All life shares the following basic characteristics: …is made up of cells. …can reproduce. …grows and develops over time. …produces and uses energy. …responds to changes in environment. …moves (internal or external). …passes genetic info on to next generation. …is highly organized.

6. Many Living Organisms • Having established what “being alive” looks like, we have another problem… there’s a lot of life on earth! • Scientists have identified more than 2 million unique types of organisms on earth. • It is estimated that 40 million species inhabit the earth. • There may be millions of types of living organisms in the tropical rain forest and oceans yet undiscovered. Every year, thousands of new species are discovered. • In order to make sense of all this life in our world, we need a way to organize living organisms into groups.

7. The Purpose of Classifying • There are two purposes to having a classification system for living organisms: • To assign a single, unique, and universal name to each organism. • To place organisms into groups that have real biological meaning. That is to say, we want organisms that are biologically similar to be in the same group. • A universal system is necessary to have clear communication among scientists worldwide. We can’t have scientists in Canada using one system and scientists in Europe using a completely different one. If that were the case, they wouldn’t be able to easily cooperate or share their work.

8. Taxonomy • Taxonomy is the branch of biology that deals with classifying living organisms. • There have been several attempts through history to develop an appropriate classification system for living organisms… • …and scientists are still working on it, as we will see.

9. Aristotle’s Taxonomy • Organisms were first classified more than2,000 years ago by Greek philosopherAristotle. • He classified organisms as either plant or animal. • Animals were further divided into blood and bloodless. He also divided animals into 3 groups according to how they moved - walking, flying, or swimming (land, air, or water). • He grouped plants based on shape and stem, into categories such as trees, shrubs, and herbs. • His system was used into the 1600s, but is no longer used today. • Aristotle’s system made sense for his time, but as science advanced, some problems appeared: • There were problems using common names for organisms • These names could vary based on country and language. • Sometimes names were unclear (Malus meant apple, and MalusPersica meant peach). • Sometimes the names were long and cumbersome. • Many new organisms were being discovered as the world was explored by Europeans. • In the late 1500s and early 1600s, scientists began developing the first microscopes, and saw types of life Aristotle never imagined.

10. Binomial Nomenclature • The two-name system in common use today is called the binomial system of nomenclature. • Binomial = 2 names = genus and species. • The first word of the name is the genus name, and the second word is the species identifier. It is often an adjective describing the organism, its geographic location, or the person who discovered it. • Using this system, the domestic dog is Canis familiaris. • Canis is the genus name for the group of animals that includes dogs, wolves, coyotes, and jackals. • The word familiaris acts as a descriptor to further differentiate the domestic dog from its wild cousins. • Every organism has its own name, and related organisms are grouped together. • This system is called the Linnean System, after Carolus Linnaeus, the Swedish naturalist who developed it in the mid-1700s.

11. Genus and Species • We still use the Linnean system of binomial nomenclature today. • Scientific name of an organism consists of its genus and species (for example, the scientific name of humans is Homo sapiens). • A species is the smallest group of organisms which can produce offspring capable of reproduction. • A genus is a group of closely related, similar species. • Latin is used because it is a dead language (does not change) and can be used in many countries. • When we use the Latin name for an organism, we always capitalize the genus but not the species Identifier. We also print the name in italics or underline them. • For example: • Acer rubrum is the red maple tree. • Acer is the Latin name for maple (genus) • rubrum is the Latin word for red (species) • The name can be abbreviated as A. rubrum.

12. Seven Levels of Classification • Just a genus and species, however, doesn’t make a classification system. • Remember, today we have 2 million species to classify, and we can expect to add many more in the future. • The Linnean System included seven levels of grouping to organize similar organisms together: • Kingdom • Phylum (Division in the plant kingdom) • Class • Order • Family • Genus • Species

13. King Phillip Cried Out… Kingdom King Phillip Cried Out "For Goodness Sake!" Phylum / Division Class Order Family Genus Species

14. 5 Kingdoms • Linnaeus classified all organisms into two kingdoms, plantae and animalia. • Modern taxonomists recognizes that many organisms are neither plant or animal. • Today, we have 5 major kingdoms: • Monera • Protista • Fungi • Animalia • Plantae • Organisms are sorted into one of these 5 based on their characteristics.

15. Five Kingdoms

16. Linnean Classification of a Human Being • Kingdom: Animalia (with eukaryotic cells having cell membrane but lacking cell wall, multicellular, heterotrophic) • Phylum: Chordata (all animals with a notochord) • Class: Mammalia (vertebrate, hair, warm-blooded, bears live young) • Order: Primates (collar bone, eyes face forward, grasping hands with fingers, two types of teeth: incisors and molars) • Family: Hominidae (upright posture, large brain, flat face, hands and feet have different specializations) • Genus:Homo (s-curved spine, "man") • Species:Homo sapiens (high forehead, well-developed chin, skull bones thin)

17. Characteristics Used to Determine Kingdom • Prokaryotic or Eukaryotic • Autotrophic or Heterotrophic • Unicellular, Multicellular, or Colonial • Motile or Sessile

18. Prokaryotes vs. Eukaryotes • Prokaryotes are the simplest cells • The prokaryotic cell is bounded by a cell membrane, but does not contain any internal membrane-bound organelles. • Instead of a nucleus, it contains a region rich in DNA called a nucleoid. • Surrounding the nucleoid is a region of cytoplasm rich in ribosomes, small structures which do the job of synthesizing proteins. • Finally, surrounding the plasma membrane is a cell wall • Prokaryotes can have surface appendages which do particular jobs. Flagella are used for locomotion, for example. • Bacteria (monerans) are prokaryotes. • Prokaryotes can be either autotrophic or heterotrophic. • There are no multicellular prokaryotes. • Eukaryotic cells are much more complex • Much of the cell is taken up by organelles bound by their own membranes (mitochondrea, chloroplasts, nucleus, vacuoles, lysomes, etc.) • Eukaryotic cells have a nucleus which contains all of the cell's DNA. • Both cell types have many, many ribosomes, but the ribosomes of the eukaryotic cells are larger and more complex than those of the prokaryotic cell. • Eukaryotic cells are larger than prokaryotes. • There are multicellular and unicellular eukaryotes. • Like prokaryotes, eukaryotes can also be either autotrophic or heterotrophic. • Protists, fungi, plants, and animals are all eukaryotes. • “Eukaryote” means “true nucleus” while “prokaryote” means “before the nucleus”.

19. Diagram of Eukaryotic and Prokaryotic Cells

20. Common Features of Prokaryotes and Eukaryotes • The common features of prokaryotic and eukaryotic cells are: • DNA, the genetic material contained in one or more chromosomes and located in a nonmembrane bound nucleoid region in prokaryotes and a membrane-bound nucleus in eukaryotes • Plasma membrane, which separates the cell from the surrounding environment and functions as a selective barrier for the import and export of materials • Cytoplasm, the rest of the material of the cell within the plasma membrane, excluding the nucleoid region or nucleus, that consists of a fluid portion called the cytosol and the organelles and other particulates suspended in it • Ribosomes, the organelles on which protein synthesis takes place

21. Diagram - Common Features of Prokaryotes and Eukaryotes

22. Autotrophic vs. Heterotrophic • These terms relate to how an organism gets its food. • Autotroph - organism that makes organic compounds from inorganic sources. Plants, some bacteria, and some protista make their own food using light energy (photosynthesis). Some organisms are also capable of synthesizing energy chemically (chemosynthesis). • Heterotroph - organism that cannot make organic compounds from inorganic sources. They obtain their organic compounds by consuming other organisms. Almost all animals, fungi and some Protista and bacteria. • All food molecules come ultimately from autotrophs, either directly or indirectly.

23. Unicellular vs. Multicellular vs. Colonial • These terms refer to how many cells an organism has. • Unicellilar – one-celled. Bacteria and most protists are unicellular, and a few fungi are also unicellular. • Multicellular – many-celled, with different types of specialized cells. All animals and plants and most fungi are multicellular. • Colonial – many-celled, but all exactly the same type of cell. Some protists (algae) are colonial.

24. Sessile vs. Motile • Whether the organism is stationary (sessile) or capable of self-propelled motion (motile). • Fungi and plants are sessile. • Bacteria, protists, and animals are motile.

25. Chart Showing Classification into Kingdoms

26. General Rules for Classifying into Kingdoms • Yes, I know it looks like a lot to remember. Here are a couple generalizations that may help you keep some of that table straight: • Only one kingdom has organisms that are prokaryotic (the moneran kingdom). • For the most part, any organism that is unicellular and eukaryotic is a protist (one exception is yeast, a unicellular fungus) . • Fungi have the same characteristics as plants, except that Fungi are heterotrophic and plants are autotrophic, and their cell walls are different . • Animals are the only motile multicellular group. • Most of the autotrophic organism we study have chlorophyll which gives them a greenish appearance. So being "green" is an important clue --- it indicates they are autotrophic (ex: blue-green algae, algae, plants).

27. Three Domains of Life(To Complicate Matters) • Starting in the early 1970s, scientists began to find evidence for a previously unknown group of single-celledorganisms. • These organisms lived in extreme environments - deep sea hydrothermal vents, "black smokers", hot springs, the Dead Sea, acid lakes, salt evaporation ponds - environments that scientists had never suspected would contain much life (It was there all along, we had just never thought to look for it!). • These unusual organisms were considered to be bacteria and named archaebacteria ('ancient' bacteria). They did not need sunlight or oxygen to grow, instead making all of their food from hydrogen sulfide and other chemicals spewing from the volcanic vents, living in a complex ecosystem with many other living organisms near the warm, mineral-rich waters of the vents. • However, as scientists studied the archaebacteria, they found that their DNA is more than 50% different from the DNA of the Monera. To put this in perspective, archaea have more DNA in common with eukaryotic organisms than they do with bacteria. • Based on this, scientists propose that there should be a new category of classification of life - the Domain, a classification category above Kingdom.

28. Three Domain System • All eukaryotes are members of the domain eukarya. • Prokaryotes are seperated into two domains: • Traditional bacteria are members of the domain eubacteria. • Archaea are members of the domain archaea.

29. Three Domains

30. Three Domains

31. About Archaea • Archaea look like bacteria - that's why they were classified as bacteria in the first place. The unicellular organisms have the same sort of rod, spiral, and marble-like shapes as bacteria. • Archaea and bacteria share some DNA, so they function similarly in some ways. But archaeans also share DNA with eukaryotes, as well as having some DNA that is completely unique. • Archaea are known for their preferred living conditions. They are often referred to as “extremophiles”, or “extreme lovers”. • Some of these organisms live in hot acidic environments; they are referred to as thermoacidophiles. • Those living in salty environments are called “halophiles”(halo=salt). • Methanogens are archaea that produce methane. Methonogens live in anaerobic conditions such as mash bottoms, intestines and in underground rocks.

32. Cell Theory • Cell theory states: • All living organisms are made up of cells and the products of those cells. • All cells carry out their own life functions. • New cells come from other living cells.

33. Relative Size of Cells

34. General Characteristicsof Cells • Cells are complex and highly organized • They contain numerous internal structures Some have membrane bound organelles while others do not. • Cells contain genetic instructions (DNA) and machinery to use it • Genes are instructions for cells to create specific proteins • All cells have ribosomes, which are used to make proteins • Cells acquire and utilize energy • Cells can perform a variety of chemical reactions • Transform simple organic molecules into complex molecules • Breakdown complex molecules to release energy • Metabolism = all reactions performed by cells • Cells can engage in mechanical activities • Cells can move • Organelles can move • Cells can respond to stimuli (chemotaxis - movement towards chemicals, phototaxis - movement towards light, hormone responses, touch responses) • Cells can regulate activities • Cells control DNA synthesis and cell division • Cells make specific proteins only when needed • Cells all contain the following structures: • Plasma membrane - separates the cell from the external environment • Cytoplasm - fluid-filled cell interior • Nuclear material - genetic information stored as DNA

35. Different Types of Cells • Though all organisms are made up of cells, they aren’t all made up of the same types of cells. • For our purposes, we’re going to examine three major categories of cell: • Bacteria • Plant • Animal • The cells we’ll be examining are generalized – they are a “typical” bacterial, plant, and animal cell. In reality, there is a lot of specialization for particular purposes.

36. Features of Prokaryotic Cells • Capsule - outer sticky protective layer • Cell Wall - rigid structure which helps the bacterium maintain its shape • this is not the same as the cell wall of a plant cell • Plasma membrane - separates the cell from the environment • Mesosome - infolding of plasma membrane to aid in compartmentalization • Nucleoid - region where DNA is found loose within the cell • Cytoplasm • semi-fluid cell interior • no membrane-bound organelles • location for metabolic enzymes • location of ribosomes for protein synthesis • Flagella (singular flagellum) - One or many threadlike motile structures (locomotion) • Pili (singular, pilus) - small hairlike projections emerging from the outside cell surface, assist bacteria in attaching to other cells and surfaces, specialized pili are used for conjugation, during which two bacteria exchange fragments of DNA.

37. Prokaryote Cell Diagram

38. Features Common to Plant and Animal Cells • Plasma Membrane - All living cells have a plasma membrane that encloses their contents. In prokaryotes and plants, the membrane is the inner layer of protection surrounded by a rigid cell wall. These membranes also regulate the passage of molecules in and out of the cells. • Nucleus - The nucleus is a highly specialized organelle that serves as the information processing and administrative center of the cell. This organelle has two major functions: it stores the cell's hereditary material, or DNA, and it coordinates the cell's activities, which include growth, intermediary metabolism, protein synthesis, and reproduction (cell division). • Endoplasmic Reticulum - The endoplasmic reticulum is a network of sacs that manufactures, processes, and transports chemical compounds for use inside and outside of the cell. It is connected to the double-layered nuclear envelope, providing a pipeline between the nucleus and the cytoplasm. In plants, the endoplasmic reticulum also connects between cells via the plasmodesmata. • Golgi Apparatus - The Golgi apparatus is the distribution and shipping department for the cell's chemical products. It modifies proteins and fats built in the endoplasmic reticulum and prepares them for export as outside of the cell. • Microfilaments - Microfilaments are solid rods made of proteins. These filaments are an important part of the cytoskeleton. • Microtubules - These straight, hollow cylinders are found throughout the cytoplasm of all eukaryotic cells and carry out a variety of functions, ranging from transport to structural support. • Mitochondria - Mitochondria are oblong shaped organelles found in the cytoplasm of all eukaryotic cells. They release stored chemical energy in a process called cellular respiration. • Ribosomes - All living cells contain ribosomes, which may be found either along the rough endoplasmic reticulum or floating loose in the cytoplasm.

39. Unique Features of Animal Cells • Centrioles - Centrioles are self-replicating organelles made up of nine bundles of microtubules and are found only in animal cells. They appear to help in organizing cell division, but aren't essential to the process. • Cilia and Flagella - For single-celled eukaryotes, cilia and flagella are essential for the locomotion of individual organisms. In multicellular organisms, cilia function to move fluid or materials past an immobile cell as well as moving a cell or group of cells. • Lysosomes - The main function of these microbodies is digestion. Lysosomes break down cellular waste products and debris from outside the cell into simple compounds, which are transferred to the cytoplasm as new cell-building materials. • Vacuoles – Animal cells may have several small vacuoles used for storage and transport of materials.

40. Animal Cell Diagram

41. Another Animal Cell Diagram

42. Unique Features of Plant Cells • Cell Wall - Like their prokaryotic ancestors, plant cells have a rigid wall surrounding the plasma membrane. It is a far more complex structure, however, and serves a variety of functions, from protecting the cell to regulating the life cycle of the plant organism. • Chloroplasts - The most important characteristic of plants is their ability to photosynthesize, in effect, to make their own food by converting light energy into chemical energy. This process is carried out in specialized organelles called chloroplasts. • Plasmodesmata - Plasmodesmata are small tubes that connect plant cells to each other, providing living bridges between cells. • Vacuole - Each plant cell has a large, single vacuole that stores compounds, helps in plant growth, and plays an important structural role for the plant.

43. Plant Cell Diagram

44. Another Plant Cell Diagram

45. What is DNAand Why is it Important? • DNA stands for deoxyribonucleic acid. • DNA is found in all living organisms, including most cells in our bodies. • Specifically, whenever a cell has a nucleus, it will have DNA. Mitochondrea and chloroplasts also have their own DNA. • DNA is organized into chromosomes. Different organisms have different numbers of chromosomes – humans have 46. • DNA contains the instructions for how an organism looks and acts – the complete makeup of an organism is stored within its DNA. • DNA is passed from parent organism to child organism in a process known as inheritance. • DNA is sometimes also called “the genetic code” because information is stored in DNA molecules using a chemical code.

46. Uniqueness of DNA • Every organism’s DNA is unique, except for identical twins. • The DNA of similar organisms will be similar, but not identical. • DNA has been used by law enforcement to identify blood and hair as belonging to a particular person. DNA evidence is now widely accepted in courts. • Scientists hope that by understanding DNA, they may be able to find cures to some inherited diseases.

47. A DNA Molecule • DNA has a very unique shape called a “double helix”… though students tend to think of it as a spiral staircase. • Unravelled, the structure of DNA looks like a ladder.

48. Structure of DNA • The two sides of the ladder are made of sugar and phosphate molecules. The sugar in DNA is deoxyribose, which is where the molecule gets its name. • The rungs of the ladder are the most important because they give the cell its information. Each rung is made of two nucleotide bases joined together. • There are four possible nucleotide bases in DNA. • adenine (A) • guanine (G) • cytosine (C) • thymine (T) • These bases pair up to form the rungs of the DNA molecule: • A always joins to T • C always joins to G • A base pair refers to either a pair of A and T or a pair of G and C. • A nucleotide refers to one base plus the phosphate and sugar it is attached to.

49. Diagram of DNA Molecule

50. Another Diagram of DNA