The information in this document is meant to cover Topic 2 and Topic 4.2.1-4.2.3 of the IB Syllabus. Characteristics of Living Things (summary) Living organisms obtain and use energy to power activities such as movement and growth. heterotrophs consume other organisms or their products autotrophs convert sunlight to food Living organisms try to maintain a constant internal environment. e.g. body temperature, water balance Living organisms reproduce. Living organisms are made of cells. The Cell Theory was originally proposed by Matthias Schleiden & Theodor Schwann (~1840) The cell theory states: 1. All life forms are made from one or more cells. 2. Cells only arise from pre-existing cells. 3. The cell is the smallest form of life. Note: Some biologists consider unicellular organisms to be acellular. Skeletal muscle and fungal hyphae are multinucleate not technically organised into cells. Evidence for the Cell Theory Cells had been observed as early as the 1600 s (by Robert Hooke in 1662 and Anthony van Leeuwenhoek in 1680) by using simple microscopes. By the 1800 s there was sufficient evidence that biologists were able to state the cell theory: Concept Living things are made of cells Cells are the smallest units of life Cells come from pre-existing cells Evidence The branch of biology which studies cells specifically is called histology. Histologists can observe cells using light and electron microscopes, and have studied many unicellular and multicellular organisms to learn about cellular structure. Viruses are crystalline, non-cellular particles that may only reproduce themselves by infecting a cell and taking over its metabolic processes. They are made of components that are found in cells (DNA or RNA and protein), but are not cells themselves. Organelles are sub-structures found in cells. Some (e.g. chloroplasts) have been shown to survive outside the cell for only brief periods of time in laboratory experiments. Louis Pasteur demonstrated that spontaneous generation (life from non-living substances) does not occur, using a simple experiment. Sterilised broth only grew bacteria when it had been exposed to air meaning that the microbes had to have come from the air itself, and couldn t just magically appear. A. De Jong/TFSS 2008 1 of 19
Some microorganisms have a dormant spore phase as part of their life cycles this allows for survival during unfavourable conditions, and could account for living things magically appearing when conditions are favourable again. Observations of cells during mitosis and meiosis; one cell becomes two (or more). Cells contain a blueprint for growth, development and behaviour Cells are the site of the chemical reactions of life Observations on the behaviour of chromosomes provided insight into the nature of genes (DNA) and both day-to-day activity and heredity. Experimental evidence of the effect of gene transfer between organisms (genetic engineering). Enzymes are biological catalysts responsible for almost all cellular processes, and most importantly those involved in extracting energy from food (cellular respiration, fermentation). Biochemical synthesis of macromolecules such as proteins (from amino acids) and complex carbohydrates (from sugars). Cell ultra-structure, the presence of discrete organelles with specific functions. This also includes the discovery that certain biochemical processes are restricted to particular regions or organelles within the cell. Unicellular Organisms carry out all the functions of life. This includes metabolism, response (to stimuli), homeostasis, growth, reproduction and nutrition. Multicellular Organisms have cells that are organized into tissues and organs. During early development, cells differentiate by turning off certain genes and leaving other genes turned on. All body cells of a multicellular organism still have the same DNA, but a skin cell doesn't need to have the insulin gene turned on. Tissues are groups of cells that develop in the same way, with the same structure and function. (e.g. heart muscle) Organs are groups of tissues that have combined to form a single structure. In an organ the tissues work together to perform an overall function. (e.g. the heart) Organ systems are groups of organs within an organism that together carry out a process. (e.g. cardiovascular system) Multicellular organisms show emergent properties, which is a result of the interactions between component parts. In essence, the whole is greater than the sum of its parts. Life itself can be seen as an emergent property. Stem Cells Most of the cells in a multicellular organism are highly specialised, and may not continue to divide once they have reached maturity. Some specialised cells never divide (e.g. brain neurons), and others only divide when damaged (e.g. liver cells). Stem cells are unspecialised cells that may continue to divide A. De Jong/TFSS 2008 2 of 19
throughout the life of the organisms. Adult stem cells can divide an unlimited number of times, producing a new stem cell and a body tissue cell each time. This is how blood cells are produced in the bone marrow. Stem cell researchers use embryonic stem cells, which may grow into any type of cell, unlike adult stem cells. These researchers hope that stem cell therapy will be used to treat diseases such as Parkinson s, Alzheimer s and Type I diabetes. It is also possible that stem cell therapy could be used to treat spinal cord injuries. Prokaryotic and Eukaryotic Cells All cells can be classified as either prokaryotic or eukaryotic. Prokaryotic cells do not have a nucleus. Instead they have a loop of naked DNA (nucleoid). Eukaryotic cells DNA is contained within a membrane, forming a nucleus. Eukaryotic chromosomes are linear, not loops. Both prokaryotic and eukaryotic cells are organized into discrete structures called organelles, which have specific functions within the cell. Eukaryotic cells have more, and they are more complex. Note: Any eukaryotic cell is more similar to any other eukaryotic cell than any prokaryotic cell. Prokaryotic Cells These cells do not have a membrane-bound nucleus, just a simple loop of DNA. They also have very few organelles. Functions of Prokaryotic Cell Structures: cell wall: forms a protective outer layer that prevents damage from outside and bursting if internal pressure is too high plasma membrane: controls exchange of substances (nutrients and waste) between cytoplasm and extra-cellular environment; some may be pumped in by active transport mesosome: increases the area of the membrane (internally) for ATP production; may be involved in moving DNA to the cell's poles before cell division cytoplasm: contains enzymes that catalyze the chemical reactions of metabolism and DNA in a region called the nucleoid A. De Jong/TFSS 2008 3 of 19 http://www.biologyforlife.com/ib Biology/Units/Classification and Diversity/bacteria diagram.jpg
ribosomes: synthesize proteins by translating messenger RNA; some proteins stay in the cell while others may be secreted naked DNA: stores the genetic information that controls the cell and is passed on to the daughter cells pili: hair-like structures that enable attachment to surfaces and to other bacteria Prokaryotes (bacteria) may be classified according to their metabolism: Photosynthesis: Blue-green bacteria make their own food by photosynthesis making them photoautotrophs. Nitrogen fixation: Nitrogen-fixing bacteria convert nitrogen gas from the air into nitrogen compounds. Fermentation: Many bacteria absorb organic substances, convert them into other organic substances and release them. For example, the bacteria which is used to produce yoghurt converts lactose (sugar) into lactic acid. All prokaryote cells are capable of extremely rapid growth when conditions are favourable to them this occurs by binary fission and can result in doubling every 20 minutes. Eukaryotic Cells Eukaryotic cells have a nucleus which is enclosed by a membrane, and many organelles, some of which are also membrane-bound. DNA is enclosed within the nucleus. The liver cell below is a typical eukaryotic cell. Functions of Eukaryotic Cell Structures Image from http://library.thinkquest.org/c004535/media/liver_cell.gif ribosomes: may be free-floating in the cytoplasm, or attached to the endoplasmic reticulum; they perform protein synthesis by translating information on mrna Golgi apparatus: modifies proteins which are being exported from the cell; produces lysosomes A. De Jong/TFSS 2008 4 of 19
lysosomes: contain digestive enzymes; used to digest food particles brought in to the cell or may break open to digest the cell when it becomes damaged ( suicide sac ) rough endoplasmic reticulum (RER): is the site of protein synthesis for any proteins which are being exported from the cell (free-floating ribosomes make proteins for use within the cell) mitochondrion: is the site of aerobic cellular respiration nucleus: contains the cell's genetic material (chromosomes) within the nuclear membrane nucleolus: makes ribosomes for the cell In addition to these internal components, there may also be extra-cellular structures such as glycoproteins for support and adhesion (in animal cells) and a cell wall for support and maintaining shape (in plant cells). Comparing Plant & Animal Cells Feature Animal Plant Cell wall Not present. Animal cells only have a plasma membrane. Cell wall and plasma membrane are both present. Cell wall is composed of cellulose (polysaccharide) fibres. Chloroplasts Not present. Present in plant cells involved in photosynthesis (i.e. Not found in root cells). Carbohydrate storage Carbohydrates are stored as glycogen. Vacuoles Shape Cell division Small and temporary. May not be present at all. Usually rounded, but able to change shape. Centrioles present form the spindle apparatus during mitosis. Cleavage furrow forms during cytokinesis and cells pinch apart. Carbohydrates are stored as starch (amylose). Large and permanent the fluid-filled vacuole helps support the plant. Usually square, and does not change shape. Centrioles absent spindle apparatus formed from cytoskeleton. New cell wall forms between daughter cells. Comparing Prokaryotic and Eukaryotic Cells Feature Prokaryote Eukaryote Size Extremely small, 5-10 µm Larger, 50-150 µm Type of genetic material Location of genetic material A naked loop of DNA. In the cytoplasm, in a region called the nucleoid. Chromosomes consisting of strands of DNA associated with protein (chromatin). Four or more chromosomes present. In the nucleus inside a double nuclear membrane called the nuclear envelope. A. De Jong/TFSS 2008 5 of 19
Cell wall Mitochondria Generally present, made of peptidoglycan Not present. The plasma membrane and mesosomes are used for cellular respiration. Present only in plants (cellulose) and fungi (chitin) Always present. Ribosomes Smaller (70S) Larger (80S) Organelles bounded by a single membrane Few or none are present. *Usually none Many are present including ER, Golgi apparatus and lysosomes Motile organelles Some may have simple flagella, 20 nm in diameter Some may have cilia or flagella with internal structures, 200 nm in diameter Most cells are too small to see with the naked eye. How Small is Small? Eukaryotic Cell 10 100 µm Prokaryotic Cell 1 5 µm Nucleus 10 20 µm Chloroplast 2 10 µm Mitochondrion 0.5 5 µm Large Virus (HIV) 100 nm Ribosome 25 nm Cell Membrane 7.5 nm thick DNA Double Helix 2 nm thick H atom 0.1 http://www.biology.arizona.edu/cell_bio/tutorials/cells/graphics/size_comp.gif In order to observe cells, we can use magnifying lenses (hand lens, microscopes) to bring them into focus... Microscopes Light microscopes were the first type to be developed, and are in wide use still today. They use light and glass lenses to magnify the image of a cell or tissue being observed. Electron microscopes use narrow beams of electrons instead of light, and produce highly magnified images. There are two types of electron microscope: Transmission Electron Microscope (TEM): an electron beam passes through a very thin section of material. An image is formed because some electrons pass through and others do not, similar to how light microscopes work. Scanning Electron Microscope (SEM): a beam of electrons is scanned in a series of lines across the surface of the specimen. This results in a three-dimensional image of the specimen. A. De Jong/TFSS 2008 6 of 19
Limitations to Cell Size Cells cannot continue growing indefinitely. Once they reach a maximum size, they usually divide. If a cell becomes too large, it develops problems related to its surface area-to-volume ratio: as the overall size of the cell increases, its surface area-to-volume ratio decreases. Since the surface area represents the cell's plasma membrane (through which all nutrients and oxygen enter, and wastes exit) and the volume represents the cell's cytoplasm & organelles (which require nutrients and oxygen, and produce wastes), it is important for cells to have a high surface area-to-volume ratio. Example: One 2 cm x 2 cm x 2 cm cell VS. eight 1 cm x 1 cm x 1 cm cells : SA = 6(2 cm x 2 cm) SA = 8 x 6(1 cm x 1 cm) = 6(4 cm 2 ) = 8(6 cm 2 ) = 24 cm 2 = 48 cm 2 V = 2 cm x 2 cm x 2 cm V = 8(1 cm x 1 cm x 1 cm) = 8 cm 3 = 8 cm 3 SA:V = 24:8 SA:V = 48:8 = 3:1 = 6:1 The eight smaller cells have the same total volume, but double the membrane, and so overall have a better surface area-to-volume ratio. This is a recurring theme in biology, and not strictly related to the size of cells. Calculating Magnification When viewing images of microscopic objects such as cells, it is often useful to know the magnification at which you are viewing said object. The linear magnification is one way to indicate the size of an object: 1. Measure the cell's length or diameter on your drawing. 2. Measure the cell's actual length or diameter (may involve estimating size using FOV). 3. Make sure both measurements are in the same units. 4. Divide the diagram size by the actual or estimated size this value is your magnification. A scale bar ( ) may also be used to indicate size similar to the scale on a map, it represents a specific distance on the diagram or photograph. A. De Jong/TFSS 2008 7 of 19
Biological Membranes Biological membranes, whether they are the plasma (cell) membrane, or a part of the endoplasmic reticulum, all have a similar structure. They are composed of amphiphilic fats called phospholipids in a bilayer. There are also various proteins embedded within the bilayer. This model of the plasma membrane is called the Fluid Mosaic Model. Image from http://bio.winona.edu/berg/illust/memb-mod.jpg phospholipids are amphiphilic, which means that they are both hydrophobic (the fatty acids) and hydrophilic (the phosphate) it is because of this unique structure, that the phospholipid molecules arrange themselves in a bilayer the hydrophilic heads arrange themselves facing the watery extracellular fluid and cytoplasm, while the hydrophobic tails hide in the middle, away from water membrane proteins may be peripheral (attached to the surface) or integral (embedded within the bilayer) some integral proteins, called transmembrane proteins, pass all the way through the membrane hormone receptor sites allow the hormone to bind on the surface of the cell, and transmit a signal to the inside of the cell enzymes located in the membrane catalyse reactions inside or outside the cell, depending on the location of the active site electron carriers are arranged in chains and pass electrons from one to the next in a series of redox reactions (chemiosmosis) cell adhesion proteins allow cells to stick together (cell-cell recognition sites) pumps are used for active transport, using energy to move substances across the membrane channels are usually gated (to motion, binding of a ligand, or changes in voltage) and allow facilitated diffusion through the membrane A. De Jong/TFSS 2008 8 of 19
Membrane Transport There are various mechanisms by which substances pass through the membrane. Passive Transport is the movement of particles across a membrane with the concentration gradient with no additional input of energy. Diffusion is the passive movement of particles from a region of higher concentration to a region of lower concentration, as a result of the random motion of particles. Particles in a liquid or gas are in constant motion this kinetic energy is the driving force behind diffusion. This is also known as Brownian movement and increases with temperature. Particles can diffuse across a membrane that is permeable to them. Plasma membranes are permeable to oxygen gas, carbon dioxide, and water. Dialysis is the diffusion of solutes across a semi-permeable membrane. Oxygen and carbon dioxide move across the cell membrane by dialysis. Osmosis is the passive movement of water molecules from a region of lower solute concentration (i.e. higher water concentration) to a region of higher solute concentration (i.e. lower water concentration) across a partially permeable membrane. Osmosis occurs in response to a high concentration of a substance that cannot cross the membrane freely, and water moves to that side of the membrane in an attempt to achieve equilibrium. Because water is a polar molecule, special pores called aquaporins allow water through. Hypertonic solutions have a lower water concentration (higher solute concentration) than cytoplasm. Salt water is generally hypertonic to cytoplasm. Hypotonic solutions have a higher water concentration (lower solute concentration) than cytoplasm. Distilled water is hypotonic to cytoplasm. Isotonic solutions have the same water concentration (and therefore solute concentration) as cytoplasm. Extracellular fluid (ECF) and blood plasma are both isotonic to cytoplasm. Facilitated diffusion occurs when a transmembrane channel protein forms a fluid-filled passageway for ions and small hydrophilic molecules such as glucose to pass through. These channels are not constantly open they open in response to a trigger such as a substance other than the one passing through the channel binding to a receptor site. Opening the channel may require some energy, due to changing the protein's shape, but transport through occurs passively, by diffusion. Active Transport Active Transport is the movement of substances across membranes using energy from ATP. Active transport can move substances against the concentration gradient (i.e. from low to high concentration). Protein pumps in the membrane are used for active transport. Each pump only transports a specific substance or substances. The sodium/potassium ion (Na + /K + ) pump is a typical example. (See next page for diagram.) A. De Jong/TFSS 2008 9 of 19
Image from http://www.mun.ca/biology/desmid/brian/biol2060/biol2060-13/0812.jpg Protons (H + ) are also transported actively across the membrane, during chemiosmosis in mitochondria (electron transport chain) Image from and chloroplasts (light-dependent reactions). Summary: http://fig.cox.miami.edu/~cmallery/150/memb/c8x16types-transport.jpg A. De Jong/TFSS 2008 10 of 19
Bulk Transport During bulk transport, substances are transported across the membrane, or within the cell, enclosed within a bubble of membrane called a vesicle. The fluidity of the membrane allows vesicles to form from the plasma membrane or join with it (or the Golgi apparatus) quite easily. Endocytosis is the transport of materials from the ECF to the cytoplasm by wrapping a portion of the plasma membrane around it, and bringing it inside the cell. There are two forms of endocytosis: Phagocytosis cell eating occurs when the membrane engulfs relatively large particles. Some white blood cells (e.g. macrophages), and Amoeba use phagocytosis. Pinocytosis cell drinking occurs when the membrane engulfs droplets of ECF and dissolved particles. All cells use pinocytosis. Exocytosis is the reverse of endocytosis. Materials made inside the cell (hormones or neurotransmitters, for example) are brought to the membrane in a vesicle, which joins the plasma membrane, releasing the contents to the ECF. Substances can also be transported within the cell inside vesicles. Proteins made on the rough endoplasmic reticulum bud off inside a vesicle and move to the Golgi apparatus. Here, they fuse with the Golgi apparatus, and become modified sugars or lipids may be added. Then, another vesicle buds off the Golgi apparatus and moves to the plasma membrane. A. De Jong/TFSS 2008 11 of 19
The Cell Cycle Image from http://bhs.smuhsd.org/bhsnew/academicprog/science/vaughn/student%20projects/paul%20&%20marcus/cycle.jpg The cell cycle involves three distinct phases: Interphase is a period when the cell is not actively dividing. It is a period of growth for the cell. Protein synthesis, metabolism of food, and other biochemical processes occur during this time. Replication of DNA in preparation for cell reproduction also occurs during this time. It is divided into three stages: G 1 is a period of growth and normal metabolic functions, which occurs directly after cytokinesis. S is a period of synthesis, or DNA replication in preparation for mitosis. G 2 is a period of further growth and preparation for mitosis. Mitosis is the replication of a cell's nucleus in preparation for cell division. It is during this time that chromosomes become visible with a light microscope. Mitosis produces two genetically identical nuclei. Prophase is the first stage of mitosis in cells. The centrioles separate and move towards the poles of the cell, while extending microtubules that form the spindle apparatus. Chromatin super-coils around itself (like winding up a ball of yarn), resulting in visible bodies called chromosomes these are identical sister chromatids joined by a centromere. The nuclear membrane begins to break down. Metaphase is the second stage of mitosis. The chromosomes are attached to the spindle by their centromeres, and align along the cell's equatorial plate. The nuclear membrane is no longer present. A. De Jong/TFSS 2008 12 of 19
Anaphase is the third stage of mitosis. The centromeres have split, and the spindle fibres begin to contract, pulling the identical sister chromatids to opposite ends of the cell (the poles). Telophase is the final stage of mitosis. The sister chromatids have reached the poles of the cell. The spindle fibres begin to break down, and the nuclear membrane reforms. Chromosomes begin to uncoil and are no longer visible once again they are called chromatin. Telophase is followed by cytokinesis. Image from http://www.dartmouth.edu/~cbbc/courses/bio4/bio4-1997/images/mitosis.jpg Cytokinesis is the splitting of the original (parent) cell into two new (daughter) cells. Cytokinesis is different in plant and animal cells due to the presence (or absence) of a cell wall. In animal cells, the plasma membrane begins to pull inwards at the equatorial plate after anaphase. By the end of telophase, the membrane has met in the middle, and two cells are formed as the membrane pinches off from itself. In plant cells, a new cell wall begins to form after anaphase, at the equatorial plate. Formation of the cell wall divides the original cell into two. A. De Jong/TFSS 2008 13 of 19
Comparison of Cytokinesis in Plant & Animal Cells: Image from http://fig.cox.miami.edu/~cmallery/150/mitosis/c7.12.9cytokinesis.jpg Mitosis is used in eukaryotes whenever it is necessary to produce identical cells: growth of multicellular organisms (e.g. bone cells, muscle cells) embryonic development repair of damaged tissues (e.g. new skin cells to repair a wound) asexual reproduction How Mitosis ensures that Identical Cells are produced: During interphase (S), an exact copy of each chromosome is made by DNA replication, forming two identical sister chromatids. The sister chromatids remain attached to each other by their centromeres during metaphase, when each gets attached to a spindle fibre. In anaphase, the centromeres split and one chromatid from each pair moves towards opposite poles of the cell. The chromosomes at the poles become the nuclei of the daughter cells, each with identical sets of chromosomes. Cytokinesis splits the parent cell in between the two new nuclei, forming two cells with exact copies of the original nucleus. A. De Jong/TFSS 2008 14 of 19
When Mitosis Fails Mitosis, like any other process in cells, needs to be controlled. Normally, cells only undergo mitosis when new cells are needed (e.g. for growth or repair). Sometimes, the control mechanisms fail, and cells begin to divide uncontrollably. Repeated divisions cause the number of cells to quickly increase, forming a mass of cells called a tumour. This can occur in any organ or tissue in the body. Tumours can grow to a large size, and if cells break off from the tumour, they can spread to other parts of the body and form more tumours (this is called metastasis). Cancer is a disease caused by the growth of tumours. Tumours are harmful to the body because they use up nutrients and oxygen required by healthy cells, killing healthy cells as they take over. Image from http://www.medicalook.com/diseases_images/cancer.gif A. De Jong/TFSS 2008 15 of 19
Meiosis Reduction Division In mitosis, the daughter cells produced have the same number of chromosomes as the parent cell two of each type. This condition is called diploidy cells with two copies of each chromosome are diploid (2n). Mitosis is useful for growth, development and repair even asexual reproduction sexual reproduction requires another method of cell division to produce gametes. Gametes (sex cells) combine with other gametes during fertilization. Because of this, they must have only one set of chromosomes a condition known as haploidy. When two haploid (n) gametes combine, the resulting cell is diploid. Meiosis is the process by which gametes are formed, and is called a reduction division because the parent cells are diploid, but the resulting gametes are haploid. How does meiosis work? Meiosis involves two divisions of the nucleus, known as meiosis I and meiosis II. These divisions are similar to the process of mitosis. Both mitosis and meiosis begin with duplication of a cell s chromosomes: From this point, a cell may progress through mitosis (to regenerate diploid cells) or meiosis (to produce gametes). Meiosis I is the first stage of meiosis. It begins with prophase I, in which homologous chromosomes pair up (forming tetrads). At this time, crossing over may occur, a process in which pieces of non-sister chromatids are exchanged. A. De Jong/TFSS 2008 16 of 19
Prophase I is also when the centrioles separate and move to opposite poles of the cell. In metaphase I, the chromosomes migrate to the cell s equatorial plate, attaching to the spindle fibres. Homologous chromosomes are pulled apart by the shortening of the spindle fibres in anaphase I. The centromeres remain intact. A. De Jong/TFSS 2008 17 of 19
During telophase I, the chromosomes are divided into two separate cells. The centrioles and spindle fibres disappear. Each cell has one homologous pair (bivalent). There is no additional replication of DNA between meiosis I and meiosis II. Meiosis II very closely resembles mitosis, and occurs in both cells formed by cytokinesis after telophase I. The end result after telophase II is four haploid cells: All images in this section from: http://www.slh.wisc.edu/wps/wcm/connect /extranet/genetics/basics_mitosis.html A. De Jong/TFSS 2008 18 of 19
Two processes ensure that the four daughter cells produced by meiosis are genetically different: independent assortment of maternal and paternal homologous chromosomes o bivalents line up randomly at the cell s equator in metaphase I o separation of homologous chromosomes is independent the new cells will have a mixture of maternal and paternal chromosomes crossing over of segments of non-sister chromatids (between maternal and paternal chromosomes) o this results in new combinations of genes on the chromosomes of the gametes produced http://www.emc.maricopa.edu/faculty/farabee/biobk/crossover.gif A. De Jong/TFSS 2008 19 of 19