IB Biology Unit 3 ( 1.1 - 1.6)

Q: How often do I like jokes about chemistry?

A: Periodically

(1.1) Outline the cell theory and the evidence supporting it. Use examples to show that the cell theory is a generalization that applies to most but not all organisms

Cell theory states that all living organisms are made of cells, the cell is the smallest unit of life, and all cells arise from preexisting cells. Most organisms that we know follow this pattern and conform with cell theory. In 1838, Matthias Schleiden stated that all plants were composed of cells. In 1839, Theodore Schwann stated that all animals are composed of cells. In 1855, Rudolf Virchow discovered that all cells come from cells. There are several exceptions to cell theory. Striated Muscle fibers can grow up to 30 cm in length and have hundreds of nuclei. Giant Algae can have cells of up to 10 cm long. Aseptate fungi are also multi nucleated.

(1.3) Describe how cholesterol regulates membrane fluidity and permeability.

Cholesterol is a component of animal cell membranes. Most of the molecule is hydrophobic, but there is a hydrophilic end so it fits into the bilayer. The cholesterol molecule restricts the movement of phospholipid molecules, reducing the fluidity of the membrane and permeability of the membrane to hydrophilic particles. This is significant since animal cells must maintain concentration differences of these molecules across the membranes and thus diffusion must be restricted.

(1.6) Explain the regulation of the cell cycle by cyclins.

Cyclins are proteins that ensure that tasks of the cell cycle are performed at the correct time. They bind to cyclin-dependent kinases (CDKs) enabling them to act as enzymes. These activated enzymes cause the cell to move from G1 to S to G2 to M. The points where cyclin activated CDKs function are called checkpoints.

(1.4) Describe and explain how particles move across membranes by diffusion, facilitated diffusion osmosis and active transport.

Diffusion is the passive movement of particles from regions of higher concentration to lower concentration. If the membrane is permeable to the particle, that particle will naturally diffuse until concentrations across either side of the membrane approach equilibrium. Since membranes are only semi-permeable, some molecules cannot freely pass through the membrane and rely on protein channels for facilitated diffusion. These channel proteins only allow one type of molecule to pass through. Sometimes, a cell needs to move molecules against their concentration gradient. Active transport is the movement of substances across membranes requiring energy from ATP. Protein pumps are used for active transport.

(1.4) Describe active transport using the sodium-potassium pump and facilitated diffusion using potassium channels in axons.

During the resetting of the neuron, potassium ions must be transported into the axon and sodium ions must leave the axon against their concentration gradients. Thus the sodium potassium pump is needed. One ATP molecule provides enough energy to pump two potassium ions into the cell and three sodium ions out of the cell. During repolarization, facilitated diffusion is needed to return the axon to its original resting potential and allow potassium ions to diffuse out of the cell. Once the outside of the axon achieves a net negative charge, parts of the channel are positively charged and attracted, thus opening the channel. After the potassium ions diffuse out, the channel is closed by a globular sub unit.

(1.5) Explain the endosymbiotic theory for the origin of eukaryotic cells and the evidence for it. Know that the almost universal nature of the genetic code indicates a common origin of life.

Endosymbiotic theory states that about 2 billion years ago, an aerobically respiring bacterial cell took up residence within an anaerobically respiring cell by endocytosis. The two cells formed a symbiotic relationship, supplying both itself and the larger cell with ATP, giving the larger cell a competitive advantage with more effective respiration. Eventually, the bacterial cell evolved into the mitochondrion. Later, a heterotrophic cell took in a smaller photosynthetic bacterium which later evolved into the chloroplast. This explains why both bacteria and mitochondria grow and divide like bacterial cells (binary fission), have a naked loop of DNA, synthesize their own 70s ribosomes, and have double membranes (as if they were taken in by endocytosis). The universality of the genetic code allows for the success of this endosymbiosis, since the genetic code has essentially the same meaning in terms of amino acids produced, and the DNA of mitochondria and chloroplasts more closely resembles bacteria than eukaryotic cells.

(1.2) Describe the structure and function of a eukaryotic cell, e.g. liver cell.

Eukaryotic cells, unlike prokaryotes, are compartmentalized. This allows enzymes and substrates that are used in a specific process to remain concentrated in a small area, with pH and other conditions at an optimum level, and with no other enzymes to disrupt it. Eukaryotic cells have several different organelles and structures. The plasma membrane is a semi-permeable phospholipid bilayer between the cell and the external environment, with proteins that act as channels and receptors. The nucleus is a membrane-bound sphere containing DNA and the nucleolus (dense, solid structure involved in ribosome synthesis). Nuclear pores allow communication between the nucleus and the rest of the cell. Plant cells have cell walls- rigid walls made of cellulose (or chitin) and are permeable boundaries that act as structure and support. The cytoskeleton is a network of thin, fibrous elements of microtubules and microfilaments that acts as a support system for organelles and maintains cell shape. Centrioles are associated with nuclear division and are composed of microtubules. They are found in an area known as the centromere (centrioles absent in higher plant cells). Ribosomes consist of two subunits made of protein and RNA. They are either free in the cytoplasm or associated with the rER and are the site of protein synthesis. The ER is a system of membranes, tubules, and sacs. The rER (adjacent to nucleus) makes large amounts of proteins for export since they are covered in ribosomes. the sER is involved in the synthesis of lipids and breakdown of toxic substances and has no ribosomes. The Golgi Apparatus is a set of stacked flattened stacks receives vesicle bound proteins from rER, processes them, packages them, and ships them to other organelles or out of the cell. Lysosomes are spherical organelles that contain digestive (hydrolytic) enzymes break down food particles, invading food particles, or worn out cell parts. Vacuoles are sacs of fluid surrounded by a membrane which are used for temporary storage of wastes, nutrients, and water. Mitochondria are folded membrane (cristae) within an outer membrane that converts chemical energy stored in food to ATP (respiration). Chloroplasts contain stacked sacs (thylakoids) that contain chlorophyll surrounded by a double membrane that carries out photosynthesis (conversion of light energy to chemical energy stored in the bonds of glucose).

(1.1) Explain how multicellularity results in the emergence of new properties. Explain how specialized tissues develop by cell differentiation during development.

Every cell in a multicellular organism has the organism's entire genome. However, during development, the cells are stimulated to express only specific aspects of the genome as the cell differentiates to perform a specific function. Differentiated cells continue to divide to form tissues and organs. Once a cell begins on a pathway of development it cannot change as it is said to be 'committed.'

(1.3) Analyze evidence from electron microscopy supporting the current mosaic fluid model of membrane structure (and falsification of previous models).

Freeze-fracture electron micrographs have shown that globular proteins were embedded in the bilayer. Analysis of proteins showed that some parts were hydrophobic and thus would be positioned in the bilayer and sometimes extend from one side to the other. Fusion of cells with membrane proteins tagged with different colored fluorescent markers showed that they can move within the membrane as the colors mixed after the cells were combined.

(1.1) Explain the significance of surface area to volume ratio to cell size.

Generally, volume increases faster than surface area does as cell size grows. For any cell, nutrients must be brought in and waste must be excreted. Instead of larger cells, smaller cells with high surface area to volume ratios are better for nutrient transport and waste removal. Too much volume causes inability to effectively take in and dispose of substances. Larger cells have a greater metabolism, thus more substrate is needed to facilitate the additional reactions and more waste must be removed. Cells often increase surface area by having extensions or folds in the membrane, flattening into long and thin disks, and dividing cytoplasm into small volumes. A large cell, compared with a small cell, has relatively less surface area to bring in materials that are needed and get rid of waste. Thus cells are limited in the size they can reach and still be able to carry out the functions of life.

(1.4) Demonstrate the effect of osmosis using hypertonic and hypotonic solutions.

Hypertonic: water moves in. Hypotonic: water moves out. Isotonic: equal water movement in and out.

(1.6) Recognize stages in the eukaryotic cell cycle: interphase, mitosis, cytokinesis. Describe the events occurring during the interphase stages: G1, S, and G2.

Interphase is the most active period of a cells life. In the G1 phase, the cell begins to grow. At the S phase, the DNA is replicated. G2 is the second growth phase and preparation for mitosis, where organelles increase in number, DNA starts to condense from chromatin, and microtubules start to form. Mitosis is the actual division of the cell and separation of the replicated DNA. During cytokinesis, the fluid filled plasma membrane pinches to form cleavage furrows in animal cells and a cell plate in plant cells. It separates the cell into two genetically identical diploid daughter cells.

(1.5) Understand that cells can only form by division of pre-existing cells. Explain how Pasteur's experiments dispelled the idea of spontaneous generation.

Louis Pasteur placed samples of broth containing many microorganisms into flasks with swan necks. The contents of some of the flasks were then boiled and let sit, and compared with the contents of unboiled flasks (controls). While the control flasks exhibited signs of life, the boiled flasks showed no microorganisms for extended periods of time, even with exposure to air. Only after the neck of the glass was broken were organisms found. Pasteur concluded that the swan necks prevented organisms in the air from getting into the flasks and no organisms appeared spontaneously.

(1.1) Calculate the magnification of drawings and the size of cell structures in light and electron micrographs and in drawings.

Magnification = size of image(with ruler)/size of specimen(with scale) Allot p2: 500x p2: 12 um p4: 230um p4: 300 um

(1.1) Discuss the ethics of producing and using stem cells for therapeutic use.

Main argument in favor: it improves the quality of life of patients suffering from otherwise incurable conditions. Few objects from using an adult's own stem cells or from a volunteer. Newborn babies, however, cannot give informed consent for stem cells to be harvested from their umbilical cord. It becomes especially controversial when taking stem cells from specially created embryos since it is a human life, even at the earliest stage, and if the embryo dies then a life has been ended and the benefits of stem cell therapeutic use do not justify this. Counter-arguments: early-stage embryos are just balls of cells without essential features of human life, they lack nervous system and feel no pain, if they were produced deliberately the individual would have no chance of life anyways, large numbers of embryos are produced by IVF and are never implanted, instead of killing them they could be used to treat diseases and save lives.

(1.1) Explain how stem cells can be used to treat disease (Stargardt's + another)

Many degenerative conditions like Stagardt's macular dystrophy, Parkinson's, and Leukemia can be treated with stem cells. These cells can be utilized for regenerating lost or damaged tissue to return an individual to normal body function. For leukemia, a patient's bone marrow stem cells are removed and high levels of chemotherapy are used to eliminate all cancer cells. The stem cells are then replaced to allow the individual to continue producing red and white blood cells. In Stagardt's macular dystrophy (mutation causing membrane protein in retina cells to malfunction, causing vision to degenerate). Researchers have developed methods for making embryonic stem cells develop into retina cells. Initial tests were successful, after implanting 50,000 retina cells (differentiated from embryonic stem cells), vision improved slightly with no side effects. Parkinson's and Alzheimer's are the result of malfunctioning brain cells, and it is hoped that implanted stem cells could replace many of these lost or defective brain cells.

(1.6) Describe the outcome of mitotic division and explain its role in eukaryotes.

Mitotic division results in the formation of two genetically identical daughter cells. In eukaryotes, this involves the supercoiling and replication of chromosomes. Mitotic division can help prevent a cell from growing too large and have to small of a surface area to volume ratio. It is part of the cell cycle, and is a crucial aspect of a multicellular organisms It is responsible for growth, tissue repair, embryonic repair, and asexual reproduction.

(1.6) Identify phases of mitosis from micrographs. Determine the miotic index of a cell from micrographs.

Mitotic index = total number of cells in mitosis/total number of cells

1.2 Ultrastructure of cells

Subtopics; - The resolution of electron microscopes - Prokaryotic cell structure - Cell division in prokaryotes - Eukaryotic cell structure

(1.6) Explain how mutagens and oncogenes are involved in the development of primary tumours.

Mutagens are factors, like radiation or chemicals, that increase the mutation rate of a cell. Mutations in genes responsible for controlling cell division (oncogenes) can cause uncontrolled cell division, or cancer. When uncontrolled cell division causes a mass of cells it is called a primary tumor.

(1.4) Explain why tissues used in medical procedures must be bathed in solutions with the same osmolarity as the cytoplasm.

Osmosis is the diffusion of water from regions of low solute concentrations to high solute concentrations (low osmolarity to high osmolartiy). If a tissue has a higher osmolarity than the cytoplasm (hypertonic), the cells in the tissue will rapidly flood with water to attempt to even out osmolarity and vice versa.

(1.2) Compare and contrast the structure of typical plant and animal cells.

Plant and animal cells are both eukaryotic cells. Animal cells do not have cell walls or chloroplasts. They store glucose as glycogen and have no vacuoles. Since they do not have cell walls, they can change shape but are usually rounded. Plant cells have cell walls and chloroplasts. They store in starch and use cellulose for structure. They have a large fluid-filled vacuole and a fixed, regular shape.

1.1 Introduction to cells

Subtopics: - The cell theory - Unicellular organisms - Limitations on cell size - Multicellular organisms - Cell differentiation in multicellular organisms - Gene expression and cell differentiation - Stem cells

(1.2) Describe the process and purpose of binary fission in prokaryotes.

Prokaryotes divide by binary fission - splitting in two. Bacterial chromosome is replicated so that there are two copies, which are subsequently moved to opposite ends of the cell. The wall and plasma membrane are pulled inwards so the cell pinches apart to form two identical cells. This can happen as fast as every 20 minutes in some cells.

(1.2) Describe the structure and function of a prokaryotic cell, e.g. E. coli. Draw the ultrastructure of a prokaryotic cell based on electron micrographs.

Prokaryotic cells are much smaller and simpler than eukaryotic cells, with no compartmentalization. They have a single, circular strand of DNA that is naked(not associated with proteins. Many have a plasmid that can be exchanged between bacteria. Prokaryotes have cell walls (peptidoglycan), plasma membranes, and ribosomes (70s). They also have pili(for attachment or joining of bacterial cells to prepare for the transfer of DNA [sexual reproduction]), and flagella for locomotion. The nucleoid is the region containing the naked DNA.

(1.6) Describe mitosis as a continuous process, with distinct stages. Recognize and describe the events in the following stages in mitosis: prophase, metaphase, anaphase, telophase.

Prophase is the first stage of mitosis. This is the preparation phase for chromosome separation. The supercoiling and condensing of chromosomes occurs here. The nuclear membrane and nucleolus disappears. In animal cells the centrosomes move to opposite ends of the cell and centrioles form. During metaphase, chromosomes line up along the middle of the cell. Spindle fibers travel all the way across the cell and push the centrioles apart while others connect with the centromeres of chromosomes (one from each centriole) and pull them to the center/equator of the cell. During anaphase, the spindle fibers pull apart the sister chromatids and split the centromere. During Telophase, chromosomes are at each pole, the nuclear membrane begins to reform, chromosomes begin to elongate to form chromatin, the spindle apparatus disappears, and the cell elongates.

(1.3) Describe the diversity and roles or proteins in the plasma membrane.

Proteins have a variety of functions in the plasma membrane. There are integral proteins (embedded in the bilayer) and peripheral proteins (on the surface). Some integral proteins are hormone receptors, protein transport, immobilized enzymes, channels, and pumps. Peripheral proteins can be used for electron transport or receptors.

(1.2) Explain the higher resolution of electron microscopes relative to light microscopes and relate this to the greater cellular detail that can be seen.

Resolution of a microscope depends on the wavelength of the rays used to form an image. The shorter the wavelength, the higher the resolution. Electrons have a much shorter wavelength than light, so they can produce a sharper image at much higher magnifications. Since resolution is the ability of the microscope to show two close objects separately in an image, it is able to better reproduce small details within cells.

(1.4) Describe how endocytosis and exocytosis are possible because of the fluid nature of the plasma membrane. Describe how vesicles move material around within the cell.

Since the membrane is fluid, it can move and change shape. Small pieces of the membrane can be pinched off to form vesicles in the process of endocytosis. These vesicles can also move to the plasma membrane and fuse with it, ejecting the contents out of the cell in the process of exocytosis.

(1.5) Explain how the first cells might have originated, and describe any supporting evidence.

Since there is no evidence today of cells arising from nonliving material (as proved by Pasteur's experiment), it is unknown how the first cells may have originated. Miller and Urey's experiment illustrated that, given the conditions of the early earth, many organic molecules could have formed naturally, providing the basic materials from which the first living organisms arose. From these molecules, other macromolecules could have arosed, including RNA and later DNA. The first cells are presumed to have risen from the enclosure of self-replicating RNA in a phospholipid membrane.

(1.1) Describe the properties of stem cells and expain their role in embryonic development.

Stem cells are populations of cells within an organism that retain the ability to divide and differentiate into different cell types. Pluripotent, or embryonic stem cells have the ability to differentiate into any and all adult cell types. A human embryo is initially consisted of only stem cells, and then the cells begin to differentiate to form various body parts and tissues. Small numbers of stem cells persist in the human body in tissues like bone marrow, the skin, and liver.

1.5 The origin of cells

Subtopics: - Cell division and the origin of cells - Origin of the first cells - Endosymbiosis and eukaryotic cells

1.4 Membrane transport

Subtopics: - Endocytosis - Vesicle movement in cells - Exocytosis - Simple diffusion - Facilitated diffusion - Osmosis - Active Transport

1.3 Membrane structure

Subtopics: - Phospholipid bilayers - Membrane proteins - Cholesterol in membranes

1.6 Cell division

Subtopics: - The role of mitosis - Interphase - Supercoiling of chromosomes - Cytokinesis - Cyclins and the control of the cell cycle - Tumor formation and cancer

(1.3) Describe the fluid mosaic model of the plasma membrane, explaining why the phospholipids form a bilayer. Draw a diagram to illistrate the fluid mosaic model, including cholesterol and embedded proteins.

The fluid mosaic model includes a phospholipid bilayer with proteins as receptors and channels embedded in the bilayer. The phospholipid molecules have a phosphate head with two fatty acid tails. The head is hydrophilic, and likes to be associated with the water-based cytoplasm and intracellular fluid. the fatty acid tails are hydrophobic and face inwards, away from the water solution. When placed in water, the phospholipid molecules naturally form a bilayer to remain stable.

(1.6) Explain the role of metastasis in the spread of cancer and the development of secondary tumours.

The process of detaching of cells from a primary tumor and carrying of those cells elsewhere in the body is known as metastasis. These cells soon form secondary tumors in other parts of the body. Unless this is treated, once a tumor has metastasized, it can cause death.

(1.1) Describe the criteria for life as demonstrated by unicellular organsims. Investigate life functions using Parameciumand Scenedesmus.

The seven basic functions of life are metabolism, response, homeostasis, growth, nutrition, excretion, and reproduction. Paramecium is a common protozoan that lives in freshwater and marine environments. It has cilia for movement and an anal pore for excretion. Its oral grove enables it to consume food (bacteria and protists). It has food vacuoles to store indigested food and contractile vacuoles to regulate water balance. It also has nuclei that carry out different functions. Scenedesmus is a freshwater algae that forms colonies. It has many chloroplasts to obtain food, and spikes in the cell wall to keep unwanted material out and protect against predation (to allow it to reproduce before death). Both organisms are protists and can reproduce either asexually through binary fission or sexually through the fusion of gametes to produce a zygote.

(1.6) Discuss the correlation between smoking and the incidence of cancer.

There is a positive correlation between cigarette smoking and death rate due to cancer. More cigarettes smoked per day often causes more chance of developing cancer in the lungs and other organs. Although the correlation does not imply causation, there is evidence that tobacco smoke contains mutagenic and therefore carcinogenic chemicals.