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Learning Objectives Cells: Cell theory & cells; Eukarya, Bacteria and Archaea:

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York University
BIOL 1000
Tamara Kelly

Topic LOs Cells: Cell theory & cells; Eukarya, Bacteria and Archaea: • Describe the cell theory. [Knowledge, Comprehension] - Three generalizations which made up the cell theory 1. All organisms are composed of one or more cells: unicellular organisms can carry out the functions of life with one cell. The complex multicellular organisms divide the life functions 2. The cell is the smallest unit that has the properties of life: the cell properties are lost if the cell is broken apart. (functional units) 3. Cells arise only from growth and division of preexisting cells: the process of cell division even though DNA and RNA contain the info for manufacture. • Relate the cell theory to the theory of evolution. [Comprehension, Analysis] Darwin‟s theory of evolution: importance of variation and a mechanism ( Natural Selection) tht can be tested using data from nature. The theory is based on observations made by naturalists especially Darwin. Evolution (biological): descend w/ modifications, change in the genetic characteristics(ex.allele freq.) of a pop over time • Define DNA, RNA, protein, metabolism, anabolism and catabolism. [Knowledge] - DNA: (Deoxyribonucleic Acid) is a large helical, double stranded that has 4 letter (A,T,G,C) which provides instructions for assembling components of the cell. - RNA: ( ribonucleic acid): polymer assembled from repeating nucleotide monomers in which the 5-carbon sugar is ribose. There are 3 types: mRNA, tRNA and rRNA. - Protein: Molecules tht carry out the most activities of life, including the synthesis of other biological molecules. A protein consists of one or more polypeptides. - Metabolism: the biochemical rxn that allow a cell or organism to extract energy from its surroundings and use tht energy to maintain itself, grow, and reproduce. - Anabolism : set of anabolic pathways, which are metabolic rxns that require energy to make larger macromolecules from smaller units. - Catabolism : set of catabolic pathways, which are metabolic rxns in which energy is released as larger macromolecules are broken into simpler molecules. • Describe the "information system" of the cell, including the roles of DNA and RNA in this system. [Knowledge, Comprehension] Grandmother‟s cookbook (DNA) – we don‟t want to remove this from the kitchen, long term storage of genetic information. DNA is a very stable molecule and there are many mechanisms that allow it to guard the main copy of all the information that goes into encoding all the proteins in the cell. We have temporary copies of the recipe – these are going to be the mRNA or messenger RNA (sometimes called a gene transcript) It is called a transcript because it is made by transcription. (Going from DNA to mRNA is called transcription) – The cell uses the mRNA‟s instructions to make proteins. Proteins are built using mRNA‟s instructions. Made of amino acids (these are our ingredients in the kitchen) (polypeptide = polymer of a.a (amino acids)) Now our kitchen equipment to make proteins are: ribosomes + tRNA. - The process is as follows 1. The info of the DNA is copied on to the RNA 2. RNA directs the productions of protein molecules. 3. The translation of RNA into protein - Enzymes are used as catalysts in the process. - Information is preserved form generation to generation as it is passed on from parents to their offspring‟s • Describe the structure of DNA, using the appropriate terminology for components and characteristics of this molecule. [Knowledge, Comprehension] DNA – two strands of nucleic acid in double helix. Note that it would be correct to call single strand “DNA” but not a “DNA molecule” – a DNA molecule has TWO strand of DNA. DNA is organized in nucleotides that are joined to make strand. Parts of a nucleotide: - Sugar (deoxyribose sugar) that has 5 carbons in it - Phosphate - Nitrogenous base attached to the sugar (which can be a purine/pyrimidine) The backbone of a DNA strand is made of the sugar and the phosphates. Phosphates are the bridge between the adjacent sugars. Bases are inside the helix. Complementary base pairings are done through H bonds. Sugars are linked to phosphates by phosphodiester bond (this is a covalent bond). Within a nucleotide the links are covalent. Adenine connects to Thymine Cytosine connects to Guanine DNA and RNA = nucleic acids. Chromosome is particular DNA molecule that is arranged in a special way and has proteins associated with it. (DNA is a more stable molecule than RNA which is perhaps why it has become the preferred genetic molecule; however, as stable as DNAs are, there still is room for errors and mutations) RNA is very similar to DNA but it has one more oxygen, RNA has sugar and ribose RNA has Uracil base (instead of thymine) Uracil is less stable than thymine. (See the purple pages) • Describe, at a general level, metabolism.[Comprehension] - ATP plays a key role Redox reactions move electrons from molecule to molecule. Redox reactions are common to all the pathways that are part of metabolism. Metabolism: all the biochemical reactions occurring in an organism or cell to sustain life. It includes 1) Catabolism: (catabolic reactions break down complex molecules to smaller parts – there is energy release in catabolism) – We need every to sustain our lives and catabolic reactions provide a way for us to supplement that energy. (Cellular respiration is catabolic) 2) Anabolism: building or synthesis of larger biomolecules from smaller ones. This will require input. (Photosynthesis is anabolic) • Describe how oxidation-reduction reactions are important in cells, providing an example. [Comprehension] - Oxidation-reduction reactions in primitive cells. - In our cells, we oxidize food molecules (sugar) and use the energy(electrons) to reduce other molecules. (example: synthesizing proteins) - Oxidation in primitive cells: electrons removed in a oxidation would have been transferred directly to the substance being reduced in one-step process. The one- step process causes a lot of energy loss - Multistep process release energy slowly ( example: cellular respiration) - Adenosine triphosphate (ATP): coupling agent- links energy-releasing rxns of those requiring energy • Provide an overview of photosynthesis and cellular respiration. [Comprehension] Although all living cells will have some sort of metabolism, not all will carry out cellular respiration or photosynthesis. Cellular respiration happens in a step-wise fashion. This allows a controlled energy release that can be captured. There are a series of molecules that are able to accept molecules with different electron affinities and as you donate/receive electrons (electron transfer) then you get release of energy that cells can capture. ATP is one way of capturing that energy. ATP is the most common molecule that is used in capturing energy (though not the only one). ATP allows coupling of reactions that release energy with those that require energy. ATP ó ADP + Pi (inorganic phosphate) (This releases energy – this energy can be coupled with a reaction that needs energy like one used to make proteins or amino acids etc) There is a constant flux of ATP/ADP ADP è ATP + Pi (requires energy) • Explain, at a general level, the role of ATP in metabolism. [Comprehension] - Role of ATP in metabolism: Used for energy, used to store energy – a coupling agent links the reactions that need energy with the ones that release energy. • Describe the basic structure of all biological membranes. [Comprehension] Structure of a membrane is something that we call a phospholipid bilayer. Phosphate head (this head is polar and it is hydrophilic or water loving / [Presentation slides] the dark circles are the ribosomes. [Video about translation] tail: is hydrophobic (water hating). This structure (going from bottom to top): Hydrophilic à Hydrophobic (inside) à Hydrophilic dictates what happens around membranes. Although all membranes have this basic similarity, different membranes have different characteristics due; in part, to the proteins that are inserted inside or outside of membranes, or certain sugars or carbohydrates. Other lipids may be embedded inside membranes (for example cholesterol) • List the common components and characteristics of all cells. [Knowledge] Common to all cells: - DNA – DNA is usually found in the form of chromosome - Ribosomes - Plasma membrane - RNA – rRNA, tRNA and mRNA - ATP plays a key role in metabolism and it is found in all types of living cells Capsule is an extra cellular structure found in bacteria. It is made up of things like sugar; it helps bacteria to stick to things. It is often sticky and thick and makes them hard to treat with antibiotics. Ribosomes are present in all cells – we need them for making proteins. Chromosomes: all organisms have at least one chromosome. Flagella: we find these in many bacteria, some protists, some animal cells (like the sperm), some plant cells and some Archaea. Cilia are flagella like structures which are shorter (these two are used in cell movement) Mitochondria: animals, plants and most Euks have these Mitochondria are mostly associated with Euks. Chloroplasts: algae and plants have them. Cyanobacteria è (Endosymbiotic event) è Chloroplasts (Cyanobacteria are possibly the evolutionary ancestors of chloroplasts) Aerobic bacterium è (Endosymbiotic event) è Mitochondrion (Aerobic bacteria are possibly the evolutionary ancestors of Mitochondria) • Define organelle, nucleus, rough endoplasmic reticulum, smooth endoplasmic reticulum, endosymbiosis, motor protein, cytoskeleton. [Knowledge] Describe the structure and functions of organelles (including the nucleus and other elements of the endomembrane system; lysosomes; mitochondria; chloroplasts) in eukaryotic cells. [Knowledge, Comprehension] An organelle is the nucleus and other specialized internal structures and compartments of Euk cells. Most definitions agree that these are membrane bound. Organelles also have specialized functions according to most definitions as well. Organelles are found in Euks. Organelles are in the cytoplasm (compartments, discrete) and that‟s what we will stick to in this course Nucleus has an inner and an outer membrane that form the nuclear envelope. The outer membrane of the nucleus is connected with the other parts of the endomembrane system; it is linked with the ER. The envelope encloses the DNA; the chromosomes and necessary/associated proteins. Nuclear pores allow transfer of molecules/complexes between nucleus and cytoplasm (e.g. mRNA) In most cells, the nucleus is the biggest organelle. Reticulum refers to a network, and when we say Endoplasmic Reticulum we are talking about stuff inside the cytoplasm that forms a network. Cytoplasm: everything inside the cell except the nucleus, a liquid matrix (Cytosol) and other organelles suspended within (e.g. mitochondria) Endoplasmic reticulum can be rough/smooth. The rough part of the ER has lots of ribosomes embedded in it – lots of protein synthesis happens in this part. Not all proteins are made here though; there are free floating ribosomes in the cytosol and those ones can create proteins that are going to be used in the cytosol itself or sometimes proteins that will be imported into the Chloroplast or mitochondria but if something is going to be secreted from the cell or if it is a protein that is going to stay in a membrane it will be made on the rough ER. In short, secreted proteins, membrane proteins will be synthesized in this area. The smooth ER does NOT have any involvement in protein synthesis. Smooth ER is involved in the synthesis of lipids, certain fats, steroid hormones and phospholipids. There is also a role in detoxification of certain drugs in this area. The inside of the ER is called the lumen. (Lumen usually means the “inside” of certain things in biology) Jumping ahead: The cytoplasm will include the cytoskeleton. The cytoskeleton provides some support inside the cell. It also provides a network for transport inside the cell. Specific proteins polymerize to form long fibres/tubes. Certain forms of cell movement require the cytoskeleton. The Golgi complex Let‟s say we are going to synthesize a protein for secretion – here are the steps: mRNA will be exiting the nucleus; ribosomes on the rough ER will translate that mRNA into a protein. The protein will be in the ER and it will have to travel to the next area where it is processed. It travels by the formation of a vesicle. This vesicle will move to the receiving part of the Golgi complex. Golgi apparatus/complex/body. It looks like a stack of pitas, sacs. One side receives proteins from the RER by vesicles, processing occurs in the middle and there is a shipping area on the other side where vesicles leave. The Golgi modifies proteins: - Molecular tags are sometimes put on the protein (for sorting) so that it knows where to go - Addition of sugars to proteins - The Golgi does not only work with proteins, some other molecules are also packaged for secretion Vacuole: in certain animals and yeasts, this structure is involved in the storage of certain things. Most plant cells have a big vacuole called the central vacuole, which has storage, but the main role is to help maintain the shape and support the plant. When central vacuoles lose water they lose Turgor pressure and that‟s why plants wilt when they don‟t get enough water. Some protists have contractile vacuoles. Lysosomes: Some vesicles that come off the Golgi will turn into Lysosomes; specialized vesicles that have hydrolytic or digestive enzymes in them. These break down large molecules. If anything has to be broken down in the cell, for example an engulfed bacteria, or a damaged organelle, the Lysosomes will fuse with that object and will release the enzymes. • Compare and contrast the features of plant and animal cells. [Comprehension,Analysis] Animal and Plant cell parts - structure found in animal cell not plant cell: centriole - structure found in plant cells: chloroplasts, cell wall and vacuoles( may be found in animal cells sometimes) - Gogli complex puts the finishing touches on the protein - Nucleus: inner and outer membrane which forms the nuclear envelope, encloses chromosomes and necessary proteins. - Nuclear pores allow transfer of molecules/complex between nucleus and cytoplasm(e.g mRNA) - Outer membrane is cont with endoplasmic ret. - ER- a inner connected network - Cytoplasm: everything inside the cell except the nucleus. : inclues the cytosol + other organelles suspended within( for example: mito.) - ER has two types: refer to the PP for extra notes** 1. Rough ER: embedded with ribosome which means protein synthesis. starting place for protein that stays in the cell( membrane protein) or secreted pro. 2. Smooth ER: making lipids, steroid hormones, phospholipids, detox of some drugs or toxins - inside of ER: lumen - cytoskeleton: support in parts of cell., network for transport inside the cell, specific proteins for long fibres/tubes. And certain movements depend on the CS. *** more on CS later. Proteins in ER move to Gogli via Gogli complex:** refer to diagram in textbook on ch.2) explains well**** • Explain the relationship (and connections) between the plasma membrane, endoplasmic reticulum and Golgi complex. [Comprehension] • Describe the endosymbiotic theory of the origin and evolution of mitochondria and chloroplasts and the evidence supporting this theory. [Knowledge, Comprehension] Evidence for endosymbiosis: Mt and cp (mitochondria and chloroplast) are about the same size and shape as bacteria. Their double layer indicates that at some point they were taken in the cell and part of the cell membrane stayed with them (remnants of endosymbiosis) We do have DNA in both organelles and they ARE circular. The nucleus is very likely the product of many years of evolution – the theory of endosymbiosis does not really apply to the nucleus. This compartmentalization of the nucleus with a membrane along with the acquisition of aerobic bacteria which were capable of synthesizing ATP happened very early on in the evolution of Euks. Mt are thought to have appeared before Cp but with Cp, this appearance happened several times (there probably was not a single origin for Cp). Endosymbiotic theory: Chloroplast and mitochondria are descended from bacterial ancestors that lived within host cell. Chloroplast: some protists are able to steal chloroplast from other organisms. After acquiring the cp the protist eats the Cp but doesn‟t seem to be able to use some of the stuff that is made by it. Mt and Cp are about the same dimensions as bacteria – their morphology (shape) is also very similar. We have DNA in Mt and Cp and it is circular. Mt DNA = similar to DNA sequences in aerobic bacteria Cp DNA = similar sequence to that of Cyanobacteria (these are photosynthetic bacteria that generate oxygen). Another piece of info to support endosymbiosis is the fact that Mt and Cp divide by binary fission (just like bacteria) Mt and Cp have their own electron transport chains (ETC) again very similar to bacteria. (ETC in bacteria are usually found on the membrane or folds on the membrane) Mt and CP have ribosomes (16s) but they are a little different and slightly smaller than Eukaryotic ribosomes (which are 18s) NB: Mt, Cp can‟t survive outside of a ruptured cell – this is because while they create some proteins on their own, they rely on the nucleus for the synthesis of some other proteins – which shows that this is no longer a symbiosis, rather, Mt and Cp have become organelles. • Describe the extracellular structures (cell surface specializations) of animal and plant cells (extracellular matrix and cell wall). [Comprehension] ECM (extra cellular matrix) – this is something that we see outside of animal cells. It is secreted by animal cells – It is made up of proteins, polysaccharides. Their nature will vary depending on which tissue you are looking at. Blood is a connective tissue, as well as bone and cartilage. Their main role is to provide strength (and sometimes signaling) Cell wall (cell surface specialization) plant cell walls are made of cellulose that provides strength; they are rigid but have openings that let stuff to pass between adjacent cells. Fungi and bacteria as well other organisms have cell walls too which are made of different components. List and describe the major eukaryotic cytoskeletal elements, and their roles in the cell/organism. [Knowledge, Comprehension] Inside Euks, we have scaffolding (cytoskeleton) – we have microfilaments and microtubules that can assemble and disassemble as they are needed. Intermediate filaments are much more stable and they don‟t break down and build up the same way as the other two. • Compare and contrast kinesin, dynein and myosin. [Analysis] Microtubules and microfilaments provide “tracks” or some sort of stability. The motor proteins move. There are several kinds of moving proteins. A Kinesin motor protein is the “walker” – Kinesin interacts with the microtubule. It binds with the MT and binds to another organelle, and then walk along the MT. In order for this to happen, ATP has to be hydrolyzed, and that drives this process. http://www.youtube.com/watch?v=686qX5yzksU&feature=bf_play&list=FLMNyv2yLU Ev4&index=1 Muscle cells (contractility) – organisms that have muscles have specialized muscle cells that have a lot of both: è Actin MFs AND è Myosin motor proteins (Kinesin protein have a “walk-like” motion” but these have a ratchet-like motion Myosin motor proteins move along MFs while Kinesin proteins move along MTs. http://www.youtube.com/watch?v=vJ9ffKeUCvE Dynein has to be present for motion to take place. Kinesin and Myosin are not directly involved in flagellar movement (human being don`t have a lot of flagellin – the bacteria inside us do however) In the lung cilia move the mucus (cilia are essentially the same as flagellum) which means if you have problem with dynein, you will also have problem in your lungs (see clicker question above) In the 9 + 2 system, the centre microtubules are not joined together. Defective dynein will mean that we lose the organization that normally exists in the flagella. Keratin à intermediate filaments (you find these in nails, hair cells etc) Intermediate filaments are not involved in movement or contractility; they are basically there to provide support. Multi-cellularity: one advantage of being multicellular is that cells can work together (more surface area) and they can each have their own specialized functions. • Explain why cytoskeletal elements associate with motor proteins for certain cellular processes, providing examples of two different processes. [Knowledge, Comprehension] These two are made of proteins. Microtubules are made of a protein called Tubulin (“in” usually is associated with structural proteins). There are tubulin subunits that get assembled into a hollow tube and make up the microtubule. Microfilaments are made up of Actin subunits. (Actin microfilaments) Intermediate filaments are made of different proteins and they are stronger and more stable that microtubules and microfilaments. All the above are present in animal cells but in plant cells we don`t usually see intermediate filaments. Motility (movement) and contractility (cells contracting) happen via cytoskeleton. Cytoskeletons need: - - - Microtubules (MT from now on) OR Microfilament (AMF from now on) Motor proteins + ATP • Compare and contrast the bacterial flagellum and the eukaryotic flagellum
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