THE CELL (eukaryotic)

1. THE CELL (eukaryotic) The IB Biology Juniors

2. Nucleus • Definition: Region of the cell containing chromosomes, surrounded by a double membrane, in which there are pores; provides for storage and protection of chromosomes; contains DNA and RNA • Functions • Stores hereditary material referred to as chromatin • Stores proteins and RNA in the nucleolus • Site for transcription in which mRNA is produced • Site for exchange of hereditary molecules (DNA and RNA) between the nucleus and the rest of the cell • During the cell division, chromatins are arranged into chromosomes in the nucleus • Production of ribosomes in the nucleolus • Selective transportation of regulatory factors and energy molecules through nuclear pores

3. The nucleus is like the brain of the cell.

4. Left Cell: Undergoing Mitosis; Right and Central Cells are in interphase

5. Structure/Contents • Nuclear Membrane: Double-layered structure that encloses the contents of the nucleus; The outer layer is connected to the endoplasmic reticulum • Nuclear Pores: The nucleus communicates with the remaining of the cell or the cytoplasm through several openings called nuclear pores; Such nuclear pores are the sites for exchange of large molecules (proteins and RNA) between the nucleus and cytoplasm • Chromosomes: Present in the form of strings of DNA and histones (proteins) called chromatin • Nucleolus: A dense, spherical-shaped structure present inside the nucleus; Produces ribosomes; Disappears when a cell undergoes division and is reformed after the completion of cell division

6. Miscellaneous • Prokaryotic vs. Eukaryotic DNA is stored in the nucleus of eukaryotic cells. Prokaryotic cells lack a nucleus. Their DNA is located in an area of cytoplasm called the nucleoid region. • Transcription This nucleus contains the genetic materials such as DNA and RNA. These materials actively participate in the process of protein synthesis. The DNA transcription takes place inside the nucleus. In the process mRNA is formed. Then the transcribed mRNA comes out of the nucleus pore into the cytoplasm. The translation process takes place and thus completes the process of protein synthesis. • Haploid/Diploid Differences – See Next Slide

7. Haploid an Diploid refer to the number of chromosomes in a cell. Haploid cells have one set of chromosomes and diploid cells have two sets. Humans have 46 chromosomes or 23 pairs. One set of each pair comes from the mother, and the other from the father. The only haploid cells in the human body are gametes (sperm/egg cells). All other cells in the human body are diploid cells. For a more thorough explanation: http://www.youtube.com/watch?v=1yu1Zuy_uEQ

8. Endoplasmic Reticulum • Definition: The endoplasmic reticulum is a network of membranous tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane. It usually has ribosomes attached and is involved in protein and lipid synthesis. • It takes up more than 10% of the cell, partially surrounding the nucleus. • The endoplasmic reticulum manufactures, processes, and transports a wide variety of biochemical compounds for use inside and outside of the cell. Some proteins are simply wandering, and some are known as ‘resident proteins’, which are constantly trapped in the lumen. The resident proteins contain a specialized retention signal consisting of a specific sequence of amino acids that enables them to be retained by the organelle.

9. Rough ER vs. Smooth ER Rough ER Smooth ER The smooth ER is from where most proteins exit the ER from the vesicles. It is much smaller than the rough ER. Smooth endoplasmic reticulum is chiefly involved, however, with the production of lipids (fats), building blocks for carbohydrate metabolism, and the detoxification of drugs and poisons.  It stores calcium which is involved in calcium metabolism.  In muscle cells, smooth endoplasmic reticulum releases calcium to trigger muscle contractions. • The surface of the rough ER is covered with ribosomes, making it look bumpy under a microscope. • It is directly continuous with the nuclear envelope. • Its job is to produce proteins that will be secreted from the cell. •  The ribosomes assemble amino acids into protein units, which are transported into the rough endoplasmic reticulum for further processing. These proteins may be either transmembrane proteins, which become embedded in the membrane of the endoplasmic reticulum, or water-soluble proteins, which are able to pass completely through the membrane into the lumen.

10. Micrograph vs. Representation Images

11. Ribosomes Structure and Function • Do not have an exterior membrane • Carry out protein synthesis in the cell • Structures maybe found in the cytoplasm • May be attached to the surface of endoplasmic reticulum • Composed of a type of RNA and protein

12. Prokaryotic vs. Eukaryotic Cells Ribosomes • Ribosomal subunits are synthesized by the nucleolus • Ribosomes of eukaryotic cells are larger and denser than prokaryotic • Eukaryotic and prokaryotic ribosomes are composed of two subunits • The eukaryotic two subunits are 80S • The prokaryotic two subunits only equal 70S • These two subunits join together when the ribosome attaches to messenger RNA (mRNA) during protein synthesis • Ribosomes along with another RNA molecule, transfer RNA (tRNA), help to translate the protein-coding genes in mRNA into proteins.

13. Proteins Produced: Free vs. Bound Free Ribosomes • Free ribosomes are located in the cytoplasm of the cell. They are not attached to any structure, but they may group together with other ribosomes to form polysomic. • In the cytoplasm, ribosomes are free floating. They can move all around the cell. Bound Ribosomes • Bound ribosomes are located on the surface of the endoplasmic reticulum • The endoplasmic reticulum that contains ribosomes is described as the rough endoplasmic reticulum because of the bumpy surface • Bound ribosomes can not move to other areas of the cell • They are attached to the cytosolic side of the endoplasmic reticulum

14. Golgi Apparatus Contents/Structure • Flattened membranous sacs called cisternae • Two sides of apparatus • Cis Face - side closest to rough ER • Trans face – gives rise to vesicles

15. Functions • Function in collection, packaging, modification and distribution of materials synthesized in cell • Cisside receives materials from the rough ER (proteins, carbs, lipids ect.) • Materials are modified as they move through the apparatus before being packaged at the Trans side • Vesicles are then created at the Trans side with the material within that are either taken to various points within the cell or outside the cell • Also manufactures some macromolecules that when coming out of the Trans side within vesicles fuse with the plasma membrane

17. Lysosomes • Definition: Lysosomes are cellular organelles that contain enzymes that break down waste materials (individual proteins or entire microorganisms) and cellular debris. The “stomach of the cell.” • They are found in animal cells, while their existence in yeasts and plants is disputed. • For example, lysosomes digest foreign material and engulfed viruses and bacteria presenting in phagosomes during the process of phagocytosis. In addition, lysosomes destroy targeted organelles, such as mitochondria, and injured cells via autolysis.

18. Picture/Diagram: • **Vesicles: Lysosomes ARE specialized vesicles. Excretory vesicles (E.V.) excrete waste from the cell (on outer edge).

19. Mitochondrion • Definition: Organelles surrounded by two membranes, the inner of which is folded inwards. * Remember: Prokaryotic cells do not have mitochondria!*

20. Function • The production of Adenosine Triphosphate (ATP) • “The raw materials used to generate ATP are the foods that we eat, or tissues within the body that are broken down in a process called catabolism.” • Programmed Cell Death or APOPTOSIS is another function of the mitochondria. • Example: The main function of the mitochondrion is _________. a. the production of proteins b. the “packaging” of proteins c. to break down waste materials in the cell d. to produce ATP through cellular respiration Answer: D

21. Structures • The mitochondria is composed of an inner and outer membrane • The outer membrane is smooth while the inner is folded into cristae (singular, crista) • Inside the inner membrane there is a semi-fluid called the matrix • The matrix is home to ribosomes and enzymes that assist in the production of ATP

22. Chemiosmosis - Definition • The subsequent movement of ions from an area of higher concentration to an area of lower concentration through transport proteins on the selectively-permeable membrane as a result of a proton gradient that forms across the membrane that is not readily permeable to ions; the diffusion of hydrogen ions (protons) across the biological membrane via the ATP synthase *Chemiosmosis occurs in the mitochondria and plays an important role in the electron transport chain (ETC)*

23. The Krebs Cycle - Overview • The Krebs Cycle takes place between the cristae of the mitochondrion within the matrix • Before the Krebs Cycle can take place, Glycolysis reduces glucose (a six carbon chain compound) to pyruvate (a three carbon chain compound) • The Pyruvate molecule is then reduced by the Krebs cycle to Acetyl-CoA (a two carbon chain) • It is then merged with Oxaloacetic Acid (a four carbon chain compound) to produce a Citric Acid (a six carbon chain compound) • *To understand the products of this reaction and to fully understand the concept, please watch http://www.youtube.com/watch?v=juM2ROSLWfw*

24. Comparison Mitochondrion Chloroplast Plant Cells Contains thylakoid membranes and pigment molecules Photosynthesis Uses light to convert carbon, derived from carbon dioxide into sugar • Both Plant and Animal Cells • Contains respiratory enzymes • Cellular Respiration • Breaks down simple sugars into carbon dioxide and release energy • Both • Produce energy for the cell to use during its functions

25. Chloroplasts • A plastid containing chlorophyll and other pigments, occurring in plants and algae that carry out photosynthesis

26. About… Calvin Cycle Link: http://www.science.smith.edu/departments/Biology/Bio231/calvin.htmal A granum is made up of numerous thylakoids stacked like a pile of coins. Thylakoids are flattened membrane sacs with the necessary componts for absorption of light Stroma contains many enzymes and chemicals needed to complete photosynthesis

27. Chloroplast vs. Mitochondria Chloroplasts Mitochondria Mitochondria has respiratory enzymes Mitochondria are located in the cytoplasm Mitochondria break down simple sugars into CO2 and release energy Mitochondria are found in plant and animal cells Produce ATP Self-sustaining, manufacturing own food • Chloroplasts have thylakoid membranes and pigment molecules • Chloroplasts are part of plant cells • Chloroplasts use light to convert carbon into sugar • Chloroplasts are larger and more complex • Only found in plant cells • Dependent on sunlight as primary source of food

29. Photosynthesis • Converts light energy to chemical energy into sugar • Only needs Carbon Dioxide, water and light energy • Takes place in plant leaves • Chlorophyll looks green because it absorbs red and blue light, making it unavailable to our eyes • The red and blue are used for photosynthesis

30. Chlorophyll: Green Coloration in Leaves

31. Cell Membranea.k.a. Plasma membrane, Cellular Membrane, Cell Surface Membrane Cell Membrane composition Phospholipids Proteins

32. Phospholipids • A Hydrophobic and hydrophilic head which makes a lipid bilayer. • Hydrophobic meaning water hating, this side faces the outside • Hydrophilic meaning water loving, this side faces the inside • The phospholipid heads are joined together by fatty acids. • However, fatty acids aren’t cemented together, they are flexible to allow materials to come in and out of the cell • These all line up together to make a lipid bilayer

33. Functions • The Cell membranes structure directly correlates with its function. • The cell membrane controls entry and removal of specific molecules from the cell. (What they let in and out) • In addition the cell membrane is responsible to endocytosis and exocytosis. • Endocytosis- process of cellular absorption: the process by which a cell membrane folds inward to take in substances bound to its surface • Exocytosis- passage of material to cell surface: the release to a cell surface of substances such as waste or secretions through vesicles

34. Proteins on the Cell Membrane • The Cell Membrane also has membrane proteins. The major two types are: Integral Proteins Peripheral

35. Integral Proteins • Integral or “Integrated” meaning that the protein goes through the outside of the cell to the inside of the cell.

36. Peripheral Proteins • Said to be “anchored” to the surface • Don’t touch the inside of the cell

37. Functions of the Proteins made Simple • These proteins in and on the cell membrane have purpose! • These functions can be remembered by a simple acronym….. • Cell communications • Channels for passive transport • Hormone binding sites • Enzymatic activity • Adhesion to other cells • Pumps for active transport

38. These functions in action • Active and passive transport • Channel integrated proteins

39. Active and Passive transport • Active transport -Use of ATP to pump molecules against the concentration gradient • Primary and secondary, some use protein channels to actively move through the cell membrane • Passive transport- Movement of molecules with the concentration gradient • Diffusion, facilitated diffusion, filtration, osmosis.

40. The fluid Mosaic Model • Now we under stand the parts, which will help us understand the whole.

41. Cell Wall Composition Function The function of the cell wall is to protect the cell and maintain its shape. • The cell wall is composed of cellulose fiber, polysaccharides, and proteins. When new cells are formed, their cell wall is thin and not very rigid. This allows the cell to grow.

42. Sources http://hyperphysics.phy-astr.gsu.edu/hbase/biology/lysosome.html http://en.wikipedia.org/wiki/Lysosome http://www.rndsystems.com/molecule_group.aspx?g=711&r=4 http://biology.clc.uc.edu/courses/bio104/photosyn.htm http://www.thefreedictionary.com/Chloroplasts http://www.buzzle.com/articles/cell-nucleus-structure-and-functions.html http://en.wikipedia.org/wiki/Cell_nucleus http://www.buzzle.com/articles/where-does-transcription-occur.html