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EXAM II

EXAM II . EXAM II is on MARCH 15 Covers Weeks 4, 5 and 6. What is a substrate?. A substrate is a reactant for an enzymatic reaction. A substrate attaches to an enzyme at the active site. 

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EXAM II

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  1. EXAM II EXAM II is on MARCH 15 Covers Weeks 4, 5 and 6

  2. What is a substrate? • A substrate is a reactant for an enzymatic reaction. • A substrate attaches to an enzyme at the active site.  • The substrate is the reactant in that the enzymatic reaction only occurs once the substrate attaches with the enzyme that is specific for that particular substrate.  • Remember, we are talking about molecules here.  All of the big blobs you see that I've drawn are representations or cartoons of what are actual molecules.  • These molecules undergo a reaction to produce a PRODUCT.  Then, that product can be used as the reactant or SUBSTRATE for the next enzymatic reaction. 

  3. Enzyme Active Site In general only the “active site” of the enzyme binds to the substrate I. II. III. A slight change at the active site allows for the attachment of the substrate Active Site of the Enzyme

  4. WEEK 5 Continued

  5. Adenosine Triphosphate (ATP) ATP is a nucleotide The base of the nucleotide is adenine The sugar of the nucleotide is ribose Tri refers to the 3 phosphate groups attached to the ribose sugar - The last two Phosphate bonds are UNSTABLE, easily broken - In cells, the end phosphate is hydrolyzed to release energy which results in ADP, adenosine diphosphate and a Phosphate molecule

  6. ATP and the Electron Transport Chain ATP is produced via the electron transport chain (ETC) Chloroplasts in plant cells use solar energy to generate ATP using ETC Mitochondria in animal cells use glucose to generate ATP using ETC The ETC is a series of transfers of electrons whereby high energy electrons are transported through a series of steps to release energy for the synthesis of ATP

  7. Energy comes from the transfer of electrons

  8. WEEK 6 Chpt 18 (pg320-327)- Cell Evolution and multicellularity Chpt 20 (all)- Viruses, Bacteria and Archaea Chpt 4 (pg68-84)- The Eukaryotic Cell Chpt 5 (all)- Membranes and Transport

  9. Mitochondria and Chloroplasts Energy is created in the Mitochondria in animal cells and in the Chloroplasts of Plant cells

  10. How do we know this? Using Microscopy, scientists have discovered the organelles and molecular structures responsible for cell structure 1- All organisms are composed of cells 2- Cells are the basic units of structure and function in organisms 3- Cells come only from preexisting cells because cells are self-reproducing

  11. Fig. 4.2

  12. Cell Size Cells are small- approximately 1 micron (µm) This is 1,000th of a millimeter Cells are the smallest unit of living matter

  13. Fig. 4.3 SURFACE AREA TO VOLUME RATIOS

  14. Why are cells so small and Why is having a large surface area so important? 1. A Smaller cell has more surface area per volume than a large cell Small cells have more surface area for exchanging wastes for nutrients because of its greater surface-area-to-volume ratio.

  15. Two Types of Cells Bacteria and Archaea

  16. YOU ARE RESPONSIBLE FOR UNDERSTANDING THE DIFFERENCE BETWEEN PROKARYOTIC AND EUKARYOTIC CELLS AND HOW ANIMAL CELLS DIFFER FROM PLANT CELLS

  17. Chpt. 18 CELLULAR EVOLUTION Protocellcontaining DNA Genes  true cell Plasma membrane forms Polymers aggregate within the plasma membrane= protocell Monomers joined to form Polymers (proteins, RNA) Abiotic Synthesis created Small organic molecules (ex. Amino acids, nucleotides) 4.6 BYA

  18. Chpt. 18, page 325 First Prokaryotes arose 3.5 BYA Eukaryotic cells arose 2.1 BYA Eukaryotes contain Mitochondria which are believed To have been independent , free living aerobic bacteria The endosymbiotic theory states that a nucleated cell Engulfed these free living aerobic bacteria which later Became organelles or ‘MITOCHONDRIA’

  19. Heterotrophs cannot produce Own food and practice Sexual reproduction The eukarya arose from ARCHAEA Heterotrophic protistsarose when eukaryotic cells engulfed aerobic bacteria

  20. THE EUKARYOTIC CELL

  21. http://www.wisconline.com/Objects/ViewObject.aspx?ID=AP11403 ANIMAL CELLS HAVE A PLASMA MEMBRANE

  22. THE NUCLEUS Chromosomes Condensed Chromatin Contains genetic information/ Genes Composed of DNA Set number per species (humans Have 23 pairs or 46 Chromosomes) Nuclear Envelope Surrounds Nucleus Composed of two layers Has nuclear pores to permit The passage of ribosomal Subunits and mRNA out of the nucleus Nucleolus Contains ribosomal RNA which aids in production of protein http://library.thinkquest.org/12413/structures.html

  23. THE CYTOPLASM Golgi Apparatus Packages Protein Near Nucleus Cell division Centrioles Involved in Cell division Endoplasmic Reticulum Fused to Nuclear Membrane 2 types-Smooth Rough Produces protein Chloroplasts (Plants ONLY) Contains Green Chlorophyll where Photosynthesis occurs Vacuoles Store, digest and Removes cell Waste Plants have a Large Central Vacuole Lysosome Digests Proteins Lipids, Carbs Transports waste to cell membrane Made by Golgi Cytoskeleton Composed of micro- tubules Supports cell and Gives shape Ribosomes Particles where protein synthesis Occurs Composed of 2 Subunits (large and small) Mitochondria Produces ATP Has 2 membranes Folds are cristae CHAPT 4 http://library.thinkquest.org/12413/structures.html

  24. THE CYTOSKELETON Intracellular protein Matrix Ropelike fibrous polypeptides Made of tubulin- a globular protein Now called ACTIN filaments= Actin monomers, twisted in a helical manner

  25. http://www.wisconline.com/Objects/ViewObject.aspx?ID=AP11403 ANIMAL CELLS HAVE A PLASMA MEMBRANE

  26. PLANT CELL (eukaryote) PLANT CELLS HAVE A CELL WALL AND CHLOROPLASTS

  27. THE PROKARYOTIC CELL

  28. PROKARYOTES HAVE A CELL WALL, NO NUCLEUS!

  29. Prokaryote fossils date to 3.5 BYA Extremely diverse in structure and metabolic capabilities Some prokaryotes move with the use of ‘FLAGELLA’ Flagella= strands of flagellin protein wound in a helix Many prokaryotes adhere to cells with the use of ‘FIMBRIAE’Fimbriae= short bristlelike fibers on the surface Prokaryotes DO NOT HAVE A NUCLEUS Prokaryotes have a dense area called a NUCLEOID where a Single chromosome of circular DNA exists Some prokaryotes also have accessory rings of DNA called Plasmids Prokaryotes reproduce ASEXUALLY via BINARY FISSION Generation time can be as little as 12 minutes Prokaryotes are HAPLOID- one copy of each gene  Mutations are highly vulnerable to Natural selection! Prokaryotes can exchange genetic information via CONJUGATION- when two bacteria are temporarily linked together, genetic information is passed from one to the other = Transduction Pg. 364 in text

  30. BACTERIA ARCHAEA Found practically in every environment on earth Protected by a cell wall that contains PEPTIDOGLYCAN-polysaccharides linked by amino acids Bacteria are classifed by whether they are: 1-Gram +, thick layer of peptidoglycan 2-Gram -, thin layer of peptidoglycan 3 shapes: Spirilli (spiral shaped), Bacilli (rod) Cocci (round/spherical) Some bacteria are: 1- Obligate anaerobes- unable to grow in the Presence of O2 2- Facultative anaerobes- able to grow in the Presence or absense of O2 Bacteria and Arachaea can be: 1- Photoautrotrophs 3- Chemoheterotrophs 2- Chemoautotrophs Became a distinct domain in 1977 because ribosomal RNA of Archaea differs from Bacteria Eukarya are more closely related to archaea than to bacteria Archaea contain lipids that allow them to Exist in high temperatures Cell walls do NOT have peptidoglycan Types of Archaea: 1-methanogens, 2- halo- philes, 3- thermoacidophiles Methanogens- Methane makers Halophiles- need high salt concentration to grow, ex. The Dead Sea Thermoacidophiles- found in hot springs, Highly acidic conditions

  31. Photoautotrophs- Are photosynthetic and use light energy to assemble the organic molecules they require • Primitive photosynthesizing bacteria us only photosystem I and DO NOT GIVE OFF O2 • Advanced photosynthesizing bacteria (ex. Cyanobacteria) use photosys. I and II • And give off O2 • Chemoautotrophs- Make organic molecules by using energy derived from the oxidation of inorganic compounds in the environment • -Ex. Methanogens can be found at the deep hydrothermal vents, H2S • -They can produce methane from hydrogen gas and CO2 • -Nitrifying bacteria oxidize ammonia (NH3) to nitrites (NO2) and nitrites to nitrates (NO3) • Chemoheterotrophs- Most free-living bacteria are chmoheterotrophs, they take up Pre-formed organic nutrients • -Bacteria produce chemicals such as ethyl alcohol, acetic acid, butyl alchol, acetones • -Bacteria action produces butter, chees, sauerkraut, rubber, cotton, silk, coffee

  32. CELL MEMBRANE STRUCTURE AND FUNCTION Fig. 5.1 Chpt 5 pg 86 Plasma Membrane of an Animal Cell -Proteins inserted into plasma membrane are INTEGRAL proteins -PERIPHERAL proteins are on the cytoplasmic side of the membrane The membrane is ‘fluid’ Current model to describe fluidity= Fluid-Mosaic Model Cells must be fluid and pliable, rigidity can be caused by cholesterol Glycoprotein- a phsopholipid with a carbo- hydrate or sugar chain attached Protects cell, facilitates adhesion btwn cells

  33. TYPES AND FUNCTIONS OF PROTEINS (chpt 5 pg 88)

  34. The Plasma Membrane The plasma membrane is permeable and regulates the passage of molecules in and out of the cell The plasma membrane is ‘SELECTIVE’ or ‘Differentially Permeable’ or ‘Selectively Permeable’ Some molecules passively cross the plasma membrane (NO ENERGY REQUIRED) while others are actively transported across the membrane (ATP IS REQUIRED) Small, non-charged particles freely pass the membrane barrier: Carbon Dioxide (CO2) Oxygen (O2) Glycerol Alcohol (These molecules follow their concentration gradient) Water passively moves across via a protein called AQUAPORIN Ions and polar molecules like glucose and amino acids slowly cross membrane, BUT often need assistance by carrier proteins

  35. PASSIVE TRANSPORT Concentration gradient- Movement of material from an area of high concentration to an area of low concentration Diffusion- the movement of molecules from a higher to a lower concentration Fig. 5.5 page 91

  36. OSMOSIS Diffusion is the movement of molecules from an area of high to low concentration OSMOSIS is the movement of WATER across a membrane due to concentration differences of solutes OSMOTIC PRESSURE is the pressure that develops in a system due to osmosis

  37. ISOTONIC SOLUTION Solute and water concentration inside and outside of the cell are equal No gain or loss of water HYPOTONIC SOLUTION Solutions that cause cells to swell and burst The net movement of water is from the outside to the inside of the cell HYPERTONIC SOLUTION Solutions that cause a cell to shrink or shrivel due to loss of water The net movement of water out of the cell

  38. More Solute inside cell swells as water moves in to dilute solute Equal solute inside and out More Solute outside cell Shrivels as water moves out to dilute solute

  39. Fig. 5.8 page 93

  40. Gases and small non-polar molecules can easily diffuse across the membrane Larger molecules like glucose and amino acids need protein assistance

  41. ACTIVE TRANSPORT Movement of molecules or ions across the membrane AGAINST their concentration gradient CHEMICAL ENERGYor ATP is required for active transport Carrier proteins are needed for active transport Proteins that assist in the active transport of molecules across the membrane are called ‘PUMPS’ The most studied PUMP is the ‘SODIUM-POTASSIUM PUMP’ Na+ Moves Outside Cell K+ Moves Inside Cell

  42. IMPORTANCE OF Na+ - K+ PUMP • Essential in maintaining the electrochemical gradient across the cell membrane. • The electrochemical gradient generated by transporting Sodium OUT and Potassium INis used in secondary active transport • Maintanenceof osmotic balance, and most importantly • Action potential generation and propagation in muscle and nerve cells/ Cell • signalling. http://wiki.answers.com/Q/Why_is_a_sodium_potassium_pump_important_in_organisims#ixzz1FwvJ9yD6

  43. Fig. 5.10 page 95

  44. BULK TRANSPORT- TRANSPORT OF LARGE MACROMOLECULES

  45. Very specific form of pinocytosis Vitamins, peptide hormones and lipoproteins can bind to the receptors Ex. Cholesterol is taken into the cell by a coated pit

  46. THE EXTRACELLULAR MATRIX (ECM) AND CELL JUNCTIONS Provides protection Collagen and Elastin -Proteins in the ECM -Provide structure Integrin - Protein connected to fibronectin - Plays a role in cell signaling - Influences shape and activities of the cell

  47. ANIMAL CELL JUNCTIONS HOW ARE CELLS CONNECTED TO EACH OTHER?? Tight Junction Membrane proteins attach to each other Desmosome Cells joined by Intracellular filaments Gap Junction Occurs when identical plasma membrane proteins join together

  48. HOW DO PLANT CELLS COMMUNICATE? Plasmodesmata- narrow, membrane-lined Channels that pass through the cell wall. http://www.mcb.uct.ac.za/tutorial/virusentplant.htm

  49. VIRUSES

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