Cell Structure and Function Exploration Guide

1. Basics: What are cells made from and how does this determine their function? 8/26 and 8/28 • How big are cells and what determines their size? • The 20 amino acids: Name, Type, Relative Charge, Structure, and functional groups • What makes the plasma membrane work? • How do the internal structures of a prokaryotes and eukaryotes differ? • What is the function of the different organelles? • How does a cytoskeleton hold the parts together? • What are the limitations and advantages of having organelles? • BE SURE TO READ/REVIEW CH 1,2 and 3!

2. What do cells need to survive? A few items: Reproduction Energy Intake Energy Expenditure Water What did Hooke and Van Leeuwenhoek contribute to Cell Theory? How Big are Cells??

4. What is the Surface to Volume Ratio? Why is it such a big deal to oncologists? Important Surface Area and Volume formulas: CUBE: Surface Area=(L)(L)X 6 Volume=(L)3 Big cell: 500 um per side SA= Vol= SA Ratio= 1500000/125000000 = 0.012 SA= 500X500 X 6 sides = 1,500,000 um2 Volume 500 X 500 X 500 = 125,000,000 um3 Tiny cell: 5 um per side SA= Vol= SA Ratio= SA= 5X5 X 6 sides = 150 um2 Volume 5 X 5 X 5 = 125 um3 SA Ratio???? Sa/volume = 150/125 = 1.2 Which cell (large or small) is best with respect to: Providing quick response to environmental change? Providing rapid diffusion of waste/oxygen? Which are most fragile? Providing nutrient storage? Why is might this be useful to an oncologist treating your cancer?

5. Water content determines cell size! How do these factors modify cellular water content? Content molecule polarity: Ions/Hydrogen bonds? Which molecules carry spheres of hydration? Which molecules do not carry water? Cellular Protein Content: What is the charge on the amino acids? Each of the 20 amino acids has a unique R-group that gives it its characteristic charge and function. Why does charge determine protein function? Hypertonic or Hypotonic exterior environment: Crenation or Lysis? Cell Contents are contained by a Cell Wall with or without a lipid bilayer Plasma Membrane.

6. Environment effects what is inside the cell (cell volume)! WHY is this so?

7. Practice Quiz: How does lecture content become test content? 1) A typical human egg would be how big in diameter? 1 um 10 um 100 um 1000 um 2) Which cell would be best able to remove it’s metabolic waste? Why Cell sizes: 1X10X100 um 10X10X1000 or 100X100X100 3) If a cell had excessive chloride ions accumulate inside what would happen to its diameter? Why? 4) If the above cell had a cell wall (tree) would it have to increase its size? Why? 5) If a cells external environment pulled water out of a cell, its environments would be a _____environment. a) Hypertonic b) Hypotonic c) Isotonic d) Lytic

8. Proteins are made of 20 different kinds of amino acids. Peptide bonds link amino acids together. Write the Amino-group (-NH3+) on left and Terminal Carboxyl-group (-COO-) on right.

9. 5 Non-polar amino acids can make proteins relatively hydrophobic(water fearing/lipid loving).

10. 3 amino acids contain hydroxyl-groups on their side chains! 2 amino acids contain sulfur! (moderately hydrophyllic, targets for phosphorylation and disulfide linkages across peptide chains)

11. There are 4 acidic amino acids. They tend to have negative charges (-COO-) at physiological pH.

12. 3 basic amino acids that tend to have positive (+) charges at physiological pH.

13. 4 amino acids have phenolic rings and one (proline) is technically an “imino” acid because of its kinked nature.

14. Be sure to memorize the structures, charges and basic function of the 20 amino acids. You will be given a structure and asked for its name OR given a name and asked to draw its structure on the quiz/exam. What works best is practice writing the 20 amino acid names till you have memorized all of their names. Then practice drawing their structures till you have memorized all of their structures. There really is not other way. :o(

15. What properties of the lipid bilayer allow it to control the passage of materials into/out of cells? • What is an amphipathic molecule? • What are phospholipids? • How do hydrophobic tails minimize water contact? • Please don’t forget that even with a PL bilayer, the PM is STILL quite permeable to water, the PM leaks!! • What materials permit controlled passage between the two sides? • What is the Fluid Mosaic Model of how proteins and PL move about on a membrane?

16. What does a membrane look like in cross-section?Protein Location: integral, peripheral and/or transmembrane

17. We talk about relative concentrations of Na+, K+, Ca++, Cl- and H2PO4- quite a bit, so we just need to memorize their relative concentrations (mM) on the inside and outside of typical cell membranes. Be sure to know these approximate values.

18. Prokaryotes were here first! Their advantage is a simple design so they can quickly replicate when the conditions are just right! Why is bacteremia and septic shock so sudden? • Main Parts of a Bacteria: • Plasma Membrane- • Nucleoid- • Ribosomes- • Cell Wall- • Doubling time relative to eukaryotes? • Everything else pretty much just rolls around! • In Cell Biology 308 we mostly talk about Eukaryotic cells. 

19. Eukaryotic compartmentalization slows the replication rate but increases the ability of a cell to respond to changes in the environment. This increases cellular adaptability and survivability! Rat Hepatocyte Below:

20. Eukaryotes have organelles and are more complicated!Eukaryotes carry more genes on their DNA.DNA is in chromosomes located in a nucleus.Nucleoplasm: fluid within nuclear envelopeThe most active DNA is found in the nucleolus.

21. DNA is transcribed into mRNA>mRNA exits nucleus via Nuclear Pore> mRNA translated to protein on a ribosome on Rough Endoplasmic Reticulum>Protein MAY be modified for export in Golgi apparatus>Protein leaves via Secretory vesicle

22. Lysosomes: Golgi endosome- Contain enzymes/acids- Digest PM Infoldings- Digest Cellular junk- Digest Pathogens- Products small enough to diffuse to cytosol/outside Inappropriate rupture can cause cellular injury!!!! Peroxisomes: Produce hydrogen peroxide! H2O2 This can kill bacteria/cell itself This can chemically modify toxic compounds This can help metabilize long chain fatty acids Catalase protects cell from H2O2 Yes the two activities seem to work in opposition to each other! Implicated in cellular apoptosis! Eukaryotes can internalize and digest things using two organelles called peroxisomes and lysosomes.

23. Vacuoles are fluid filled and store things like water • Phagocytosis- • Endocytosis- • Exocytosis- • Water removal: • Generation of turgor pressure:

24. Chloroplasts and Mitochondria are essential for eukaryotes to manage energy! • Special/Unique Origins inside Eukaryotes! • Endosymbiont Theory: • DNA similar to that of bacteria! • Mitochondria: • Dark color from iron/enzyme content! • Chloroplast: • Green color from chlorophyll/coenzyme content! Plants can have both mitochondria and chloroplasts Animals can only have mitochondria

27. The cytoskeleton is an intricate array of proteins that help hold the sides of the cell to each other and anchor proteins/organelles within the cell.

28. Why should you review the material in CH4?You should already understand CH 1,2 and 3… right? • In cell biology we talk about this stuff constantly • We assume that you are familiar with the basics • We need to be fluent in the basics to understand the “finer points”, that what Cell Biology 308 is supposed to look at • We will spend most of the rest of the semester discussing these “finer points”