BI202: Study Guides

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Study Guide for Exam 1 - Pending! Please start adding outlines at will!

Review for Cell Biology:

  • Note: the symbol * means that this is question asked in class or a topic that we need to understand from the notes or textbook
 CHAPTER 1 (Lecture and Textbook)
       Review Figures (1, 2, 8, 9, 13, 14, 17, 18, 30, 32-34, 38-41)
      

Terms: 1. Micrometer μm: a measurement of length; approximately 10 -6 times that of a meter

  • What is the average diameter of a cell? 5 – 20 μm

2. Cell: A small membrane enclosed unit (the fundamental units of life) that usually has an aqueous solution of chemicals inside of it and has the ability to reproduce by splitting into two units. 3. DNA: Deoxyribonucleic Acid 4. RNA: Ribonucleic Acid 5. Transcription: Turns DNA to RNA 6. Translation: Turns RNA to proteins 7. Genome: the entire library of genetic information in a cell’s DNA 8. Microscope: A device used to look at cells

  • Robert Hooke first looked at a piece of cork with it in 1665

a. Light Microscope: use light to illuminate the specimen b. Electron Microscope: invented in the 1930’s; shoots beams of electrons onto the specimen to get better details of cells i. Scanning Electron Microscope (SEM): the specimen is coated with a heavy metal (ex. Gold) to create very detailed images, sometimes even in 3D ii. Transmission electron Microscope (TEM): requires a vacuum and a very thin specimen to shoot beams of electron to get a detailed image. Usually the specimen can be coated with a dye. c. Confocal Microscope: creates the image of a specimen by scanning it with a laser beam which allows fluorescence from the specimen to bounce back for greater resolution. Can create semi 3D images. 9. Prokaryotes: Simple cells with no membrane bound organelles like a nucleus a. Bacteria: a typical prokaryotic cell that have simple structures with little organelles within it. b. Archea: Remotely related to bacteria yet are known to live in extreme environments like high temperature areas 10. Cell Wall: A protective coat that surrounds the plasma membrane of a prokaryotic cell 11. Eukaryotes: Cells that have membrane bound organelles and a nucleus, seen in more complicated animal and plant cells 12. Nucleus: enclosed by two membranes that create the nuclear envelope, it contains the DNA molecules of a cell and it’s individual chromosomes 13. Mitochondria: Present in nearly all eukaryotic cells that contain their own DNA, reproduce by dividing in two, produce ATP, and were thought to originate as a engulfed bacteria in a eukaryotic cell 14. ATP: Adenosine Triphosphate 15. Chloroplasts: green organelles present in plant and algae cells that contain chlorophyll 16. Endoplasmic Reticulum (ER): a maze of interconnected spaces enclosed by a membrane, can by rough or smooth 17. Cytoskeleton: a network of filaments criss-crossing the cytoplasm of eukaryotic cells a. Actin Filaments: generate contractile forces b. Microtubules: the thickest filaments that act as tubes c. Intermediate Filaments: mechanically strengthen the cell 18. Homologous: when two genes from a common ancestor have a high probability that they will be in future offspring

Important Notes:

  • Recall the Hawkmoth larva and adult stage: do they have the same genes?

They have the same genes but they are expressed differently

  • How are genes expressed?
	Proteins encoded in DNA
  • DNA is transcribed (nucleus) in RNA that is translated (cytoplasm) to proteins
  • Cells have different genes expressions for specialized functions that they perform like creating substances or burning fuel to do work
  • The term cell was invented by Robert Hooke in 1665 after looking at cork. Later Antoni van Leewenhoek determined that they were “living animals”
  • 1838 = When Schleiden and Schwann developed “Cell Theory”
  • 1952 = first look at a focused surface features by a TEM
  • Florescence Microscopy uses colors and dyes to label structures within a cell
  • Look at TABS 1-1 in the textbook; it helps us tell the difference between TEM and SEM
  • There are many differences between Prokaryotic and Eukaryotic cells; the main difference is what can be found inside of them:
  • What is Phagocytosis?
         When a cell eats another cell
  • Myostatin = the protein that is irregularly expressed with cause unrestricted muscle growth
  • The list of model organisms: what traits make us use them in experiments?

1. Some mammals (mice, dogs) 2. E. coli 3. S. Cerevisiae 4. A. thaliana 5. D. melanogaster 6. C. elegan 7. zebrafish

  • What has more DNA, flowers or Humans?
Flowers, not all DNA codes for genes
  • Check out the Essential Concepts page (35) at the end of Chapter 1 in the book.

Chapter 2

Review Figures (1, 4, 6, 10 - 13, 16 (movie), 17, 19, 20)

Terms: 1. Elements: what matter is composed of that cannot be broken down or converted 2. Protons: positively charged particle in nucleus of an atom 3. Neutron: in the nucleus of an atom with no charge 4. Electron: negatively charged particle in the electron cloud of an atom 5. Atomic Number: the number of protons in an atom 6. Atomic Weight: the essential mass of an atom 7. Avogadro’s Number: used to measure mols 8. Chemical Bonds: a. Ionic: when electrons are donated from one element to another b. Electrostatic Attraction: the attractive force that occurs between oppositely charged atoms c. Covalent: when electrons are shared between elements d. Polar Covalent: when one atom attracts more electrons than another e. Hydrogen: A weak bond that occurs when the positive hydrogen atoms are attracted to a negatively charged one (water) 9. Bond Strength: the amount of energy that must be supplied to break a bond 10. Hydrophilic: water loving 11. Hydrophobic: water hating 12. Macromolecules: organic molecules used by the cells. These include proteins, fats, sugars and nucleic acids 13. Sugars: a. Monosaccharide: simple sugars (glucose) b. Polysaccharide: complex sugars (glycogen) 14. Condensation Reaction: when water is expelled as a bond is made 15. Hydrolysis: when water is consumed in a bond 16. Fats: a. Fatty Acids: contains a hydrocarbon tail and a hydrophilic head b. Saturated: c. Unsaturated 17. Proteins: a. Amino Acids (A.A.): contain a carboxyl and amino group and create proteins b. Peptide bonds: covalent linkage of two adjacent A.A. 18. Nucleotides: a. DNA b. RNA 19. Macromolecules: polymers constructed by covalently linking small molecules (Monomers and Polymers) 20. Conformation: the shape of a constructed molecule

Important Notes:

  • Which model organisms are good for looking at protein deficiencies?
  • Describe an Ionic and Covalent Bond. Give an example
  • According to the textbook, are covalent bonds weak or strong in aqueous solutions?
  Covalent bonds are 10-100 times stronger in aqueous solution (important for cell function) (47)
  • Recall the structure for Double Bonds
  • What does a polar molecule look like? What is the partial dipole?
  • What do bonds of acids look like?

(Pg. 49)

  • There are 4 building blocks of a cell: Sugars, Fatty Acids, Nucleotides and A.A. What are the macromolecules for each building block?
  • Compare Hydrolysis and Condensation reactions
  • How are fats stored and used by cells?
  • Recall the Sperm Whale
  • Draw a phospholipid
  • What are the 3 components of a nucleic acid?

A phosphate, a sugar and a nitrogen base

  • In DNA, the base pairs are connected by hydrogen bonds

A – T, C – G

  • Look at the essential concepts section at the end of chapter 2

CHAPTER 4 (pg 119 – 157)

Review Figures (1, 2, 4, 5, 7, 10, 12, 13, 15, 27, 37, 39, 41, 43) Terms: 1. Enzymes: promote intracellular chemical reactions 2. Protein: referred to as a polypeptide chain and carry out multiple functions such as structure, storage, receptor, motor, ect) 3. A.A. Sequence: the unique order that A.A are in 4. Polypeptide backbone: made from the repeating A.A 5. Side Chains: the parts of A.A. that are involved in forming the peptide bond

  • Long peptide chains are very flexible

6. Conformation: The final folded structure 7. Denatured: when a protein is unfolded 8. Natured: When a protein is folded 9. α helix: a common secondary structure with a backbone consisting of hydrogen bonds every four A.A. 10. β sheet: a common secondary structure with regular bonding interactions within a peptide bond that provide strong structural stability 11. Coiled Coil: when multiple α helices wrap around each other 12. Protein Levels of Organization: a. Primary Structure: the A.A. sequence b. Secondary Structure: the segments of polypeptide chains that include α helix and β sheets c. Tertiary Structure: the full 3D structures of a protein d. Quaternary Structure: When a protein molecule is formed with more polypeptide chains to create a complex structure 13. Ligand: the particular molecule that a protein binds to

  • Proteins are able to bind to a few ligands out of thousands

14. Binding Site: The region of a protein that associates with a ligand 15. Antibodies: Y-shaped proteins produced by the immune system that target certain molecules to bind to (foreign pathogens) 16. Feedback Inhibition: a type of negative regulation. Where enzymes act to prevent the reaction of a certain pathway. 17. Allosteric: when proteins can adopt two or more different conformations 18. Protein phosphorylation: controls the activity of proteins in cells a. * 1000’s of reactions occur each second 19. Kinase: the catalysis of Phosphorylation 20. Dephosphorylation: the reverse of Phosphorylation 21. Phosphatase: the catalysis of Dephosphorylation 22. GDP: Guanosine Diphosphate 23. GTP: Guanosine Triphosphate 24. GTP – Binding Proteins: Hydrolyzes GTP to GDP and releases a phosphate, turning the molecule inactive

Important Notes:

  • When A.A. folds, what types of bonds are present?

Ionic, Hydrogen, Van der waals, hydrophobic interactions

  • Protein function is dependent on its shape
  • When a protein folds, what side is hydrophobic and what side is hydrophilic?
  • The form of a protein is determined by its A.A. sequence
  • What do an alpha helix and beta sheet look like?
  • Beta sheets alternate directions in the sequence
  • Draw a coiled-coil
  • explain the anti-freeze beta sheet arrangement
  • Compare Globular and Fibrous Proteins
  • Look at an antibody and describe how it binds to foreign molecules in our bodies
  • Protein function is regulated by:

1. Feedback (inhibition) 2. Phosphorylation 3. Nucleotide Binding 4. Allosteric reactions

  • Review the essential concepts in the back of chapter 4

CHAPTER 11