BIOL 1406

Cellular and Molecular Biology

Dr. Sal Tavormina

Objectives for Unit 2
The Cellular Basis of Life

A. Basic Cell Structure and Function

1.      Describe the general plan of cellular organization common to all cells.

2.      List and explain the 3 principles of the cell theory.

3.      Describe some factors that act to limit cell size.

4.      Describe the structure of a typical prokaryotic cell.  Be sure to discuss the following: size, plasma membrane, cell wall, capsule, cytoplasm, ribosomes, nucleoid, pili, and flagellum.

5.      Describe the structure of a typical eukaryotic cell.  Be sure to discuss all of the following features, and explain the similarities and differences between animal and plant cells:
a) size
b) plasma membrane
c) cell wall
d) extracellular matrix
e) cytoplasm
f) ribosome
g) nucleus with nuclear envelope, nuclear pore, nucleoplasm, chromosome, chromatin, nucleolus
h) endoplasmic reticulum (rough and smooth)
i) Golgi apparatus or dictyosome
j) vesicle, including transport vesicle, secretory vesicle, and endocytic vesicle
k) lysosome
l) microbody including peroxisome
m) vacuole, including storage vacuole, food vacuole, contractile vacuole, and central vacuole
n) mitochondrium
o) plastid including chloroplast
p) cytoskeleton including microfilament, microtubule, and intermediate filament
q) cilium, flagellum, centriole

6.      Describe the similarities and differences between prokaryotic and eukaryotic cells.

7.    Name and describe the types of surface markers that give cells identity.

8.    Explain what cell junctions are, and discuss the following types of cell junctions:
a)  tight junction
b)  anchoring junction
d)  communicating junction 

B. Viruses

9.      Explain the similarities and differences between viruses and living organisms.

10.      Describe the structure of a typical virus.  Be sure to discuss the following: nucleic acid core, protein coat or capsid, envelope, viral-specific enzymes.

11.      Explain what a bacteriophage is, and be able to name and describe the 2 types of reproductive cycles found in bacteriophages.

12.    Describe the life cycle of a representative animal virus, such as HIV.

C. Membranes and Cell Transport

13.    Describe the Fluid Mosaic Model of membrane structure.

14.    List and describe the various functions of membrane proteins.

15.    Explain the importance of cell transport.

16.    Explain what passive transport is, and describe the following methods of passive transport across membranes:
a) simple diffusion
b) dialysis
c) osmosis (distinguish between isotonic, hypotonic, and hypertonic solutions)
c) facilitated diffusion (also called protein-mediated passive transport)

17.    Explain what active transport is, and describe the following methods of active transport across membranes:
a) membrane pumps (also called protein-mediated active transport)
b) coupled transport (also called cotransport)

18.    Explain what bulk transport is, and describe the following methods of bulk transport:
a) endocytosis including phagocytosis, pinocytosis, and receptor-mediated endocytosis
b) exocytosis 

D. Energy and Metabolism

19.    Define the term "energy" and distinguish between potential and kinetic energy.

20.    State the first and second laws of thermodynamics and explain how they apply to living organisms.

21.    Explain what a chemical reaction is and discuss how chemical equations are used to describe the changes that take place during a chemical reaction.

22.    Distinguish between endergonic and exergonic reactions and explain how they are coupled in living organisms. Describe the roles of ATP and ADP in the coupling of chemical reactions.

23.    Explain the concepts of chemical equilibrium, transition state, and activation energy.

24.    Describe some methods that can be used to speed up chemical reactions.

25.    Describe the structure, function, and characteristics of enzymes.

26.    Explain how the following factors can affect enzyme activity:
a)  temperature
b)  pH
c)  inhibitors and activators
d)  cofactors

27.    Define the terms "metabolism" and "metabolic pathway" (or "biochemical pathway") and explain how metabolic pathways are regulated.

E. How Cells Harvest Energy

28.    Identify the following terms and explain how each is involved in the transfer of energy within a cell:
a) oxidation-reduction reactions
b) electron carriers
c) electron transport chain
d) ATP

29.    Describe the following methods that are used by cells to make ATP:
a) substrate-level phosphorylation
b) electron transport phosphorylation (= chemiosmotic phosphorylation or chemiosmosis)

30.    Explain why chemiosmotic phosphorylation is sometimes called oxidative phosphorylation. 

31.    Distinguish between aerobic respiration, anaerobic respiration, and fermentation.

32.    Write a summary chemical equation for aerobic respiration and describe the origin and fate of each substance involved.

33.    Identify the 4 main stages of aerobic respiration.  For each stage discuss:
a) the cellular location
b) the main events that take place
c) whether 02 is required
d) starting substances and end products
e) the major enzymes involved and the type of reaction each catalyzes
f) the number of ATPs, NADHs, and FADH2s produced (or used up) per glucose molecule

34.    Describe the process of anaerobic respiration.

35.    Describe the process of fermentation and distinguish between alcoholic fermentation and lactic acid fermentation.

F. Photosynthesis

36.    Write a summary chemical equation for photosynthesis and describe the origin and fate of each substance involved.

37.    Explain the role and importance of photosynthesis for life on earth, and identify the main types of cells that carry out this process.

38.    Identify the 2 main stages of photosynthesis and indicate where each stage takes place in both prokaryotic and eukaryotic cells.

39.    Describe the light-dependent (energy capturing) reactions of photosynthesis with respect to:
a) how pigment molecules in the antenna complexes are used to capture light energy
b) how the captured energy is used for the production of ATP and NADPH during non-cyclic photophosphorylation
c) how the captured energy is used for the production of ATP during cyclic photophosphorylation

40.    Describe the following events of the carbon fixation reactions (also called the Calvin or C3 cycle) of photosynthesis:
a) carbon fixation
b) the reduction of PGA to form G3P (also called PGAL)
c) the production of glucose from G3P
d) the regeneration of RuBP from G3P 

G. Cell Communication

41.    Explain how cells communicate with each other, and describe the following types of cell communication:
a) direct contact
b) paracrine signaling
c) endocrine signaling
d) synaptic signaling

42.    Describe the process of signal transduction

43.    Distinguish between intracellular receptors and cell surface receptors.

44.    Explain how the following types of intracellular receptors work: 
a)  receptors that act as gene regulators
b)  receptors that act as enzymes

45.    Explain how the following types of cell surface receptors work:
a)  chemically gated ion channels
b)  enzymic receptors
c)  G-protein-coupled receptors

46.    Discuss how second messengers may be used to relay a signal into a target cell, and explain how the relayed signal may be amplified.