1. Chp 2. The Chemistry of Life
Flipped

2. Concepts What overarching concepts are covered in this chapter?
Slide 2
What overarching concepts are covered in this chapter?
Concepts

3. Overarching Concepts To Know
Slide 3
Overarching Concepts To Know
Polarity
including solubility, properties of water, and the aqueous environment,
Basic biological chemistry:
bonds, nature of carbon, chemical formulas & representations, functional groups, acids/bases & related topics (pH, ionization, buffers)
should be a review of high school science and BIOL 111
Biological macromolecules:
structure (understanding & recognizing), function, understanding chemical nature, interactions
Membranes:
structure, differences, function, how selective permeability is achieved

4. See Worksheet:
Getting Started

5. PolARITY Polarity means something different depending on the context.
Slide 5
Polarity means something different depending on the context.
What common feature does polarity have to do with in these different contexts?
PolARITY

6. Slide 6
Physical Models
Water kit

7. Basic biological chemistry
Slide 7
See also supplementary materials under Class Notes
Basic biological chemistry

8. Basic Biological Chemistry: Questions
Briefly in groups
Slide 8
Basic Biological Chemistry: Questions
You should know: covalent, ionic, hydrogen bond, but what are ‘hydrophobic interactions’?
Classify these bonds and interactions based on their strength in an aqueous solution.
Why have weak bonds or interactions? Aren’t these supposed to hold things together? Mention examples.
What is so great about carbon?
You should know what pH is and why is pure water is pH 7 (think about the word ionization). You may want to look at the Review of Biological Chemistry and consider coming to the review. Draw a chemical reaction to illustrate pH.
What is a buffer? How does it work?
Hydrophobic interactions can sometimes to mean more than one thing and what is meant is not always clear so lets separate this into two pieces:
-Hydrophobic effect (that results primarily due to entropy and from a lack of interactions in an aqueous environment)
-weak van der Waals forces between nonpolar molecules or groups

9. Slide 9
Apply what you know…
Which of the following will form H bonds and what are they?
Water, nucleotide, amino acid, carbohydrate/monosaccharide, cholesterol, water, triglyceride, glycolipid, fatty acid

10. Biological macromolecules
Slide 10
Structure determines function
Chemical nature & resulting shape will determine interactions and reactivity
Biological macromolecules

11. Apply what you know… pH Scale
Briefly in groups
Slide 11
Apply what you know…
If the pH of a solution is 8, what is the relationship of the proton and hydroxide concentration?
If the pH of one solution is 3 and another is 6, how much more or less is the proton concentration? 7 14
Acidic
> [H3O+]
Basic
< [H3O+]
< [OH–]
> [OH–]
pH Scale
Neutral
[H3O+] = [OH–]
pH is a log scale

12. Understanding Structure
Cn3D from NCBI:
Jmol Tutorials: see our webpage
Physical models available in lab
Class & S2 demo and explain

13. Biological Macromolecules
Briefly in groups
Slide 13
Biological Macromolecules
How will you recognize them?
You should know the basic function and structure of each of the 4 groups of biological macromolecules have. How would you describe the structure of each?
Carbohydrates Ques #3-6
Lipids Ques #8
Nucleic acids Ques #12
Proteins
Physical Models:
Molecules of Life

14. Building on what you know, p 1
Worksheet:
Building on what you know, p 1

15. What bonds/interactions hold things together?
Briefly in groups
Slide 15
Biological Macromolecules
What bonds/interactions hold things together?
carbohydrates to the solvent/water
amino acids in a peptide
Two strands of DNA
between H and O in a single water molecule
between 2 polypeptides
between H and O in separate water molecules

16. Asymmetry is critical in biology Think of some examples
Slide 16
Biological Macromolecules
Asymmetry is critical in biology Think of some examples

17. -Carbohydrates -Proteins -DNA
Slide 17
Biological Macromolecules
Asymmetry allows directionality. What is the basis of directionality in… ? How do we refer to the two ends?
-Carbohydrates
-Proteins
-DNA

18. Now consider the structure of Proteins and NA
See Worksheet:
Building on what you know, p 2

19. Protein Structure: Think about it…
Briefly in groups
Slide 19
Biological Macromolecules
Protein Structure: Think about it…
Briefly describe the hierarchy of structure in proteins.
What is the difference between a polypeptide and a protein? Given a multisubunit protein, how can you tell how many polypeptides it has?
If there are four levels in the hierarchy of protein structure, then what is a domain?

20. Protein Domains

21. What aspects would you want to consider?
Slide 21
Biological Macromolecules
Compare & Contrast NA
What aspects would you want to consider?
See homework
Physical Models:
DNA vs. RNA

22. Slide 22
The aqueous environment drives the structure of biological membranes.
These membranes create compartments that not only allow cells to create an environment conducive to life, but also allows the creation of membrane enclosed organelles that are the hallmark of eukaryotic cells.
MEMBRANES

23. Slide 23
Membrane Proteins
In the diagram, identify an example of each of the following membrane proteins.
Peripheral
Integral
Transmembrane
Lipoproteins
Glycoproteins
Fig 2.25

24. Selective Permeability
Briefly in groups
Slide 24
Selective Permeability
How is this feature created?
Is selective permeability all or none?
Chemical nature (lipid bilayer)
Passages through proteins
Fig 2.28
Permeability varies

25. Consider: What does it mean to be fluid?
Slide 25
Membrane Fluidity
Describe features of P-lipids that determine fluidity of membranes. Do other lipids affect fluidity? Why is this important?
Consider:
What does it mean to be fluid?

26. Crossing a biological membrane…
Briefly in groups
Crossing a biological membrane…
Through what route can items cross biological membranes?
Make a table to organize and describe membrane transport mechanisms.
What terms would you include?
Include the terms: simple diffusion, facilitated diffusion, active transport, passive transport, exocytosis, endocytosis

27. More info provided in class

28. See Worksheet
Membranes