Bke2 Biochemistry Exercises

Group exercise: Basic Principles

"Organic chemistry is the chemistry of carbon compounds.
Biochemistry is the study of carbon compounds that crawl."
Mike Adams

The General Principles group excercise attempts to remind you about:

very basic chemistry, as it relates to biochemistry
very basic facts and concepts about cells
very basic mathematics of relevance to biochemistry

Questions:

List the six most common elements found in biological molecules. What effect will the fact that there are so few elements involved have on the chemistry you have to remember?
Where do we get these elements from? Do all organisms have the same solution to that problem?
How many covalent bonds does each of the types of atoms named above usually make?
Which of the atoms you named are electronegative? What does the term "electronegative" mean?
Look at the list of functional groups, etc., on p. 6 (2nd ed) or p. 7 (3rd ed) of Horton. Make sure you can recognise these when we talk about them. If you had a nucleophilic attack of the oxygen from a hydroxyl group on a carbonyl group, what would the product look like?
What is the difference between a covalent bond and a non-covalent interaction? Name the primary non-covalent forces involved in holding biological molecules together; describe how each one works. Rank them in order of approximate strength. How do they compare to covalent bonds, in terms of the energy it takes to break them?
What is a van der Waals radius? How does it differ from a van der Waals contact distance? How do the attractive and repulsive components of a van der Waals interaction vary with distance?
Find the polar (hydrophilic) and non-polar (hydrophobic) portions of this molecule:

What type of molecule is this, and what special properties might it have?
Given that the dielectric constant (D) of pure water is around 80, and that D inside a membrane about 1/10th of that number, as well as the relationship describing the force of an electrostatic attaction:

F = q₁ q₂/r² D

where

q₁ and q₂ are charges on the two groups
r is their separation
D is the dielectric constant

what would you expect for the relative strength of an electrostatic interaction in water, compared to that inside a membrane?
What is an acid? What is a base? What is a pKa? More generally, what is a dissociation constant (K_d)? If the [H⁺] in a solution is 10^-10 M, what is the pH? What is the [OH^-]? Is this solution acidic or basic?
What is physiological pH, buffer, salt? Why are these parameters important? Do you think that the inside of a cell is like the solution in a test tube? What might be different? What about the situation in a membrane?
Name (at least) two ways that water affects the chemistry of the cell.
BRIEFLY define: proteins, carbohydrates, lipids, nucleotides. What is a polymer, and why are they important? What jobs do these different molecules perform in your cells?
Which of the following belong in a procaryotic cell? In a eucaryotic cell? What are their basic functions?
DNA, RNA, proteins, membranes, nucleus, endoplasmic recticulum, organelles, cytoplasm, chloroplasts, mitochondria, Golgi apparatus, cytosol, chromosomes.
Which of the following is(are) correct?
a) nM > mM > M
b) m > Å > nm
c) nM < mM < M
d) mg < g < mg
All cells of a given organism usually have the exact same kind and quantity of DNA. So, why are there so many kinds of cells in the average organism?

Reading material: Chapters 1 and 2 of Horton (other useful sources: Stryer Chapter 1, and Appendix to Chapter 2; Chapter 1 of Alberts, 3rd edition for more on cells)

Lectures:
Zoom in: inside cells
Basic principles

Links:
Suggested answers

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