Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2001
Lecture Notes:: 27 August	© R. Paselk 2001
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FIRST DAY: INTRODUCTION

Introduction

 

Tentative Schedule

Grading

Text

 

Who am I?

• Education in Biophysics (NMR of Proteins etc in Grad Sch)
• Current favorite biochem topics are metabolism and its control, protein folding, genesis and fate of cell components
• Also teach Biochemical Toxicology; Chemical Instrumentation and all intro Chem courses
• Interests in history of science and technology, particularly scientific instrumentation and apparatus (Museum in HSU Library and on Web).

 

How to study:

• Notes are key-nearly everything you will need to know I will cover in lecture. So how can you get the most out of your notes?
• Don't rely on/be seduced by on-line notes.

 

Course intent:

• Lecture will be initially black box biochemistry-describe system, but very little about how we got to know what we know. However, in lab we will look at how we know what we know, both in experiments and in lab lectures. Of course we will create linkages between the two. Lecture exams will emphasize biological systems and how they work. They will not cover lab material. How we know will be covered in lab exams and take-homes.
• Life at the molecular level.
• You will be expected to do some synthesis and problem solving in doing this course.

I will focus on eukaryotes, specifically humans, not because I'm a chauvinist, but because I want you to understand a functional system with all of the regulation etc. it requires. We will look at eukaryotes because they involve intracellular compartmentation and humans because I want a system with multiple intercommunicating organs and cell types, and because the human system is probably the best understood eukaryote system.

THE ELEMENTS OF LIFE

But first, we will start with the basic requirements of an idealized, simplest life form and ask why life should use the particular atoms and molecules we see dominating in living organisms.

The following observations may be made regarding the elements of life:

• Life is largely a phenomena of hydrogen and the second period of the Periodic Table. That is, the major component elements (red) in all known organisms are from these periods. Why these four elements? First we might observe that H, O, N, and C are the smallest elements capable of forming 1, 2, 3, and 4 bonds. Smallest is important because that means they can form the strongest covalent bonds. So these atoms are going to be capable of forming some of the most stable molecules, an important consideration for something that needs to grow and reproduce in a hostile environment. C, N, and O are also the only elements capable of forming strong multiple bonds (carbon and nitrogen can form triple bonds, all three can form double bonds). Thus we can hypothesize that these elements were chosen for their special properties, specifically strong covalent bond formation (to enable the formation of stable biomolecules), the ability of carbon to form large branched molecules, and for C, N, and O the formation of multiple bonds which provides chemical flexibility (step-wise oxidations, different hybridization geometries etc.).
• The next important elements to life occur in Period 3: P and S (orange). These are the smallest elements capable of multiple covalent bonds to H, C, O and N, and which also have available d-shells. The d-shells allow additional transition states and reaction mechanisms. P and S are particularly important in the capture, storage, and distribution of chemical energy.
• The "essential" elemental ions found in all studied species (blue), Ca (II), Mg (II), K (II), Na (I) and Cl (-) were probably chosen more on the basis of availability in the primordial oceans then for any specific properties: other ions are very similar.
• The trace elements required by all studied organisms (violet) are all used as co-catalysts and/or ligands. Thus they were probably chosen for their specific electronic structures as well as their availability on the early earth.
• A variety of other elements are required by at least a few organisms, and are shown on the table in black. The grayed elements are not known to be of biological importance, but are shown as "place-markers" to help us keep track on the Table.

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Last modified 27 August 2001