Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes 4:

Thermodynamics in Metabolism, cont.

Remember that for chemists and biologists the thermodynamic term generally of most interest is the Free Energy for a reaction, that is the energy available to do work.

The free energy is defined as: G = G_products- G_reactants = H - T S.
When the free energy is negative we say the reaction is spontaneous, which simply means the reactants are favored in the reaction equation as written.
Note when a reaction is at equilibrium then the G is zero.

Since free energy depends on conditions, chemists tabulate free energies under Standard Conditions, (G°): 298 K, 1 atm., with all concentrations at 1 M.

For biological systems we define a slightly different standard free energy with [H⁺] = 10^-7 M (pH=7), G° '.
For non-standard conditions we can find the free energy of a reaction using: G = G° ' + RT lnQ.
For the special case of equilibrium, the free energy is zero, so G° ' = -RT lnK', G° ' = -5700 log K (in joules). Thus free energy is related to the equilibrium constant, K.
To provide a quantitative feeling for this relationship some values are tabulated below:

K	log K	G°' (calories)	G°' (joules)
10^-3	-3	4,089	17,100
10^-1	-1	1,363	5,700
1	0	0	0
10³	3	-4,089	-17,100

For non-equilibrium situations we can find the energy available for work using G = G° ' + RT lnQ, where Q is the mass action expression, Q = ([C][D])/([A][B]) for the reaction A + B C + D.

One advantage of using free energy is that it is easier to evaluate the overall equilibrium/energy for a series of sequential reactions (its additive instead of multiplicative): G_tot = [G]. Often use to predict feasibility of pathways, possible energy yields, and to determine when individual reactions are not at equilibrium (important for determining potential control steps etc.).

Note that the overall free energy determines spontaneity of the reaction - the pathway doesn't matter! As noted above thermodynamics is pathway independent. Thus can drive unfavorable reactions by linking with favorable reactions. This can be done:

Sequentially: , where the reaction of B to C pulls A to B; or
In parallel: , where the two reactions are linked

Example: glucose + phosphate to G-6-P (G= +3300 cal) and ATP + water to ADP + P_i (G= -7600 cal); mix together, no G-6-P (G= -4300 cal). But link with enzyme, Glu + ATP G-6-P + ADP (G= -4300 cal). All of metabolism depends on such coupled reactions. In essence catabolic reactions drive anabolic reactions etc. via direct, and more commonly, indirect, multi-step, coupling.

Metabolism would be extremely complex if coupled processes directly, however. Instead use an intermediate energy carrier: ATP. Thus catabolic processes make ATP which can then be used for anabolic processes, locomotion, pumping ions across cell membranes (major contribution to basal metabolic rate or BMR), etc. Note that ATP is not used to store energy however. (Often compared to electricity's role in our culture).

FYI – Origin of Life

The oldest fossil evidence for life on Earth dates to about 3.7 by (billion years ago). The Earth itself formed about 4.5 by with the formation of our solar system. It is thought that the Earth was too hot and chaotic to support life until perhaps 3.8 by (intense bombardment of the earth did not end until 3.9 by, thus life arose quite quickly, essentially as soon as possible!

How did this occur? Obviously guess work - no one was there, and there is no record in the rocks that we could even be certain of. However, we have good guesses as to Earth's early environment (atmosphere of H₂O, NH₃, CO₂ and smaller amounts of CH₄, NH₃, SO₂, and H₂. If you treat such an atmosphere with any high energy source in the laboratory (as was first done by Miller in 1953) you will get a mixture of organic molecules including many important to organisms today. Interestingly, we also find small precursor molecules all over the Universe - in ancient rocks, meteors, comets etc. Evidence of small precursor molecules (amino acids, nitrogenous bases etc.) also occurs in interstellar space, the atmospheres of carbon stars, gas giant planets etc.

The formation of polymers is more problematic. A major difficulty is that biopolymers are all thermodynamically unstable relative to their hydrolysis products. Some theories, but no certainty as to how polymers may have formed, though polymers have been synthesized under conditions which may have occurred on the early Earth.

The biggest problem for the origin of life is the issue of how we go from polymers to living "systems."

Consider the probelm of protein biosynthesis:
- Going from DNA (information archive) to RNA (usable information) requires a rather complex system to assure accurate transcription today. However, we could assume a much simpler system in the early, low-competition, Earth.
- Going from RNA to protein incredibly complex:
  - Need adaptor molecules (t-RNA) because there isn't any natural relationship between RNA codes (sequences) and particular amino acids.
  - Need enzymes to match specific amino acids to specific tRNA's because even the tRNA's are not specific to amino acids in term of recognizing them.
    - as a result, need 20 tRNAs + 20 proteins!
  - Need a complex molecular machine, the Ribosome, to read off the mRNA message using the tRNAs and make proteins:
  - Ribosome consists of
    - 1-2 small RNAs + two large, complexly folded, RNAs,
- The chance of such a system arising spontaneously is truly infinitesimal.
"RNA World" has been potulated to solve these dificulties.
- In this scenario RNA-based life preceeds "modern" life.
- First "life" combined information and catalytic properties in single RNA-protein molecules.
- Later there was a transition where proteins took over much of machinery over time.

Pre-Cambrian Life:¹

3.8 - microfossils?
3.46 - stomatolites (Australia) [3.5-3.3 microfossils of cyanobacteria?]
2.8 kerogens with low ¹³C/¹²C indicative of O₂ use by methanogens
2.7-2.5 2-methyl-hopane "fossils" (cyanobacterial markers); steranes (eukaryotic molecular marker, oxygen needed for synthesis)
2.5 -> stromatolite reefs rivaling modern reefs in size and architecture
0.6 Ediacaran fauna
0.54 Phanerozoic begins with deposits of "small shelly fossils" in early Cambrian
- 0.53-0.52 "Cambrian explosion" – the invention of all or nearly all animal body-plans (basis of animal phyla)

¹A slightly enhanced treatment, with photos of specimens at our natural history museum is available by clicking on the link.

Cells and Organelles

Systems Biology

Let's look at a couple of the concepts of systems biology:

1) Robustness

Complex, generalized organisms such as E. coli exhibit an amazing level of redundancy in enzymes etc. For example, of the approximately 4,000 genes in E. Coli less than 300 have been found to be "essential," where essential means the organism cannot grow on rich medium if the gene is deleted. Many genes also appear to be "silent: under more restrictive conditions as well - that is the organism often has more than one pathway to accomplish a given metabolic activity. (Cornish-Bowden & Cárdenas, Nature 14 Nov 2002, p 129)

2) Modularity

We will see that cells are designed at a number of hierarchical levels in a modular fashion, including functional localizations within cells as shown in cell structure.

There are two main cell types: prokaryote and eukaryote.

A typical idealized prokaryote cell is shown in Figure 2.7 on p 39 of Text.

Let's review E. coli for a moment just to recall its size, and also to get an idea of the sizes of various molecules Moodle pics.

prokaryote cell image

public domain image via Wikipedia Creative Commons

Cool facts about E. coli :70% water, 15% protein, 7% nucleic acids, 3% polysaccharides, 3%, lipids, 1% inorganic ions, & 0.2% metabolites.

Compartmentation in Eukaryotes

As mentioned earlier we will be focusing on eukaryotes in the rest of this course. Eukaryotes differ from prokaryotes in having a nucleus and cell organelles (their cells are physically compartmentalized). As a point of reference, an E. coli cell is about the size of a typical mammalian mitochondria.

Eukaryote cells: anatomy and organelles – Power Point presentation of McKee Chap 2b - Eukaryote Cells.

Let's look at where different major metabolic pathways occur in a "typical" liver cell.

eukaryote cell image

public domain image via Wikipedia Creative Commons

Nucleolus: localized region of the nucleus in which ribosomal RNA's are synthesized and processed.
Nucleus: DNA replication, synthesis and processing of messenger RNA's.
Ribosome: Ribonucleoprotein machines for translating RNA information into proteins.
Vesicle:small membrane enclosed vessels used in transporting proteins between different organelles (e.g. sER and Golgi etc.)
Rough Endoplasmic Reticulum: Biosynthesis and modification of membrane and export proteins.
Golgi Complex: Further modification of membrane and export proteins.
Cytoskeleton: multi-subunit fibrous proteins such as actin and microtubulin providing support for cell shape
Smooth Endoplasmic Reticulum: Lipid Synthesis; Steroid synthesis; Phase one detoxification reactions.
Mitochondria: Kreb's Citric Acid Cycle; Electron transport system and Oxidative Phosphorylation; Fatty acid oxidation; Amino acid catabolism; Interconversion of carbon skeletons.
Lysosomes: Hydrolytic (digestive) enzyme localization.
Cytosol: Glycolysis and most of gluconeogenesis; Pentose Phosphate shunt; Fatty acid biosynthesis.
Peroxisomes: Amino acid oxidases, catalase-oxidative degradation reactions.
Centrioles within Centrosome: Centrioles are barrel-shaped structures composed of nine microtular triplet-strands. A pair of associated centrioles in amorphous stuff makes up the centrosome which is involved in organizing the mitotic spindle in cell division in animal and most fungal cells (they are not present in plants). It is also essential for flagella and celia formation.
Plasma Membrane: Active and passive transport systems; receptors and signal processing systems (synthesis of various second messengers etc.).