Introduction

Chemistry of life processes; study life processes at the molecular level; biochemists are interested in the molecular interactions of biomolecules.
American Society for Biochemistry and Molecular Biology, ASBMB, has this definition on their web page: Molecular basis of life processes

The molecules that comprise living organisms conform to all of the familiar laws of chemistry BUT they also interact with each other in accordance with another set of principles.
Albert Lehninger, a biochemist of some renown who worked on energy transduction in mitochondria and who wrote one of the first comprehensive textbooks of biochemistry, refers to The Molecular Logic of Life
In BICH 107 we will discuss the Principles of Biochemistry involved in the molecular logic of life.
These principles do NOT involve any new or as yet undiscovered principles of physical or chemical laws that govern the Universe.
Instead they are a set of principles that characterize the nature, function and interaction of biomolecules.

In the introduction to his textbook Lehninger asks two questions:

How do these molecules confer the remarkable combination of characteristics we call life?
How can a living organism appear to be more than the sum of its inanimate parts?

He writes that the basic goal of Biochemistry is to answer these questions: it is ultimately concerned with the wonder of life itself.
But can biochemists ever hope to answer such questions?
I think not!
Biochemists are reductionists! They study molecular interactions of isolated biomolecules.
A reductionist approach cannot hope to answer such fundamental questions. Only a broad based approach can do that!

So, if biochemists study the molecular basis of life processes, then

What is Life?
What distinguishes Life from non-life, Animate from In-animate?

1. Living things are structurally complicated, highly organized, with complicated internal structures and many kinds of complex molecules.
2. Living things contain structures with a functional purpose (eg, mitochondria, nucleus, ribosomes).
3. Living things use their complex molecular structure to extract, transform and utilize energy from the environment, either chemical or radiant energy. The interplay between the complex molecules is dynamic with changes in one set of components causing changes in another.
4. Living things have the property of precise self-replication and self-assembly.
   Ah! But what about crystals -- not a true analog -- a seed crystal is often needed to initiate the events, and crystals are less complex, static and not dynamic.

Cell Structure

What are the classes of organisms?

with and without a nuclear envelope, eukaryotes and two groups of prokaryotes, the eubacteria and the archaea (archaebacteria)

• Eukaryotes
• Prokaryotes:
  • Eubacteria
  • Archaea

• Eubacteria 1-2 µm
• Eukaryotes 10 - 30 µm

• Diffusion of metabolites, gases, input and output of molecules (exchange of matter and energy with the environment) is limited by the surface area to volume ratio -- as the diameter increases, the surface area does not increase proportionally.

What are three structural features shared by all organisms?

Cells of all kinds share three common features:

1. a plasma membrane defines the periphery of the cell and separates the internal structures from the surround environment; it provides a barrier to movemnet and penetration; it is flexible and allows changes in shape; it contains transporters for movement of solutes, receptors and signal transducers for responding to the environment.
2. a cytoplasm which is a concentrated aqueous solution of biomolecules; a cytosol with dissolved or suspended components plus insoluble componenets; it is not a dilute aqueous solution (the form in which it is studied by most biochemists) but a complex quasi-crystalline gel-like structure containing proteins, vitamins, and a variety of organic compounds.
3. supramolecular structures and complexes such as ribosomes and a nucleus, or nucleoid, containing the genome.

What are the habitats colonized by organisms?

• Archaea -- primitive or harsh or extreme environments
• Eubacteria and eukaryotes -- all the other environments

Sub-groups may be distinguished by habitat and energy source

• aerobic -- anaerobic
• obligate -- facultative
• chemotrophs = obtain energy from chemical fuel
• phototrophs = obtain energy from sunlight
• autotrophs = can grow utilizing only very simple inorganic compounds such as CO2, NH3
• heterotrophs = require some of their organic nutrients preformed

• Chemoheterotrophs: Organic compounds + oxygen --> cell growth + CO2
• Chemoautotroph: CO2 + electron donar --> cell growth + electron acceptor
  Ferrous, H2S --> Ferric, S
• Photoheterotroph: Organic + radiant energy --> cell growth
• Photoautotroph: CO2 + radiant energy --> cell gowth + O2

What is the structure of a typical Prokaryote?

E.coli, 2µm x 1µm

cell envelope: outer membrane (lipids and proteins)
periplasmic space = peptidoglycans (sugars and proteins)
inner membrane = plasma membrane (lipids and proteins)
Inner membrane contains transport proteins, electron transport proteins, cytochromes for energy transduction.
Outer membrane contains pili for adherence, flagellae for movement.
Inner membrane major site for trapping chemical energy in the form of ATP.

Cytoplasm contains ribosomes, proteins, and metabolites.

Nucleoid contains the genome, a single chromosome
a single, circular nucleic acid molecule (DNA) occupying approx 1µm x 0.5µm
it is approx 1000-times the length of the E.coli, or 2µm x 1000 = 2mm in length.

NOTE the division of labor in this primative cell.

• The cell envelope regulates entry and exit of materials, and acts as a barrier.
• Plasma membrane contains cytochromes for energy transduction.
• Cytoplasm contains ribosomes for protein synthesis.
• Nucleoid stores and transmits the genetic information.

eukaryotic cells are much larger than prokaryotes, approx 10-30µm

What three things happened as prokaryotes evolved into eukaryotes?

1. more DNA necessitating more compact folding of the DNA, necessitating an association with proteins (histones), to neutralize the charges on DNA, producing what is called chromatin. The condense packaging of the chromatin produces a chromosome which is composed of a single DNA molecule tightly wound around histones. The 23 chromosomes of a human cell contain 3x10E9 base pairs and have a contour length of 1m.
2. development of intracellular membrane systems, specialized compartments for specialized functions, eg the nuclear membrane separates DNA and RNA synthesis from protein synthesis, the peroxisome segregates molecular oxygen and harmful oxygen radicals for drug detoxification.
3. symbiotic associations: mitochondria in chemoheterotrophs and chloroplasts in photoautotrophs

What is the structure of a typical Eukaryote?

• Generally no cell wall in animal cells, cellulose (sugar or carbohydrate) cell wall in plant cells

• The outer plasma membrane is composed of lipids, proteins, and carbohydrates (phospholipids, glycoproteins, and lipoproteins). As in prokaryotes it contains transporters and receptors for signal transduction as well as self-recognition molecules. An example of a transporter is the LDL receptor for binding and transport into the cell of serum lipoproteins in cholesterol metabolism. An example of a receptor is the acetylcholine receptor which is required for signal transduction in the nervous stimulation of muscle contraction (nerve gas poisons interfere with this process).

• A number of different Intracellular Membranes and membrane-bound organelles
  • The Endoplasmic Reticulum is a 3-D network of double membranes enclosing a lumen. It is contiguous with the nuclear membrane. The rough ER has ribosomes for protein synthesis: proteins for export are extruded into the lumen. The smooth ER synthesizes other compounds such as lipids; it is also involved in drug detoxification.
  • Nuclear membrane: a double membrane enclosing the nucleus, sequestering the genome (chromosomes), contiguous with the ER and containing nuclear pores for entry and exit.

  • The Golgi apparatus is a smooth, double membrane system contiguous with the ER. It has a cis end near the ER and a trans end near the plasma membrane. Proteins synthesized on the rough ER transit through the Golgi and are modified by addition of sulfate, carbohydrate, and lipid. These tags, together with the structure of the protein itself, act as address labels that direct the modified protein to specific intracellular compartments or into membrane vesicles for export from the cell (a process called exocytosis).
  • Lysosomes: a single membrane enclosing digestive enzymes = acid pH optimum hydrolases
  • Peroxisomes: a single membrane enclosing oxidases and peroxidases, and free radicals
  • Mitochondria: double mebrane vesicle for energy transduction; contains its own DNA, RNA and ribosomes for mitochondrial protein synthesis; carries out oxidations by removal of electrons and H to reduce oxygen to H2O; conserves the energy of oxidation in the formation of ATP.
  • Chloroplasts: double membrane system for energy transduction; contains its own DNA. RNA and ribosomes; uses energy of the photon to synthesize chemical energy (ATP) at the same time oxidizing H2O to molecular O2 (the single most important reaction of the biosphere); also fixes CO2 to synthesize carbohydrate.

• Cytoskeleton: molecular motor; actin and myosin filaments; give the cell shape; provide for cytoplasmic streaming and the movement of vesicles and membrane systems.

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Bich 107 lecture notes on Cell Structure last updated 09/05/06

Comments to Martyn Gunn