Chapter 1.1: Introduction to Cell biology

A. What is a cell - Water, carbon, elements.

B. Size of Cells.

C. What is the difference between elements?

D. What is living?

E. What is interesting about Cell biology?

---

What is a cell?

Cells are structural units that make up plants and animals, also there many single cell organisms. What cells all have in common is they are small 'sacks' composed mostly of water. The 'sacks' are made from a phospholipid bilayer (which will be explained in detail in chapter 2). The membrane is semi-permeable (allowing some things to pass in or out of the cell and blocking others), there are also other methods of transport that we will get into later.

So what is in a cell? The cell as we mentioned is a fluid like membrane that surrounds the contents of the cell. Each component will be discussed in more detail later.

Cells are 90% fluid (cytoplasm) which consists of free amino acids, proteins, glucose, and numerous other molecules. The cell environment (ie. the contents of the cytoplasm, and the nucleus, as well as, they way the DNA is packed) affect the gene expression/regulations, and thus are VERY important parts of inheritance, below are approximations of other
components:

Elements:

59% Hydrogen (H)

24% Oxygen (O)

11% Carbon (C)

4% Nitrogen (N)

2% Others - Phosphorus (P), Sulphur (S), etc.

As far as molecules that make up the cell:

50% protein

15% nucleic acid

15% carbohydrates

10% lipids

10% Other

A picture of a cell:

What is inside the cell is the cytoplasm which is:

Cytosol - a lot of water - it is everything except the organelles.

Organelles (which also have membranes) in 'higher' eukaryote organisms:

Nucleus (in eukaryotes) - where genetic material (DNA) is located, RNA is transcribed.

Endoplasmic Reticulum (ER) - Important for protein synthesis. It is a transport network for

molecules destined for specific modifications and locations.
There are two types:

Rough ER - has ribosomes, and tends to be more in 'sheets'.

Smooth ER - Does not have ribosomes and tends to be more of a tubular network.

Ribosomes - half are on the Endoplasmic Reticulum, the other half are 'free' in the cytosol, this is

where the RNA goes for translation into proteins.

Golgi Apparatus - important for glycosylation, secretion.

Lysosomes - Digestive sacks - the main point of digestion, these are only found in animal cells.

peroxisomes - Use oxygen to carry out catabolic reactions, in both plant and animals.

Microtubules - made from tubulin, and make up centrioles,cilia,etc.

Cytoskeleton - Microtubules, actin and intermediate filaments.

Mitochondria - convert foods into usable energy. (ATP production) A mitochondrion does this through aerobic respiration. They have 2 membranes, the inner membranes shapes differ between different types of cells, but they form projections called cristae. The mitochondrion is about the size of a bacteria, and it carries its own genetic material and ribosomes.

Vacuoles - More commonly associated with plants. Plants commonly have large vacuoles.

Found in Plants and not in animals:

Plastids - minute granules found in plant cells which have their own membrane, ribosomes

and DNA. The most commonly know is the chloroplast.

Chloroplasts - convert light/food into usable energy. (ATP production)

Cell Wall - found in prokaryotic plants and it provides structural support and protection.

---

Size of Cells

Eukaryotes are typically 10 times the size of prokaryotic cells. Plant cells are on average some of the largest cells, which may be because of the large water filled vacuoles in some plant cells.

So, you ask, what are the relative sizes of biological molecules and cells?

These are all approximations:

Small

0.1 nm (nanometer) diameter of a hydrogen atom

0.8 nm Amino Acid

2 nm Diameter of a DNA Alpha helix

4 nm Globular Protein

6 nm microfilaments

10 nm thickness cell membranes

11 nm Ribosome

25 nm Microtubule

50 nm Nuclear pore

100 nm Large Virus

200 nm Centriole

200 nm (200 to 500 nm) Lysosomes

200 nm (200 to 500 nm) Peroxisomes

1 um (micrometer)

(1 - 10 um) the general sizes for Prokaryotes

1 um Diameter of human nerve cell process

2 um E.coli - a bacterium

3 um Mitochondrion

5 um length of chloroplast

6 um (3 - 10 micrometers) the Nucleus

9 um Human red blood cell

10 um

(10 - 30 um) Most Eukaryotic animal cells

90 um Amoeba

100 um Human Egg

1 mm (1 millimeter, 1/10th of a centimeter)

1 mm Diameter of the squid giant nerve cell

2 mm Diameter of a frog egg

Large

---

What is the difference between elements/compounds?

The various elements that make up the cell are:

59% Hydrogen (H)

24% Oxygen (O)

11% Carbon (C)

4% Nitrogen (N)

2% Others - Phosphorus (P), Sulphur (S), etc.

The difference between these elements is their respective weights, electrons and in general their properties. A given element can only have so many other atoms attached. For instance carbon (C) had 4 electrons in its outer shell and thus can only bind 4 atoms, Hydrogen only has 1 electron and thus can only bind to one other atom. An example would be Methane which is CH4. Oxygen only has 2 free electrons, but will some times form a double bond, which is a 'ester' (which typically smell good or bad).

   Methane    Water   Methanol (Methyl Alcohol)
   -------    -----   -------------------------
      H       H   H      H
      |        \ /       |
    H-C-H       O      H-C-O-H
      |                  |
      H                  H

As far as molecules that make up the cell:

50% protein

15% nucleic acid

15% carbohydrates

10% lipids

10% Other

Here is a list of Elements, symbols, weights and biological roles.

ELEMENT (Symbol)Atomic Weight   Biological role

Calcium   (Ca)  40.1            Bone; muscle contraction
Carbon    (C)   12.0            Constituent(backbone) of
                                organic molecules
Chlorine  (Cl)  35.5            Digestion and photosynthesis
Copper    (Cu)  63.5            Part of Oxygen-carrying
                                pigment of mollusk blood.
Fluorine  (F)   19.0            For normal tooth enamel
                                development
Hydrogen  (H)    1.0            Part of water and all organic
                                molecules
Iodine    (I)  126.9            Part of thyroxine (a hormone)
Iron      (Fe)  55.8            Hemoglobin, oxygen caring
                                pigment of many animals
Magnesium (Mg)  24.3            Part of chlorophyll, the photo-
                                synthetic pigment; essential
                                to some enzymes.
Manganese (Mn)  54.9            Essential to some enzyme actions.
Nitrogen  (N)   14.0            Constituent of all proteins and
                                nucleic acids.
Oxygen    (O)   16.0            Respiration; part of water; and
                                in nearly all organic molecules.
Phosphorus(P)   31.0            High energy bond in ATP.
Potassium (K)   39.1            Generation of nerve impulses.
Selenium  (Se)  79.0            For the working of many enzymes.
Silicon   (Si)  28.1            Diatom shells; grass leaves.
Sodium    (Na)  23.0            Part of Salt; nerve conduction
Sulfur    (S)   32.1            Constituent of most proteins.
                                Important in protein structure:
                                Sulfide bonds are strong.
Zinc      (Zn)  65.4            Essential to alcohol oxidizing
                                enzyme.

---

What is living?

This is a topic that is been of many long discussions and it depends on your initial definitions. Some definitions are:

1. The quality that distinguishes a vital and functional being from a

dead body or purely chemical matter.

2. The state of a material complex or individual characterized by the
capacity to perform certain functional activities including metabolism,
growth, and reproduction.

3. The sequence of physical and mental experiences that make up the
existence of an individual.

Under these varying definitions life may or may not include a virus that is only 'alive' if it can insert its genetic material into a living cell. To me live is the substance that can react to its environment, grow, improve and reproduce. To have less of a definition would include to much to have more would not include some cells.

---

What is interesting about Cell biology?

What makes cell biology particularly interesting is that there is so much that is not understood. Cells are a complex system in and of themselves. And when you add to a individual cell its environment, whether that is the single celled organism or multicellular, there is a complex web reactions. One organism, like the human, can have the same genetic material in every cell, yet, there are over 200 types of cells in the human, that are different shapes, sizes and and carry out very different functions. And ALL of these cells were developed from 1 (one) cell.

Food for thought - to be discussed in the final chapters.

Biology is the understanding of complex systems. Which is how in basic terms how we get a functional system when things tend to move toward lower energy states. For example, if you took food scraps and left them in a compost pile they cells and proteins would break down to more basic compounds. The system maintains and generates new proteins. Without constantly breaking down and building new proteins, enzymes, DNA, cells, the larger system would
break down.

Complexity - A cell is more like a balanced eco-system then a simple unit.

inter-relations of cells - between cells in multi-cellular or organisms
there is communication, exchanges of information and needed resources.
(like a red blood cell bringing oxygen, other cells producing a hormone,
or one bacterium transferring a plasmid to another).

Intra-relations of a cell - Within a cell organelles, gene expression
work together to maintain the cell.

The cell and its environment - The environment around the cell influences
and is required at times how, when or if a gene is expressed. It is not
as simplistic as the 'gene' causes A or B, it is the entire cell, the cells
around and the larger environment.

Its ability to Live and reproduce.

Its ability to grow and change.

It is what makes up you and the food you eat.

---

Please send questions/comments/suggestions to: Mark Dalton at markwdalton@gmail.com.