Basic Cellular Chemistry

Atom-The smallest unit that cannot be divided chemically (can be divided in other ways)
3 most important characteristics;

Name	Size	Location	Charge
Neutron	1 A.M.U.	Nucleus	0
Proton	1 A.M.U.	Nucleus	+
Electron	----------	Orbitals	-

1AMU=1 dalton=1.7x10 -23
Electron = 1/2000 dalton
in an atom there is an electrical balance
atomic number = # of protons and therefore #electrons
atomic mass = # of protons + # of neutrons

Orbitals - location of electron around the nucleus

Orbitals are stacked into energy shells

Shell	# of orbitals	# of electrons
1	1	2
2	4	8
3	4	8

Atoms react to fill their outer shell (octet rule, typically more than1 orbital)

Atoms are like small children regarding electrons

Isotopes - Atoms of an element with different numbers of neutrons i.e. same atomic number different atomic mass

Radioactive isotopes, nuclei lose particles
Can be used for:
-Diagnostic studies (imagery)
-Tracers
-Disease cures
-Radioactive dating i.e. Carbon 14 has a half life of 5 600 yrs

Molecules
Types of Atomic bonds
1. Ionic -and atom steals 1 or more electrons from another atom (therefore the electrical charges of the protons and electrons are no longer balanced) this creates positive and negative ions. Ions of opposite charge are electrically attracted
2. Covalent- 2 or more atoms share electrons
-Equal sharing- non-polar, no charge across the molecule
-unequal sharing creates a charge across the molecule (it is polar), a polar covalent bond
covalent bonds are stronger bonds because they are physically sharing mass
3. Hydrogen bonding-this weak bond creates a slightly positive hydrogen, due to a polar covalent bond, electrically attaches to anything negative this usually happens when H bonds to O, N or F.

Water properties
1 a polar molecule = Oxygen (-) and 2 Hydrogens (+)
2 105 degree bond not 90 degrees allows water to bond to many things at once.
3 cohesion - water to water( H bonding between 2 water molecules)
-Liquid form 0 to 100 degrees C
-high specific heat - water does not change temperature easily
-1 cal the amount of energy it takes to raise 1 gm of water up 1 degree
-Cal or Kcal =1 000cal
-1cal= 4.184 joule (j)
-high heat of vaporization- 540 cal/gm
-heat of fusion - 80 cal/gm to take 1gm below 0 C gives off heat
- capillary action- waters ability to climb a tube (also uses adhesion)
- surface tension - water molecules at the surface have a higher affinity for each other than air, this creates a "film"
4 Maximum density 4 degrees C - molecules are closest together - to close and molecules repel( causes insulation)
5 Adhesion- water to others + cohesion water to water adds to capillary action
-universal solvent except lipids (fats waxes and oils)
-breaks ionic bonds

Solution Terminology
solution is a homogenous mixture of 2 or more substances that look and act as one
solvent-is the dissolving agent
solute-is the substance being dissolved
aqueous solution-solution with water as the solvent
hydrophillic-dissolves in water- water loving
hydrophobia-does not dissolve in water-water hating

pH = -log[H+]

measure of acidity- anything that gives off a hydrogen ion is and acid H+
anything that releases OH (hydroxy) more that H+ is a base
7 is neutral = # of H+ = OH-
it is a logorythmic scale

Biological Molecules = organic chemistry

Monomers- 1 part molecules (ex. a sugar)

Polymers-many part molecules (ex. a large carbohydrates) made through condensation (dehydration) reactions. Breaking down polymers is called Hydrolysis - giving the H and OH back to the monomers

Carbohydrates-sugars and sugar polymers with a ratio of C1:H2:O1
The function of carbohydrates is energy storage and structural molecules (plant cell walls are made of celulose a carbohydrate)

monosaccarides-1 sugar carbohydrates a monomer that others are made of
-3 carbon minimum
-ex. glucose, fructose, lactose
disaccarides- 2 sugar carbohydrate
-sucrose= 1 glucose + 1 fructose (table sugar)
-maltose= 2 glucose (grain sugar)
-lactose= 1 glucose + 1 galactose (milk sugar)

polysaccarides- many sugars
-greater that 20 sugars typically hundreds
-commonly called starch
-linkage between sugars is critical

cellulose- major component in the cell walls of plants
glycogen- animals make this starch for energy (stored in the liver)

Proteins
Proteins are the biological polymers of Amino Acids
-20 unique amino acids joined with bonds -C-N-C-
-C-N-C is a peptide bond
-poly peptide with N not O covalent bond
- 3 positive soluble or hydrophillic
- 2 negative hydrophillic
- 6 hydrophillic
- 8 hydrophobic
- cystine forms sulpher bonds

Proteins
4 levels of protein structure
primary structure- sequence of the amino acids (altering the primary sequence totally changes the amino acid)

secondary structure- typically a type of helix, allows for hydrogen bonding
tertiary structure- folded back on itself makes a reactive 3D structure
quaternary structure - aggregate of two or more peptides interlocking or interfolding gives it the ability to react with other parts of itself.

Denature-a proteins perminent change in shape
-extremes of pH and temperature in relation to the protein

function of proteins
structural-collegen , keratin
enzymes- run chemical reations
antibodies
toxins-snake venom
cytochromes- transport electrons
transport across membranes
ferritin-stores iron in spleen
hemoglobin
actin & myosin- muscle contractions

Lipids

-all lipids are hydrophobic but may not be structurally similar
-fats, oils, waxes -triglycerides
-fats- solid at room temp
-wax- has a higher melting point ( kanuba best wax, highest melting point)
phospholipids

Steriods have a 4 ring structure
Terpenes certain types of pigments (retina)

Saturated- higher melting point saturated with hydrogen, harder to digest, has a straight matrix
Unsaturated- C=C double bond (oleic acid) tails bend, lowers melting point, easier to metabolize
Polyunsaturated-many double bonds many C=C double bonds

Steriods
1used to produce bile- helps in digestive process , to digest other lipids
2 produces vitamin D-needed for bone developement
3used to produce sex hormones
4 keeps membranes permeable
phospholipids-slight charge makes the head attracte4d to water-tails are tatty acid allwas orient themsteves in double layered sheets makes the basic structure of a cell membrane

Nucleic acids

Polymers of nucleotides

Ribose-RNA Nucleotides=sugar always ribose , nitrogen base
Deoxyribose-DNA=sugar sides are always anteparalell

Specific functions of DNA

-herditary direction
controlls all cellular activites- determines protein synthesis

ATP- Adenosine Triphosphate - the energy tranfer (currency) that cells have to use or convert to be able to use for energy
ADP- Adenosine Diphosphate- gives off enery by gleaning off the 1 Phosphate group

Origins of life-

Earth is 4.6-4.8 billion years old

Why here?
1. correct size to hold and atmosphere
2. proper distance from the sun to keep water liquid
3. proper raw elements to build biological molecules

charecteristics of the primative atmosphere

-carbon monoxide, carbon dioxide, water vapor, sulfur dioxide, nitrogen, methane, ammonia, little or no oxygen

reducing atmosphere
reduce-add H+ or e- to an atom or molecule
monomers produced naturally

oxydation-remove H ions and electron oxygen is a powerful mover of electrons
(these are opposites someone gets -can't have one without the other oxidation/reduction reaction)

Monomers form polymers need a matrix like clay to be able to keep the polymer from makin a loop Clay holds small polymers to make big polymers called microspheres or protobionts
These can increase mass, divide and perform 1 or 2 step pathways, may run small chemical reations has no genetic material. Needs a self replicating system/molecule.

DNA => RNA => Protein

RNA- World theory

1. Easier to produce Protein
2. Smaller and simpler than DNA(2.9 billion base pairs)
3. Some RNA can self replicate

years ago first fossil evidences of cells- Prokaryote
they were heterotrophic-( other feeder) feeding on the environment
and they were anaerobic-without oxygen- less efficient than an aerobic metabolizm

Photosynthesis-3.8 billion years ago has a competitive advantage may have evolved in a microsphere- by product is that it produces oxygen.

2.5 years ago atmosphere becomes oxydizing( to remove the H+ or e- from an atom or molecule) creates oxygen

1.5 bya oldest Eukaryote fossils from prokaryotes via endosymbiosis.

Endosymbiosis-(inside relationship) highly evolved relationship between two organisms
-all multicellular organisms are Eukaryotes and have a division of labor (plants, fungi etc.)

Hydrogen Hypothesis (a new spin on endosymbiosis and eukaryote origins)
Catagorize groups of organisms

Domain Eubacteria-Prokaryote cells
DomainArchea or Archeabacteria-does things slightly different , very different from Eubacteria
Domain Eukarya-
-mitochondria(most)- Aerobic, organic molecules and generates ATP
-hydrogenosomes-Anaerobic- takes Carb (pyruvate)into ATP this process gives off Hydrogen, Acetate Carbon Dioxide
-intercellular parasites (vary rare) Neither

-cells with hydrogenosomes are seen with methanogens metagen feeds on Carbon Dioxide, Hydrogen and acetate -producing methat

Hydrogenosomes and Mitochondria have a common origin through endosymbiosis and the "host " cell was a Archeon- could be the precurser to the Eukaryote cells

Main argument in the last few years is wheter or not the Pre Eukaryote posses a nucleas (prior to this new discussion called the hydrogen hypothesis)

1. An Archeon unable to break down organic molecules(needs a non biological source of Hydrogen, Carbon Dioxide and Acetate) would be attracted to the Eubacteriun that gives off all three
2. As they mave to areas w/out natural sources of H, CO2 and Acetate the Archeon dependant on the Eubacteria so it holds on
3. If the Archeon would completely engulf the Eubacteria cutting off the organic molecule supply to do this the Archeon must "learn " to feed the Eubacteria. Probably by stealing the Genes from the Eubacteria. O, M converted into pyruvate.

Now the Eubacteria is dependant on the Archeon

4. If Oxygen is present the Eubacteria becomes a Mitochondria , If no Oxygen is present the Eubacteria becomes a Hydrogenosome.
5. This merging produced the need to form a nucleus and cytoskeliton (Eukaryote cell)

Evidence
1. Few Eukaryotes w/ hydrogenosomes like oxygen poor environments(mitochondria like oxygen)
2. Trichonomads-Anaerobic, no mitochondria but have the Hydrenosomes , they have genes similar to those used by the mitochondria and the protein they produce are used in the Hydrogenosomes
3. Microsporide and Diplomonads( single cellular Eukaryotes intercellular parasites) also have mitochondrial genes(had the precurser but shed it with the parasitic life style (vestigial or leftover)
4. These two organells have in common the Archeon bacteria precursor to Eukaryote cells.

Cells-general
Robert Hooke invented the first light microscope while usung the refractive lenses wanted to know why cork floats. He saw the cell walls of the dead cork bark and called them cells after the monastery cubicles they lived in
Ancient Greeks documented a theory of cells smaller parts or units
Cell Theory came form Schleidon and Schwann (Schwann cells)
Schleidon saw a botanist and Schwann was an animal biologist. They thought that all cells more or less looked alike

Cell Theory
1. a cell has three things, 1 cell membrane, 2 genetic material (DNA) 3 cytoplasm (living matrix that is very reactive)

2. All organisms are made of cells and cell products (Hair, fingernails, ligaments tendons bones etc.)

3. All cells come from preexisting cells ( at that time period this was considered blasphemy and you would be killed for saying things like this)

4. All activities of a multicellular organism are cellular in origin, ( movement, muscle cells starts on a cellular level, only the correct ones are used- highly organized cellular activity)

Prokaryote-(before + nucleus) primitive type oldest fossil type is 3.9 bya
Domain Archea-Archeabacteria(has RNA cell wall Gly attachments)
Domain Eubacteria-true bacteria, bacteria, cyanobacteria(blue-green Algae)
Characteristics of Prokaryote cells
1. No nucleus
2. DNA in a single circular strand(252 unique types of protein) will not form a chromosome)
3. No membrane bound organelles (have organelles not surrounded by membrane)
4. Ribosomes(assemble aminos to make protein)are smaller than Eukaryotes by 25%
Not attached to a membrane, are free floating
5. The cell wall is Peptidoglycan
-no cellulose (different origins not plant material which is a structural carbohydrate
6. May or may not have a flagella the structure is solid if divided end to end .

Eukaryote cells- true nucleus
Eu -true Karyote-Nucleus

-an advanced condition - oldest fossil evidence is 1.5 bya (fairly new)
-All multicellular organisms with a division or labor (specializing)

Domain eukaryote
Kingdoms(4, at least)

Plantae
Animalia
Micota
Protoctista-Protozoa

Characteristics of a Eukaryote cell

1. Nucleus- contains/protects the DNA
2. DNA in strands assoc. With proteins called chromatin, that will form chromosomes during division. (miles of DNA strand will wrap around a protein that is what is called a chromosome) also the number and size of the DNA strand does not determine the complexity of the result.
3. Has various membrane bound organelles
4. Ribosomes are large may or may not be attached to a membrane 25% larger than Prokaryote
5. May or may not have cell wall usually with cellulose
6. May or may not have a flagella with a 9+2 arrangement of microtubes (protein rods running through the flagella)

Cell membranes
1 contains the cell
2 protects the cell ( flexible, is not rigid, fluid)
3 regulates transport in and out of the cell, selectively permeable
phospholipids are the base structure of a membrane, with proteins scattered throughout as receptors cholesterol found in all cell membranes helps keep the membrane fluid and permeable( no cholesteral free diets)
glycocalyx- covering on the outside sugar (important in recognition) glycoprotein, glycolipids(last four terminationg sugars) wrong ones can give you a imune response and can kill you if given the wrong blood type
extracellular matrix- optional common in animals cells not found in plant cells
protein fibers attach the proteins to the membrane some proteins can move, some have to move to function

Molecular Transport
Passive mechanizms- cell does not expend energy for transfer to occur (it happens naturally)
-diffusion- random movement (bumper cars) natural ricocheting makes them tend to move from high concentration to low concentration. (Perfume) will occur until they reach a point of equilibrium, then collisions stop.(the only way to stop atoms and molecules from moveing completely is to drop the temperature to absolute zero(0 kelvin)
or (@-273 degrees Celcius) coldest place on the planet is in the physics lab in Gainsville. Must be insulated against the footssteps of other students in other buildings they are so temperature sensitive.
Osmosis- diffusion of water across a membrane from a higher concentration to a lower consentration of water. Biologically speaking for water only.