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What is matter? Where does it come from?
How do atoms interact with each other?
How do the interactions of atoms lead to the emergence of the raw materials necessary for life?
Why are you mostly made of water?
How does water function in biological systems?
How does the structure of water determine its properties?
Why is Carbon a fundamental atom in biological systems?
How does the structure of carbon allow for functionally infinite complexity in the structure of molecules that contain it?
Atoms with unstable nuclei are "radioactive"
Radioactive atoms spontaneously emit high energy particles until stability is reached.
Excess radiation is damaging to biological systems (why?)
Radiation is used in biology as molecular labels
1. It's abundant
2. It's versatile
Specific heat:
How much heat is absorbed/released before an increase/decrease in temp.
Water: 4.18 J/g C
Ethanol:1.24 J/g C
Iron: 0.449 J/g C
Why so high?
So what? Big What!
Energy interacts with atoms in different ways.
Vitalism- belief in a "life force"
Mechanism- theory that there is nothing special about how life is built.
Stanley Miller:
Simulated Early Earth Conditions
Produced hydrocarbons, amino acids.
So long vitalism (at least as far as molecules go)
Carbon is tetravalent.
It makes 4 bonds to get stable
This leads to infinite variety
Cohesion: Sticking together
Adhesion: Sticking to other things
Water is both. Why?
Is there anything that water can't stick to?
Solid water is less dense than liquid water (weird!)
Why?
What would happen if the reverse were true?
Earth is unique in its amount of liquid water
The properties of a compound can be very different from the properties of the elements that make them
Bonding is accomplished by electrons interacting between atoms (due to valence considerations).
2 major kinds of bonds hold atoms together.
The chemistry of life is a solution-based chemistry
The majority of any organism is water.
Emergence: increasing levels of complexity in a system can demonstrate novel properties not seen in the levels below them.
Shows up repeatedly in science (especially in biology).
Ionic Bonds: Transfer of e-'s
Not many possible combinations.
Kind of boring.
Covalent Bonds: Sharing of e-'s.
Functionally infinite combinations.
All important biological molecules
(eg. glucose, DNA) are covalently
bonded.
Structural-
Same formula, different order.
Cis-Trans-
Same formula, different positioning
around a double bond.
Enantiomers-
Same formula, mirror image
positioning around a central carbon
Isomers- Molecules with the same molecular formula, but different structures
Any molecule more complex than propane has at least one isomer.
Isomerism is another example of an emergent property!
Water is one of the few substances that exists in all three phases at normal terrestrial conditions
Atoms = The smallest fundamental unit of matter
(worth considering in biology)
There are ~120 different kinds of atoms ("elements").
Biology is made of 4 major (CHON), ~10 minor, & ~30-50 trace elements
Biological systems tend to use only one of any two enantiomeric forms.
All cells use D-sugars, and L-amino acids
Can you explain why this is?
It's a bad scene if you don't get your elements
There are many.
All of them are due to the polarity of water (and its resulting hydrogen bonds)
Polarity:
The unequal sharing of electrons in a covalent bond
Leads to unequal distribution of
charge in the molecule
Functional Groups modify the properties of organic molecules
Biological systems can only tolerate a narrow range of pH.
Extreme variations in pH have bad effects at all levels of organization
There is no "universal solvent"
But water comes close (why?)
Is there anything water can't dissolve?
Polar Molecules are attracted to other polar molecules.
Hydrogen Bonds: The strongest attractions between the most polar molecules.
Common in Biological Systems
In any reaction, mass, energy, and charge are conserved.
...and shape is very, very important in Biology!
Structure & Function are ALWAYS related.
The entire difference in the physical appearance of the sexes is due to the effects of these two hormones!
Because it is so polar, water can easily break apart.
This produces a hydronium (H3O+) and hydroxide (OH-) ion.
In pure water, the concentration of these ions is equal.
"Acids"- donate protons: [H3O+] > [OH-]
"Bases"- accept protons: [H3O+] < [OH-]
Explain how the structure of the Carbon atom leads to the emergence of complexity in carbon containing compounds
Identify all of the functional groups discussed in this presentation.
Explain how each of the functional groups discussed contributes to the properties of the molecules that contain them.
Explain why water is necessary for biological systems.
Explain why water is polar
Draw a water molecule, assign polarity to the different atoms of the molecule, and show how water molecules hydrogen bond with each other.
Explain how each of the properties of water discussed in this presentation are a function of water's polarity/its capacity for hydrogen bonding.
Provide two examples of how each of the properties of water discussed in this presentation are used by organisms to maintain their homeostasis.
Identify different elements and explain how they are different from each other.
Explain the processes of ionic and covalent bonding and why they occur.
Explain why a compound demonstrates emergent properties.
Compare polar and non-polar bonds and describe how they affect the substances that they occur in.
Explain the relationship between bonding, shape and function of molecules.
Provide some examples of the uses of radioactive isotopes in biology
pH: a measure of acidity.
You should be able to calculate pH/pOH if given the [H3O+] or [OH-] concentration