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Chemistry: Atoms, Water, & Carbon
Transcript of Chemistry: Atoms, Water, & Carbon
Atoms & Bonds
What are these atoms of which we speak?
= The smallest fundamental unit of matter
(worth considering in biology)
Two simplistic models of atoms
There are ~120 different kinds of atoms ("
Biology is made of 4 major (
), ~10 minor, & ~30-50 trace elements
Bonding is accomplished by electrons interacting between atoms (due to
2 major kinds of bonds hold atoms together.
Energy & Atoms
interacts with atoms in different ways.
Energy holds e-'s to the nucleus.
When atoms absorb energy, e-'s are moved to
higher energy levels
The movement of e-'s back to
lower energy levels
releases energy (as
: Transfer of e-'s
Unstable in water. Dissolve.
: Sharing of e-'s.
Functionally infinite combinations.
All important biological molecules (eg
glucose, DNA) are covalently bonded
Compounds & Emergence
The properties of a compound can be very different from the properties of the elements that make them
Sodium: explosive metal
Chlorine: toxic gas
Delicious table salt!
: 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).
Not all bonds are created equal
The unequal sharing of electrons in a covalent bond
Leads to unequal distribution of
charge in the molecule
Polar Molecules are attracted to other polar molecules.
: The attraction between two different polar molecules.
Common in Biological Systems
All Chemical Reactions result in the breaking and forming of bonds.
In any reaction, mass, energy, and charge are conserved.
Bonds Determine Shape
...and shape is very, very important in Biology!
Structure & Function are ALWAYS related.
Atoms with unstable nuclei are "
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
It's a bad scene if you don't get your elements
" comes from too little iodine in the diet
Various nutrient defficiencies in plants
Now that we have all these atoms...
...Just what are we supposed to do with them?
Make Sure You Can
Because it is so polar, water can easily break apart.
This produces a
In pure water, the concentration of these ions is equal.
"- donate protons: [H3O+] > [OH-]
"- accept protons: [H3O+] < [OH-]
: a measure of acidity.
the -log of the [H3O+]
In all (aq) solutions [H3O+] x [OH-] = 10E-14
You should be able to calculate pH/pOH if given the [H3O+] or [OH-] concentration
pH & Biology
Biological systems can only tolerate a narrow range of pH.
Extreme variations in pH have bad effects at all levels of organization
The effect of ocean acidification on coral reef biodiversity:
Why is water such a big deal?
Water ice in the track of a Mars rover
Water is needed for life
The chemistry of life is a solution-based chemistry
The majority of any organism is water.
Earth is unique in its amount of liquid water
Water is one of the few substances that exists in all three phases at normal terrestrial conditions
Water's Unique Properties
There are many.
All of them are due to the
of water (and its resulting
Cohesion & Adhesion
: Sticking together
: Sticking to other things
Water is both. Why?
Is there anything that water can't stick to?
The cohesiveness of water gives it a very high
: The movement of water through trees. A BIG Deal!
A High 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!
Water as Temp.
Solid water is less dense than liquid water (weird!)
What would happen if the reverse were true?
Water is a great solvent!
There is no "
But water comes close (why?)
Is there anything water can't dissolve?
A large protein in solution
The dissolution of salt
Getting To Know
The Functional Groups
Biology = Carbon Based
1. It's abundant
2. It's versatile
It makes 4 bonds to get stable
This leads to infinite variety
There is nothing special about life's building blocks
Vitalism- belief in a "life force"
- theory that there is nothing special about how life is built.
Simulated Early Earth Conditions
Produced hydrocarbons, amino acids.
Organic Soup Model
- 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!
3 Kinds of isomers
Same formula, different order.
Same formula, different positioning
around a double bond.
Same formula, mirror image
positioning around a central carbon
Biological systems tend to use only one of any two enantiomeric forms.
All cells use
Can you explain why this is?
A little difference goes a long way!
modify the properties of organic molecules
The entire difference in the physical appearance of genders is due to the effects of these two hormones!
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?
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
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?
Make Sure You Can
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.
Make Sure You Can
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.
** Do not need for exam.