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Chemistry 1: Atoms, Water, & Carbon

Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license. Derived from content by David Knuffke
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Thomas Hattori

on 24 August 2015

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Transcript of Chemistry 1: Atoms, Water, & Carbon

Chemistry
Atoms & Bonds
Water
Carbon
What are these atoms of which we speak?
Atoms
= The smallest fundamental unit of matter
(worth considering in biology)
Two simplistic models of atoms
There are ~120 different kinds of atoms ("
elements
").

Biology is made of 4 major (
CHON
), ~10 minor, & ~30-50 trace elements
electrons (-)
Nucleus:
Protons (+)
Neutrons(0)
electron "orbitals"
electron "cloud"
Atoms Bond
Bonding is accomplished by electrons interacting between atoms (due to
valence
considerations).

2 major kinds of bonds hold atoms together.
Energy & Atoms
Energy
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
EM radiation
)
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
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!
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).
Not all bonds are created equal
Polarity
:
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.

Hydrogen Bonds
: The strongest attractions between the most 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.
Radioactivity
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
It's a bad scene if you don't get your elements
a "
goiter
" comes from too little iodine in the diet
Various nutrient defficiencies in plants
Water Dissociates!
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-]
pH
: 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:
Healthy Reef
Sick Reef
Dead Reef
Bleaching!
Why is water such a big deal?
Water ice in the track of a Mars rover
Any Questions?
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 the only 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
polarity
of water (and its resulting
hydrogen bonds
)
Why is Water Wet?
Cohesion
: Sticking together
Adhesion
: 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
surface tension
Transpiration
: The movement of water through trees. A BIG Deal!
A High Specific Heat
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!
Evaporative Cooling
Water as Temp.
Buffer
Ice Floats!
Solid water is less dense than liquid water (weird!)
Why?
What would happen if the reverse were true?
Water is a great solvent!
There is no "
universal solvent
"
But water comes close (why?)
Is there anything water can't dissolve?
A large protein in solution
The "
Hydration Shell
"
The dissolution of salt
Getting To Know
The Functional Groups
Biology = Carbon Based
Why Carbon?
1. It's abundant
2. It's versatile
Carbon is
tetravalent
.
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"

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)
Stanley Miller
Isomerism
Isomers
- Molecules with the same molecular formula, but different structures

Any molecule more complex than propane has at least one isomer.
3 Kinds of isomers
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
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?
About Enantiomers
A little difference goes a long way!
Functional Groups
modify the properties of organic molecules
Teststerone
Estrogen
The entire difference in the physical appearance of genders is due to the effects of these two hormones!
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