Unit 1 emergent properties Atoms, Water, & Carbon

A measure of the strength of attraction of one atom for the valence electrons of another atom.

Importance of EN

EN determines polarity

Polarity determines how molecules will interact

slippery or sticky

Polarity:

The unequal sharing of electrons

Leads to unequal distribution of

charge in the molecule

Polar Molecules are attracted to other polar molecules. (sticky)

Non-Polar Molecules are not attracted to any other molecules (slippery)

Hydrogen Bonds: The strongest attractions between the most polar molecules.

Chemistry

Now that we have all these atoms...

Kabloom!

...Just what are we supposed to do with them?

Carbon

Atoms & Bonds

Water

Biology = Carbon Based

Why is water such a big deal?

Water ice in the track of a Mars rover

Big Questions

What is matter? Where does it come from?

How do atoms interact with each other?

Explain how the interactions of atoms lead to the emergence of the molecules 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?

Any Questions?

A High Specific Heat

Radioactivity

There is nothing special about life's building blocks

Why Carbon?

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?)

Energy & Atoms

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!

Water as Temp. Buffer

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

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)

Evaporative Cooling

Ice Floats!

Cohesion & Adhesion

Stanley Miller

Transpiration: The movement of water through trees. A BIG Deal!

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?

The cohesiveness of water gives it a very high surface tension

Atoms Bond

Compounds & Emergence

Water is needed for life

Isomerism

3 Kinds of isomers

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

occurs b/w metal and non-metal

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

What are these atoms of which we speak?

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)

Delicious table salt!

Sodium: explosive metal

Chlorine: toxic gas

About Enantiomers

electrons (-)

electron "orbitals"

electron "cloud"

There are ~120 different kinds of atoms ("elements").

Biology is made of 4 major (CHON), ~10 minor, & ~30-50 trace elements

Nucleus:

Protons (+)

Neutrons(0)

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?

Two simplistic models of atoms

Water's Unique Properties

It's a bad scene if you don't get your elements

Electronegativity

Various nutrient defficiencies in plants

a "goiter" comes from too little iodine in the diet

There are many.

All of them are due to the polarity of water (and its resulting hydrogen bonds)

Getting To Know

The Functional Groups

All Chemical Reactions result in the breaking and forming of bonds.

A little difference goes a long way!

pH & Biology

Water is a great solvent!

Functional Groups modify the properties of organic molecules

Bonds Determine Shape

Make Sure You Can

The dissolution of salt

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?

A large protein in solution

Teststerone

Estrogen

The effect of ocean acidification on coral reef biodiversity:

...and shape is very, very important in Biology!

Structure & Function are ALWAYS related.

In any reaction, mass, energy, and charge are conserved.

The "Hydration Shell"

Bonds b/w atoms of the same element are

non-polar covalent.

Bonds between atoms of different elements are usually polar covalent.

important exception: C-H

Water Dissociates!

Bleaching!

Healthy Reef

Sick Reef

Dead Reef

The entire difference in the physical appearance of genders is due to the effects of these two hormones!

Any Questions?

Make Sure You Can

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.

• 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

Not all covalent bonds are equal