Atoms, Bonds, and Molecules

What is “stuff” made of?

Atoms and Bonds

I. Atoms

A. Matter

    1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions.

Atoms and Bonds

I. Atoms

A. Matter

    1. ‘Elemental’ forms of matter, or ‘the elements’, are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions. There are 92 naturally occurring elements…

Atoms and Bonds

I. Atoms

A. Matter

    1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions.

    2. The smallest unit of an element that retains the properties of that element is an atom.

Atoms and Bonds

I. Atoms

A. Matter

    1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions.

    2. The smallest unit of an element that retains the properties of that element is an atom.

3. Atoms are WICKED SMALL and are mostly SPACE. The material ‘things’ in atoms are protons and neutrons in the nucleus, orbited by electrons:

Proton: in nucleus; mass = 1, charge = +1 - Defines Element

Neutron: in nucleus; mass = 1, charge = 0

Electron: orbits nucleus; mass ~ 0, charge = -1

NOT TO SCALE

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

1. Subatomic Particles

Proton: in nucleus; mass = 1, charge = +1 - Defines Element

Neutron: in nucleus; mass = 1, charge = 0

Electron: orbits nucleus; mass ~ 0, charge = -1

Orbit at quantum distances (shells)

Shells 1, 2, and 3 have 1, 4, and 4 orbits (2 electrons each)

Shells hold 2, 8, 8 electrons = distance related to energy

Neon (Bohr model)

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

1. Subatomic Particles

2. Mass = protons + neutronsO

8

15.99

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

1. Subatomic Particles

2. Mass = protons + neutrons

3. Charge = (# protons) - (# electrons)...

If charge = 0, then you have an ...ION

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

4. Isotopes -

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

4. Isotopes - 'extra' neutrons... heavier

Some are stable

Some are not... they 'decay' - lose the neutron

These 'radioisotopes' emit energy (radiation)

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

4. Isotopes - 'extra' neutrons... heavier

Some are stable

Some are not... they 'decay' - lose protrons/neutrons

These 'radioisotopes' emit energy (radiation)

So, K40, with 19 protons and 21 neutrons, decays to Ar40 (18 protons, 22 neutrons) with the conversion of a proton into a neutron. As neutrons weigh slightly less than protons, the mass that is lost in this conversion is lost as energy

(E = mc2)

Atoms and Bonds

I. Atoms

A. Matter

B. Properties of Atoms

4. Isotopes - 'extra' neutrons... heavier

Some are stable

Some are not... they 'decay' - lose the neutron

These 'radioisotopes' emit energy (radiation)

This process is not affected by environmental conditions and is constant; so if we know the amount of parent and daughter isotope, and we know the decay rate, we can calculate the time it has taken for this much daughter isotope to be produced.

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

    1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles.

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

    1. atoms chemically react with one another and form molecules - the atoms are "bound" to one another by chemical bonds - interactions among electrons or charged particles.     2. Bonds form because atoms attain a more stable energy state if their outermost shell is full. It can do this by loosing, gaining, or sharing electrons.  This is often called the 'octet rule' because the 2nd and 3rd shells can contain 8 electrons.

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

B. Covalent Bonds - atoms are shared

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

B. Covalent Bonds - atoms are shared

C. Ionic Bond - transfer of electron and attraction between ions

ClNa

Atoms and Bonds

I. Atoms

II. Bonds

A. Molecules

B. Covalent Bonds - atoms are shared

C. Ionic Bond - transfer of electron and attraction between ions

D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

D. Hydrogen Bonds - weak attraction between partially charged hydrogen atom in one molecule and a negative region of another molecule

Biologically Important Molecules

Biologically Important Molecules

I.Water

Biologically Important Molecules

I.WaterA. Structure

- polar covalent bonds

Biologically Important Molecules

I.WaterA. Structure

- polar covalent bonds

Biologically Important Molecules

I.WaterA. Structure

- polar covalent bonds - partial charges

Biologically Important Molecules

I.WaterA. Structure

- polar covalent bonds - partial charges - hydrogen bonds

I. WaterA. StructureB. Properties

- 1. cohesion“water sticks to itself through H-bonds”

I. WaterB. Properties - 2. adhesion

“water sticks to other charged surfaces”

I. WaterB. Properties - consequences of cohesion/adhesion

Capillary action – rotating water water molecules stick to the inner surface of thin tubes, and act as a fulcrum for other water molecules that can spin and contact the surface above them… through cohesion, those in contact with the new surface are themselves a surface for now water molecules to attach.

- important in the mvmt of soil water up from the water table to the root zone, and up vascular plants in xylem tissue.

I. WaterB. Properties - 3. High specific heat

‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories).

I. WaterB. Properties - 3. High specific heat

‘specific heat’ is the amount of energy change required to change the temperature of 1 g of that substance 1oC. By definition, a calorie is a change in heat energy needed to change 1ml (or g) of water 1oC. (Dietary “calories” are usually kilocalories).

Water has a high specific heat because of the hydrogen bonds, which must be broken before the molecules can move faster (increase temperature).

I. WaterB. Properties - consequences of water’s high specific heat

Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution).

I. WaterB. Properties - consequences of water’s high specific heat

Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution).

So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…)

I. WaterB. Properties - consequences of water’s high specific heat

Water is an excellent thermal buffer - aqueous solutions change temperature more slowly than air (less dense aqueous solution).

So, aqueous environments are more thermally stable (air temps vary more dramatically than water temps…)

So, terrestrial organisms change temperature more slowly than the environment, giving them time to adjust behaviorally (like leaving!)

I. WaterB. Properties - 4. High heat of vaporization

Quantity of heat a liquid must absorb for 1 g of it to change to a gas.

Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy

without changing state.

I. WaterB. Properties - 4. High heat of vaporization

Quantity of heat a liquid must absorb for 1 g of it to change to a gas.

Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy

without changing state. - when it does change state, the most energetic molecules

evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling.

I. WaterB. Properties - 4. High heat of vaporization

Quantity of heat a liquid must absorb for 1 g of it to change to a gas.

Water’s high heat of vaporization means that: - water doesn’t change state quickly; it can absorb a lot of energy

without changing state. - when it does change state, the most energetic molecules

evaporate and leave the liquid (or surface); so the average kinetic energy (temperature) of the liquid or surface drops dramatically – this is evaporative cooling.

- evaporative cooling keeps water bodies cooler than air, and cools living organisms (evapotranspiration, perspiration).

I. WaterB. Properties - 6. solvent

Ionic and polar compounds dissolve in water

Salts dissolve in water when their constituent ions separate and bond to water molecules instead of each other.

I. WaterB. Properties - 7. Water dissociates

Although the H+ is always bound to another water molecule (as a hydronium ion), we represent it (H+) and it’s concentration as if it is ‘free’. In pure water, the concentration is 1 x 10-7.

I. WaterB. Properties - 7. Water dissociates

In all aqueous solutions at 25oC,The product of [H+][OH-] = 1 x 10-14

So, if the pH is 6.0, the concentration ofOH- ions is 1 x 10-8

I. WaterC. Water and Life

Why Life on Earth in Water?

I. WaterC. Water and Life

Life on Earth is inconceivable without water.Life requires rapid and continuous chemical reactions

facilitated by a dissolution of reactants in a liquid solvent.Water’s solvent properties are ideal.Water is a liquid over a wide temperature range that is very

common on Earth. (High specific heat, vaporization).Water is abundant on Earth, covering over 70% of the surface.Water is a thermally stable internal/external environment.No surprize that life probably originated in water, and did not

adapt to exploit the desiccating terrestrial environments until the last 10% of Earth history.

Biologically Important Molecules

I.WaterII.Carbohydrates

II. CarbohydratesA. Structure

1. monomer = monosaccharidetypically 3-6 carbons, and CnH2nOn formula

II. CarbohydratesA. Structure

1. monomer = monosaccharidetypically 3-6 carbons, and CnH2nOn formulahave carbonyl and hydroxyl groups

II. CarbohydratesA. Structure

1. monomer = monosaccharidetypically 3-6 carbons, and CnH2nOn formulahave carbonyl and hydroxyl groupscarbonyl is either ketone or aldehydein aqueous solutions, they form rings

II. CarbohydratesA. Structure

1. monomer = monosaccharide2. polymerization:

dehydration synthesis reaction

II. CarbohydratesA. Structure

1. monomer = monosaccharide2. polymerization3. Polymers = polysaccharides

Disaccharides

Polysaccharides

Polysaccharides

Polysaccharides

The ‘cross-linkages’ in cellulose are not digestible by starch-digesting enzymes, so animals cannot eat wood unless they have bacterial endosymbionts. Decomposing fungi and bacteria also have these enzymes, and can access the huge amount of energy in cellulose.

Polysaccharides

H-bonds link cellulose molecules together

Polysaccharides

glucosamine

II. CarbohydratesA. StructureB. Function

- energy storage (short and long) - structural (cellulose and chitin)

CO2

H2O

Glucose, Cellulose,Starch

Biologically Important Molecules

I.WaterII.CarbohydratesIII.Lipids

III. Lipids - not true polymers or macromolecules; an assortment

of hydrophobic, hydrocarbon molecules classes as fats, phospholipids, waxes, or steroids.

III. LipidsA. Fats - structure

glycerol (alcohol) with three fatty acids

(or triglyceride)

III. LipidsA. Fats - structure

-saturated fats (no double bonds)

Straight chains pack tightly; solid at room temperature like butter and lard.

Implicated in plaque build-up in blood vessels (atherosclertosis)

Animal fats (not fish oils)

III. LipidsA. Fats - structure

-unsaturated fats (no double bonds)

Plant and fish oils

Kinked; don’t pack – liquid at room temperature.

“Hydrogenation” can make them saturated and solid, but the process also produces trans-fats (trans conformation around double bond) which may contribute MORE to atherosclerosis than saturated fats)

III. LipidsA. Fats - structure - functions

- long term energy storage (dense) not vital in immobile organisms (mature

plants), so it is metabolically easier to store energy as starch. But in seeds and animals (mobile), there is selective value to packing energy efficiently.In animals, fat is stored in adipose cells

III. LipidsA. Fats - structure - functions

- long term energy storage (dense) - insulation (subcutaneous fat) - cushioning

III. LipidsA. FatsB. Phospholipids

- structure

Glycerol 2 fatty acids phosphate group (and choline)

Hydrophilic and hydrophobic regions

III. LipidsA. FatsB. Phospholipids

- functionselective membranes

In water, they spontaneously assemble into micelles or bilayered liposomes.

III. LipidsA. FatsB. PhospholipidsC. Waxes

- structureAn alcohol and fatty acid

Wax Alcohol Fatty Acid

CarnubaCH3(CH2)28CH2-OH CH3(CH2)24COOH

BeeswaxCH3(CH2)28CH2-OH CH3(CH2)14COOH

SpermaceticCH3(CH2)14CH2-OH CH3(CH2)14COOH

III. LipidsA. FatsB. PhospholipidsC. Waxes

- structure - function

Retard the flow of water (plant waxes)Structural (beeswax)Signals – waxes on the exoskeleton can signal an insect’s

sexual receptivity.

III. LipidsA. FatsB. PhospholipidsC. WaxesD. Steroids

- structuretypically a four-ring structure with side groupscholesterol and its hormone derivatives

Cholesterol

Biologically Important Molecules

I.WaterII.CarbohydratesIII.LipidsIV.Proteins

IV. ProteinsA. structure

- monomer: amino acids

IV. ProteinsA. structure

- monomer: amino acidsCarboxyl group

Amine group

IV. ProteinsA. structure

- monomer:

amino acids

20 AA’s found in proteins, with different chemical properties. Of note is cysteine, which can form covalent bonds to other cysteines through a disulfide linkage.

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration

synthesis

The bond that is formed is called a peptide bond

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration

synthesis- polymer: polypeptide

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration

synthesis- polymer: polypeptideMay be 1000’s of aa’s longNot necessarily functional (“proteins” are functional polypeptides)Sequence determines the function

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration

synthesis- polymer: polypeptide- protein has 4 levels of structure

1o (primary) = AA sequence

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration synthesis- polymer: polypeptide- protein has 4 levels of structure

1o (primary) = AA sequence2o (secondary) = pleated sheet or

helix

The result of H-bonds between neighboring AA’s… not involving the side chains.

Some proteins are functional as helices - collagen

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration synthesis- polymer: polypeptide- protein has 4 levels of structure

1o (primary) = AA sequence2o (secondary) = pleated sheet or

helix3o (tertiary) = folded into a glob

The three dimensional structure of the protein is stabilized by all types of bonds between the side chains… ionic between charged AA’s, Hydrogen bonds between polar AA’s, van der Waals forces, and even covalent bonds between sulfurs.

IV. ProteinsA. structure

- monomer: amino acids- polymerization: dehydration synthesis- polymer: polypeptide- protein has 4 levels of structure

1o (primary) = AA sequence2o (secondary) = pleated sheet or

helix3o (tertiary) = folded into a glob4o (quaternary) = >1 polypeptide

Actin filament in muscle is a sequence of globular actin proteins…

http://3dotstudio.com/prenhall/muscle.jpg

50 myofibrils/fiber (cell)

IV. ProteinsA. structureB. functions! - catalysts (enzymes) - structural (actin/collagen/etc.) - transport (hemoglobin, cell membrane) - immunity (antibodies) - cell signaling (surface antigens)

IV. ProteinsA. structureB. functions!C. designer molecules

If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it?

IV. ProteinsA. structureB. functions!C. designer molecules

If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it?

Folding is critical to function, and this is difficult to predict because it is often catalyzed by other molecules called chaparones

IV. ProteinsA. structureB. functions!C. designer molecules

If protein function is ultimately determined by AA sequence, why can’t we sequence a protein and then synthesize it?

Folding is critical to function, and this is difficult to predict because it is often catalyzed by other molecules called chaparones

Perhaps by analyzing large numbers of protein sequences and structures, correlations between “functional motifs” and particular sequences will be resolved.