chapter 2 - the chemical basis of life new aim: what’s the matter? figure 2.1

Chapter 2 - The Chemical Basis of Life NEW AIM: What’s the matter?

Figure 2.1

AIM: What’s the matter?

What isMATTER?

Chapter 2 - The Chemical Basis of Life

- Anything that takes up space and has mass


The smallest chemically unbreakable unit of MATTER?


An atom

Fig. 2.1

AIM: What’s the matter?Chapter 2 - The Chemical Basis of Life


Elements


- The various types of atomsEx. Carbon, Oxygen, Nitrogen, etc…

Table 2.1


“Minerals”

Fig 2.3b



A lack of iodine in one’s diet can cause swelling of the thyroid gland resulting in a GOITER. The condition is reversible if iodine is taken. (Don’t worry, we iodize salt)

Iodine is used by thyroid cells to make hormones (chemicals released by one cell into the blood and bind to a receptor on another cell, which is one way cells talk to each other).

Fig 2.3b


Element

Compoundvs

(Emergent Properties)



Elements – composed of the same types of atoms

Compounds – composed of two or more types of atoms


Element

CompoundEx) a bar of pure gold, nitrogen gas (N2), oxygen gas (O2)

- Any substance composed of two or more elements


- Any substance composed of only ONE element

Ex) Na+Cl- (table salt), H2O, CO2


EMERGENT PROPERTIES (EP’s)


+ =

Pure sodium (element)Chlorine (Cl2) gas (element)Na+Cl- Table Salt (Compound)

Fig 2.2


The forces and energy



What are atoms made of and how are they organized?


(The Bohr Model)

Niels BohrDanish Physicist1885-1962


Nucleus Organization:


protonneutronelectron

chargemass+10-1

1 amu (dalton)

1 amu (dalton)

1/1836th an amu (dalton)

amu = atomic mass unit

1 amu or 1 dalton = 1.67 x 10-27 kg

Subatomic particles(sub = below, below the atom level)


How are the electrons “held” to the nucleus? Why do they not just shoot away?

Electrons are held to the nucleus by the electromagnetic (EM) force since electrons are negative and the nucleus is positive – opposite charges attract / like charges repel.


How are the protons “held” together in the nucleus? Why do they not break apart due to the EM force?

The strong force holds the nucleus together. The strong force is only “felt” at extremely small distances, which is why the electrons do not feel it. You would need to be on the nucleus to feel it. For example, if gravity were like this, you would only feel it on Earth, but if you jumped up a few feet, you would no longer be pulled down by it...


Electron Organization:

Electrons are present in shells and move around the nucleus at a speed of ~2200 km/s. They can only be in these shells and nowhere else!!The first shell (n=1) can hold up to 2 electrons. That means it can have 0, 1 or 2 electrons in it at any time.

The second shell (n=2) can hold up to 8 electrons.

There are many more shells, but you only need to know the first three for AP Bio.

n=1n=2

The third shell (not shown, n=3) can also hold up to 18 electrons.

2n2


What is the current model of the atom?


(The Quantum Model)



Which shell contains higher energy electrons, shell 1 (n=1) or shell 2 (n=2)? Explain.Shell 2. The further from the nucleus the electron, the further it can fall toward the nucleus and therefore it has more energy (a greater ability to accelerate matter) than shell 1 electrons.

n=1n=2



Electrons can jump between shells (called a quantum leap)

In order to get an electron to “leap” from n=1 to n=2, what is required?

n=1n=2



Electrons can jump between shells (called s quantum leap)

n=1

n=2

n=3

The nucleus is charged and therefore is pulling on the electron. It will take energy to pull the electron away from the nucleus and move it further away to shell 2. This is analogous to picking up a bowling ball. Earth is pulling on the bowling ball like the nucleus is pulling on the electron. It takes energy to pick up a bowling ball.

Fig 2.7



Electrons can jump between shells (called s quantum leap)

n=1

n=2

n=3

What occurs when an electron leaps in the opposite direction from n=2 to n=1?Energy is emitted or lost from the electron (in the form of light).

Fig 2.7


How big are atoms?


(size)

1/100,000,000,000th mm

1/10,000,000th mm

Analogy: If the nucleus were enlarged to the size of a golf ball, the first electron shell would be over ½ mile away. What does this tell you about the composition of an atom or matter in general as we know it on Earth?

Matter as we know it is 99.999999999% empty space and therefore has an extremely low density.

.0.62 miles


Then what is matter at the microscopic level?


Mostly empty space with tiny spaced out dots of matter (protons/neutrons/electrons) held together by the electromagnetic and strong force.


If we are just a collection of dots, why can’t we pass through each other? Why don’t I just fall through the floor?


Quizicule1. Identify the four forces of the Universe.

2. What is a force?

3. What does the term “energy” imply?

4. What force do we as humans use when we apply force to objects?5. Why do we rely of the force of gravity in order to make our bodies move around? Be brief.

6. If a nucleus of an atom were scaled to the size of a golf ball, how far away would the first electron need to be placed approximately?


602,300,000,000,000,000,000,0006.023

x 10

23or


A mole(Avogadro’s Number)

Aside: Make sure you know scientific notation and unit conversions…


602,300,000,000,000,000,000,0006.023

x 10

23or

(scientific notation)


A mole of money spent at 1 billion dollars per second would take 19 million years to spend…


602,300,000,000,000,000,000,0006.023

x 10

23or


A mole(Avogadro’s Number)

WHY?


Mass (amu) If you have a mole… Mass (grams) conclusion

1 proton(1 amu)

X 6.02x1023 = (1 mole)

1 gram 1 mole of protons has a mass of 1 gram(1 amu…1 gram)

1 neutron(1 amu)

X 6.02x1023 = (1 mole)

1 gram 1 mole of neutrons has a mass of 1 gram (protons and neutrons have essentially the same mass)

2 protons(2 amu)

X 6.02x1023 = (1 mole)

2 grams If one mole of protons is one gram then a mole of 2 protons will be 2 grams(2 amu…2 grams)

2 protons and 2 neutrons(4 amu)

X 6.02x1023 = (1 mole)

4 grams I hope you are seeing it now…(4 amu…4 grams)

Carbon-12 atom(12 amu)

X 6.02x1023 = (1 mole)

12 grams

NaCl(22.99+35.45 amu)

X 6.02x1023 = (1 mole)

58.44 grams


You learned in chemistrythat if you know the amu of a

substance then you know the number of grams/mole (gram formula mass).


(size)

You should not be able to explain why this works so nicely…explain


How many water moleculesare in 18ml of water?


(size)


Quizicule

1. How many marbles do I have if I have 2 moles of marbles?2. What is the significance of a mole? (Why is a mole defined as 6.02e23?3. Identify the two forces at play within the nucleus.4. If the nucleus were scaled to the size of a golf ball, approximately how far away would the first electron be?


Questions

1. How many grams of KCl would you need to weigh out in order to have 1 mol of KCl’s?2. If I have 180g of glucose, how many moles of glucose do I have? How many glucose molecules do I have?3. How many ml of water would I need in order to have 3 moles of water molecules?


What determines the elemental identity of an atom?


Explain why.


Always has 2 protons

Always has 6 protons


Memorize the first 20 – Hydrogen to Calcium


What determines the elemental identity of an atom?Chapter 2 - The Chemical Basis of Life

The number of protons = atomic number (Z)

Element?


Charge?

Mass?



The atomic mass (A)Why do we not add the electrons mass?

Electrons are soooo small relative to protons and neutrons (1/2000th the size) that we ignore them.

= protons + neutrons


The atomic chargeCompare number of protons to the number of electrons.

Ex. If there are 10 protons (+10) and 7 electrons (-7) the overall charge is +3


What happens if wechange the number of protons?


You change the identity of the atom (becomes a different element) as well as the mass.


What happens if wechange the number of neutrons?


You change the mass and perhaps the stability....


Isotopes are atoms that have the same elemental identity (same number of protons/same properties), but different number of neutrons.


Certain ratios of protons to neutrons are unstable resulting in breakdown of the nucleus (nuclear radiation).

Ex. 6 protons and 6 neutrons in a nucleus (Carbon-12) is stable, but 6 protons and 8 neutrons (carbon-14) is unstable and will undergo radioactive decay to become stable. C-14 is called a radioactive isotope.

stable stable unstable


Radioactive decay


Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7 neutrons in a nucleus is stable. An electron is shot out during the decay making it dangerous and useful.

Radioactive decay


How can we use radioactivityto our

advantage?


Example:3H (tritium) = radioactive isotope of hydrogen. How many protons and neutrons?1 proton, 2 neutrons

1. Add tritiated thymidine (thymidine with 3H hydrogens) to human cells undergoing mitosis in petri dishes. (tritiated thymidine will be converted to the nucleotide dTTP (T) and used to make DNA)

2. Place dishes at different temperatures for a couple hours. 3. Remove dishes, put cells in test tubes and centrifuge down cells and measure radioactivity. What would you predict to observe?

At what temperature is DNA replication most efficient in humans?


Example:3H (tritium) = radioactive isotope of hydrogen. How many protons and neutrons?1 proton, 2 neutrons

What would you predict to observe?Cells growing at 37C performed DNA replication the quickest as human enzymes typically work best at body temperature. Therefore these cells with have the greatest amount of radioactivity. Cell at greater than 50C or less than 20C will have little to no radioactivity as DNA replication enzymes will not work at these temps.


We can send molecules like fluorodeoxyglucose (FDG) (glucose with radioactive fluorine (F-18) in place of a hydroxyl (-OH) group) containing radioactive elements into your body. For example, cancer cells use lots of glucose and therefore the glucose will build up where tumors are found. The radioactive elements will be shooting out particles (electrons or others) like a billion microscopic flare guns that we can detect (in this case using PET scanning).

Tumor (mass of unregulated dividing cells) with concentrated radioactive glucose.

PET scan


We can potentially trace (follow) any radioactive molecule we put into you.

Tumor (mass of unregulated dividing cells) with concentrated radioactive glucose.


What if we alter thenumber of electrons

?


If you alter the electrons, you simply change the charge of the atom


Quizicule1. What determines the elemental identity of an atom?2. Why is a mole equal to 6.02e23?

6. How many grams of sodium bicarbonate (NaHCO3) would I need to mass out if I wanted to have 1.5 moles in my possession?

4. Atoms of the same elemental identity, but differ in their number of neutrons are known as __________________. 5. If sucrose has a total of 342 protons and neutrons of which 182 are protons , and I have 182g of sucrose, how many moles of sucrose am I sporting?

3. Draw the bohr model of a carbon atom with a charge of -1 in its lowest energy state.


Review:1. Draw an oxygen atom with a charge of -2 and an atomic mass of 18


2. What is the atomic number of this atom?

3. Draw a neutral isotope of the above atom.


Review:

4. How many protons, neutrons and electrons does the above element contain?



Review:

5. Which of the following models is correct according to the Bohr model of the atom?



Review:6. You have an atom and determine its mass to be 150 amu and to have 90 neutrons. The atom has an overall charge of -3. How many electrons does the atom have?



Review:7. What is a mole? Why is this number important? From where did it originate?



What determines the Chemical reactivity of a given atom

?Chapter 2 - The Chemical Basis of Life

(how an atom will interact with another atom)

The number of electrons in the valence shell (outer shell). This is logical as you would expect the outer surfaces of atoms to interact with each other. Of course, the number of protons determines the number of electrons and therefore it boils down to the number of protons in the nucleus, which is why protons determine the element.


Valence shell


Climbing the Hierarchy

AIM: How do atoms interact with each other?


When are atomsmost happy ?

When their valence shell is full.

Chapter 2 - The Chemical Basis of Life AIM: How do atoms interact with each other?

To be “happy” (stable) the sodium atom will need to either get 7 electrons or lose 1. Which is easier?

The sodium will give away its outer shell electron.


Chlorine needs one electron for its outer shell to be full.


Chlorine has a higher AFFINITY for the electron and therefore the electron will “fall” from sodium to chlorine.


When the piece of elemental sodium (countless numbers of sodium molecules) is placed in the chlorine gas in the video, all those ridiculous number of electrons jump to the countless chlorines. This causes all the molecules to move around violently (heat up) and electrons to jump between shells (give off light).


ions

Cation vs Anion

Ionic bond


When sodium loses an electron it becomes positively charged (a cation). When chlorine picks it up it becomes negatively charged (a anion). Cations and Anions are collectively called ions = fully charged atoms/molecules.


ions

Cation vs Anion

Ionic bond


The sodium and chloride ions are now attracted to each other and form an ionic bond.ionic bond = bond between two oppositely charged ions


Salt crystals


Na+Cl- crystals are repeating arrays of Na+ and Cl- held together by the electromagnetic force.


SaltAIM: How do atoms interact with each other?

-general name given to ANY ionic compound (not just sodium chloride (Na+Cl-) held together in a lattice structure.Na+Cl-

K+Cl-

Mg2+Cl2-

Mn2+Cl2-

Ca2+CO32-


http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55

AIM: How do atoms interact with each other?How else can atoms fill their outer shells?





Single Covalent Bond

In this case, to be stable and fill their outer shells, unlike in an ionic bond, the atoms will SHARE their electrons to form a covalent bond.

H-H or H2



F-F or F2


Double Covalent Bonds (double bond)

O=C=O or CO2


Draw :CH4 or H2O



Why is oxygen gas O2 and

nitrogen gas N2


?O=O and N=N-

Triple bond > Double bond > Single bond

Covalent bond strengths:


Fig. 2.11

MOLECULE


A molecule is two or more atoms held together by COVALENT bonds. If you see a covalent bond, it is a molecule. Period. The End.


Displayed formulaskeletal formula Ball-and-stick

C9H8O4= Molecular formula

Structural formula:


An aspirin molecule


C9H8O4= Molecular formula

Why is the molecular formula not usually enough to tell us what molecule is being indicated?


Because the atoms can be attached in different ways and different structures will give us different molecules with different functions called structural isomers or constitutional isomers.

Chapter 2 - The Chemical Basis of Life AIM: How do atoms interact with each other?An antibody molecule (a type or protein) compared to an aspirin molecule (the smaller one).


Drawing molecules 1. Lewis-dot diagram (valence)2. Display3. Skeletal


Draw the structure of H2CO

Draw the structure of C2H6

H-C-C-HHH

HH

H-C=OH


Draw the structure of H6C3O

Draw the structure of C6H6


Number of bonds formed by each element:

Element Number of Covalent Bonds it will form to be “happy” (stable)

Hydrogen

Oxygen

Nitrogen

CarbonThe element will form as many bonds as it needs electrons in its valence shell. For example, carbon needs four electrons and therefore it will make four covalent bonds (it will share 4 electrons) with other elements.

123

4


Using the terms element, compound and/or molecule, characterize the following:

C6H6

This is certainly a molecule because there will be covalent bonds. It is also a compound because there is more than one type of element.



Na+Cl-

This is not a molecule since there are no covalent bonds present. It is a compound since there is more than one type of atom present.



O2

This is a molecule because there is a covalent bond (a double covalent bond in this case). It is not a compound since there is only oxygen, which would make it an element.


Quizicule1. Draw a possible molecule with the molecular formula C3O3H4 in both lewis-dot (valence shells only), displayed form (all atoms indicated), and skeletal form. (6 points)

Chapter 3 - The Molecules of Cells

Aside: To what is DNA analagous?AIM: How can we observe cells?

DNA stores information…books store information…both are pointless without…

AIM: How is all life united?Chapter 1 - Introduction: The Scientific Study of Life Chapter 1 - Introduction: Exploring Life

AIM: What are the major characteristics of life?


What is this human analogous to?

AIM: How can we observe cells? …something to read them.



Protein…proteins are molecules that do all the work in the cell…they are like people…the workers / little machines…they build the cell, maintain the cell, divide the cell, read the DNA, and much more.


How large are proteins and DNA relative to the cell?

AIM: How can we observe cells?

Imagine Madison Square Garden (MSG) is a single cell…how big is a protein in this cell?

A protein would be about the size of a tennis ball in MSG and the DNA would be a string with a thickness of 2mm and a length of 1200 miles!!!




Another way to draw molecules/atoms: spacefill


Another structure/function example:

Fig. 2.17

The structure of a molecules determines its function...In the example to the right, endorphin (a naturally occuring chemical in your brain that reduces the sensation of pain) has its structure mimicked by morphine (a chemical found in opium poppy).

This allows morphine to bind the endorphin receptor on the surface of neurons in the brain making it a very popular painkiller.

Opium poppy fruit that has been cut revealing the fluid containing morphine.


Another structure/function example:

Fig. 2.17

The structure of a molecules determines its function...The structure of hemoglobin allows it to carry four oxygen (O2) molecules.

Like the structure of a hammer allows it to hits nails…


Biochemical Pathways…an introduction

They are a lot like factory lines:proteins (enzymes) in blue = yellow robotsMolecules being modified = cars and parts

Equilibrium vs homeostasisMetabolism

Basic Research


Biochemical Pathways…an introduction

Basic Research turned Applied Research

Professor Akira Endo

Mevastatin


Another structure/function example:The structure of a molecules determines its function...Lovastatin treats hypercholesterolemia (high cholesterol level).It was first isolated in 1978 from the fungus Asperfillus terreus.

Worth a read…

Mevastatin


Another structure/function example:The structure of a molecules determines its function...Cholesterol Biosynthesis – you don’t need to eat cholesterol. Your enzymes make it.

Lovastatin binds to and inhibits HMG-CoA reductase – remember that enzyme names will usually end in –ase.

**Enzymes are in blue.**Substrates/Products are in black with final products in GREEN.


Another structure/function example:The structure of a molecules determines its function...

Lovastatin has a structure that allows it to bind to the active site of this enzyme thereby giving it its function as an inhibitor and in turn reducer of blood cholesterol.

Alpha helices are in blue.Beta sheets in purple.Loops in yellow.

HMG-CoA reductase with lovastatin bound:


Another structure/function example:The structure of a molecules determines its function...

This is the reaction normally catalyzed by this enzyme. Compare the natural substrate (HMG CoA) to Lovastatin. Could you guess that this molecule would bind to this protein?


Another structure/function example:Lipitor (Atorvastatin}

Born from the understanding of fungal statins…


Top 20 selling drugs 2014 -


Quizicule1. Define Equilibrium. How is it different from homeostasis?2. What are statins?

3. A) What was the rationale behind the discovery of the first statin? B) In what type of organism was the first statin discovered?4. What is the difference between basic and applied research? Give an example using statins.

5. Give an analogy for biochemical pathways.


Chemical Reaction

The transformation of one set of chemical substances to another…


Chemical Reactions and Chemical EquilibriumSome reactions proceed to completion (irreversible reaction) indicated by the single arrow:

However, many proceed in both directions (reversible reaction) as indicated by the double arrow in the reaction diagram reaching an equilibrium.

CaCO3 + 2HCl → CaCl2 + H2O + CO2

or


Define Equilibrium…The rates are the same in both directions…

In this case, the rate of the reaction to the right is the same as the rate of the reaction to the left…they are occurring at the same speed essentially…If the sustances are being formed as quickly as they are being used then what can you say about the concentrations of all substances?

Concentrations are not changing…


Chemical Reactions and Chemical EquilibriumBiological Example:

Glycolysis is shown to the right. The circled numbers are enzymes.

Which reactions are reversible?Which reactions are irreversible?

Those catalyzed by enzymes 3, 4, 6, 7, 8, 9, 10, and 11

Those catalyzed by enzymes 1, 2, 5 and 12

chapter 2 - the chemical basis of life new aim: what’s the matter? figure 2.1

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