Chapter 2

The Chemical Context of Life

1. What is an atom?– Smallest unit of matter that retains the physical & chemical

properties of its element– Element – a substance that cannot be broken down into other

substances by chemical rxn

2. What is an atom made of?– Proton – (+1) charge, found in nucleus, 1 amu/1 dalton– Neutron – no charge, found in nucleus, 1 amu/1 dalton– Electron – (-1) charge, orbit nucleus, mass negligible

Chapter 2 The Chemical Context of Life

Figure 2.4 Simplified models of a helium (He) atom

Nucleus

(a) (b)

Cloud of negativecharge (2 electrons)

Electrons

1. What is an atom?

2. What is an atom made of?

3. What do these numbers mean?23Na 12C

11Na 6C

4. What is an isotope? Radioisotope?– Atoms of an element that have the same atomic # but different

atomic mass (due to different #s of neutrons)– Unstable isotope where the nucleus spontaneously decays

emitting subatomic particles &/or energy as radioactivity.

5. What are radioisotopes used for?

Chapter 2 The Chemical Context of Life

Atomic mass = protons + neutrons

Atomic # = # of protons

1. What is an atom?

2. What is an atom made of?

3. What do these numbers mean?

4. What is an isotope? Radioisotope?

5. What are radioisotopes used for? Radiation cancer therapy (“nuclear medicine”)

- http://www.rsc.org/chemistryworld/News/2011/May/11051102.asp

Cell research (trace path of protein from ribosome-to-final destination)

6. How are atoms held together?

Chemical bonds!!!

7. What are the different types of bonds?– Covalent – sharing of electrons

• Polar covalent – UNequal sharing• Non-polar covalent – equal sharing

– Ionic – complete transfer of electrons

Chapter 2 The Chemical Context of Life

Figure 2.10

• Formation of a covalent bondHydrogen atoms (2 H)

Hydrogenmolecule (H2)

+ +

+ +

+ +

In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.

1

When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.

2

The two electronsbecome shared in a covalent bond,forming an H2

molecule.

3

(a)

(b)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

H H

O O

Figure 2.11 A, B

• Single and double covalent bonds

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

(c)

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

(d)

HO

H

H H

H

H

C

Figure 2.11 C, D

• Covalent bonding in compounds

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)Figure 2.13

• An ionic bond– Is an attraction between anions and cations

1. What is an atom?

2. What is an atom made of?

3. What do these numbers mean?

4. What is an isotope? Radioisotope?

5. What are radioisotopes used for?

6. How are atoms held together?

7. What are the different types of bonds?

8. What is electronegativity?– Atom’s ability to attract & hold electrons– In Biology – most concerned with N & O

Chapter 2 The Chemical Context of Life

Figure 2.12

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

• In a polar covalent bond– The atoms have differing electronegativities– Share the electrons unequally

–

Hydrogen Bonds

– +

+

Water(H2O)

Ammonia(NH3)

OH

H

+

–

N

HH H

A hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.+ +

Figure 2.15

• A hydrogen bond– Forms when a hydrogen atom covalently

bonded to one electronegative atom is also attracted to another electronegative atom

• Molecular shape– Determines how biological molecules recognize

and respond to one another with specificity

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

OxygenNaturalendorphin

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Figure 2.17

1. What is an atom?

2. What is an atom made of?

3. What do these numbers mean?

4. What is an isotope? Radioisotope?

5. What are radioisotopes used for?

6. How are atoms held together?

7. What are the different types of bonds?

8. What is electronegativity?

9. How are bonds created between atoms?

Chapter 2 The Chemical Context of Life

Reactants Reaction Product

2 H2 O2 2 H2O

+

+

• Chemical reactions– Convert reactants to products