Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings AP Biology Ch. 2 The Chemical Context of Life Bombardier Beetle’s Defense: Ejecting

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

AP Biology Ch. 2 The Chemical Context of Life

Bombardier Beetle’s Defense:

Ejecting a spray of hot irritating chemicals, an example of the interconnectedness of biology and chemistry.

•Essential elements of life

•Structure of atoms

•Chemical bonding

•Chemical reactions


25 Essential Elements of Life

96% of living matter –

O, C, H, N

Table 2.1 Naturally Occurring Elements in the Human Body


Effects of essential-element deficiencies

(a) Nitrogen deficiency (b) Iodine deficiency –trace element

Trace elements – required only in minute quantities

deficiency results in great consequences0.15 mg iodine required

Malaysian woman – can be reversed with iodine

supplementsFigure 2.3


An element’s properties depend on the structure of its atoms.

• Atom – smallest unit of matter

• Mass number

– sum of protons + neutrons

• Atomic number

– Number of protons in the nucleus; 2He

• Atomic weight

– Mass number; 4He

• Isotopes

– 2 atoms of same element; differ in # of neutrons

Nucleus

Cloud of negativecharge (2 electrons)

Electrons

Model of Helium


Radioactive isotopes

• Unstable nuclei decay, emitting particles & energy

• Applications: date fossils trace atoms through metabolic processes diagnose disorders


Figure 2.5 Research Method Radioactive Tracers

Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA.

APPLICATION

DNA (old and new)

Ingredients includingradioactive tracer (bright blue)

Human cells

Incubators1 2 3

4 5 6

987

10°C 15°C 20°C

25°C 30°C 35°C

40°C 45°C 50°C

TECHNIQUE

2

1

The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed.

1 2 3 4 5 6 7 8 9

Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H.

Radioactive isotopes –

elements with unstable nuclei; give off particles and energy as

they decay


Placed in a Scintillation Chamber

Temperature (°C)

The frequency of flashes, - counts per minute, proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.

10 20 30 40 50

Optimumtemperaturefor DNAsynthesis

30

20

10

0

Co

un

ts p

er

min

ute

(x 1

,00

0)

RESULTS

In scintillators the part of the energy lost by a particle is converted into the energy of a light flash


Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

Chemical Behavior - determined by it’s electron configuration. Valence electrons – only unpaired electrons are involved

Atoms with the same # of valence e- have similar chemical behaviors.

nonreactiveFigure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table.


Formation & function of molecules depend on chemical bonding between atoms.

• Chemical bonds (4)

– Covalent bond –

– Ionic bond –

– Hydrogen bonds –

– van der Waals interactions –


Covalent bonding – atoms sharing e-

Name(molecularformula)

Electron-shell

diagram

Structuralformula

(c)

H

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

Space-fillingmodel

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

(a)

H H

O O

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

(b)

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

O H

H

H H

HO

H

O O

H

HH C H

H

H

HC

(d)

Pair of equally shared e-

Pair of unequally shared e-

polar (e- shared unequally) vs. nonpolar (e- shared equally)


Polar / Nonpolar Covalent Rules

• Nonpolar – e- shared equally -b/t 2 atoms of same element – H-H -b/t atoms w/similar electronegativity – CH4

• Polar – e- shared unequally ex. H2O; oxygen – higher electronegativity

• Electronegativity – attraction of an atom for the shared e- of a covalent bond (strong electronegative atoms attempt to pull the shared e- toward themselves)


Figure 2.12 Polar covalent bonds in a water molecule

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.


Ionic bond– one atom strips e- from another

cations (atom w/+ charge) anions (atom w/- charge)

– The attraction between oppositely charged atoms, or ions, is an ionic bond.

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 uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium ion(a cation)

Sodium chloride (NaCl)


Hydrogen bonds –

– H atom of one compound is attracted to another compound

– Holds water together

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.

+

+

+


van der Waals interactions –

Molecules in close proximity exert attraction in concert

Hair tip molecules and the molecules of the wall’s surface are so numerous, collectively they form strong bonding patterns temporarily.

Gecko lizard – walks up

walls


Molecule’s biological function -related to its shape

• Biological molecules:

– Recognize, interact with one another with a specificity based on molecular shape.

Ex. morphine affects pain perception and emotional state by mimicking the brain’s natural endorphins.

Naturalendorphin

Morphine

Endorphinreceptors


Chemical reactions make / break chemical bonds.

• Change reactants into products conserving matter

• Most are reversible.

• Chemical equilibrium is reached - when the forward and reverse reaction rates are equal

Elodea, a freshwater plant, produces sugar by rearranging the atoms of carbon dioxide and water in the chemical process

known as photosynthesis. Much of the sugar is then converted to other food molecules. Oxygen gas is a by-product of

photosynthesis; hence the bubbles of oxygen escaping from the leaves.

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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings AP Biology Ch. 2 The Chemical Context of Life Bombardier Beetle’s Defense: Ejecting