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Chapter 2. The Chemical Context of Life. Matter. Takes up space and has mass Exists as elements (pure form) and in chemical combinations called compounds. Elements. Can’t be broken down into simpler substances by chemical reaction Composed of atoms

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chapter 2

Chapter 2

The Chemical Context of Life

matter
Matter
  • Takes up space and has mass
  • Exists as elements (pure form) and in chemical combinations called compounds
elements
Elements
  • Can’t be broken down into simpler substances by chemical reaction
  • Composed of atoms
  • Essential elements in living things include carbon C, hydrogen H, oxygen O, and nitrogen N making up 96% of an organism
other elements
Other Elements
  • A few other elements Make up the remaining 4% of living matter

Table 2.1

trace elements
Trace Elements
  • Trace elements Are required by an organism in only minute quantities
  • Minerals such as Fe and Zn are trace elements
deficiencies
Deficiencies

(b) Iodine deficiency (Goiter)

(a) Nitrogen deficiency

  • If there is a deficiency of an essential element, disease results
compounds
Compounds

+

Sodium

Chloride

Sodium Chloride

  • Are substances consisting of two or more elements combined in a fixed ratio
  • Have characteristics different from those of their elements

Figure 2.2

properties of matter
Properties of Matter
  • An atom is the smallest unit of matter that still retains the properties of a specific element
  • An element’s properties depend on the structure of its atoms
subatomic particles
Subatomic Particles
  • Atoms of each element Are composed of even smaller parts called subatomic particles
  • Neutrons, which have no electrical charge
  • Protons, which are positively charged
  • Electrons, which are negatively charged
subatomic particle location
Subatomic Particle Location
  • Protons and neutrons
    • Are found in the atomic nucleus
  • Electrons
    • Surround the nucleus in a “cloud”
simplified models of an atom
Simplified models of an Atom

Cloud of negative

charge (2 electrons)

Electrons

Nucleus

This model represents the

electrons as a cloud of

negative charge, as if we had

taken many snapshots of the 2

electrons over time, with each

dot representing an electron‘s

position at one point in time.

(a)

In this even more simplified

model, the electrons are

shown as two small blue

spheres on a circle around the

nucleus.

(b)

Figure 2.4

atomic number
Atomic Number
  • Is unique to each element and is used to arrange atoms on the Periodic table
  • Carbon = 12
  • Oxygen = 16
  • Hydrogen = 1
  • Nitrogen = 17
atomic mass
Atomic Mass
  • Is an approximation of the atomic mass of an atom
  • It is the average of the mass of all isotopes of that particular element
  • Can be used to find the number of neutrons (Subtract atomic number from atomic mass)
isotopes
Isotopes
  • Different forms of the same element
  • Have the same number of protons, but different number of neutrons
  • May be radioactive - spontaneously giving off particles and energy
  • May be used to date fossils or as medical tracers
slide15

APPLICATION

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.

TECHNIQUE

Ingredients including

Radioactive tracer

(bright blue)

Incubators

1

2

3

10°C

15°C

20°C

Human cells

4

5

6

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.

25°C

30°C

35°C

1

7

8

9

45°C

50°C

40°C

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

2

DNA (old and new)

2 3 4 5 6 7 8 9

1

slide16

A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter.

3

The frequency of flashes, which is recorded as counts per minute, is 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.

RESULTS

RESULTS

Optimum

temperature

for DNA

synthesis

30

20

Counts per minute

(x 1,000)

10

0

10

20

30

40

50

Temperature (°C)

Figure 2.5

other uses
Other uses

Cancerous throat tissue

Figure 2.6

  • Can be used in medicine to treat tumors
energy
Energy
  • Energy
    • Is defined as the capacity to cause change
  • Potential energy

- Is the energy that matter possesses because of its location or structure

  • Kinetic Energy

- Is the energy of motion

electrons and energy
Electrons and Energy

(a)

A ball bouncing down a flight

of stairs provides an analogy

for energy levels of electrons,

because the ball can only rest

on each step, not between

steps.

Figure 2.7A

  • The electrons of an atom
    • Differ in the amounts of potential energy they possess
energy levels of electrons
Energy Levels of Electrons
  • An atom’s electrons Vary in the amount of energy they possess
  • Electrons further from the nucleus have more energy
  • Electron’s can absorb energy and become “excited”
  • Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels
energy levels
Energy Levels

Third energy level (shell)

Second energy level (shell)

Energy

absorbed

First energy level (shell)

Energy

lost

Atomic

nucleus

(b)

An electron can move from one level to another only if the energy

it gains or loses is exactly equal to the difference in energy between

the two levels. Arrows indicate some of the step-wise changes in

potential energy that are possible.

Figure 2.7B

  • Are represented by electron shells
why do some elements react
Why do some elements react?
  • Valence electrons
    • Are those in the outermost, or valence shell
    • Determine the chemical behavior of an atom
covalent bonds
Covalent Bonds

Hydrogen atoms (2 H)

In each hydrogen

atom, the single electron

is held in its orbital by

its attraction to the

proton in the nucleus.

+

+

2

3

1

When two hydrogen

atoms approach each

other, the electron of

each atom is also

attracted to the proton

in the other nucleus.

+

+

The two electrons

become shared in a

covalent bond,

forming an H2

molecule.

+

+

Hydrogen

molecule (H2)

  • Sharing of a pair of valence electrons
  • Examples: H2

Figure 2.10

covalent bonding
Covalent Bonding
  • Electronegativity
    • Is the attraction of a particular kind of atom for the electrons in a covalent bond
  • The more electronegative an atom
    • The more strongly it pulls shared electrons toward itself
covalent bonding1
Covalent Bonding
  • In a nonpolar covalent bond
    • The atoms have similar electronegativities
    • Share the electron equally
covalent bonding2
Covalent Bonding

Because oxygen (O) is more electronegative than hydrogen (H),

shared electrons are pulled more toward oxygen.

d–

This results in a

partial negative

charge on the

oxygen and a

partial positive

charge on

the hydrogens.

O

H

H

d+

d+

H2O

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

Figure 2.12

ionic bonds
Ionic Bonds
  • In some cases, atoms strip electrons away from their bonding partners
  • Electron transfer between two atoms creates ions
  • Ions
    • Are atoms with more or fewer electrons than usual
    • Are charged atoms
slide29
Ions
  • An anion
    • Is negatively charged ions
  • A cation
    • Is positively charged
ionic bonding
Ionic Bonding

The lone valence electron of a sodium

atom is transferred to join the 7 valence

electrons of a chlorine atom.

Each resulting ion has a completed

valence shell. An ionic bond can form

between the oppositely charged ions.

+

1

2

Cl

Na

Na

Cl

Cl–

Chloride ion

(an anion)

Na+

Sodium on

(a cation)

Na

Sodium atom

(an uncharged

atom)

Cl

Chlorine atom

(an uncharged

atom)

Sodium chloride (NaCl)

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

Figure 2.13

ionic substances
Ionic Substances

Na+

Cl–

Figure 2.14

  • Ionic compounds
    • Are often called salts, which may form crystals
weak chemical bonds
Weak Chemical Bonds
  • Several types of weak chemical bonds are important in living systems
hydrogen bonds
Hydrogen Bonds

H

Water

(H2O)

O

A hydrogen

bond results

from the

attraction

between the

partial positive

charge on the

hydrogen atom

of water and

the partial

negative charge

on the nitrogen

atom of

ammonia.

H

 +

 –

Ammonia

(NH3)

N

H

H

d+

+

H

Figure 2.15

  • A hydrogen bond
    • Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

 –

 +

 +

van der waals interactions
Van der Waals Interactions
  • Van der Waals interactions
    • Occur when transiently positive and negative regions of molecules attract each other
weak bonds
Weak Bonds
  • Weak chemical bonds
    • Reinforce the shapes of large molecules
    • Help molecules adhere to each other
molecular shape and function
Molecular Shape and Function
  • Structure determines Function!
  • The precise shape of a molecule
    • Is usually very important to its function in the living cell
    • Is determined by the positions of its atoms’ valence orbitals
shape and function
Shape and Function
  • Molecular shape
    • Determines how biological molecules recognize and respond to one another with specificity
slide38

Nitrogen

Carbon

Hydrogen

Sulfur

Oxygen

Natural

endorphin

Morphine

(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.

Natural

endorphin

Morphine

Endorphin

receptors

Brain cell

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

Figure 2.17

chemical reactions
Chemical Reactions
  • Chemical reactions make and break chemical bonds
  • A Chemical reaction
    • Is the making and breaking of chemical bonds
    • Leads to changes in the composition of matter
chemical reactions1
Chemical Reactions

+

2 H2O

2 H2

+

O2

Reactants

Reaction

Product

  • Chemical reactions
    • Convert reactants to products
chemical reactions2
Chemical Reactions
  • Photosynthesis
    • Is an example of a chemical reaction

Figure 2.18

chemical reactions3
Chemical Reactions
  • Chemical equilibrium
    • Is reached when the forward and reverse reaction rates are equal