1. Essential Chemistry in Biology Mrs. Norris
Topics Discussed in these notes
Matter, Elements and Compounds
Periodic Table of the Elements: Metals vs. Nonmetals
Atomic Structure
Chemical Bonding: Ionic vs. Covalent Bonding
Chemical Reactions and Chemical Equations
The Structure of Water
Water as a Solvent
The Importance of Water to Living Things
Acids, Bases and pH
Self-test/Review Questions

2. BASIC CHEMISTRY
Organisms and all other things in the universe consist of matter
Matter: Elements and Compounds
Matter is anything that occupies space and has mass
Matter is composed of chemical elements and compounds
Elements: substances that cannot be broken down into other substances
There are 92 naturally occurring elements on Earth
What are compounds? Examples?

3. Periodic table of the elements
Location of....
Metals?
Nonmetals?

4. 25 Elements are essential to life
C, H, O, N: 96% of the weight of the human body

5. Some Elements React to Form Compounds
Elements can combine chemically to form compounds
Compounds contain two or more elements chemically combined in a fixed ratio
Examples of Compounds:
Table salt (sodium chloride): NaCl
Water: H2O
Glucose: C6H12O6

6. Each element consists of one kind of atom
Atom: smallest unit of matter that retains the properties of an element
Each element consists of one kind of atom
(a) Hydrogen atom
(b) Carbon atom
(c) Oxygen atom
Proton
Neutron
Electron
First
shell
Second
shell
Atomic nucleus
Fig. 2.02

7. The subatomic particles of an atom
Atomic Structure
The subatomic particles of an atom
Electron
 Negative charge
Proton
• Participates in chemical
reactions
 Positive charge
 Determines element
• Outer-shell electrons
determine chemical
behavior
Neutron
 No charge
 Determines isotope
Nucleus
• Consists of neutrons and protons

8. Atomic Number: number of protons
Elements
differ in the number of subatomic particles in their atoms
Atomic Number: number of protons
determines which element it is
Mass number
sum of the number of protons and neutrons

9. Chemical Properties of Atoms
Electrons
Located outside the nucleus of an atom in specific electron shells (energy levels)
The number of electrons in the outermost shell determines the chemical properties of an atom

10. Atoms of the four elements most abundant in life
First
electron shell:
can hold
2 electrons
Outermost
electron shell:
can hold
8 electrons
Electron
Hydrogen (H)
Atomic number = 1
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8

11. Orbital Diagrams of the First 18 Elements
1st Shell
2nd Shell
3rd Shell 2 8 8

12. Chemical Bonding and Molecules
Chemical reactions:
Atoms give up or acquire electrons in order to complete their outer shells
Result in atoms staying close together to form molecules
Chemical bonds hold molecules together
Ionic Bonds
Covalent bonds

13. Ionic Bonds: form between metals and nonmetals
When an atom loses or gains electrons, it becomes electrically charged
Charged atoms are called ions
Ionic bonds are formed between oppositely charged ions
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na)
Chloride ion (Cl)
Sodium chloride (NaCl)

14. Atoms: electrically neutral Ions: Electrically charged
(a) Hydrogen atom (H)
(b) Hydrogen ion (H+)
1 electron
No electron
1 proton
1 proton
No net electrical charge
(c) Sodium atom (Na)
(d) Sodium ion (Na+)
11 electrons
10 electrons
11 protons
11 protons
No net electrical charge
Fig. 2.03

15. Covalent Bonds: form between nonmetallic atoms
A covalent bond forms when two atoms share one or more pairs of outer-shell electrons

16. Covalent bonding in water
Water molecule (H2O)
Oxygen atom with unfilled shell
Full shell with 8 electrons –
Slightly negative
Covalent bond
(shared pair
of electron) + +
Slightly positive
Full shells with 2 electrons each
Hydrogen atoms with unfilled shells
Fig. 2.04a

17. Chemical Reactions
Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones
Such changes in the chemical composition of matter are called chemical reactions
Hydrogen gas
Oxygen gas
Water
Reactants
Products

18. Chemical Equations: symbolize chemical reactions
Reactants: on the left side of the equation
the starting materials
Products: on the right side of the equation
the ending materials (the stuff produces)
Law of Conservation of Mass
Chemical reactions do not create or destroy matter—they only rearrange it!

19. The abundance of water is a major reason Earth is habitable
WATER AND LIFE
The abundance of water is a major reason Earth is habitable
Modern life still remains tied to water
Your cells are composed of 70%–95% water

20. The Structure of Water The water molecule:
two hydrogen atoms joined to one oxygen atom by single covalent bonds H H O

21. Water: a polar molecule
The electrons of the covalent bonds are shared unequally between oxygen and hydrogen
unequal sharing of electrons makes water a polar molecule
hydrogen atoms: partially positive (d ) Why?
oxygen atom: partially negative (d -) Why?
(d )
(d )
(d )

22. The Structure of Water
The polarity of water results in weak electrical attractions between neighboring water molecules
These interactions are called hydrogen bonds
()
Hydrogen bond
()
()
()
()
()
()
()
(b)

23. Water’s Life-Supporting Properties
The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties
Versatility of water as a solvent
Water’s cohesive nature
Water’s ability to moderate temperature
Floating ice

24. Water as the Solvent of Life
A solution is a liquid consisting of two or more substances evenly mixed
The dissolving agent is called the solvent
The dissolved substance is called the solute
Salt crystal
Ion in solution

25. Dissolving of Sodium Chloride (NaCl) in Water
Salt
Electrical
attraction
Water molecules dissolve NaCl,
breaking ionic bond
Water
Water
molecules
(H2O)
Hydrogen
bonds
Edge of one
salt crystal
Ionic bond

26. Water molecules stick together as a result of hydrogen bonding
The Cohesion of Water
Water molecules stick together as a result of hydrogen bonding
This is called cohesion
Cohesion is vital for water transport in plants
Microscopic tubes

27. Surface tension
is the measure of how difficult it is to stretch or break the surface of a liquid
Hydrogen bonds give water an unusually high surface tension
Figure 2.13

28. Water Moderates Temperature
Because of hydrogen bonding, water has a strong resistance to temperature change
Water can absorb and store large amounts of heat while only changing a few degrees in temperature
Earth’s Oceans cause temperatures to stay within limits that permit life

29. constantly break and re-form
The density of ice is lower than liquid water
This is why ice floats
Hydrogen bond
Ice
Liquid water
Stable hydrogen bonds
Hydrogen bonds
constantly break and re-form

30. The Biological Significance of Ice Floating
When water molecules get cold, they move apart, forming ice
A chunk of ice has fewer molecules than an equal volume of liquid water
Since ice floats, ponds, lakes, and even the oceans do not freeze solid
Marine life could not survive if bodies of water froze solid

31. Acids, Bases, and pH Acid Base
A chemical compound that donates H+ ions to solutions
Base
A compound that accepts H+ ions and removes them from solution

32. The pH scale is used to describe the acidity of a solution
Oven cleaner
Household bleach
Household ammonia
Acidic: pH < 7
H+ > OH-
Basic: pH > 7
H+ < OH-
Neutral: pH = 7
H+ = OH-
Basic
solution
Milk of magnesia
Seawater
Human blood
Pure water
Neutral
solution
Urine
Tomato juice
Grapefruit juice
Lemon juice;
gastric juice
Acidic
solution

33. CheckPoint
Which of the following are compounds? Elements?: C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I
What is the difference between an atom and an ion? Give examples of each to support your response.
Which subatomic particle determines the identity of an atom?
Which subatomic particle determines the chemical properties of an atom?
Explain the difference between an ionic and covalent bond in terms of what happens to the electrons in the outer shell of the participating atoms.

34. Chemical Reactions and Enzymes

35. Chemical Reactions
A chemical reaction is a process that changes one set of chemicals into another set of chemicals.
The elements or compounds that enter into a chemical reaction are known as the reactants.
The elements or compounds produced by a chemical reaction are known as products.

36. Energy in Reactions
Chemical reactions can either release energy or absorb energy.
An exergonic reaction releases energy and will often occur spontaneously.
An endogonic reaction absorbs energy and will not occur spontaneously.

37. Activation energy is the energy required to get a chemical reaction started.
Burning glucose (sugar): an exergonic reaction
high
high
activation energy needed
to ignite glucose
glucose
activation
energy from
light captured
by photosynthesis
glucose + O2
energy
content of
molecules
energy
content of
molecules
net energy
captured by
synthesizing
glucose
energy released
by burning glucose
Figure :6-2
Title:
Energy relations in exergonic and endergonic reactions
Caption:
(a) An exergonic (downhill) reaction, such as the burning of sugar, proceeds from high-energy reactants (here, glucose) to low-energy products (CO2 and H2O). The energy difference between the chemical bonds of the reactants and products is released as heat. To start the reaction, however, an initial input of energy—the activation energy—is required. (b) An endergonic (uphill) reaction, such as photosynthesis, proceeds from low-energy reactants (CO2 and H2O) to high-energy products (glucose) and therefore requires a net input of energy, in this case from sunlight. Question In addition to heat and sunlight, what are some other potential sources of activation energy?
CO2 + H2O
CO2 + H2O
low
low
progress of reaction
progress of reaction
Photosynthesis: an endergonic reaction

38. Enzymes speed up chemical reactions that take place in cells.
Copyright Pearson Prentice Hall

39. “on” or “off” keys (binding proteins)
Regulation of Enzyme Activity
allosteric
regulator
molecule
Allosteric
inhibition pH
Temperature
“on” or “off” keys (binding proteins)
Up: Enzyme “off”
Down: Enzyme “on”
Competitive
inhibition
Enzyme
structure
active site
substrate
enzyme
allosteric
regulatory site
Figure :6-11
Title:
Enzyme regulation by allosteric regulation and competitive inhibition
Caption:
(a) Many enzymes have an active site and an allosteric regulatory site on different parts of the molecule. (b) When enzymes are inhibited by allosteric regulation, binding by a regulator molecule alters the active site so the enzyme is less compatible with its substrate. (c) During competitive inhibition, a molecule somewhat similar to the substrate fits into the active site and blocks entry of the substrate.
Competitive- key
Fits lock, but wont
Open door
Up: Enzyme “off”

40. Enzymes are proteins that act as biological catalyst
A Catalyst is a substance that speeds of the rate of a chemical reaction
high
activation energy
without
catalyst
activation energy
with catalyst
energy
content of
molecules
reactants
Figure :6-8
Title:
Catalysts lower activation energy, increasing the rate of reactions
Caption:
A high activation energy (black curve) means that reactant molecules must collide very forcefully in order to react. Only very fast-moving molecules will collide hard enough to react, so reactions with high activation energies proceed slowly at low temperatures, where most molecules move relatively slowly. Catalysts lower the activation energy of a reaction (red curve), so a much higher proportion of molecules move fast enough to react when they collide. Therefore, the reaction proceeds much more rapidly. Question Can a catalyst make a non-spontaneous reaction occur spontaneously?
Enzymes are proteins that act as biological catalyst
products
low
progress of reaction

41. Enzymes provide a site where reactants can be brought together and aligned properly to react.
- the reactants of an enzyme catalyzed reaction.

42. substrates active site of enzyme enzyme Figure :6-9 Title:
The cycle of enzyme–substrate interactions
Caption:
Question How would you modify reaction conditions if you wanted to increase the rate at which an enzyme-catalyzed reaction produced its product?

43. “on” or “off” keys (binding proteins)
Regulation of Enzyme Activity
allosteric
regulator
molecule
Allosteric
inhibition pH
Temperature
“on” or “off” keys (binding proteins)
Up: Enzyme “off”
Down: Enzyme “on”
Competitive
inhibition
Enzyme
structure
active site
substrate
enzyme
allosteric
regulatory site
Figure :6-11
Title:
Enzyme regulation by allosteric regulation and competitive inhibition
Caption:
(a) Many enzymes have an active site and an allosteric regulatory site on different parts of the molecule. (b) When enzymes are inhibited by allosteric regulation, binding by a regulator molecule alters the active site so the enzyme is less compatible with its substrate. (c) During competitive inhibition, a molecule somewhat similar to the substrate fits into the active site and blocks entry of the substrate.
Competitive- key
Fits lock, but wont
Open door
Up: Enzyme “off”