The Chemistry of Life

1
The Chemistry of Life

• Essential Questions
• 1. Describe atoms and how they bond
  together.
  2. What elements and compounds are important
  to living things. 3. What are
  the functions of the major groups of organic
  compounds? 4. How do enzymes speed up
  chemical reactions within the cell?

2
TERMS

• Organic, inorganic, glucose, carbohydrates, amino
  acids, proteins, nucleic acids, water, polarity,
  cohesion, starch, glycogen, chemical bond,
  element, compound, acid, base, pH, lipid, ATP,
  photosynthesis, respiration, starch,
  monosaccharide, mitochondria, chloroplast,
  aerobic, anaerobic, biological catalyst,
  recycled, enzyme, substrate, -ase, optimal
  temperature, synthesis, breakdown, lock and key

3
The Nature of Matter

• The basic unit of matter is the atom.
• What are atoms made of?
• Protons()
• Neutrons(0)
• Electrons(-)

Found in the nucleus
Orbiting the nucleus
4
The Atom
What atom is this? Hint 2 protons
5
What do you know about this equation?

• C6H12O6 6O2 --gt CO2 H2O

• Summary equation for cellular respiration
• Glucose reacts with oxygen to form carbon dioxide
  and water
• The reactants are to the left / the products are
  to the right
• The number and types of atoms

How many are there?
6
Elements and Isotopes

• An Element is a pure substance consisting
  entirely of one type of atom (found on the
  periodic table of elements)
• What determines what type of element it is?

The Atomic Number or number of protons
How many protons does Hydrogen have? Carbon?
Nitrogen? Oxygen? Phosphate?
7
Elements and Isotopes

• The mass number is the number of protons plus the
  number of neutrons
• It is written like this

Mass number (PN)
How many neutrons are there?
12
C
6
Atomic Number ( of P)
8
Elements and Isotopes

• Remember - the number of protons determines what
  element it is
• What happens if we change the number of neutrons?
  
• It is an isotope.

6 neutrons
7 neutrons
8 neutrons
12
C
13
C
14
C
6
6
6
All Carbon Atoms
9
Elements and Isotopes

• Because they have the same number of protons and
  electrons, isotopes have the same chemical
  properties
• Some isotopes are radioactive - their nuclei are
  unstable and want to break apart at a constant
  rate
• Radioactive elements can be dangerous to living
  things, but science has a lot of important uses
  for radioactive isotopes
• Treat cancer / age rocks / tracers

10
Chemical Compounds

• A compound is a substance formed by the
  combination of two or more elements
• Smallest unit of most chemical compounds is known
  as a molecule
• Molecule of water - H2O

Chemical properties of compounds are usually
different than the individual atoms that make it
up
O
H
H
11
Chemical Compounds

• Chlorine - poisonous gas
• Sodium - silver metal that reacts explosively
  with water
• Combine them you get

Sodium Chloride (NaCl) or table salt
12
Chemical Bonding

• Atoms in compounds are held together by chemical
  bonds
• Formed by the valence electrons (outer most
  electrons)
• types that we will study are
• Covalent Bonds
• Ionic Bonds
• and some hydrogen bonds

13
Covalent Bonds

• Sharing of electrons
• In living cells, covalent bond help to form large
  molecules with many thousands of atoms
• In molecular drawings, a single covalent bond
  (sharing 2 electrons) is represented by a single
  line / a double covalent bond (sharing 4
  electrons) is represented by a double line

Butadiene
H
H
H
H
H
Methane
C C C C
C
H
H
Single Bond
H
H
H
Double Bond
14
Covalent Bonds
Sharing Electrons Makes Them Happy
15
Ionic Bonds
Atoms with a positive or negative charge are
known as ions

• Transfer of 1 or more electrons from one atom to
  another
• What happens when an atom loses an electron?
• What happens to an atom that gains an electron?

0
It loses a negative so it becomes positively
charged
1
-
-


It gains a negative, so it becomes negatively
charged
0
-1
-
-
-
-
16
Ionic Bonds
Opposites Attract
17
Water
O
H
H

• What are the atoms that make up a water molecule?
• How many protons and electrons are there?
• Sounds normal, but

1 Oxygen and 2 Hydrogen
10 Protons, 10 Electrons
18
Water

• The hydrogen atoms are on the same side of the
  oxygen atom
• The oxygen atom is much larger than the two
  hydrogen atoms
• The 8 Protons of the oxygen atom attract the
  electrons more than the 2 Protons of the Hydrogen
• This gives the molecule a negative charge on one
  side and a positive charge on the other

What side will have what charge?
19
Water

• So, what does all that mean?

Water is a Polar Molecule
Negative side
O
O
H
H
Positive side


20
Hydrogen Bonds

• Opposites attract - the side will be attracted
  to the side of another water molecule
• Not as strong as covalent or ionic
• This gives water a lot of its characteristics

Cohesion is the attraction between molecules of
the same substance
Adhesion is the attraction between different
substances
21

• Cohesion

2 water molecules attracted to each other
Causes surface tension
Water goes up the glass straw
Capillary action
Adhesion
22
Solutions and Suspensions

• Mixture - two or more elements or compounds mixed
  together but not chemically combined
• Solution - mixture where one substance is
  dissolved into another substance
• Suspension - a mixture where small particles do
  not settle out (not dissolved)

Blood - cells and other materials are suspended
23

• Solutions

Water is the universal solvent
Solvent
Material that does the dissolving
CLICK HERE (NaCl H2O)
Solute
Salt and Water
http//www.chem.iastate.edu/group/Greenbowe/sectio
ns/projectfolder/flashfiles/thermochem/solutionSal
t.htmllocate
Material that is dissolved
24
Acids and Bases

• Acids
• Turn litmus paper RED and usually taste sour
• Ex. Coffee, soda, vinegar, lemons, oranges
• Have an excess of H ions
• Lower than 7 on the pH scale

25
Acids and Bases

• Bases
• Turn litmus paper BLUE, is slippery to the touch,
  and tastes bitter
• Has excess OH ions
• Ex. Ammonia, oven cleaner, soap
• Higher than 7 on the pH scale

26
pH Scale
Acids
Bases
27
Living Things and Acids and Bases

• Strong acids and bases can be harmful to living
  things
• Living things need to maintain homeostasis or a
  stable internal environment
• Cells have dissolved substances that help prevent
  sharp changes in our pH (cells are usually around
  6.5 to 7.5 on the pH scale) - these substances
  are called buffers

28
Neutralization Reaction

• When you combine an acid and a base, they
  neutralize (go back to 7 on the pH scale)
• They produce a salt and water

Acid Base --gt Salt Water
HCl NaOH --gt NaCl H2O
29
Carbon Compounds (Organic Chemistry)

• Carbon has 4 electrons in the outermost energy
  level - it wants 8
• It can either lose the 4 that it has, or it can
  gain 4 (this is unlikely - instead, it will share
  its 4 electrons with other atoms) what kind of
  bond is that?

Covalent
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Macromolecules

• giant molecules
• May consist of thousand, even hundreds of
  thousands, smaller molecules
• Formed by polymerization - large compound made by
  combining smaller compounds
• Monomers Polymers

Polymerization
31
Organic Compounds

• Carbohydrates
• Lipids
• Nucleic Acids
• Proteins

32
Carbohydrates
CHO

• Made of Carbon, Hydrogen, and Oxygen
• Usually a 121 ratio
• Sugars and Starches
• Living things use them to store energy
• Plants use them for structure (cellulose)

33
Carbohydrates(Monosaccharides)

• Single simple sugar (mono 1)
• C6H12O6
• Glucose, galactose (found in milk), and fructose

34
Carbohydrates(Disaccharides)

• 2 simple sugars (di 2)
• C12H24O12
• Sucrose (table sugar)

35
Carbohydrates(Polysaccharides)

• 3 or more simple sugars
• Animals store excess sugar as glycogen in the
  liver and muscles
• Plants store sugars as starch
• Plants also make cellulose for structure (cell
  walls)

36
Lipids

• Made of mostly Carbon and Hydrogen (some Oxygen)
• Fats, Oils, Waxes, and Steroids
• Used to store energy, insulation, and biological
  membranes

H
H
H
H
H
H
H
H
H
O
C
C
C
C
C
C
C
C
H
C
O
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
H
O
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
O
C
C
C
C
C
C
C
C
H
C
H
H
H
H
H
H
H
H
H
37
Glycerol
H
H
H
H
H
H
H
H
H
O
C
H
C
C
C
C
C
C
C
C
C
O
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
H
O
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
O
H
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
Fatty Acid
38
Lipids(Saturated vs.. Unsaturated)

• Unsaturated
• If there are double carbon bonds - it is
  unsaturated (many double carbon bonds makes it
  polyunsaturated)
• Saturated
• Contains the maximum number of hydrogen atoms

39
Nucleic Acids

• Carbon, Hydrogen, Oxygen, Nitrogen, and
  Phosphorous
• Made of monomers known as nucleotides
• DNA and RNA DNA - deoxyribose / RNA - ribose
• Nucleotides have 3 basic parts
• 5-carbon sugar
• Phosphate group
• Nitrogenous base

Nitrogenous Base
P
A
5- carbon sugar
40
Nation Human Genome Research Institute
41
Proteins

• Carbon, Hydrogen, Oxygen, and Nitrogen
• Growth and repair, energy, buffers to keep pH
  constant
• Monomers called amino acids
• Amino acids are composed of
• Amino group
• Carboxyl group
• R-group

R-Group
H H O N C C H R OH
Amino Group
Carboxyl Group
42
Proteins

• Amino Acids
• 20 different amino acids found in nature
• Can join end to end
• R-Group - many different kind / change the
  properties of the proteins

43
Amino Acids
R-Groups
44
Chemical Reactions and Enzymes

• Chemical reaction changes one set of chemicals
  into another set of chemicals
• Involves changes in chemical bonds
• Reactant - enter the chemical reaction
• Products - produced by the chemical reaction

45
Chemical Reaction
Product
Reactant
CO2 H2O ---gt H2CO3
Because carbon dioxide is not very soluble in
water, this reaction enables carbon dioxide to be
carried in the blood. The compound that is
produced is soluble in water (Carbonic Acid).
When the carbonic acid gets to the lungs, the
reaction is reversed.
H2CO3 ---gt CO2 H2O
46
Chemical Reactions (Energy)

• Some reactions release energy (exothermic),
  others absorb energy (endothermic)
• Activation energy is the energy needed t start a
  chemical reaction

----------------
---------------
----------------
Energy
----------------
----------------
----------------
Reactants Products
Reactants Products
47
Enzymes

• Biological Catalyst
• Essential to life
• Speed up virtually every important chemical
  reaction in cells w/out entering the reaction
• Most enzymes end in - ase
• Lower activation energy

48
____________
Reaction w/out enzyme
-----------
-----------------
Energy
Reaction with enzyme
Activation Energy
-----------------
Course of reaction
49
How Enzymes Work

• The reactants in an enzyme-catalyzed reaction are
  known as substrates
• Substrates attach or bind to an enzyme at the
  activation site forming an enzyme-substrate
  complex
• Enzyme is shaped so that it only locks up with
  specific substrates
• Often referred to as the lock and key

Enzyme
Substrate
Enzyme-substrate complex
50
Enzymes

• Temperature, pH, and concentration strongly
  influence enzyme action
• If either pH or temp. is too high or low, the
  reactions will be slowed
• If temperature gets too high the proteins that
  make the enzyme can denature - change their shape
  so the activation site no longer fits
• If there are only so many enzymes and a large
  amount of substrate the reaction will level off

51
Pictures Cited

• http//www.historyoftheuniverse.com/he.html
• http//www.theodoregray.com/PeriodicTable/Elements
  /017/
• http//www.mii.org/Minerals/photosalt.html
• http//www.uni.edu/iowawet/H2OProperties.htm
• http//kentsimmons.uwinnipeg.ca/cm1504/water.htm
• http//www.accessexcellence.org/RC/VL/GG/nucleotid
  e2.htm
• http//folding.stanford.edu/science.html