Download CP-Bio Ch 3(Chemistry of Life)

Chapter 3
The Chemistry of Life
Atoms
• Atoms- the smallest particles that make up
all matter
– Protons(+): positively charged particles found
in the nucleus of an atom
– Neutrons(o): neutral particles found in the
nucleus of an atom
– Electrons(-): negatively charged particles
found outside of the nucleus
Model of the Atom
Elements
• Elements are substances made of only one
type of atom
– Ex: O2(oxygen)
H2(hydrogen)
O3(ozone)
Ions
• Ions are atoms that have lost or gained
electrons
• Ions have a positive(+) or negative(-) charge
Lose
Na
Electron
Na
+
Positive ion
_
Gain
Cl
Electron
Cl
Negative ion
Compounds & Molecules
• Compounds and Molecules are formed
when 2 or more different elements are
bonded together
• Ex: Compound- Salt(NaCl)
Molecule- Water(H2O)
Molecular Formulas
• Molecular formulas show the kind and # of
atoms in a molecule
– H2O = 2 hydrogen atoms + 1 oxygen atom
– CO2 = 1 carbon atom + 2 oxygen atoms
– C6H12O6 = 6 carbon atoms + 12 hydrogen atoms
+ 6 oxygen atoms
– NaCl = 1 sodium ion(Na) + 1 chlorine ion(Cl)
Physical Changes
• A physical change is a change in the size,
shape, or state of a substance
– Ex: melting, freezing, molding clay, cutting wood
Chemical Change
• Chemical change occurs when atoms combine or
separate to create new substances
• Chemical changes use or give off energy
• Ex: Combustion(burning)
C3H8 + O2

CO2
+ H2O
propane + oxygen  carbon dioxide + water
• Ex: Oxidation(rusting)
Fe + O2  Fe2O3
iron + oxygen  ironoxide(rust)
Bonding
• Bonding is a force of attraction holding
atoms together
• Types of Bonding:
– Covalent Bonds
– Ionic Bonds
– Hydrogen Bonds
Covalent Bonds
• Covalent bonds form when 2 or more
neutral atoms share electrons to form a
molecule
– Ex: H2O(water)
-Ex: CO2(carbon dioxide)
Ionic Bonds
• Ionic bonds form when 2 or more ions
become held together by their opposite
charges
• Ex: NaCl(salt)
– Positive ions are attracted to negative ions
Hydrogen Bonds
• Hydrogen bonds hold together water
molecules
Types of Chemical Reactions
Condensation Reactions- combine simple
molecules to make a more complex molecule
* Water(H2O) is produced as a byproduct
Hydrolysis Reactions- break apart complex
molecules into simpler molecules
* Water(H2O) and enzymes are often used to break
the complex molecules down
Examples of Reaction Types
Condensation Reaction:
Hydrolysis Reaction:
2 H2O2 --> O2 + 2 H2O
Acids & Bases
• Acids- contain large amounts of
hydrogen(H+) ions
– Acids turn pH paper RED
Ex: stomach acid(HCl), vinegar, citric acid
• Bases- contain large amounts of
hydroxide(OH-) ions
– Bases turn pH paper BLUE
Ex: bleach, ammonia, soap
Neutral Substances
• Neutral substances have equal amounts of
hydrogen(H+) and hydroxide(OH-) ions
Ex: water (H2O), alcohol (C2H5OH), oil
- neutral substances do not change pH paper
Biochemistry
Chemistry pertaining to
Biology
Inorganic= molecules derived from nonliving things
Organic = molecules derived from living things
18
Organic Compounds
• Compounds that contain CARBON
are called organic.
• Macromolecules are large organic
molecules.
19
Carbon (C)
• Carbon has 4 electrons in outer
shell. Can bond in many ways
• Carbon can form covalent bonds
with as many as 4 other atoms
Usually with C, H, O or N.
• C joins with other C atoms to
form chains or rings
• Example: C6H12O6(glucose)
20
Macromolecules
• Large organic molecules.
• Also called POLYMERS.
• Made up of smaller “building blocks”
called MONOMERS.
• Examples:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids (DNA and RNA)21
Carbohydrates
22
Carbohydrates
• Small sugar molecules to large
complex carbohydrates.
• Monosaccharides typically have a
formula that is CH2O
• Carbohydrates have 2:1 Ratio of
Hydrogen to Oxygen atoms
• Examples:
A.
B.
C.
monosaccharide(glucose)
disaccharide(sucrose)
polysaccharide(cellulose)
23
Carbohydrates
Monosaccharide: one sugar unit
Examples:
glucose
glucose (C6H12O6)
deoxyribose
ribose
Fructose
Galactose
24
Isomers
• Glucose and Fructose are
isomers containing same atoms
but in different arrangements
giving them different properties
25
Carbohydrates
Disaccharide: two sugar unit
Examples:
– Sucrose (glucose+fructose)
– Lactose (glucose+galactose)
– Maltose (glucose+glucose)
glucose
glucose
26
Carbohydrates
Polysaccharide: many sugar units
Examples: starch (bread, potatoes)
glycogen (beef, muscle)
cellulose (lettuce, corn)
glucose
glucose
glucose
glucose
cellulose
glucose
glucose
glucose
glucose
27
Lipids
28
Lipids
• General term for compounds which are
not soluble in water.
• Lipids are soluble in hydrophobic
solvents.
• Remember: “stores the most energy”
• Examples: 1. Fats
2. Phospholipids
3. Oils
4. Waxes
5. Steroid hormones
29
6. Triglycerides
Lipids
Six functions of lipids:
1. Long term energy storage
2. Protection against heat loss
(insulation)
3. Protection against physical shock
4. Protection against water loss
5. Chemical messengers (hormones)
6. Major component of membranes
(phospholipids)
30
Lipids
Triglycerides:
composed of 1 glycerol and 3
fatty acids.
H
O
H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
O
H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
O
fatty acids
H-C----O C-CH -CH -CH -CH
2
2
2
H
glycerol
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Fatty Acids
There are two kinds of fatty acids you may see
these on food labels:
1. Saturated fatty acids: no double bonds
saturated
O
C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
2. Unsaturated fatty acids: double bonds
(“good fats”)
unsaturated
O
C-CH2-CH2-CH2-CH
32
Proteins
• Made from: carbon(C), hydrogen(H), oxygen(O),
& nitrogen(N)
33
Proteins (Polypeptides)
• Amino acids (20 different kinds of aa)
bonded together by peptide bonds
(polypeptides).AA=monomer
• Six functions of proteins:
1. Storage:
albumin (egg white)
2. Transport:
hemoglobin
3. Regulatory:
hormones
4. Movement:
muscles
5. Structural:
membranes, hair, nails
6. Enzymes:
cellular reactions
34
Proteins (Polypeptides)
Four levels of protein structure:
A.Primary Structure
B. Secondary Structure
C. Tertiary Structure
D.Quaternary Structure
35
Primary Structure
Amino acids bonded together
by peptide bonds (straight
chains)
Amino Acids (aa)
aa1
aa2
aa3
aa4
aa5
aa6
Peptide Bonds
36
Secondary Structure
• 3-dimensional folding arrangement of a
primary structure into coils and pleats
held together by hydrogen bonds.
• Two examples:
Alpha Helix
Beta Pleated Sheet
Hydrogen Bonds
37
Tertiary Structure
• Secondary structures bent and folded
into a more complex 3-D arrangement
of linked polypeptides
• Bonds: H-bonds, ionic, disulfide
bridges (S-S)
• Call a “subunit”.
Alpha Helix
Beta Pleated Sheet
38
Quaternary Structure
• Composed of 2 or more
“subunits”
• Globular in shape
• Form in Aqueous environments
• Example: enzymes (hemoglobin)
subunits
39
Nucleic Acids
• Made from: carbon(C), hydrogen(H), oxygen(O),
nitrogen(N), & phosphorus(P)
40
Nucleic acids
• Two types:
a. Deoxyribonucleic acid (DNAdouble helix)
b. Ribonucleic acid (RNA-single
strand)
• Nucleic acids are composed of long
chains of nucleotides linked by
dehydration synthesis. (condensation)
41
Nucleic acids
• Nucleotides include: (are monomers)
phosphate group
pentose sugar (5-carbon)
nitrogenous bases:
adenine (A)
thymine (T) DNA only
uracil (U) RNA only
cytosine (C)
guanine (G)
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Nucleotide
Phosphate
Group
O
O=P-O
O
5
CH2
O
N
C1
C4
Sugar
(deoxyribose)
C3
C2
Nitrogenous base
(A, G, C, or T)
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DNA
double
helix
O
5
3
O
P
5
3
O
C
G
1
P
5
3
2
4
4
2
3
1
P
T
5
A
P
3
O
O
P
5
O
3
5
P
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How are all these molecules formed ?
• Reactions that create complex molecules:
Condensation Reactions(remove water)
• Monomers split/break down from each
other by Hydrolysis(add water)
45
Enzymes!!!
Enzymes are biological catalysts – they speed up the
chemical reactions that take place inside all cells, but
without being used up in the process.
There are many thousands of different types of enzyme,
and each one catalyzes a different reaction.
Enzymes occur naturally in all organisms, but they are
increasingly being used in industrial processes.
Enzymes speed up reactions
Enzymes speed up reactions by lowering the activation
energy (Ea) of a reaction. The activation energy is the
energy needed to start a reaction.
Different reactions have different activation energies.
energy (kJ)
Ea without enzyme
Ea with enzyme
reaction (time)
Shape is VERY Important
The shape of an enzyme is very important because it has
a direct effect on how it catalyzes a reaction.
An enzyme’s shape is
determined by the sequence of
amino acids in its structure, and
the bonds which form between
the atoms of those molecules.
Different types of enzymes have different shapes and
functions because the order and type of amino acids in
their structure is different.
Enzymes are Specific
Enzymes are very specific about which reactions they
catalyze. Only molecules with exactly the right shape will
bind to the enzyme and react. These are the reactant, or
substrate, molecules.
The part of the enzyme to
which the reactant binds is
called the active site.
This is a very specific shape
and the most important part
of the enzyme.
What happens at the active site?
In the same way that a key fits into a lock, so a substrate
is thought to fit into an enzyme’s active site. The enzyme
is the lock, and the reactant is the key.
↔
+
enzyme
+
reactant
↔
↔
enzyme-reactant
complex
+
↔
enzyme
+
products
The lock and key model
Factors affecting enzymes
The rate of enzyme-catalyzed reactions depends on
several factors. What are some of these?
Factors that affect the rate of a reaction include:
 temperature
 substrate concentration
 pH
 surface area
 enzyme concentration
 pressure.
All enzymes work best at only one particular temperature
and pH: this is called the optimum.
Different enzymes have different optimum temperatures
and pH values.
Factors affecting enzymes
If the temperature and pH changes sufficiently beyond an
enzyme’s optimum, the shape of the enzyme irreversibly
changes.
This affects the shape of the active site and means that
the enzyme will no longer work.
When this happens the enzyme is denatured.
heat
pH
normal
denatured
Enzymes and temperature
Enzymes: true or false?
Co-Enzymes
Co-Enzymes- help enzymes to perform
properly
- Vitamins often function as co-enzymes
- These molecules help the enzyme and
substrate fit together better at their active
sites