Biochemistry
Chapter 3
What does “Organic” mean?
One version of “Organic”
Organic
=Substance having Carbon and Hydrogen
Can also have:
1.
2.
3.
4.
5.
6.
7.
8.
Phosphorus
Sulfur
Iron
Calcium
Sodium
Chlorine
Magnesium
Potassium
Organic Compounds
• Glucose (C6H12O6)
• CH4
• CH3CH2OH
Inorganic Compounds
•
•
•
•
H20
CO2
H2SO4
NaCl
Water Facts
• What percent of our
body weight is water?
65%
Can we live without water?
Why Not?
Chemical Reactions
• Need to occur in water (ie. In solution)
Chemical Properties of Water
• Cohesion
Cohesion in Life
Water drop shape
Surface Tension
Cohesion
• High Boiling Point
• Can absorb much
heat before
evaporation
• Sweating
Chemical Properties of Water
• Adhesion
– Water molecules
attracted to
substances other than
water
– Ex. Capillary Action
Classes of Organic Compounds
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic Acids
Major Elements
C, H, O
C, H, O
C, H, O, N
C, H, O, N
Carbohydrates
• C, H, O
• H:O ratio of 2:1
• Monomer= Most Simple Subunit
– Monosaccharide (simple sugar) C6H12O6
• The –ose molecules
• Energy role in life
Monosaccharide
Glucose
Monosaccharide
Monosaccharide
Disaccharides
=a double sugar
=two simple sugars connected
Disaccharides
Disaccharides
Disaccharides
Lactose
Oligosaccharides
• 3-20 monomers
• Found in vegetables
• Ex. Raffinose and Stachyose
Polysaccharides
• Many simple sugars connected
• Polymer
Polysaccharides
Starch
Polysaccharides
Cellulose
Polysaccharides
Polysaccharides
Glycogen (“animal starch”)
How do we connect monomers?
Dehydration Synthesis
Dehydration Synthesis
• Glucose= C6H12O6
• Maltose= C12H22O11
How do we break apart polymers?
Hydrolysis
Water & Enzymes
Uses of Carbohydrates?
Lipids
• C,H,O
• H:O ratio much greater than 2:1
– Ex. C17H35COOH (Stearic Acid)
• Examples:
– Fats ( ex.Triglycerides),
– Oils (Olive, canola),
– Waxes (Bees, Ear)
– Steroids (Testosterone)
– Terpenes (Bio Pigments, Rubber)
Monomers of Lipids
• Glycerol
3 hydro-carbons with 3
hydroxyl groups
Monomers of Lipids
•Fatty Acid
=chain of hydro-carbons with a carboxyl
group at the end
Lipid Triglyceride(Polymer)
Saturated
Unsaturated
Dehydration Synthesis to
get O-bridge
Loss of 3 waters
Lipid –Phospholipid (Polymer)
Saturated vs. Unsaturated Fats
Saturated Fats
•
•
•
•
•
•
Butter
Lard
Whole Milk
Other Animal Products
Rich diet leads to increased cholesterol
Rich diet leads to Heart Disease and
Arteriosclerosis
Hydrogenated fats
=add Hydrogen to liquid
unsaturated fats to make them
solid saturated fats
Uses of fats?
•Cushioning
•Warmth
•Secondary energy source
•Part of cell membranes (lubrication)
Proteins
• C,H,O,N
• Make up cartilage, bone, muscles
• Make up hormones, antibodies and
enzymes
Amino Acid or Peptide (Monomer)
(R-Group)
20 kinds of amino acids
Vary in R-Group
How do you connect multiple
peptides?
Dehydration Synthesis
Dipeptide
Peptide Bond
Polypeptide
Chain of amino acids
Shape and Proteins
• Shape determines your job!
• Proteins are not functional until they have
reached their final shape
• Lose of shape=Lose of function
Sequence of Shape Formation
1. Primary Structure= Peptides connected
by peptide bonds
Sequence of Shape Formation
2. Secondary Structure: Alpha-Helix and Beta Pleated
sheet structure held by Hydrogen Bonds
Hydrogen Bonding
Much H-bonding
Less H-bonding
Protein Structure
3. Tertiary Structure: Globular or Fibrous
shape held in place by Hydrogen bonds,
Hydrophobic/Hydrophilic Interactions, ionic
bonds, disulfide bonds
Protein Shape
4. Quaternary Structure=Multiple
polypeptide chains connected
Multiple bond types hold
chains together
Heat Shock Proteins:Molecular
Chaperons
Heat Shock Proteins
• 1962 Ferruccio Ritossa
• Heated flies and noticed some genes being
expressed
• HSPs are an ancient survival mechanism
• Activated during stress (heat, cancer,pathogens)
• Help protein chains fold
• Escorts protein chains to their mates
• Protects proteins from falling apart in heated
situations
• Help recycle damaged proteins
Enzymes-Great Examples of
Proteins!
• Biological Catalysts=affect rate of reaction
without being consumed or changed by
the reaction
• Very Specific
• The “ase” people (ex. Maltase, Sucrase..)
Note: Reactions can also be catalyzed by
RNA
Enzymes
Active Site
Models of Enzyme Action
Vs.
Lock and Key vs. Induced Fit (Both Occur)
Both Reversible
(On/Off Switch)
Enzyme Inhibition
• Sarin Nerve Gas
– Permanent blocking
– Blocks acetylcholinesterase function
– Muscles permanently contracted
What affects the speed of enzyme
action?
1. Temperature
Optimal Temp
What affects the speed of enzyme
action?
2. pH
Optimal pH
What affects the speed of enzyme
action?
3. Substrate Concentration Video Click Here
What affects the speed of enzyme
action?
4. Coenzymes (organic ex. Vit. B6, B12,
NAD, FAD) and Cofactors (Inorganic ex.
Mn, Fe, Mg, Zn)
Enzymes lower Activation Energy
(Energy to break old bonds)
Nucleic Acids
• C,H,O,N
• Genetic Material=blueprint of body passed
from parent to child
Monomer
• Nucleotide
Types of Nitrogenous Bases
Pyrimidines
Purines
Polymer- Nucleic Acid
• DNA=Deoxyribonucleic Acid
– Genetic Material=blueprint of body passed
from parent to child
• RNA=Ribonucleic Acid
– Rough copy of DNA
DNA Structure
• Double-stranded alpha helix
• Has the sugar, deoxyribose
• Structure “discovered” by Watson and
Crick (Really Rose Franklin)
• All DNA of a human cell lined up would
span 2 meters
– Diameter of cell’s nucleus only 0.000005
meters…
DNA
Hydrogen Bonds
Phosphodiester
Linkages
Base Pairing Rules
• TAGC
Genes
Segments of
DNA that are the
codes for certain
characteristics
Chromosomes
=DNA and Histones
• If you were to write out your own genome
using four letters to represent the four
nucleotides, you would write more than 3
billion letters. Using 12 point font, you
would fill about a thousand textbooks
RNA
• Single-stranded
• Has the sugar, ribose
• Many forms: transfer RNA (t-RNA),
ribosomal RNA (r-RNA), messenger RNA
(m-RNA)
• Lacks Thymine
• Has in place Uracil instead of Thymine
RNA
RNA act as an enzyme?
• Yes!
• Ribozymes=catalytic RNA
• Can help assemble RNA chains or cut
RNA or form peptide linkages