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Chapter 3: Biological Molecules
Stanley Miller - 1953
• Spontaneous synthesis of
complex organic compounds
Stanley Miller experiment
Early earth
volcanic gases
organic molecules
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Carbon is the main component of organic molecules.
• Organic molecules = carbon skeleton
• Inorganic molecules = no carbon skeleton
• What makes carbon special?
�Carbon has four electrons in the valence (outer) shell.
• This allows carbon to potentially bind with four different atoms or molecules.
�Allows for single, double or triple bonds.
C C C C
Carbon is the main component of organic molecules.
• Carbon atoms can form single, double and triple bonds.
• This characteristic allows carbon chains, rings and many branches = very diverse molecules!
�Branches can be different molecules. These molecules act as functional groups.
• Functional Groups: Determine characteristics of molecules
Molecular diversity arising from carbon
skeleton variation
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Functional Groups (Table 3.1)
A) Methyl Group
B) Hydroxyl Group
C) Carboxyl Group
• Non-polar (hydrophobic)
• Lipids
• Polar (hydrophilic)
• Carbohydrates
• Acidic (H+ dissociates)
• Fatty acids / amino acids
D) Amino Group
• Basic (H+ bonds)
• Amino acids / Nucleic acids
Chapter 3: Biological Molecules
What about silicon?
• Silicon is located just below carbon.
• Silicon also has four electrons in its valence shell.� So why don’t we have silicon based life forms?
Silicon-based life from
star trek.
Two reasons:� Silicon does not form double and
triple bonds
�Silicon precipitates in water
�Another versatile solvent
would be needed.
Some life does utilize silicon to
form shells.
� DiatomsSilicon used by diatoms
on earth
Ok, Carbon is versatile. So what?
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Nearly all biological molecules can be grouped into one of four general categories (Table 3.2):
Category General Function
1) Carbohydrates • Energy source• Structural material
2) Lipids • Energy storage• Structural material
3) Proteins • Structural material• Catalyze cell processes
4) Nucleic Acids • Store genetic material• Transfer genetic material
How are Organic Molecules Synthesized?
Answer: They are synthesized by a modular approach
• Sub-units are added one to another
• Single sub-unit = monomer (“one part”)
• Long chains of monomers = polymer (“many parts”)
Monomer (glucose) Polymer of glucose monomers (polysaccharides)
Polymer diversity
• 10,000’s of different macromolecules
• Very small number of monomers
Proteins
20 monomers
Nucleic Acids
5 monomers
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How are Organic Molecules Synthesized?
• Biological molecules subtract or add water as they
are joined together or broken apart.
• Subtract water = dehydration reaction
�Joins monomers to form polymer chain.
• Add water = hydrolysis reaction
�Breaks apart polymers into individual monomers.
Dehydration Synthesis: To form by removing water
Hydrolysis: To break apart with water
How are Organic Molecules Synthesized?
The Carbs
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What Are Carbohydrates?
• Molecules composed of carbon, hydrogen, andoxygen (1:2:1)
• Composed of water-soluble sugar molecules:
• Monosaccharide = Single sugar (e.g. glucose)
• Disaccharide = Two sugars (e.g. sucrose)
• Polysaccharide = Many sugars (e.g. starch / glycogen)
• Important as:
1) Energy source for most organisms
2) Structural support (plants / insects)
Biological Molecules: Carbohydrates
Carbohydrates - Monosaccharides:
• Backbone of 3 - 7 carbons = (CH2O)n
Monosaccharide Types:
• Fold up into rings in solution:
(e.g. glucose)
2) 5-C Backbone (C5H10O5)
• Ribose / Deoxyribose
1) 6-C Backbone (C6H12O6)
• Glucose (most common)
• Fructose (corn sugar)
• Galactose (milk sugar) RNA DNA
Biological Molecules: Carbohydrates
Functional roles of monosaccharides
• Fuel (especially
glucose)
• Raw material for
synthesis of other
monomers
�Amino acids
�Fatty acids
Glucose is the primary fuelfor your brain
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Hypoglycemia
• Low blood sugar
�Glucose levels are below normal
• Symptoms of hypoglycemia
�Shakiness
�Anxiety
�Mood changes
�Dizziness
�Fatigue
• Many of these occur because the brain is starved for glucose.
Carbohydrates - Disaccharides:
• Two sugar molecules linked (dehydration synthesis):
Disaccharide Types:
1) Sucrose = Glucose + Fructose
2) Lactose = Glucose + Galactose
3) Maltose = Glucose + Glucose
• Short-term energy storage
(Figure 3.1)
Biological Molecules: Carbohydrates
Carbohydrates - Polysaccharides:
• Multiple sugar molecules linked together
1) Long term energy storage:
A) Starch (1000 - 500,000 glucose molecules)
• Found in roots and seeds (plants)
(Figure 3.3)
Biological Molecules: Carbohydrates
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• Carbohydrates - Polysaccharides:
� Multiple sugar molecules linked together
• Long term energy storage:
� Glycogen (1000 - 100,000 glucose
molecules, often with many branches)
� Found in skeletal muscle and liver
(animals)
• Humans can store ~ 2000 calories worth
of glycogen.
Biological Molecules: Carbohydrates
• Structural Material:
� Cellulose (Plants - composes cell wall)
� Not digestible by most animals �dietary fiber = prevents colon cancer
Starch(Digestible)
Cellulose(Indigestible)
Biological Molecules: Carbohydrates
Termites can digest cellulose
Ruminants
• Rumen:
�Main organ for digestion
of cellulose
�The first compartment of
a ruminant’s stomach
�Microbes in the rumen
digest cellulose into
mono or disaccharides.
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• Structural Material:
� Chitin
�Exoskeleton - insects / crabs / spiders
�Fungus cell walls
• Nitrogen functional groups attached to glucose sub-units
(Figure3.5)
Biological Molecules: Carbohydrates
The Fats
Lipids
• Composed of
�1 Glycerol
�A sugar alcohol.
�3 fatty acids
(triglycerides)
• Dehydration reaction
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Fatty Acids
• Long hydrocarbon skeleton
• Terminal carboxyl group
�Palmitic acid : Palm oil
Fatty Acids
• Hydrocarbon (HC) skeleton may vary in:
�Length (number of carbon atoms)
�Number and location of double bonds.
�The 3 fatty acids may be same or different.
Types of fatty acids
• Saturated fatty acid: No C=C double bonds
�Think of it as saturated with single bonds.
• Unsaturated fatty acids: 1 or more C=C double bonds.
�Double bonds add “kinks” to the chain.
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Types of fatty acids
• Saturated fatty acids
�Butter, Lard, Coconut oil, Palm kernel oil
• Mostly solid at room temperature
�Straight chains pack tightly together.
Types of fatty acids
• Monounsaturated fatty acids
�One and only one double bond in chain.
�Liquid at room temperature, but will solidify if refrigerated.
�Olive oil, Peanut oil Olive Oil
Types of fatty acids
• Poly unsaturated fatty acids
�Tend to be liquid at room
temperature
�Omega 3 oils, canola oil,
safflower oil, corn oil
Canola oil
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Melting points of fatty acids
Types of fatty acids
• Unsaturated fats are liquid at room temperature because
the double bonds create kinks
�Prevents tight packing of molecules.
• Types of Lipids:
� Oils & Fats
� Waxes:
� Similar in structure of saturated fats (solid at room temp.)
• Functions of waxes :
� Form waterproof outer covering
� Structural material
Biological Molecules: Lipids
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Essential Fatty Acids (humans)
• Humans cannot make them, must be obtained from diet.
�was called Vitamin F before analyses found that they were more associated with lipids instead of vitamins.
Hydrogenated fats: What are those?
• Hydrogenated fats are polyunsaturated oils that have been exposed to hydrogen gas.
�This breaks double bonds and adds the hydrogen atoms.
�This process makes the polyunsaturated oil more solid at room temperature.
Function of lipids
• Mammals:
�Store tissues in adipose cells
• Also used for cushioning & insulation
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Types of Lipids:
� Similar in structure to fats / oils except 1 of 3 fatty acidsreplaced by phosphate group
1) Oils & Fats
2) Waxes:
3) Phospholipids:
(Figure 3.8)
� Found in plasma membrane of cells
Biological Molecules: Lipids
Phospholipids
• Hydrophilic head
• Hydrophobic tail
• The main component of
the plasma membrane.
Know this molecule well, you will see it again in future chapters!
Types of Lipids:
1) Oils & Fats
2) Waxes:
3) Phospholipids:
4) Steroids:
• 4 rings of carbon with functional
groups attached
Cholesterol
Hormones
Biological Molecules: Lipids
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Other lipids
• The steroids
�Including cholesterol.
• Are these lipids good or bad for humans???
Cholesterol
• Membrane component
�Regulates cell fluidity over a
temperature range.
�Involved with bile
manufacturing
�Aids in absorbing fat soluble
vitamins (A, D, E & K)
Lipid function
• Hormones
�Precursor of hormones is
cholesterol.
• Includes sex hormones
�Estrogen, Testosterone
• Cortisol
�Stress hormone
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Different steroids have different functional groups
Estradiol and testosterone differ only by the
function group at the left.
What are anabolic steroids?
• Anabolic steroids are analogs of natural hormones
�Almost all of them are androgenic (testosterone)
• Used in normal dosages, can help with certain
diseases
�Bone marrow stimulation
�Wasting diseases (AIDS, Cancer)
�Male puberty delay
IF you were offered a drug that promised 5
years of making gold medals, but the drug
would kill you in 7 years…
would you still take it?
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Anabolic steroid abuse
• When excess anabolic steroids are administered:
�Greater muscle mass
�More hair (especially in female athletes)
�More aggression (‘roid rage)
�Testicular atrophy
�Cardiac pathologies
�Hypertension (high blood pressure)
Admitted Steroid abuser
Did anabolic steroids kill Lyle Alzado?
• Former NFL player in the 70’s and 80’s
• Died of brain cancer in 1992 at age 43.
• Convinced steroids caused his cancer, spoke out against steroid use.� But doctors state that there is no link to
brain cancer and steroid abuse.
• Used growth hormones harvested from corpses, instead of synthetic steroids.
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Steroids
• Steroids are necessary for life (even cholesterol!)
�Testerosterone and estrogen necessary for reproduction
�Cholesterol is needed for structural integrity of cell
membrane, absorption of vital vitamins.
• But as with all things, moderation is best!
The proteins
Proteins
• Have many structures, resulting in a wide range of
functions
�10,000’s of different proteins
�Most structurally complex molecule known
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Polypeptides
• Polypeptides are polymers of amino acids.
• Amino acids are made up of 4 components
attached to central alpha (α)carbon
C
HOH
CO
R
NH
H
Variable R-group
• Molecules composed of 1 or more chains of amino acids
Amino Acids:
• A central carbon with four bonds:
3) A hydrogen1) An amine group (-NH2)
2) A carboxyl group (COOH) 4) A variable group (R)
Biological Molecules: Proteins
• 20 unique amino acids
• Amino acid characteristics depend on variable (R) groups
Amino Acids:
Hydrophilic Hydrophobic Disulfide Bonds
Biological Molecules: Lipids
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Amino acid polymers = polypeptides
• Amino acids joined together
by a dehydration reaction.
• Resulting covalent bond =
peptide bond.
Polypeptides have different ends
• N-terminus (amino)
�Located at the beginning of the polypeptide.
�Amino end always has the nitrogen atom.
• C-terminus (carboxyl)
�Located at the end of the polypeptide.
�Carboxyl end always has the carbon.
H2N- -COOH
Polypeptide backbone
• NCCNCCNCC…
polymer chain of
proteins.
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Protein Structure Dictates Protein Function!
Levels of Protein Structure:
1) Primary
Sequence of
amino acids
3) Tertiary
Disulfide bondsbetween AAs
Hydrophilic / phobicinteractions
between AAs
HelixPleated Sheet
2) Secondary
Hydrogen bonds
between AAs
4) Quaternary
Hydrogen bondsbetween peptide
chains (2 or more)
(Hemoglobin)
Denaturing = loss of secondary / tertiary structure
Four levels of protein structure
• Primary (10)
�Is the unique sequence of all
amino acids in the
polypeptide chain.
Four levels of protein structure
• Secondary (20)
• Folding patterns that result
from H-bonding of the
backbone atoms.
α-helixβ-pleated
sheet
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Polypeptides can be a mix
• Polypeptides are
often a mix of the
two secondary
structures.
Four levels of protein structure
• Tertiary (30)
�Folding patterns due to interactions between R
GROUPS (mostly).
Four levels of protein structure
• Quaternary (40)
• Aggregation of two or more polypeptides
�Polypeptides = “protein subunits”
• Same structure as tertiary, only combined with other tertiary protein subunits.
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Hemoglobin: example of quaternary structure
• Final shape of the protein is very important for proper function.
Protein conformation alterations
• Protein conformation can be affected by a single
mutation, resulting in an amino acid change.
�E.g. sickle cell disease
Caused by a single amino acid change, which changed the
folding pattern of the protein.
Effect: blood cell sickling >> severe anemia
Physical/chemical conditions
• Changes in pH, salt concentration, and
temperature can cause proteins to denature
�Unwind from folded structures.
denaturation
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Renaturation: refolding
• Spontaneous for some simple proteins.
�But not for more complex proteins.
Misfolded proteins and disease
• Dementia associated with 2 misfolded proteins
�ββββ-amyloid
Causes plaques
• Tau protein
�Causes neurofibrillary tangles
normal Alzhemiers
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Functions of Proteins (Table 3.3):
1) Catalyze Chemical
Reactions (e.g. amylase)
2) Structure
(e.g. keratin)
3) Energy Storage
(e.g. albumin)
4) Transport
(e.g. hemoglobin)6) Hormones
(e.g. insulin)
5) Movement
(e.g. muscle fibers)7) Poisons
(e.g. venom)
The Story Behind Hair...
Nucleic acids
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• Molecules composed of nucleotides:
What Are Nucleic Acids?
1) 5-carbon sugar (Ribose or deoxyribose)
2) Phosphate group
3) Nitrogen-containing base (5 types)
Biological Molecules: Nucleic Acids
Nucleic Acid Types (based on sugar in nucleotide):
1) Deoxyribonucleic Acid (DNA)
• Sequence of nucleotides housingthe genetic code for an organism
2) Ribonucleic Acid (RNA)
• A copy of the genetic code whichdirects the synthesis of proteins
Biological Molecules: Nucleic Acids
Polymerization of nucleic acids
• NTs joined via a dehydration
reaction.
• Bonds connecting NTs:
phosphodiester linkage
� sugar-phosphate backbone
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DNA
• Double-stranded double helix
�Strands held together by
hydrogen bonds
�Hydrogen bonds = base-pairing
between complementary bases
(aka nucleotides).
�Cytosine = Guanine
�Thymine = Adenine
Roles of nucleic acids
• Information storage
�A gene encodes the amino acid sequence of a
polypeptide.
�Stored in a linear sequence of dNTs (nucleotides)
A gene is a
region of DNA
Functions of DNA
• Information transmission (gene expression)
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Other Functions of Nucleotides:
Cyclic Nucleotides
cAMP
• Intracellularmessengers
ATP
Nucleotides with ExtraPhosphate Groups Coenzymes
• Energy transfer molecules • Assist enzyme
action
Case study: Prions
� Infectious agents in animals
� Proteinaceous infectious particles.
• Cause degenerative brain diseases:
�Kuru (humans)
�Scrapie (sheep)
�BSE (“mad cow disease”)
�Wasting disease (deer, elk)
�Creutzfeld-Jacob disease (humans)
Misfolded form of a normal
brain protein (PrPc)
�Remember that protein
folding is CRUCIAL for
proper function!
Agent is a protein (no genome, no genes!)
PrPc Prion
Cellular function of
the prion is unknown
at this time
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Disease mechanism
2. PrPc misfolding
Fig 18.13
1. Prion binds to PrPc
3. Chain reaction
Exposure to prions causes normal proteins to misfold and become prions.
Effect of prions on brain morphology
brain tissue infected with prions
Normal brain tissue
Consuming prion-infected tissue
(mostly neural tissue like brains)
Transmission of BSE
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Prion disease transmission
• Kuru
�Occurred in New Guinea among the Fore tribe.
�Medical puzzle that stumped researchers because it affected mostly women and children.
�Mystery solved in the 1950s when it was discovered that the Fore tribe was cannibalistic, eating their dead relatives’s brains as a funeral rite.