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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Chapter 3: Biological Molecules
Functional Groups (Table 3.1)
A) Methyl Group
• Non-polar (hydrophobic)
• Lipids
B) Hydroxyl Group
• Polar (hydrophilic)
• Carbohydrates
C) Carboxyl Group
• Acidic (H+ dissociates)
• Fatty acids / amino acids
D) Amino Group
• Basic (H+ bonds)
• Amino acids / Nucleic acids
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?
Two reasons:
Silicon does not form double and
triple bonds
Silicon-based life from
star trek.
Silicon precipitates in water
Another versatile solvent
would be needed.
Some life does utilize silicon to
form shells.
Diatoms
Silicon 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):
General Function
Category
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.
How are Organic Molecules Synthesized?
Dehydration Synthesis: To form by removing water
Hydrolysis: To break apart with water
The Carbs
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Biological Molecules: Carbohydrates
What Are Carbohydrates?
• Molecules composed of carbon, hydrogen, and
oxygen (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
• Fold up into rings in solution:
(e.g. glucose)
Monosaccharide Types:
1) 6-C Backbone (C6H12O6)
• Glucose (most common)
2) 5-C Backbone (C5H10O5)
• Ribose / Deoxyribose
• Fructose (corn sugar)
• Galactose (milk sugar)
RNA
DNA
Functional roles of monosaccharides
• Fuel (especially
glucose)
• Raw material for
synthesis of other
monomers
Amino acids
Fatty acids
Glucose is the primary fuel
for 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.
Biological Molecules: Carbohydrates
Carbohydrates - Disaccharides:
• Two sugar molecules linked (dehydration synthesis):
(Figure 3.1)
• Short-term energy storage
Disaccharide Types:
1) Sucrose = Glucose + Fructose
2) Lactose = Glucose + Galactose
3) Maltose = Glucose + Glucose
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)
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Biological Molecules: Carbohydrates
• 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
Termites can digest cellulose
Starch
(Digestible)
Cellulose
(Indigestible)
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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Biological Molecules: Carbohydrates
• Structural Material:
Chitin
Exoskeleton - insects / crabs / spiders
Fungus cell walls
• Nitrogen functional groups attached to glucose sub-units
(Figure3.5)
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.
Biological Molecules: Lipids
• 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
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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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Biological Molecules: Lipids
(Figure 3.8)
Types of Lipids:
1) Oils & Fats
2) Waxes:
3) Phospholipids:
Similar in structure to fats / oils except 1 of 3 fatty acids
replaced by phosphate group
Found in plasma membrane of cells
Phospholipids
• Hydrophilic head
• Hydrophobic tail
• The main component of
the plasma membrane.
Know this molecule well, you will see it
again in future chapters!
Biological Molecules: Lipids
Types of Lipids:
1)
2)
3)
4)
Oils & Fats
Waxes:
Phospholipids:
Steroids:
Cholesterol
• 4 rings of carbon with functional
groups attached
Hormones
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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
H
H
H
C
N
OH
C
O
R
Variable R-group
Biological Molecules: Proteins
• Molecules composed of 1 or more chains of amino acids
Amino Acids:
• A central carbon with four bonds:
1) An amine group (-NH2)
2) A carboxyl group (COOH)
3) A hydrogen
4) A variable group (R)
Biological Molecules: Lipids
Amino Acids:
• 20 unique amino acids
• Amino acid characteristics depend on variable (R) groups
Hydrophilic
Hydrophobic
Disulfide Bonds
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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
2) Secondary
Sequence of
amino acids
Hydrogen bonds
between AAs
3) Tertiary
Disulfide bonds
between AAs
Hydrophilic / phobic
interactions
between AAs
4) Quaternary
Hydrogen bonds
between peptide
chains (2 or more)
(Hemoglobin)
Helix
Pleated Sheet
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.
β-pleated
sheet
α-helix
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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
β
β-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)
4) Transport
(e.g. hemoglobin)
3) Energy Storage
(e.g. albumin)
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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Biological Molecules: Nucleic Acids
What Are Nucleic Acids?
• Molecules composed of nucleotides:
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 housing
the genetic code for an organism
2) Ribonucleic Acid (RNA)
• A copy of the genetic code which
directs the synthesis of proteins
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
A gene is a
region of DNA
• Information storage
A gene encodes the amino acid sequence of a
polypeptide.
Stored in a linear sequence of dNTs (nucleotides)
Functions of DNA
• Information transmission (gene expression)
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Other Functions of Nucleotides:
cAMP
ATP
Cyclic
Nucleotides
Nucleotides with Extra
Phosphate Groups
• Intracellular
messengers
• Energy transfer molecules
Coenzymes
• 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)
Agent is a protein (no genome, no genes!)
Misfolded form of a normal
brain protein (PrPc)
Remember that protein
folding is CRUCIAL for
proper function!
Cellular function of
the prion is unknown
at this time
PrPc
Prion
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Disease mechanism
Fig 18.13
1. Prion binds
to PrPc
2. PrPc misfolding
3. Chain
reaction
Exposure to prions causes normal
proteins to misfold and become prions.
Effect of prions on brain morphology
Normal brain tissue
brain tissue infected
with prions
Transmission of BSE
Consuming prion-infected tissue
(mostly neural tissue like brains)
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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.
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