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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

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?

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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• 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


The Carbs

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)


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)


• 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.


• Structural Material:

� Cellulose (Plants - composes cell wall)

� Not digestible by most animals �dietary fiber = prevents colon cancer

Starch(Digestible)

Cellulose(Indigestible)


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)


The Fats

Lipids

• Composed of

�1 Glycerol

�A sugar alcohol.

�3 fatty acids

(triglycerides)

• Dehydration reaction

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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• Saturated fatty acids

�Butter, Lard, Coconut oil, Palm kernel oil

• Mostly solid at room temperature

�Straight chains pack tightly together.


• 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


• Poly unsaturated fatty acids

�Tend to be liquid at room

temperature

�Omega 3 oils, canola oil,

safflower oil, corn oil

Canola oil

Melting points 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

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


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


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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

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.

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 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.


• Secondary (20)

• Folding patterns that result

from H-bonding of the

backbone atoms.

α-helixβ-pleated

sheet

Polypeptides can be a mix

• Polypeptides are

often a mix of the

two secondary

structures.


• Tertiary (30)

�Folding patterns due to interactions between R

GROUPS (mostly).


• 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

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

• 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)

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 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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