The Molecules of Life

What is a molecule?

Molecules <1 nm
 Ecologyisstudyofrelationshipsoforganismstoeach
otherandenvironment
Organismsingivenareaaretermedacommunity

LIVING
NonLIVING
(cells,organisms
(abiotic)
Communitiesetc.

TogethercompriseanECOSYSTEM(seeChp30)
 Atoms and Elements
Atoms
Basic unit of all
matter
Made up of three
major components
Protons
Positively charged
Electrons
Negatively charged
Neutrons
Uncharged
 Atom
Protons and neutrons are found in the nucleus
Account for the weight of the atom
Atomic mass
Electrons orbit the nucleus
Have relatively little mass
Do not contribute to the mass of the atom
Approximately 2,000 electrons = 1 proton
Protons and electrons are equal in a uncharged
atom
 Atoms and Elements
Elements
Substance that consists of a single type
of atom
92 naturally occurring elements
99% of all living matter by weight made up of four
Carbon
Hydrogen
Oxygen
Nitrogen
Phosphorus and sulfur make up additional 0.5%
 Oxygen radical formation
(reactive oxygen species -ROS)

http://www.healthinternetwork.org/antioxidants-winning-the-fight-against-free-radicals/
The most abundant element in the
universe is hydrogen, which makes
up about 3/4 of all matter! Helium
makes up most of the remaining
25%. Oxygen is the third most
abundant element in the universe.
All of the other elements are
relatively rare.
Determinants of atmosphere that can
sustain life; what are the problems in
Venus and Mars?

https://www.ucar.edu/learn/images/plangas.gif
www.mysciencebox.org/book/export/html/526
Deep Sea Hydrothermal Vent Communities -black smokers
 Chemical Bonds and the
Formation of Molecules
Atoms are most stable when the outer orbital
contains the maximum number of electrons
2, 8, 8 etc.
To fill outer orbitals atoms form bonds with
other atoms to fill outer orbitals
Bonds are formed with the sharing or the gain or
loss of electrons
Molecules are formed when atoms bond together
 Chemical Bonds and the
Formation of Molecules
There are several types of chemical bonds
They also vary in strength
Chemical bonds include

Covalent bonds
Ionic bonds
Hydrogen bonds
 Covalent Bonds

Achieve stability through the

sharing of electrons
between atoms
Creates a strong bond
Difficult to break
Requires significant energy
usually in the form of heat
Never break spontaneously at
physiological temperatures
Enzyme required to break at
lower temperature
Bonds can be polar or non-
polar
Chemical Compounds of the Cell

Most important molecule is water

Makes up over 70% of all living organisms
by weight
Importance of water depends on it unusual
bonding properties
physical laws on a large scale are due to
chaos on a small scale. the order-from-
disorder principle.
 Hydrogen Bonds
Weakest of the biological bonds
Constantly being formed and broken at room
temperature
At room temperature the average lifetime of a
single hydrogen bond is a fraction of a second
Large numbers of hydrogen bonds can hold
molecules together firmly
Like numerous stitches in clothing
One stitch wont hold a shirt together but numerous
stitches will
 Bonding Properties of Water
Hydrogen bonds
form between
positively charged
hydrogen of one
molecule and
negatively charged
oxygen of another
Hydrogen bonding
produces a polar
molecule
 IONs are CHARGED atoms
Polar nature accounts for ability
to dissolve numerous
compounds
Water is known as universal solvent
Molecules that dissolve in water
must contain charged atoms
- attraction due to opposite
charges
NaCl readily dissolves in water
forming Na+ ions and Cl- ions
Ions become surrounded by water
Na+ and Cl- ions no longer able to
bond to each other

Ionicbonding
http://www.youtube.com/watch?v=QqjcCvzWwww
 pH
Acidity is measured as pH
Defined as concentration of H+
ions
potential Hydrogen
Measured on logarithmic scale
of 0 to 14
0 highly acid
14 highly alkaline (basic)
Acidity based on ionization of
water to H+ and OH- ions
When H+ and OH- ions are equal
solution is neutral
High H+ = acid
High OH- = base
We could wipe out all of the plants and
animals in the world, and life would
eventually return. However, if we wiped
out all of the microbes, our planet would
be as barren as the surface of the moon

Lynn Margulis
The meme has started.
https://www.nasa.gov/content/nasas-journey-to-mars
 Small Molecules in the Cell
All cells contain small organic and inorganic molecules
Approximately 1% of dry weight of bacteria composed of
inorganic ions
Na+, K+, Mg2+, Ca2+, Fe2+, Cl-, PO43- and SO42-
Certain enzymes require positively charged ions for proper
functioning
Negatively charged phosphate ions are essential in energy
metabolism
Small organic molecules act as precursor metabolites
These are converted to the building blocks of
macromolecules
 Macromolecules and Their
Subunits
All macromolecules are polymers
Poly = many
Large molecules formed by
joining smaller subunits
together
Joining subunits together
involves dehydration
reaction
H2O is removed during
chemical reaction
Reaction termed
dehydration
synthesis
What is the definition of organic?
4 major classes of biological
macromolecules

Nucleic acids

Proteins

Carbohydrates

Fatty acids/lipids
 Reverse
Transcription
e.g. HIV

The Blueprint

A second messenger

Central Dogma
Enzymes, cell building blocks
 Nucleic Acids
Two types of nucleic acid
DNA
Carries genetic code in all cells
RNA
Decodes sequence of amino acids to produce
proteins
Subunits of nucleic acids are nucleotides
 Master molecule
DNA
Determines specific properties of
the cell
Nucleotides are composed of three
units
Nitrogen containing ring
compound
Nitrogenous base
Purine
Adenine and guanine
Pyrimidine
Thymine and cytosine
Five carbon sugar molecule
Deoxyribose
Phosphate molecule
 DNA
DNA in living organisms is a double
stranded helical molecule
Strands are held together by hydrogen
bonding between the nitrogen bases
Specific pairing between bases
Adenine binds to thymine
A-T or T-A
Guanine binds to cytosine
G-C or C-G
Bases are complementary
 Does arsenic
equal
phosphorus?

Nature 474:19; June

2, 2011;
go.nature.com/oaetjq
Mono lake
http://www.webelements.com/
http://www.nasa.gov/topics/universe/features/astrobiology_toxic_chemical.html

http://www.popsci.com/science/article/2010-12/nasas-arsenic-loving-bacteria-doesnt-love-arsenic-after-all-critics-say
http://blogs.discovermagazine.com/loom/2011/08/02/didrosie
redfieldjustrefutearseniclifeonherblog/
 RNA
Involved in decoding DNA
Structure is similar to DNA
Differs in a number of ways
Thymine is replaced by uracil
There is no thymine base in RNA
The sugar is ribose in place deoxyribose
RNA is generally shorter
Exists as a single stranded molecule not double
stranded
 Lipids
Critical component of the cell membrane
Membranes act a gatekeepers to the cell
Often determines what enters or leaves the cell
Heterogeneous group of molecules
Made up of different subunits
Defining feature
Insoluble in water
Smallest of the four macromolecules
Can be divided into two general classes
Simple lipids
Compound lipids
 Simple Lipids
Contain only carbon,
hydrogen and oxygen
Most common are called
fats Fatty acids bond to glycerol
Solid at room temperature covalently through dehydration
Made of glycerol and fatty synthesis
acids
Fatty acids are long
hydrocarbon chains
(R) plus an acid group
(COOH) at the end
Glycerol is carbon hydrogen
chain with three hydroxyl
(OH) groups attached
Allows for the binding of
three fatty acids to one
glycerol
Triglyceride
 Simple Lipids
Steroids are also considered
simple lipids
Differ from fats in structure
and function
Structure consists of
four- membered ring
Classified as lipid because
steroids are insoluble in
water
If one of the rings has a
hydroxyl (OH) group
attached it is classified as a
sterol
Example: cholesterol
Compound Lipids
Contain fatty acids, glycerol
and other elements
Phospholipid most
important compound lipid
Phospholipid is made up of a
phosphate and two fatty acids
attached to a glycerol
molecule
Phosphate head is polar
and soluble in water
Hydrophilic
Fatty acids are non polar
and insoluble in water
Hydrophobic
 Separating inside from outside
Phospholipids
Major component in lipid cell
membrane
Membrane is a double or
bilayer of phospholipids
Hydrophilic heads orient
towards internal and
external environments
Hydrophobic tails orient
themselves away from
aqueous environment
towards each other
Membrane acts as a barrier
to the entry and exit of
cellular substances

http://www.youtube.com/watch?v=Qqsf_UJcfBc
New research on smart molecules

http://www.youtube.com/watch?v=zpgMIh6q2os
Proteins
 Proteins and Their Functions
Constitute over 50% of cell dry weight
Made up of amino acid subunits
Most versatile
Some responsibilities include
Catalyzing reactions
Composition and shape of certain bacterial
structures
Gene regulation
Nutrient procurement
 Amino Acid Subunits
Proteins are composed of numerous
combinations of 20 amino acids
Protein function depends on the shape
of the protein
Protein shape depends on the sequence of
amino acids
 Amino Acid Subunits
All amino acids have the
following shared features
A carboxyl group
(COO-)
An amino group (NH2+)
A central carbon
A side chain
The side chain
differentiates the
amino acids Amino acids are
subdivided
based on similarities of
the side chain
Study Table 2.4 for functional groups
So there is directionality in the peptide chain
 Protein Structure
Proteins have four structures

Primary
Secondary
Tertiary
Quaternary
 What were the primary take home
messages of chapter (2)?

Atoms, elements and molecules comprise living systems

Elements are joined by chemical bonds

Which element is more reactive - C, H or O, and why?

4 major biological molecules

Which ones used for energy

Which are most common carbohydrates on the planet?
Proteins are 3 DIMENSIONAL
2ndary structures
ENZYME

Lock and Key model

YPPang2006
Inositolphosphatase
mRNA Amino acid
Carbohydrates

Carbohydrates serve as energy stores,

fuels, and metabolic intermediates
(e.g. starch, glycogen)
Lustic, RH et al, Nature
(2012)
Sucralose (Splenda)
Chemical structure: Sugar combined with chlorine
Safety: It is safe and no reason to think it will cause harm
Calories: none. Our bodies cannot burn sucralose for energy HAS BEEN FOUND offshore

Sugar Alcohols (maltitol, sorbitol, xylitol, lactitol, isomalt, erythritol etc.)

Chemical structure: Hydrogen atom added to sugars.
Safety: Considered safe but large amounts may give you diarrhea, bloating and gas.
Calories: Some are poorly absorbed (hence the diarrhea) and provide very few calories while others may provide
75% of calories. They dont raise blood sugars as rapidly as sugar but they will still provide calories.

Aspartame (SweetN Low, Equal, Nutrasweet)

Chemical structure: 2 amino acids combined (phenylalanine and aspartic acid)
Safety: Pretty sure it is safe but there is still some question. Some experience headaches. No supporting evidence
related to claims on the internet about aspartame causing multiple sclerosis, Alzheimers or cancer.
Calories: it is so sweet that only tiny amounts are needed to sweeten foods

Stevia (sweet leaf)

Chemical Structure: Derived from a plant
Safety: Animal studies have found increase testicular cell proliferation and reduced sperm production in male rats
and found smaller and fewer offspring in female rats
Calories: Our bodies cant metabolize it.

Saccharin (Hermesetas)
Chemical Structure: Synthetic chemical
Safety: Unsafe. May cause bladder cancer in humans
Calories: our bodies cant metabolize it

Cyclamate (Sugar Twin, SweetN Low (pink packet)

Chemical Structure: synthetic chemical
Safety: Banned for use in foods. Seems to increase potency of carcinogens. Cyclamates may also damage the male
reproductive organs. Also not recommended during pregnancy. Still available as tabletop sweetener.
Calories: Not metabolized

http://www3.telus.net/eatingforenergy/081704.htm
Carbs are in abundance!
Carbohydrates are probably not involved in
early chemical evolution because,

Polymerization of carbs require enzyme catalysis;

possible ribozyme that can form glycosidic linkages
not yet identified

Carbohydrate structure is too simple - lack diversity

of functional groups found in amino acids

Self-replication not possible - no coding information

or complimentary base pairing
 Carbohydrates contain carbon, hydrogen and
oxygen in 1:2:1 ratio
Each carbon atom is bound to two hydrogen atoms
and one oxygen atom
CH2O
Polysaccharide
large molecules made of carbohydrate molecules
Oligosaccharide
short chains of carbohydrates
Monosaccharide
Single carbohydrate molecule
 Carbohydrate Properties
Monosaccharide
Classified by number of carbons in
molecule
Most common monosaccharides
5 and 6 carbon sugars
5 carbon sugars = pentose
Ribose and deoxyribose

6 carbon sugars = hexose

Glucose, fructose and
galactose
 Disaccharides
Produced by joining two monosaccharides
through dehydration synthesis
Lactose and sucrose most common in
nature
Lactose = Glucose + galactose
Sucrose - Glucose + fructose
Maltose less common
Glucose + glucose = maltose
 Polysaccharides
Serve different function
Cellulose most abundant organic molecule on earth
Polymer of glucose molecules
Principle constituent in plant cell wall
Glycogen is carbohydrate storage molecule of
animals and some bacteria
Polymer of glucose subunits
Dextran storage molecule for carbon and energy for
some bacteria
Polymer of glucose subunits
Polymers are multiple sugar units covalently bound
ModelBacterium
CELL WALL AND CYTOPLASMIC MEMBRANE
All bacteria except the mycoplasmas have cell walls
that protect and determine the shape of the cell.
Cell wall of eubacteria contain a polymer known as
PEPTIDOGLYCAN (PDG) ;PDG is made up of
repeating disaccharride units attached to amino acids
The monosaccharides forming the disaccharides are
N-acetyl glucoseamine (NAG) and N-acetylmuramic
acid (NAM)
NAG and NAM are linked in rows to form the
carbohydrate backbone and adjacent rows are linked
by the amino acids.
Bacteria are divided into two groups based on the
chemical components outside the peptidoglycan layer
i.e Gram staining characteristics
N-acetylmuramic acid N-acetyl glucoseamine
 Basis of Human
H ABO blood Group
Antigen system
--> Type of
carbohydrate
(glycoprotein)
expressed on
blood cells
B Depends on
enzyme
yellow shade: minimal
determinant or core
structure; blue arrow:
residue added by blood

A group gene product;

Dark brown = GalNAc

Pink = Gal
Red= Fuc
Pale= GlcNAc
http://www.bioc.aecom.yu.edu/bgmut/abo.htm
Question of the Day*:
Which type of the
four major molecules
type makes the best
vaccine ?