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
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?
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)?
YPPang2006
Inositolphosphatase
mRNA Amino acid
Carbohydrates
Saccharin (Hermesetas)
Chemical Structure: Synthetic chemical
Safety: Unsafe. May cause bladder cancer in humans
Calories: our bodies cant metabolize it
http://www3.telus.net/eatingforenergy/081704.htm
Carbs are in abundance!
Carbohydrates are probably not involved in
early chemical evolution because,