Transcript The Chemical Basis of Life Chapter 2 What’s Matter? Nothing…what’s matter with you? • Any substance that has mass and occupies space it matter •

The Chemical Basis of Life
Chapter 2
What’s Matter?
Nothing…what’s matter with you?
• Any substance that has mass and
occupies space it matter
• An element is the purest form of matter – it
cannot be broken down into a simpler
substance
• Matter is composed of atoms, or one can
say an Element is represented by a
specific type of atom
92 Natural Elements
Ag
S
Hg
• Silver, Sulfur and Mercury are examples of
naturally occurring elements
• Others are laboratory synthesized radioactive
elements - some of these decay rapidly.
Technitium, a radioactive silver-gray metal was
first to be synthesized. Plutonium, Promethium,
Francium are other examples. Some of these
man made elements (like Francium) actually do
occur in nature in extremely minute amounts
Tc - Technitium
87
Francium
25 Elements Needed for Life
• 25 of the 92 elements are found
in all life forms
• The 4 most common elements
make up 96% of a cell. They are:
Hydrogen (H), Oxygen (O),
Carbon (C), Nitrogen (N)
• Others such as Phosphorus (P),
Sulphur (S), Potassium (K),
Calcium (Ca), etc. account for the
remaining 4%
• Trace elements are those
required in minute quantities. Eg.
Boron, Iodine, Iron, chromium,
zinc, manganese, selenium,
silicon, tin, vanadium,
molybdenum, cobalt, copper and
flourine.
Goiter – Thyroid enlargement
Atoms and subatomic particles
Particle
electron
Representation
Relative
charge
Relative
mass
-1
1
1800
proton
+1
1D
neutron
o
1D
• Atoms are the smallest units of
matter that have the properties of
the element they represent
• An atom can be split into many
different subatomic particles, but
only three are stable enough to
have been studied for many
decades: Protons, Neutron and
Electrons
• Protons – positively charged, have a mass of about 1 dalton
• Neutrons – electrically neutral, mass close to 1 dalton
• Electrons – negatively charged; their mass is about 1/1800 of
protons and neutrons, so it can be ignored
• So the mass of an atom = number of protons + number of
neutrons
• The atomic number = the number of protons
ATOMS
• Atoms are the smallest units of matter that have all the
characteristics of an element – they cannot be broken
down into simpler substances without losing the
properties of the element they represent
• All matter solid, liquid or gas is made up of atoms
• Atoms are made up of sub-atomic particles
For example, an iron atom is the smallest unit
of iron that has all the characteristics of the
element iron. A helium atom (right) is the
smallest unit of helium that has all the
characteristics of the element helium.
Atoms are the building blocks of everything in
the universe.
Sub-atomic Particles
Most atoms are made up of three subatomic particles:
1. A positively charged particle called a Proton
2. A particle with no charge (neutral) called a neutron
3. A negatively charged particle called an electron
Protons and neutrons are found packed together, in the
center of the atom, called the nucleus.
Electrons orbit around the nucleus in their own orbitals, at
speeds close to that of light – they are so fast in fact, that
the region around the nucleus where they are found is
called the electron cloud.
Protons :Atomic number
• Protons are found in the nucleus
• They have a positive (+) charge
• Each atom of the same element is characterized by a certain
number of protons in the nucleus. That number is called the
atomic number.
• Atomic number (number of protons) cannot change for the
same element! In other words, all oxygen atoms will have 8
protons, all carbon atoms will have 6 protons
• Protons have a mass of 1 amu (atomic mass unit) each
Neutrons – subatomic glue
• Neutrons are also found in the nucleus –
they are tightly bound to the protons, and
keep the protons from repelling each other
• They have zero charge – they are neutral
• Atoms of the same element can have
different number of neutrons – these are
called isotopes
• Neutrons also have a mass of 1 amu each
• The sum of the masses of protons and
neutrons in the nucleus is called the
atomic mass number
Isotopes of Hydrogen
Hydrogen 1 (hydrogen)
Hydrogen 2 (deuterium)
Hydrogen 3 (tritium)
1 proton, 0 neutrons
Mass number = 1
1 proton, 1 neutron
Mass number = 2
1 proton, 2 neutrons
Mass number = 3
SAME ELEMENT – DIFFERENT ATOMS BECAUSE OF DIFFERENT
NUMBER OF NEUTRONS.
Chemical Bonds
When atoms complete their valence shell by either sharing or
transferring unpaired valence electrons, they tend to stay close together
– this is a chemical bond
Covalent Bonds
Sharing of valence electrons by atoms –
Extremely strong bonds
a. Non-polar – electrons shared equally –
hydrophobic
- single, double and triple bonds
b. Polar – electrons spend more time closer to
the more electronegative atom - hydrophilic
Electronegativity is the tendency of an atom to attract electrons.
IONIC BONDS
When electrons are lost or gained by atoms, they become charged atoms or
ions. A negatively charged ion is an anion, a positively charged ion is a
cation. Anions and cations are attracted to each other and form an ionic
bond. These bonds are weaker than covalent bonds.
Difference between Covalent and Ionic bonds
Water
In liquid water at 37 ˚ C, each water molecule has hydrogen bonds with 4
other water molecules. These weak bonds constantly break and form with
other water molecules nearby – this gives water its fluidity.
Water – the solvent of life
• The polarity of a water molecules helps it dissolve ionic and
hydrophilic substance easily
Water molecules dissociate
• Because oxygen is so
electronegative, in water
molecules all the
electrons (even those of
hydrogen) spend more
time around the oxygen
molecule
• Sometimes, the oxygen
molecule dissociates from
one hydrogen, but keeps
its electron – so the
hydrogen is now a proton
(H+) and the hydroxide
molecule is (OH-)
The pH Scale
• pH stands for Potential of Hydrogen
• It is a measure of the concentration of H+ in
a solution
• Acids have high concentrations of H+ and
low OH-, whereas bases have the opposite
• The pH of pure water is 7, or neutral – it
has equal number of H+ and OH- ions
Increasing [H+]
Decreasing [OH-]
[H+] and [OH-] equal
Increasing [OH-]
Decreasing [H+]
Acids and Bases
• Acids taste sour, are corrosive to metals,
change litmus (a dye extracted from lichens) red,
and become less acidic when mixed with bases
– Acids have low pH values 0 - 6.9
• Bases feel slippery, change litmus blue, and
become less basic when mixed with acids
– Bases have high pH values – 7.1 - 14
Biological Macromolecules
• Carbohydrates
– Sugars
– Starch, Glycogen
– Cellulose, Chitin
• Lipids
– Triglycerides, Phospholipids, Steroids
• Proteins
• Nucleic Acids
Carbohydrates
• The building blocks of carbohydrates are
simple sugars or monosaccharides (single
sugars) and disaccharides (double sugars)
• Important monosaccharides are: Glucose,
Fructose and Galactose
Structure of some Monosaccharides
(also known as dextrose)
Sugars are named for the number of carbons in the backbone
Sugars end in “ose”
Linear versus Ring forms
Sugars tend to change into ring
forms when placed in an aqueous
solution. Here is an example of
straight chain glucose changing
into its ring form.
α and β forms of glucose
OH group on top
OH group on the bottom
When the glucose molecule takes on a ring form, it can form one
of 2 isomers. The tiny difference between these two isomers of
the same molecule means that the polysaccharide that they form
is different. The 2 isomers, α and β forms of glucose is evident
in the diagrams above.
Making Disaccharides
• 2 glucose molecules bond covalently to form maltose
• 1 fructose and 1 glucose bond to form sucrose (table sugar)
• 1 glucose and 1 galactose bond to form lactose (found in milk
and dairy products)
People who are lactose intolerant, do not
make lactase, an intestinal enzyme that
hydrolyzes lactose into its constituent
monosaccharides, glucose and galactose
which can then be easily absorbed into
the blood, across the intestinal lining.
When lactose cannot be broken down, it
ferments in the gut and causes bloating,
diarrhea, flatulence, etc.
70% of the world population is lactose
intolerant. However, only 10% of
Europeans are.
Making Polysaccharides
• Multiple monosaccharides form chains by
forming covalent bonds through
dehydration synthesis. These covalent
bonds are called glycosidic linkages.
• Polysaccharides can be considered either
“storage polysaccharides” or “structural
polysaccharides”, based on their structure
and role in cells.
Storage Polysaccharides
• Starch
Plants store their sugars as starch – a
polysaccharide (pennies vs. dollars)
- Starch is made up of α-Glucose
-Starch is stored in chloroplasts
• Glycogen
Animals store their sugars as glycogen
– Glycogen is also made of α-Glucose
– Animals store glycogen in the liver and muscle cells
Starch and glycogen – storage
polysaccharides
Structural Polysaccharides
• Cellulose
Plants have cellulose in their cell walls, which
protects their cells from damage
Cellulose is made from β-Glucose
• Chitin
Fungal cell wall contain chitin, as do the
exoskeletons of arthropods such as insects,
crustaceans, arachnids, etc. Chitin is made from
β-Glucose
Cellulose – a structural polysaccharide
Most animals cannot digest cellulose
(fiber). Cows, sheep, termites and
many other animals rely on bacteria in
their intestinal tracts to breakdown
cellulose into glucose monomers for
them. Bacteria are one of the few
organisms that produce an enzyme
called cellulase, which hydrolysis the
glycosidic bonds between betaglucose monomers. This is mutualistic
symbiosis.
Chitin – a structural polysaccharide
Starch is made up of
alpha-glucose
molecules
In cellulose, every other
beta-glucose molecule
is upside down.
Lipids
• The lipid family consists of fats, oils,
waxes, phospholipids and steroids.
• All lipids are hydrophobic (completely or
partially)
• Lipids are an important storage
macromolecule. They also are good
insulators and shock absorbers.
Fatty acids are the building blocks
of lipids
No double or triple
bonds – filled with
hydrogens – fatty
acid is straight
Contains double or
triple bonds – not
filled with
hydrogens – fatty
acid is bent
Triglycerides
• Are made up of 3 fatty acids covalently bound to a 3carbon alcohol called glycerol
• The 3 covalent bonds are formed through dehydration
synthesis – 3 H2O molecules are lost
• The fatty acids can be saturated or unsaturated
Triglycerides
• Saturated triglycerides are found in animals –
butter, lard, etc.
They are solid at room temperature, because
the fatty acids are straight (no double bonds)and
can “pack” together
• Unsaturated triglycerides are found in plants and
fish – they are called oils and are liquid at room
temperature – because the fatty acids are bent
(double or triple bonds) and cannot “pack”
together
Saturated vs. unsaturated
triglycerides or fats vs. oils!!
Saturated: found
in animals and is
solid at room
temperature
Unsaturated:
found in plants
and fish; is liquid
at room
temperature
Phospholipids
• Phospholipids are 2 fatty acids and a phosphate group
that are covalently bonded to a glycerol
• The Fatty acids tails are hydrophobic and the phosphate
head is hydrophilic
• Phospholipids compose cell membranes
Phospholipid Bilayers
• The hydrophilic phosphate regions (Heads) interact with
the water inside and outside the cell. The fatty acids of
the phospholipids (Tails) interact and form a
hydrophobic center of the bilayer.
Steroids
• Another major class of
lipids is steroids, which
have structures totally
different from the other
classes of lipids.
• Lipid steroids include
such well known
compounds as
cholesterol, sex
hormones (estrogen
and testosterone), birth
control pills, etc.
Proteins
• Proteins can be categorized into several
different families, depending on their role
in a living organism
• Amino acids are the building blocks of
proteins
• There are over 150 amino acids, only 20
of which are used in protein building, by all
organisms
An amino acid
2 is in the Zwitterion state – when a compound can exist as an
anion and a cation at the same time
Dipeptides, Polypeptides
• Amino acids are joined end – to –end by
enzymes through dehydration synthesis, to
form polypeptides (releasing a water
molecules as a by product)
• The covalent bond that forms between the
carbon of one amino acids and the nitrogen
of another is called a peptide bond.
Polypeptides
• A long chain of covalently bonded amino acids is
called a polypeptide (many peptide bonds).
N-terminus
C-terminus
Protein structure
• Once a polypeptide forms, it tends to fold
into several possible structures
• These structures form due to various types
of bonding and chemical interactions
between the amino acids in the chain
Primary Structure
• The first level of structure is called
primary structure.
• The primary structure of a peptide or
protein is simply the sequence of
amino acids or the polypeptide chain.
• The primary structure is held together
by peptide (covalent) bonds
Secondary Protein Structure
-Helix and -pleated sheets
•Depending on the sequence of amino
acids, a polypeptide chain can fold in a
number of ways.
•In an  - helix, hydrogen bonding between
every fourth amino acid maintains the
structure
•In -pleated sheets, the hydrogen bonding
is between adjacent amino acids
•Secondary structures are held together by
hydrogen bonds
Secondary Protein Structure
-Helix and -pleated sheets
•In an  - helix, hydrogen bonding between every fourth amino acid maintains the structure
•In -pleated sheets, the hydrogen bonding is between adjacent amino acids in parallel rows
Tertiary Structure
• This occurs when the protein folds into a
complex 3-dimensional shape
• It involves many different kinds of bonds
and interactions between amino acids side
chains
• These proteins are usually called globular
and are soluble in water
• Enzymes are examples of globular
proteins
Tertiary Structure
Quaternary Structure
• When multiple tertiary
structures interact to
form a more complex
globular protein, it is
called a quaternary
structure
• Hemoglobin is a protein
made up of 4 tertiary
protein chains
• The quaternary structure
is usually held together
by hydrogen bonds
between the chains
Protein Structure Summary, cont’d.
Nucleic Acids
• Category consists of DNA and RNA
• DNA = Deoxyribonucleic Acid, RNA = Ribonucleic Acid
• DNA is double stranded, contains the sugar deoxyribose and
the nitrogenous bases Thymine, Adenine, Guanine and
Cytosine
• RNA is single stranded (usually), contains the sugar ribose and
the nitrogenous bases Uracil, Adenine, Guanine and Cytosine
Incorporation of Nucleotides into DNA
The Nitrogenous Bases
• They are Nitrogen-containing
compounds that are basic in
nature – but overall, DNA is
mildly acidic
• Divided into Purines and
Pyrimidines
• Purines are larger in structure
than pyrimidines
• Adenine and Guanine are
purines
• Cytosine, Thymine and Uracil
are pyrimidines
• A and T or A and U can form 2
Hydrogen bonds
• G and C form 3 Hydrogen bonds
(a stronger alliance than A-T)
Guanine and Cytosine
Adenine and Thymine
3’ to 5’ direction
Sugar-phosphate backbone
5’ to 3’ direction
Sugar-phosphate backbone
DNA is antiparallel.
One strand runs 5’ to
3’ and the other 3’ to
5’. This is the only
configuration that will
allow proper H bond
formation and
distances between
the bases.
DNA in a nutshell
• 2 antiparallel strands
• Sugar-Phosphate backbone
held together by
phosphodiester bonds
• Sugar phosphate backbones
on the outside
• Bases stacked on the inside
• Purine-pyrimidine pairing,
stabilized by H bonds (G=C)
and (A=T)
DNA - View from the top
DNA gets packaged into
a chromosome
Types of RNA
THE END