Lecture 2
Cell chemistry and
biosynthesis
CHEMISTRY OF LIFE
• Elements: simplest form of a
substance - cannot be broken
down any further without
changing what it is
• Atom: the actual basic unit composed of protons, neutrons,
and electrons
THE ATOM
• Just like cells are the basic unit of life,
the ATOM is the basic unit of matter.
• They are very small. If placed side by
side one million would stretch a
distance of 1cm.
• The atom is made up of 3 particles.
Particle
Charge
PROTON
+
NEUTRON
NEUTRAL
ELECTRON
-
• Electrons are not present within the atom,
instead THEY REVOLVE AROUND THE NUCELUS
OF THE ATOM & FORM THE ELECTRON CLOUD
• Draw a helium atom. Indicate where the
protons, neutrons and electrons are.
NEUTRONS
-
ELECTRONS
PROTONS
+
ATOMIC # = 2
(PROTONS)
+
-
ATOMIC MASS = 4
(PROTONS &
NEUTRONS)
COMPOUNDS
• a substance formed by the chemical
combination of 2 or more elements in definite
proportions
– Ex: water, salt, glucose, carbon dioxide
TWO TYPES OF COMPOUNDS
• Organic - Contain C, H, and O in
some ratio (usually referred to as
chemicals of life)
–
Carbohydrates, Proteins, Lipids, Nucleic Acids
• Inorganic - usually "support" life - no
specific ratio of C, H, and O
–
Water (H2O), Carbon Dioxide (CO2)
IONIC BONDS
• Occur when 1 or more electrons are
TRANSFERRED from one atom to another.
• When an atom loses an electron it is a
POSITIVE charge.
• When an atom gains an electron it is a
NEGATIVE charge
• These newly charged atoms are now called
IONS
– Example: NaCl (SALT)
COVALENT BONDS
• Occur when electrons are SHARED by atoms.
• These new structures that result from covalent
bonds are called MOLECULES
• ** In general, the more chemical bonds a
molecule has the more energy it contains
SHARING IS CARING!
70% of a cell’s weight is water
Cells contain four major families of small organic molecules
Glucose monomer
Monosaccharide to
disaccharide
Maltose = Glucose + Glucose
Sucrose= Glucose + Fructose
Lactose = Glactose + Glucose
PolysaccharideGlycogen
Fatty acids are usually
covalently linked other
molecules by their
carboxyl group in a cell
Lipids and phospholipids
Lipids: a loosely defined collection of biological molecules
which are insoluble in water while being soluble in fat and
organic solvents such as benzene. They either contain
long hydrocarbon chains, as in the fatty acids and isoprenes,
or multiple linked aromatic rings,
such as in the steroids.
Examples: fatty acids and their derivative such as triacylglycerols
Phospholipids: amphipathic
Some fatty acids contain double bonds between carbons
Essential structure
of a cell!!!
Amino acids and proteins
Nucleotides and nucleic acids
FUNCTIONAL GROUPS
• There are certain groups of atoms that are frequently
attached to the organic molecules we will be studying,
and these are called functional groups.
• These are things like hydroxyl groups which form
alcohols, carbonyl groups which form aldehydes or
ketones, carboxyl groups which form carboxylic acids,
and amino groups which form amines.
Macromolecules are abundant in cells
Noncovalent bonds specify both the precise shape of a
macromolecule and its binding to other molecules
Metabolic pathways and
their interconnections
500 reactions
Two opposing streams
of chemical reactions
As we age, the
balance slowly shifts
towards a more
catabolic dominant
metabolism
Second law of thermodynamics
Greater
entropy
Oxidation of Organic Molecules
The carbon cycle
Oxidation and Reduction Involve
Electron Transfer
Oxidation: Removal of electron
Example: Fe2+  Fe3+
Reduction: Addition of electron
Example: Cl  Cl-
Enzymes lower the activation energy,
thus speed up chemical process
A peptide bond
The 20 amino acids found in proteins
Three types of noncovalent bonds driving protein folding
Polar amino acid side chains gather on the outside
Secondary structure: α helix
Formed by hydrogen bonds in the polypeptide backbone
Secondary structure: β sheet
Formed by hydrogen bonds in the polypeptide backbone
Coiled-coil:
from hydrophobic α helices
Protein domains (40-350 aa): modular units
Protein Dimerization: It is a quaternary structure of a protein
A “tetramer”
A tetramer of two different subunits
Sizes and shapes of domains and proteins
Actin polymers:
important components
of cytoskeleton!
Self-assembly of a macromolecule aggregate
Proteins don’t work alone: Protein-protein interactions
between functional groups of proteins-challenges in “post-genome” era