Chemical Foundations
Cell Chemistry
 Molecules are compounds
 The interaction of these molecules with each other
determines how the cell works
 The types of interactions that molecules have with
each other depend on the chemical properties of each
of the molecules
 Understanding the types of interactions allows one
to understand and predict the functions of the
molecules
The Chemistry of Water
• The intracellular environment is aqueous
• 70-80% of cellular weight is water
• Water is the most abundant molecule in
biological systems
• This is the medium in which the chemistry
of life happens
Water: How Does It Make You Feel?
• Hydrophilic
I
WATER
• Hydrophobic
I
WATER
• Amphipathic
I
WATER
Biomolecules are defined in part by how they relate to water.
Time to “Bond”
• Covalent Bonds
Connect atoms into a molecule: within molecule bonds
• Noncovalent Interactions
Stabilize groups of atoms into functional structure: within
and between molecule interactions
–
–
–
–
Ionic bond
Hydrogen bonds
van der Waals interactions
hydrophobic effect
Covalent Bonds
• Strong forces that hold atoms together into molecules
• Form when atoms share (one pair or multiple pairs of ) electrons
• Have fixed or specific geometric orientation
Polar Covalent Bonds
• What happens if one atom has a greater affinity for the
electron?
Water: polar molecule
• Covalent Bonds
Connect atoms into a molecule: within molecule bonds
• Noncovalent Interactions
Stabilize groups of atoms into functional structure: within
and between molecule interactions
–
–
–
–
Ionic bond
Hydrogen bonds
van der Waals interactions
hydrophobic effect
Ionic Interactions
• Attractions between oppositely charged ions (cation+anion)
• Do not have a specific geometry associated with them
• Weaker than covalent bonds
Hydration shell
Hydrogen Bonds
• Interactions of a positively charge
H atom in a molecular dipole with
unpaired electrons from another
atom
• This can occur within the same
molecule or a different molecule
• Properties of water:
– High melting/boiling points
– Ability to interact with other
molecules
Hydrogen Bond
Potential Hydrogen Bond Interactions
• Solubility of uncharged substances in an aqueous environment
largely depends on the ability of that substance to form H
bonds with water
(Ionic Interactions)
• Charged molecules and ions that
interact with the dipole in water
(Hydrogen Bond Interactions)
can dissolved in water
• Molecules with polar bonds that
can easily form H bonds with
water
So, these molecules are hydrophilic (water liking)
So how about nonpolar molecules?
• Non-polar molecules
– Do not contain charged groups
– Do not possess a dipole moment
– Do not become hydrated
(do not interact well with water)
− In biology, most common nonpolar molecules
are the hydrocarbons (C – C; C – H)
These molecules are hydrophobic (water fearing)
Hydrophobic Interactions
• Hydrophobic chemicals
don’t form interactions
with water
– non-polar, uncharged
• H-bonds form between
water molecules,
excluding hydrophobic
substances
– hydrophobic
molecules end up
clumped together
Van der Waals Interactions
• Weak, nonspecific attractive force created when
two atoms approach each other closely
• Occurs in all types of molecules, both polar and
nonpolar
• Particularly responsible for the cohesion between
nonpolar molecules
• ↑Distance ↓Strength
• Strength in numbers
Done !
• Covalent Bonds
Connect atoms into a molecule: within molecule bonds
• Noncovalent Interactions
Stabilize groups of atoms into functional structure: within
and between molecule interactions
–
–
–
–
Ionic bond
Hydrogen bonds
van der Waals interactions
hydrophobic effect
Brief
Summary
Polar vs. Nonpolar
Polar = parts are negatively charged and other parts are
positively charged
– This can be a formal charge (-) or (+)
– This can be separation of charge but overall neutral
molecule.
Nonpolar = no separation of charge (neutral)
- In biology, most common nonpolar molecules are the
hydrocarbons
- These molecules do not interact well with water
Amphipathic
- molecule having a polar and a nonpolar part
Brief
Summary
Relative Bond Strengths
Complementary shapes
Macromolecules
Major Biological Molecules:
Proteins
Nucleic Acids
Carbohydrates
Lipids
How big is big?
Molecular weight
Oxygen = 16, Carbon = 12
Carbon dioxide = 44
Proteins - 5,000 to 150,000
Macro = large
Chemical Building Blocks
Biological macromolecules formed by covalent bonds
between monomers in a dehydration reaction
– Proteins
– Nucleic Acids
– Polysaccharides
Phospholipids form the basic bilayer structure of
biomembranes by non-covalent interactions
Biological macromolecules formed by covalent bonds
between monomers in a dehydration reaction
– Proteins
– Nucleic Acids
– Polysaccharides
MONOMERS
POLYMER
polymerization
• Amino Acids
• Nucleotides
• Sugars
Proteins
Nucleic Acids
Polysaccharides
Proteins
 Proteins are made up of small subunits called
amino acids
 There are 20 different types of amino acids
Proteins do most of the jobs in cells
Antibodies
Enzymes
Carry oxygen
Transporters
Structure (cell cytoskeleton)
and many, many more…
 They can be hooked up in different orders to
make a different protein
Side Chain
R
H
N
C
C
H
H
O
Amino Group (H2N)
OH
Carboxyl Group (COOH)
Amino acid
Each protein has an amino and a carboxyl group on it
Proteins as Words
ANALOGY: each amino acid is like a letter of the alphabet.
Words are constructed by putting together letters in different orders
(and different lengths)
Sample words:
and
perform
explanation
supercalifragilisticexpialidocious
Sample proteins
Insulin - 51 a.a
Rubisco - hundreds of a.a.
Amino Acids
The 20 AAs:
Alanine (A)
Arginine (R)
Aspartate (D)
Asparagine (N)
Cysteine (C)
Glycine (G)
Glutamate (E)
Glutamine(Q)
Histidine (H)
Isoleucine (I)
Leucine (L)
Lysine (K)
Methionine (M)
Phenylalanine (F)
Proline (P)
Serine (S)
Threonine (T)
Tryptophan (W)
Tyrosine (Y)
Valine (V)
The amino acids can be grouped in terms of their chemical properties.
−Ionized @ pH of 7 are the most hydrophilic
−(+) Basic; (-) Acidic
Amino Acids
− Nonpolar side chain are hydrophobic and so poorly soluble in water
− The larger the nonpolar side chain, the more hydrophobic the amino acid
Protein Conformation
• Primary structure: linear AA sequence
• Secondary structure: folding of adjacent AAs into
3D shapes (α-helix, β sheets)
– Hydrogen bonding
β sheets
α-helix
Protein Conformation
• Tertiary structure: overall conformation; domains
– Non-covalent ionic interactions
– Disulfide bridges
Protein Conformation
• Quaternary structure: multiple subunits
(completely different polypeptide strings)
Reminder:
MONOMERS
POLYMER
polymerization
•
•
•
Amino Acids
Nucleotides
Sugars
Proteins
Nucleic Acids
Polysaccharides
Nucleic Acids
Four building blocks in DNA
Adenine
Cytosine
Guanine
Thymine
Four building blocks in RNA
Adenine
Cytosine
Guanine
Uracil
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
It’s amazing - isn’t it?
Only 4 different building blocks
make up all of the code for us.
AND each of us is different even
though there are only 4 types of
building blocks.
What makes us different????
Nucleotides
Common structure: phosphate + five carbon sugar + base
O
Base
5-C sugar
RNA
How many types of base?
DNA
Nucleotides
Common structure: phosphate + five carbon sugar + base
O
Base
5-C sugar
AGC found in both DNA and RNA
T is found only in DNA
U only found in RNA
Nucleotides Polymerization
Nucleotides are hooked together
through a phospodiester bond
Its all of the phosphodiester bonds
that make the phosphate backbone
of nucleic acids
Water is lost during this reaction too!
Reminder:
MONOMERS
POLYMER
polymerization
•
•
•
Amino Acids
Nucleotides
Sugars
Proteins
Nucleic Acids
Polysaccharides
Polysaccharides
The building blocks of polysaccharides are simple sugars, or monosaccharides
e.g. glucose, galactose, etc.
Polysaccharides can be used:
to store energy - glycogen, starch,
as protection - chitin (bugs)
as support - cellulose (plants), and to make glycoproteins
Disaccharides, Polysaccharides
Disaccharides- 2 monosaccharides
Lactose= glucose + galactose
Sucrose= glucose + fructose
Cellulose
Long chains arrayed in parallel sheets
for strength
• Glycosidic bonds ( C-O-C) link
multiple sugars in a chain
– water is lost in bond formation
Summary
Chemical Building Blocks
Biological macromolecules formed by covalent bonds
between monomers in a dehydration reaction
– Proteins
– Nucleic Acids
– Polysaccharides
Phospholipids form the basic bilayer structure of
biomembranes by non-covalent interactions
Phospholipids
• Biomembranes- large flexible sheets
– Boundries of cells and intracellular organelles
– Assembled by non-covalent interactions
• Phospholipids are the primary building blocks of biomembranes
Amphipathic
• Saturated vs. Unsaturated
– absence or presence of double bonds in carbon chain
– affects melting point
– affects the shape of fatty acids
Solid at room temp.
Trans fats: solid margarine sticks
Similarities and Differences of
Biological Macromolecules
Let’s name some things that each of the previous
molecules have in common and are different in
terms of polymerization.
Lipids are not true macromolecules because they
don’t undergo polymerization (but they are big!)