MCB 181R Sec 3/4H

(August 24 – September 16)

• The Science of Biology

• Review of Chemistry
• Organic Chemistry
• Macromolecules
• Cells
• Functions of Cell Membranes
• Review for Exam 1
• Exam 1 -- Study Sessions 1-6 (September 16)
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(polynucleotides)

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Polymers are made by condensation (dehydration) reactions and
broken down by hydrolysis.

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 Today we will consider the four classes of large (macro)
molecules found in all living things.

• Proteins provide structure, catalysis,

regulation, movement, transport, and
recognition in cells.
• Polysaccharides are used for energy storage
and building materials.
• Nucleic Acids store and transmit hereditary
information.
• Lipids are diverse hydrophobic molecules
which function as hormones (steroids), as part
of biological membranes (phospholipids) and 4
 Proteins provide structure, catalysis, regulation, movement,
transport, and recognition in cells.

• A protein consists of one or more polypeptide

chains folded into a specific conformation (shape).
• A polypeptide is a long chain or polymer of amino
acids connected in a specific sequence.
• The information that specifies the sequences of
amino acids in the thousands of different kinds of
proteins in cells is stored in genes (DNA of
chromosomes).

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 Cells build proteins with 20 different amino acids!

• All amino acids have an

amino and a carboxyl
group linked to an alpha
(α) carbon atom.
• The 20 different amino
acids have the same
general structure but
have different “R” groups
(side chains) that impart
unique characteristics.

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In neutral conditions (pH 7), the amino and carboxyl
groups ionize to NH3+ and COO–, respectively—
this helps amino acids stay in solution and makes
them more reactive.

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The twenty amino acids of proteins are grouped according to
chemical properties of the side chain!

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(hydrophobic)

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(hydrophylic)

*has a special role

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(hydrophylic)

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A protein (one or more polypeptides) consists of amino acids
linked together by peptide bonds!

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Within the polypeptide, the peptide bonds form a “backbone” with three key
characteristics:
• R-group orientation: Side chains can interact with each other or water.
• Directionality:
– Free amino group, on the left, is called the N-terminus.
– Free carboxyl group, on the right, is called the C-terminus.
• Flexibility: Single bonds on either side of the peptide bond can rotate, making the
entire structure flexible.
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 A functional protein has up to four levels of structure:
Primary and Secondary structures
• Primary structure refers
to the sequence or order
of the 20 different amino
acids in the polypeptide
chain.
• As a result of hydrogen
bonding, the polypeptide
can coil (α helix) or fold
(β-pleated sheet) to give
the secondary structure.

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 Tertiary structure
• Polar, nonpolar and ionic side chains of the various amino
acids can interact to superimpose a three dimensional
shape on the polypeptide referred to as the tertiary
structure.

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 A disulfide bridge

The terminal—SH group of

cysteine can react with
another cysteine side
chain to form a disulfide
bridge, or disulfide bond
(—S—S—).

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 A functional protein has up to four levels of structure!

• Polar, nonpolar and ionic side chains of the various amino

acids can interact to superimpose a three dimensional
shape on the polypeptide referred to as the tertiary
structure.

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Hydrophobic and van der Waals interactions within proteins

• Hydrophobic Interactions: interactions of nonpolar R

groups within protein in the presence of a polar
solvent (water). Hydrophobic side chains tend to
form globular masses. Weaker than hydrogen bonds.
• van der Waals Interactions: interactions of electrons
of nonpolar R groups within protein. Weakest type of
interactions. But a large number of van der Waals
interactions tend to occur within a polypeptide with
many hydrophobic residues. Many interactions add
up to a significant increase in stability of the
polypeptide.
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 A functional protein has up to four levels of structure!

• Quaternary structure is
the overall protein
structure resulting from
aggregation of more than
one polypeptide. The
hemoglobin protein in
human red blood cells
consists of four
polypeptides.

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Figure 3.7 The Four Levels of Protein Structure

Primary Structure: Amino acid monomers are joined, forming polypeptide chains.

Amino acid monomers Peptide bond

Figure 3.7 The Four Levels of Protein Structure

Secondary Structure: Polypeptide chains may form a helices…

α-Helix

Hydrogen bond
Figure 3.7 The Four Levels of Protein Structure

…or β-pleated sheets.

β-Pleated sheet

Hydrogen bond
Figure 3.7 The Four Levels of Protein Structure

Tertiary Structure: Polypeptides fold, forming specific shapes.

Folds are stabilized by bonds and disulfide bridges.

β-Pleated sheet

Hydrogen bond

α-Helix Disulfide bridge

Figure 3.7 The Four Levels of Protein Structure

Quaternary Structure: Two or more polypeptides assemble to form larger protein

molecules. The hypothetical molecule here is a tetramer, made up of four polypeptide
subunits.
 One-minute-break slide!
My office hours:
Tues & Thurs 1-2 pm
Wed 9-11 am
or by appointment.
Location: Marley 441D

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 Today we will consider the four classes of large (macro)
molecules found in all living things.

• Proteins provide structure, catalysis,

regulation, movement, transport, and
recognition in cells.
• Polysaccharides are used for energy storage
and building materials.
• Nucleic Acids store and transmit hereditary
information.
• Lipids are diverse hydrophobic molecules
which function as hormones (steroids), as part
of biological membranes (phospholipids) and 28
Polysaccharides (carbohydrates) are used for energy storage and
building materials.

• A polysaccharide consists of a long chain or

polymer of monosaccharides (simple sugars) such
as glucose.
• Cells make polysaccharides by using catalytic
proteins called enzymes which perform a
condensation (dehydration) reaction to link simple
sugars together.
• Polysaccharides are carbohydrates that contain
carbon, hydrogen and oxygen in the proportion
CH2O.
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Sugars exist in linear and ring forms
 Monosaccharides Are Simple Sugars

Glyceraldehyde is
the smallest
monosaccharide
and exists only as a
linear-chain form. Ribose and
deoxyribose each
have five carbons,
but they have very
different chemical
properties and
These hexoses have biological roles.
the same
molecular formula
as glucose
(C6H12O6), but they
have a different
arrangement of
atoms resulting in
isomers with
different
properties.
Cells build polysaccharides by linking monosaccharides together
by a glycosidic bond!

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Cellulose, starch and glycogen are all polysaccharides made of
glucose!

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Cellulose, starch and glycogen are all polysaccharides made of
glucose!

Plant cell wall Starch granules in plant Glycogen deposits in

cells human liver
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 Today we will consider the four classes of large (macro)
molecules found in all living things.

• Proteins provide structure, catalysis,

regulation, movement, transport, and
recognition in cells.
• Polysaccharides are used for energy storage
and building materials.
• Nucleic Acids store and transmit hereditary
information.
• Lipids are diverse hydrophobic molecules
which function as hormones (steroids), as part
of biological membranes (phospholipids) and 36
 Nucleic acids store and transmit hereditary information!

• Nucleic acids consists of a long chain or polymer

of nucleotides.
• There are two types of nucleic acids:
Deoxyribonucleic Acid (DNA) and Ribonucleic Acid
(RNA)

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A nucleotide consist of a nitrogen-containing base, a
pentose sugar and one or more phosphate groups!

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Nucleotides are joined by a dehydration (condensation)
reaction to form a phosphodiester linkage.

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• The sugar-phosphate backbone
of a nucleic acid is directional—
one end has an unlinked 5′
carbon, and the other end has
an unlinked 3′ carbon.

• The nucleotide sequence is

written in the 5′  3′ direction.
This reflects the sequence in
which nucleotides are added to
a growing molecule.

• This nucleotide sequence

comprises the nucleic acid’s
primary structure.

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A DNA molecule consists of two polynucleotide strands held
together by hydrogen bonds between the nitrogenous
bases!

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 The secondary structure of DNA is a double helix.

http://www.youtube.com/watch?v=ZGHkHMoyC5I 42
 Today we will consider the four classes of large (macro)
molecules found in all living things.

• Proteins provide structure, catalysis,

regulation, movement, transport, and
recognition in cells.
• Polysaccharides are used for energy storage
and building materials.
• Nucleic Acids store and transmit hereditary
information.
• Lipids are diverse hydrophobic molecules
which function as hormones (steroids), as part
of biological membranes (phospholipids) and 43
 Fats store large amounts of energy!
• Fats (triglycerides) are made from two kinds of molecules (glycerol and
fatty acids) by a condensation (dehydration reaction).

These fatty acid chains

can have different
hydrocarbon chain
length or structure,
some saturated and
some unsaturated. 44
 Fatty acids vary in length and they may be saturated or
unsaturated!
• Saturated fatty acids: no
double bonds between
carbons—it is saturated
with H atoms.
• Unsaturated fatty acids:
some double bonds in
carbon chain.
• monounsaturated: one
double bond
• polyunsaturated: more
than one
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 Phospholipids are building blocks of cell membranes!

• Phospholipids have 2 rather

than 3 fatty acids with a
phosphate group on the third
position on the glycerol
molecule.
• Additionally, small charged or
polar molecules (e.g. choline)
are linked to the phosphate
group.
• The resulting phospholipid is
amphipathic with both
hydrophobic and hydrophilic
portion of the molecule.
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Phospholipids spontaneously form a bilayer structure in water

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Phospholipids spontaneously form a bilayer structure in water
with their hydrophobic hydrocarbon tails clustered together
and the polar phosphate head groups associated with water
molecules.

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Lipid bilayers show selective permeability

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Fatty acid structure changes the permeability of membranes

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 Steroids are lipids that regulate many aspects of growth!
• Steroids are characterized by a carbon skeleton consisting of four fused rings.
• Cholesterol is a common component of human cell membranes and is
essential for synthesis of other sterols.
• Sex hormones like testosterone are made from cholesterol.

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 Bonds, bonds and more bonds!
• Covalent – shared pair of electrons
• Ionic – electrostatic attraction between anions and cations
• Hydrogen – attraction between hydrogen and oxygen or
nitrogen
• Peptide – links amino acids together in polypeptides
• Disulfide – bond between two S atoms stabilizing tertiary
structure of polypeptides
• Ester – linkage between fatty acids and glycerol of
triglycerides
• Glycosidic – linkage between sugars in polysaccharides
• Phosphodiester – linkage between nucleotides in
polynucleotides (DNA and RNA)
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