16/11/2023

AMINO ACIDS,
PEPTIDES, AND
PROTEINS
CHEM05 Biochemistry and
Analytical Chemistry

182

Amino Acids
• General structure of amino acids

• For amino acids, the R-group is often called the “side-

chain” or “variant group.”

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Amino Acids
• α-carbon atom is thus a chiral center

• For all the common amino acids except glycine, the α-carbon is
bonded to four different groups: a carboxyl group, an amino
group, an R group, and a hydrogen atom
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Amino Acids
• amino acids have two possible stereoisomers - enantiomers

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Amino Acids
• Twenty different amino acids are commonly found in proteins.
• All the amino acids have trivial or common names, in some cases
derived from the source from which they were first isolated.
• Asparagine was first found in asparagus
• Glutamate in wheat gluten;
• Tyrosine was first isolated from cheese ( Greek tyros, “cheese”)
• Glycine (Greek glykos, “sweet”) was so named because of its sweet
taste.

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Classification of Amino Acids

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Classification of Amino Acids

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Classification of Amino Acids

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Classification of Amino Acids

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Classification of Amino Acids

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Classification of Amino Acids

PVT TIM HALL

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Classification of Amino Acids

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Amino Acids Can Act as Acids and Bases

Amino acids are amphoteric

When an amino acid is dissolved in water, it exists in solution as the
dipolar ion, or zwitterion (German for “hybrid ion”)
Acid (proton donor) Base (proton acceptor)

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Amino Acids Can Act as Acids and Bases

• Amino acids vary in their acid-base properties and have characteristic

titration curves.
• Monoamino monocarboxylic amino acids (with nonionizable R
groups) are diprotic acids ( +H3NCH(R)COOH) at low pH and exist in
several different ionic forms as the pH is increased.
• Amino acids with ionizable R groups have additional ionic species,
depending on the pH of the medium and the pKa of the R group

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Amino Acids Have Characteristic Titration Curves

Titration curve of Glycine
• The plot has two distinct stages,
corresponding to deprotonation of
two different groups on Gly
• At very low pH, the predominant
ionic species of glycine is the fully
protonated form, +H3N-CH2-COOH.

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Amino Acids Have Characteristic Titration Curves

Titration curve of Glycine
• At the midpoint in the first stage of
the titration, in which the –COOH
group of glycine loses its proton,
equimolar concentrations of the
proton-donor (+H3N-CH2-COOH)
and proton-acceptor (+H3N-CH2-
COO-) species are present.
• pKaCOOH = 2.34

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Amino Acids Have Characteristic Titration Curves

Titration curve of Glycine
• The second stage of the titration
corresponds to the removal of a
proton from the -NH3+ group of
glycine.
• equimolar concentrations of the
proton-donor (+H3N-CH2-COO-) and
proton-acceptor (H2N-CH2-COO-)
species are present.
• pKaNH3 = 9.6
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Amino Acids Have Characteristic Titration Curves

Titration curve of Glycine
• The point at which the removal of
the first proton is essentially
complete and removal of the
second has just begun.
• At this pH glycine is present largely
as the dipolar ion +H3N-CH2-COO-

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Amino Acids Have Characteristic Titration Curves

Titration curve of Glycine
• The characteristic pH at which the
net electric charge is zero is called
the isoelectric point or isoelectric
pH, designated pI.
• For glycine, which has no ionizable
group in its side chain, pI is equal
mean of the two pKa values:

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Amino Acids Differ in Their Acid-Base Properties

Amino acids with ionizable R
groups
• Have three pKa values
• The additional stage for the
titration of the ionizable R group
merges to some extent with the
other two.

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Amino Acids Differ in Their Acid-Base Properties

Titration curve of Glutamate
• pI = 3.22

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Amino Acids Differ in Their Acid-Base Properties

Titration curve of Histidine
• pI = 7.59

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Sample Problem
Determine the pI of Aspartic acid (Asp)

pKa1 = 2.0
pKa2 = 10
pKaR = 3.9

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Sample Problem
Determine the pI of Aspartic acid (Asp)
Approach:
(1) Draw the fully protonated structure off
the amino acid

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Sample Problem
Determine the pI of Aspartic acid (Asp)
Approach:
(2) Write out structures for sequential
deprotonation and place pKa values over
the equilibrium arrows. pKa2 = 10

• pKa1 = 2.0
pKa1 = 2.0 pKaR = 3.9
• pKa2 = 10
• pKaR = 3.9

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Sample Problem
Determine the pI of Aspartic acid (Asp)
Approach:
(3) Determine the net charge on each
ionized form

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Sample Problem
Determine the pI of Aspartic acid (Asp)
Approach:
(4) Find the structure that has no net
charge

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Sample Problem
Determine the pI of Aspartic acid (Asp)
Approach:
(4) Take the average of the pKa’s that are
around the structure

pI = (2.0 + 3.9)/2 pKa1 = 2.0 pKaR = 3.9

pI = 2.95

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Formation of Peptide Bond

• Step 1
one oxygen and two
hydrogen atoms are
removed

• Step 2
a new bond is made

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Peptide Terminology
• The end of the peptide structural formula that has a quaternary
ammonium group is called the N-terminus, and the end that has a
carboxylate group is called the C-terminus.

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Peptide Terminology

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Primary Protein Structure

-order in which the amino acids are covalently linked together
-the primary structure is the one-dimensional first step in specifying
the three-dimensional structure of a protein

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Primary Protein Structure

Why is it important to know the primary structure of protein?
- The amino acid sequence of a protein determines its 3D structure,
which, in turn, determines its properties.
- In every protein, the correct three-dimensional structure is needed
for correct functioning.

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Primary Protein Structure

Example
Sickle-cell anemia
-In this genetic disease, red blood cells
cannot bind oxygen efficiently.
-The red blood cells also assume a
characteristic sickle shape.
-These drastic consequences stem from a
change in one amino acid residue in the
sequence of the primary structure.

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Primary Protein Structure

Example
Sickle-cell anemia

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Secondary Protein Structure

• hydrogen-bonded arrangement of the
backbone of the protein
• the bonds in the peptide backbone plays an
important role here
• Phi φ - the bond between the α-carbon and the
amino nitrogen of that residue
• Psi ψ - the bond between the α-carbon and the
carboxyl carbon of that residue.
• only the backbone is considered in the
secondary structure.

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Secondary Protein Structure

Two common types of secondary structures:

alpha helices beta sheets

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Secondary Protein Structure

Two common types of secondary structures:

The a-helix and b-pleated sheet are periodic structures: their

features repeat at regular intervals.

• The α-helix is rod-like and involves only one polypeptide chain.

• The β-pleated sheet structure can give a two-dimensional array and can
involve one or more polypeptide chains.

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Secondary Protein Structure

Supersecondary Structures
-combinations of α- and β-strands
Motif – repetitive secondary structure

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Tertiary Protein Structure

• Three-dimensional arrangement of all the atoms in the molecule.
• The conformations of the side chains and the positions of any
prosthetic groups are parts of the tertiary structure

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Tertiary Protein Structure

Forces that stabilize the tertiary structure of proteins

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Tertiary Protein Structure

• (1) Hydrophobic Interactions

Nonpolar side-chains are attracted

to other nonpolar sidechains

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Tertiary Protein Structure

• (2) Hydrogen bonding

• can occur between polar side

chains

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Tertiary Protein Structure

• (3) Salt Bridges

• attractive force between the

positive formal charge on polar
basic amino acid residue and a
negative formal charge on a
polar acidic residue.

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Tertiary Protein Structure

• (4) Disulfide bridges

• cysteine residue contains a thiol group in its side-chain that is

capable of forming a disulfide bridge with another cysteine
residue

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Tertiary Protein Structure

How can the three-dimensional structure
of a protein be determined?
X-ray crystallography
• Pure protein crystal is exposed to a
beam of X rays
• A diffraction pattern is produced on a
photographic plate or a radiation
counter.

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Tertiary Protein Structure

How can the three-dimensional structure of
a protein be determined?
Nuclear magnetic resonance spectroscopy
• uses protein samples in aqueous solution
rather than crystals.
• this environment is closer to that of
proteins in cells,

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Quaternary Protein Structure

• final level of protein structure and pertains to proteins that consist of
more than one polypeptide chain.
• each chain is called a subunit.
• the number of chains can range from two to more than a dozen, and
the chains may be identical or different.
• Oligomer - a molecule made up of a small number of subunits

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Quaternary Protein Structure

• The chains interact with one
another noncovalently via
electrostatic attractions, hydrogen
bonds, and hydrophobic
interactions.
• subtle changes in structure at one
site on a protein molecule may
cause drastic changes in properties
at a distant site → allosteric

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The Structure of Insulin

Primary structure

Insulin in its mature form has two polypeptide chains, named A and B, connected by
disulfide linkages. Thus, the sequence of amino acids in chains A and B form the primary
level of structure of insulin
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The Structure of Insulin

Secondary and tertiary structure

• the secondary structure seen in insulin is

three alpha-helices and the rest of the
region as a random coil.
• the A and B chains of functional insulin
monomer form a wedge-shaped tertiary
level of structure.

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The Structure of Insulin

Quaternary structure

• The quaternary level of structure is six

monomeric insulins group around two Zn2+
ions forming an oligomeric protein
stabilized by hydrophobic interactions of
the subunits

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Protein Denaturation and Renaturation

Cristian Anfinsen
Anfinsen proved that the sequence of amino acids determines 1972 Nobel Prize in Chemistry
the way the chain folds itself

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Protein Denaturation and Renaturation

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Protein Denaturation and Renaturation

Denaturing agents
Heat
• An increase in temperature favors vibrations within the molecule, and
the energy of these vibrations can become great enough to disrupt
the tertiary structure

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Protein Denaturation and Renaturation

Denaturing agents
Heat
• An increase in temperature favors vibrations within the molecule, and
the energy of these vibrations can become great enough to disrupt
the tertiary structure

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Protein Denaturation and Renaturation

Denaturing agents
pH
• At either high or low extremes of pH, at least some of the charges on
the protein are missing, hence the electrostatic interactions that
would normally stabilize the native, active form of the protein are
drastically reduced

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Protein Denaturation and Renaturation

Denaturing agents
Chemical denaturants
• Detergents tend to disrupt hydrophobic interactions. If a detergent is
charged, it can also disrupt electrostatic interactions within the
protein.

Sodium dodecyl sulfate beta-mercaptoethanol urea

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Enzymes
CHEM05 Biochemistry and
Analytical Chemistry

240

Enzymes
Enzymes are biological catalysts
• An enzyme is a macromolecule that acts as a catalyst, a chemical agent
that speeds up a reaction without being consumed by the reaction
• Almost all every biochemical reaction is catalyzed by an enzyme.
• With the exception of a few catalytic RNAs, all known enzymes are
proteins

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Classification of Enzymes

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Oxidoreductase

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Isomerase

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Hydrolases

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Ligase

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Transferase

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Lyases

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Classification of Enzymes
Nomenclature

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Classification of Enzymes
Nomenclature

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Classification of Enzymes
Nomenclature

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Enzyme Structure
Coenzymes are organic
molecules and quite often bind
loosely to the active site of an
enzyme and aid in substrate
recruitment
Cofactors are "helper molecules"
and can be inorganic or organic in
nature.

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How enzymes work?

An enzyme catalyzes a reaction by lowering the activation energy barrier
enabling the reactant molecules to absorb enough energy to reach the
transition state even at moderate temperatures
Activation energy – amount of energy required for a reaction to occur

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How enzymes work?

AB + CD → AC + BD
Reactants Products

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How enzymes work?

The difference between the
energy levels of the ground
state and the transition
state is the activation
energy, ∆G‡.

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How enzymes work?

Enzymes enhance reaction
rates by lowering activation
energies

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Enzymes are substrate-specific

The reactant an enzyme
acts on is referred to as the
enzyme’s substrate.
The enzyme binds to its
substrate(s) forming an
enzyme-substrate complex
The pocket or groove on
the surface of the enzyme
where catalysis occurs is
called the active site

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Enzymes are substrate-specific

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Enzyme Inhibition
Competitive inhibition
• When the inhibitor can bind
to the active site and block
the substrate’s access
Non-competitive inhibition
• When inhibitor binds to the
enzyme at a site other than
the active site and, as a
result of binding, causes a
change in the structure of
the enzyme, especially
around the active site

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Enzymes Kinetics
Enzyme Kinetics
• is the study of the chemical reactions that are catalyzed
by enzymes
• in enzyme kinetics, the reaction rate is measured and the
effects of varying the conditions of the reaction are
investigated.

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Enzymes Kinetics
Enzyme activity
• expressed in terms of the
initial reaction rates or
initial velocity
Initial velocity, Vo
• Instantaneous rate of P
formation or of S
disappearance with time (t)
• Measured at the beginning
of the reaction in which the
rate of substance
disappearance or product
formation is linear with t

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Enzymes Kinetics
Initial velocity, Vo
• Instantaneous rate of P
formation or of S
disappearance with time
(t)
Vo = -∆[S] / ∆t
= ∆[P] / ∆t

Enzyme activity

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Factors affecting enzyme activity

• Substrate concentration
• Enzyme concentration
• pH
• Temperature
• Coenzyme concentration
• Inhibitor concentration
• Activator concentration
• Buffer

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Factors affecting enzyme activity

Temperature

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Factors affecting enzyme activity

pH

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Factors affecting enzyme activity

Inhibitors and Activators

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Factors affecting enzyme activity

Substrate Concentration

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Factors affecting enzyme activity

Enzyme Concentration

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(1-2) Draw the general structure of an amino acid

(3-5) Draw the structure of a dipeptide. Indicate
the R-groups as R1 and R2.

270

Determine whether the following structures

belong to the primary, secondary, tertiary, and
quaternary structure
6. PVALGEDE
7. hemoglobin
8. αβα fold

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9-10. Calculate the IpH of Lysine

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274

Nucleotides
and
Nucleic Acids
CHEM05 Biochemistry and
Analytical Chemistry

275

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Nucleotides
Nucleotides
• Building blocks of nucleic acids
• Three components
• Pentose sugar
• Nitrogenous base
• Phosphate

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Nucleotides

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Pentoses in nucleotides

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Nucleotides
Nitrogenous base
• Flat aromatic rings
• Basic
• Have conjugated double bonds
• Have multiple sites for hydrogen
bonding

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Nucleotides
Nitrogenous base: Purines
• Heterocyclic aromatic compound
• Pyrimidine fused with an
imidazole ring (double ring)
• Adenine (6-aminopurine)
• Guanine (2-amino-6-oxypurine)

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Nucleotides
Nitrogenous base: Pyrimidines
• Heterocyclic aromatic compound
similar to benzene and pyridine
(single ring)
• N atoms at position 1 and 3
• Thymine (2,4-dioxy-5-
methylpyrimidine (or
• Cytosine (2-oxy-4-aminopyrimidine)
• Uracil (2,4-dioxy-pyrimidine)

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Nucleotides
Formation of nucleotides

282

Nucleotides
Formation of nucleotides
Linkages in nucleotides
• Phosphoester bond
• N-glycosidic bond

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Nucleotides
Phosphate Groups
• Component of the backbone of the
polynucleotide together with the
pentose
• Imparts negative charge to the
DNA
• Enables DNA to associate with
proteins (e.g. histones)

284

Nucleotides
Phosphate Groups
• Component of the backbone of the
polynucleotide together with the
pentose
• Imparts negative charge to the
DNA
• Enables DNA to associate with
proteins (e.g. histones)

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Structure of the DNA

Primary Structure
• Linear sequence of
deoxyribonucleotides
• Two complementary strands held
together by hydrogen bonds
• Linked together by phosphodiester
linkage
• By convention, DNA sequence is
read from the 5’ to 3’ direction
5’-ATGCGTCGG-3’

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Structure of the DNA

Secondary Structure
• Double helix
• Two intertwined strands antiparallel
to each other

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Structure of the DNA

Secondary Structure
• Major and minor grooves

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Structure of the DNA

Secondary Structure
• Mostly are right-handed helix
• Some are left-handed helix

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Structure of the DNA

Secondary Structure
• Maximizes hydrophobic interactions for
greater stability
• Distance between two base pairs: 3.4 Å
• Helix diameter: 20 Å; Maintained by the
right pairing of bases

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Structure of the DNA

Secondary Structure
• Base pairing
• A=T
• G=C

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Structure of the DNA

Secondary Structure
• Base pairing
• A=T
• G=C

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Structure of the DNA

DNA Conformations
• A,B,Z conformations
are common in
nature

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Structure of the DNA

DNA Conformations
• A,B,Z conformations
are common in
nature

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Structure of the DNA

Watson-Crick model for the structure of DNA

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Structure of RNA
- single stranded
- Ribose sugar
- Uracil instead of Thymine

- Generally shorter than DNA

(usually hundreds to thousand
bases)
- Base pairing may occur forming
double stranded regions

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Forces stabilizing
Nucleic Structures
Stacking
• van der Waals forces
• Ionic interactions
• Hydrophobic interactions
Double strand stabilization
• Hydrogen bonding between
base pairs
Intrastrand bonds
• Covalent bonds
(phosphodiester bond)

298

Biological Functions of Nucleotides

Nucleotides have a variety of roles in cellular metabolism.

• the energy currency in metabolic reactions,
• the essential chemical links in the response of cells to hormones
and other stimuli, and
• the structural components of a variety of enzyme cofactors and
metabolic intermediates.
• constituents of the nucleic acids, deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).

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Biological Functions of Nucleotides

Segments of DNA specifying the synthesis of a functional protein or RNA product
are called genes.
The storage and transmission of biological information are the only known
functions of DNA. RNAs have a broader range of functions.
Ribosomal RNAs (rRNAs) are structural and catalytic components of ribosomes.
Messenger RNA (mRNAs) carry genetic information specifying the sequences of
proteins.
Transfer RNAs (tRNAs) are adaptor molecules that participate in translating the
information in mRNA into a specific sequence of amino acids in a polypeptide.
There is also a wide variety of special-function RNAs, including some called
ribozymes that have enzymatic activity.

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Biological Functions of Nucleotides

The storage and transmission of biological information are the only known
functions of DNA. RNAs have a broader range of functions.
Ribosomal RNAs (rRNAs) are structural and catalytic components of ribosomes.
Messenger RNA (mRNAs) carry genetic information specifying the sequences of
proteins.
Transfer RNAs (tRNAs) are adaptor molecules that participate in translating the
information in mRNA into a specific sequence of amino acids in a polypeptide.
There is also a wide variety of special-function RNAs, including some called
ribozymes that have enzymatic activity.

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(1-3) What are the three components of a nucleotide?

(4) What is the major difference between the sugar of RNA and DNA?
(5) In a double-stranded DNA, the two strands are held together by __?
(6) Which RNA carries the amino acid corresponding to the codons in
the mRNA?
(7) The simplest sugar has ___ carbons
(8) Pair of molecules that exist in two forms that are mirror images of
one another
(9) Cyclic sugars are depicted using _____ projection
(10) Draw the linear structure of D-glucose

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Carbohydrates
CHEM05 Biochemistry and
Analytical Chemistry

304

Carbohydrates
• “Hydrates of carbon”
• Also called “saccharides”
• Monosaccharides - one unit
• Di-, tri-, etc.: ≥ 2 units
• Larger polymers: polysaccharides
• Can be modified with other groups to
contain N, P, etc.
• General formula: (CH₂O)n; n ≥ 3
• Simplest have 3 carbons

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Classifying Carbohydrates
• By functional group
• Aldose = aldehyde
• Ketose = ketone

306

Classifying Carbohydrates
• By number of C atoms
• Triose = 3C
• Tetrose = 4C
• Pentose = 5C
• Hexose = 6C
• Etc.

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Classifying Carbohydrates
• By number of C atoms
• Triose = 3C
• Tetrose = 4C
• Pentose = 5C
• Hexose = 6C
• Etc.

308

Chirality
• Chiral carbon → C atom surrounded by
four different groups
• Several chiral carbons in carbohydrates
• D- and L- conformations are determined by
the chirality of the penultimate carbon
• Chirality at the other carbons determines penultimate C
identity

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Chirality
D- and L- Configurations
• Based on the chirality of the
penultimate C
• Enantiomers - pair of molecules
that exist in two forms that are
mirror images of one another but
cannot be superimposed one upon
the other

310

Glucose

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Glucose

312

Threose

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314

Chirality
Enantiomers
• Enantiomers have identical
physical properties (mp, bp, etc)
• Can only distinguish them by:
• Interactions with other chiral
substances
• Rotation of plane-polarized light
• Most naturally-occurring sugars are
the D enantiomer

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Chirality
Epimers
• Carbohydrates that differ in
configuration around only 1C other
than the enantiomeric one
• Diastereomers

316

Cyclization
Cyclical sugars are non-planar.

317

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Cyclization of Glucose

• Since the aldehyde group has rotational freedom about the C1-C2 bond,
anomers are possible
• β-D-Glucose is most prevalent in biochemistry
• More stable conformation

318

Cyclization

• The anomeric carbon is always bound to 2 O atoms

• 5-membered ring – furanose
• 6-membered ring – pyranose

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Reducing sugars
• any sugar that is capable
of acting as a reducing
agent
• due to the presence of
reducing aldehyde or
ketone groups
• Sugars which form open
chain structure with free
carbonyl group

320

Non-Reducing Sugars
Sucrose
• Disaccharide of glucose and
fructose
• Anomeric C occupied in the
bond

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Polysaccharides
• Chains or polymers of carbohydrates formed by glycosidic bonds
• glycan chains
• Can be used to modify other molecules,
• e.g. glycoproteins or glycolipids
• Can be joined in a variety of ways
• Multiple -OH groups with different bonding arrangements makes this
possible
• Need way to classify and understand them that includes this level of
complexity
• Polysaccharides are common fuel-storage molecules

322

Disaccharides
• Disaccharides occur in nature most commonly as breakdown products of
polysaccharides
Example
Lactose

• Secreted in milk of lactating mammals

• Galactose-ß -1,4-glucose
• Joined by glycosidic bond between 1C of galactose and the
4C of glucose (left to right)

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Fuel Storage Carbohydrate

Starch (plants)
• Polymers of glucose joined by α(1-4) linkages
• Amylose
• Linear (unbranched) form of starch
• Linkages create "kink" in structure
• Leads to helical shape

324

Fuel Storage Carbohydrate

Starch (plants)
• Polymers of glucose joined by α(1-4) linkages
• Amylopectin
• Branched, larger molecule
• Includes α(1-6) linkages every 20-30
residues to generate branching

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Fuel Storage Carbohydrate

Starch (plants)
• Polymers of glucose joined by α(1-4) linkages
• Amylopectin
• Branched, larger molecule
• Includes α(1-6) linkages every 20-30
residues to generate branching

326

Fuel Storage Carbohydrate

Glycogen (animals)
• Polymer that resembles amylopectin, but branches are ~ every 12
residues
• Highly branched form allows it to be rapidly assembled or disassembled

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Structural Carbohydrate
Cellulose
• Glucose polymer formed between 1C
and 4C atoms - like amylose – but
linkages are β
• Makes for very profound differences in
structure
• instead of compact granules
(storage form), form extended fibers
• Provides rigidity and strength for
plant cell walls

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Structural Carbohydrate
Cellulose
• Extensive hydrogen bonding network within and between adjacent chains
• Most animals cannot digest cellulose
• Ruminant and capable because of their rumen microflora

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Structural Carbohydrate
Chitin
• β(1-4) linkages of glucose derivative,
N-acetylglucosamine
• Part of the exoskeletons of insects
and crustaceans
• Part of the cell walls of many fungi

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Structural Carbohydrate
Chitin
• β(1-4) linkages of glucose derivative,
N-acetylglucosamine
• Part of the exoskeletons of insects
and crustaceans
• Part of the cell walls of many fungi

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Glycoproteins
• Proteins that carry a carbohydrate group
• Most surface proteins or those that are excreted carry sugar moieties
• Eukaryotic glycoproteins usually N-linked to Asn or O-linked to Ser or Thr

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Glycoproteins
N-glycosylation
• Chain of 14 residues added as
polypeptide comes off ribosome
in RER (rough endoplasmic
reticulum)
• At Golgi apparatus, glycosidases
remove some residues and
glycosyltransferases add new
monosaccharides
• Highly specific process
• Gives tremendous variety and
specificity to molecules

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Glycoproteins
Purpose of Glycosylation
• Variety of molecules
• Highly hydrophilic and conformationally flexible
• Intracellular signaling
• Stability of proteins
• Basis of ABO blood groups

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Lipids
CHEM05 Biochemistry and
Analytical Chemistry

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Lipids
• Highly hydrophobic molecules
• Mostly insoluble in water
• Cannot form polymers
• Do not have defined functional
groups
• Some are amphiphatic
• Both polar and non-polar
regions

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Lipids
Functions
• Cellular barrier
• Membrane fluidity
• Water proofing
• Signaling agents
• Storage of energy

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Biological Functions of Lipids

• Storage of energy
–Reduced compounds: lots of available energy
–Hydrophobic nature: good packing

• Insulation from environment

–Low thermal conductivity
–High heat capacity (can “absorb” heat)
–Mechanical protection (can absorb shocks)

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Biological Functions of Lipids

• Water repellant
–Hydrophobic nature: keeps surface of the organism dry

• Prevents excessive wetting (birds)

• Prevents loss of water via evaporation

• Buoyancy control and acoustics in marine mammals

–Increased density while diving deep helps sinking –Spermaceti organ
may focus sound energy

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Biological Functions of Lipids

• Cofactors for enzymes
–Vitamin K: blood clot formation
–Coenzyme Q: ATP synthesis in mitochondria

• Signaling molecules
–Paracrine hormones (act locally)
–Steroid hormones (act body-wide)
–Growth factors
–Vitamins A and D (hormone precursors)

• Pigments
–Color of tomatoes, carrots, pumpkins, some birds

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Classification of Lipids
Based on the structure and function
• Lipids that do not contain fatty acids: cholesterol, terpenes
• Lipids that contain fatty acids (complex lipids)
– can be further separated into:

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Fatty Acids
• Carboxylic acids with hydrocarbon chains containing between 4 to 36
carbons
• Almost all natural fatty acids have an even number of carbons
• Most natural fatty acids are unbranched
• Saturated: no double bonds between carbons in the chain
• Monounsaturated: one double bond between carbons in the alkyl chain
• Polyunsaturated: more than one double bond in the alkyl chain

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Structure of Fatty Acids

• Fatty acids are carboxylic acids with long-chain hydrocarbon
parts.

• Fatty acids typically contain between twelve and twenty

carbon atoms.

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Structure of Fatty Acids

• Specific example is lauric acid

• carbons that are single bonded to

each other in a linear sequence,
abbreviated as (CH2)n, where n is
equal to the number of times that
the CH2 is repeated

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Conformation of Fatty Acids

•The saturated chain

tends to adopt extended
conformations

•The double bonds in

natural unsaturated fatty
acids are commonly in
cis configuration, which
kinks the chain

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monounsaturated

polyunsaturated

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•Trans fatty acids form by partial

dehydrogenation of unsaturated
fatty acids

•Consuming trans fats

increases risk of
cardiovascular disease

•Trans fatty acids can

pack more regularly and
show higher melting
points than cis forms

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Melting Point and Double Bonds

• Saturated fatty acids pack in a fairly orderly way
–extensive favorable interactions
•Unsaturated cis fatty acid pack less orderly due to the kink
–less-extensive favorable interactions

–unsaturated cis fatty

acids have a lower
melting point

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Melting Point and Double Bonds

• melting points of fatty acids are
related to the size

• Another factor that

influences the melting points
of fatty acids is their degree
of saturation.
• The more carbon-carbon double bonds that are present in a
fatty acid, the lower the melting point.

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Check your Understanding!

Which fatty acid would you expect to have the higher melting point,
oleic acid or palmitoleic acid?
Answer: oleic acid

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Check your Understanding!

Which fatty acid would you expect to have the higher melting point,
oleic acid or linoleic acid?
Answer: oleic acid

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Triacylglycerols
•Majority of fatty acids in biological
systems are found in the form of
triacylglycerols

-Solid ones are called fats

-Liquid ones are called oils

•The primary storage form of lipids

(body fat)

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Triacylglycerols
• Triglycerides are formed in the esterification reaction of three
fatty acid molecules with glycerol (an alcohol with three hydroxyl
groups – a triol).

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Cross section of four guinea pig

adipocytes

Cross section of a cotyledon cell

from a seed of the plant Arabidopsis

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Metabolism of Lipids
• Our body can produce all the fatty acids except essential
fatty acids.

Fatty acids synthesis: in cytoplasm

Degradation of fatty acids: in mitochondria

Excess food Acetyl CoA Fatty acids Lipid (fat)

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Digestion of Triglycerides
• triglycerides are first hydrolyzed to diglycerides, then
to monoglycerides

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Digestion of Triglycerides
• each one of these reactions produces a fatty acid

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Digestion of Triglycerides
• referred to as “partial hydrolysis” because one of the
fatty acid residues remains bound to carbon number 2 of
glycerol in the monoglyceride

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Digestion of Triglycerides
• triglyceride digestion begins in the mouth where lingual
lipase catalyzes the partial hydrolysis

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Digestion of Triglycerides

• majority of dietary
triglycerides are
digested in the small
intestine

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Digestion of Triglycerides

• after being absorbed into the

intestine walls, the fatty acids
and monoglycerides are then
re-assembled back into
triglycerides

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Glycerophospholipids

• the main lipid component of

biological membranes, contain
• two fatty acids esterified to a
glycerol phosphate backbone

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Glycerophospholipids

• Phosphatidyl choline

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Glycerophospholipids

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Sterols

• Characterized by the four fused

carbon rings in their structure

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Sterols

• cholesterol

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Sterols

• Bile acids synthesized from

cholesterol

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Sterols

• Other sterols are synthesized

from cholesterol

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Sphingolipids
• a class of lipids containing a backbone of sphingoid bases, which are a set of
aliphatic amino alcohols that includes sphingosine
• major constituents of the plasma membrane, where they are known to form
lipid microdomains with cholesterol.

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Sphingolipids

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Waxes

• A monoester formed from the

reaction of a long chain
monohydroxy alcohol with a fatty
acid molecule.
• They function as protective coating.
• The structure involves a head and
two nonpolar tails.

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Waxes

• Waxes are water-insoluble due to

the weakly polar nature of the ester
group.
• As a result, this class of molecules
confers water-repellant character to
animal skin, to the leaves of certain
plants, and to bird feathers.

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