SIMPLE LIPIDS
Triglycerides – Fats & Oils
lipids
•a heterogeneous class of naturally occurring
organic compounds classified together on
the basis of common
solubility properties.
•insoluble in water, but soluble in organic
solvents
including diethyl ether, dichloromethane,
and acetone
•Lipids include
•fatty acids, triglycerides, sphingolipids,
basis of, and glycolipids
•lipid-soluble vitamins
•prostaglandins, leukotrienes,
thromboxane’s cholesterol, steroid
hormones, and bile acids
PROPERTIES OF LIPIDS
ds may be either liquids or non-crystalline
solids at
room temperature
•Pure fats and oils are colorless, odorless,
and tasteless
•They are energy-rich organic molecules
•Insoluble or immiscible in water
•Soluble in organic solvents like alcohol,
chloroform,
acetone, benzene, etc.
•No ionic charges
•Solid triglycerols (fats) have high
proportions of saturated
fatty acids.
•Liquid triglycerols (oils) have high
proportions of unsaturated fatty acids.
TRIGLYCERIDES
1. Predominate form of fat in
foods and major storage form of fat in the body
2. Structure – composed of 3 fatty acids +
glycerol
Fatty acids
•Organic acid (chain of carbons with hydrogens
attached) that has an acid group at one end & a
methyl group at the other end
Fatty Acids carbon chains vary in:
and
1. Length – affects absorption
2. Saturation –chemical structure; affects
cooking & storage properties and health
Saturation
Saturated fatty acid – carbon chains filled with
hydrogen atoms (no C=C double bonds)
1. Saturated fat: triglyceride containing 3
saturated fatty acids, such as animal fats
(butter, lard) & tropical oils (palm, coconut)
2. Appear solid at room temperature
FATTY ACIDS
unsaturated fatty acid
carbon chains lack some hydrogen
(>1 C=C double bond)
1. Monounsaturated fat: triglyceride containing
fatty acids w/1double bond
Examples: canola & olive oil
2. Polyunsaturated fat: triglycerides containing
a high % of fatty acids with >2 double bonds
Examples: corn, safflower, soybean, sunflower FATTY ACIDS
oils, and fish;
Hydrogenated: addition of hydrogen to
3. Appear liquid at room temperature unsaturated fat

FATTY ACIDS 1. Makes it more “solid” or firm

Location of double bonds 2. Affects stability and protects against

oxidation; more “shelf-stable”
•Omega number – refers to the position
3. Widely used by food industry in margarine,
of the double bond nearest the methyl (CH3)
shortening, peanut
end of the carbon chain
butter, baked goods, and snack foods
•Omega-3 fatty acid

•Omega-6 fatty acid

Hydrogenated: addition of hydrogen to
unsaturated fat

1. Makes it more “solid” or firm

2. Affects stability and protects against

oxidation; more “shelf-stable”

3. Widely used by food industry in margarine,

shortening, peanut

butter, baked goods, and snack foods

glycerides

Physical properties depend on the fatty acid

components:

1.

o •Melting points of fatty acids

increases as the number of
carbons in the hydrocarbon
chains increases and as the
number of double bonds
decreases.

o •Triglycerides rich in
unsaturated fatty acids are
generally liquid at room
temperature and are called oils.

o •Triglycerides rich in saturated

fatty acids are generally
 semisolids or solids at room
temperature and are called fats.
Triglycerides
The lower melting points of
triglycerides rich in unsaturated fatty
acids are related to differences in
their three-dimensional shape.
•Hydrocarbon chains of saturated
fatty acids can lie parallel with strong
London dispersion forces between
their chains; they pack into well-
ordered, compact crystalline forms
and melt above room temperature
•Because of the cis configuration of
the double bonds in unsaturated
fatty acids, their hydrocarbon chains
have a less ordered structure and
London dispersion forces between
them are weaker; these triglycerides
have melting points below room
temperature.
melting points of fatty acids are
dependent on the length of the
carbon chains and the number and
types of double bonds
.•Cis double bonds cause a kink in
the chain that disrupts the London
Dispersion Forces between the
chains and lowers the melting point
of oleic acid (18:1) compared to the
saturated acid stearic acid (18:0).
•The trans fatty acid (18:1)
resembles a saturated acid and does
not disrupt the chain as much as the
cis acid. Thus, melting point would
be predicted to be higher.
•Actual melting points: 18:0 (700 C);
18:1 trans (450 C); 8:1 cis (160 C)
In general, melting points of
compounds within the same class
increase with molecular weight.
•The melting point indicates how
much energy is required to break up
the close packing of the solid.
•The greater the molecular weight
of a compound, the greater are the
attractive forces holding the
molecules together.
THE LONDON DISPERSION FORCE
• The weakest intermolecular force
• -a temporary attractive force that
results when the electrons in 2
adjacent atoms occupy positions that
make the atoms form temporary dipole
Hydrogenation
•Hardening: reduction of some or all of
the carbon-carbon double bonds of an
unsaturated triglyceride using
H2/transition metal catalyst.
•In practice, the degree of hardening is
carefully controlled to produce fats of a
desired consistency.
•The resulting fats are sold for kitchen
use (Crisco, Spry, Dexo, and others).
•Margarine and other butter substitutes
are produced by partial hydrogenation of
polyunsaturated oils derived from corn,
cottonseed, peanut, and soybean oils
 Hydrogenation
•Cis vs. trans-fatty acidsIn nature, most
double bonds are cis meaning that the
hydrogens next to the double bonds are
on the same side of the carbon chain.
When a fat is partially hydrogenated,
some of the double bonds change from
cis to trans
COMPLEX LIPIDS
complex lipids
• Phospholipids
• contain an alcohol, two fatty acids, and a
phosphate ester
• In glycerophospholipids, the alcohol is glycerol
• In sphingolipids, the alcohol is sphingosine
• Glycolipids
• Complex lipids that contain a carbohydrate
membranes
• Complex lipids form the membranes around
cells and small structures within cells.
• In aqueous solution, complex lipids
spontaneously form into a lipid bilayer, with a
back-to-back arrangement of lipid monolayers.
• Polar (hydrophilic) head groups are in contact
with the aqueous environment.
• Nonpolar (hydrophobic) tails are buried within
the bilayer and shielded from the aqueous
environment.
• The major force driving the formation of lipid
bilayers is hydrophobic interaction.
• The arrangement of hydrocarbon tails in the
interior can be rigid (if rich in saturated fatty
acids) or fluid (if rich in unsaturated fatty acids).
➢ The hydrophilic head group and
hydrophobic tails are the keys to
phospholipid function.
➢ n aqueous solution, phospholipids
spontaneously form into a lipid bilayer,
with a back-to-back arrangement of lipid
monolayers.
➢ phospholipids
➢ • Phospholipids: similar to triglycerides
in
➢ structure except only 2 fatty acids +
choline
➢ Phospholipids in foods: Lecithin, egg
yolks, soybeans, wheat germ, and
peanuts
phospholipids
1. Functions: part of cell
membranes and acts as an
emulsifier (helps keep fats in
solution)
2. Not a dietary essential; made by
the liver
glycerophospholipids = phosphoglycerides
the second most abundant group of naturally
occurring lipids
• Found almost exclusively in plant and animal
membranes, which typically consist of 40% -50%
phosphoacylglycerols and 50% - 60% proteins.
• The most abundant glycerophospholipids are acids.
derived from phosphatidic acid, a molecule in
• contributes to the fluidity of the plasma
which glycerol is esterified with two molecules
membrane by disrupting the London forces
of fatty acid and one of phosphoric acid.
between the carbon chains of the fatty acids. It
• The three most abundant fatty acids in disrupts the interactions similarly to a cis double
phosphatidic acids are palmitic (16:0), stearic bond, thus raising fluidity.
(18:0), and oleic (18:1).
lipoproteins
glycerophospholipids
• Cholesterol, along with fats, are transported by
• A phosphatidic acid
Lipoproteins
• The fatty acid on carbon 2 of glycerol is always
TYPE OF LIPOPROTEIN
Unsaturated
Lipoproteins are particles that contain
sphingolipids
triacylglycerol, cholesterol, phospholipids, and
• Found in the coatings of nerve axons (myelin)
amphipathic proteins called apolipoproteins.
• Contain the long-chain aminoalcohol,
Lipoproteins can be differentiated on the basis of
sphingosine,
their density, but also by the types of
from which this class of compounds is named.
apolipoproteins they contain. The degree of lipid
A sphingomyelin in a lipoprotein affects its density - the lower the
density of a lipoprotein, the more lipid it contains
relative to protein.
glycolipids

a complex lipid that contains a carbohydrate

cholesterol transport
• The carbohydrate is either glucose or galactose.
• Transport of cholesterol from the liver starts
• The cerebrosides are ceramide mono- or
with VLDL.
Oligosaccharides
• VLDL is carried in the serum.
steroids
• As fat is removed, its density increases and it
a group of plant and animal lipids that
becomes LDL. LDL stays in the plasma for about
have this tetracyclic ring structure
2.5 days.
cholesterol
• LDL in the bloodstream is delivered to cells by
• is the most abundant steroid in the human
binding to LDL receptor proteins in areas called
body, and also the most important.
coated pits on cells surface. After binding, the
• a component of plasma membranes in all
animal cells. LDL is transported inside the cells (endocytosis)

• the precursor of all steroid hormones and bile where cholesterol and cholesteryl esters are
released by enzymatic degradation of the LDL.
Cholesterol transport
• High-density lipoproteins (HDL) transport
cholesterol from peripheral
tissues to the liver and also transfer cholesterol
to LDL.
• While in the serum, free cholesterol in HDL is
converted to cholesteryl esters.
• In the liver, HDL binds to the liver cell surface
and transfers its cholesteryl esters to the cell.
• These esters are used for the synthesis of
steroid hormones and bile acids.
• After LDL has delivered its cholesteryl esters to
liver cells, it reenters circulation.
Levels of LDL and HDL
• Most of the cholesterol is carried by LDL.
• Normal plasma level: 175 mg/100 mL
• If there are sufficient LDL receptors on the
surface of cells, LDL is removed from circulation
and its concentration in blood plasma drops.
• The number of LDL receptors is controlled by a
negative feedback mechanism.
• When the concentration of cholesterol inside
cells is high, the synthesis of LDL receptors is
suppressed.
• In the disease called hypercholesterolemia,
there are not enough LDL receptors and plasma
levels of cholesterol may be as high as 680
mg/100 mL.
Levels of LDL and HDL
• High levels of cholesterol can cause premature
atherosclerosis and heart attacks.
• In general, high LDL means high cholesterol
content in
the plasma because LDL cannot get into cells.
• Therefore, high LDL together with low HDL is a
symptom of faulty cholesterol transport and a
warning of possible atherosclerosis.
• The serum cholesterol level controls
cholesterol synthesis in the liver. When serum
cholesterol is high, its synthesis in the liver is low,
and vice versa.
The commonly used statin drugs inhibit the
synthesis of cholesterol by blocking HMG-CoA
reductase.
• Our cholesterol levels are an important
measure of heart health. For HDL cholesterol, or
"good" cholesterol, higher levels are better.
• High-density lipoprotein (HDL) is known as the
"good" cholesterol because it helps remove other
forms of cholesterol from the bloodstream.
Steroid Hormones
Androgens: male sex hormones
• synthesized in the testes
• responsible for the development of male
secondary sex characteristics
AMONG THE SYNTHETIC ANABOLIC STEROID
ARE:
➢ METHANDIENONE
➢ METHENOLONE
➢ 4-Androstene-3,17-dion
steroid hormones
Estrogens: female sex hormones
• synthesized in the ovaries from
progesterone
• responsible for the development of female
secondary sex characteristics and control of
the menstrual cycle
 Steroid Hormones
glucorticoid hormones
• synthesized in the adrenal cortex
• regulate metabolism of carbohydrates
• decrease inflammation
• involved in the reaction to stress
bile salts
the oxidation products of cholesterol
• synthesized in liver, stored in gallbladder,
and secreted into intestine where they
emulsify dietary fats and aid in their
absorption and digestion
prostaglandins
• a family of compounds that have the 20-
carbon skeleton of prostanoic acid
are not stored in tissues as such, but are
synthesized frommembrane-bound 20-carbon
polyunsaturated fatty acids inresponse to specific
physiological triggers.
• One such polyunsaturated fatty acid is
arachidonic acid
COX enzymes
• The COX (cyclooxygenase) enzyme occurs in
two forms:
• COX-1 catalyzes the normal physiological
production of prostaglandins.
• COX-2 is responsible for the production of
prostaglandins in inflammation.
When a tissue is injured or damaged, special
inflammatory cells invade the injured tissue and
interact
with resident cells, for example, smooth muscle
cells.
This interaction activates COX-2 and
prostaglandins are synthesized.
thromboxanes
are also derived from arachidonic acid
• Thromboxane A2 induces platelet aggregation
and vasoconstriction.
• Aspirin and other NSAIDs inhibit the synthesis
of thromboxanes by inhibiting the COX enzyme
are also synthesized from arachidonic acid.
• They occur mainly in leukocytes.
• They produce muscle contractions, especially in
the lungs and thereby can cause asthma-like
attacks.
• In this regard, they are 100 times more potent
than histamine.
• Several recently-developed anti-asthma drugs
inhibit the synthesis of leukotrienes
PROTEIN
Proteins serve many functions. Among the most
important
functions are:
1. Structure: collagen and keratin are the 2
important structural
proteins, chief constituents of skin, bone, hair,
and nails;
function for protection and support, forming
connective tissue,
tendons, bone matrices, and muscle fiber.
2. Catalysts: virtually all reactions in living
systems are catalyzed
by proteins called enzymes, without enzymes –
reactions would occur so slowly as to be useless
3. Movement: muscles are made up of proteins
called myosis and actin.
4. Transport: hemoglobin, a protein in the blood,
transports oxygen from the lungs to cells; other
proteins transport molecules across cell
membranes.
5. Regulation and control: many hormones are
proteins, among them
6. Protection: when protein from outside source
blood or some foreign antigen enters the body,
the body makes its own proteins called
antibodies to counteract the foreign protein.
Antibody production is one of the major body
mechanisms that the body uses to fight diseases.
Blood clotting is carried out by protein fibrinogen.
Without blood clotting, we would bleed to death
from any small wound.
7. Storage: casein in milk and ovalbumin in eggs
store nutrients for newborn mammals and birds;
ferritin, a protein in the liver, stores iron
8. Regulation: some proteins not only control the
expression of genes (regulating the kind of
proteins to be synthesized in a cell), but also
dictate when such synthesis takes place
Two Major Types of Proteins
• fibrous proteins or Scleroproteins – insoluble in
water; used mainly for structural purposes;
Scleroprotein superfamilies include keratin,
collagen, elastin, actin, myosin, and fibrin.
• globular proteins or Spheroproteins – more or
less soluble in water; used mainly for
nonstructural purposes. Examples are
hemoglobin, insulin, immunoglobulin and many
enzymes in the body. The increased solubility of
proteins is
all down to the folding of the protein
Amino acid: a compound that
contains both an amino group
(NH2) and a carboxyl group
(COOH).
• a- Amino acid: an amino acid
in which the amino group is on the carbon
adjacent to the carboxyl group.
• Although -Amino acids are commonly written
in the un-ionized form, they are more properly
written in the zwitterion (zwi-tər-ī-ˈä-n) or
internal salt form
chirality of Amino Acids
• With the exception of glycine, all protein-
derived amino acids have at least one
stereocenter (the -carbon) and are chiral.
• The vast majority of protein-derived -amino
acids have the L-configuration at the -carbon
A molecule is chiral if it is NOT superimposable on
its mirror image.
• Most chiral molecules can be identified by their
lack of a plane of symmetry or a center of
symmetry.
• Our hand is a chiral object, as it does not have
either of these types of symmetry. Can
you superimpose one hand exactly onto the
other?
NO!
this C atom is superimposable on its mirror
image due to its identical substituents such as the
2 methyl groups
1. All 20 are a-amino acids.
2. For 19 of the 20, their -
amino

group is primary; for proline, it is secondary. peptides

3. With the exception of glycine, the -carbon of
each is a stereocenter.
4. Isoleucine and threonine
Each contain a second stereocenter.
In 1902, Emil Fischer proposed: proteins are long
chains of amino acids joined by amide bonds.
• peptide bond: The special name given to the
amide bond between

the -carboxyl group of one amino acid and the

-amino group of another
IONIZATION VS. PH
Peptide: A short polymer of amino acids joined by
The net charge on an amino acid depends on the
peptide bonds; they are classified by the number
pH of the solution in which it is dissolved.
of amino acids in the chain.
• If we dissolve an amino acid in water, it is
• Dipeptide: A molecule containing two amino
present in the aqueous solution as its zwitterion.
acids joined by a peptide bond.
• If we now add a strong acid such as HCl to bring
• Tripeptide: A molecule containing three amino
the pH of the solution to 2.0 or lower, the strong
acids joined by peptide bonds.
acid donates a proton to the - COO- of the amino
acid turning the zwitterion into a positive ion • Polypeptide: A macromolecule containing many
amino acids joined by peptide bonds.
If we add a strong base such as NaOH to the
solution and bring its pH to 10.0 or higher, a • Protein: A biological macromolecule containing
proton is transferred from the NH3+ group to the at least 30 to 50 amino acids joined by peptide
base turning the zwitterion into a negative ion bonds.

Writing Peptides

Isoelectric Point (pI) • By convention, peptides are written from the

left,
• The pH at which the majority of
beginning with the free -NH3+ group and ending
molecules of a compound in solution have no net
with the
charge.
free -COO- group on the right.
cysteine
• C-terminal amino acid: the amino acid at the
• The -SH (sulfhydryl) group of cysteine is easily
end of the chain having the free -COO- group.
oxidized to an -S-S- (disulfide).
• N-terminal amino acid: the amino acid at the
other amino acids end of the chain having the free -NH3+ group.

• Hydroxylation (oxidation) of proline, lysine, and

tyrosine, and iodination for tyrosine, give these
nonstandard amino acids

peptides and proteins
• Proteins behave as zwitterions.
• Proteins also have an isoelectric point, pI.
• At its isoelectric point, the protein has NO net
charge.
• At any pH above (more basic than) its pI, it has
a net - charge.
• At any pH below (more acidic than) its pI, it has
a net + charge.
• Hemoglobin, for example, has an almost equal
number of acidic and basic side chains; its pI is
6.8.
• Serum albumin has more acidic side chains; its
pI is 4.9.
• Proteins are least soluble in water at their
isoelectric points and can be precipitated from
solution at this pH.
Four Levels of Structural Organization of Proteins
• Primary structure: basic structure which is a
linear sequence of amino acids in a polypeptide
chain; read from the N-terminal amino acid to the
C-terminal amino acid.
• Secondary structure: conformations of amino
acids in localized regions of a polypeptide chain;
examples are α-helix, β-pleated sheet, and
random coil
• Tertiary structure: the complete three-
dimensional arrangement of atoms of a
polypeptide chain
• Quaternary structure: the spatial relationship
and interactions between subunits in a protein
that has more than one polypeptide chain
PRIMARY STRUCTURE
is the linear sequence of amino acids in a
polypeptide chain, the two-dimensional
component of the eventual 3-D shape
• the number peptides possible from the 20
protein-derived amino acids is enormous.
• there are 20 x 20 = 400 dipeptides possible
• there are 20 x 20 x 20 = 8000 tripeptides
possible
• the number of peptides possible for a chain of
n amino acids is 20n.
• for a small protein of 60 amino acids, the
number of proteins possible is 2060 = 1078,
which is possibly greater than the number of
atoms in the universe
primary structure
• Just how important is the exact amino acid
sequence?
• Human insulin consists of 2 polypeptide chains
having a total of 51 amino acids; the 2
polypeptide chains are connected by 2 interchain
disulfide bonds.
• In the table, are differences between 4 types of
insulin Vasopressin and oxytocin are both
nonapeptides but have quite different biological
functions.
• Vasopressin is an antidiuretic hormone -a
chemical produced in the brain that causes the
kidneys to release less water, decreasing the
amount of urine produced. A high ADH level
causes the body to produce less urine.
A low level results in greater urine production.
• Oxytocin affects contractions of the uterus in
childbirth and the muscles of the breast that aid
in the secretion of milk
 Secondary structure:
conformations of amino acids in localized
regions of a polypeptide chain; the way that the
linear sequence of amino acids folds upon itself.
The most common types of motifs or patterns of
secondary structure are α- helix and β-pleated
sheet.
• α-Helix: a type of secondary structure
in which a section of polypeptide
chain coils into a spiral, most
commonly a right-handed spiral.
• β-Pleated sheet: a type of secondary
structure in which 2 polypeptide
chains or sections of the same
polypeptide chain align parallel to
each other; the chains may be parallel
or antiparallel; stabilized by H bonds
in a section of -helix
• There are 3.6 amino acids per turn of the helix.
• The 6 atoms of each peptide bond lie in the
same plane.
• N-H groups of peptide bonds point in the same
direction, roughly parallel to the axis of the helix.
• C=O groups of peptide bonds point in opposite
direction, also roughly parallel to the axis of the
helix.
• The C=O group of each peptide bond is
hydrogen bonded to the N-H group of the
peptide bond 4 amino acid units away from
b-Pleated Sheet
In a section of β-pleated sheet:
• The 6 atoms of each peptide bond lie in the
same plane
• The C=O and N-H groups of peptide bonds from
adjacent chains point toward each other and are
in the same plane so that hydrogen bonding is
possible between them
• All R- groups on any one chain alternate, first
above, then below the plane of the sheet, etc.
Reminder: R group: an abbreviation for any
functional group
in which a carbon or hydrogen atom is attached
to the rest of the molecule.
Sometimes used more loosely, to include other
elements such as halogens, oxygen, or nitrogen.
Methyl group (CH3) is a common group
represented by R
ollagen triple helix (tropocollagen)
• Basic structural unit of collagen; of
approximately 1000 amino acid residues each
measuring 3000 Angstrom (Å) long by 15 Å wide
• Consists of 3 polypeptide chains wrapped
around each other in a ropelike twist to form a
triple helix
• 30% of amino acids in each chain are: Pro and
L-hydroxyproline (Hyp); glycine also occurs
• The 3 strands are held together by hydrogen
bonding.
• With age, collagen helices become cross linked
by covalent bonds formed between side chains of
Lys residues
ertiary structure
• Is the overall conformation of an entire
polypeptide chain
• Tertiary structure is stabilized in 4 ways:
• Covalent bonds, as for example, the formation
of disulfide bonds between cysteine side chains.
• Hydrogen bonding between polar groups of
side chains, as for example between the -OH
groups of serine and threonine.
• Salt bridges, as for example, the attraction of
the -NH3+ group of lysine and the -COO- group of
aspartic acid.
• Hydrophobic interactions, as for example,
between the nonpolar side chains of
phenylalanine and isoleucine.
The tertiary structure of a native conformation
refers to the 3- dimensional organization of all
the atoms - including side chain atom - in a
protein.
• Perhaps the best way to visualize what tertiary
structure looks like is to imagine taking an amino
acid sequence with primary and secondary
structure and crumpling it up into a ball. Just as
each type of protein has its own unique primary
and secondary structure, it also has its own
unique tertiary structure
The quaternary
structure of a native conformation refers to the
3-D organization of all the atoms in a multi-
subunit protein.
• Multi-subunit proteins consist of 2 or more
individual amino acid chains, each with their
own primary, secondary, and tertiary structures.
• The way these individual chains fit together into
an overall three dimensional arrangement is
called quaternary structure.
• Only multi-subunit proteins have quaternarY
structure.
Quaternary Structure
• the arrangement of polypeptide chains into a
noncovalently bonded aggregation; describes the
bonding between multiple polypeptides
• The individual chains are held in together by
hydrogen bonds, salt bridges, and hydrophobic
interactions.
• Hemoglobin
• Adult hemoglobin: 2 alpha chains of 141 amino
acids each and 2 beta chains of 146 amino acids
each
Each chain surrounds an iron- containing heme
unit
• Fetal hemoglobin: 2 alpha chains and 2 gamma
chains; fetal hemoglobin has a greater affinity for
oxygen than does adult hemoglobin.
The 4° Structure of Hemoglobin
• The term for a completely and properly folded
up protein is called the proper conformation of a
protein.
• To achieve the proper conformation, there
must be correct primary structure, secondary,
tertiary, and quaternary structure.
• Many proteins function as monomers and so do
not require quaternary structure to be
considered properly folded.
Quaternary Structure
Integral membrane protei of rhodopsin made of
a-helices.
• The b-barrel of an integral membrane protein
of the outer membrane of a mitochondrion is
made of 8 b-pleated sheets
 Denaturation
• the process of destroying the native
conformation of a protein by chemical or physical
means. Some denaturations are reversible, while
others permanently damage the protein.
• Heat increases the kinetic energy and causes
the molecules to vibrate rapidly and violently so
that the hydrogen bonds and non-polar
hydrophobic interaction are broken.
• proteins or nucleic acids lose the quaternary
structure, tertiary structure, and secondary
structure which is present in their native state, by
application of some external stress or denaturing
compounds
• If proteins in a living cell are denatured, this
results in disruption of cell activity and possibly
cell death.
Denatured proteins lose their 3-D structure and
thus cannot function.
• Denatured proteins can exhibit a wide range of
characteristics, from conformational change and
loss of solubility to aggregation due to the
exposure of hydrophobic groups
Heat: disrupts hydrogen bonding; in globular
proteins, heat can cause unfolding of
polypeptide chains - coagulation and
precipitation may take place
Aqueous 6 M Urea: disrupts hydrogen
bonding
Surface-active agents: detergents such as
sodium Dodecylbenzenesulfate (SDS) disrupt
hydrogen bonding; detergents generally
affects the hydrophobic regions
Reducing agents: 2-Mercaptoethanol
(HOCH2CH2SH) cleaves disulfide bonds by
reducing -S-S- groups to -SH groups
Heavy metal ions: transition metal ions such
as Pb2+, Hg2+ and Cd2+ form water-insoluble
salts with -SH groups; Hg2+ for example forms -
S-Hg-S-
Salts: affect both salt bridges and hydrogen
bonds of proteins
denaturating agents
Alcohol or Chloroform: 70% ethanol, e.g., which
denatures proteins, is used to sterilize skin before
injections. An alcohol content greater than 60% is
necessary to break down the envelope protein
wall of the bacteria and viruses.
Ethanol
• safe to use on food-grade surfaces
• has a quick drying time and does not leave a
residual solvent
• safest method of sanitizing in any food or
pharmaceutical setting 70% Solution is Preferred
Even though ethanol is diluted to a 70% solution,
it’s still effective at killing
microbes, bacteria, and other microorganisms on
the surfaces of counters andfood manufacturing
equipment.
Two types commonly available in industry:
70% and 95% - also known as 140 proof and 190
proof.
100% but it’s harder to obtain and is only used for
specific scientific purpose
Pure Ethanol Prevents Cell Death
Testing has been done to show that when pure
ethanol (at 100%) is
poured onto a single celled organism, it will
coagulate (clot) its protein.
The ethanol penetrates its cellular wall in all
directions. The protein located just within the cell
wall is what coagulates. It’s much like a defense
mechanism.
This ring of coagulated protein actually prevents
the ethanol from penetrating deeper into the cell
wall of the organism. No more coagulation takes
place.
Basically, this renders the organism dormant, but
doesn’t kill it. If the ethanol were to be washed
away, then it’s possible the organism would come
back to life. This process defeats the purpose of
using ethanol to kill microbes. Instead, scientists
have found a way to trick these microbes with a
lower percentage of ethanol
What Microbes Can 70% Ethanol Kill?
Water that’s been mixed into ethanol slows the
drying time, creating a longer contact time.
Ethanol needs to have a contact time of at least
10 seconds to kill Staphylococcus aureus and
Streptococcus pyogenes. At a 10 second drying
time, ethanol kills:
• Pseudomonas aeruginosa
• Serratia marcescens
• E. coli
• Salmonella typhosa
• Staphylococcus aureus
• Streptococcus pyogenes
Pouring egg whites into a beaker of acetone will
also turn egg whites translucent and solid.
• The skin that forms on curdled milk is another
common example of denatured protein.
• Keratin in human hair contains high % of
disulfide bonds that are responsible for the
shape of the hair – straight/curly. A reducing
agent cleaves the S-S bonds, allowing molecules
to lose their rigid orientation and become more
flexible. Oxidizing agent reverses the process.
Chemical Connections
• Aspartame (marketed under the trade name
NutraSweet) – too
sweet peptide
• The Use of Human Insulin
• Sickle Cell Anemia
• Protein/Peptide Conformation-Dependent
Diseases
• Proteomics
• Quaternary Structure and Allosteric Proteins
• Laser Surgery and Protein Denaturation
• State example of an inherited error in protein
structure that results in a happy ending rather
than a debilitating disease.
Soybeans: the only plant food that could serve as
a person's sole source of
protein because they contain all 8 essential
amino acids.
Quinoa (keen-wah) is native to the Andes in
South America. Chenopodium
quinoa plant comes from the same botanical
family as sugar beets and
spinach, and not the grass family like wheat, rice,
and the other grains we
typically think of as being cereals.
There are 8 essential amino acids (9 for children) • Ligases: the joining to two molecules
— essential in the sense that they cannot be
synthesized by the body so they must be supplied
by what we eat each day. Quinoa is a better
source of these amino acids than many other
grains. It contains more lysine than wheat or rice
does, and lysine is the amino acid most lacking in
these two major sources of dietary protein for Characteristics of Active Site
many people in the world. But the protein in soy
contains substantially more lysine than the • site where substrate binds to enzyme
protein in quinoa, and by some standards, quinoa • generally has groups that extend into the
falls just short of the lysine needed to be
classified as a complete provider of all 8 essential active site to help catalyze the reaction – often
amino acids. So quinoa is quite good when it histidine
comes to amino acids, but not quite as good as
• substrate “fits” into site
soybeans.
• substrate held by weak, noncovalent
ENZYMES interactions in binding site
What are enzymes? • site is very specific – only substrate that fits into
The cells in our body are chemical factories. site will undergo reaction

Only a few of the thousands of compounds • enzyme specificity is the ability of an enzyme to
necessary for the operation of the human bind only on one (or a very few) substrates and
organism are obtained from the diet. Instead, thus catalyze only one reaction
most of these substances are synthesized within
the cells, which means that hundreds of chemical
reactions take place in our cells very second of Levels of Specificity Absolute
our life. Nearly all of these reactions are catalyzed
•One substrate only Group
by enzymes, which are large molecules that
increase the rates of •Similar compounds (hexoses)
Enzymes are commonly named after thereaction Linkage Recognize bond
or reactions they catalyze Example : lactate
(linkage) types
dehydrogenase, acid phosphatase
Stereochemical
The 6 Major Groups of Enzymes
•D- or L-isomer
• Oxidoreductases: oxidation-reduction reactions
Terms in Enzyme Chemistry
• Transferases: group transfer reactions
• Activation: any process that initiates or
• Hydrolases: hydrolysis reactions
increases the activity of an enzyme.
• Lyases: addition of groups to a double bond, or
• Inhibition: any process that makes an active
Removal of groups to create a double bond enzyme less active or inactive.

• Isomerases: isomerization reactions

• Competitive inhibitor: any substance that binds
to the active site of an enzyme thereby
preventing binding of substrate.
• Noncompetitive inhibitor: any substance that
binds to a portion of the enzyme other than the
active site and thereby inhibits the activity of the
enzyme.
Apoenzyme: the protein part of an enzyme.
• Cofactor: a nonprotein portion of an enzyme
that is necessary for catalytic function;
examples are metallic ions such as Zn2+ and
Mg2+.
• Coenzyme: a nonprotein organic molecule,
frequently a B vitamin, that acts as a
cofactor.
• Substrate: the compound or compounds
whose reaction an enzyme catalyzes.
• Active site: the specific portion of the enzyme
to which a substrate binds during reaction.
• Holoenzyme: Active enzyme
ACTIVATING ENZYMES
Coenzyme binds temporarily to catalytic site to
help catalyze reaction (often has vitamin
component)
• Coenzyme binds to apoenzyme first.
• Substrate binds second
• Both product and coenzyme are
released after reaction
Enzyme Activity
• Enzyme activity: a measure of how
much a reaction rate is increased.
• We examine how the rate of an enzyme-
catalyzed reaction is affected by:
• enzyme concentration
• substrate concentration
• temperature
• Ph
ENZYME ACTIVITY
The effect of enzyme concentration on the rate
of an enzyme-catalyzed reaction.
Substrate concentration, temperature, and pH
are constant. Keeping the concentration of
substrate constant while increasing the
concentration of enzymes will increase the rate
linearly. That is, if the enzyme concentration
doubles, the rate doubles as well. If the enzyme
concentration triples, the rate also triples.
This is practically the case in all enzyme reactions
because the molar
concentration of enzyme is almost always much
lower than that of substrate.
➢ Keeping the concentration of enzyme
constant while increasing the
concentration of substrate, we will get an
entirely different type of curve called
saturation curve.
MECHANISM OF ACTION
Lock-and-key model of enzyme mechanism.
•The enzyme is a rigid three- dimensional
body.
•The enzyme surface contains the active site.
Induced-fit model
•The active site becomes modified to
accommodate the substrate.

The mechanism of competitive inhibition.
• the inhibitor fits into the active site, thereby
preventing the substrate from entering
Mechanism of noncompetitive inhibition.
•the inhibitor binds to a site other than
the active site, thereby changing the
conformation of the active site. The substrate no
longer fits
Mechanism of Action
• Both the lock-and-key model and the induced-
fit model emphasize the shape of the active site.
• However, the chemistry of the active site is the
most important.
• Just five amino acids participate in the active
sites in more than 65% of the enzymes studies to
date.
• These five are His > Cys > Asp > Arg > Glu.
• Four of these amino acids have either
acidic or basic side chains; the fifth has a
sulfhydryl group (-SH)
Catalytic Power
Enzymes provide an alternative pathway for
reaction, one with a significantly lower activation
energy and, therefore, a fast
Enzyme Regulation
Feedback control
•an enzyme-regulation process where the
product of a series of enzyme-catalyzed
reactions inhibits an earlier reaction in the
sequence.
•the inhibition may be competitive or
Noncompetitive
Enzyme Regulation
Zymogen (proenzyme): an inactive form of an
enzyme that must have part of its polypeptide
chain hydrolyzed and removed before it becomes
active.
• An example is trypsin, a digestive enzyme.
• It is synthesized and stored as trypsinogen,
which has no enzyme activity.
• It becomes active only after cleaving off 6
amino acids (hydrolyzed & removed from N-
terminal end of its chain)
• Removal of this small fragment changes in not
only the primary structure but also the tertiary
structure, allowing the molecule to achieve its
active form.
Enzyme Regulation
Allosterism: enzyme regulation based on an
event
occurring at a place other than the active site but
that
creates a change in the active site.
• An enzyme regulated by this mechanism is
called an allosteric enzyme.
• Allosteric enzymes often have multiple
polypeptide chains.
• Negative modulation: inhibition of an allosteric
enzyme.
• Positive modulation: stimulation of an allosteric
enzyme.
because it was created using a transition state
• Regulator: a substance that binds to an
analog as an immunogen.
allosteric enzyme
The allosteric effect:
Binding of the regulator to a site other than the
active site changes the shape of the active sit
Enzyme Regulation
Protein modification: the process of affecting
enzyme activity by covalently modifying it.
• The best known example of protein
modification involves
phosphorylation/dephosphorylation.
Example: Pyruvate kinase (PK) is the active
form of the enzyme; it is inactivated by
phosphorylation to pyruvate kinase
phosphate (PKP)
Isoenzyme: an enzyme that occurs in multiple
forms; each catalyzes the same reaction.
• Example: lactate dehydrogenase (LDH)
catalyzes the oxidation of lactate to pyruvate.
• The enzyme is a tetramer of H and M chains.
• H4 is present predominately in heart muscle.
• M4 is present predominantly in the liver and in
skeletal muscle.
• H3M, H2M2, and HM3 also exist.
• H4 is allosterically inhibited by high levels of
pyruvate while M4 is not.
• H4 in serum correlates with the severity of
heart attack.
Transition State Analogs
Abzyme: an antibody that has catalytic activity
➢ the abzyme is then used as a catalys
NEUROTRANSMITTERS AND
HORMONES
Chemical Communication
Terms and definitions:
• neuron: a nerve cell.
• neurotransmitter: a chemical messenger
between a neuron and another target cell;
neuron, muscle cell or cell of a gland.
• hormone: a chemical messenger released
by an endocrine gland into the bloodstream
and transported there to reach its target cell.
• The distinction between a
neurotransmitter and a hormone is
physiological, not chemical; it depends on
whether the molecule acts over a short
distance (across a synapse) or over a long
distance (from the secretory organ, through
the blood, to its site of action).
A large percent of drugs used in human
medicine influence chemical communication
• Antagonist: a molecule that blocks a natural
receptor and prevents its stimulation.
• Agonist: a molecule that competes with a
natural messenger for a receptor site; it binds
to the receptor site and elicits the same
response as the natural messenger.
• A drug may decrease or increase the
effective concentration of messenger.
 Chemical Messengers • When Ca2+ concentration becomes more
that about 0.1 mM, the vesicles that contain
• There are five classes of chemical
ACh fuse with the presynaptic membrane of
messengers:
nerve cells and empty ACh into the synapse.
• cholinergic messengers
• ACh travels across the synapse and is
• amino acid messengers absorbed on specific receptor sites.

• adrenergic messengers Action of the acetylcholine (cont’d)

• peptidergic messengers • The presence of ACh on the postsynaptic

receptor triggers a conformational change in
• steroid messengers the receptor protein.
• Messengers are also classified by how they • This change opens an ion channel and
work; they may: allows ions to cross membranes freely.
• activate enzymes. • Na+ ions have higher concentration outside
• affect the synthesis of enzymes. the neuron and pass into it.

• affect the permeability of membranes. • K+ ions have higher concentration inside

the neuron and leave it.
• act directly or through a secondary
messenger. • This change of Na+ and K+ ion
concentrations is translated into a nerve
Acetylcholine- the main cholinergic signal.
messenger is acetylcholine
• After a few milliseconds, the ion channel
Cholinergic receptors closes.
• There are two kinds of receptors for Acetylcholine
acetylcholine.
Removal of ACh
• We look at the one that exists in motor end
plates of skeletal muscles or in sympathetic • ACh is removed from the receptor site by
ganglia hydrolysis catalyzed by the enzyme
acetylcholinesterase
Acetylcholine
CONTROL OF NEUROTRANSMITTER
• Storage and release of acetylcholine (ACh).
Acetylcholinesterase is inhibited irreversibly
• The nerve cells that bring messages contain by the phosphonates in nerve gases and
ACh stored in vesicles. some pesticides (ChemCom 24B).
• The receptors on muscle neurons are called • It is also inhibited by these two compounds:
nicotinic receptors because nicotine inhibits
them. Succinylcholine

• The message is initiated by calcium ions, Decamethonium bromide

Ca2+.
 This receptor is a ligand-gated ion channel.

Control of transmission (cont’d) • When Glu binds to the receptor, the ion
channel opens, Na+ and Ca2+ ions flow in,
• Another control is to modulate the action
and K+ ions flow out.
of the ACh receptor.
• The gate of this channel is closed by Mg2+
• Because ACh enables ion channels to open
ion.
and propagate signals, the channels
themselves are called ligand-gated ion Adrenergic Messengers
channels.
Monoamine messengers
• The binding of the ligand to the receptor is
• These monoamines transmit signals by a
critical to signaling.
mechanism whose beginning is similar to the
• Nicotine in low doses is a stimulant; it is an
agonist because it prolongs the receptor’s action of acetylcholine
biochemical response.
When norepinephrine is absorbed onto the
• Nicotine in large doses is an antagonist and receptor site,
blocks the action of the receptor.
• The active G-protein hydrolyzes GTP.

• The energy of hydrolysis activates

Amino Acids adenylate cyclase.
• Amino acid messengers Cyclic AMP (cAMP)
• Some amino acids are excitatory • cAMP is synthesized in cells from ATP
neurotransmitters; examples are Glu, Asp,
and Cys. ADRENERGIC MESSENGER

• Others are inhibitory neurotransmitters; • cyclic-AMP activates protein kinase by

they reduce neurotransmission. Examples dissociating the regulatory (R) unit from
are Gly and these three, none of which is the catalytic (C) unit.
found in proteins. • The catalytic unit phosphorylates the
ion-translocating protein
➢ TAURINE • that blocks the channel ion flow.
➢ B-ALANINE • The phosphorylated ion-translocating
➢ Y-AMINOBUTYRIC ACID protein changes its shape and position
Amino Acid Messengers and opens the ion gate
• Removal of the signal:
Each amino acid has its own receptors:
• When the neurotransmitter or hormone
• Glu has at least five subclasses of receptors. dissociates from the receptor, the adenylate
• The best known receptor among these is cyclase stops the synthesis of cAMP.
the N-methyl- • The cAMP already produced is destroyed by
D-aspartate (NMDA) receptor the enzyme phosphodiesterase, which
catalyzes the hydrolysis of one of the
phosphodiester bonds to give AMP.
• The amplification through the secondary
messenger (cAMP) is relatively slow. It may
take from 0.1 s to a few minutes.
• In cases where transmission must be fast, a
neurotransmitter such as acetylcholine, acts
on membrane permeability directly without a
second messenger.
Control of neurotransmission:
• The G-protein—adenylate cyclase cascade
in transduction signaling is not limited to
monoamine messengers.
• A variety of other neurotransmitters and
peptide hormones use this signaling
pathway, including glucagon, vasopressin,
luteinizing hormone, enkephalins, and P-
protein.
• A number of enzymes can be
phosphorylated by protein kinases and the
phosphorylation controls whether these
enzymes will be active or inactive.
Removal of neurotransmitter:
• The body inactivates monoamines by
oxidation to an aldehyde, catalyzed by
monoamine oxidases (MAOs)
• The action of histamine is similar to that
of other monoamines. It is synthesized
from His by decarboxylation
• H1 receptors are found in the respiratory
tract where they affect the vascular,
muscular, and secretory changes associated
with hay fever and asthma; antihistamines
that block H1 receptors relieve these
symptoms.
• H2 receptors are found mainly in the
stomach and affect the secretion of HCl;
cimetidine and ranitidine block H2 receptors
and thus reduce acid secretion.
Peptidergic Messengers
• The first brain peptides isolated were the
enkephalins.
• These pentapeptides are present in certain
nerve cell terminals.
• They bind to specific pain receptors and
seem to control pain perception.
• Neuropeptide Y, a potent orexic, affects the
hypothalamus.
• Substance P, an 11-amino acid peptide is
involved in the transmission of pain signals.
Tyr-Gly-Gly-Phe-Leu Leucineenkephalin
Tyr-Gly-Gly-Phe-Met Methionineenkephalin
All peptidergic messengers, hormones, and
neurotransmitters act through secondary
messengers.
• Glucagon, luteinizing hormone, antidiuretic
hormone,
angiotensin, enkephalin, and substance P use
the G-protein-adenylate cyclase cascade.
• Others such as vasopressin use membrane-
derived phosphatidylinositol (PI) derivatives
Steroid Messengers
• A large number of hormones are steroids.
• These hormones are hydrophobic and,
therefore, cross plasma membranes by
diffusion.
• Steroid hormones interact inside cells with
protein receptors.
• Most of these receptors are located in the
nucleus, but
 small numbers also exist in the cytoplasm. • A nucleotide is composed of:
• a base, a monosaccharide, and a
• Once inside the nucleus, the steroid-
phosphate.
receptor complex can either bind directly to
DNA or combine with a transcription factor. PYRAMIDINE/PURINE BASE

NUCLEIC ACID AND HEREDITY

The Molecules of Heredity

• Each cell of our bodies contains thousands of

different proteins.

• How do cells know which proteins to synthesize

out of the extremely large number of possible
amino acid sequences?

• From the end of the 19th century, biologists

suspected that the transmission of hereditary

information took place in the nucleus, more

specifically in structures called chromosomes.

• The hereditary information was thought to Nucleosides

reside in genes within the chromosomes. • Nucleoside: a compound that consists of

• Chemical analysis of nuclei showed D-ribose or 2-deoxy-D-ribose bonded to a

chromosomes are made up largely of proteins
purine or pyrimidine base by a -N-
called histones and nucleic acids
glycosidic bond
By the 1940s, it became clear that
deoxyribonucleic acids (DNA) carry the Nucleotide: a nucleoside in which a molecule
hereditary information.
of phosphoric acid is esterified with an -OH
• Other work in the 1940s demonstrated that
each gene controls the manufacture of one of the monosaccharide, most commonly either
protein.
the 3’ or the 5’-OH.
• Thus the expression of a gene in terms of an
enzyme protein led to the study of protein • deoxythymidine 3’-monophosphate (3’-
synthesis and its control. Dtmp
here are two kinds of nucleic • adenosine 5’-triphosphate (ATPATP)
acids in cells: serves as a
• ribonucleic acids (RNA) • common currency into which energy
• deoxyribonucleic acids (DNA) gained
• Both RNA and DNA are polymers built • from food is converted and stored.
from monomers called nucleotides.
Schematic diagram • Chromatin fibers are organized into loops,
and the loops into the bands that provide the
of a nucleic acid molecule. The four bases of
superstructure of chromosomes
each nucleic acid
The three differences in structure
are arranged in various specific sequences.
between DNA and RNA are:
• base sequence is read from the 5’ end to • DNA bases are A, G, C, and T; the RNA bases
the 3’ end are A, G, C, and U.
• The sugar in DNA is 2-deoxy-D-ribose; in
RNA
DNA - 2° Structure it is D-ribose.
• Secondary structure: the ordered • DNA is always double stranded; there are
arrangement of nucleic acid several kinds of RNA, all of which are
strands. single-stranded.
• the double helix model of DNA 2° REPLICATION, TRANSCRIPTION,
structure was proposed by James TRANSLATION
Watson and Francis Crick in 1953.
• Double helix: a type of 2° .
structure of DNA in which two
polynucleotide strands are
coiled around each other in a
screw-like fashion.

Higher Structure of DNA

• DNA is coiled around proteins called

histones.

• Histones are rich in the basic amino acids

Lys

and Arg, whose side chains have a positive

charge.

• The negatively-charged DNA molecules and

positively-charged histones attract each

Genes, Exons, and IntronsIntrons
other and form units called nucleosomes.
• Gene: a segment of DNA that carries a
• Nucleosome: a core of eight histone base sequence that directs the
molecules around which the DNA helix is synthesis of a particular protein,
wrapped. tRNA, or mRNA.
• There are many genes in one DNA
• Nucleosomes are further condensed into
molecule.
chromatin. • In bacteria the gene is continuous.
• In higher organisms the gene is
discontinuous. Replisomes are assemblies of “enzyme
• Exon: a section of DNA that, when factories”.
transcribed, codes for a protein or
Component Function
RNA.
• Intron: a section of DNA or mRNA that Helicase Unwinds the DNA double
does not code for a protein helix

Primase synthesizes rimers

DNAReplication Clamp protein threads leading strand
• Replication involves separation of the
two original strands and synthesis of DNA polymerase joins assembled
two new daughter strands using the nucleoticides
original strands as templates. Ligase Joins Okazaki fragments
• DNA double helix unwinds at a specific lagging strand
point called an origin of replication.
• Polynucleotide chains are synthesized in
both directions from the origin of
replication; that is, DNA replication is
bidirectional. DNA Replication
• At each origin of replication, there are two 1. Opening up the superstructure.
replication forks, points at which new During replication, the very condensed
polynucleotide strands are formed. superstructure of chromosomes is opened by
a signal transduction mechanism.
One step of this mechanism involves
DNA Replication DNA Replication acetylation and deacetylation of key lysine
• DNA is synthesized from its 5’ -> 3’ end residues.
(from • Acetylation removes a positive charge and
the 3’ -> 5’ direction of the template). thus weakens the DNA-histone interactions.
• The leading strand is synthesized
continuously acetylation
in the 5’ -> 3’ direction toward the deacetylation
replication fork.
• The lagging strand is synthesized 2. Relaxation of higher structures of
semidiscontinuously as a series of Okazaki DNA.
fragments, also in the 5’ -> 3’ direction, but
away from the replication fork. •TropoisomerasesTropoisomerases (also
• Okazaki fragments of the lagging strand are called(also called gyrasesgyrases))
joined by the enzyme DNA ligase.
facilitate the relaxation of supercoiled DNA by
• Replication is semiconservative: each
introducing either single strand of double strand
daughter
breaks in the DNA.
strand contains one template strand and one
newly synthesized strand • Once the supercoiling is relaxed by this break,
the broken ends are joined and the
tropoisomerase diffuses from the location of the
replication fork.
3. Unwinding the DNA double helix.
• Replication of DNA starts with unwinding of
the double helix.
• Unwinding can occur at either end or in the
middle.
polymerases can synthesize only short
fragments,
becausee these enzymes only work from 5’ -
3’.
• These short fragments are called Okazaki
fragments.Okazaki fragments.

• Unwinding proteins called • Joining the Okazaki fragments and any

helicaseshelicases attach remaining nicks is catalyzed by DNA
ligase.DNA ligase.
themselves to one DNA strand and cause
The viability of cells depends on DNA
separation of the double helix. repair enzymes that can detect,
• The helicases catalyze the hydrolysis of ATP recognize, and repair mutations in DNA.
• Base excision repairBase excision repair
as the DNA strand moves through; the energy (BER)(BER): one of the
of hydrolysis promotes the movement. most common repair mechanisms.
• A specific DNA glycosylase recognizes the
Primer/primases damaged base.
• Primers/Primers are short • It catalyzes the hydrolysis of the -NN-
oligonucleotides— 4 to 15 glycosidic bond between the incorrect base
nucleotides long. and its deoxyribose.
• They are required to start the synthesis of • It then flips the damaged base, completing
both daughter strands. the excision
• Primases/Primases are enzymes that • The sugar-phosphate backbone remains
catalyze the intact.
synthesis of primers.
• Primases are placed at about every 50 BER (cont’d)
nucleotides in the lagging strand synthesis. • At the APAP (apapurinic or apapyrimidinic)
sitesite
thus created, an endonucleasendonuclease
DNA polymerases are key enzymes in catalyzes the
hydrolysis of the backbone
replication.
• An exonucleaseexonuclease liberates the
• Once the two strands have separated at the sugar-phosphate
unit of the damaged site
replication fork, the nucleotides must be
• DNA polymerase inserts the correct
lined up in proper order for DNA synthesis.
nucleotide
• In the absence of DNA polymerase, • DNA ligase seals the backbone to complete
alignment is slow. the repair
• NERNER (nnucleotide eexcision rrepair)
• DNA polymerase provides the speed and
removes and repairs up to 24-32 units by
specificity of alignment.
similar mechanism involving a number of
• Along the lagging (3’ -> 5’) strand, the repair enzymes
 ➢ RNA
➢ Replication
Transcription
Cloning :Transcription: the process by which
• Clone: a genetically identical information encoded in a DNA
population. molecule is copied into an mRNA
• Cloning: a process whereby DNA is molecule.
amplified by inserting it into a host • Transcription starts when the DNA
and having the host replicate it along double
with the host’s own DNA. helix begins to unwind near the gene
• Polymerase chain reaction (PCR): an to be
automated technique for amplifying DNA transcribed.
using a heat-stable DNA polymerase from • Only one strand of the DNA is
a thermophilic bacterium. transcribed.
• Ribonucleotides assemble along
the unwound
DNA strand in a complementary
sequence.
• Enzymes called polymerases
polymerases (poly)(poly) catalyze
transcription: poly I for rRNA
formation,
poly II for mRNA formation, and poly
III for
tRNA formation.

GENE EXPRESSION AND PROTEIN A eukaryotic gene has two parts:

SYNTHESIS • A structural genestructural gene
that is transcribed into
The central dogma of molecular biology RNA; the structural gene is made of
• Information contained in DNA molecules is exons and
introns.
expressed in the structure of proteins. • A regulatory generegulatory gene
• Gene expression is the turning on or that controls
transcription; the regulatory gene is
activation of a gene. Protein not
transcribed but has control
Transcription Translation
elements, one of
DNA which is the promoter.promoter.
• A promoter is unique to each gene.
replication
• There is always a sequence of bases
DNA mRNA on the
DNA strand called an initiation
Reverse transcriptase
signal.initiation signal.
• Promoters also contain consensus The RNA products of transcription
sequences,consensus sequences, are not
such as the TATA box,TATA box, in necessarily functional RNAs.
which the two • They are made functional by post-
nucleotides T and A are repeated transcriptionpost-transcription
many times. modification.modification.
• Transcribed mRNA is capped at
A TATA box lies approximately 25 both ends.
base pairs • The 5’ end acquires a methylated
upstream (Figure 25.2). guanine.
• All three RNA polymerases interact • The 3’ end acquires a polyA tail that
with their promoter regions via may
transcriptiontranscription contain from 100 to 200 adenine
factorsfactors that are binding residues.
proteins. • Once the two ends are capped, the
• After initiation, RNA polymerase introns are
zips up the spliced out.
complementary bases in a process • tRNA is similarly trimmed, capped,
called elongation.elongation. andmethylated.
• Elongation is in the 5’ -> 3’ • Functional rRNA also undergoes
direction. post-transcription methylation
• At the end of each gene is a
termination sequence RNA in Translation
• mRNA, rRNA, and tRNA all
participate in translation.
Poly II has two different forms: • Protein synthesis takes place on
• At its C-terminal domain, it has Ser ribosomes.
and Thr • A ribosome dissociates into larger
repeats that can be phosphorylated. and a smaller
• When poly II starts initiation, it is body.
unphosphorylated. • In higher organisms, the larger
• Upon phosphorylation, it catalyzes body is called a 60S
elongation. ribosome; the smaller body is called
• After termination of the a 40S ribosome.
transcription, it • The 5’ end of the mature mRNA is
is dephosphorylated by a bonded to the 40S
phosphatase. ribosome and this unit then joined to
• In this manner, poly II is constantly the 60S
recycled between its initiation and ribosome.
elongation roles. • Together the 40S and 60S
ribosomes form a unit on
which mRNA is stretched out.
• Triplets of bases on mRNA are
called codons.codons.
• The 20 amino acids are then for His.
brought to the mRNA- • By 1967, the genetic code was
ribosome complex, each amino acid broken.
by its own
particular tRNA. Features of the Code
• All 64 codons have been assigned.
tRNA • 61 code for amino acids.
• Each tRNA is specific for only one • 3 (UAA, UAG, and UGA) serve as
amino acid. termination signals.
• Each cell carries at least 20 specific • AUG also serves as an initiation
enzymes, each specific for one signal.
amino acid. • Only Trp and Met have one codon
• Each enzyme recognizes only one each.
tRNA. • More than one triplet can code for
• The enzyme bonds the activated the same amino acid; Leu, Ser, and
amino acid to Arg, for example,
the 3’ terminal -OH group of the are each coded for by six triplets.
appropriate • The third base is irrelevant for
tRNA by an ester bond. Leu,Val, Ser, Pro, Thr, Ala, Gly, and
• At the opposite end of the tRNA Arg
molecule is a For the 15 amino acids coded for by
codon recognition site.codon 2, 3, or
recognition site. 4 triplets, it is only the third letter of
• The codon recognition site is a the codon that varies. Gly, for
sequence of example, is
three bases called an coded for by GGA, GGG, GGC, and
anticodon.anticodon. GGU.
• This triplet of bases aligns itself in a • The code is almost universal: it the
complementary fashion to the codon same in
triplet on viruses, prokaryotes, and
mRNA. eukaryotes; the
only exceptions are some codons in
The Genetic Code mitochondria.
• Assignments of triplets is based on
several types of experiments. Translation:
• One of these used synthetic mRNA. Translation: the process whereby a
• If mRNA is polyU, polyPhe is base sequence of mRNA is used to
formed; the create a protein.
triplet UUU, therefore, must code for • There are four major stages in
Phe. proteinSynthesis:
• If mRNA is poly ---ACACAC---, •Activation
poly(Thr-His) •Initiation
is formed; ACA must code for Thr, •Elongation
and CAC • Termination
 • Gene regulation:

Gene regulation: the various methods

used by organisms to control which
genes will be expressed and when.
• Some regulations operate at the
transcriptional leveltranscriptional level
(DNA -> RNA)
• Others operate at the translational
Amino Acid Activation
leveltranslational level
• Requires
(mRNA -> protein).
• amino acids
• tRNAs
• aminoacyl-tRNA synthetases
Transcriptional Level
• ATP, Mg2+
• In eukaryotes, transcription is
• Formation on an aminoacyl-tRNA
regulated by three elements: promoters,
➢ Amino Acid Activation enhancers, and response elements.
• The activated amino acid is bound to •Promoters located adjacent to the
its own particular tRNA by an ester transcription site are defined by an initiator
bond between the carboxyl group of the and conserved
amino acid and the 3’-OH of the tRNA sequences such as TATA or GC boxes.
• Different transcription factors transcription
This two-stage reaction allows selectivity at
factors bind to
two levels
different modules of the promoter.
• the amino acid:the amino acid: The • Transcription factors allow the rate of
aminoacyl-AMP remains synthesis of mRNA (and from there the target
protein) to vary by a factor of up to a
bound to the enzyme and binding of the million.
correct amino acid is verified by an

editing site on the tRNA synthetase. Promoters

• tRNA:tRNA: There are specific binding sites
on tRNAs that are recognized by aminoacyl-
tRNA synthetases.
Termination
• Chain termination requires:
• Termination codons (UAA, UAG, or UGA) of
mRNA.
• Releasing factors that cleave the
polypeptide chain from the last tRNA and
release the tRNA from the ribosome
• Transcription factors find their targeted
sites by twisting their protein chains so
that a certain amino acid sequence is
present at the surface.
• One such conformational twist is provided
by metal-binding fingers metal-binding
fingers (next screen).
• Two other prominent transcription factor
conformations are the helix-turn-helix and
the leucine zipper leucine zipper.
• Transcription factors also possess
repressors, which reduce the rate of
transcription.
 Enhancers
• Enhancers speed up transcription:
They may be several thousand nucleotides
away from the transcription site; a loop in
DNA brings the enhancer to the initiation
site.
Response elements are activated by
their transcription factors in response
to an outside stimulus.
• The stimulus may be heat shock, heavy metal
toxicity, or a hormonal signal.
• The response element of steroids is in front
of and about 250 base pairs upstream from
the starting point of transcription.
• Certain proteins called chaperones help
newly synthesized proteins to fold properly.
• If rescue by chaperones fails, proteasomes may
degrade the misfolded protein
Mutations and mutagen
Mutation: a heritable change in the base
sequence of DNA.
• It is estimated that, on average, there is one
copying error for every 1010 bases.
• Mutations can occur during replication.

• Base errors can also occur during transcription

Translational Level in protein synthesis (a nonheritable error).

• During translation, there are a number
• Consider the mRNA codons for Val, which are
of mechanisms that ensure quality
CAT, CAC, CAG, and CAA.
control.
• AARS control • If the original codon is CAT, it may be
• Each amino acid must bond to the proper transcribed onto mRNA as GUC which codes for
tRNA. Val.
• Enzymes called aminoacyl-tRNA
• Other errors in replication may lead to a change
synthaseaminoacyl-tRNA synthase
(AARS)(AARS) catalyze this bonding. in protein structure and be very harmful.
• Each AARS recognizes its tRNA by specific
nucleotide sequences. Mutagen: a chemical that causes a base
• Further, the active site of each AARS has change in DNA.
two sieving sites.
• Many changes in base sequence caused by
Termination control
radiation and mutagens do not become
• The stop codons must be recognized by
mutations because cells have repair
release factors release factors.
mechanisms called nucleotide excision
• The release factor combines with GTP and nucleotide excision repair (NER)
binds to the ribosomal A site when that site • NER can prevent mutations by cutting out
is occupied by the termination codon. damaged areas and resynthesizing them.
• Post-translational control • Not all mutations are harmful.
• In most proteins, the Met at the N-terminal • Certain ones may be beneficial because they
end is removed by Met-aminopeptidase.
enhance the survival rate of the species. GENE THERAPHY VIA RETROVIRUSES

Recombinant DNA:

DNA from two sources that have been combined

into one molecule.

• One example of the technique begins with

plasmids found in the cells of Escherichia coli.

•plasmid: a small, circular, double-stranded DNA

molecule of bacterial origin.

• A class of enzymes called endonucleases cleave

DNA at specific locations.

• One, for example, may be specific for cleavage

of the bond between A-G in the sequence -

CTTAAAG-.

In this example “B ” stands for bacterial

gene, and “H for human gene.
• The DNA is now double-stranded with two
“sticky ends”, each with free bases that can
pair with a complementary section of DNA.
• Next, we cut a human gene with the same
restriction endonuclease; for example, the CLONING DNA
gene for human insulin

The human gene is now spliced into the

plasmid by the enzyme DNA ligase.
• Splicing takes place at both ends of the
human gene and the plasmid is once again
circular.
• The modified plasmid is then put back into
the bacterial cell where it replicates
naturally every time the cell divides.
• These cells now manufacture the human
protein, in our example human insulin, by
transcription and translation
RECOMBINANT DNA