SIMPLE LIPIDS TRIGLYCERIDES

Triglycerides – Fats & Oils

lipids 1. Predominate form of fat in
•a heterogeneous class of naturally occurring
organic compounds classified together on foods and major storage form of fat in the body
the basis of common 2. Structure – composed of 3 fatty acids +
solubility properties.
•insoluble in water, but soluble in organic glycerol
solvents Fatty acids
including diethyl ether, dichloromethane,
and acetone •Organic acid (chain of carbons with hydrogens
•Lipids include
attached) that has an acid group at one end & a
•fatty acids, triglycerides, sphingolipids,
basis of, and glycolipids methyl group at the other end
•lipid-soluble vitamins
Fatty Acids carbon chains vary in:
•prostaglandins, leukotrienes, and
thromboxane’s cholesterol, steroid 1. Length – affects absorption
hormones, and bile acids
2. Saturation –chemical structure; affects
cooking & storage properties and health
PROPERTIES OF LIPIDS
Saturation
ds may be either liquids or non-crystalline
solids at Saturated fatty acid – carbon chains filled with
room temperature hydrogen atoms (no C=C double bonds)
•Pure fats and oils are colorless, odorless, 1. Saturated fat: triglyceride containing 3
and tasteless saturated fatty acids, such as animal fats
•They are energy-rich organic molecules (butter, lard) & tropical oils (palm, coconut)
•Insoluble or immiscible in water
•Soluble in organic solvents like alcohol, 2. Appear solid at room temperature
chloroform, FATTY ACIDS
acetone, benzene, etc.
•No ionic charges unsaturated fatty acid
•Solid triglycerols (fats) have high carbon chains lack some hydrogen
proportions of saturated
fatty acids. (>1 C=C double bond)
•Liquid triglycerols (oils) have high 1. Monounsaturated fat: triglyceride containing
proportions of unsaturated fatty acids. 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 In general, melting points of
temperature and are called fats. compounds within the same class
increase with molecular weight.
Triglycerides
•The melting point indicates how
The lower melting points of much energy is required to break up
triglycerides rich in unsaturated fatty the close packing of the solid.
acids are related to differences in
•The greater the molecular weight
their three-dimensional shape.
of a compound, the greater are the
•Hydrocarbon chains of saturated attractive forces holding the
fatty acids can lie parallel with strong molecules together.
London dispersion forces between
THE LONDON DISPERSION FORCE
their chains; they pack into well-
ordered, compact crystalline forms
and melt above room temperature
• The weakest intermolecular force
•Because of the cis configuration of • -a temporary attractive force that
the double bonds in unsaturated results when the electrons in 2
fatty acids, their hydrocarbon chains adjacent atoms occupy positions that
have a less ordered structure and make the atoms form temporary dipole
London dispersion forces between Hydrogenation
them are weaker; these triglycerides •Hardening: reduction of some or all of
have melting points below room the carbon-carbon double bonds of an
temperature. unsaturated triglyceride using
H2/transition metal catalyst.
melting points of fatty acids are
•In practice, the degree of hardening is
dependent on the length of the
carefully controlled to produce fats of a
carbon chains and the number and
desired consistency.
types of double bonds
•The resulting fats are sold for kitchen
.•Cis double bonds cause a kink in use (Crisco, Spry, Dexo, and others).
the chain that disrupts the London •Margarine and other butter substitutes
Dispersion Forces between the are produced by partial hydrogenation of
chains and lowers the melting point polyunsaturated oils derived from corn,
of oleic acid (18:1) compared to the cottonseed, peanut, and soybean oils
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)
 Hydrogenation • Nonpolar (hydrophobic) tails are buried within
•Cis vs. trans-fatty acidsIn nature, most the bilayer and shielded from the aqueous
double bonds are cis meaning that the environment.
hydrogens next to the double bonds are
• The major force driving the formation of lipid
on the same side of the carbon chain.
bilayers is hydrophobic interaction.
When a fat is partially hydrogenated,
some of the double bonds change from • The arrangement of hydrocarbon tails in the
cis to trans 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
COMPLEX LIPIDS ➢ • Phospholipids: similar to triglycerides
in
➢ structure except only 2 fatty acids +
complex lipids choline
• Phospholipids ➢ Phospholipids in foods: Lecithin, egg
yolks, soybeans, wheat germ, and
• contain an alcohol, two fatty acids, and a peanuts
phosphate ester phospholipids
• In glycerophospholipids, the alcohol is glycerol 1. Functions: part of cell
• In sphingolipids, the alcohol is sphingosine membranes and acts as an
• Glycolipids emulsifier (helps keep fats in
• Complex lipids that contain a carbohydrate solution)
membranes 2. Not a dietary essential; made by
• Complex lipids form the membranes around the liver
cells and small structures within cells.
glycerophospholipids = phosphoglycerides
• In aqueous solution, complex lipids
spontaneously form into a lipid bilayer, with a the second most abundant group of naturally
back-to-back arrangement of lipid monolayers. occurring lipids

• Polar (hydrophilic) head groups are in contact • Found almost exclusively in plant and animal
with the aqueous environment. 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. the plasma because LDL cannot get into cells.

Cholesterol transport • Therefore, high LDL together with low HDL is a

• High-density lipoproteins (HDL) transport symptom of faulty cholesterol transport and a

cholesterol from peripheral warning of possible atherosclerosis.

tissues to the liver and also transfer cholesterol • The serum cholesterol level controls
to LDL. cholesterol synthesis in the liver. When serum
cholesterol is high, its synthesis in the liver is low,
• While in the serum, free cholesterol in HDL is
and vice versa.
converted to cholesteryl esters.
The commonly used statin drugs inhibit the
• In the liver, HDL binds to the liver cell surface
synthesis of cholesterol by blocking HMG-CoA
and transfers its cholesteryl esters to the cell.
reductase.
• These esters are used for the synthesis of
• Our cholesterol levels are an important
steroid hormones and bile acids.
measure of heart health. For HDL cholesterol, or
• After LDL has delivered its cholesteryl esters to "good" cholesterol, higher levels are better.
liver cells, it reenters circulation.
• High-density lipoprotein (HDL) is known as the
Levels of LDL and HDL "good" cholesterol because it helps remove other
forms of cholesterol from the bloodstream.
• Most of the cholesterol is carried by LDL.
Steroid Hormones
• Normal plasma level: 175 mg/100 mL
Androgens: male sex hormones
• If there are sufficient LDL receptors on the
surface of cells, LDL is removed from circulation • synthesized in the testes
and its concentration in blood plasma drops.
• responsible for the development of male
• The number of LDL receptors is controlled by a secondary sex characteristics
negative feedback mechanism.
AMONG THE SYNTHETIC ANABOLIC STEROID
• When the concentration of cholesterol inside ARE:
cells is high, the synthesis of LDL receptors is
➢ METHANDIENONE
suppressed.
➢ METHENOLONE
• In the disease called hypercholesterolemia, ➢ 4-Androstene-3,17-dion
there are not enough LDL receptors and plasma
steroid hormones
levels of cholesterol may be as high as 680
mg/100 mL. Estrogens: female sex hormones

Levels of LDL and HDL • synthesized in the ovaries from

progesterone
• High levels of cholesterol can cause premature
• responsible for the development of female
atherosclerosis and heart attacks.
secondary sex characteristics and control of
• In general, high LDL means high cholesterol the menstrual cycle
content in
 Steroid Hormones with resident cells, for example, smooth muscle
cells.
glucorticoid hormones
This interaction activates COX-2 and
• synthesized in the adrenal cortex
prostaglandins are synthesized.
• regulate metabolism of carbohydrates
thromboxanes
• decrease inflammation
are also derived from arachidonic acid
• involved in the reaction to stress
• Thromboxane A2 induces platelet aggregation
and vasoconstriction.

bile salts • Aspirin and other NSAIDs inhibit the synthesis

of thromboxanes by inhibiting the COX enzyme
the oxidation products of cholesterol
are also synthesized from arachidonic acid.
• synthesized in liver, stored in gallbladder,
and secreted into intestine where they • They occur mainly in leukocytes.
emulsify dietary fats and aid in their
• They produce muscle contractions, especially in
absorption and digestion
the lungs and thereby can cause asthma-like
prostaglandins attacks.

• a family of compounds that have the 20- • In this regard, they are 100 times more potent
than histamine.
carbon skeleton of prostanoic acid
• Several recently-developed anti-asthma drugs
are not stored in tissues as such, but are inhibit the synthesis of leukotrienes
synthesized frommembrane-bound 20-carbon
polyunsaturated fatty acids inresponse to specific
physiological triggers.
PROTEIN
• One such polyunsaturated fatty acid is
arachidonic acid Proteins serve many functions. Among the most
important
COX enzymes
functions are:
• The COX (cyclooxygenase) enzyme occurs in
two forms: 1. Structure: collagen and keratin are the 2
important structural
• COX-1 catalyzes the normal physiological
production of prostaglandins. proteins, chief constituents of skin, bone, hair,
and nails;
• COX-2 is responsible for the production of
prostaglandins in inflammation. function for protection and support, forming
connective tissue,
When a tissue is injured or damaged, special
tendons, bone matrices, and muscle fiber.
inflammatory cells invade the injured tissue and
interact 2. Catalysts: virtually all reactions in living
systems are catalyzed
by proteins called enzymes, without enzymes – all down to the folding of the protein
reactions would occur so slowly as to be useless
Amino acid: a compound that
3. Movement: muscles are made up of proteins
contains both an amino group
called myosis and actin.
(NH2) and a carboxyl group
4. Transport: hemoglobin, a protein in the blood,
transports oxygen from the lungs to cells; other (COOH).
proteins transport molecules across cell
membranes. • a- Amino acid: an amino acid

5. Regulation and control: many hormones are in which the amino group is on the carbon
proteins, among them adjacent to the carboxyl group.

• Although -Amino acids are commonly written

in the un-ionized form, they are more properly
6. Protection: when protein from outside source written in the zwitterion (zwi-tər-ī-ˈä-n) or
blood or some foreign antigen enters the body, internal salt form
the body makes its own proteins called
antibodies to counteract the foreign protein. chirality of Amino Acids
Antibody production is one of the major body • With the exception of glycine, all protein-
mechanisms that the body uses to fight diseases. derived amino acids have at least one
Blood clotting is carried out by protein fibrinogen. stereocenter (the -carbon) and are chiral.
Without blood clotting, we would bleed to death
from any small wound. • The vast majority of protein-derived -amino
acids have the L-configuration at the -carbon
7. Storage: casein in milk and ovalbumin in eggs
store nutrients for newborn mammals and birds; A molecule is chiral if it is NOT superimposable on
ferritin, a protein in the liver, stores iron its mirror image.
8. Regulation: some proteins not only control the • Most chiral molecules can be identified by their
expression of genes (regulating the kind of lack of a plane of symmetry or a center of
proteins to be synthesized in a cell), but also symmetry.
dictate when such synthesis takes place
• Our hand is a chiral object, as it does not have
Two Major Types of Proteins either of these types of symmetry. Can
• fibrous proteins or Scleroproteins – insoluble in you superimpose one hand exactly onto the
water; used mainly for structural purposes; other?
Scleroprotein superfamilies include keratin,
collagen, elastin, actin, myosin, and fibrin. NO!

• globular proteins or Spheroproteins – more or this C atom is superimposable on its mirror

less soluble in water; used mainly for
image due to its identical substituents such as the
nonstructural purposes. Examples are
hemoglobin, insulin, immunoglobulin and many 2 methyl groups

enzymes in the body. The increased solubility of 1. All 20 are a-amino acids.
proteins is
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 In 1902, Emil Fischer proposed: proteins are long
each is a stereocenter.
chains of amino acids joined by amide bonds.
4. Isoleucine and threonine
• peptide bond: The special name given to the
Each contain a second stereocenter. 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
 PRIMARY STRUCTURE

peptides and proteins is the linear sequence of amino acids in a

polypeptide chain, the two-dimensional
• Proteins behave as zwitterions.
component of the eventual 3-D shape
• Proteins also have an isoelectric point, pI.
• the number peptides possible from the 20
• At its isoelectric point, the protein has NO net protein-derived amino acids is enormous.
charge.
• there are 20 x 20 = 400 dipeptides possible
• At any pH above (more basic than) its pI, it has
• there are 20 x 20 x 20 = 8000 tripeptides
a net - charge.
possible
• At any pH below (more acidic than) its pI, it has
• the number of peptides possible for a chain of
a net + charge.
n amino acids is 20n.
• Hemoglobin, for example, has an almost equal
• for a small protein of 60 amino acids, the
number of acidic and basic side chains; its pI is
number of proteins possible is 2060 = 1078,
6.8.
which is possibly greater than the number of
• Serum albumin has more acidic side chains; its atoms in the universe
pI is 4.9.
primary structure
• Proteins are least soluble in water at their
• Just how important is the exact amino acid
isoelectric points and can be precipitated from
sequence?
solution at this pH.
• Human insulin consists of 2 polypeptide chains
Four Levels of Structural Organization of Proteins
having a total of 51 amino acids; the 2
• Primary structure: basic structure which is a polypeptide chains are connected by 2 interchain
linear sequence of amino acids in a polypeptide disulfide bonds.
chain; read from the N-terminal amino acid to the
• In the table, are differences between 4 types of
C-terminal amino acid.
insulin Vasopressin and oxytocin are both
• Secondary structure: conformations of amino nonapeptides but have quite different biological
acids in localized regions of a polypeptide chain; functions.
examples are α-helix, β-pleated sheet, and
• Vasopressin is an antidiuretic hormone -a
random coil
chemical produced in the brain that causes the
• Tertiary structure: the complete three- kidneys to release less water, decreasing the
dimensional arrangement of atoms of a amount of urine produced. A high ADH level
polypeptide chain causes the body to produce less urine.

• Quaternary structure: the spatial relationship A low level results in greater urine production.
and interactions between subunits in a protein
• Oxytocin affects contractions of the uterus in
that has more than one polypeptide chain
childbirth and the muscles of the breast that aid
in the secretion of milk
 Secondary structure: b-Pleated Sheet

conformations of amino acids in localized In a section of β-pleated sheet:

regions of a polypeptide chain; the way that the
• The 6 atoms of each peptide bond lie in the
linear sequence of amino acids folds upon itself.
same plane
The most common types of motifs or patterns of
secondary structure are α- helix and β-pleated • The C=O and N-H groups of peptide bonds from
sheet. adjacent chains point toward each other and are
in the same plane so that hydrogen bonding is
• α-Helix: a type of secondary structure
possible between them
in which a section of polypeptide
• All R- groups on any one chain alternate, first
chain coils into a spiral, most above, then below the plane of the sheet, etc.

commonly a right-handed spiral. Reminder: R group: an abbreviation for any

functional group
• β-Pleated sheet: a type of secondary
in which a carbon or hydrogen atom is attached
structure in which 2 polypeptide
to the rest of the molecule.
chains or sections of the same
Sometimes used more loosely, to include other
polypeptide chain align parallel to
elements such as halogens, oxygen, or nitrogen.
each other; the chains may be parallel
Methyl group (CH3) is a common group
or antiparallel; stabilized by H bonds
represented by R
in a section of -helix
ollagen triple helix (tropocollagen)
• There are 3.6 amino acids per turn of the helix.
• Basic structural unit of collagen; of
• The 6 atoms of each peptide bond lie in the approximately 1000 amino acid residues each
measuring 3000 Angstrom (Å) long by 15 Å wide
same plane.
• Consists of 3 polypeptide chains wrapped
• N-H groups of peptide bonds point in the same around each other in a ropelike twist to form a
direction, roughly parallel to the axis of the helix. triple helix

• C=O groups of peptide bonds point in opposite • 30% of amino acids in each chain are: Pro and
L-hydroxyproline (Hyp); glycine also occurs
direction, also roughly parallel to the axis of the
• The 3 strands are held together by hydrogen
helix. bonding.
• The C=O group of each peptide bond is • With age, collagen helices become cross linked
hydrogen bonded to the N-H group of the by covalent bonds formed between side chains of
peptide bond 4 amino acid units away from Lys residues

ertiary structure
• Is the overall conformation of an entire structure.
polypeptide chain
Quaternary Structure
• Tertiary structure is stabilized in 4 ways:
• the arrangement of polypeptide chains into a
• Covalent bonds, as for example, the formation
noncovalently bonded aggregation; describes the
of disulfide bonds between cysteine side chains.
bonding between multiple polypeptides
• Hydrogen bonding between polar groups of
side chains, as for example between the -OH • The individual chains are held in together by
groups of serine and threonine.
hydrogen bonds, salt bridges, and hydrophobic
• Salt bridges, as for example, the attraction of interactions.
the -NH3+ group of lysine and the -COO- group of
aspartic acid. • Hemoglobin

• Hydrophobic interactions, as for example, • Adult hemoglobin: 2 alpha chains of 141 amino
between the nonpolar side chains of acids each and 2 beta chains of 146 amino acids
phenylalanine and isoleucine. each

The tertiary structure of a native conformation Each chain surrounds an iron- containing heme
refers to the 3- dimensional organization of all unit
the atoms - including side chain atom - in a • Fetal hemoglobin: 2 alpha chains and 2 gamma
protein.
chains; fetal hemoglobin has a greater affinity for
• Perhaps the best way to visualize what tertiary
structure looks like is to imagine taking an amino oxygen than does adult hemoglobin.
acid sequence with primary and secondary The 4° Structure of Hemoglobin
structure and crumpling it up into a ball. Just as
each type of protein has its own unique primary • The term for a completely and properly folded
and secondary structure, it also has its own up protein is called the proper conformation of a
unique tertiary structure protein.

The quaternary • To achieve the proper conformation, there

must be correct primary structure, secondary,
structure of a native conformation refers to the tertiary, and quaternary structure.
3-D organization of all the atoms in a multi-
subunit protein. • Many proteins function as monomers and so do
not require quaternary structure to be
• Multi-subunit proteins consist of 2 or more considered properly folded.
individual amino acid chains, each with their Quaternary Structure
own primary, secondary, and tertiary structures. Integral membrane protei of rhodopsin made of
• The way these individual chains fit together into a-helices.
an overall three dimensional arrangement is • The b-barrel of an integral membrane protein
called quaternary structure. of the outer membrane of a mitochondrion is
• Only multi-subunit proteins have quaternarY made of 8 b-pleated sheets
 Denaturation reducing -S-S- groups to -SH groups

• the process of destroying the native Heavy metal ions: transition metal ions such
conformation of a protein by chemical or physical
as Pb2+, Hg2+ and Cd2+ form water-insoluble
means. Some denaturations are reversible, while
others permanently damage the protein. salts with -SH groups; Hg2+ for example forms -
• Heat increases the kinetic energy and causes S-Hg-S-
the molecules to vibrate rapidly and violently so
that the hydrogen bonds and non-polar Salts: affect both salt bridges and hydrogen
hydrophobic interaction are broken. bonds of proteins
• proteins or nucleic acids lose the quaternary denaturating agents
structure, tertiary structure, and secondary
structure which is present in their native state, by Alcohol or Chloroform: 70% ethanol, e.g., which
application of some external stress or denaturing denatures proteins, is used to sterilize skin before
compounds
injections. An alcohol content greater than 60% is
• If proteins in a living cell are denatured, this
results in disruption of cell activity and possibly necessary to break down the envelope protein
cell death. wall of the bacteria and viruses.

Denatured proteins lose their 3-D structure and Ethanol

thus cannot function.
• safe to use on food-grade surfaces
• Denatured proteins can exhibit a wide range of
• has a quick drying time and does not leave a
characteristics, from conformational change and residual solvent
loss of solubility to aggregation due to the
• safest method of sanitizing in any food or
exposure of hydrophobic groups
pharmaceutical setting 70% Solution is Preferred
Heat: disrupts hydrogen bonding; in globular
Even though ethanol is diluted to a 70% solution,
proteins, heat can cause unfolding of
it’s still effective at killing
polypeptide chains - coagulation and
precipitation may take place microbes, bacteria, and other microorganisms on
the surfaces of counters andfood manufacturing
Aqueous 6 M Urea: disrupts hydrogen
equipment.
bonding
Two types commonly available in industry:
Surface-active agents: detergents such as
70% and 95% - also known as 140 proof and 190
sodium Dodecylbenzenesulfate (SDS) disrupt proof.

hydrogen bonding; detergents generally 100% but it’s harder to obtain and is only used for
specific scientific purpose
affects the hydrophobic regions
Pure Ethanol Prevents Cell Death
Reducing agents: 2-Mercaptoethanol
Testing has been done to show that when pure
(HOCH2CH2SH) cleaves disulfide bonds by ethanol (at 100%) is
poured onto a single celled organism, it will • Keratin in human hair contains high % of
coagulate (clot) its protein.
disulfide bonds that are responsible for the
The ethanol penetrates its cellular wall in all
shape of the hair – straight/curly. A reducing
directions. The protein located just within the cell
wall is what coagulates. It’s much like a defense agent cleaves the S-S bonds, allowing molecules
mechanism.
to lose their rigid orientation and become more
This ring of coagulated protein actually prevents
the ethanol from penetrating deeper into the cell flexible. Oxidizing agent reverses the process.
wall of the organism. No more coagulation takes
place.
Chemical Connections
Basically, this renders the organism dormant, but
doesn’t kill it. If the ethanol were to be washed • Aspartame (marketed under the trade name
away, then it’s possible the organism would come NutraSweet) – too
back to life. This process defeats the purpose of sweet peptide
using ethanol to kill microbes. Instead, scientists
have found a way to trick these microbes with a • The Use of Human Insulin
lower percentage of ethanol
• Sickle Cell Anemia

• Protein/Peptide Conformation-Dependent
What Microbes Can 70% Ethanol Kill? Diseases

Water that’s been mixed into ethanol slows the • Proteomics

drying time, creating a longer contact time.
• Quaternary Structure and Allosteric Proteins
Ethanol needs to have a contact time of at least
10 seconds to kill Staphylococcus aureus and • Laser Surgery and Protein Denaturation
Streptococcus pyogenes. At a 10 second drying
• State example of an inherited error in protein
time, ethanol kills:
structure that results in a happy ending rather
• Pseudomonas aeruginosa than a debilitating disease.

• Serratia marcescens Soybeans: the only plant food that could serve as
a person's sole source of
• E. coli
protein because they contain all 8 essential
• Salmonella typhosa
amino acids.
• Staphylococcus aureus
Quinoa (keen-wah) is native to the Andes in
• Streptococcus pyogenes South America. Chenopodium

Pouring egg whites into a beaker of acetone will quinoa plant comes from the same botanical
family as sugar beets and
also turn egg whites translucent and solid.
spinach, and not the grass family like wheat, rice,
• The skin that forms on curdled milk is another and the other grains we
common example of denatured protein. 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 much a reaction rate is increased.
to the active site of an enzyme thereby
• We examine how the rate of an enzyme-
preventing binding of substrate.
catalyzed reaction is affected by:
• Noncompetitive inhibitor: any substance that
binds to a portion of the enzyme other than the • enzyme concentration
active site and thereby inhibits the activity of the
enzyme. • substrate concentration

Apoenzyme: the protein part of an enzyme. • temperature

• Cofactor: a nonprotein portion of an enzyme • Ph

that is necessary for catalytic function; ENZYME ACTIVITY

examples are metallic ions such as Zn2+ and The effect of enzyme concentration on the rate
of an enzyme-catalyzed reaction.
Mg2+.
Substrate concentration, temperature, and pH
• Coenzyme: a nonprotein organic molecule, are constant. Keeping the concentration of
substrate constant while increasing the
frequently a B vitamin, that acts as a
concentration of enzymes will increase the rate
cofactor. linearly. That is, if the enzyme concentration
doubles, the rate doubles as well. If the enzyme
• Substrate: the compound or compounds
concentration triples, the rate also triples.
whose reaction an enzyme catalyzes.
This is practically the case in all enzyme reactions
• Active site: the specific portion of the enzyme because the molar

to which a substrate binds during reaction. concentration of enzyme is almost always much
lower than that of substrate.
• Holoenzyme: Active enzyme
➢ Keeping the concentration of enzyme
ACTIVATING ENZYMES constant while increasing the
concentration of substrate, we will get an
entirely different type of curve called
Coenzyme binds temporarily to catalytic site to saturation curve.
help catalyze reaction (often has vitamin
component) MECHANISM OF ACTION

• Coenzyme binds to apoenzyme first. Lock-and-key model of enzyme mechanism.

• Substrate binds second •The enzyme is a rigid three- dimensional

body.
• Both product and coenzyme are
•The enzyme surface contains the active site.
released after reaction
Induced-fit model
Enzyme Activity
•The active site becomes modified to
• Enzyme activity: a measure of how accommodate the substrate.
 sequence.

The mechanism of competitive inhibition. •the inhibition may be competitive or

• the inhibitor fits into the active site, thereby Noncompetitive

preventing the substrate from entering Enzyme Regulation

Mechanism of noncompetitive inhibition. Zymogen (proenzyme): an inactive form of an

•the inhibitor binds to a site other than enzyme that must have part of its polypeptide

the active site, thereby changing the chain hydrolyzed and removed before it becomes
conformation of the active site. The substrate no
active.
longer fits
• An example is trypsin, a digestive enzyme.
Mechanism of Action
• It is synthesized and stored as trypsinogen,
• Both the lock-and-key model and the induced-
fit model emphasize the shape of the active site. which has no enzyme activity.
• However, the chemistry of the active site is the • It becomes active only after cleaving off 6
most important.
amino acids (hydrolyzed & removed from N-
• Just five amino acids participate in the active
sites in more than 65% of the enzymes studies to terminal end of its chain)
date. • Removal of this small fragment changes in not
• These five are His > Cys > Asp > Arg > Glu. only the primary structure but also the tertiary
• Four of these amino acids have either structure, allowing the molecule to achieve its
acidic or basic side chains; the fifth has a active form.
sulfhydryl group (-SH) Enzyme Regulation

Allosterism: enzyme regulation based on an

Catalytic Power event

Enzymes provide an alternative pathway for occurring at a place other than the active site but
that
reaction, one with a significantly lower activation
creates a change in the active site.
energy and, therefore, a fast
• An enzyme regulated by this mechanism is
Enzyme Regulation called an allosteric enzyme.
Feedback control • Allosteric enzymes often have multiple
polypeptide chains.
•an enzyme-regulation process where the
• Negative modulation: inhibition of an allosteric
product of a series of enzyme-catalyzed
enzyme.
reactions inhibits an earlier reaction in the
• Positive modulation: stimulation of an allosteric Abzyme: an antibody that has catalytic activity
enzyme.
because it was created using a transition state
• Regulator: a substance that binds to an
analog as an immunogen.
allosteric enzyme
➢ the abzyme is then used as a catalys
The allosteric effect:

Binding of the regulator to a site other than the

active site changes the shape of the active sit NEUROTRANSMITTERS AND
Enzyme Regulation HORMONES
Protein modification: the process of affecting Chemical Communication
enzyme activity by covalently modifying it.
Terms and definitions:
• The best known example of protein
modification involves • neuron: a nerve cell.
phosphorylation/dephosphorylation. • neurotransmitter: a chemical messenger
Example: Pyruvate kinase (PK) is the active between a neuron and another target cell;
neuron, muscle cell or cell of a gland.
form of the enzyme; it is inactivated by
• hormone: a chemical messenger released
phosphorylation to pyruvate kinase by an endocrine gland into the bloodstream
and transported there to reach its target cell.
phosphate (PKP)
• The distinction between a
Isoenzyme: an enzyme that occurs in multiple
neurotransmitter and a hormone is
forms; each catalyzes the same reaction. physiological, not chemical; it depends on
whether the molecule acts over a short
• Example: lactate dehydrogenase (LDH)
distance (across a synapse) or over a long
catalyzes the oxidation of lactate to pyruvate. distance (from the secretory organ, through
the blood, to its site of action).
• The enzyme is a tetramer of H and M chains.
A large percent of drugs used in human
• H4 is present predominately in heart muscle. medicine influence chemical communication
• M4 is present predominantly in the liver and in • Antagonist: a molecule that blocks a natural
skeletal muscle. receptor and prevents its stimulation.

• H3M, H2M2, and HM3 also exist. • Agonist: a molecule that competes with a
natural messenger for a receptor site; it binds
• H4 is allosterically inhibited by high levels of to the receptor site and elicits the same
pyruvate while M4 is not. response as the natural messenger.

• H4 in serum correlates with the severity of • A drug may decrease or increase the
effective concentration of messenger.
heart attack.

Transition State Analogs

 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 cimetidine and ranitidine block H2 receptors
phosphodiester bonds to give AMP. and thus reduce acid secretion.

• The amplification through the secondary Peptidergic Messengers

messenger (cAMP) is relatively slow. It may
• The first brain peptides isolated were the
take from 0.1 s to a few minutes.
enkephalins.
• In cases where transmission must be fast, a
• These pentapeptides are present in certain
neurotransmitter such as acetylcholine, acts
nerve cell terminals.
on membrane permeability directly without a
second messenger. • They bind to specific pain receptors and
seem to control pain perception.
Control of neurotransmission:
• Neuropeptide Y, a potent orexic, affects the
• The G-protein—adenylate cyclase cascade
hypothalamus.
in transduction signaling is not limited to
monoamine messengers. • Substance P, an 11-amino acid peptide is
involved in the transmission of pain signals.
• A variety of other neurotransmitters and
peptide hormones use this signaling Tyr-Gly-Gly-Phe-Leu Leucineenkephalin
pathway, including glucagon, vasopressin,
luteinizing hormone, enkephalins, and P- Tyr-Gly-Gly-Phe-Met Methionineenkephalin
protein.

• A number of enzymes can be All peptidergic messengers, hormones, and

phosphorylated by protein kinases and the
phosphorylation controls whether these neurotransmitters act through secondary
enzymes will be active or inactive. messengers.

Removal of neurotransmitter: • Glucagon, luteinizing hormone, antidiuretic

hormone,
• The body inactivates monoamines by
oxidation to an aldehyde, catalyzed by angiotensin, enkephalin, and substance P use
monoamine oxidases (MAOs) the G-protein-adenylate cyclase cascade.

• The action of histamine is similar to that • Others such as vasopressin use membrane-
of other monoamines. It is synthesized derived phosphatidylinositol (PI) derivatives
from His by decarboxylation Steroid Messengers
• H1 receptors are found in the respiratory
tract where they affect the vascular, • A large number of hormones are steroids.

muscular, and secretory changes associated • These hormones are hydrophobic and,
with hay fever and asthma; antihistamines therefore, cross plasma membranes by
that block H1 receptors relieve these diffusion.
symptoms. • Steroid hormones interact inside cells with
• H2 receptors are found mainly in the protein receptors.
stomach and affect the secretion of HCl; • 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. polymerases can synthesize only short
fragments,
• Replication of DNA starts with unwinding of
becausee these enzymes only work from 5’ -
the double helix.
3’.
• Unwinding can occur at either end or in the
• These short fragments are called Okazaki
middle. 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 • Transcription factors find their targeted
on tRNAs that are recognized by aminoacyl- sites by twisting their protein chains so
tRNA synthetases. that a certain amino acid sequence is
present at the surface.
• One such conformational twist is provided
Termination by metal-binding fingers metal-binding
• Chain termination requires: fingers (next screen).
• Termination codons (UAA, UAG, or UGA) of • Two other prominent transcription factor
mRNA. conformations are the helix-turn-helix and
• Releasing factors that cleave the the leucine zipper leucine zipper.
polypeptide chain from the last tRNA and • Transcription factors also possess
release the tRNA from the ribosome repressors, which reduce the rate of
transcription.
 Enhancers • Certain proteins called chaperones help
• Enhancers speed up transcription:
newly synthesized proteins to fold properly.
They may be several thousand nucleotides
away from the transcription site; a loop in • If rescue by chaperones fails, proteasomes may
DNA brings the enhancer to the initiation degrade the misfolded protein
site.
Mutations and mutagen
Response elements are activated by
their transcription factors in response Mutation: a heritable change in the base
to an outside stimulus. sequence of DNA.
• The stimulus may be heat shock, heavy metal
toxicity, or a hormonal signal. • It is estimated that, on average, there is one
• The response element of steroids is in front copying error for every 1010 bases.
of and about 250 base pairs upstream from
the starting point of transcription. • 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