CHEM 2N LAB l BIOHEMISTRY LAB

CHEM 2N LAB l ENDTERM

• STEROIDS

REVIEWER o Derivatives of cholesterol

• EICOSANOIDS
o Derivatives of the Fatty acid arachidonic
UNIT 5 - BIOLOGICAL MOLECULES I
acid
LIPIDS • MEMBRANES
o Formed from phospholipids and
glycolipids
• Like organic molecules, biological molecules
are grouped into families.
• There are four major families of biological
FATTY ACIDS
molecules, including PROTEINS, NUCLEIC
ACIDS, CARBOHYDRATES, AND LIPIDS. • Fatty acids contain a carboxylic acid group
• The lipids are the subject of this unit. o This should make them quite polar
• Of these four families, the lipids are the • However, they also contain a long
structurally the most diverse. hydrocarbon tail
• This is because unlike members of the other o Which overall, makes them nonpolar.
three families, members of this families do no • Fatty acids typically contain between 12 and
share a common structural feature, but rather 20 carbons
share a common physical property; they are o The number is usually always even
HYDROPHOBIC.

INTRODUCTION

MELTING POINTS FOR SATURATED FATTY ACIDS:

LIPIDS

• are hydrophobic, nonpolar molecules.

o They are soluble in nonpolar solvent.
o They are insoluble in polar solvents, such
as water
• They are isolated from the other biological
molecules by extracting them with nonpolar
solvents

THE TYPES OF LIPIDS THAT WE WILL LOOK AT

SOME FATTY ACIDS CONTAIN DOUBLE BONDS
INCLUDE

• FATTY ACIDS
o In the carboxylic acid family
• WAXES
o Fatty Acids + Alcohols
• TRIGLYCERIDES
o 3 Fatty acids + glycerol
• PHOSPHOLIPIDS AND GLYCOLIPIDS
o 2 fatty acids + glycerol + phosphate + X

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

THE COMMON FATTY ACIDS FOUND IN
BIOLOGICAL SYSTEMS ARE SHOWN IN TABLE 8.1
• The NEGATIVE CHARGE makes the polar
OF RAYMOND
head portion of the fatty acid even MORE
POLAR AND HYDROPHILIC.

Linolenic acid is one of the omega-3 fatty acids.

• The salts of fatty acids are also called SOAPS,

• NORMALLY THE DOUBLE BONDS ARE CIS
and are considered AMPHIPATHIC, meaning
o This lowers the melting points for fatty
acids containing double bonds. they have a part that is VERY HYDROPHOBIC
along with a part that is VERY HYDROPHILIC.
o In Unit 3 we discussed how amphipathic
molecules form interesting structures
when exposed to water.

WAXES

• Waxes are made by combining FATTY ACIDS

WITH LONG CHAIN ALCOHOLS.
o In Unit 2 we discussed how carboxylic
acids react with alcohols to from esters

• The CIS DOUBLE BONDS PRODUCE KINKS,

which disrupt the London forces by preventing
the tails from packing close to one another

ALCOHOLS, CARBOXYLIC ACIDS & ESTERS (UNIT 2)

• We look now at three families that are

distinguished by a functional group that
contains the element oxygen.

• As acids, the carboxylic acid group in fatty ESTERS

acids can react with a base to produce a
• Chemically, esters can be synthesize by
carboxylate ion
reacting a carboxylic acid with and alcohol:
• By donating its proton (H+) to the base
the fatty acid becomes negatively charged.
WAXES

• Waxes are esters

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 • Because one of the products of the hydrolysis
is a carboxylic acid, in base catalyzed
hydrolysis the base undergoes a second
acid/base reaction with the carboxylic acid to
produce a carboxylate ion.
• The base catalyzed hydrolysis of esters is also
called SAPONIFICATION
• We will be discussing acids and bases in Unit 6

TRIGLYCERIDES

• Triglycerides are a storage form of FATTY

ACIDS IN MAMMALS.
o Often when blood tests are done, they
• When two more molecules combine to form a measure your triglyceride levels.
larger molecule, the word RESIDUE is used to o HIGH TRIGLYCERIDE levels in the blood
indicate which molecule that part of the larger are a risk indicator for
molecule came from ATHEROSCLEROSIS.

• Triglycerides are a combination of THREE 3

FATTY ACID MOLECULES with a glycerol
molecule

• Waxes are very hydrophobic and are used by

plants and animals for protective, water-proof
coatings

REACTIONS INVOLVING WATER (UNIT 4)

HYDROLYSIS • GLYCEROL, which is also called GLYCERIN, is

an alcohol with three hydroxyl groups.
• Hydrolysis can also be catalyzed using a base o As with the waxes, the fatty acids can react
(OH-) with the hydroxyl groups to form esters.

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 o Since there are three hydroxyl groups, o FAT can store almost twice as much
three fatty acids can react to form three energy per gram as carbohydrates and
esters. proteins
• IN MAMMALS the fats are stored in the
• For triglycerides, all three hydroxyls of the ADIPOSE TISSUE.
glycerol have a fatty acid residue attached to it • ADIPOSE TISSUE also functions to protect
organs from shock and cold.

REACTIONS THAT INVOLVE TRIGLYCERIDES

INCLUDE:

o Hydrogenation
o Oxidation
o Base-catalyzed hydrolysis (saponification)

• HYDROGENATION OF TRIGLYCERIDES
o This is the same reaction that we saw in
Unit 4 with the hydrogenation of alkenes.
▪ UNSATURATED FATS AND OILS
contain alkenes and can be
hydrogenated to produce
• Just as with fatty acids, where the presence of SATURATED FATS.
cis double bonds lower the melting points, o Commercially, VEGETABLE OILS are often
triglycerides made from UNSATURATED hydrogenated to produce a solid product
FATTY ACIDS have lower melting points than that has better qualities for making baked
those made from SATURATED FATTY ACIDS. goods.
o TRIGLYCERIDES FROM ANIMALS tend to ▪ ANIMAL FATS, such as BUTTER
have a higher proportion of SATURATED AND LARD, which are NATURALLY
FATTY ACIDS. SATURATED, can also be used, but
▪ Most are solids at room temperature unlike the vegetable oils, they come
and are called FATS. with cholesterol, which is undesirable
▪ Examples include: butter, lard and for health reasons.
bacon grease
o TRIGLYCERIDES FROM PLANTS tend to
have a higher proportion of OXIDATION AND REDUCTION (UNIT 4)
UNSATURATED FATTY ACIDS.
▪ Most are liquids at room
temperature and are called OILS. HYDROGENATION
▪ Examples include: corn oil, canola
• Another type of oxidation/reduction reaction is
oil, peanut oil and olive oil.
the HYDROGENATION reaction:
o In this example, an ALKENE IS REDUCED
TO AN ALKANE.
TRIGLYCERIDES AS PRIMARILY USED AS A FORM ▪ This is considered reduction, because
OF STORED ENERGY. the hydrogen is bringing in additional
• This is why when you eat more than you need electrons to the molecule.
to meet your energy requirements, the excess o THE ALKANE that is produced in this
energy is STORED IN THE FORM OF FAT. reaction is considered “SATURATED”

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 because it can no longer absorb any more • Partial hydrogenation cab produce trans fats.
hydrogen atoms. o Trans fats have been found to lower your
HDL (“Good cholesterol”) levels

TRIGLYCERIDES

HYDROGENATION OF TRIGLYCERIDES
SATURATED VS UNSATURATED FATS

• This is the same reaction that we saw in Unit 4

with the hydrogenation of alkenes.
• UNSATURATED FATS AND OILS contain
alkenes and can be hydrogenated to produce
SATURATED FATS.
• Commercially, VEGETABLE OILS are often
hydrogenated to produce a solid product that
has better qualities for making baked goods.
o ANIMAL FATS, such as butter and lard,
which are naturally saturated, can also be
used in baking, but unlike the VEGETABLE
OILS, they come with cholesterol, which is
undesirable for health reasons.

TOTAL HYDROGENATION

PARTIAL HYDROGENATION

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 PHOSPHOLIPIDS AND GLYCOLIPIDS

• PHOSPHOLIPIDS AND GLYCOLIPIDS are the

stuff that biological membranes are made of.
o Like the SOAPS, these molecules are
highly APHIPATHIC, and when mixed
with water spontaneously form
membranes that are described as LIPID
BILAYERS.

OXIDATION OF TRIGLYCERIDES

• Unsaturated triglycerides can react with

oxygen to produce small change fatty acids
another small molecules.
o These often do not smell very good
o This is what happens when butter goes
PHOSPHOSPHOLIPIDS
rancid.
• This makes solid fats and oils more stable than o There a are two types of phospholipids
liquid oils and is why the solid fats are ▪ Glycerophospholipids
preferred for deep frying ▪ Sphingolipids

SAPONIFICATION OF TRIGLYCERIDES

• SAPONIFICATION is the base-catalyzed

hydrolysis of the ester bonds in a triglyceride.
• We also discussed this reaction in Unit 4
• This cleaves the esters back into carboxylic • The Glycerophospholipids have a structure
acids (fatty acids) and an alcohol (glycerol). similar to triglycerides, with one of the fatty
• Because the reaction is base-catalyzed, the acids replaced with a phosphate.
base also reacts with the carboxylic acids to
from carboxylate ions

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 • The SPHINGOLIPIDS function similarly to the
glycerophospholipids, but structurally they are
different.
o There is not GLYCEROL CORE
o The glycerol and one of the fatty acids
found in GLYCEROPHOSPHOLIPIDS is
replaced with a molecule called
SPHINGOSINE.

• The Glycerophospholipids have a structure

similar to triglycerides, with one of the fatty
acids replaced with a phosphate.

• The SPHINGOLIPIDS are found in the MYELIN

MEMBRANES that INSULATE THE NERVE
CELLS.
• Some sphingolipids use sugars for the alcohol
portion of the molecule
o These are called GLYCOLIPIDS

STEROIDS

• STEROIDS are a type of lipid that is not

derived form a fatty acid.
o They are based instead on a system of
FIVE CYCLOALKANE RINGS that are
FUSED TOGETHER.

• Phospholipids are used commercially as

EMULSIFYING AGENTS.
o An emulsifying agent stabilizes an
EMULSION.
o An emulsion is a COLLOIDAL SUSPENSION
of one liquid in another.
▪ An example is MAYONNAISE, which is a
colloidal suspension of oil and water.
• LECITHIN, which is another name for the • CHOLESTEROL is the steroid that used as the
phospholipid phosphatidylcholine, is used as starting POINT FOR THE SYNTHESIS of other
an emulsifying agent in mayonnaise and other steroids.
prepared foods.

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 ▪ This is why HDL is sometimes
referred to AS “GOOD
CHOLESTEROL”
➢ 40 mg/dL is good.
o HIGH LEVELS OF LDL is considered BAD
▪ This is why LDL is sometimes
referred to as “BAD
• CHOLESTEROL is ONLY FOUND IN ANIMALS CHOLESTEROL”
• Besides being used to synthesize the other ▪ 100 mg/dL is bad.
steroids, cholesterol is DISSOLVED IN
MEMBRANES TO KEEP THEM FLUID.
o PLANTS use the alternative strategy of
using POLYUNSATURATED FATTY ACIDS
to make their PHOSPHOLIPIDS.

LIPOPROTEINS

• LIPOPROTEINS are used to transport THE

WATER INSOLUBLE LIPIDS such as
triglycerides, phospholipids and cholesterol, IN
THE BLOOD.
o Lipoproteins contain lipids and proteins.
o They include:
▪ CHYLOMICRONS transport primarily
triglycerides from the digestive track.
▪ LDLS (LOW DENSITY LIPOPROTEINS)
transport cholesterol, triglycerides and
phospholipids from the liver to other
tissues.
▪ HDLS (HIGH DENSITY
LIPOPROTEINS) transport cholesterol
and phospholipids back to the liver. EICOSANOIDS

• EICOSANOIDS are derived from

ARACHIDONIC ACID

• The HDL AND LDL levels in the blood can be

used to assess ones risk for
ATHEROSCLEROSIS.
o HIGH LEVELS OF HDL is considered
GOOD

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 ENZYMES

WHAT ARE ENZYMES?

• are PROTEINS (tertiary and quaternary

structures)

• Each enzyme has a unique 3-D shape,

including a surface groove called an ATIVE SITE
• The enzyme works by binding a specific
chemical reactant SUBSTRATE to its active site,
causing the substrate to become unstable and
react.
• The resulting PRODUCT (s) is then released
WHAT DO ENZYMES DO? from the active site.

• Enzymes act as CATALYSTS in cellular

reactions.
• Q: What does a catalyst do?

ENZYMES

• Are SPECIFI for what they catalyze

• Fit the substrate like a LOCK and KEY

When an enzyme is interacting with its substrate,

during the chemical reaction, together they are
referred to as the

HOW TO ENZYMES WORK?

• Enzymes catalyze reactions by weakening

chemical bonds, which LOWERS activation
energy.
• are REUSABLE

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

• They are not consumed (used up) in the FACTORS THAT INFLUENCE ENZYME ACTIVITY
reactions they catalyze.
• Temperature
• pH
• Enzymes are like tiny machines within living
• Cofactors & Coenzymes
things.
• Inhibitors
• The more cans (substrate), the more $
(product). The more recycling machines
(enzymes), the faster the cans turn into $.
TEMPERATURE AND Ph
• Have names that usually end in -ASE.
o Sucrase • Think about what kind of cell or organism an
o Lactase ENZYME may work in
o Maltase • Temperatures far above the normal range
DENATURE enzymes. (This is why very high
fevers are so dangerous. They can cook the
WHY ARE ENZYMES SO IMPORTANT? body’s proteins.)
• Most enzymes work best near NEUTRAL pH (6
• Why are we devoting one whole lecture topic
to 8).
to a protein molecule?
• Nearly all chemical reactions in biological cells
need enzymes to make the reaction occur fast
enough to support life.

FORMATS FOR WRITING AN ENZYMATIC

REACTION

TEMP AND PH AFFECTS ENZYMES

HOW DO YOU STOP AN ENZYME?

• DENATURE it
• Alteration of a protein shape through some
form of external stress
• Example, by applying heat or changing pH.
• Denatured protein can’t carry out its cellular
function.

COFACTOS AND COENZYMES

NON-PROTEIN substances (zinc, iron, copper,

vitamins) are sometimes need for proper enzymatic
activity.

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 • COENZYME VS COFACTOR: What’s the (say a-si-’tell-de-hide) during the metabolism of
difference? alcohol. Elevated acetaldehyde levels cause symptoms
• COFACTOR more general term. Includes of nausea and vomiting.
inorganic and organic molecules.
NON-COMPETETIVE INHIBITOR
• COENZYME type of cofactor, but specifically
organic molecules. Ex. Vit B12 • Do not enter active site, but bind to another
part of the enzyme, causing the enzyme &
active site to change shape.
• Usually reversible, depending on concentration
of inhibitor & substrate

INHIBITORS
EXAMPLE: You may know that compounds containing
TWO TYPES OF ENZYME INHIBITORS
heavy metals such as lead, mercury, copper or silver
are poisonous. This is because ions of these metals are
non-competitive inhibitors for several enzymes.
COMPETETIVE INHIBITOR

• Chemicals that resemble an enzyme’s normal

substrate and compete with it for the active ENZYME INHIBITORS
site.
• Blocking an enzyme's activity can kill a
• Reversible depending on concentration of
pathogen or correct a metabolic imbalance.
inhibitor and substrate.
• Many MEDICATIONS are enzyme inhibitors.
• Enzyme inhibitors are also used as
HERBICIDES and PESTICIDES

EXAMPLE:

• Another example of competitive inhibition is

protease inhibitors.
• They are a class of anti-retroviral drugs used
to treat HIV.
• The structure of the drug ritonavir (say ri-
TAHN-a-veer) resembles the substrate of
HIV protease, an enzyme required for HIV to
be made.
EXAMPLE: The drug Antabuse is used to help
alcoholics quit drinking. Antabuse inhibits aldehyde
oxidase, resulting in the accumulation of acetaldehyde

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 ENZYME: CATECHOLASE • Remember, hydrolysis cuts molecule by adding
water…the reverse of the hydration synthesis
• Catecholase is present in most FRUITS and
pictured to the left.
VEGETABLES
• It is the enzyme that facilitates the
BROWNING of cut or bruised fruits and
vegetables by CATALYZING the following
reaction:

Bromelain is used as a meat tenderizer. Breaks down the

collagen in meat.
LEMON juice and other acids are used to preserve
color in fruit, particularly apples, by lowering the Ph So what do you think could happen to your tongue
when you eat fresh pineapple?
and removing the COPPER (cofactor) necessary for the
enzyme to function.

REACTION:

ENYZME: BROMELAIN

• Pineapple contains enzyme bromelain, which

can digest protein
• Jell-O® is made of gelatin, a processed version
of a STRUCTURAL PROTEIN called
COLLAGEN found in many animals, including
humans.
• Collagen = big, fibrous molecule makes skin,
bones, and tendons both strong and elastic.
• Gelatin you eat in Jell-O ® comes from the
collagen in cow or pig bones, hooves, and
connective tissues. (Yummie!)

• Bromelain is a PROTEASE enzyme that

facilitates hydrolysis of protein.

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 NUCLEIC ACIDS

NUCLEIC ACIDS

• Complex molecules containing elements of

carbon, hydrogen, oxygen, phosphorus, and
nitrogen.

TWO TYPES OF NUCLEIC ACIDS: NITROGENOUS BASES

DNA (DEOXYRIBONUCLEIC ACID)

• Found within the nucleus

• Storage and transfer of genetic information
• Passed from one cell to another during cell
division

RNA (RIBONUCLEIC ACID)

• Occurs in all parts of the cell

• Primary function is to synthesize the proteins PHOSPHATE
• Monomer units are nucleotides
• Derived from phosphoric acid (H3PO4)
• Under cellular pH conditions, the phosphoric
acid is fully dissociated to give a hydrogen
NUCLEOTIDE BUILDING BLOCKS phosphate ion (HPO42-)
• Nucleic Acids: Polymers in which repeating
unit is nucleotide
• A Nucleotide has three components:
o Pentose Sugar - Monosaccharide
o Phosphate Group (PO43-)
o Nitrogenous Base

NUCLEOTIDE FORMATION

PENTOSE SUGAR

• Ribose is present in RNA and 2-deoxyribose is

present in DNA NUCLEOTIDE NOMENCLATURE

STRUCTURAL DIFFERENCE:

• a —OH group present on carbon 2’ in ribose

• a —H atom in 2-deoxyribose

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 PRIMARY NUCLEIC ACID STRUCTURE

• Two nucleotides are joined through

phosphodiester bond to give a dinucleotide.
• Sugar-phosphate groups are the nucleic acid
backbone DNA DOUBLE HELIX
• Sugars are different in DNA and RNA
• Two strands/ polynucleotide chains run anti-
parallel (opposite directions: 5’-3’ and 3’to 5’)
and coiled around each other to form a double
helix
• Discovered by Watson and Crick in 1953

RNA

• Nucleotide polymer in which each of the

monomers contains ribose, a phosphate
group, and one of the nitrogenous bases
adenine, cytosine, guanine, or uracil.

DNA
BASE PAIRING
• Nucleotide polymer in which each of the
monomers contains ribose, a phosphate • A pyrimidine is always paired with purine
group, and one of the nitrogenous bases • Fits inside the DNA double strand
adenine, cytosine, guanine, or thymine. • Hydrogen bonding is stronger with A-T and G-
C
• A-T and G-C are called complementary bases

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 DNA SEQUENCE

• the sequence of bases on one polynucleotide PROTEN SYNTHESIS

is complementary to the other polynucleotide.
• Complementary bases are pairs of bases in a
nucleic acid structure that can hydrogen-bond
to each other.

Example:

• List of bases in sequential order in the

direction from the 5’ end to 3’ end of the
segment:
• 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’ RIBONUCLEIC ACID (RNA)
• Complementary strand of this sequence will
be: • Ribonucleic acid (RNA) is a nucleic acid which

• 3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’ is directly involved in protein synthesis.

• Its main role is to act as a messenger
conveying instructions from DNA for
controlling protein synthesis.
DNA REPLICATION

• DNA molecules produce exact copies of

themselves
• takes place when a cell divides producing two
identical daughter cells each containing the
same number of chromosomes as the original
cellS

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 RIBOSOMAL RNA (rRNA)

• combine with specific proteins to form

ribosomes, the physical sites for protein
synthesis.

TRANSFER RNA (tRNA)

• Delivers amino acids to the sites for protein

synthesis; the smallest

TYPES OF RNA
MUTATIONS

• An error in base sequence reproduced during

HETEROGENOUS NUCLEAR RNA (hnRNA) DNA replication
• Errors in genetic information is passed on
• Formed directly by DNA transcription.
during transcription.
MESSENGER RNA (mRNA) • The altered information can cause changes in
amino acid sequence during protein synthesis
• Carries instruction for protein synthesis and thereby alter protein function.
(genetic information) to the sites of proteins • MUTAGEN – substance or agent that causes a
synthesis. change in the structure of a gene
SMALL NUCLEAR RNA (snRNA) • Radiation and chemical agents

• Facilitates the conversion of heterogenous

nuclear RNA to Mrna

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB

 VIRUSES

• Tiny disease-causing agents with outer protein

envelope and inner nucleic acid core
• Invade their host cells to reproduce and in the
process disrupt the normal cell’s operation
• Many human diseases are of viral origin, e. g.
common cold, smallpox, rabies, influenza,
hepatitis, and AIDS

VACCINES

KATHLEEN JAN M. LOS BAÑEZ I BSN1- C I CHEM2N LAB