Digital Portfolio

in
Biochemistry

Valerie Joyce I. Faller

TABLE OF CONTENTS

Introduction ................................. 1
Biochemistry Activity 1 ................................. 2
Bio Reading Essentials ................................. 4

Water: Unique properties of water

Laboratory Report in Water .................................. 7
Laboratory Report 1: Water Properties Experiment ......................... 8

Proteins
20 Common Amino Acids ................................ 13

Enzymes
Biochemistry Activity 2 ................................ 15
Laboratory Report 2: How do enzymes work? ................................ 19
Pineapple Enzymes and Gelatin Experiment ............................... 22

Nucleic Acids
Formative Quiz .............................. 23

Lipids
Laboratory Report 3: Saponification .............................. 29
 INTRODUCTION

Biochemistry, as the name implies, is a branch of science that

combines the two classical disciplines of biology and chemistry. If
chemistry is the science of matter, then biochemistry is the science of
living matter.

It is considered a central science since it integrates biology,

environmental sciences, medicine, and mathematics. Biochemistry is
essential to human survival since it improves the provision of basic
necessities such as health, food, energy, clothes, shelter, and clean
water and air. Biochemistry discusses how atoms, molecules, and ions
interact to affect structure, size, and even how individuals feel.
Biochemistry knowledge is used to contribute to current civilization
solutions such as producing new medicines, comparing the nutrient
content of foods, and establishing the safety of drinking water.
Biochemistry is utilized to better understand metabolic processes and
DNA molecules, which helps in gene therapy. Food additives contain
biomolecules such as lipids. Biochemistry knowledge is utilized to
substitute biomolecules, such as in the manufacturing of artificial
sweeteners. Biochemistry leads to a number of job options, allowing
students to find work.

All life on Earth depends on biochemical reactions and processes.

By integrating this scientific knowledge with practical strategies to
maintain health, understand diseases, identify potential treatments,
and enhance our understanding of the origins of life on earth,
biochemistry is and will remain one of the most important areas of
science.

Page 1
 Biochemistry Activity 1

C2HCl3O – Trichloroethanal Na2SO4 – Sodium sulfate C2H4O2 – Acetic Acid

C65H102N18O21 – Collagen NH4OH- Ammonium hydroxide
HCN - hydrogen cyanide CaCl2 – Calcium chloride CO2 – Carbon dioxide
CN- - Cyanide H3PO2 – Phosphinic acid C7H7NO – Benzamide
C₆H₁₂O₆ - glucose C6H10O5 – Glycogen H2CrO4 – Chromic acid
Cr2O7 2− - dichromate C6H10O5 – amylose C₆H₁₂O₆ - Galactose
HMnO4 - Permanganic acid Al(OH)3 - Aluminum hydroxide
H2CO3 – Carbonic acid

Organic Compounds Inorganic Compounds

1. C2HCl3O – Trichloroethanal 1. CaCl2 – Calcium chloride

2. C65H102N18O21 – Collagen 2. H3PO2 – Phosphinic acid
3. C6H10O5 – Glycogen 3. Al(OH)3 - Aluminum hydroxide
4. C6H10O5 – Amylose 4. NH4OH- Ammonium hydroxide
5. C7H7NO – Benzamide 5. Na2SO4 – Sodium sulfate
6. C₆H₁₂O₆ - Galactose 6. CO2 – Carbon dioxide
7. C2H4O2 – Acetic Acid 7. H2CrO4 – Chromic acid
8. C₆H₁₂O₆ - Glucose 8.H2CO3 – Carbonic acid
9. HCN - hydrogen cyanide
10.HMnO4 - Permanganic acid
11.Cr2O7 2− - dichromate
12. CN- - Cyanide

Page 2
Essential Question:

1. How will you classify organic compounds and inorganic

compounds?

The basic distinction between organic and inorganic

compounds is that organic substances always contain a carbon atom,
whereas most inorganic compounds do not. Carbon-hydrogen or a
simple C-H bond can be found in almost all organic molecules. The
most common distinction between the two is that organic
substances are primarily the outcome of a living being's actions.
Inorganic chemicals, on the other hand, are derived by natural
processes that are unrelated to any of the Earth's life forms or the
results of human laboratory operations. Plants and plant materials,
proteins and fat that make up our bodies, and DNA in our bodies are
all examples of organic molecules. Salts, metals, and related
chemicals are examples of inorganic compounds.

Page 3
Cellular Structure and Function

Page 4
Cellular Structure and Function

Page 5
Cellular Structure and Function

Page 6
Laboratory
Report in
Water

Page 7
 BIOCHEMISTRY
LABORATORY REPORT 1
Water Properties Experiment

Introduction

Water is made up of two hydrogen Each water molecule in the drop is

molecules and an oxygen molecule that is drawn to the other water molecules in
covalently linked to the hydrogens. This is the drop. As a result, the water pulls
because oxygen desires to fill its outer shell itself into a shape with the least
with electrons and is eager to steal them amount of surface area. Water is sticky
from hydrogens. Without the presence of and elastic, clumping together in
water, life on Earth would be extinct. Water drops rather than spreading out in a
is so important that it is the foundation of thin sheet. Adhesion and cohesion are
human life, animal life, and a stable two more fundamental water
environment. Water is a plentiful resource properties that influence how water
on Earth, constituting the great majority of behaves everywhere, from plant
the planet, our anatomy, and other life leaves to your own body. Water is
forms. Water's special properties ensure attracted to water in cohesion, but
that life on Earth continues to thrive.
water is attracted to other things in
adhesion.
Water is a highly effective solvent. The
polarity of water contributes to its
remarkable dissolving capacity. However, in
nature, all compounds do not combine with
water. Hydrophilic substances are those
that can mix with water, while hydrophobic
substances are those that cannot mix with
water. Surface tension is one of the unique
properties of water that allows life to exist
on Earth. The cohesiveness of water
molecules at the surface of a body of water
is referred to as surface tension.

Page 8
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Page 9
 Conclusion

We began this coin and water experiment by placing one of each coin on
a paper towel and estimating how many drops it would retain. Pennies are
surrounded by a little ridge. When you put water on a coin, it builds a dome on
it. Because of surface tension, this is conceivable. The water will eventually
become too much for the penny, causing it to leak.

As a result, I infer that the structure of the water molecule itself is

responsible for why a dome forms when water is poured onto a coin and why
the dome eventually collapses. Water is a polar molecule, which means it has
both a positive and a negative end. The negative end of one molecule is
attracted to the positive end of another molecule (much like a magnet), causing
the molecules to adhere closely together. The molecules on the surface are
drawn inward and form a dome as a result of their strong bonding. This is
referred to as surface tension.

Post Laboratory Questions:

1. What other things besides size affect
the number of drops each coin can hold?
Write down what you thought was going
to happen and what did happen.
Aside from the size of the penny,
we also considered the side of each coin,
the angle of the droppers, the location of
our experiments, if it is on a windy
portion, and lastly, the pinching of
rubber of the droppers. These are the
additional factors that determine the
number of drops each coin may hold for
us. There are instances when we expect
the largest coin to have twice as many
drops as the smallest coin, yet it was just
two drops ahead of the smaller coins.
2. What coin/penny can hold the highest
number of water drops? Explain
The coin/penny that can hold the
most water drops is always the third
penny or 20 pesos coin. It is evident that
it can retain more droplets than the two
smallest coins due to its size and space.
3. Explain how cohesion and adhesion
play a role in surface tension. Give an
example of how surface tension is
important in real life.
Cohesion is the attraction of like
molecules to one another, whereas
adhesion is the attraction of unlike
molecules to one another. Cohesion

Page 10

holds hydrogen bonds together to create surface
tension on water. Since water is attracted to
other molecules, adhesive forces pull the water
toward other molecules.
Surface tension, also known as interfacial
tension, is a very essential phenomenon that
plays a crucial part in everyday life. There are
various cases when surface tension is
important. One of the best examples is the soap
and detergents. Soaps and detergents appear to
be simple items that can be found in our
bathrooms, laundry rooms, or cleaning supplies.
However, the chemistry underlying this
occurrence is not so simple. Soaps and
detergents are really complicated compounds
that function in an unusual way. Water
molecules tend to adhere to one another via
intermolecular forces. Soaps and detergents aid
cleaning by reducing the surface tension of the
water, allowing it to more easily penetrate pores
and dirty regions. Soap molecules are made up
of lengthy chains of carbon and hydrogen
atoms, as well as other ionic compounds. At one
end of the chain is an atom configuration that
prefers to be in water (hydrophilic). The other
end, on the other hand, avoids water
(hydrophobic) but easily adheres to grease.
During washing, the "grease-loving" end of the
soap molecule binds to the oil or fat on the stain,
allowing water to flow underneath. The stain
particles become loose and surrounded by soap
molecules, and are swept away by a rush of
water.
4. Plants must get water from their roots
to their highest branches. Explain how
cohesion and adhesion might help a plant
get water from the ground to its upper
leaves.
Plant growth is frequently limited by
the lack of water. As a result, plants have
evolved an efficient system for absorbing,
translocating, storing, and utilizing water.
The forces of adhesion and cohesion act in
the plant's xylem to transfer water to the
farthest leaf in order to get water up to all
the branches and leaves. Adhesion aids in
the movement of sticking in the stems,
whilst cohesion pushes water down into
the roots. This is known as capillary
action, and it allows plants to receive
nutrients from water as it travels down
the stem. Capillary action is also required
for the drainage of the eye's constantly
produced tear fluid.
Page 11
BTS!
Behind The Scene

Page 12
 20 Common Amino Acids

The building blocks of proteins in Amino acids account for 75% of the human
living organisms are the amino acids. body. They are required for practically every
Amino acids bind together to form bodily function, and every chemical process
polypeptide chains, and these that occurs in the body is dependent on them
polypeptides fold and coil together into
and the proteins that they produce.
specific conformations to form proteins.
There are over 500 amino acids found in
nature, but the human genetic code only
encodes 20 directly. Non-essential amino
acids can be synthesized in the body,
while 'essential' amino acids must be
obtained from the diet.

Proteins are made up of 20 different

types of amino acids, with the types
determining the shape of the proteins.
Glutamine, glycine, phenylalanine,
tryptophan, and valine are some of the
most well-known. Humans require three
of these amino acids: phenylalanine,
tryptophan, and valine; the others are
isoleucine, leucine, lysine, methionine,
and threonine. Because this type cannot
be produced by the body, it must be
consumed through food. Tryptophan is a
well-known necessary amino acid that
serves various important activities in
humans. It aids in the induction of regular
sleep, the reduction of anxiety,
depression, and the risk of arterial
spasms, and the production of a stronger
immune system. Tryptophan is arguably
best recognized for its function in the
production of serotonin, which is famed
for putting people to sleep after a massive
holiday feast.

Page 13
 20 Common Amino Acids

This chart only shows those amino acids for which the human genetic
code directly codes for. Selenocysteine is often referred to as the 21st amino
acid, but is encoded in a special manner. In some cases, distinguishing
between asparagine/aspartic acid and glutamine/glutamic acid is difficult. In
these cases, the codes asx (B) and glx (Z) are respectively used.

Page 14
 Enzymes
Activity 1: “Formulate Your Answer”

1. What are the characteristics of enzymes?

Enzymes are biological molecules (mostly proteins) that serve as

catalysts in the body and are created by living organisms. It increases any
chemical or metabolic reaction that is taking place in any part of the body.
The finest part is that it participates in practically all cellular reactions
while being structurally unchanged. Another feature of enzymes is that
they are generally complex macromolecules of globular proteins, many
enzymes have additional non-protein (inorganic or organic) substances
associated with them for their activity called co-factors, enzymes are
protein macromolecules with a very high molecular weight, enzyme-
controlled reactions are reversible, and enzymes can only affect the rate of
biochemical reactions, not the direction of the reactions.

2. Explain the structure of enzymes.

Enzymes are made up of a linear chain of amino acids that form a

three dimensional structure. The sequence of amino acids defines the
structure, which in turn identifies the enzyme's catalytic activity.
When heated, the structure of the enzyme denatures, resulting in a
decrease in enzyme activity that is normally associated with temperature.
Enzymes are often enormous in comparison to their substrates, with sizes
ranging from 62 amino acid residues to an average of 2500 residues seen in
fatty acid synthase. Only a small portion of the structure, located around
the binding sites, is engaged in catalysis. The active site of the enzyme is
made up of the catalytic and binding sites. There are a few ribozymes that
act as RNA-based biological catalysts. It interacts with proteins in
complexes.

Page 15
3. Discuss the nomenclature and classification of enzymes.

Enzymes are categorized into six classes based on the reaction being catalyzed. The
Enzyme Commission established the nomenclature in 1961 (with the most recent
modification being in 1992), therefore all enzymes are issued a "EC" number.
The classification ignores amino acid sequence (i.e., homology), protein structure, and
chemical process. EC numbers are four digits long, such as a.b.c.d, where "a"
represents the class, "b" represents the subclass, "c" represents
the sub-subclass, and "d" represents the sub-sub-subclass. The
"b" and "c" digits describe the reaction, while the
"d" digit differentiates between distinct enzymes with the same function
dependent on the substrate in the reaction.

EC1. Oxidoreductases, also known as oxidases, dehydrogenases, or reductases, catalyze

the transfer of hydrogen or oxygen atoms or electrons from one substrate to another. It
should be noted that because these are 'redox' reactions, an electron
donor/acceptor is also required to complete the reaction. (Transfer of electrons).
EC2. Transferases, with the exception of oxidoreductases, catalyze group transfer
processes (which transfer hydrogen or oxygen and are EC 1). These take the following
↔
general form: A-X + B BX + A (Transfer of a radical)
EC3. Hydrolases are enzymes that catalyze hydrolytic reactions. Lipases, esterases,
nitrilases, and peptidases/proteases are examples. These take the general form: A-X +
H2O X-OH + HA. (Addition or removal of water)
EC4.Lyases — catalyze the non-hydrolytic (EC 3) removal of functional groups from
substrates, which frequently results in the formation of a double bond in the product; or
the reverse reaction, i.e. the addition of function groups across a double bond. In the
removal direction, there are decarboxylases and aldolases, while in the addition
direction, there are synthases. (Splitting or forming a C-C bond)
EC5. Isomerases — enzymes that catalyze isomerization reactions such as racemization’s
and cis-tran isomerization’s. (Changing geometry or structure of a molecule)
EC6. Ligases are enzymes that catalyze the formation of different (mainly C-X) bonds
while also breaking down energy-containing substrates. (Joining two molecules through
hydrolysis of pyrophosphate bond in ATP or other tri-phosphate)

4. Cite models of enzyme action.

Biochemists have long been interested in enzyme action. There are two
models for how enzymes work: The Lock and Key model and the Induced fit
model are the two models used to explain the activity of enzymes with
substrates. The enzyme is the lock in lock and key, while the substrate is the key.
The shapes must be complementary, just like a lock and the key that opens it,
and this shape cannot alter. Induced fit considers enzyme active sites to be
slightly more flexible and initially uncomplimentary. It proposes that the binding
of the substrate to the enzyme causes the active site to change shape and allow
the enzyme-substrate complex to form.

Page 16
 Activity 2: “Enzyme Practice”

Answer:

a. Substrate
b. Active Site
c. Enzyme
d. Products

Answer:

1. Arrows point to the active sites of the enzyme.

2. Substrates bind to the active sites of the enzyme -- [enzyme-
substract] complex forms
3. Enzyme-substracts turns into enzyme-products.
4. Products are released after catalyzed reaction.

Page 17
 Answer true of false to the following statements:

a. true Enzymes interact with specific substrates

b. false Enzymes change shape after a reaction occurs
c. true Enzymes speed up reactions.
d. false One enzyme can be used for many different types of
chemical reactions.
e. true Enzyme reactions can be slowed or halted using
inhibitors.

Circle the correct effect.

a. Raising the temperature slightly will [ increase | decrease |
not change] the rate of reaction.
b. Boiling temperature will [ increase | decrease | not change]
the rate of reaction.
c. Changing the pH toward the optimal pH will [ increase |
decrease | not change] the rate of reaction.
d. Introducing a competitive inhibitor will [ increase | decrease
| not change] the rate of reaction.

Place a check mark next to the things that are expected to

INCREASE the rate of an enzymatic reaction

√
a. Add more enzyme
√
b. Add more substrate
√
c. Adjust pH to optimal level
d. __Add a non-competitive inhibitor
e. __Freezing

Page 18
 PROTEINS & ENZYMESBiochemistry: How do Enzymes Work?

GUIDE QUESTIONS:

1. What can you say about the enzymatic reactions in cups 2 to 4?

Cup 2 has a lower enzymatic reaction than Cup 4. In cup 4, the number
of bubbles generated during the reaction is double that of cup 2. Also, the
reaction in cup 2 is slower than the response in cup 4, however when the yeast
is poured in cup 4, the reaction in the solution is faster than the prior reaction.

2. Describe the reaction that happened in cup 1 after you added 1 tablespoon
of H2O2?

There isn't much that happens after pouring peroxide into dishwashing
solutions; simply a few bubbles form.

3. What do you think is the limiting factor for the catalase reaction in a cup?

The limiting factor for the catalase reaction in a cup is the substrate
availability, because catalase chemical reaction occurs when the substrate
concentration ratio is less, equal, or greater than the solution. The greater the
size of the substrate, the more chemical reactions occur.

4. Why is the amount of foam different in each cup? Why do you think this is
the case? Based on your results, what caused the difference in the activity of
the catalase enzyme in each cup?

Because each cup contains a varied amount of hydrogen peroxide, the

foam in each cup differs. The larger the concentration of peroxide, the greater
the foam that will create. However, no reaction occurs in cup 1 due to the
absence of yeast, whose primary function is to act as a catalyst in hydrogen
peroxide.

Page 19
5. Make a graph of cups 1 to 4, indicating the differences in enzymatic
reactions.

The reaction is weaker in the first cup, but the amount of foam formed
doubled on the second, third, and fourth cup.

6. Based on your laboratory activity, how do you define enzymes and

substrates?

Enzymes are proteins that interact with substrate molecules to

reduce the activation energy required for a chemical reaction to occur by
stabilizing the transition state. This stabilization accelerates reaction rates
and allows them to occur at physiologically meaningful rates. Enzymes bind
substrates at active sites, which are critical points in their structure. They are
often very selective, binding only specific substrates for specific reactions.

Page 20
 Conclusion

What is the importance of enzymes in the lives of living organisms?

What did you realize after exploring enzymatic activity?
What if no enzymes? What do you think will happen to us and to other
living forms?

Enzymes operate as catalysts for a wide range of biological reactions

that are essential for the survival of living organisms. Due to the large
activation energy required, such reactions would occur very slowly or not
at all in the absence of enzymes. Enzymes provide an additional channel for
certain processes, allowing them to finish. After analyzing enzymatic
activity, I realized that enzymes are necessary for humans to survive. It
works with vitamins and minerals as a catalyst to speed up chemical
processes because most chemical reactions in living cells happen too
slowly. Enzymes do more than just function as a catalyst. The body can
protect itself and repair the harm caused by practically all degenerative
disease conditions when it has an abundance of enzymes. Without
enzymes, we age faster, develop disease earlier, and develop physical and
mental limitations as our systems deteriorate. A human or an animal
cannot exist without enzymatic function. As if it were the most important
aspect of life and the source. Enzymes are responsible for the majority of
biochemical processes in living things. The likelihood of those reactions
occurring would be low in the absence of enzymes. Without enzymes to
catalyze biological reactions, there is no prospect of the emergence and
evolution of living things.

Page 21
 Pineapple Enzymes and Gelatin
Experiment
Enzymes operate as a biological catalyst
in a variety of bio-reaction processes in the
human body, including the production of
energy in cells through the breakdown of big
starch molecules, proteins, lipids, the
production of hormones, digestion, and so
on. Enzymes are also utilized as catalysts in
certain industrial processes. Because
bromelain is a protein digesting enzyme,
similar reactions between pineapple and
gelatin occur. Since gelatin is formed of
proteins, bromelain digests the collagen.
When you add hot water to gelatin, the
heat causes the long chains of proteins to
unwind. As the gelatin cools and solidifies,
the collagen reforms messy and tangled,
trapping water in the middle of the long
chain proteins, turning what started as a
liquid into a wiggly mass of semi solid
protein. Gelatin will remain a semi solid.
Bromelain, a proteolytic enzyme, is found in
pineapple and seems to be a
combination of enzymes that degrade
proteins. Chemical reactions are
accelerated in the presence of biological
catalysts. As the long-chain proteins are cut
up into smaller proteins, trapped water is
gradually released, returning solution to a
liquid state. Bromelain breaks down at
boiling temperatures and is no longer able
to digest the proteins in gelatin. The longer
the fresh pineapple and bromelain enzymes
are in contact with the gelatin, the more
proteins will be broken down and the more
liquid will be left on the surface of the semi
solid gelatin.
Enzymes' catalytic activity is
dependent on their substrate binding to
create an enzyme-substrate complex. The
substrate binds to the active site, which is a
specific area of the enzyme. The substrate
is transformed into the reaction product
while bound to the active site, and the
enzyme is subsequently released. I
recognized that enzymes are necessary
because without them, most reactions
would be too slow and the cell would be
unable to meet biochemical needs.
Page 22
 Formative Quiz!
Nucleotides & Nucleic Acids

The components and structures of common nucleotides are

compared. (Questions 1-5)

Which structural feature is shared by

both uracil and thymine?

a) Both contain two keto groups.

b) Both contain one methyl group.
c) Both contain a five-membered ring.
d) Both contain three nitrogen atoms.

Which component is found in both

adenosine and deoxycytidine?

a) Both contain a pyranose.

b) Both contain a 1,1’-N-glycosidic bond.
c) Both contain a pyrimidine.
d) Both contain a 3’-OH group.

Which property is shared by both GDP

and AMP?

a) Both contain the same charge at

neutral pH.
b) Both contain the same number of
phosphate groups.
c) Both contain the same purine.
d) Both contain the same furanose.
Which characteristic is shared by purines
and pyrimidines?
a) Both contain two heterocyclic rings
with aromatic character.
b) Both can form multiple non-covalent
hydrogen bonds.
c) Both exist in planar configurations with
a hemiacetal linkage.
Which property is found in nucleosides and d) Both exist as neutral zwitterions under
nucleotides? cellular conditions.
a) Both contain a nitrogenous base, a pentose, and at
least one phosphate
group.
b) Both contain a covalent phosphodister bond that is
broken in strong acid.
c) Both contain an anomeric carbon atom that is part
of a β-N-glycosidic
bond.
d) Both contain an aldose with hydroxyl groups that
can tautomerize.

Page 23
The structures of nucleotides and their components are studied.
(Questions 6-10)

Which characteristic is shared by both

adenine and cytosine?

a) Both contain one methyl group.

b) Both are anomeric.
c) Both contain one keto group.
d) Both are heterocyclic.

Which component is found in both

guanosine and uridine?

a) Both contain an aldohexose.

b) Both contain three hydroxyl groups.
c) Both contain a 1’,9 - bond.
d) Both contain a pyranose.

Which property is shared by both CTP and

dTDP?

a) Both contain the same sugar.

b) Both contain the same charge at cellular
pH.
c) Both contain a planar six-membered ring.
d) Both contain phosphodiester bonds.

Which characteristic is found in both purines and

pyrimidines?

a) They both have aromatic rings that undergo

substantial tautomerization at
neutral pH.
b) They both are weak bases that can be positively
charged at neutral pH.
c) They both have multiple pKa values that result in
zwitterion forms.
d) They both can form stable N-glycosidic bonds with β
D-ribofuranose.

Which is a general property of both

nucleosides and nucleotides?
a) Both contain a pentose in the form of a
furanose.
b) Both contain at least one 5’-phosphate
group.
c) Both contain a nitrogenous base that forms
covalent H-bonds.
d) Both contain a hemiacetal or hemiketal
bond.

Page 24
A single-stranded DNA molecule contains 40 nucleotides with
equal amounts of A, C, G, and T. This DNA strand can combine
with a complementary DNA strand to form a double-stranded
DNA molecule. (Questions 11-16)

Which structural feature is found in the single-stranded

DNA molecule?
a) It can have a negatively-charged backbone composed of
nitrogenous bases.
b) Each 3’,5’-phosphodiester bond will contain one
phosphate group thinking two deoxyribose sugars.
c) It can have one end with a 5’-phosphate group while the
other end has a 2’-hydroxyl group.
d) Each purine and pyrimidine will be paired with a
complementary base.

Which is a possible sequence and structure for this DNA molecule?

a) If the single-stranded molecule has the sequence 5’-(ATGC)10, then

its double- stranded form could assume a Z-DNA structure.
b) If the single-stranded molecule has the sequence 5’-(GATC)10, then
its double-stranded form could assume an H-DNA structure.
c) If the single-stranded molecule has the sequence 5’-(CTGA)10, then
its double-stranded form could assume a hairpin structure.
d) If the single-stranded molecule has the sequence 5’-(TGAC)10, then
its double-stranded form could assume a cruciform structure.

Which characteristic does this double-stranded

molecule have when it forms a B-
DNA structure?

a) The two strands will have parallel orientation and

identical sequences.
b) The helix will be right-handed with 12 base-pairs
per turn.
c) Every base-pair will contain one purine and one
pyrimidine.
d) There are both covalent and non-covalent bonds
between the two chains.
Which of the following double-stranded DNA molecules
would denature at a lower temperature than the 40 base-
pair double-stranded molecule described above?
Which force can stabilize a DNA double-helix?
a) Hydrophobic bases are found in the interior of the
helix where each base-pair is stabilized by the same
number of hydrogen bonds.
b) Hydrophilic sugar-phosphate groups are found on
the exterior of the helix where they can interact with
water.
c) Non-covalent N-glycosidic bonds can form between
nitrogenous bases in opposite strands in the helix.
d) Covalent base-stacking interactions can occur
between adjacent bases
within the same strand in the helix.

a) a 40 base-pair molecule in which 25% of the bases are

adenines
b) a 30 base-pair molecule in which 40% of the bases are
guanines
c) a 20 base-pair molecule in which 10% of the bases are
thymines
d) a 10 base-pair molecule in which 20 % of the bases are
cytosines

Page 25
 Which characteristic will this double-stranded
DNA molecule share with a double-stranded
RNA molecule of the same size?

a) Both will have secondary structure.

b) Both will contain inverted repeats.
c) Both will be degraded by base.
d) Both will contain four types of base-pairs.

A single-stranded DNA molecule contains 40 nucleotides and has

the sequence 5’-(GA)20-3’. (Questions 17-22)

Which will be a characteristic of this one single strand?

a) The single-stranded chain will contain both ribose and

deoxyribose.
b) The single-stranded chain will contain both purines and
pyrimidines.
c) The single-stranded chain will contain one 5’-end and one
3’-end.
d) The single-stranded chain will contain multiple
phosphodiester bonds each
linking a 2’-carbon and a 5’-carbon.

When this single strand binds to a complementary

DNA strand,

a) the complementary strand has the sequence 5’-

(CT)20-3’ and a cruciform structure could form.
b) the complementary strand has the sequence 5’-
(CT)20-3’ and a Z-DNA structure could form.
c) the complementary strand has the sequence 5’-
(TC)20-3’ and an H-DNA structure could form.
d) the complementary strand has the sequence 5’-
(TC)20-3’ and a hairpin structure could form.
When this single strand binds to a complementary DNA strand
to form a B-DNA structure,

a) half the base-pairs will be A-G pairs and half will be C-T pairs.
b) each base will form at least two hydrogen bonds with a base
in the opposite strand.
c) the two strands will form an antiparallel left-handed helix
with 12 base-pairs per turn.
d) there will be covalent phosphodiester bonds between the
two strands.

Which of the following forces can stabilize a normal DNA

double-helix?
a) Base-stacking is a non-covalent interaction that occurs
between the relatively hydrophobic bases in the interior of the
helix.
b) Base-pairing is a non-covalent interaction that occurs
between adjacent bases in the same strand of the DNA
molecule.
c) The hydrophilic sugar-phosphate groups are on the exterior
of the helix where they can interact with each other.
d) The deoxyribose rings form N-glycosidic bonds with the
phosphate groups that link neighboring nucleotides.

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 Which of the following double-stranded DNA molecules
would denature at about the same temperature as the
double-stranded molecule containing a 5’-(GA)20-3’
strand?

a) a molecule which contains a (GC)20 strand

b) a molecule which contains a (TA)20 strand
c) a molecule which contains a (GACT)10 strand
d) a molecule which contains a (GGGA)10 strand

Which characteristic will be shared when comparing

the single 5’-(GA)20-3’ strand to another single-
stranded DNA molecule with the sequence 5’-(AT)20-
3’?

a) Both contain a palindromic sequence.

b) Both can form the same secondary structures.
c) Both could hybridize to the same RNA molecule.
d) Both will have the same overall charge.

Genetic material is examined in several organisms. (Questions 23-

28)

Which of the following experimental results, if obtained, would

be evidence against proteins being the genetic material?

a) The viral components labeled with 35S are found inside the
bacterial cell during a successful infection.
b) The viral components labeled with 32P are found outside the
bacterial cell during a successful infection.
c) The transforming factor isolated from a virulent bacterium is
resistant to proteases.
d) The transforming factor isolated from a virulent bacterium is
resistant to deoxyribonucleases.

Assume that DNA molecules are studied in a variety of

organisms and found to have the following properties. Which
property would be consistent with the hypothesis that genetic
material is composed of DNA?

a) DNA in all organisms is composed of the same nucleotides.

b) DNA in an organism remains constant as the organism ages.
c) DNA from two different organisms has the same base
composition.
d) DNA is different in two different cells of the same organism.

A new virus, virus X, is isolated and studied. Which

molecule is most likely to be the genetic material of
virus X?

a) a linear DNA molecule containing 10,000 base-pairs

b) a linear RNA molecule containing plasmids
c) a circular DNA molecule containing nucleosomes
d) a circular RNA molecule with a molecular weight of
10 billion

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 Which are characteristics of bacterial genetic
material?

a) It is double-stranded and supercoiled.

b) It is single-stranded and relaxed.
c) It is circular and compacted into
palindromes.
d) It is linear and attached to a protein scaffold.

Which describes the structural properties of a

eukaryotic chromosome?

a) It contains a double-helix composed of nucleosomes

each with four million base-pairs.
b) It is one double-stranded linear DNA molecule
bound to proteins for compaction.
c) It is arranged into a 30 nm fiber which is attached to
the cell membrane.
d) It contains linker regions which are arranged into
loops and coiled to form a helix.

Which property is shared by the five histone proteins?

a) They are acidic proteins with relatively large

molecular weights.
b) They are multimeric proteins with high levels of Arg
and Lys.
c) They are fibrous proteins with high amounts of α-
helix.
d) They are globular proteins with a positive charge.

Genetic material is examined in several organisms. (Questions 29-

30)

If the following experimental results were obtained, this would

be evidence against DNA being the genetic material?

a) The base composition of DNA is the same in two different cells

of the same organism.
b) The viral components labeled with 32P remain outside the cell
during a successful infection.
c) The transforming factor isolated from a virulent bacterium is
sensitive to deoxyribonucleases.
d) The base composition of DNA in an organism remains
constant as the organism ages.

Which is a property of both viral genetic material and

bacterial genetic material?

a) Both can be double-stranded, circular DNA.

b) Both can be single-stranded, linear RNA.
c) Both can be compacted into inverted repeats.
d) Both can be compacted into plasmids.

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 LIPIDS
SAPONIFICATION: The Process of Making Soap
Guide Questions

1. What are lipids?

Lipids are organic substances that contain carbon, hydrogen,

and oxygen, such as fats, oils, and waxes. The same three components
are present in the structure of carbohydrates, although the amount of
oxygen in the molecule is substantially lower. Because water is a polar
molecule, these organic compounds are soluble exclusively in
nonpolar solvents and insoluble in water. These molecules can be 2. Explain saponification.
produced in the human body and are found in oil, butter, whole milk,
cheese, fried meals, and some red meats. They are small molecules in
comparison to polysaccharides, but because they are insoluble, they
bind together to form globules.

Saponification is derived from the Latin word sapo, which

3. When you touched the beaker with the coconut oil and
NaOH solution, what did you feel? Is the reaction
endothermic or exothermic, as you believe? Why is this
the case?
signifies soap. The process of creating soap is known as saponification.
Soaps are lengthy chains of sodium and potassium salts of fatty acids.
Saponification is defined in chemistry as the reaction of an ester with
water and a base such as NaOH or KOH to create alcohol and an acid's
sodium or potassium salt. A hard soap is formed when sodium
hydroxide is utilized. The use of potassium hydroxide produces a soft
soap. Saponification is the chemical reaction that occurs when any fat
reacts with sodium hydroxide.

When I touched the beaker with the coconut oil and NaOH
solution, it felt warm to the touch, but I believe this depends on how
quickly you stir. One solution could be friction caused by strong
stirring. Another reason is because the two chemicals in the beaker are 4. What changes in the mixture have you
undergoing an exothermic chemical reaction. The saponification seen while the beaker is on the hot plate?
reaction should be exothermic since it involves the production of an

ionic molecule that is quite polar and hence soluble in the polar solvent
in which the reaction is often carried out. This is due to the release of
heat throughout the procedure. Wrapping the soap to retain the heat
generated by this reaction speeds up the reaction.
Before heating, the coconut oil and NaOH solution seems to be
a clear colorless liquid, but after boiling the mixture has a soft, greasy
appearance and when it starts to form, and as it ages the wax hardens
and turns brittle it forms soap molecules or soap salts. This waxy
material, turning it into a soap mummy. However, we are unable to
shape the soap salt totally because the wax solidifies.

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 5. What colors did you see after dipping the
litmus paper in the suspension? What do the
colors mean?

Soap is a sodium salt of fatty acids found naturally. A

saponification or basic hydrolysis reaction of a fat or oil produces it. To
neutralize the fatty acid and convert it to salt, sodium carbonate or
sodium hydroxide are now employed. After dipping the litmus paper
in the suspension, I see that the blue litmus paper does not change
color, however the red litmus paper changes color and turns blue. It
leads to the conclusion that soap solutions are naturally alkaline.
Because fatty acids are weak acids and sodium hydroxide is a strong
base, the salt that is formed here is a salt of weak acid and strong base,
which is basic in nature. As a result, the soap solution will be alkaline in
nature.

Conclusion:

Personal and public health depend on soaps and detergents. They securely remove
bacteria, soils, and other impurities, allowing us to stay healthy while also improving our
environment. Fats and oils, or their fatty acids, are used to make soap.

Many organisms store energy in the form of fats and oils. Lipids in the body store
energy and help to form cell membranes. They are fundamental building blocks found in
the stratum corneum, the skin's outermost layer. These lipids build layers around and in
between skin cells, forming a barrier that prevents natural moisture from escaping.
Without lipids to maintain collagen, matrix skin becomes thin and dry, revealing fine lines
and wrinkles. Sagging skin occurs as the lipid layer becomes thinner. The stratum
corneum is made up of dead skin cells bound together by lipids, and it serves as an
environmental barrier that protects clients from the elements. Lipids serve a critical role in
our bodies. They make up the cell membrane's structural framework. They assist our
bodies to manufacture hormones and provide energy. They aid in appropriate meal
digestion and absorption. If consumed in sufficient quantities, they are a healthy part of
our diet. They play a vital function in signaling as well.

Saponification is significant to industrial users because it allows them to

determine the amount of free fatty acid in a food material. The amount of free fatty acid
can be determined by calculating how much alkali must be added to the fat or oil to
neutralize it.

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Process

Page 31
Page 32
 At the axis of the body-mind relationship, biochemists and
psychologists collide. If we want to fully comprehend
perfumery, we need to take into account both the
physiological and psychological aspects. Biochemistry is
concerned with the actual body, whereas psychology is
concerned with thoughts and feelings, or an imaginary body.
Any change in biology is frequently mirrored in psychological
changes.

Many concerns about how our brain and behavior are

linked remain unanswered, but biologists and chemists have
discovered that our entire body, including the brain, is made
up of proteins that perform certain activities and are
expressed through our genes. Those proteins control
everything else in our body, including its functions. One of the
most significant scientific triumphs of the last century was the
discovery of genetics, which is also a profoundly biological
concept. Genetic influences on f.e. are increasingly being
considered by modern psychologists. Susceptibility to
addiction or mental diseases Biochemistry and biochemical
approaches are heavily used in neuroscience, which can be
understood as an attempt to explain psychological events on a
biological basis.

In psychological research, laboratory experiments are

extremely important. It enable us to discover a cause-and-
effect link between variables that would be impossible to
discover using many other study methodologies. To
summarize, I feel that laboratory experiments are among the
most significant pieces of psychological research since they
allow us to see a direct cause and effect link while also
reducing the impacts of extraneous variables. They provide
great dependability and objective data collection.

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