Biochemistry Topic: Introduction to Protein Conformation Secondary and Tertiary Structures

By: Aldrin Dela

Cruz Merlyn
Edillor
Professor: Armando M. Lamboloto, Jr.
What do I need At the end of this module, the learner should be able to:
to learn? 1. Define protein conformation and its structures
2. Identify secondary structures whether ( a-helix, b-sheet, b-turn, or random coil )
Perform a simple observation to identify the specific property of water involved in a
given scenario.

What do I need Introduction:

to know? Proteins structures are made by condensation of amino acids forming peptide bonds.
The sequence of amino acids in a protein is called its primary structure. The
secondary structure is determined by the dihedral angles of the peptide bonds, the
tertiary structure by the folding of protein chains in space. Association of folded
polypeptide molecules to complex functional proteins results in quaternary structure.
Protein structure is defined as a polymer of amino acids joined by peptide bonds.

Protein conformation may be defined as the arrangement in space of its

constituent atoms which determine the overall shape of the molecule. The
conformation of the protein arises from the bonding arrangements within its
structure Protein conformation may be defined as the arrangement in space of its
constituent atoms which determine the overall shape of the molecule. The
conformation of the protein arises from the bonding arrangements within its
structure

Types and Different Structure of Protein Conformation

Primary structure
The simplest level of protein structure, primary structure, is simply the sequence
of amino acids in a polypeptide chain. For example, the hormone insulin has two
polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown
here is cow insulin, although its structure is similar to that of human insulin.) Each
chain has its own set of amino acids, assembled in a particular order. For instance,
the sequence of the A chain starts with glycine at the N-terminus and ends with
asparagine at the C-terminus, and is different from the sequence of the B chain.

The sequence of a protein is determined by the DNA of the gene that encodes the
protein (or that encodes a portion of the protein, for multi-subunit proteins). A
change in the gene's DNA sequence may lead to a change in the amino acid
sequence of the protein. Even changing just one amino acid in a protein’s
sequence can affect the protein’s overall structure and function.
In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the
amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of
amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern
of bonding pulls the polypeptide chain into a helical structure that resembles a
curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups
of the amino acids stick outward from the α helix, where they are free to interact
\[^3\]
.
In a β pleated sheet, two or more segments of a polypeptide chain line up next to
each other, forming a sheet-like structure held together by hydrogen bonds. The
hydrogen bonds form between carbonyl and amino groups of backbone, while the
R groups extend above and below the plane of the sheet.

. The strands of a β pleated sheet may be parallel, pointing in the same direction
(meaning that their N- and C-termini match up), or antiparallel, pointing in
opposite directions (meaning that the N-terminus of one strand is positioned next
to the C-terminus of the other).
Certain amino acids are more or less likely to be found in α-helices or β pleated
sheets. For instance, the amino acid proline is sometimes called a “helix breaker”
because its unusual R group (which bonds to the amino group to form a ring)
creates a bend in the chain and is not compatible with helix formation.

Proline is typically found in bends, unstructured regions between secondary

structures. Similarly, amino acids such as tryptophan, tyrosine, and phenylalanine,
which have large ring structures in their R groups, are often found in β pleated
sheets, perhaps because the β pleated sheet structure provides plenty of space for
the side chains.
.
Many proteins contain both α helices and β pleated sheets, though some contain
just one type of secondary structure (or do not form either type).In an α helix, the
carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an
amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would
form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls
the polypeptide chain into a helical structure that resembles a curled ribbon, with
each turn of the helix containing 3.6 amino acids.

The R groups of the amino acids stick outward from the α helix, where they are
free to interact.
In a β pleated sheet, two or more segments of a polypeptide chain line up next to
each other, forming a sheet-like structure held together by hydrogen bonds. The
hydrogen bonds form between carbonyl and amino groups of backbone, while the
R groups extend above and below the plane of the sheet.

The strands of a β pleated sheet may be parallel, pointing in the same direction
(meaning that their N- and C-termini match up), or antiparallel, pointing in
opposite directions (meaning that the N-terminus of one strand is positioned next
to the C-terminus of the other).
Certain amino acids are more or less likely to be found in α-helices or β pleated
sheets. For instance, the amino acid proline is sometimes called a “helix breaker”
because its unusual R group (which bonds to the amino group to form a ring)
creates a bend in the chain and is not compatible with helix formation

Proline is typically found in bends, unstructured regions between secondary

structures. Similarly, amino acids such as tryptophan, tyrosine, and phenylalanine,
which have large ring structures in their R groups, are often found in β pleated
sheets, perhaps because the β pleated sheet structure provides plenty of space for
the side chains.
Many proteins contain both α helices and β pleated sheets, though some contain
just one type of secondary structure (or do not form either type).

For instance, a single amino acid change is associated with sickle cell anemia, an
inherited disease that affects red blood cells. In sickle cell anemia, one of the
polypeptide chains that make up hemoglobin, the protein that carries oxygen in
the blood, has a slight sequence change. The glutamic acid that is normally the
sixth amino acid of the hemoglobin β chain (one of two types of protein chains that
make up hemoglobin) is replaced by a valine. This substitution is shown for a
fragment of the β chain in the diagram below.

.
Secondary structure
The next level of protein structure, secondary structure, refers to local folded
structures that form within a polypeptide due to interactions between atoms of the
backbone. (The backbone just refers to the polypeptide chain apart from the R
groups – so all we mean here is that secondary structure does not involve R group
atoms.) The most common types of secondary structures are the α helix and the β
pleated sheet. Both structures are held in shape by hydrogen bonds, which form
between the carbonyl O of one amino acid and the amino H of another.
You'll learn more about the reasons behind the behavior of water as you progress
through this subject. You will discover the details of its unique structure and how
these attributes are influenced by it. Ready to delve into the secrets of water?
Together, let's explore as we begin!

BIOLOGICAL AND MEDICAL IMPORTANCE

1. A necessary component of all living forms is water.
2. Every cell contains water. It serves as the medium for all cellular activity.
3. Enzyme activity and solute transport inside the body depend on it.
4. Proteins and nucleic acids, among other macromolecules, fold more easily
when wet.
5. The body's semi-fluid condition results from water.
6. Body temperature is regulated by water.
7. Water provides ions, which speed up biological operations.
8. Dehydration and edema cause changes in the body's water content.

WATER PROPERTIES AND REACTION IN WATER

I. POLARITY OF WATER
Molecular Structure
Covalent Bonds: In water (H₂O), oxygen and hydrogen atoms share electrons
through covalent bonds.
Bond Angle: The angle between the bonds is 104.5°.
Electronegativity: Oxygen, being more electronegative than hydrogen, attracts
electrons more strongly, leading to a polar covalent bond.
Dipole Formation: This creates a permanent dipole in the molecule.

Effects of Polarity
Solubility: The principle "like dissolves like" explains why polar substances dissolve in
water, whereas nonpolar substances do not.

II. HYDROGEN BONDS

Formation
Interaction: Water molecules attract each other due to their polar covalent bonds.
Bond Characteristics: Hydrogen bonds occur between a slightly positive hydrogen
atom in one water molecule and a slightly negative oxygen atom in another.
These bonds are about 25 times weaker than covalent bonds.
Bonding Capacity: Each water molecule can form hydrogen bonds with up to
four other water molecules.

Consequences of Hydrogen Bonds

Melting Point: The high melting point of water is due to hydrogen bonding.
Density and Expansion: As water freezes, it forms a less dense structure (ice) with an
open lattice of molecules.
Specific Heat Capacity: Hydrogen bonds contribute to water’s high specific heat
capacity,
which stabilizes temperature changes.
Heat of Vaporization: A considerable amount of heat is required to convert water
from a liquid to a gas due to the need to break hydrogen bonds.

A. Unique Properties of Water As A Consequence of The Hydrogen Bond

Water has special qualities because its molecules create hydrogen bonds with one
another. These various characteristics are important for earthly life. Due to the
hydrogen bond, water has the following special qualities.

a. It is a liquid at room temperature with a high boiling point.

Because hydrogen bonding, an extremely potent intermolecular force, holds
water's molecules together, water has a high boiling point. The hydrogen
bonds that hold water molecules together must be broken by greater kinetic
energy or temperature in order for the water molecules to escape as steam.
Raising the liquid's temperature causes the molecules' kinetic energy to increase,
causing the liquid to boil. The molecules can become gaseous by escaping the
intermolecular interactions that keep them together as a liquid when their kinetic
energy increases. As the intensity of the intermolecular force grows, so does the
amount of kinetic energy needed to break it. A substance with stronger
intermolecular interactions has a higher boiling point because they need more
energy to break.

Hydrogen bonding, an extremely potent intermolecular force, holds water

molecules together. Because the hydrogen atoms have a partial positive charge
and the oxygen atoms have a partial negative charge, every water molecule is
polar. One water molecule's partial negative charge attracts another water
molecule's partial positive charge with great power. The molecules must be
given enough kinetic energy to break free of the strong hydrogen bonds
between them in order for water to boil. The molecules' kinetic energy can only be
enhanced by raising the temperature. This raises the boiling point of water due to
the hydrogen bonding.

b. Because of its high specific heat, it needs a lot of heat to evaporate.

This explains why there aren't many temperature fluctuations on Earth that could
change the climate. Because it takes a lot of heat energy to break the hydrogen
bonds that exist within a water molecule, water has a high heat capacity. The
water molecule heats up once the hydrogen bonds are broken because most of
the heat energy is focused on rupturing the bonds.

The water molecule itself can absorb the extra heat energy once the hydrogen
bonds inside it have heated up to the point of breaking. The water molecule is then
vibrated by this extra heat energy, which enables it to collide with other water
molecules to disperse the heat energy from a heat source. Since the vibrating
water molecule needs to transfer enough heat energy to break the hydrogen
bonds in the surrounding water molecules, the dispersion of heat energy occurs
slowly. The water cools, but only very slowly, once the heat source is removed.

Just as significant energy is required to break the hydrogen bonds in a water

molecule, significant energy is likewise required to re-form them. Only when
the water molecule achieves a low enough temperature to allow the hydrogen
bonds to re-form does the water molecule release the heat energy. This process of
warming and cooling explains why water slowly heats up and cools down.

c. It is the only substance that contracts when cooled because of its more open
structure in the solid form. The density of ice is less than liquid water, hence, it floats
on water.

When a liquid is cooled, more and more molecules are brought closer together and
need to be accommodated in a smaller area. This gives most solids more density
than their liquid form.
However, in the case of water, the negatively-charged oxygen atoms repel each
other (when

brought together in a smaller space) to prevent the ice from becoming any denser.
This is the reason that density actually decreases as temperature continues to fall
below 4 degrees Celsius.

d. It has high heat of vaporization. This causes a large drop in temperature during
evaporation.

Due to hydrogen bonding, water molecules cling to each other (cohesion) and
remain in liquid state under temperatures that are favorable to plants and other
living organisms. Liquid water has a boiling temperature of 100°C and freezes
at 0°C at 1 atmospheric pressure. When it boils, the hydrogen bonds are
broken and the molecules separate from each other. But without these
hydrogen bonds, water will boil at temperature of -80°C and freeze at -100°C
(Mader 1993).

The hydrogen-bonding property of water is therefore vital to life, particularly to

plants which generally survive within a temperature range from 0 to 50°C.
Otherwise, plants will be deprived of liquid water because the water inside will
change to gas even at low temperatures. In the process of changing 1 gram of
liquid water at 0°C to solid form or ice at 0°C, 80 calories of heat energy is lost.
This is the latent heat of fusion of water. The heat that is given off when water
freezes keeps the atmospheric temperature higher. Likewise, 1 gram of ice at 0°C
uses 80 calories of heat energy to convert to 1 gram of liquid water at 0°C. This is
water's latent heat of melting.

But a very high quantity of heat energy is needed for evaporation. This amount
of heat is called heat of vaporization. When molecules of water absorb heat
energy, they move fast in water. Eventually, the speed of movement of some
molecules becomes so fast allowing them to overcome the intermolecular
attraction, detach from the multimolecular water, form bubbles, and leave the
water surface in gas state.

Water has latent heat of vaporization of 540 calories per gram, the amount of heat
energy that is necessary to convert 1 g of liquid water at 100°C to steam at
100°C, or 40.71 kJ/mol or about 2,260 kJ/kg water. The heat energy is used in
breaking the hydrogen bonds which hold the molecules of liquid water together.

This property of water helps to cool down the body of living organisms. This is
called evaporative cooling. In humans, body heat is used to vaporize sweat, in
plants, heat is likewise used in converting liquid water to water vapor which
then escapes into the atmosphere. This natural process of vaporizing plant water
is called transpiration (it is the evaporation of water from plants).

e. It has a high surface tension.

This allows water to move from the roots to the top of a very tall tree. Water
molecules want to cling to each other. At the surface, however, there are fewer
water molecules to cling to since there is air above (thus, no water molecules).
This results in a stronger bond between those molecules that actually do come in
contact with one another, and a layer of strongly bonded water (see diagram).
This surface layer (held together by surface tension) creates a considerable
barrier between the atmosphere and the water. In fact, other than mercury,
water has the greatest surface tension of any liquid. (Source: Lakes of Missouri)

Surface tension in water owes to the fact that water molecules attract one
another, as each molecule forms a bond with the ones in its vicinity. At the
surface, though, the outmost layer of molecules, has fewer molecules to cling to,
therefore compensates by establishing stronger bonds with its neighbours, this
leading to the formation of the surface tension.

Within a body of a liquid, a molecule will not experience a net force because the
forces by the neighboring molecules all cancel out (diagram). However, for a
molecule on the surface of the liquid, there will be a net inward force since there
will be no attractive force acting from above. This inward net force causes the
molecules on the surface to contract and to resist being stretched or broken.
Thus the surface is under tension, which is probably where the name "surface
tension" came from. (Source: Woodrow Wilson Foundation)

Due to the surface tension, small objects will "float" on the surface of a fluid, as
long as the object cannot break through and separate the top layer of water
molecules. When an object is on the surface of the fluid, the surface under
tension will behave like an elastic membrane.

III. WATER AS A UNIVERSAL SOLVENT

Solubility
Polar and Ionic Compounds: Water dissolves polar compounds and electrolytes due
to its ability to interact with them.
Solvation Spheres: Water molecules form a shell around ions, aiding their
dissolution.

Organic Molecules
Solubility Factors: Molecules’ solubility in water depends on their polarity and
capacity to
form hydrogen bonds.
Functional Groups: Groups such as carboxylates, protonated amines, amino, hydroxyl,
and carbonyl enhance solubility.

Hydrophobic Interactions
Nonpolar Molecules: Nonpolar molecules do not dissolve in water and tend to
cluster together, a phenomenon known as the hydrophobic effect.
Amphipathic Molecules: Detergents and surfactants, which have both hydrophilic and
hydrophobic parts, exhibit this property.

4. NONCOVALENT INTERACTIONS IN BIOMOLECULES

Hydrogen Bonds
Structural Stability: Essential for stabilizing structures such as proteins and nucleic
acids.
Hydrophobic Interactions

Protein Structure: Although weak, these interactions are crucial for the shape of
proteins and the structure of membranes.

Charge-Charge Interactions (Ionic Bonds)

Strength: The strongest noncovalent interaction, occurring between oppositely
charged particles.
Impact of Water: Water can weaken these bonds by interfering with the interactions
between charged particles.

Van der Waals Forces

Attractive and Repulsive Forces: These forces occur between neutral atoms and
vary based on distance. They are weaker compared to hydrogen bonds.

5.NUCLEOPHILIC NATURE OF WATER

Nucleophiles
Definition: Electron-rich species that are attracted to electron-deficient areas
(electrophiles).
Examples: Includes oxygen, nitrogen, sulfur, carbon, and water (to a lesser extent).

Reactions
Hydrolysis: Water participates in hydrolysis reactions, breaking larger molecules into
smaller ones.
Condensation: During condensation reactions, water is released as smaller
molecules combine to form larger ones (e.g., protein synthesis).

6.Ionization of Water

Properties
 Ionization: Pure water slightly ionizes and can function as both an acid (proton donor)
and a base (proton acceptor).
Biological Relevance: This ionization is crucial for maintaining pH balance in living
organisms.

What does Title of Research: Water Structure, Properties and Some Applications – A Review
research say First Published: June 2022
about this?
Researchers: Georgios M. Kontogeorgis, Andrew Holster, Nomiki Kottaki, Evangelos
Tsochantaris, Frederik Topsøe, Jesper Poulsen, Michael Bache, Xiaodong Liang,
Nikolaj Sorgenfrei Blom, and Johan Kronholm

Abstract
This study provides an in-depth examination of water's structure, properties, and
applications, with a particular focus on recent scientific advancements and
controversial theories. It highlights key findings from both well-established
research and emerging hypotheses. The review distinguishes between
experimental evidence and theoretical claims, emphasizing water's anomalous
properties, its role in thermodynamics, and the less conventional areas of water
bridges and exclusion zones. Despite some hypotheses remaining unproven, the
review presents a comprehensive overview of the current state of water
science. By integrating diverse perspectives and summarizing both mainstream
and controversial viewpoints, it aims to offer a clearer understanding of water's
complex behavior and its significance across various scientific disciplines.

Water in
Reaction
 Reference: Kontogeorgis, G. M., Holster, A., Kottaki, N., Tsochantaris, E.,
Topsøe, F., Poulsen, J., Bache, M., Liang, X., Blom, N. S., & Kronholm, J.
(2022). Water structure, properties and some applications – A review.
Chemical Thermodynamics and Thermal Analysis, 6, 100053.
https://doi.org/10.1016/j.cta.2022.100053
What Insights I- Reflect
and Learning 1. What impact does water's unique characteristics—such as its high
have I gained in specific heat, surface tension, and freezing-thawing density—have on
this topic? its ability to control temperature in biological systems and
environmental processes?
2. What effect do the unusual characteristics of water, like its high
vaporization heat and anomalous density, have on our comprehension
of the function of water in industrial and natural processes?
3. Water has special qualities. similar to you. Additionally, you possess
special qualities. What sets you apart from the others. How can you
motivate others with your uniqueness?
What do I need OBSERVATION (GROUP ACTIVITY)
to do? Conduct a simple observation to identify the specific property of water involved in a
given scenario. Then, answer the following questions.

1.

 a. Why does water has high boiling point than ethanol?

 b. What property of water is shown in the picture?

2.

 Which will release heat slower? Why?

 What property is exhibited by the water?
 3.
a. Why does the ice float?
b. How will you describe the molecular structure of water in solid form?

4.

a. How does colored water change the color of the flower?

b. What are properties involved in this action?
Where can I get Ayson, Marissa F. et al., General Chemistry 2 Textbook. Quezon City: Vibal Group,
additional Inc., 2016.
information Teaching Guide for Senior High School General Chemistry 2. Commission on
about this? Higher Education, 2016.
https://www.usgs.gov/special-topic/water-science-school/science/surface-tension-
and- water?qt-science center objects=0#qt-science center objects
https://wwwww.cropsreview.com/heat-of-.htmlhttps://www.cropsreview.com/
transpiration.html https://www.reference.com/science/water-high-heat-capacity-
7937c9c620e6f810