Im-4 Genbiochem1

Republic of the Philippines
NUEVA VIZCAYA STATE UNIVERSITY

Bayombong, Nueva Vizcaya
INSTRUCTIONAL MODULE
IM: GENBIOCHEM1-1STSEM-2023-2024
COLLEGE OF ARTS AND SCIENCES

Bayombong Campus
DEGREE CERTIFICATE IN COURSE NO. GEN BIOCHEM1
PROGRAM AGRICULTURE SCIENCE
SPECIALIZATION AGRICULTURE SCIENCE COURSE TITLE GENERAL BIOCHEMISTRY
YEAR LEVEL 2 TIME FRAME 3 HRS WK NO. 8 IM NO. 4
I. CHAPTER 4: AMINO ACIDS AND PROTEINS
II. LESSON TITLE: Amino Acids and Proteins

4.1 Introduction
4.2 Amino Acids
4.3 Acid-base behavior of amino acids
4.4 Peptides
4.5 Biologically active peptides
4.6 Four Levels of Structure of Proteins
4.7 Protein Classification Based on Shape and Function
4.8 Protein hydrolysis and Denaturation
III. LESSON OVERVIEW
Of the four major groups of biomolecules- lipids, carbohydrates, proteins, and nucleic acids-proteins have
the widest array of functions. Keratin and collagen, for example, form long insoluble fibers, giving strength and
support to tissues. Hair, horns, and fingernails are all made up of keratin. Collagen is found in bone, connective
tissue, tendon, and cartilage. Membrane proteins transport small organic molecules and ions across cell
membranes. Insulin, the hormone that regulates blood glucose levels, and hemoglobin, which transports oxygen
from the lungs to tissues, are proteins.
In this chapter, the discussions will begin with the structures and chemical properties of the common
amino acids, including their stereochemistry, and end with the brief summary of the structure and functions of
some related compounds.
IV. DESIRED LEARNING OUTCOMES
At the end of the chapter, students should be able to:
1. Identify the general structural features and the acid-base properties of amino acids
2. Draw simple peptides from individual amino acids.
3. Identify the levels of protein structure and explain how a protein’s structure affects its properties.
4. Describe the features of fibrous and globular proteins.
5. Describe the protein’s denaturation.
V. LESSON CONTENT
4.1 INTRODUCTION
Proteins are
biomolecules that contain many
amide bonds, formed by joining
amino acids together.
The word protein comes from the Greek proteios meaning “of first importance”. Proteins occur widely in
the human body, according for approximately 50% of its dry weight. Fibrous proteins, like keratin in hair,
skin and nails and collagen in connective tissue, give support and structure to Tissues and cells. Protein
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hormones and enzymes regulate the body’s metabolism. Transport proteins carry substances through
the blood, and storage protiens store elements and ions in organs. Contractile proteins control muscle
movements, and immunoglobulins are protiens that defend the body against foreigh substances.
Recommneded Daily Protein Intake
Group Daily Protein Intake (g protein/kg body weight)

Children (1-3 years) 1.1
Adult 0.8
Source: Date from U.S. FDA
4.2 AMINO ACIDS
General Features of Amino Acids
Amino acids contain two functional group—an amino group (NH2) and a carboxyl group
(COOH). In most naturally occurring acids, the amino group is bonded to the α carbon, the carbon
adjacent to the carbonyl group, making them α-amino acids.
Amino group Carboxyl group
glycine
α-amino acid the simplest amino acid
The 20 amino acids that occur naturally in proteins differ in the identity of the R group bonded to the α
carbon. The R group is called the side chain of the amino acid. The simplest amino acid, called glycine,
has R = H. Other side chains may be simple alkyl groups, or have additional functional groups such as
OH, SH, COOH, or NH2’
• Amino acids with additional COOH group in the side chain are called acidic amino acids.
• Those with an additional basic N atom in the side chain are called basic amino acids.
• A nonpolar amino acid is an amino acid that contains one amino group, on carboxyl group, and
a nonpolar side chain.
• A polar neutral amino acid is an amino acid that contains one amino group (NH 2), one carboxyl
group, and a side chain that is polar but neutral. In solution at physiological pH, the side chain of
a polar neutral amino acid is neither acidic or basic.
All amino acids have common names, which are abbreviated by a three-letter or one-letter
designation. For example, glycine is often written as the three-letter abbreviation Gly, or the one-letter
abbreviation G.
Amino acids never exist in nature as neutral molecules with uncharged atoms. Since amino acids
contain a base (NH2 group) and an acid (COOH), proton transfer from the acid to the base forms as salt
called zwitterion, which contains both a positive and a negative charge. These salts have high melting
points and are water soluble.
(+) and (-) charges in the same
compounds
zwitterion
This neutral form of an amino a salt

acid does not exist This salt is the neutral form of
an amino acid
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20 Common Naturally Occurring Amino Acids

Nonpolar Amino Acids
Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L)

Glycine (Gly, G) Proline (Pro, P)
Isoleucine (Ile, I)
Methionine (Met, M) Phenylalanine (Phe, F)
Tryptophan (Trp, W)
Polar Neutral Amino Acids
Serine (Ser, S) Threonine (Thr, T) Aspargine (Asn, N) Glutamine (Gln, Q)
Cysteine (Cys, C)
Tyrosine (Try, Y)
Polar Acidic Amino Acids Polar Basic Amino Acid
Glutamic Acid (Glu, E) Aspartic Acid (Asp, D)

Lysine (Lys, K) Histidine (His, H) Arginine (Arg, R)
Humans can synthesize only 10 of the 20 amino acids needed for proteins. The remaining 10,
called essential amino acids, must be obtained from the diet and consumed on a regular, almost daily
basis. Diets that include animal products readily supply all of the needed amino acids. Since no one plant
source has sufficient amount amounts of all the essential amino acids, vegetarian diets must be carefully
balanced. Grains-wheat, rice, and corn-are low in lysine, and legumes-beans, peas, and peanuts-are low
in methionine, nut a combination of these foods provides all the needed amino acids.
Stereochemistry of Amino Acids
All amino acids have a chirality center (except for glycine)- a carbon bonded to four different
groups- on α carbon. Thus, amino acids like alanine (R=CH3) has two possible has two possible
enantiomers, draws below in both in three-dimensional representations with wedges and dashed bonds,
and Fischer projections.
Naturally occurring enantiomer

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• L-Amino acids have the –NH3+ group on the left side in the Fischer projection. Common naturally
occurring amino acids are L- isomers.
• D-Amino acids have the –NH3+ group on the right side in the Fischer projection. D- Amino acids
occur infrequently in nature.
4.3 ACID-BASE BEHAVIOR OF AMINO ACIDS
An amino acid contains both a basic amino group (NH 2) and an acidic carbonyl group (COOH).
As a result, proton transfer from the acid to the base forms a zwitterion, a salt that contains both positive
and a negative charge. The zwitterion is neutral: that is, the net charge on the salt is zero.
The lone pair can
bond to a proton
zwitterion
The carboxyl group can donate a proton

An amino acid can exist in different forms, depending on the pH of the aqueous solution in which it is
dissolved. When pH of a solution is around 6, alanine (R=CH 3) and other neutral amino acids exist in
their zwitterionic form (A), having no net charge. In this form, the carboxyl group bears a net charge—it
is a carboxylate anion—and the amino group bears a net positive charge (NH 4+).
alanine-no net charge

A (pH=6)
When strong acid is added to lower the pH 2 or less, the carboxylate anion gains a proton and the amino
acid has a net positive charge (form B).
The carboxylate anion picks up a proton.
Adding acid:
Overall +1 charge
A B
When strong base is added to A to raise the pH to 10or higher, the ammonium cation loses a proton and
the amino acid has a net negative charge (from C).
The ammonium cation loses a proton.

Adding base:
Overall -1 charge
A C
Thus, alanine exists in one three different in one of three different forms depending on the pH in
which it is dissolved. At the physiological pH of 7.4, neutral amino acids are primarily in their zwitterions.
• The pH at which the amino acid exists primarily in its neutral from is called its isoelectric point,
abbreviated as pI.
The isoelectric points of neutral amino acids are generally around 6. Acidic amino acids which have an
additional carboxyl group that can lose a proton, have lower pI values (around 3). The three basic amino
acids, which have an additional basic nitrogen atom that can accept proton, have higher pI values (7.7-
10.8)
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Sample Problem
Draw the structure of the amino acid glycine at each pH: (a) 6; (b) 2; (c) 11.
Solution
(a) At pH=6, the neutral, (b) at pH=2, glycine has a net (c) At pH = 11, glycine has a
zwitterionic form of glycine +1 charge. net -1 charge.
predominates.
4.4 PEPTIDES
When amino acids are joined together by amide bonds, they form larger molecules called
peptides and proteins.
• A dipeptide has two amino acids joined together by one amide bond.
• A tripeptide has three amino acids joined together by two amide bond
(Amide bonds are

shown in red)
Polypeptides and proteins both have many amino acids joined together in long linear chains, but the
term protein is usually reserved for polymers of more than 40 amino acids.
• The amide bonds in peptides and proteins are called peptide bonds.
• The individual amino acids are called amino acids residues.
To form a dipeptide, the –NH3+ group of one amino acid forms an amide bond with the carboxylate
(–COO-) of another amino acid, and the elements of H 2O are removed. Because each amino acid
has both functional groups, two different dipeptides cab ne formed. This is illustrated with alanine (Ala)
and serine (Ser) to from dipeptides A and B.
1. The –COO- group of alanine can combine with the –NH3+ group of serine.
new amide bond
reacting functional groups

2. The –COO- group serine can be combine with –NH3+ group of alanine.
new amide bond
reacting functional groups
Dipeptides A and B are constitutional isomers of each other. Both have an ammonium cation
(–NH3+) at one end of their chains and a carboxylate anion (–COO-) at the other.
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• The amino acid with the free –NH3 group on the α carbon is called the N-terminal amino acid.
+
• The amino acid with the free –COO- group on the α carbon is called the C-terminal amino acid.
By convention, the N-terminal amino acid is always written as the left end of the chain and the C-terminal
amino acid at the right.
B
A
• Name all other amino acids from left to right as substituents of the C-terminal amino acid. Change
the –ine or –ic ending of the amino acid name to the suffix-yl.
Thus, peptide A, which has serine as its C-terminal amino acid, is named as alanylserine (Ala-Ser).
Peptide B, which has alanine as its C-terminal amino acid, is named as serylalanine (Ser-Ala).
4.5 BIOLOGICALLY ACTIVE PEPTIDES
Many relatively simple peptides have important biological functions.
Enkephalins, pentapeptides synthesized in the brain, act as pain killers and sedatives by binding
to pain receptors. Two enkephalins that differs in the identity of only one amino acid are known. Met-
enkephalins contains a C-terminal methionine residue, whike leu-enkephalin contains a C-terminal
leucine.
Tyr-Gly-Gly-Phe-Met Tyr-Gly-Gly-Phe-Leu
Met-enkephalin Leu-enkephalin
The addictive narcotic analgesic morphine and heroin bind to the same receptors as the
enkephalins, and thus produce a similar physiological response. Enkephalins, however, produce only
short-term pain-relieving effects because their peptide bonds are readily hydrolyzed by enzyme in the
brain. Morphine and heroin, on the other hand, are not readily hydrolyzed, do they are biologically active
for a much longer time period.
Enkephalin are related to a group of larger polypeptides called endorphins that contain amino
acids. Endorphins also block pain and are through to produce the feeling of wee-being experience by an
athlete after excessive or strenuous exercise.
Peptide Hormones
Oxytoxin and vasopressin are cyclic nonapeptide hormones secreted by the pituitary
gland. Their sequences are identical except for two amino acids, yet this is enough to give them very
different biological activities.
Oxytoxin stimulates the contraction of uterine muscles, and it initiates the flow of milk in
nursing mothers. Oxytoxin, sold under the trade names Pitocin and Syntocinon, is used to induce labor.
Vasopressin, also called antidiuretic hormone (ADH), targets the kidneys and help to
keep electrolytes in body fluids in the normal range. Vasopressin is secreted when the body is
dehydrated and causes the kidneys to retain fluid, thus decreasing the volume of the urine.
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4.6 FOUR LEVELS OF STRUCTURE OF PROTEINS
Primary Structure of Proteins
The primary structure of a protein is the particular sequence of amino acids that is joined together
by peptide bonds.
The carbonyl carbon of the amide had trigonal planar geometry. All six atoms involved in the
peptide bond lie in the same plane. All bond angles are 120 0 and the C=O and N-H bonds are oriented
1800 from each other. As a result, the backbone of the protein adopts a zigzag arrangement as shown in
the three-dimensional structure of a portion of protein in molecule,
The primary structure of a protein –the exact sequence of amino acids –determines all
properties and function of proteins.
Secondary Structure of Proteins
The three-dimensional arrangement of localized regions of aprotien is called its secondary

structure. These regions arise due to hydrogen bonding between the N-H proton of one amide and the
C=O oxygen of another. Two arrangement that are particularly stable are called the α-helix and the β-
pleated sheet.
α-Helix
The α-helix forms when a peptide chain twists into a right-handed or clockwise spira as shown in the
figure below. Several important features characterize an α-helix.
• Each turn of the helix has 3.6 amino acids.
• The N-H and C=O bonds point along the axis of the helix in opposite directions.
• The C=O group of one amino acid is hydrogen bonded to an N-H group four amino acid residues
farther along the chain.
• The groups of the amino acids extend outward from the core of the helix.
Both the myosin in muscle and the α-keratin in hair are proteins composed entirely of α-helices.
β-Pleated Sheet
The β-pleated sheet forms when two or more peptide chains, called strands, line up side-by-side
as shown in the figure below. All β-pleated sheets have the following characteristics.
• The C=O and N-H bonds lie in the plane of the sheet.
• Hydrogen bonding often occurs between the N-H and C=O groups nearby amino acids residues.
• The R groups are oriented above and below the place of the sheet, and alternate from one side
to the other along a given strand.
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2 Different Illustrations of the α-Helix The β-Pleated Sheet
a. The right handed α- b. the backbone of the c. The β-pleated sheet consists of extend strands of the peptide chains
helix α-helix held together by hydrogen bonding. The C=O and the N-H bonds lie in the
plane sheet, while the R groups alternate above and below the plane.
Tertiary Structure of Proteins
Tertiary protein structure is the overall three-dimensional shape of a protein that results from
the interactions between amino acids chains (R groups) that are widely separated from each other
within a peptide chain.
Interactions Responsible for Tertiary Structure
Four types of attractive interactions contribute to the tertiary structure of a protein:
a) Disulfide Bond, the strongest of the tertiary-structure interactions, results from the –SH
groups of two cysteine residues reacting with each to form a covalent disulfide bond. This type of
interaction is only one of the four tertiary-structure interactions that involves a covalent bond. Disulfide
bond formation may involve two cysteine units in the same peptide chain (an intermolecular disulfide
bond.
Disulfide bonds can form in two different ways
Intermolecular disulfide bond
Insulin, for example, consist of two separate polypeptide chains that are covalently linked by
two intermolecular disulfide bonds. The A chain, which also has an intermolecular bond, has 21 amino
acid residues, whereas the B chain has 30.
interchange disulfide
linkage
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Synthesized by groups of cells in the pancreas called the islets of Langerhans, insulin is the
protein that regulated blood glucose levels.
A relative or complete lack of insulin results in diabetes. Many of the abnormalities associated
with this disease can be controlled by the injection of insulin. Until the recent availability of human
insulin through genetic engineering techniques, all insulin used by diabetics was obtained from pigs
and cattle. The amino acid sequence of these insulin proteins are slightly different from that of human
insulin. Pig insulin differs in one amino acid only, while bovine insulin has three different amino acids.
This is shown in the accompanying table.
Chain A Chain B
Position of Residue → 8 9 10 30
Human insulin Thr Ser Ile Thr
Pig insulin Thr Ser Ile Ala
Bovine insulin Ala Ser Val Ala
b) Electrostatic interactions, also called salt bridges, always involve the interactions between
an acidic side chain (R group) and a basic side chain (R group). The side chains of acidic and basic
amino acids, at the appropriate pH, carry charges, with the acidic side chain being negatively charged
and the basic side chain being positively charged. The side chain charges occur when –COOH group
becomes a –COO- group and when a –NH2 group becomes a –NH3+ group. The interaction between
the two types of side chains is a positive-negative ion-ion attraction.
c) Hydrogen bonds can occur between amino acids with polar R groups. A variety of polar
side chains can be involved, especially those that possess the following functional groups. Hydrogen
bonds are relatively weak and more easily disrupted by changes in pH and temperature.
d) Hydrophobic interactions result when two nonpolar chains are close to each other. In
aqueous solution, globular proteins usually turn their polar groups outward, toward the aqueous
solvent, and their nonpolar groups inward, away from the water molecules. The nonpolar groups prefer
to interact with each other, excluding water from these regions. The result is a series of hydrophobic
interactions. The attractive forces are London forces resulting from the momentary uneven distribution
of electrons within the side chains.
Four types of interactions between
amino R groups produce the
tertiary structure of a protein. (a)
disulfide bonds, (b) electrostatic
interactions (salt bridges), (c)
hydrogen bonds, (d) hydrophobic
interactions.
The stabilizing Interactions in Secondary and Tertiary Protein Structure
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Hydrophobic interaction Hydrophobic interaction
Quaternary Structure of Proteins
Quaternary structure is the highest level of protein organization. It is found only in multimeric
proteins. Such proteins have strictures involving two or more peptide chains that are independent of each
other –that is, not covalently bonded to each other. Quaternary protein structure is the organization
among the various peptide chains in a multimeric protein.
Most multimeric proteins contain an even number of subunits (two subunits= adimer four subunits
= a tetramer, and so on. The subunits are held together mainly by hydrophobic interaction between amino
acid R groups.
An example of a protein with quaternary structure is hemoglobin, the oxygen-carrying protein in
blood.It is a tetramer in which there are two identical α chains and two identical β chains. Each chain
enfolds a heme group, the site where oxygen binds to the protein.
A schematic diagram showing the tertiary The heme group present

and quaternary structure of the oxygen- hemoglobin
carrying protein hemoglobin.
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The Primary, Secondary, Tertiary, and Quaternary Structure of Proteins
Primary protein structure is

sequence of a chain of amino
groups. Tertiary protein structure
occurs when certain
attraction are present
between α helices and
pleated sheets.
Secondary protein structure

occurs when the sequence of
amino acids is linked by hydrogen Quaternary protein structure is a
bonds. protein consisting more than one
amino acid chain.
4.7 PROTEIN CLASSIFICATION BASED ON SHAPE AND FUNCTION
Protein Classification Based on Shape

Based on molecular shape, which is determined primarily by tertiary and quaternary structure
feature, three are three main types of proteins:
a) Fibrous protein is a protein whose molecules have an elongated shape with one dimension
much longer than the others. Fibrous proteins tend to have simple, regular, linear structures, there is
tendency for such proteins to aggregate to form macromolecular structures.
b) Globular protein is a protein whose molecules have peptide chains that are folded into
spherical or globular shapes. The folding in such proteins is such that most of the amino acids with
hydrophobic side chains (nonpolar R groups) are in the interior of the molecule and most of the
hydrophobic side chains (polar groups) are on the outside of the molecule. Generally, globular proteins
are water-soluble substances.
c) Membrane protein is a protein that is found associated with a membrane system of a cell.
Membrane protein structure is somewhat opposite that of globular proteins, with most of the hydrophobic
amino acid side chains oriented outward. Thus, such proteins tend to be water-insoluble and they usually
have fewer hydrophobic amino acids than globular proteins.
Some Common Fibrous and Globular Proteins
Name Occurrence and Function

Fibrous proteins (insoluble)
keratins found in wool, feather, hooves, silk, and fingernails
collagens found in tendons, bones, and other connective tissue
elastins found in blood vessels and ligaments
myosins found in muscle tissue
fibrin found in blood cloths
Globular proteins (soluble)
Insulin regulatory hormone for controlling glucose metabolism
Myoglobin involved in oxygen storage in muscles
hemoglobin involved in oxygen transport in blood
tranferrin involved in iron transport in blood
immunoglobulins involved in immune system responses
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Protein Classification Based on Function
Proteins play crucial roles in almost all biochemical process. The diversity of functions exhibited by
proteins far exceeds that of other major types of biochemical molecules. The functional versatility of proteins
stems from (1) their ability to bind small molecules specifically and strongly to themselves, (2) their ability to
bind other protein, often other like proteins, to from fiber-like structures, and (3) their ability to bind to, and
other become integrated into, cell membranes.
The following list gives a number of the major categories based on function.
1.Catalytic proteins. Proteins are probably best known for their role as catalysts. Proteins with the role
of biochemical catalysts are called enzymes. Enzymes participate in almost all of the metabolic reactions that
occur in cells.
2. Defense proteins. These proteins, also called immunoglobulins or antibodies, are central to the
functioning of the body’s immune system. They bind to foreign substances, such as bacteria and viruses, to
help combat invasion of the body by foreign particles.
3. Transport proteins. These proteins bind to particular small biomolecules and transport them to other
locations in the body and then release the small molecules as needed at the destination location. The most
well-known example of a transport protein is hemoglobin, which carries oxygen form the lungs to other organ
tissues. Another transport protein is transferrin, which carries iron from the liver to the bone marrow.
4. Messenger proteins. These proteins transmit signals to coordinate biochemical processes between
different cells, tissues, and organs. A number of hormones that regulate body processes are messenger
proteins, including insulin and glucagon. Human growth hormone is another example of a messenger protein.
5. Contractile proteins. These proteins are necessary for all forms of movement. Muscles are composed
of filament-like contractile protein that, in response to nerve stimuli, undergo conformation changes that
involve contraction and extension. Actin and myosin are examples of sperm. Sperm can “swim” because of
long flagella made up of contractile proteins.
6. Structural proteins. These proteins confer stiffness and rigidity to otherwise fluid like biochemical
systems. Collagen is a component of cartilage and α keratin gives mechanical strength as well as protective
covering to hair, fingernails, feather, hooves, and some animal cells.
7. Transmembrane proteins. These proteins, which span a cell membrane help control the movement
of small molecules and ions through the cell membrane. Many such proteins have channels through which
molecules can enter and exit a cell. Such protein channels are very selective, often allowing passage just one
type of molecules or ion
.
8. Storage proteins. These proteins bind (and store) small molecules for future use. During degradation
of hemoglobin the iron atoms present are released and becomepart of ferritin, an iron-storage protein, which
saves the iron for use in the biosynthesis of new hemoglobin molecules. Myoglobin is an oxygen-storage
protein present in muscles; the oxygen so stored is reserve oxygen source fro working muscle.
9. Regulatory proteins. These proteins are often forum “embedded in the exterior surface of cell
membranes. They act as sites at which messenger molecules, including messenger proteins such as insulin,
can bind and thereby initiate the effect that the messenger “carries”. Regulatory protein are often the
molecules that bind to enzymes (catalytic proteins), thereby turning them “on” “off”, and thus controlling
enzymatic action.
10. Nutrient proteins. These proteins are particularly important in the early stages of life, from embryo
to infant. Casein, found in milk, and ovalbumin, found in egg white, are two examples of such proteins. The
role of milk in nature is to nourish and provide immunological protection for mammalian young. Three-fourths
of the protein in milk is casein. Over 505 of the protein in egg white is ovalbumin.
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4.8 PROTEIN HYDROLYSIS AND DENATURATION
Protein Hydrolysis
Like other amide bonds, the peptide bonds in proteins are hydrolyzed by treatment with aqueous acid,
base, or certain enzymes
• The hydrolysis of the amide bonds in a protein forms the individual amino acids that comprise the
primary structure.
For example, hydrolysis of the amide bonds in the tripeptide Ile-Gly-Phe forms the amino acids isoleucine,
glycine, and phenylalanine. When each amide bond is broken, the elements of H2O are added, forming a
carboxylate anion (–COO-) in one amino acid and an ammonium cation (–NH3+) in the other.
Break the peptide bonds
The first step in the digestion of dietary protein ins hydrolysis of the amide bonds of the protein backbone.
The enzyme pepsin in the acidic gastric juices of the stomach cleaves some of the amide bonds to form
smaller peptides, which into the small intestines and are further broken down into individual amino acids by
the enzymes- trypsin and chymotrypsin.
Proteins in the diet serve a variety of nutritional need. Like carbohydrates and lipids, proteins can be
metabolized for energy. Moreover, the individual amino acids formed by hydrolysis are used as starting
materials to make new proteins that the body need. Likewise, the N atoms in the amino acids are incorporated
into other biomolecules that contain nitrogen.
Protein Denaturation
When the secondary, tertiary, or quaternary structure of a protein is disturbed, the properties of a protein
are also altered and the biological activity is often lost.
• Denaturation is the process of altering the shape of a protein without breaking the amide bonds
that form the primary structure.
High temperature, acid, base, and even agitation can disrupt the noncovalent interactions that hold a
protein in a specific shape. Heat breaks up weak London forces beaten nonpolar amino acids. Heat, acid,
and base disrupt hydrogen bonding interactions between polar amino acids, which account for much of the
secondary and tertiary structure. As a result, denaturation causes a globular protein to uncoil into an undefined
randomly lopped structure.
Loose coils
and loops
Coiled globular protein
Denaturation often makes proteins less water soluble. Globular proteins are typically folded with
hydrophobic regions in the interior to maximize the interaction of polar residues on the outside surface
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with water. This makes them water soluble. When the protein is denatured, more hydrophobic regions
are exposed and the protein often loses water solubility.
We witness examples of protein denaturation in the kitchen. As milk ages it becomes sour from
enzymes than produce lactic acid. The acid also denatures milk proteins, which precipitate as an insoluble
curd. Ovalbumin, the major protein in egg white, is denatures when egg is boiled or fried, forming a solid.
Even vigorously whipping eggs whites denatures its protein, forming the stiff meringue used to top a
lemon meringue pie.
Selected Physical and Chemical Denaturing Agents
Denaturing Agent Mode of Action

heat Disrupts hydrogen bonds by making molecules vibrate too
violently; produces coagulation, as in the frying of an egg
Microwave radiation Causes violent vibrations of molecules that disrupt hydrogen
bonds
Ultraviolent radiation Operates very similarly to the action of heat (e.g., sun burning)
Violent whipping or shaking Causes molecules in globular shapes to extend to longer lengths,
which then entangle (e.g., beating egg white into meringue)
detergent Affects R-group
Organic solvents (e.g., Interfere with R-group interactions because these solvents also
ethanol, 2-propanol, acetone) can form hydrogen bonds; quickly denature proteins in bacteria,
killing then(e.g., disinfectant action of 70% ethanol)
Strong acids and bases Disrupt hydrogen bonds and salt bridges; prolonged action leads
to actual hydrolysis of peptide bonds
Salts of heavy metals (e.g., Metal ions combine with –SH groups and from poisonous salts
salts of Hg2+, Ag+, Pb2+)
Reducing agents Reduce disulfide linkages to produce –SH groups
VI. LEARNING ACTIVITIES
Identify at least 5 essential amino acids and their role/function(s) in the human body?
VII. EVALUATION (On separate sheet)
VIII. ASSIGNMENT
What are the structural differences between oxytocin and vasopressin? How do they differ in
physiological function?
Note: Limit your discussions in 1 (short) bond paper only.
IX. REFERENCES
1. Campbell, M.K., Farrell, S.O., 2010. Biochemistry, 7th Edition, Belmont, California, USA: Brooks/Cole
2. Smith, J.G., (2010). General, Organic, and Biological Chemistry. McGraw Hill Education
3. Voet,J., Voet, J.D., Pratt, C.W. 2013. Fundamentals of Biochemistry-Life at the Molecular Level, 4th
Edition. Rosewood Drive, Danvers, Ma, USA: John Wiley & Sons Inc.
NVSU-FR-ICD-05-00 (081220)
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Im-4 Genbiochem1

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Republic of the Philippines

NUEVA VIZCAYA STATE UNIVERSITY

COLLEGE OF ARTS AND SCIENCES

I. CHAPTER 4: AMINO ACIDS AND PROTEINS

II. LESSON TITLE: Amino Acids and Proteins

III. LESSON OVERVIEW

IV. DESIRED LEARNING OUTCOMES

At the end of the chapter, students should be able to:

Recommneded Daily Protein Intake

Group Daily Protein Intake (g protein/kg body weight)

4.2 AMINO ACIDS

General Features of Amino Acids

Amino group Carboxyl group

This neutral form of an amino a salt

20 Common Naturally Occurring Amino Acids

Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L)

Serine (Ser, S) Threonine (Thr, T) Aspargine (Asn, N) Glutamine (Gln, Q)

Polar Acidic Amino Acids Polar Basic Amino Acid

Glutamic Acid (Glu, E) Aspartic Acid (Asp, D)

Naturally occurring enantiomer

4.3 ACID-BASE BEHAVIOR OF AMINO ACIDS

The carboxyl group can donate a proton

alanine-no net charge

The ammonium cation loses a proton.

(Amide bonds are

reacting functional groups

reacting functional groups

4.5 BIOLOGICALLY ACTIVE PEPTIDES

Many relatively simple peptides have important biological functions.

Primary Structure of Proteins

Secondary Structure of Proteins

The three-dimensional arrangement of localized regions of aprotien is called its secondary

Tertiary Structure of Proteins

Interactions Responsible for Tertiary Structure

Four types of attractive interactions contribute to the tertiary structure of a protein:

Disulfide bonds can form in two different ways

Intermolecular disulfide bond

The stabilizing Interactions in Secondary and Tertiary Protein Structure

Hydrophobic interaction Hydrophobic interaction

Quaternary Structure of Proteins

A schematic diagram showing the tertiary The heme group present

Primary protein structure is

Secondary protein structure

4.7 PROTEIN CLASSIFICATION BASED ON SHAPE AND FUNCTION

Protein Classification Based on Shape

Some Common Fibrous and Globular Proteins

Name Occurrence and Function

Break the peptide bonds

Coiled globular protein

Denaturing Agent Mode of Action

VI. LEARNING ACTIVITIES

VII. EVALUATION (On separate sheet)

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