PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
PROTEINS
● Greek word proteios meaning “of
first importance”
● provide structure in membranes
● build cartilage, connective tissues
● transport oxygen in blood, muscle
● direct biological reactions as
enzymes
● defend the body against infection
● control metabolic process as
hormones
● provides nitrogen and sulfur, unlike
fats and carbohydrates
● most abundant cellular component
AMINO ACIDS
● monomer unit of proteins
● 20 structurally similar amino acids
● α-amino acids
○ have carboxyl group and
amino acid bonded to same
carbon (α-carbon)
○ only differ in R group
○ R group vary in structure,
size, electric charge, and
solubility of AA in water
OPTICAL ISOMERISM
● α-carbon is chiral center
● four different groups bonded
○ carboxyl group
○ amino group
○ R group
○ hydrogen atom
● all AA except glycine are chiral and
optically active
● two possible stereoisomers, L & D
● the nonsuperposable mirror image
forms are enantiomers
● all AA in proteins in our body are
L-isomer
● D AAs are extremely rare; cell
walls of a few types of bacteria
● L-isomer if NH3 at the left
● D-isomer if NH3 at the right
CLASSIFICATION OF AMINO ACIDS
● grouped into five main classes
based on properties of R groups
● specifically their polarity, or
tendency to interact with water at
biological pH (near pH 7.0)
● Nonpolar, Aliphatic R Groups
○ side chains of alanine,
valine, leucine, isoleucine
cluster together within
proteins, stabilizing protein
structure by means of
hydrophobic interactions
○ glycine, simplest structure,
small side chain has no
real contribution to
hydrophobic interactions
○ methionine contains
sulfur, has nonpolar
thioether group on its side
chain
○ proline has an aliphatic
side chain with distinct
cyclic structure, the
secondary imino group of
proline residues reduces
the structural flexibility in
polypeptide regions that
contain proline
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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
○ polarity of cysteine
contributed by sulfhydryl
group; a weak acid makes
weak H bond with O and N
○ cysteine is oxidized to form
covalently linked dimeric
AA cystine (two cystine
are joined by disulfide
bond)

● Aromatic R Groups
○ has aromatic side chains
○ relatively nonpolar
○ hydroxyl group of tyrosine
can form H bonds, which is
an important functional
group in some enzymes
○ tyrosine and tryptophan
are significantly more
polar than phenylalanine,
● Positively Charged R Groups
due to tyrosine hydroxyl
○ basic, most hydrophilic
group and nitrogen of
○ positive charge at pH 7.0
tryptophan indole ring
○ lysine has second primary
amino group at the ϵ
position on aliphatic chain
○ arginine has + charged
guanidinium group
○ histidine has aromatic
imidazole group
○ histidine may be positively
charged or uncharged at ph
7.0 due to ionizable side
chain pKa near neutrality,
thus can be proton donor or
acceptor in reactions
● Polar, Uncharged R Groups
○ more soluble in water,
since they contain
functional groups that form
H bonds with water
○ polarity of serine and
threonine contributed by
hydroxyl groups
○ asparagine and glutamate
are amides of aspartate
and glutamate which are
hydrolyzed by acid or base
● Negatively Charged R Groups

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
○ acidic, most hydrophilic (vegetable source), usually lysine,
○ negative charge at pH 7.0 tryptophan, or methionine
○ aspartate and glutamate
have second carboxyl
group

NONSTANDARD AMINO ACID

● 20 amino acids are standard AA
● nonstandard amino acids are
residues that have been
chemically modified after
incorporated in a polypeptide;
amino acids that occur in living
organism but not found in proteins
ESSENTIAL AMINO ACIDS ● 4-hydroxyproline, 5-hydroxylysine
○ structural constituent of
● 20 amino acids but 10 can be fibrous protein collagen
synthesized by our body, ○ most abundant protein in
● nonessential amino acids if we mammals
don't need to get it from food
● essential amino acids if it must
be obtain from proteins in diet
● 10 essential amino acids
○ Phenylalanine
○ Valine
○ Threonine
○ Tryptophan
○ Isoleucine
○ Methionine
○ Histidine
○ Arginine
○ Leucine ● γ-carboxyglutamic acid
○ Lysine ○ constituent of several
proteins involved in blood
clotting

COMPLEMENTARY PROTEINS
● complementary protein foods
contain all essential amino acid in
proper amount (animal source)
● incomplete protein is low in one
or more of essential amino acid

● O-phosphoserine
○ presence of P regulates the
activity of proteins

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
● cystine
○ made of two cysteine joined
by disulfide bond
○ the bond play special role in
structure of many proteins
(e.g. hair) by forming
covalent cross-links
● ornithine, citrulline
○ metabolites of urea cycle
ISOELECTRIC POINT
● zwitterion
○ AA lacks ionizable R group
○ dissolved in water at
neutral pH
○ exist as dipolar ion in soln.
● isoelectric point
○ pH of AA at zwitterion form
○ at this pH, molecule is
neutral
● zwitterions can act as acid and
base when placed below or above
their isoelectric point
● having this dual (acid-base) are
amphoteric and called
ampholytes
● when acid is added to zwitterion,
zwitterion picks up H+ and
becomes positive ion
●
● when base is added to zwitterion,
OH- is neutralized by H+ and
becomes negative ion
FORMATION OF PEPTIDE
● peptide bond
○ a chain of AA held by
peptide or amide bonds
○ occur between carboxylic
group and amino of
different AA with H2O loss
○ AA units that remain after
peptide bond formed is
amino acid residue
○ dipeptide (two AA),
tripeptide (three AA),
tetrapeptide (four AA),
polypeptide (long AA)
● N-terminal end is free amino group
(NH3+), while C-terminal is end
with free carboxyl group (COO-)
● repeating chain of amide linkage is
called backbone of the protein
● amino side chains are called
substituents of the backbone
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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
NAMING OF PEPTIDE
● all AA end with -yl (except C
terminal AA)
● named as one word
● peptide
○ AA polymer of short
chain length
● polypeptide
○ AA polymer polymer of
intermediate chain length
(up to 50 AA residues)
● protein
○ AA polymer of more than
50 AAs
● amino acid residue
○ AA part of protein chain
● N-terminal residue
○ AA on end chain that has
free amino group
● C-terminal residue
○ AA on end chain that has
free carboxylate group
BIOLOGICALLY IMPORTANT PEPTIDES
● glutathione
○ γ-glutamyl-L-cysteinylglycine
○ a tripeptide
○ contains γ-glutamate
○ found in almost all organism
○ protein and DNA synthesis
○ drug and environment toxin
metabolism
○ amino acid transport
○ a reducing agent
● oxytocin, vasopressin
○ AA sequences differ only
by two residues (3 ile-phe,
and 8 leu-arg)
○ both nonapeptide and
produced in hypothalamus
○ after synthesis, transported
down nerve tracts to
posterior pituitary gland,
where it is stored
○ secreted in response to
signals from hypothalamus
oxytocin
○ stimulate contraction of
uterine muscles during
childbirth
○ stimulates ejection of milk
by mammary glands during
lactation
○ in males, regulatory role in
synthesis of testosterone
○ has mild antidiuretic activity
vasopressin
○ also known as antidiuretic
hormone (ADH)
○ secreted in response to low
blood pressure or high
blood Na+ conc.
○ act by stimulating kidneys
to retain water
○ has some oxytocin like
activity
● met-enkephalin, leu-enkephalin
○ belong to a group of
peptides called opioid
peptides; molecules that
relieve pain and produce
pleasant sensations
○ found predominantly in
tissue cells
○ pentapeptide, differs only in
C-terminal AA residues
● atrial natriuretic factor,
Substance P, Bradykinin
○ has opposing functions
atrial natriuretic factor
○ produced by specialized
cells in heart and nervous
system
○ stimulates production of
dilute urine (opposite of
vasopressin)
Substance P, Bradykinin
○ stimulate perception of pain
(opposite of opioid peptide)
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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
POLYPEPTIDES IN THE BODY
● enkephalins and endorphins
○ natural painkillers
produced in the body
○ polypeptides that bind to
receptors in brain to give
relief from pain
● enkephalins
○ found in thalamus and
spinal cord
○ smallest molecule with
opiate activity
○ AA sequence of met-
enkephalin found in
longer AA of endorphins
● endorphins
○ prevents the release of
substance P
four types:
○ α-endorphin (16 AA)
○ β-endorphin (31 AA)
○ γ-endorphin (17 AA)
○ δ-endorphin (27 AA)
LEVELS OF PROTEIN STRUCTURE
● Primary Structure
○ sequence of AA linked by
peptide bonds
● Secondary Structure
○ various ways that proteins
fold into shapes essential
for their function
● Tertiary Structure
○ various ways that proteins
fold into shapes essential
for their function
● Quaternary Structure
○ various ways that proteins
fold into shapes essential
for their function
PRIMARY STRUCTURE
● proteins’ AA sequence that
determines its overall shape,
function, and properties
● translation of information
contained in genes
● each protein has different
primary structure with different
AA in different places along the
chain
● change of only one AA out of
several hundreds can drastically
alter protein’s biological
properties (example below)
SICKLE CELL ANEMIA
● RBCs assume a sickle shape
● due to substitution of AA in primary
structure (Glu → Val)
● caused by defective (mutant)
hemoglobin
● in β-chain of HbS, valine replaces
glutamic acid
● carries oxygen well, but when
deoxygenated, HbS changes
shape and bind with other HbS
protein to form long polymer that
distort RBC to crescent shape
● occurs when individual inherit gene
for HbS from both parents
● sickle cells get stuck in capillaries,
which can clog blood flow and
result in damage to many organs
especially bone and kidney
● causes anemia; deficiency in RBC
● people with sickle cell has less
severity of malaria
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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
AMINO ACID SEQUENCING
1. Cleavage of all disulfide bonds 4. Cleavage of polypeptide in
- oxidation with performic acid is fragments
commonly used - long polypeptides cannot be directly
2. Determination of N-terminal AA sequenced, thus its broken in smaller
- several methods are available to peptides
determine the N-terminal AA - use of several reagents cuts chain at
● Sanger’s Method different sites, creates overlapping sets of
○ polypeptide chain reacts w/ fragments
1-fluoro-2,4-dinitrobenzene ● Trypsin
(DNFB) ○ pancreatic enzyme (most
reliable)
○ cleaves arg and lys (AA1)
● Chymotrypsin
○ pancreatic enzyme
○ cleaves phe, try, trp (AA1)
● Pepsin
○ cleaves phe, tyr, trp, asp
glu, ile (AA2)
○dinitrophenyl (DNP) is ● Cyanogen Bromide
isolated ○ cleaves met (AA1)
● Edman degradation
○ uses phenylisothiocyanate
(PITC), often referred to as
Edman’s reagent

5. Ordering the polypeptide fragments

- AA sequence information derived from
two or more sets of polypeptide fragments
are examined for overlapping segments

Significance of sequence analysis

○ cleaves the N-terminal
1. essential for understanding the protein’s
phenylthiohydantoin
mechanism of action (biological activity)
residue derivative
2. important for the study of gene structure
○ carried out by using a
3. recognition of amino acid sequence has
computer - programmed
led to the chemical synthesis of medically
machine called
useful polypeptide
sequenator
3. Determination of C-terminal AA
- enzymes called carboxypeptidases are
used to identify C-terminal residue PEPTIDE BOND IS RIGID & PLANAR
- secreted by pancreas, hydrolyze ● α-carbons of adjacent AA residues
peptides one residue at a time from the C- are separated by three covalent
terminal end bonds, Cα-C-N-Cα
● Carboxypeptidase A
○ cleaves peptide bonds
when an aromatic AA is the
C-terminal residue
● Carboxypeptidase B
○ cleaves basic AA residues

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
● nitrogen and carboxyl group
(peptide bond) are coplanar
● six atoms in single plane on each
side of Cα
● no free rotation in peptide bond
(rigid), but bonds coming from Cα
atom can rotate
● phi (Φ) and psi (ψ) are dihedral
angles (angle between two
intersecting plane)
● for Φ and ψ remove atoms that are
not included (free amino group and
free carboxylic group)
● phi (Φ)
○ rotation occur around N-Cα
○ H point to the left, CH3
point to the right
○ O moves
● psi (ψ)
○ rotation occur around Cα-C
○ H point to the right, CH3
point to the left
○ N moves
● both Φ and ψ are defined at ±180°
when polypeptide is fully extended
and all peptide groups are in the
same plane
● increases 0° to 180° clockwise
from starting position until 6 clock
hand
● increases -180° to 0° clockwise
from 6 clock hand to starting
position
● Ramachandran plot
○ defined by values of Φ & ψ
○ predicts what secondary
structure of AA
○ dark blue represents
conformations that involve
no steric overlap thus fully
allowed
○ medium blue indicates
conformations allowed at
extreme limits for
unfavored atomic contacts
○ light blue indicates
conformations that are
permissible if a little
flexibility is allowed in the
dihedral angles
○ yellow regions are
conformations not allowed
SECONDARY STRUCTURE
● local conformation of some parts of
a polypeptide chain
● result of H bonding between amide
hydrogen and carbonyl oxygen of
peptide bonds
● different regions of protein may
have different type of secondary
structure (arrow = β-pleated sheet,
coil = α-helix)
● α-helix and β-pleated sheet most
common because they maximize H
bonding in backbone (triple helix
not common)

α-helix

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
● most common type ○ disulfide bond broken with
● backbone forms spiral shape with reducing agent (performic
3.6 AA per turn of helix acid)
● amide group interact with another ○ oxidizing agent form new
amide group 3 residues above and disulfide bond (curly hair)
3 residues below, locking to place
● because of many H bonds in the
polypeptide, the chain is pulled into
coil looking like spring / phone cord
● R groups pointing out

● myosin
○ one of the major muscle
proteins
○ rodlike structure
○ two α-helices coiled around
one another
● fibrous proteins β-pleated sheet
○ structural proteins arranged ● two or more polypeptide chain
in fibers or sheets segments line side by side
○ has only one type of 2° ● individual segment is β-strand
○ e.g α-keratin; covering of ● all carbonyl oxygen and amide
most land animals hydrogens involved in H bond
● α-keratin ● backbone near complete extended
○ hair example of structure ● two orientations:
○ hair proteins consist almost parallel β-pleated sheet (N-
only of polypeptide chains termini head to head) and
coiled up into into α-helices antiparallel β-pleated sheet (N-
○ three single α-helices coil terminus aligned to C-terminus)
into bundle to give
protofibril;a three stranded
superstructure
○ protofibril part of an array
microfibril; resembles
“molecular pigtails” that
possess great mechanical
strength & insoluble in H2O
○ major structural property of
coiled coil superstructure of
α-helices is its mechanical
strength
permanent waving process
○ disulfide bridge of hair
changed
○ hair strands arranged in
desired shape

● antiparallel β-pleated sheet more

stable than parallel β-pleated sheet

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
more stable than because fully ● type I occurs more than twice as
colinear H bond form frequently as type II
● silk fibroin ● type
○ fibrous protein composed
of antiparallel β-pleated
sheet
● fibroin
○ protein of silk
○ polypeptide chains many in
β conformation
○ rich in Ala and Gly residue
thus closed packed β
sheets, interlock R groups
arrangement residue
○ stabilized by H bonding ● γ-turn
among peptide linkages turn
and Van der Waals with
○ silk doesn’t stretch since H
highly extended already bond
○ flexible due to weak
interactions unlike covalent
bond such as disulfide
bond in α-keratin

between first and third residue

triple helix
● strong structure
● three helical polypeptides woven
together like a braid to form
tropocollagen; a triple helix
● only found in collagen
● collagen
○ most abundant protein in
β-turns body (25%-35)
● ⅓ structural element of globular ○ found in connective tissue,
proteins is β-turns blood vessels, skin,
● consist of four AA residue tendons, ligaments, cornea
● carbonyl C of one residue is H- of eye, and cartilage
bonded to the amide proton of a
residue three residues away
● central two central residues don’t
participate interresidue H bonding
● rich in gly (gives flexibility) and pro
(controls rigidity movement)

● Vit C in collagen metabolism

○ collagen has gly, pro, ala
(high) and hydroxyproline,
hydroxylsine(small amount)
● type I and II β-turns are most ○ hydroxyls contain groups
common that form more H bonds in

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
peptide chains to give
strength to collagen triple
helix
○ collagen fibrils weak if diet
is low in Vit C since
enzyme form hydroxyls
need it (lesser groups,
lesser H bonding between
collagen fibrils)
○ when person ages,
collagen is less elastic due
to additional cross link form
between fibrils
TERTIARY STRUCTURE
● three-dimensional structure
● complete folding pattern
interactions that stabilize
● Van der Waals force
○ R groups of nonpolar AA
● Hydrogen bond
○ R groups of polar AA (has
OH in R group)
● Ionic bond (Salt bridge)
○ acidic and basic R group
● Covalent bond
○ thiol-containing AA
(cysteine only)
- hydrophobic residues in interior
- hydrophilic residues in exterior
- disulfide bond of cysteine can be cross-
link between different proteins, or tie two
segments within protein together
● myoglobin
○ small, oxygen-binding
protein of muscle cells
○ functions to store oxygen
and facilitate oxygen
diffusion in rapidly
contracting muscle tissue
(allows diving mammals to
remain submerged for a
long time)
○ contains single polypeptide
chain of 153 AA residues
and a heme group
○ abundant in muscles of
diving mammals; so
abundant muscle is brown
● hemoglobin
○ same heme group from
myoglobin found here
○ oxygen-binding protein of
erythrocytes
● heme group
○ single iron protoporphyrin
○ responsible for deep red-
brown color of myoglobin
and hemoglobin
QUARTERNARY STRUCTURE
● two or more polypeptide chain
● involves the combination of
different polypeptide chains that
combine to form a single structure
● chains are kept together by all the
types of bonds mentioned in
tertiary structure
● hemoglobin
○ example of 4° structure
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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
○ two identical α and β sub- Classification of proteins (composition)
units
● collagen
○ protein with quaternary
structure
● prosthetic group
○ nonprotein group that some
functional protein bind to
○ e.g. glycoproteins have
sugar groups attached
○ e.g. hemoglobin binded to
heme group simple protein - no prosthetic group
conjugated protein - has prosthetic group

Classification of proteins (function)

CLASSIFICATION OF PROTEINS
● Fibrous proteins
○ also structural proteins
○ long and narrow DENATURATION OF PROTEINS
○ insoluble in water ● unfolding of native confirmation of
○ involved in structure, protein (disrupt interactions
support, and movement between R groups that stabilize 2°,
○ include: 3°, and 4°)
■ α-keratins, ● covalent amide bonds of primary
■ β-pleated sheet of: structure not affected
➢ silk fibroin Temperature
➢ collagen ● disrupt weak interactions like H
bonds and hydrophobic interaction
● can cause coagulation (e.g. egg:
from viscous solution to solid)

● pH
○disrupt salt bridges
● Globular proteins ○blood pH drops too low,
○ functional globular proteins blood protein becomes
○ only when four peptides polycation
bound to one another is the ○ blood pH rise too high,
protein molecule functional blood protein becomes
○ round polyanion
○ soluble in water ● Organic Solvents
○ function in cells as ○ disrupt H bonds
enzymes, hormones, and ○ nonpolar regions of
antibodies solvents interfere with

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PROTEINS
Biochemistry for Health Sciences (Lecture)
CHM042 Block 160 | PROF. Luisita S. Cabanos | SEM 1 2022
hydrophobic interactions in
interior of protein
● Detergents
○ disrupt hydrophobic
interaction, causing protein
chain to unfold
● Heavy Metals
○ react with disulfide bonds
and acidic amino acid
● Agitation
○ stretches protein until
cross-links break form solid
● Mechanical Stress
○ disrupt weak interactions
that maintain protein
conformation

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