Proteins

PROTEINS (1)
Dr. Aileen B. Angcajas October 2022

Department of Chemistry
College of Science and Mathematics
MSU-Iligan Institute of Technology
Iligan City
Characteristics of Proteins
A protein is a naturally-occurring, unbranched polymer in
which the monomer units are amino acids.
Specific definition: A protein is a peptide in which at least

40 amino acid residues are present:
– The terms polypeptide and protein are often used
interchangeably to describe a protein
– Several proteins with >10,000 amino acid residues are
known
– Common proteins contain 400–500 amino acid residues
– Small proteins contain 40–100 amino acid residues
BIOCHEMISTRY I ABA, Oct 2022 | Page 2
Protein Classification Based on Chemical
Composition
Simple proteins
A protein in which only amino acid residues are present:

– More than one protein subunit may be present but all
subunits contain only amino acids
Albuminoids - keratin in skin, hair, nails; collagen in
cartilage
Albumins - egg albumin, serum albumin
Globulins - antibodies
Histones - chromatin in chromosomes
Protein Classification Based on Chemical
Composition
Conjugated (complex) proteins
A protein that has one or more non-amino acid entities

(prosthetic groups) present in its structure: Prosthetic
group may be organic or inorganic

Protein Classification Based on Shape
Fibrous Proteins: Alpha-Keratin & Collagen
The polypeptide chains are arranged in long strands or

sheets
• Have long, rod-shaped or string-like molecules that can
intertwine with one another and form strong fibers;
water-insoluble
• Structural functions

Protein Classification Based on Shape
Globular Proteins: Myoglobin & Hemoglobin
The polypeptide chains are folded into spherical or globular

shapes
• Nonpolar amino acids are in the interior, polar amino
acids are on the surface
• Water-soluble which allows them to travel through the
blood and other body fluids to sites where their activity is
needed
• Dynamic functions

Major Categories of Proteins Based on Function
• Catalytic proteins: Enzymes are best known for their catalytic role.
– Almost every chemical reaction in the body is driven by an
enzyme
• Defense proteins: Immunoglobulins or antibodies are central to
functioning of the body’s immune system.
• Transport proteins: Bind small biomolecules, e.g., oxygen and
other ligands, and transport them to other locations in the body
and release them on demand.
• Messenger proteins: transmit signals to coordinate biochemical
processes between different cells, tissues, and organs.
– Insulin and glucagon - regulate carbohydrate metabolism
– Human growth hormone – regulate body growth

•Contractile proteins: Necessary for all forms of movement.
– Muscles contain filament-like contractile proteins (actin and
myosin).
– Human reproduction depends on the movement of sperm –
possible because of contractile proteins.
• Structural proteins: Confer stiffness and rigidity
– Collagen is a component of cartilage
– Keratin gives mechanical strength as well as protective covering
to hair, fingernails, feathers, hooves, etc.
• Transmembrane proteins: Span a cell membrane and help control
the movement of small molecules and ions.
– Have channels – help molecules to enter and exist the cell.
– Transport is very selective - allow passage of one type of
molecule or ion.
• Storage proteins: Bind (and store) small molecules.
– Ferritin - an iron-storage protein - saves iron for use in the
biosynthesis of new hemoglobin molecules.
– Myoglobin - an oxygen-storage protein present in muscle
• Regulatory proteins: Often found “embedded” in the exterior surface
of cell membranes - act as sites for receptor molecules
– Often the molecules that bind to enzymes (catalytic proteins),
thereby turning them “on” and “off,” and thus controlling
enzymatic action.
• Nutrient proteins: Particularly important in the early stages of life -
from embryo to infant.
– Casein (milk) and ovalalbumin (egg white) are nutrient proteins
– Milk also provide immunological protection for mammalian young.
Amino Acid: The Building Blocks for Proteins
• Amino acid: a compound that
contains both an amino group
and a carboxyl group
•  -Amino acid has an amino
group attached to the carbon
adjacent to the carboxyl group
• -carbon also bound to side
chain group, R
• R gives identity to amino acid
• Two steroisomers of amino acids
are designated L- or D-. Based on
similarity to glyceraldehdye
– R = side chain –vary in size, shape, charge, acidity,

functional groups present, hydrogen-bonding ability, and
chemical reactivity.
– >700 amino acids are known
– Based on common “R” groups, there are 20 standard
amino acids
• All amino acids differ from one another by their R-groups
– There are 20 common (standard) amino acids
• Standard amino acids are divided into four groups based

on the properties of R-groups
• Non-polar amino acids: R-groups are non-polar
– Such amino acids are hydrophobic-water fearing
(insoluble in water)
– 8 of the 20 standard amino acids are non-polar
– When present in proteins, they are located in the
interior of protein where there is no polarity
Amino Acid Structure and Properties
• With the exception of glycine, all protein-derived amino

acids have at least one stereocenter (the α-carbon) and
are chiral (stereoisomers)
• The vast majority of α -amino acids have the L-
configuration at the α -carbon (Proline is usually D)
• Side-chain carbons in other amino acids designated with
Greek symbols, starting at a carbon (…etc)
• Amino acids can be referred to by three-letter or one-
letter codes.

Nomenclature
Common names assigned to the amino acids are currently

used.
• Three letter abbreviations - widely used for naming:
– First letter of amino acid name is compulsory and
capitalized followed by next two letters not capitalized
except in the case of Asparagine (Asn), Glutamine (Gln)
and tryptophan (Trp).
• One-letter symbols - commonly used for comparing amino
acid sequences of proteins:
– Usually the first letter of the name
– When more than one amino acid has the same letter the
most abundant amino acid gets the 1st letter.
Amino Acid Abbreviations and Codes

Learning the Names and Codes

Essential Amino Acids
Essential Amino acid: A standard amino acid needed for protein
synthesis that must be obtained from dietary sources – adequate
amounts cannot be synthesized in human body.
Nine of the 20 standard amino acids are considered essential
*Required for growth

in children and is not
essential for adults.

Essential Amino Acids
A complete protein contains all the essential amino acids in
the proper amounts.
An incomplete protein is low in one or more of the essential

amino acids, usually lysine, tryptophan, or methionine.
Except for gelatin, proteins from animal sources are complete,
whereas proteins from vegetable sources are incomplete except soy
protein.
Complementary proteins are incomplete proteins which

when served together, complement each other and provide
all the essential amino acids
Examples of Complete and Incomplete Protein Sources

All the essential amino acids are provided in a meal that consists of
a complete protein of animal origin or complementary proteins of
vegetable origin.

Nonstandard/Uncommon Amino Acids
Each derived from a
common amino acid by
a modification
• Hydroxylysine and
hydroxyproline are
found only in a few
connective tissues
such as collagen
• Thyroxine is found only

in the thyroid gland

Ionization of Amino
Acids
• In amino acid,
carboxyl group (-) and
amino group (+) are
charged at neutral
pH.
• In free amino acids
-carboxyl, and a-
amino groups have
titratable protons.
Some side chains do
as well
Ionization of Amino Acids
In neutral solution, the COOH is ionized and the NH2 is
protonated
The resulting structures have “+” and “-” charges (a dipolar
ion, or zwitterion)

Ionization vs pH
The net charge on an amino acid depends on the

pH of the solution in which it is dissolved.
If we dissolve an amino acid in water, it is present in the

aqueous solute as its zwitterion.
If we now add a strong acid such as HCl to bring the pH of

the solution to 2.0 or lower, the strong acid
-
donates a proton to the -COO of the amino acid turning
the zwitterion into a positive ion.

Ionization vs pH
If we now add a strong acid such as HCl to bring the pH of

the solution to 2.0 or lower, the strong acid
-
donates a proton to the -COO of the amino acid turning
the zwitterion into a positive ion.

Ionization vs pH
If we add a strong base such as NaOH to the solution and
bring its pH to 10.0 or higher, a proton is transferred from
the NH3+ group to the base turning the
zwitterion into a negative ion.

Ionization vs pH
to summarize:

Isoelectric Point (pI)
The pH at which the majority of molecules of a compound
in solution have no net charge.
The pH at which the concentration of Zwitterion is

maximum -- net charge is zero
– Different amino acids have different isoelectric points

– At isoelectric point - amino acids are NOT attracted
towards an applied electric field because they carry net
zero charge

To calculate the pI:
1. Draw out the complete ionization of amino acid
2. Determine net charge on each ionized form
3. Find the structure that has no net charge
4. Take the average of the pKa’s that are around the
structure
5. Note do NOT just take the average of all pKa’s.

* pKa1 = COOH
* pKa2 = NH3+
* pKaR = R group H+
The pI for glycine, for example, falls midway between

the pKa values for the carboxyl and amino groups
2.4+9.8
pI = = 6.1
2

Summary of the changes in ionic charges when acid
or base is added to a solution of amino acid at
isoelectric point

Isoelectric pH values for the 20

protein-derived amino acids

Titration of Amino Acids
When an amino acid is

titrated, the titration curve
represents the reaction of
each functional group with
the hydroxide ion

Titration of Alanine with NaOH
+1 0 -1
pI = 2.3 + 9.7
2
pI = 6.0

Titration of Histidine with NaOH

PRACTICE
Consider the following amino acid and its pKa values:
A. Draw the structure of the amino acid as the pH of the

solution changes from highly acidic to strongly basic.
A. Draw the structure of the amino acid as the pH of the
solution changes from highly acidic to strongly basic.

B. Which form of the amino acid is present at the
isoelectric point

C. Calculate the isoelectric point (pI).

PROTEINS (2)
Dr. Aileen B. Angcajas November 2022
Iligan City
Peptides and Peptide Bonds
Under proper conditions, amino acids can bond together to
produce an unbranched chain of amino acids.
– The reactions is between amino group of one amino
acid and carboxyl group of another amino acid.
• The length of the amino acid chain can vary from a few
amino acids to hundreds of amino acids.
• Such a chain of covalently-linked amino acids is called a
peptide.
• The covalent bonds between amino acids in a peptide are
called peptide bonds (amide).
ABA, Nov 2022 | Page 2



Nature of Peptide Bond
The C – N bond in the peptide linkage has partial double
bond character that makes it rigid and prevents the
adjacent groups from rotating freely; the peptide bond is
planar, and the two adjacent a-carbons lie trans to it.
The H of the amide nitrogen is also trans to the O of the
carbonyl group. Almost all the peptide bonds in proteins
are planar and have a trans configuration.

Polypeptide Structure and Trans Amide

Peptide Nomenclature
• Structure left (N-term) to right (C-term)
• Structure is based on the repeating sequence
N-C-C-N-C-C-N-C-C
N is the a-amino group; red is the α-carbon; and blue is the
carbonyl carbon.
• All the other amino acid residues have names that end in
-yl. The -yl suffix replaces the -ine or -ic acid ending of
the amino acid name, except for tryptophan, for which -
yl is added to the name.

Ala-leu-gly has the IUPAC name of alanylleucylglycine

• Peptide: the name given to a short polymer of amino
acids joined by peptide bonds; they are
classified by the number of amino acids in the
chain
• Dipeptide: a molecule containing two amino acids
joined by a peptide bond
• Tripeptide: a molecule containing three amino acids
joined by peptide bonds
• Polypeptide: a macromolecule containing many amino
acids joined by peptide bonds
• Protein: a biological macromolecule of molecular
weight 5000 g/mol or greater, consisting of
one or more polypeptide chains
PRACTICE
Given the (a) three-letter abbreviation ; (b) one-

letter symbol, and (c) name of the following
tripeptide:
BIOCHEMISTRY I ABA, Nov 2022 | Page 11

PRACTICE
Write the structure of the ff. peptides at pH 7
a) threonylcysteine
b) Isoleucylmethionylaspartate

Isomeric Peptides
Peptides that contain the same amino acids but present in
different order are different molecules (constitutional
isomers) with different properties
Two different dipeptides can be formed between alanine
and glycine
The number of isomeric peptides possible increases rapidly
as the length of the peptide chain increases

Biologically Important Peptides
Glutathione (GSH)
• Protects cells from the destructive effects of oxidation by reacting

with substances such as peroxides.
• In red blood cells: glutathione protects against formation of
methemoglobin by reducing H2O2 in a reaction catalyzed by the
enzyme glutathione peroxidase
Met-enkephalin and Leu-enkephalin
Met-enkephalin Leu-enkephalin
• Pentapeptide neurotransmitters produced by the brain

and bind receptors within the brain
• Help reduce pain
Oxytocin and Vasopressin
– Produced by the pituitary gland

– Nonapeptide (nine amino acid residues) with six of the residues held
in the form of a loop by a disulfide bond formed between two
cysteine residues
Aspartame
Dipeptide sold under trade names Equal and Nutrasweet;
~180x as sweet as sucrose

Levels of Protein Structure
1° structure: the sequence of amino acids in a polypeptide
chain, read from the N-terminal end to the C-
terminal end
2° structure: the ordered 3-dimensional arrangements
(conformations) in localized regions of a
polypeptide chain; refers only to interactions
of the peptide backbone
e. g., α-helix and β-pleated sheet
3˚ structure: 3-D arrangement of all atoms
4˚ structure: arrangement of monomer subunits with
respect to each other
Levels of Protein Structure

PROTEINS (3)
Iligan City
Primary Structure (1o) of Proteins
The order in which the amino acid residues of a peptide
molecule are linked is the amino acid sequence of the
molecule.
Differences in the chemical and physiologic properties of
peptides result from differences in the amino acid
sequence.
Bradykinin vs Boguskinin
(Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg) (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe)
partly responsible for triggering pain, - completely inactive
welt formation (as in scratches),
movement of smooth muscle, and
lowering of blood pressure
Primary Structure (1o) of Proteins
Changes in just one amino acid in sequence can alter biological
function, e.g. hemoglobin associated with sickle-cell anemia
Normal 𝛽 𝑐ℎ𝑎𝑖𝑛: Val-His-Leu-Thr-Pro-Glu-Glu-Lys-….
Sickled 𝛽 𝑐ℎ𝑎𝑖𝑛 : Val-His-Leu-Thr-Pro-Val-Glu-Lys-….

Amino Acid Sequencing Steps
Determination of 1˚ sequence of protein is routine biochemistry
lab work
1. Cleavage of all disulfide bonds–oxidation with

performic acid is commonly used.
2. Determination of the N–terminal amino acid.
a. Sanger’s method - the polypeptide chain is reacted

with 1–fluoro–2,4–dinitrobenzene (DNFB).

Sangers Method

b. Edman degradation – uses phenylisothiocyanate (PITC),
often referred to as Edman’s reagent

3. Determination of the C–terminal amino acid
A group of enzymes called the carboxypeptidases are used to identify
the C – terminal residue.
Caboxypeptidases A and B, both secreted by the pancreas, hydrolyze
peptides one residue at a time from the C–terminal end.
a. Carboxypeptidase A – preferentially cleaves peptide bonds when

an aromatic amino acid is the C–terminal residue.
b. Carboxypeptidase B – cleaves basic amino acid residues.

Because these enzymes sequentially cleave peptide bonds starting at
the C–terminal residue, the first amino acid liberated is the C–
terminal residue.
4. Cleavage of the polypeptide into fragments
a. Trypsin -cleaves peptide bonds on the carboxyl side of the two

strongly basic amino acids Arg and Lys.
b. Chymotrypsin-cleaves peptide bonds on the carboxyl side of the

three aromatic amino acids (Phe, Tyr, and Trp).
c. Pepsin - cleaves peptide bonds at the amino end of aromatic

amino acids (Phe, Trp, Tyr), acidic amino acids (Asp, Glu) and Ile.
d. Cyanogen Bromide (CNBr) - specifically cleaves peptide bonds on

the carboxyl side of methionine residues

5. Ordering the peptide fragments
The amino acid sequence information derived from two or

more sets of polypeptide fragments are next examined
for overlapping segments. Such segments make it possible
to piece together the overall sequence.

Sample Problem 1
1. Consider the following peptide:
Gly – Ile – Glu – Trp – Thr – Pro – Tyr – Gln – Phe – Arg – Lys
What amino acids and peptides are produced when the

above peptide is treated with each of the following
reagents?
a. Carboxypeptidase c. Trypsin
b. Chymotrypsin d. DNFB

Solution
a. Because carboxypeptidase cleaves at the carboxyl end of peptides,
the products are
Gly – Ile – Glu – Trp – Thr – Pro – Tyr – Gln – Phe – Arg
and
Lys
b. Because chymotrypsin cleaves peptide bonds in which aromatic

amino acids (i.e., Phe, Tyr, and Trp) contribute a carboxyl group,
the products are
Gly – Ile – Glu – Trp, Thr – Pro – Tyr,
Gln – Phe and Arg – Lys

c. Trypsin cleaves at the carboxyl end of lysine and
arginine. The products are
Gly – Ile – Glu – Tyr – Thr – Pro – Tyr – Gln – Phe – Arg
and
Lys
d. DNFB tags the amino terminal amino acid. The products:
DNP – Gly and

Ile – Glu – Trp – Thr – Pro -Tyr – Gln – Phe – Arg – Lys

Sample Problem 2

Sample Problem 2

Sample Problem 3

Sample Problem 3

Secondary (2o) Structures of Proteins
Arrangement of atoms of peptide backbone in space.

Secondary Structures of Proteins
The peptide linkages are essentially planar thus allows only two
possible arrangements for the peptide backbone for the following
reasons:
– For two amino acids linked through a peptide bond six atoms lie in
the same plane
– The planar peptide linkage structure has considerable rigidity,
therefore rotation of groups about the C–N bond is hindered
– Cis–trans isomerism is possible about C–N bond.
– The trans isomer is the preferred orientation

Secondary Structures of Proteins
The only bond responsible for the 2o structure of proteins

is H-bonding between peptide bonds, the – C = O of one
peptide group and the – N – H of another peptide linkage
farther along the backbone.
The two most common types :

alpha-helix (α-helix)
beta-pleated sheet (β-pleated sheet).

Alpha-helix (α-helix)
– H-bonding between amino acids
within the same chain –
intramolecular H-bonding
– Coiled helical spring
– R-groups stay outside of the
helix -- not enough room for
them to stay inside
– The helix is so tightly wound
that the space in the center is
too small for solvent molecules
to enter
Alpha-helix (α-helix)
• Coil of the helix is clockwise or right-
handed
• There are 3.6 amino acids per turn
• Repeat distance is 5.4Å
• Each peptide bond is s-trans and planar
• C=O of each peptide bond is hydrogen
bonded to the N-H of the fourth amino
acid away
• C=O----H-N hydrogen bonds are parallel
to helical axis
• All R groups point outward from helix

Several factors can disrupt an α -helix
• Proline creates a bend because of (1) the restricted

rotation due to its cyclic structure and (2) its α-amino
group has no N-H for hydrogen bonding
• Strong electrostatic repulsion caused by the proximity

of several side chains of like charge, e.g., Lys and Arg
or Glu and Asp
• Steric crowding caused by the proximity of bulky side

chains, e.g., Val, Ile, Thr

Beta-Pleated Sheets (β-pleated sheet)
Completely extended protein chain
segments in same or different
molecules governed by intermolecular
or intramolecular H-bonding
H-bonding between different parts of

a single chain – intramolecular H-
bonding
Side chains below or above the axis

“U-turn” structure – most frequently
encountered
Beta-Pleated Sheets (β-pleated sheet)
• Polypeptide chains lie adjacent to one another; may be
parallel or antiparallel
• R groups alternate, first above and then below plane

• Each peptide bond is s-trans and planar
• C=O and N-H groups of each peptide bond are

perpendicular to axis of the sheet
• C=O---H-N hydrogen bonds are between adjacent sheets

and perpendicular to the direction of the sheet
Antiparallel β-pleated sheet
Chains run in opposite direction; more stable because of fully
collinear H- bonds
N-terminus of one chain is aligned with the C-terminus of a second
chain (head to tail)

Parallel β-pleated sheet
Chains run in the same direction
N-termini are head-to-head

Some proteins contain bot α-helices and β-sheets
• α -helices can gradually curve,
and are not exactly straight,
and that in the β -sheet the
strands are not the same in
length, nor is each perfectly
'flat’
• some parts that do not have
either α-helical or β-sheet
character—these regions may
be 'disordered’, or may
represent a type of turn
structure
Structures of Reverse Turns
• Glycine found in reverse turns
• Spatial (steric) reasons
• Polypeptide changes direction
• Proline also encountered in reverse turns.

β Turns
- carbonyl C of one residue is H-bonded to the amide proton of a

residue three residues away
- proline and glycine are prevalent in beta turns

Not all amino acids are equally likely to be found in each
type of secondary structure

Fibrous Proteins
• Fibrous proteins: contain polypeptide chains
organized approximately parallel along a single axis.
They
• consist of long fibers or large sheets
• tend to be mechanically strong
• are insoluble in water and dilute salt solutions
• play important structural roles in nature
• Examples are
• keratin of hair and wool
• collagen of connective tissue of animals including cartilage,
bones, teeth, skin, and blood vessels

Fibrous Proteins and Secondary Structures

Fibrous Protein: Alpha-Keratin (α-Keratin)
A fibrous structural
protein consists of
~300 residues coiled
into a right-handed
helical secondary
structure, α-helix
stabilized by H-bonds
between amide N–H
groups and C=O
groups four residues
away.
Alpha-Keratin (α-Keratin)

• Provide protective coating for organs

• Major protein constituent of hair, feather, nails, horns
and turtle shells
• Mainly made of hydrophobic amino acid residues
• Hardness of keratin depends upon -S-S- bonds
– More –S-S– bonds make nail and bones hard and
hair brittle


Fibrous Protein: Collagen
- helical ("α-chain")
- left-handed, 3.3-residues per turn
- repeating tripeptide sequence
Gly-X-Pro (or Gly-X-HyPro)
- three helical strands wrap
around each other in a right-hand
sense to form a 'superhelix‘, with
H bonds extending between the
chains

Fibrous Protein: Collagen
• Most abundant proteins in
humans (30% of total body
protein)
• Major structural material in
tendons, ligaments, blood
vessels, and skin
• Organic component of bones
and teeth
• Predominant structure - triple
helix
• Rich in proline (up to 20%) –
important to maintain struct

Collagen

Fibrous Protein: Silk Fibroin
• Fibroin is a protein produced by spiders & insects
• Spider dragline silk is both flexible and strong (tensile
strength of 200,000 psi
• Structure is largely "β-sheet”

PROTEINS (4)
Iligan City
Globular Proteins
• Globular proteins: proteins which are folded
to a more or less spherical shape
• they tend to be soluble in water and salt solutions
• most of their polar side chains are on the outside
and interact with the aqueous environment by
hydrogen bonding and ion-dipole interactions
• most of their nonpolar side chains are buried
inside
• nearly all have substantial sections of α-helix and
β-sheet

Comparison of Shapes of Fibrous and Globular Proteins

Tertiary (3o) Structures of Proteins
Three-dimensional arrangements of all the atoms in
the molecule.
Polypeptide chain with its regions of secondary

structure, α-helix, and β-pleated sheet, further folds
on itself.
Tertiary structure forms spontaneously and is

maintained as a result of interactions among the R groups
of the amino acids.

Forces in 3o Structure
• Noncovalent interactions, including
• Hydrogen bonding between polar side chains, e.g., Ser and Thr
• Hydrophobic interaction between nonpolar side chains, e.g., Val
and Ile
• Electrostatic attraction between side chains of opposite charge,
e.g., Lys and Glu
• Electrostatic repulsion between side chains of like charge, e.g.,
Lys and Arg, Glu and Asp
• Covalent interactions: Disulfide (-S-S-) bonds between
side chains of cysteines

Forces in 3o Structure

Globular Proteins: Myoglobin
A single polypeptide chain of 153 amino
acids
A single heme group in a hydrophobic

pocket
8 regions of α-helix; no regions of β-sheet
Most polar side chains are on the surface
Nonpolar side chains are folded to the

interior

Heme: an oxygen-binding cofactor

Heme-Iron-Protein Interaction
Fe2+ is octahedrally coordinated. Four binding groups from the

porphyrin ring are attached to it. The remaining coordination sites
lie along an axis perpendicular to the ring. One coordination of
these sites is occupied by the nitrogen of His 93 (proximal histidine).
Myoglobin:
– An oxygen storage molecule in muscles.

– Monomer - single peptide chain with one heme unit
– Binds one O2 molecule
– Has a higher affinity for oxygen than hemoglobin.
– Oxygen stored in myoglobin molecules serves as a
reserve oxygen source for working muscles
Without the oxygen (deoxymyoglobin), the remaining

coordination site on the other side of the iron is occupied by a
water molecule. In the presence of oxygen (oxymyoglobin),
this site is occupied by oxygen.

Quaternary (4o) Structures of Proteins
Quaternary structure is the result of noncovalent
interactions between two or more protein chains.
In some cases, the quaternary structure involves binding to
a nonprotein group called a prosthetic group.
e.g. Hemoglobin has four protein chains and the
heme prosthetic group.
The chains in a quaternary structure may be identical or
different.
dimer = 2 polypeptide chains
trimer = 3 polypeptide chains
tetramer = 4 polypeptide chains
Nomenclature for Quaternary Structure

Nomenclature for Quaternary Structure

Oxygen-Binding Proteins
• Hemoglobin and myoglobin are heme-containing
oxygen transport and storage proteins (not enzymes)
– Hemoglobin (Hb) in blood
– Myoglobin (Mb) in muscle
• Hemoglobin and myoglobin have different oxygen
binding curves
• Mb is monomeric
– 153 aa, 16.7 kDa
• Hb is tetrameric (α2 β2) 64.5 kDa
– 2 α-subunits of 141 residues
– 2 β-subunits of 146 residues
Structures of Myoglobin and Hemoglobin
Each of the four chains in in

hemoglobin has a folded structure
similar to that of myoglobin and
each carries a heme.

Globular Proteins: Hemoglobin (Hb)
• Hb is a tetrameric heme protein
• The basic physiological function
of Hb is to bind oxygen in lungs
and release it in capillaries
• When a first oxygen binds to Fe
in heme of Hb, the heme Fe is
drawn into the plane of the
porphyrin ring
– Hb without a bound O2
molecule is called
deoxyhemoglobin
Oxygen Binding of Hemoglobin
• Oxygen binds to heme in hemoglobin cooperatively:
as one O2 is bound, it becomes easier for the next
to bind.
• The first oxygen causes 2,3-bisphospho-glycerate (BPG)
to leave deoxyhemoglobin. This causes shape changes
which favor more reaction with oxygen.
• H+ produced by metabolizing cells (low pH) favors
oxygen release from Hb and higher pH in the lungs
favors binding of oxygen to Hb.

pH/[CO2] Variation and CO2-binding to Hemoglobin
• Hb can bind H+ and CO2 and serves to carry
them from the tissues where they are
generated to the lungs & kidneys where
they are excreted
• At low pH (high [H+]) and high [CO2] Hb has
reduced O2 affinity
O2 & H+ have inverse binding affinities to Hb

at [O2] - releases H+ from Hb
(as in lung)
at [O2] - H+ binds Hb, O2 released
(as in peripheral tissue)

Themes in Protein Function
• Structure dictates function

– primary structure → tertiary structure → protein function
• Proteins are often flexible & dynamic

– proteins have a unique shape & architecture, but many
(aside from certain fibrous/structural proteins) are not
rigid & immobile

PROTEIN DENATURATION
Denaturation of a protein occurs when there is a change that
disrupts the interactions between R groups that stabilize the
secondary, tertiary, or quaternary structure. However, the
covalent amide bonds of the primary structure are not affected.

• Partial or complete disorganization of protein’s tertiary
structure
• Cooking food denatures the protein but does not change
protein nutritional value
• Coagulation: Precipitation (denaturation of proteins)
– Egg white - a concentrated solution of protein albumin -
forms a jelly when heated because the albumin is
denatured
• Cooking:
– Denatures proteins – Makes it easy for enzymes in our
body to hydrolyze/digest protein
– Fever: >104ºF – the critical enzymes of the body start
getting denatured
Temperature
As the temperature continues to increase, the bonds
within the proteins begin to vibrate more violently and
eventually, the weak interactions, like hydrogen bonds
and hydrophobic interactions, that maintain the
protein structure are disrupted.

Denaturation of egg protein occurs when the bonds of the tertiary

structure are disrupted.



Proteins

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Proteins

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PROTEINS (1)

Dr. Aileen B. Angcajas October 2022

Specific definition: A protein is a peptide in which at least

A protein in which only amino acid residues are present:

Conjugated (complex) proteins

A protein that has one or more non-amino acid entities

BIOCHEMISTRY I ABA, Oct 2022 | Page 4

Fibrous Proteins: Alpha-Keratin & Collagen

The polypeptide chains are arranged in long strands or

BIOCHEMISTRY I ABA, Oct 2022 | Page 6

Globular Proteins: Myoglobin & Hemoglobin

The polypeptide chains are folded into spherical or globular

BIOCHEMISTRY I ABA, Oct 2022 | Page 7

BIOCHEMISTRY I ABA, Oct 2022 | Page 9

– R = side chain –vary in size, shape, charge, acidity,

• Standard amino acids are divided into four groups based

• With the exception of glycine, all protein-derived amino

BIOCHEMISTRY I ABA, Oct 2022 | Page 20

Common names assigned to the amino acids are currently

BIOCHEMISTRY I ABA, Oct 2022 | Page 22

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*Required for growth

BIOCHEMISTRY I ABA, Oct 2022 | Page 24

An incomplete protein is low in one or more of the essential

Complementary proteins are incomplete proteins which

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• Thyroxine is found only

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The net charge on an amino acid depends on the

If we dissolve an amino acid in water, it is present in the

If we now add a strong acid such as HCl to bring the pH of

BIOCHEMISTRY I ABA, Oct 2022 | Page 31

If we now add a strong acid such as HCl to bring the pH of

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The pH at which the concentration of Zwitterion is

– Different amino acids have different isoelectric points

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5. Note do NOT just take the average of all pKa’s.

The pI for glycine, for example, falls midway between

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Isoelectric pH values for the 20

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When an amino acid is

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A. Draw the structure of the amino acid as the pH of the

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Given the (a) three-letter abbreviation ; (b) one-