Chapter 3

Chapter 3
Proteins
Chapter 20
Table of Contents
20.1Characteristics of Proteins
20.2Amino Acids: The Building Blocks for Proteins
20.3Chirality and Amino Acids
20.4Acid–Base Properties of Amino Acids
20.5Cysteine: A Chemically Unique Amino Acid
20.6Peptides
20.7Biochemically Important Small Peptides
20.8General Structural Characteristics of Proteins
20.9 Primary Structure of Proteins
20.10Secondary Structure of Proteins
20.11Tertiary Structure of Proteins
20.12Quaternary Structure of Proteins
20.13 Classification Based on Shape
20.14 Protein Classification Based on Function
20.15 Protein Hydrolysis
20.16 Protein Denaturation
20.17 Glycoproteins
20.18 Lipoproteins
Copyright © Cengage Learning. All rights reserved 2

Section 20.1
Characteristics of Proteins
• A protein is a naturally-occurring, unbranched polymer in

which the monomer units are amino acids
• Proteins are most abundant molecules in the cells after
water – account for about 15% of a cell’s overall mass
• Elemental composition - Contain Carbon (C), Hydrogen
(H), Nitrogen (N), Oxygen (O), most also contain Sulfur
(S)
• The average nitrogen content of proteins is 15.4% by
mass
• Also present are Iron (Fe), phosphorus (P) and some
other metals in some specialized proteins
Return to TOC

Section 20.2
Amino Acids: The Building Blocks for Proteins
• Amino acid - An organic compound that contains both an amino (-NH2) and
carboxyl (-COOH) groups attached to same carbon atom
– The position of carbon atom is Alpha (a)
– -NH2 group is attached at alpha (a) carbon atom.
– -COOH group is attached at alpha (a) carbon atom.
• 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
Side Chain
R  -Carbon Atom
H2N C COOH
-Carboxyl
-Amino H Group
Group Return to TOC

Section 20.2
• All amino acids differ from one another by their R-groups

• 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
Return to TOC

Section 20.2
• Polar amino acids: R-groups are polar

– Three types: Polar neutral; Polar acidic; and Polar
basic
• Polar-neutral: contains polar but neutral side chains
– Seven amino acids belong to this category
• Polar acidic: Contain carboxyl group as part of the side
chains
– Two amino acids belong to this category
• Polar basic: Contain amino group as part of the side
chain
– Two amino acids belong to this category
Return to TOC

Section 20.2
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.
• Both types of abbreviations are given in the following slides
Return to TOC

Section 20.2
Non-Polar Amino Acids
Return to TOC

Section 20.2
Polar Neutral Amino Acids
Return to TOC

Section 20.2
Polar Acidic and Basic Amino Acids
Return to TOC

Section 20.2
Practice Exercise
• Classify the following amino acids based on the polarity of their R-groups
O
O
d. H 2N CH C OH
a. H 2N CH C OH
CH2
CH3
Non-polar
O
H 2N CH C OH
Non-polar
CH2
b.
O
H 2N CH C OH
e. CH2
Polar Neutral OH
CH2
CH2
O CH2
c. H 2N CH C OH NH2
CH2
Polar Basic
Polar Acidic C O
OH
Return to TOC

Section 20.3
Chirality and Amino Acids
• Four different groups are attached to the a-carbon atom

in all of the standard amino acids except glycine
– In glycine R-group is hydrogen
• Therefore 19 of the 20 standard amino acids contain a
chiral center
• Chiral centers exhibit enantiomerism (left- and right-
handed forms)
• Each of the 19 amino acids exist in left and right handed
forms
Return to TOC

Section 20.3
• The amino acids found in nature as well

as in proteins are L isomers.
– Bacteria do have some D-amino acids
– With monosaccharides nature favors
D-isomers
• The rules for drawing Fischer projection
formulas for amino acid structures
• The — COOH group is put at the top, the
R group at the bottom to position the Designation of Mirror
carbon chain vertically handedness in standard amino
acid structures
• The — NH2 group is in a horizontal
position.
– Positioning — NH2 on the left - L
isomer
– Positioning — NH2 on the right - D
isomer. Return to TOC

Section 20.3
Practice Exercise
• Name the following amino acids with correct designation for
the enantiomer (chiral carbon is indicated by *).
A B C
COOH COOH COOH
*C *C H 2N *C H
H 2N H H NH2
CH CH3 CH2 CH2
CH2 SH
CH3
A = L-Isoleusine
B = D-Cysteine OH
C = L-Tyrosine
Return to TOC

Section 20.4
Acid-Base Properties of Amino Acids
• In pure form amino acids are white crystalline solids

• Most amino acids decompose before they melt
• Not very soluble in water
• Exists as Zwitterion: An ion with + (positive) and – (Nagetive)
charges on the same molecule with a net zero charge
– Carboxyl groups give-up a proton to get negative charge
– Amino groups accept a proton to become positive
COO- COO-
+H NH3 +
3N H H
R CH3
L D
Zwitterions
Return to TOC

Section 20.4
Acid-Base Properties of Amino Acids
• Amino acids in solution exist in three different species (zwitterions,

positive ion, and negative ion) - Equilibrium shifts with change in pH
• Isoelectric point (pI) – 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 net zero charge.
COOH COO- COO-
+
+
H3N C H H3N C H H2N C H
CH3 CH3 CH3

Low pH High pH
Zwitter Ion (net - charge)
(net + charge) (net neutral charge)
Neutral pH
Return to TOC

Section 20.5
Cysteine: A Chemically Unique Amino Acid
• Cysteine: the only standard

amino acid with a sulfhydryl
group ( — SH group).
• The sulfhydryl group imparts
cysteine a chemical property
unique among the standard
amino acids.
• Cysteine in the presence of
mild oxidizing agents dimerizes
to form a cystine molecule.
– Cystine - two cysteine
residues linked via a
covalent disulfide bond.
Return to TOC

Section 20.6
Peptides
• Under proper conditions, amino acids can bond together to

produce an unbranched chain of amino acids.
• The length of the amino acid chain can vary from a few amino
acids to many 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.
Return to TOC

Section 20.6
Peptides
• Dipeptide: bond between two amino acids

• Oligopeptide: bond between ~ 10 - 20 amino acids
• Polypeptide: bond between large number of amino acids
• Every peptide has an N-terminal end and a C-terminal end
+
H3N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COOOH
-
N-terminal end
O O CH2 O
+H
H H
3N CH C N CH C N CH C O-
CH3 CH 2 C-terminal end
Alanine Phenylalanine Serine Return to TOC

Section 20.6
Peptides
Peptide Nomenclature
• The C-terminal amino acid residue keeps its full amino
acid name.
• All of the other amino acid residues have names that end
in -yl. The -yl suffi x replaces the -ine or -ic acid ending of
the amino acid name, except for tryptophan, for which -yl
is added to the name.
• The amino acid naming sequence begins at the N-
terminal amino acid residue.
• Example:
– Ala-leu-gly has the IUPAC name of
alanylleucylglycine
Return to TOC

Section 20.6
Peptides
Isomeric Peptides
• Peptides that contain the same amino acids but present
in different order are different molecules (constitutional
isomers) with different properties
– For example, 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
Return to TOC

Section 20.7
Biochemically Important Small Peptides
• Many relatively small peptides are biochemically active:

– Hormones
– Neurotransmitters
– Antioxidants
• Small Peptide Hormones:
– Best-known peptide hormones: 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
Return to TOC

Section 20.7
Small Peptide Neurotransmitters

• Enkephalins are pentapeptide neurotransmitters
produced by the brain and bind receptor within the brain
• Help reduce pain
• Best-known enkephalins:
– Met-enkephalin: Tyr–Gly–Gly–Phe–Met
– Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu
Return to TOC

Section 20.7
Small Peptide Antioxidants

• Glutathione (Glu–Cys–Gly) – a tripeptide – is present is in high levels
in most cells
• Regulator of oxidation–reduction reactions.
• Glutathione is an antioxidant and protects cellular contents from
oxidizing agents such as peroxides and superoxides
– Highly reactive forms of oxygen often generated within the cell in
response to bacterial invasion
• Unusual structural feature – Glu is bonded to Cys through the side-
chain carboxyl group.
Return to TOC

Section 20.8
General Structural Characteristics of Proteins
• General definition: 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 used 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
• More than one peptide chain may be present in a protein:
– Monomeric : A monomeric protein contains one peptide chain
– Multimeric: A multimeric protein contains more than one peptide
chain
Return to TOC

Section 20.8
General Structural Characteristics of Proteins
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
• Conjugated protein: A protein that has one or more non-amino acid
entities (prosthetic groups) present in its structure:
– One or more polypeptide chains may be present
– Non-amino acid components - may be organic or inorganic -
prosthetic groups
– Lipoproteins contain lipid prosthetic groups
– Glycoproteins contain carbohydrate groups,
– Metalloproteins contain a specific metal as prosthetic group
Return to TOC

Section 20.9
Primary Structure of Proteins
Four Types of Structures

–
Primary Structure
–
Secondary Structure
–
Tertiary Structure
–
Quaternary
• Primary Structure: Primary structure of protein refers to
the order in which amino acids are linked together in a
protein
• Every protein has its own unique amino acid sequence
– Frederick Sanger (1953) sequenced and determined
the primary structure for the first protein - Insulin
Return to TOC

Section 20.9
Primary Structure of a Human Myoglobin
Return to TOC

Section 20.9
• Proteins of the same organism always same sequence (cows,

pigs, etc.)
• Different sources: Insulin from pigs, cows, sheep, humans similar
• Some differences:
Species Chain A Chain B

AA #8 AA #9 AA #10 AA #30
Human Thr Ser Ile Thr
Pig (porcine) Thr Ser Ile Ala
Cow (bovine) Ala Ser Val Ala
• Due to differences insulin may show some reaction over time

• Now human insulin produced from genetically engineered
bacteria
Return to TOC

Section 20.10
Secondary Structure of Proteins
• Arrangement of atoms of backbone in space.

• The two most common types : alpha-helix (a-helix) and the
beta-pleated sheet (b-pleated sheet).
• 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 Return to TOC

Section 20.10
Alpha-helix (a-helix)
• A single protein chain adopts a shape that resembles a coiled spring
(helix):
– H-bonding between same amino acid chains –intra molecular
– Coiled helical spring
– R-group outside of the helix -- not enough room for them to stay
inside
Return to TOC

Section 20.10
Beta-Pleated Sheets
• Completely extended amino acid chains
• H-bonding between two different chains – inter and/or
intramolecular
• Side chains below or above the axis
Return to TOC

Section 20.11
Tertiary Structure of Proteins
• The overall three-dimensional shape of a protein

• Results from the interactions between amino acid side
chains (R groups) that are widely separated from each
other.
• In general 4 types of interactions are observed.
Return to TOC

Section 20.11
Tertiary Structure of Proteins
Four Types of Interactions

• Disulfide bond: covalent, strong, between two cysteine
groups
• Electrostatic interactions: Salt Bridge between charged
side chains of acidic and basic amino acids
– -OH, -NH2, -COOH, -CONH2
• H-Bonding between polar, acidic and/or basic R groups
– For H-bonding to occur, the H must be attached on
O, N or F
• Hydrophobic interactions: Between non-polar side chains
Return to TOC

Section 20.12
Quaternary Structure of Proteins
• Quaternary structure of protein refers to the organization

among the various peptide chains in a multimeric
protein:
• Highest level of protein organization
• Present only in proteins that have 2 or more
polypeptide chains (subunits)
• Subunits are generally Independent of each other -
not covalently bonded
• Proteins with quartenary structure are often referred
to as oligomeric proteins
• Contain even number of subunits
Return to TOC

Section 20.13
Protein Classification Based on Shape
• Three types of proteins: fibrous, globular, and membrane

• Fibrous proteins: protein molecules with elongated shape:
– Generally insoluble in water
– Single type of secondary structure
– Tend to have simple, regular, linear structures
– Tend to aggregate together to form macromolecular structures, e.g., hair, nails,
etc
• Globular proteins: protein molecules with peptide chains folded into
spherical or globular shapes:
– Generally water soluble – hydrophobic amino acid residues in the protein core
– Function as enzymes and intracellular signaling molecules
• Membrane proteins: associated with cell membranes
– Insoluble in water – hydrophobic amino acid residues on the surface
– Help in transport of molecules across the membrane
Return to TOC

Section 20.13
Fibrous Proteins: Alpha-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
Return to TOC

Section 20.13
Fibrous Proteins: 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
structure
Return to TOC

Section 20.13
Globular Proteins: Myoglobin

• Globular Proteins: 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
Return to TOC

Section 20.13
Globular Proteins: Hemoglobin

• An oxygen carrier molecule in blood
• Transports oxygen from lungs to tissues
• Tetramer (four peptide chains) - each subunit has a
heme group
• Can transport up to 4 oxygen molecules at time
• Iron atom in heme interacts with oxygen
Return to TOC

Section 20.14
Protein Classification Based on Function
• Proteins play crucial roles in most biochemical

processes.
• The diversity of functions exhibited by proteins far
exceeds the role of other biochemical molecules
• The functional versatility of proteins stems from:
– Ability to bind small molecules specifically and
strongly
– Ability to bind other proteins and form fiber-like
structures, and
– Ability integrated into cell membranes
Return to TOC

Section 20.14
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
Return to TOC

Section 20.14

• 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 a
– 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 can enter and exist the cell.
– Transport is very selective - allow passage of one type of
molecule or ion. Return to TOC

Section 20.14

• 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.
Return to TOC

Section 20.15
Protein Hydrolysis
• Hydrolysis of proteins - reverse of peptide bond

formation:
– Results in the generation of an amine and a
carboxylic acid functional groups.
– Digestion of ingested protein is enzyme-catalyzed
hydrolysis
– Free amino acids produced are absorbed into the
bloodstream and transported to the liver for the
synthesis of new proteins.
– Hydrolysis of cellular proteins and their resynthesis is
a continuous process.
Return to TOC

Section 20.16
Protein Denaturation
• 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
– Kills microorganisms by denaturation of proteins
– Fever: >104ºF – the critical enzymes of the body start getting
denatured
Return to TOC

Section 20.17
Glycoproteins
• Conjugated proteins with carbohydrates linked to them:

– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
– Collagen and mmunoglobulins are glycoproteins
• Collagen -- glycoprotein
– Most abundant protein in human body (30% of total body
protein)
– Triple helix structure
– Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) —
derivatives
– Some hydroxylysines are linked to glucose, galactose, and their
disaccharides – help in aggregation of collagen fibrils.
Return to TOC

Section 20.17
Glycoproteins
Immunoglobulins
• Glycoproteins produced as a protective response to the
invasion of microorganisms or foreign molecules -
antibodies against antigens.
• Immunoglobulin bonding to an antigen via variable
region of an immunoglobulin occurs through hydrophobic
interactions, dipole – dipole interactions, and hydrogen
bonds.
Return to TOC

Section 20.18
Lipoproteins
• Lipoprotein: a conjugated protein that contains lipids in addition to

amino acids
• Major function - help suspend lipids and transport them through the
bloodstream
• Four major classes of plasma lipoproteins:
– Chylomicrons: Transport dietary triacylglycerols from intestine to
liver and to adipose tissue.
– Very-low-density lipoproteins (VLDL): Transport triacylglycerols
synthesized in the liver to adipose tissue.
– Low-density lipoproteins (LDL): Transport cholesterol
synthesized in the liver to cells throughout the body.
– High-density lipoproteins (HDL): Collect excess cholesterol from
body tissues and transport it back to the liver for degradation to
bile acids.
Return to TOC

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Chapter 3

Copyright © Cengage Learning. All rights reserved 2

• A protein is a naturally-occurring, unbranched polymer in

Copyright © Cengage Learning. All rights reserved 3

Copyright © Cengage Learning. All rights reserved 4

• All amino acids differ from one another by their R-groups

Copyright © Cengage Learning. All rights reserved 5

• Polar amino acids: R-groups are polar

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Copyright © Cengage Learning. All rights reserved 7

Non-Polar Amino Acids

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Polar Neutral Amino Acids

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Polar Acidic and Basic Amino Acids

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Copyright © Cengage Learning. All rights reserved 11

• Four different groups are attached to the a-carbon atom

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• The amino acids found in nature as well

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CH CH3 CH2 CH2

Copyright © Cengage Learning. All rights reserved 14

• In pure form amino acids are white crystalline solids

Copyright © Cengage Learning. All rights reserved 15

• Amino acids in solution exist in three different species (zwitterions,

CH3 CH3 CH3

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• Cysteine: the only standard

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• Under proper conditions, amino acids can bond together to

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• Dipeptide: bond between two amino acids

CH3 CH 2 C-terminal end

Alanine Phenylalanine Serine Return to TOC

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• Many relatively small peptides are biochemically active:

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Small Peptide Neurotransmitters

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Small Peptide Antioxidants

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• General definition: A protein is a naturally-occurring, unbranched

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Protein Classification Based on Chemical Composition

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Four Types of Structures

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Primary Structure of a Human Myoglobin

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• Proteins of the same organism always same sequence (cows,

Species Chain A Chain B

• Due to differences insulin may show some reaction over time

Copyright © Cengage Learning. All rights reserved 29

• Arrangement of atoms of backbone in space.

Copyright © Cengage Learning. All rights reserved 30

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