Stoker Chapter 20 Proteins Part 1
Biochemistry (Lec) (University of Science and Technology of Southern Philippines)
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CHAPTER 20
Proteins – Part 1
20.1 Characteristics of Proteins
Protein Classification Based on Shape
General definition: A protein is a naturally-occurring,
unbranched polymer in which the monomer units are amino
acids.
Fibrous Proteins: Alpha-Keratin & Collagen
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Proteins are the most abundant molecules in the
cells after water – account for about 15% of a
cell’s overall mass.
Elemental composition – contains carbon (C),
hydrogen (H), nitrogen (N), oxygen (O), and 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.
Specific definition: A protein is a peptide in which at least 40
amino acid residues are present:
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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
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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
Globular Proteins: Myoglobin & Hemoglobin
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The polypeptide chains are folded into
spherical or globular shapes
Nonpolar amino acids are in the interior, and 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
More than one polypeptide chain may be present in a protein:
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Monomeric: contains one polypeptide chain
Multimeric: contains 2 or more polypeptide chains
Simple proteins: a protein in which only amino acid residues
are present:
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More than one protein su-bunit may be present
but all subunits contain only amino acids
Albuminoids – keratin in skin, hair, and nails;
collagen in cartilage
Albumins - egg albumin, serum albumin
Globulins – antibodies
Histones – chromatin in chromosomes
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 Function
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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
Major Categories of Proteins Based on Function
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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: Binds small biomolecules, e.g.,
oxygen and other ligands, and transport them to other
locations in the body and release them on demand.
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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
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present, hydrogen- bonding abilty, and chemical
reactivity.
>700 amino acids are known
Based on common “R” groups, there are
20 standard amino acids
Major Categories of Proteins Based on Function
Contractile proteins: necessary for all forms of movement.
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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
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Collagen is a component of cartilage
Keratin gives mechanical strength as well
as a protective covering to hair, fingernails,
feathers, hooves, etc.
Transmembrane proteins: span a cell membrane and help
control the movement of small molecules and ions.
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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
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Often the molecules that bind to enzymes
(catalytic proteins), thereby turning then “on”
and “off”, and thus controlling enzymatic
action.
Nutrient proteins: particularly important in the early stages of
life from embryo to infant.
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Casein (milk) and ovalalbumin (egg
white) are nutrient proteins
Milk also provide immunological protection
for mammalian young.
20.2 Amino acids: the building blocks for proteins
Amino acid – an organic compound that contains both an
amino acid (-NH2) and a carboxyl (-COOH) group attached to
same carbon atom
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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.
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Nomenclature
The position of carbon atom is alpha
-NH2 group is attached at alpha carbon
atom.
R = side chain – vary in size, shape,
charge, acidity, functional groups
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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 in 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 acids
get the 1st letter
All amino acids differ from one another by their R-groups
Three 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
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Polar amino acids: R-groups are polar;
hydrophilic – water- loving (soluble in wate
Polar acidic: contain carboxyl group as part of the side
chains
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COMPLETE PROTEIN – contains all the essential
amino acids in the proper amounts
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INCOMPLETE PROTEIN – 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 for soy protein
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COMPLEMENTARY PROTEINS – incomplete
proteins which when served together, complement
each other and provide all the essential amino acids
Polar basic; contain amino group as part of the side
chain
20.4
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Derived amino acids (“nonstandard” amino acids)
Usually formed by an enzyme-facilitated reaction
on a common amino acid after that amino acid
has been incorporated into a protein structure
Ex. Elastin (cysteine, desmosine, and isodesmosine),
collagen (hydroxyproline, and hydroxylysine),
Prothrombin (δ-carboxyglutamate)
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Chirality and amino acids
Four different groups are attached to an alphacarbon atom in all of the standard amino acids
except glycine (R- group is Hydrogen)
Therefore 19 of the 20 standard amino acids
contain a chiral center
Molecules with chiral centers exhibit enantiomerism
(left- and right-handed forms)
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
20.3 Essential Amino Acids
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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
20.5
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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
Under physiological conditions exists as Zwitterions:
an ion with + (positive) and – (negative) charges on
the same molecule with a net zero charge
Carboxyl groups give up a proton to
get a negative charge
Amino groups accept a proton to
become positive
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ISOELECTRIC POINT (pI)
Amino acids in solution exist in three
different species (zwitterions, positive ion,
and negative ion)
Equilibrium shifts with change in pH
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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
At pH values lower than pI, the carboxylate end of the
zwitterion picks up a proton from solution, the amino
acid acquires a net + charge, and migrate to the
negative electrode in an electric field
At pH values higher than pI, a proton is removed from
the ammonium end of the zwitterion, the amino acid
acquires a net negative (-) charge and migrate to the
negative electrode
For basic and acidic amino acids, the side chain can also
acquire a charge because it contains an amino or a carboxyl
group that can, respectively, gain or lose a proton.
Because of the extra site that can be protonated or
deprotonated, acidic and basic amino acids have four charged
forms in solution.
These four forms for aspartic acid, one of the acidic amino acids, are
Isoelectric Point
The pKa1 is for the functional group that has dissociated at its
isoelectric point. If two groups are dissociated at isoelectric pH,
the pKa1 is the higher pKa of the two. Therefore, pKa2 is for
the group that has not dissociated at isoelectric pH. If there are
two groups that are not dissociated, the one with the lower pKa
is used.
20.7 Peptides
Nature of Peptide Bond
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Under proper conditions, amino acids can bond
together to produce an unbranched chain of amino
acids
The reactions between amino group of one
amino acid and carboxyl group of another
amino acid
The length of the amino acid chain can vary from s
few amino acids to hundreds of amino acids
Peptide - a chain of covalently-linked amino acids
Peptide Bonds (amide) - a covalent bond between
the carboxyl group of one amino acid and the amino
group of another amino acid
N-terminal end – the structure of peptides is
represented beginning with the amino acid whose
amino group is free
C-terminal end – other end that contains free
carboxyl group
Amino acids are added to a peptide by forming
peptide bonds with the C-terminal amino acid
residues
Small peptide neurotransmitters
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Amino acid residues - the portion of an amino acid
structure that remains, after the release of H2O,
when an amino acid participates in peptide bond
formation as it becomes part of a peptide chain
The C-N bond of the peptide linkage has a partial
double bond character that makes it rigid and
prevents the adjacent groups from rotating freely
Almost all of the peptide bonds in proteins are planar
and have a trans configuration
Polypeptide - a long unbranched chain of amino acids
Peptide Nomenclature
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The IUPAC rules for doing this are:
Rule 1: The C-terminal amino acid residue
(located at the far right of the structure)
keeps its full amino acid name.
Rule 2: All of 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
(tryptophyl), cysteine (cysteinyl), glutamine
(glutaminyl), and asparagine (asparaginyl).
Rule 3: The amino acid naming sequence
begins at the N-terminal amino acid residue
Isomeric Peptides
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Peptides that contain the same amino acids but
present in different order are different molecules
(constitutional isomers) with different properties
Ex. Two different dipeptides can be formed
between alanine and glycine
The number of isomeric peptides possibly increases
rapidly as the length of the peptide chain increases
20.8 Biochemically important small peptides
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Many relatively small peptides have been shown to
be biochemically active. Functions for them include
hormonal action, neurotransmission, and antioxidant
activity.
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Small peptide hormones:
Produced by the pituitary gland
Nonpeptide (nine amino acid residues) with
six of the residues held in the form of a
loop by a disulfide bond formed between
two cysteine
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Enkephalins are pentapeptide neurotransmitters
produced by the brain and bind receptors with the
brain
Help reduce pain
Best-known enkephalins
Met-enkephalin: Tyr-Gly-Gly-Phe-Met
Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu
Small peptide antioxidants
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Glutathione (Glu-Cys-Gly) - a tripeptide – is present
in high levels in most cells
Regulator of oxidation–reduction reactions
An antioxidant and protects cellular contents
from oxidizing agents such as peroxides and
superoxides
Unusual structural feature –Glu is bonded to Cys
through the side-chain carboxyl group
Small peptide artificial sweeteners
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Aspartame (Asp-Phe) - Dipeptide sold under trade
names Equal and Nutrasweet
Approximately 180x as sweet as sucrose