PROTEIN

Proteins

Proteins are polymers

of amino acids.

Amino acids contain

both an amine and
carboxylate group
attached to the
same carbon called
the alpha carbon.
 Protein Structure - Primary
• Protein: chain of amino acids joined by
peptide bonds
 Protein Structure - Primary
• Protein: chain of amino acids joined by
peptide bonds
• Amino Acid
– Central carbon (Cα) attached to:
• Hydrogen (H)
• Amino group (-NH2)
• Carboxyl group (-COOH)
• Side chain (R)consist of a central C that is unique to
each amino acid
General Amino Acid Structure

H 2N Cα COOH

R
General Amino Acid Structure
At pH 7.0
H

+H3N Cα COO-

R
 AMINO ACIDS: Structure
• The side group creates unique
characteristics for each amino
acid so they differ in: shape,
size, composition, electrical
charge, and pH.
 WHAT IS PROTEIN MADE OF?
Proteins are a sequence of amino acids
Of the 20 amino acids that exist,
9 are essential amino acids, and
11 are non-essential
• There are also 4 amino acids that can
be considered conditionally
essential: arginine, tyrosine,
glutamine, and cysteine
General Amino Acid Structure
Structure of Proteins
 Amino Acids
• Chiral
 Chirality: Glyceraldehyde

D-glyderaldehyde L-glyderaldehyde
 Amino Acids
• Chiral
• 20 naturally occuring; distinguishing side
chain
20 Naturally-occurring Amino Acids
 Amino Acids
• Chiral
• 20 naturally occuring; distinguishing side chain
• Classification:
• Non-polar (hydrophobic)
• Charged polar
• Uncharged polar
Alanine:
Nonpolar
 Serine:
Uncharged Polar
Aspartic Acid
Charged Polar
 Glycine
Nonpolar (special case)
Table of α-Amino Acids
Found in Proteins
 *
Table of α-Amino Acids Found in Proteins Backbone of the amino acids is red,
R-groups are black
pK1 pK2 pK R
Amino Acid Symbol Structure*
(COOH) (NH2) Group

Amino Acids with Aliphatic R-Groups

Glycine Gly – G which R = hydrogen 2.4 9.8

Alanine Ala – A If R = methyl group (CH3) 2.4 9.9

Valine Val – V 2.2 9.7

Leucine Leu – L 2.3 9.7

Isoleucine Ile – I 2.3 9.8

 Non-Aromatic Amino Acids with Hydroxyl R-Groups

(Ser) is an amino acid in which R contains

Serine Ser – S 2.2 9.2 ≈13
an alcohol functional group

Threonine Thr – T 2.1 9.1 ≈13

 Amino Acids with Sulfur-Containing R-Groups

Cysteine Cys – C (Cys) contains sulfur 1.9 10.8 8.3

Methionine Met – M 2.1 9.3

 Acidic Amino Acids and their Amides

Aspartic (Asp) contains a carboxylic acid

Asp – D 2.0 9.9 3.9
Acid functional group

Asparagine Asn – N 2.1 8.8

Glutamic
Glu – E 2.1 9.5 4.1
Acid

Glutamine Gln – Q 2.2 9.1

 Basic Amino Acids

Arginine Arg – R 1.8 9.0 12.5

Lysine Lys – K 2.2 9.2 10.8

Histidine His – H 1.8 9.2 6.0

 Amino Acids with Aromatic Rings

Phenylalanine Phe – F 2.2 9.2

Tyrosine Tyr – Y 2.2 9.1 10.1

Tryptophan Trp – W 2.4 9.4

 Imino Acids

Proline Pro – P 2.0 10.6

Schematic Diagram of a helix such as is found in
wool fibres.
The red dotted lines show the hydrogen bonds
between amino acids along the chains
maintaining the helical structure.
Schematic Diagram of a sheet found in silk. The red
dotted lines show the hydrogen bonds between
amino acids along the chains maintaining the sheet
structure.
 The Peptide Bond
Amino acids are linked to each other to form
proteins by an amide linkage between the amine of
one amino acid to the carboxylate of another amino
acid. This amide linkage is known as the peptide
bond.
 The Peptide Bond
Dipeptide is formed when two amino acids
are joined.
Tripeptides contain three amino acid units.
Polypeptides contain 10 or more amino acid
units.
Proteins may contain 10,000 or more amino
acid units.
 AMINO ACID: Sequence

• Amino acids link in specific sequences to

form strands of protein
• One amino acids is joined to the next by a
PEPTIDE bond
Peptide Bond Formation
Peptide Chain
 Peptide Bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
 Peptide bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
– Results in shorter bond length
Peptide Bond Lengths
 Peptide bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
– Results in shorter bond length
– Double bond disallows rotation
 AMINO ACID: Sequence

• Dipeptide – 2 amino acids

• Tripeptide – 3 amino acids
• Oligopeptides – 4-10 amino acids
• Polypeptide – more than 10 amino acids
• Proteins in the body and diet are long
polypeptides (100s of amino acids)
 Protein: The Machinery of Life
NH2-Val-His-Leu-Thr-Pro-Glu-Glu-
Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-
Gly-Lys-Val-Asn-Val-Asp-Glu-Val-
Gly-Gly-Glu-…..

“Life is the mode of existence of proteins, and this mode

of existence essentially consists in the constant self-
renewal of the chemical constituents of these
substances.”
Friedrich Engles, 1878
 DENATURING of PROTEINS
• Acid, alkaline, heat, alcohol, and agitation can
disrupt the chemical forces that stabilize
proteins and can cause them to lose their
shape (denature)
• Denaturing of proteins happens during food
preparation (cooking, whipping, adding acids)
or digestion (in the stomach with hydrochloric
acid)
 PROTEINS: Function
Structural Functions:
• Collagen – is the most abundant protein
in mammals, and gives bone and skin
their strength
• Keratin – provides structure to hair and
nails
 Proteins

Proteins
are
a vital
compo
nent of
all living
things.
 Proteins

Plants can synthesize proteins from carbon dioxide,

water, and minerals like nitrates or sulfates.

Animals must consume proteins as part of their diet.

Humans can synthesize some amino acids, but must

obtain essential amino acids in a normal diet.
 Protein Function in Cell
1. Enzymes
• Catalyze biological reactions

2. Structural role
• Cell wall
• Cell membrane
• Cytoplasm
Protein Structure
Protein Structure
Hemoglobin-A Protein molecule in red
blood cells
 Hemoglobin: Red Blood Cell
(Erythrocyte)
• Protein in red blood cells

• Composed of four subunits, each

containing a heme group: a ring-like
structure with a central iron atom that
binds oxygen
Heme Groups in Hemoglobin
Composed of four
subunits, each
containing a heme
group: a ring-like
structure with a central
iron atom that binds
oxygen

Picks up oxygen in
lungs, releases it in
peripheral tissues (e.g.
muscles)
Hemoglobin – Quaternary Structure

Two alpha subunits and two beta subunits

(141 AA per alpha, 146 AA per beta)
Hemoglobin – Tertiary Structure

One beta subunit (8 alpha helices)

Hemoglobin – Secondary Structure

alpha helix
 Hydrogen Bonding
And Secondary Structure

alpha-helix beta-sheet
Hemoglobin – Primary Structure

-Val-His-Leu-Thr-Pro-Glu-Glu-
NH2

Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-
Gly-Lys-Val-Asn-Val-Asp-Glu-Val-
Gly-Gly-Glu-…..
beta subunit amino acid sequence
 PROTEIN: Functions
ENZYMES
• Enzymes are proteins that catalyze chemical
reactions without being used up or destroyed in
the process
• Used in – digestion, releasing of energy from
nutrients for fuel, triggering reactions that build
muscle and tissue
 Enzymes

Enzymes are biological catalysts. Most are proteins.

Many are highly specific, only catalyzing a single
reaction or related group of reactions.

The substrate is the reactant molecule whose reaction

the enzyme catalyzes.
 Enzymes
The activity of many enzymes can be explained by the
induced fit model.

According to the induced fit model, the substrate molecule

bonds to the enzyme at the active site, forming an
enzyme-substrate complex.

This complex can then catalyze the reaction of the substrate

and form products.

Enzyme + Substrate → Enzyme-substrate complex ↔

Enzyme + Products
 Enzymes
Induced Fit Model
 Enzymes
Inhibition
The action of enzymes can be inhibited. One
mechanism of enzyme inhibition has a
molecule bonding to the enzyme protein at
another site other than the active site. This
changes the shape of the protein and prevents
the substrate from bonding at the active site.
This mechanism is used to control the action
of certain enzymes.
 Enzymes

Inhibition
 Enzymes

Cofactors: Some enzymes require another molecule to be

present for proper functioning of the enzyme. Cofactors
can be inorganic ions (Zn2+, Mg2+, …) or organic
molecules.

Coenzyme: A cofactor that is a nonprotein organic

molecule.

Apoenzyme: Pure protein part of an enzyme.

 Enzymes in Medicine
Diabetic test strips use two enzymes to measure blood sugar.
One enzyme catalyzes the oxidation of glucose, producing
hydrogen peroxide as a by-product. The other enzyme
catalyzes the breakdown of hydrogen peroxide and oxidizes a
dye to produce a color change.

Enzymes can be monitored to diagnose liver damage or heart

damage.

Enzymes can also be used to break up clots after a heart

attack or to increase clotting to treat hemophelia.
 Enzymes in Industry
Enzymes have many industrial applications
including the production of baby foods, beer,
sweeteners for soft drinks, animal feeds, and
blue jeans.
 Enzymes in Everyday Life
Enzymes are used in stain removers and meat
tenderizers. Those that are lactose-intolerant
can also take enzymes to reduce the
discomfort caused by ingesting dairy foods.
Worldwide production of enzymes is worth
more than $1 billion per year.
 PROTEIN: Functions

HORMONES
• Hormones are chemical messengers that
are made on one part of the body, but act
on cells in other parts of the body
• Insulin, Glucagon
• Antidiuretic Hormone (ADH)
 PROTEIN: Functions

IMMUNE FUNCTION
• The Immune Response is a series of steps
your body takes to mount an attack against
invaders
• Antibodies are blood proteins that attack
and inactivate bacteria and viruses
• Once an antibody has been made for a
certain invader, your body can more quickly
respond (Immunization)
 PROTEIN: Functions

FLUID BALANCE
• Fluids in the body are intracellular or
extracellular (interstitial and intravascular)
and must remain balanced
 PROTEIN: Functions

FLUID BALANCE
• Blood proteins like albumin and globulin
help to regulate this balance by remaining
in the capillaries and attracting fluid
• Edema is the result of fluid imbalance
 PROTEIN: Functions

ACID-BASE BALANCE
• Proteins help to maintain a stable pH level
in our body fluid by picking up extra
hydrogen ions when conditions are acidic,
and donating hydrogen ions when
conditions are alkaline
• Otherwise, the resulting conditions of
acidosis or alkalosis could lead to coma or
death
 PROTEIN: Functions

TRANSPORT
• Lipoproteins (chylomicrons, LDL, HDL)
• Albumin transports a variety of nutrients such
as calcium, zinc, and Vitamin B6
• Transferrin transports iron (hemoglobin – a
protein, contains iron, but it transports oxygen)
• Proteins may also acts as channels or pumps
across the cell membrane
 PROTEIN: Functions
ENERGY SOURCE
• If the diet does not provide enough energy, the
body must begin to break down its own protein
• The proteins are broken down into individual
amino acids, then deaminated, and the
remaining carbon, hydrogen, and oxygen
compounds are used to make energy or glucose
• If the diet contains too much protein, the excess
will be converted to glucose, or stored as fat
 DIGESTION

• No digestion of protein takes place in the

mouth, it begins in the stomach
• Hydrochloric acid denatures protein and
also converts pepsinogen to pepsin
• Pepsin breaks the protein down into
peptides of various lengths and some
amino acids
• Pepsin completes ~ 10-20% of digestion
 DIGESTION
• Pancreas makes trypsinogen and
chymotrypsinogen (proenzymes) in
response to protein in the small intestine
• They will be activated to trypsin and
chymotrypsin (now called proteases)
• Proteases break down polypeptides into
smaller peptides (very few peptides have
been broken down to amino acids at this
stage)
 DIGESTION and ABSORPTION

• The intestinal wall produces peptidases

which continue to split the remaining
polypeptides into tripeptides, dipeptides,
and some amino acids
• These smaller units are transported into
the enterocytes
 ABSORPTION
• In the enterocyte, other peptidases
immediately digest everything into single
amino acids which are absorbed into the
bloodstream
• Some amino acids share the same transport
system, so if you take in a large amount of
one particular amino acid, you may be
inhibiting the absorption of others
 ABSORPTION
• Most protein absorption takes place in the
duodenum and jejunum
• Most amino acids are absorbed into the
bloodstream, but some remain in the
enterocytes and are used to synthesize
enzymes and new cells
• >99% of protein enters the bloodstream as
amino acids
• Absorption of whole protein can cause a
severe allergic reaction
 PROTEINS in the BODY
• Amino Acid Pool – amino acids that are
available throughout the body (tissues and
fluids) for use when needed
• Protein Turnover – of the ~ 300 grams of
protein synthesized by the body each day, 200
grams are made from recycled amino acids
 NITROGEN EXCRETION
• Amino acid breakdown yields an amino group
(containing nitrogen)
• This molecule is unstable and is converted to
ammonia
• Ammonia is toxic, so it is excreted from the cells
and sent to the liver, where it is converted to urea
and water
• The urea is transported to the kidney, where it is
filtered from the blood and finally sent to the
bladder for excretion in the urine
• Nitrogen is also lost through hair, skin, GI cells
mucus, nails, and body fluids like sweat
 How Much Protein Do We Need?
Adults:
0.8 grams of protein per kilogram of body weight
per day

Endurance Athletes:
1.2 to 1.4 g/kg/day

Heavy Weight Trainers:

1.7 to 1.8 g/kg/day
 Protein Sources
Almonds (1 cup) 24 grams
Pinto Beans (1 cup) 15 grams
Cheese (1 oz.) 7 grams
Ham (3 oz.) 18 grams
1 Egg 6 grams
2% Milk (1 cup) 8 grams
Clams (3 oz.) 60 grams
Whole Wheat Bread 3 grams
Lean Hamburger 30 grams
Peanut Butter (1 T) 4 grams
Salmon (3 oz.) 20 grams
Tofu (4 oz.) 9 grams
Yogurt (8 oz.) 10 grams
White rice (1 cup) 4 grams
 PROTEIN QUALITY
• Complete Proteins – proteins that provide
all the essential amino acids (most animal
proteins)
• Incomplete Proteins – proteins that are
missing one or more essential amino acids
(most plant proteins except soy protein)
• Incomplete proteins can be served with a
complementary protein to make it complete
 PROTEIN: Health Effects
INSUFFICIENT DIETARY PROTEIN
• Protein-Energy Malnutrition (PEM) can occur
anywhere in the world, but is most common in
developing countries
• Kwashiorkor
• Marasmus
• In industrialized nations, PEM may exist in the
elderly population, in the poor, and those with
anorexia, cancer, AIDS, or malabsorption
syndromes
 PROTEIN: Health Effects
EXCESS DIETARY PROTEIN
• May strain the kidneys
• May cause mineral losses (especially calcium)*
• May increase risk of obesity*
• May increase risk of heart disease*
• May increase risk of cancer*
*only with animal protein
 VEGETARIANISM
• What are the PROS and CONS of
vegetarianism?
 ATKIN’S DIET
• How does it work?
• What are some of the possible negative
consequences?