Chapter 7 Proteins

Part 1 Section 7.1-7.3

Dr Bobadilla

Slides adapted from Dr. Paul Larsen

What Are Proteins?
• Complex organic molecules
– Chains of amino acids, which are composed of carbon,
hydrogen, oxygen and nitrogen

• There are 20 different amino acids, so a protein with 100

amino acids could have many different sequences.

• The specific sequence of each

protein is encoded by the gene
(DNA) for that protein.

• All cells in the body contain

proteins.
 Types and Functions of Proteins
• Structural proteins (like collagen) in cartilage, ligaments, bones, hair,
skin and nails (hair and nails are composed of the protein keratin.)
• Contractile proteins in muscles that enable muscles to move.
• Enzymes that catalyzes all the reactions inside cells and outside cells
(e.g. in the digestive system and in blood)
• Pigment proteins like melanin (determine color of eyes, hair and skin)
• Clotting proteins needed for blood to clot
• Transport proteins like hemoglobin (transports O2) and membrane
proteins that selectively let/help solutes get in/out of cells
• Some hormones are proteins, e.g., insulin and glucagon
• Hormone receptors (often on outsides of cells)
• Antibodies (components of the immune system, carried in blood)
• The body’s own proteins are not usually used for energy (except in
starvation, as a last resort when normal energy stores of carbohydrates
and lipids are exhausted).
 Amino Acids
• Proteins are made of smaller units called amino acids
• 20 different amino acids found in proteins
• Each amino acid is composed of
– An amino group (contains nitrogen)
– An acid group
– A “side chain” (R group) -- this is what is different in the 20
amino acids.

nitrogen
 Essential vs. Nonessential Amino Acids
• Essential amino acids: the 9 amino acids (out of 20 total)
that the human body cannot make, so they must be
supplied in foods we eat.
• Nonessential amino acids: the 11 amino acids that humans
can make ourselves
• We need all 20 amino acids in order to make proteins --
if we lack even 1 type of amino acid, we can’t make any
proteins at all, because virtually all proteins have some of
each of the 20 different amino acids in their structures.
 William C. Rose and Essential Amino Acids
• In the 1930s William C. Rose undertook experiments at the Univ. of Illinois
(Champaign-Urbana) that introduced the idea of an essential amino acid
into nutrition in both human and rodent diets. Nutritionists had known for a
long time that rats fed a diet in which the only protein was zein from corn
would inevitably die early.
• Rose worked with the constituent amino acids rather than proteins. He still
found, however, that the rats died regardless of the combination of amino
acids he tried. But if the milk protein casein was added to their diet, the
ailing rats recovered.
• Rose concluded that casein must contain an unknown amino acid not found
in zein that was essential to life. In a long series of experiments extracting
and testing various fragments of casein,
Rose discovered threonine, the essential amino acid
that provided a satisfactory diet for rodents when
added to other amino acids. In addition, Rose
showed that it is not synthesized by the body, but
must be obtained from the diet.

William Cummings Rose (1887-1985)

 William C. Rose and Essential Amino Acids
• Rose argued that if there was one essential amino acid, there could be
others. Over the years, he manipulated the rodent diet to establish the
primary importance of ten amino acids: lysine, tryptophan, histidine,
phenylalanine, leucine, isoleucine, methionine, valine, and arginine* in
addition to the newly discovered threonine. (*sometimes essential in
humans, too)

• Rose proved that different amino acids are essential for different
organisms.
• In the 1940s Rose undertook a ten-year research project on the human
diet, including the nutritive properties of amino acids. Most significantly,
Rose investigated the role of proteins in metabolism and the
metabolic interrelationships among amino acids. This work led to the
determination of amino acid requirements for humans (with volunteer grad
students eating specially baked wafers with defined amounts of amino
acids).
 Proteins in Foods
• Nearly all foods contain protein, but no natural food is 100%
protein.

• Animal foods typically have more protein than plant foods

– By weight, beef is ~20-30% protein; drained, water-packed tuna fish is
~25% protein; egg is only ~12% protein
– 3 oz of lean ground beef supplies ~23 g protein
– 3 oz of steamed broccoli or cooked carrots supplies only ~1 g protein

• Among plant foods, seeds, tree nuts (e.g., walnuts, cashews,

almonds, pistachios), and legumes (e.g., soybeans, peas,
peanuts, lentils and beans) supply more protein than fruit or
the edible leaves, roots, flowers, and stems of vegetables.
– 3 oz of almonds, dry-roasted peanuts, or sunflower seed kernels
supplies ~20 g of protein
 Proteins in Foods
Protein Content of Some Common Foods (per portion)
 Protein quality
• Not all dietary protein is created equal b/c
not all proteins will have all 20 amino acids

High quality (complete) Low quality (incomplete

protein: protein that protein): nutritional term
contains all of the for protein that lacks or
essential amino acids in has inadequate
amounts that support amounts of one or
normal protein synthesis more of the essential
amino acids
 Protein Quality
High quality (complete) protein:

Animal products: meat, poultry, fish, eggs, and dairy products

– Egg protein: very high protein quality; easy to digest,
with pattern (amounts per g of protein) of essential amino
acids closely resembling what is needed by humans
– Among animal proteins, gelatin, which is made from
collagen (a connective tissue protein in animals that
accounts for about 25% of the protein in mammalian
bodies) is the exception -- it is a highly incomplete
source of protein (low quality protein), because it contains
a very high proportion of just 2 amino acids (both
nonessential), and not nearly enough of the 9 essential
amino acids.
 But wait
If egg is only 12% protein, how can it be
considered a high quality complete
protein?

Think, pair, share a complete answer

 Protein Quality, continued
Low quality (incomplete) protein

Limiting amino acids: the essential amino acids not present in

high enough amounts in a dietary source of protein (often
tryptophan, threonine, lysine, and/or the sulfur-containing amino
acids methionine and cysteine)

Most plant proteins are low-quality

• Corn and other grains, and also nuts and seeds, have limiting
amounts of lysine.
• Beans and other legumes have limiting amounts of tryptophan and
methionine.

EXCEPTIONS: quinoa seeds and soy protein

• Both are excellent sources of high-quality (complete) protein.
 Does this mean the meat-based diets are
better than vegetarian since vegetarian diets
will comprise more low-quality proteins?
 Protein Quality, continued
Combinations of plant foods can result in a complete source
of essential amino acids with complementary sources of
protein.

– Combining foods from the 3 protein-rich plant groups can result in a

complete protein source without animal products:
1. legumes: such as dry beans, peas, peanuts, and lentils (soybeans
actually provide complete protein themselves)
2. grains: such as wheat, rye, rice, corn, oats, and barley
3. seeds and nuts: such as sunflower and pumpkin seeds, pecans,
and walnuts

Diets should include a variety of foods!

Remember phytochemicals?
Eat the Rainbow
 How Your Body Synthesizes Proteins
• Cells connect the combinations of the 20 amino acids in a
specific order according to information provided by genes
• Amino acids are connected by peptide bonds.
– Polypeptides: longer chains
of amino acids (> ~50)

– Each different colored

bead in the figure
represents one of
the 20 different
amino acids.
– The “links” that
connect the
amino acids are
peptide bonds.
 Abbreviated Scheme for Protein Synthesis
Protein with
DNA transcription translation specific
(gene) enzymes in mRNA amino acid •
in cytoplasm; sequence
cell nucleus requires ribosomes,
enzymes, amino acids
and tRNA molecules

Folding and
Amino acids come from diet sometimes
OR your body makes them— further
the recipe for the order of the “processing”
sequence is in your DNA

Protein in
final, folded,
functional
https://learn.genetics.utah.edu/content/basics/tra
nscribe/
form
protein synthesis video
Baking a cake analogy

DNA

RNA

protein
 3-Dimensional Shape of a Protein
After It “Folds”
• Proteins in living systems are only functional after they assume their 3
dimensional shape.
• The 3-D structure is dictated by the sequence of amino acids.
• Example: the protein hemoglobin, which is found in high concentrations in
your red blood cells, carries oxygen from your lungs through the blood to all
the tissues in your body.
• Hemoglobin has 4 chains
of amino acids (shown
schematically in different
colors), each with a heme
unit (shown in red) that has
an iron in it that binds the
oxygen.
• The need for iron in heme
(which is also found in a
number of other important
proteins) is one of the reasons
your body requires iron as a
micronutrient.
 Sometimes Wrong Amino Acids Are Inserted in Protein Sequences.
• If the abnormal amino acid sequence results from a genetic mutation
(change in the DNA sequence of the gene), then there aren't normal protein
molecules to carry out the function of that protein.

• Example: the defective hemoglobin that

results from the “sickle” mutation in the
sequence of a polypeptide chain of Sickle cell anemia is more
hemoglobin, a heritable condition. common among people of
• If 2 of the mutant (defective) chains are African, Caribbean, or
present in the 4-chain molecules, the Mediterranean ancestry.
molecules aggregate (glom together) into
long fibers, distorting the shape of the
red blood cells into “sickle” shapes,
which clog the small blood vessels and
cannot transport oxygen efficiently.
• The result is pain, organ damage, and
sometimes premature death.

a) normal red blood cell; b) sickle cell

 Protein Denaturation (Unfolding)
• Denaturation: disruption of the normal 3-D structure of a protein,
“unfolding” it, by altering the conditions
• Conditions can be altered, for example, by
– Heating, e.g.,
• Cooking raw egg white, which is a concentrated solution of mostly
protein in water, makes the egg white solidify.
• Cooking foods usually makes them more digestible by denaturing the
protein
– Mechanical denaturation, agitation, e.g.,
• Beating an egg white, or whipping
cream
– Chemical disruption of the protein
structure, e.g.,
• marinating meats in
wine (alcohol denatures
the meat proteins,
tenderizing the meat)
• treating milk with lemon juice
(acidic) curdles the protein in the
milk (useful for making lemon pie)
• acid in gastric juice denatures dietary proteins
 Proteins Require Digestion Before Absorption
Proteases: enzymes that cleave proteins; some proteases are digestive
enzymes
1. Digestion begins in the stomach
– Stomach secretes hydrochloric acid, which denatures proteins
– Pepsin (enzyme active at very acidic pH) digests proteins into smaller
polypeptides
2. Lumen of small intestine:
– digestive proteases secreted by pancreas, e.g., trypsin and
chymotrypsin, which break down polypeptides into shorter peptides
and amino acids
3. Inside absorptive cells of small intestine, final digestion (breakdown) of the
di- and tripeptides occurs into free amino acids
- absorptive cells release more proteases that break down the shortened
peptides into tripeptides (3 amino acids), dipeptides (2 amino acids), and
amino acids
– Amino acids are the end products of protein digestion.
4. Amino acids go from absorptive cells into portal vein of circulatory system,
which carries them to liver, and on into general circulation.
5. Very little dietary protein escapes digestion -- almost none excreted
Protein Digestion
and Absorption
• All the body’s
cells get the
amino acids
they need
(including the
essential
amino acids)
via the
circulatory
system.
 Protein Turnover
• We can recycle old/unneeded proteins into new ones
• Protein turnover: Breaking down old or unneeded proteins into
amino acids and recycling the amino acids
• Amino acids that are not incorporated into proteins become part
of
– Amino acid “pool”: a readily available supply of amino acids
that can be used for protein synthesis
• The liver makes most of the nonessential amino acids for the
rest of the body via two main types of reactions
– Transamination and deamination reactions that interconvert
carbon skeletons and amino acids, so body can keep pools
of amino acids balanced, adjusted to relative needs.

Protein alone is not considered a “living thing.” Our hair and nails
are made of keratin proteins. Once our hair cells make keratin we
can’t ‘fix’ that protein structure with shampoos or conditioners that
have protein—our protein comes from within
 Transamination and deamination balance supplies of AAs.
• Deamination: removal of nitrogen-containing group from an
unneeded amino acid, making the amino acid into a “carbon
skeleton” (lacking the N-containing amino group)
• Transamination: transfer of nitrogen-containing group (amino
group) from an unneeded amino acid to another carbon
skeleton, forming a different amino acid
Ammonia for making urea in liver
+
DEAMINATION

TRANSAMINATION
(reversible)

(a different carbon skeleton)

Transamination reactions don’t generate
any free ammonia, just transfer amino
group from one C skeleton to another.

Deamination

Toxic waste product

Excess amino acids (not needed) are

not stored -- they’re broken down by
deamination.
 Deamination and Urea Formation
• Deamination
– occurs primarily in the liver
– removes the amino group (NH2)
from glutamic acid to form
ammonia (NH3), a very toxic
waste product
– leaving the C skeleton for the
cell to use for energy or to build
other molecules like glucose or
fats.
• To detoxify and excrete the
ammonia, liver converts it to urea
– urea is not toxic and very water-
soluble,
– Urea travels through
bloodstream to kidneys, which
filter out the urea and eliminate
it in urine.
 If your body needs to make more alanine, a
nonessential amino acid, and has an excess of
glycine, what process would most likely occur
to increase the concentration of alanine?
 Nitrogen Balance
• You lose some N every day,
mostly as urea (and
creatinine, a N-containing
waste product made by
muscle cells)
• Some loss from growth (e.g.
hair, nails) and production of
new proteins and cells
• Even though body recycles a
lot of amino acids, some
replacement amino acids
have to come from dietary
protein.
• Nitrogen balance
(equilibrium): state in which
nitrogen intake is balanced Healthy state (body is meeting
with nitrogen losses protein and energy needs)
 Positive Nitrogen Balance
• Positive nitrogen balance: protein
turnover and nitrogen intake are
greater than nitrogen losses
• Body is gaining/retaining more N
than it loses.
• Person is eating more protein to
satisfy the increased need for amino
acids from dietary protein.
• Occurs during periods of rapid
growth, e.g.,
– Pregnancy
– Infancy and puberty
– Periods of recovery from illness
or injury
– Performing resistance exercise
• Positive nitrogen balance is
stimulated by hormones, e.g.,
increased levels of insulin,
growth hormone, or testosterone.
 Negative Nitrogen Balance
• Negative nitrogen balance: nitrogen
losses are greater than turnover and
nitrogen intake.
• Body is losing more N through the
kidneys than it is gaining/retaining.
• Person is not eating enough protein to keep
up with the demand, or is missing an
essential amino acid

• Occurs during or as a result of

– periods of starvation
– low protein diets or digestive tract
diseases that interfere with amino acid
absorption
– serious illnesses like kidney diseases
– severe injuries/blood loss
– Fever, injuries, or burns

• Negative nitrogen balance is stimulated by

different hormones, e.g., increased
amounts of thyroid hormone or cortisol (a
“stress” hormone)