Paper 3:

Fundamentals
of
Biochemistry and Biomolecules.

Unit II:
Proteins and Amino Acids

2015 RRA, FLS, JSS University, Mysuru

 What Are Proteins?
• Large molecules
• Made up of chains of amino acids
• Are found in every cell in the body
• Are involved in most of the body’s functions and
life processes
• The sequence of amino acids is determined by
DNA

2015 RRA, FLS, JSS University, Mysuru

 Structure of Proteins
• Made up of chains of amino acids; classified by
number of amino acids in a chain
– Peptides: fewer than 50 amino acids
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Polypeptides: more than 10 amino acids
– Proteins: more than 50 amino acids
• Typically 100 to 10,000 amino acids linked together
• Chains are synthesizes based on specific bodily DNA
• Amino acids are composed of carbon, hydrogen,
oxygen, and nitrogen
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Structural Differences Between Carbohydrates,
Lipids, and Proteins
The Anatomy of an Amino Acid

Figure 6.2b
Uncommon amino acids

Hydroxylysine and hydroxyproline. Collagen is a fibrous protein

made up of three polypeptides that form a stable assembly, but only if
the proline and lysine residues are hydroxylated. (requires vitamin C
for reduction of these amino acids to hydroxy form)

Thyroxine, an iodinated derivative of tyrosine, found in

thyroglobulin (produced by thyroid gland; requires iodine in diet)

g-carboxyglutamic acid (i.e. glutamic acid with two carboxyl

groups) found in certain blood clotting enzymes (requires vitamin K
for production)

N-methyl arginine and n-acetyl lysine. Found in some DNA binding

proteins known as histones
Non protein aminoacids…………..
Amino acid derivatives not found in proteins

•Serotonin (derivative of tryptophan) and g-amino butyric acid (a

derivative of glutamic acid) are both neurotransmitters

•Histamine (derivative of histidine) involved in allergic response

•Adrenaline (derivative of tyrosine) a hormone

•Various antibiotics are amino acid derivatives (penicillin)

 Peptide Bonds Link Amino Acids
• Form when the acid group (COOH) of one amino
acid joins with the amine group (NH2) of a second
amino acid
• Formed through condensation
• Broken through hydrolysis

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Condensation and Hydrolytic Reactions

Figure 6.3
Features of the peptide bond

• Partial double-bond character

• Prevents free rotation around the bond between the carbonyl carbon
and the nitrogen of the peptide bond.
• However, the bonds between the a-carbons and the a-amino or a-
carboxyl groups can be freely rotated.
• The -C=O and -NH groups of the peptide bond are uncharged, but
they are polar and involved in hydrogen bonding in secondary
structure.
 Essential, Nonessential, and
Conditional
• Essential – must be consumed in the diet
• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be synthesized
due to illness or lack of necessary precursors
– Premature infants lack sufficient enzymes needed to
create arginine

2015 RRA, FLS, JSS University, Mysuru

 Structure of the Protein
• Four levels of structure
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure

Any alteration in the structure or sequencing

changes the shape and function of the protein

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 Denaturing
• Alteration of the protein’s shape and thus
functions through the use of
– Heat
– Acids
– Bases
– Salts
– Mechanical agitation
• Primary structure is unchanged by denaturing

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Denaturing a Protein

Figure 6.5
 Quick Review
• Proteins are chains of combination of amino acids
• Amino acids contain carbon, hydrogen, oxygen,
nitrogen, and sometimes sulfur
• Unique amino acids consist of a central carbon with a
carboxyl group, a hydrogen, a nitrogen-containing
amine group, and a unique side chain
• There are 20 side chains and 20 unique amino acids
– 9 essential amino acids
– 11 nonessential amino acids
• At time these become conditionally essential
• Amino acids link together with peptide bonds by
condensation and break apart by hydrolysis
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 Reactions of Aminoacids

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 Quick Review
• Attractions and interactions between the side chains
cause the proteins to fold into precise three-
dimensional shapes
• Protein shape determines its function
• Proteins are denatured and their shapes changed by
– Heat
– Acids
– Bases
– Salts
– Mechanical agitation

2015 RRA, FLS, JSS University, Mysuru

Protein Digestion: Part 1

Figure 6.6
Protein Digestion: Part 2

Figure 6.6
Protein Digestion: Part 3

Figure 6.6
Protein Digestion: Part 4

Figure 6.6
 Amino Acid Metabolism
• Liver metabolizes amino acids, depending on
bodily needs
• Most amino acids are sent into the blood to be
picked up and used by the cells
– Amino acid pool is limited but has many uses
• Protein turnover – the continual degradation and
synthesizing of protein

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Protein Synthesis

Figure 6.8
Metabolic Fate of Amino Acids

Figure 6.7
 How Does the Body Use Protein?
• Functions of protein
– Provide structural and mechanical support
– Maintain body tissues
– Functions as enzymes and hormones
– Help maintain acid base balance
– Transport nutrients
– Assist the immune system
– Serve as a source of energy when necessary

2015 RRA, FLS, JSS University, Mysuru

 Quick Review
• Protein plays many important roles in the body,
including:
– Helping facilitate muscular contraction
– Promoting satiety and appetite control

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 How Much Protein Do You Need?
• Healthy, nonpregnant adults
– Should consume enough to replace what is used every
day
– The goal is nitrogen balance
• Pregnant woman, people recovering from surgery
or injury, and growing children
– Should consume enough to build new tissue

2015 RRA, FLS, JSS University, Mysuru

Nitrogen Balance and Imbalance

Figure 6.12
 Protein Quality
• Complete proteins
– Contain all nine essential amino acids
– Usually animal source are complete proteins
– Are considered higher quality
• Incomplete proteins
– Low in one or more essential amino acid
– Usually plant sources are incomplete

2015 RRA, FLS, JSS University, Mysuru

 Protein Needs
• Protein intake recommendations
– 10–35% of total daily kilocalories
– Adults over 18
• 0.8 g/kg daily

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 Quick Review
• Protein quality is determined by digestibility and
types and amounts of amino acids
• Plant proteins can be complemented with proteins
from other plant sources or animal source to
improve their quality
• Adults should consume 0.8 g/kg/day of protein

2015 RRA, FLS, JSS University, Mysuru

 Best Sources of Protein
• Proteins are abundant in
– Dairy foods
– Meats
– Poultry
– Meat alternatives such as dried beans, peanut butter,
nuts, and soy
• 3 oz serving of cooked meat, poultry, or fish
– Provides 21–25 grams of protein
– About 7 g/oz
– About the size of a deck of cards
– Adequate amount for one meal
2015 RRA, FLS, JSS University, Mysuru
Best Sources of Protein

Figure 6.14
 Quick Review
• A well-balanced diet can meet daily protein needs
• Best source of protein are animal products
– Eggs
– Lean meats
– Low-fat or fat-free dairy products
• Plant proteins such as soy, grains, and vegetables
supply substantial proteins
• Most people consume adequate protein from
their diet and do not need protein supplements

2015 RRA, FLS, JSS University, Mysuru

 Eating Too Much Protein
• Risk of heart disease
• Risk of kidney stones
• Risk of calcium loss from bones
• Risk of colon cancer
• Displacement of other nutrient-rich, disease
preventing foods

2015 RRA, FLS, JSS University, Mysuru

 Eating Too Little Protein
• Protein-energy malnutrition (PEM)
– Protein is used for energy rather than its other
functions in the body
– Other important nutrients are in short supply
– More prevalent in infants and children
• 17,000 children die each day as a result

2015 RRA, FLS, JSS University, Mysuru

 Too Little Protein
• Without adequate protein
– Cells lining the GI tract are not sufficiently replaced as
they slough off
– Digestive function is inhibited
– Absorption of food is reduced
– Intestinal bacteria gets into the blood and causes
septicemia
– Immune system is compromised due to malnutrition
and cannot fight infection

2015 RRA, FLS, JSS University, Mysuru

Types of PEM: Kwashiorkor
 Severe protein deficiency
• Generally result of a diet high in
grains and deficient in protein
 Symptoms range from
• Edema in legs, feet, and stomach
• Muscle tone and strength
diminish
• Hair is brittle and easy to pull out
• Appear pale, sad, and apathetic
• Prone to infection, rapid heart
rate, excess fluid in lungs,
pneumonia, septicemia, and
water and electrolyte imbalances
(Image from http://www.thachers.org/pediatrics.htm)

Figure 6.16
Types of PEM: Marasmus
 Results from a severe deficiency
in kilocalories
• Frail, emaciated appearance
• Weakened and appear apathetic
• Many cannot stand without
support
• Look old
• Hair is thin, dry, and lacks
sheen
• Body temperature and blood
pressure are low
• Prone to dehydration,
infections, and unnecessary
blood clotting
Figure 6.17
 Types of PEM: Marasmic
Kwashiorkor
• Chronic deficiency in
kilocalories and protein
– Have edema in legs and arms
– Have a “skin and bones”
appearance
– With treatment the edema
subsides and appearance
becomes more like someone
with marasmus

2015 RRA, FLS, JSS University, Mysuru

 Quick Review
• High-protein diet may play a role in increasing risk of heart
disease, kidney problems, and calcium loss from bones
• Consuming too much protein from animal sources increase
saturated fat intake
• Too much protein can displace whole grains, fruits, and
vegetables, which have been shown to reduce many chronic
diseases
• Low-protein diet can lead to loss of bone mass
• PEM is caused by inadequate protein and/or kilocalorie
intake
– Kwashiorkor – severe protein deficiency
– Marasmus – severe kilocalorie deficiency

2015 RRA, FLS, JSS University, Mysuru

 Vegetarian Diet
• People choose vegetarian diets for a variety of
reasons
– Ethical
– Religious
– Environmental
– Health

• Vegetarians must consume adequate amounts of

a variety of food and should plan meals well

2015 RRA, FLS, JSS University, Mysuru

 Putting It All Together
• Majority of daily kilocalories should come from
carbohydrate-rich foods
• Fat intake should be no more than about one-
third of daily kilocalories
• Protein should provide the rest of the daily
kilocalories

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 Titrating properties of Amino acids

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 H+ OH-

100% HA 50% HA 100% A-

Protonated 50% A- deprotonated

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2015 RRA, FLS, JSS University, Mysuru
2015 RRA, FLS, JSS University, Mysuru
2015 RRA, FLS, JSS University, Mysuru
2015 RRA, FLS, JSS University, Mysuru