Lecture 3

Jacqueline De Vera
Proteins and Amino Acids
Structural Differences Between Carbohydrates, Lipids, and Proteins

Figure 6.1
The Anatomy of an
Amino Acid

Figure 6.2b
 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
Proteins: Enzymes, Binding Proteins, Structural
Proteins – all made from Amino Acids
 Carbon Numbering System

A
 Amino Acids: Classification
• Common amino acids can be placed in five basic
groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Invented the One Letter
Amino Acid Code.
 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
 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
Condensation
and Hydrolytic Reactions

Figure 6.3
 Stereochemistry

Enantiomers
• each of a pair of molecules that are
mirror images of each other.

S ("Sinister" → Latin= "left")

R ("Rectus" → Latin= "right")
 L- isomer

D- isomer

Mirror image
L and D forms
Which Form Occurs in Water ?
Glycine Acid/Base Titration

pH, [H+]

pH.[H+]
Compare Amino Acids to Simple Carboxylic Acids
and Amines
Glutamate has 3 pKa’s
Histidine has 3 pKa’s
Uncommon Amino Acids
Peptide Bond Formation
Structure of a Simple Peptide

Ser-Gly-Tyr-Ala-Leu or SGYAL
Peptide bonds are trans!
 Naming peptides:
start at the N-terminus

• Using full amino acid names

• Serylglycyltyrosylalanylleucine
• Using the three-letter code abbreviation
• Ser-Gly-Tyr-Ala-Leu
• For longer peptides (like proteins) the one- letter code
can be used
• SGYAL
AEGK
 Peptides: A Variety of Functions
• Hormones and pheromones
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g., toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
 Proteins are:

• Polypeptides (covalently linked -amino acids) + possibly:

• cofactors
 functional non-amino acid component
 metal ions or organic molecules

• coenzymes
 organic cofactors
 NAD+ in lactate dehydrogenase

• prosthetic groups
 covalently attached cofactors
 heme in myoglobin

• other modifications
 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
 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
Secondary Structure
• Hydrogen bonding

The alpha-helix Beta-pleated sheets

intramolecular bonding intermolecular bonding

"R" groups are sticking out sideways from the main helix. "anti-parallel" sheet
Tertiary Structure

The model shows the alpha-helices in the

secondary structure as coils of "ribbon".
The beta-pleated sheets are shown as flat
bits of ribbon ending in an arrow head.

3-dimensional shape

Ionic interactions
Hydrogen bonds
van der Waals dispersion forces
Sulphur bridges
Quarternary
Structure

• clustering of several individual peptide

or protein chain
 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
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
 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
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 Absorption
• Amino acids are absorbed in the small intestine
• Amino acids are transported to the liver from the intestines via the portal vein
• In the liver, amino acids are
• Used to synthesize new proteins
• Converted to energy, glucose, or fat
• Released to the bloodstream and transported to cells throughout the body
• Occasionally proteins are absorbed intact
 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
Protein Synthesis

Figure 6.8
Protein Synthesis

Figure 6.8
Protein Synthesis

Figure 6.8
Codons
• A codon is a sequence of
three DNA or RNA
nucleotides that corresponds
with a specific amino acid or
stop signal during protein
synthesis.
 Deamination
• When the amino acid pool reaches capacity the amino acids are broken down
to their component parts for other uses
• First deamination must occur
• Carbon-containing remnants are
• Converted to glucose, if they are glucogenic amino acids, through gluconeogensis
• Converted to fatty acids and stored as triglycerides in adipose tissue
Metabolic Fate of Amino Acids

Figure 6.7
 Quick Review
• During digestion
• Proteins are broken down to amino acids with the help of
• Gastric juices
• Enzymes in the stomach and small intestine
• Enzymes from the pancreas and small intestine lining
• Limited supply of amino acids exist in the amino acid pool
• The amino acid pool acts as a reservoir for protein synthesis
• Surplus amino acids are
• Deaminated
• Used for glucose or energy
• Stored as fat
• Nitrogen is converted to urea and excreted in urine
 How Does the Body Use Protein?
Functions of protein
1. Provide structural and mechanical support
2. Maintain body tissues
3. Functions as enzymes and hormones
4. Help maintain acid base balance
5. Transport nutrients
6. Assist the immune system
7. Serve as a source of energy when necessary
Nitrogen Balance and Imbalance

Figure 6.12
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
Kwashiorkor
Pathophysiology
Decrease synthesis of ferritin
Impaired synthesis of Beta-lipoproteins
resulting to fat accumulation and eventually
to hepatomegaly(enlarged liver)

Figure 6.16
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
 Total lack of nutrition in the diet.
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
 Treatment for PEM
• Medical and nutritional treatment can dramatically reduce mortality rate
• Should be carefully and slowly implemented
• Step 1 – Address life-threatening factors
• Severe dehydration
• Fluid and nutrient imbalances
• Step 2 – Restore depleted tissue
• Gradually provide nutritionally dense kilocalories and high-quality protein
• Step 3 – Transition to foods and introduce physical activity