Proteins: Structure

and Functions

The Nitrogen Cycle

 Large molecules
 Made up of chains of amino acids
 Are found in every cell in the body-the
chief constituents of all cells in the body
 Are involved in most of the body’s
functions and life processes
 The sequence of amino acids is
determined by DNA
What are proteins
 Instrumental in about everything that an
organism does:
◦ Structural support and Movement
◦ Energy: 4 Cal/g
◦ Transport of nutrients (e.g. hemoglobin: oxgyen) and
waste products
◦ Transmission of impulses: Nerves
◦ Transmission of hereditary characteristics: nucleoproteins
◦ Assist the immune system
 Defense against infection: antibodies
◦ Regulation of metabolic processes
 Catalysis of biochemical reactions : enzymes
 Regulation of metabolic processes: hormones
◦ main enzymes in a cell and regulate metabolism by
selectively accelerating chemical reactions.
What are proteins
 “protein” is derived from the Greek word “proteios”
meaning “of first importance”

 Functions of protein
Provide structural and mechanical support:
-Building of new cells
-Maintenance of existing cells
-Replacement of old cells
-Muscular activity (contraction)
-Components of skin, hair, nails, connecting and supporting
tissues

 Source of energy (when necessary):

-1 g protein ~ 4 kcal energy
-1 g carbohydrate ~ 4 kcal energy
-1 g lipid ~ 9 kcal energy

Best Sources of Protein

How Does the Body Use Protein?

Structural Differences Between
Carbohydrates, Lipids, and Proteins
 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
Structure of Proteins
 Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L)

Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N)

Glutamine (Q) Serine Threonine (T) Tyrosine (Y) Cysteine (C)

(S)

Asparatic acid (D) Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H)

Yellow: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

The 20 Amino Acids

 must be consumed in the diet
Essential

can be synthesized in
Non-
the body
Essential

Conditional

cannot be synthesized due to illness or lack

of necessary precursors

Premature infants lack enzymes needed to synthesize arginine

Essential, Nonessential, and Conditional Amino Acids

 R Different side chains, R,
determine the properties of 20
NH3+ C COO- amino acids.

Amino group Carboxylic

acid group
H

All amino acids in proteins are

L-amino acids, except for
glycine, which is achiral

α-amino acid: The Stereochemistry Stereoisomers of α-amino acids

Amino acids with hydrophobic R groups Amino acids with hydrophilic R groups
 Some R groups are bases, others are acids.

Amino acids with charged (ionized

functional groups at cellular pH
Properties of Cysteine side chain
 Amphoterism accounts for the
ability of amino acids to act as
buffers in the blood.

Modified or Unusual Amino Acids Amphoteric Nature

Isolectric point The isoelectric points of some proteins
Isoelectric focusing
• Forms when the
acid group (-COOH)
of one amino acid
joins with the
amine group (-NH2)
of a second amino
acid

• Forms through
condensation

• Breaks through
hydrolysis

The peptide bond Condensation and Hydrolytic Reactions

Examples of Oligopeptide
 Primary Assembly

STRUCTURE

PR O C E S S
Secondary Folding

Packing
Tertiary

Quaternary Interaction

Molecular Data on Some Proteins

Protein Structures
 Primary structure
(Amino acid sequence)
↓ Any alteration in the
Secondary structure
（α-helix, β-sheet） structure or sequencing
↓ changes the shape and
Tertiary structure
（Three-dimensional structure
formed by assembly of
function of the protein.
secondary structures）
↓
Quaternary structure
（Structure formed by more than
one polypeptide chains）

Protein Structures
 -ala-glu-val-thr-asp-pro-gly- …
Primary Structure
 can be determined by amino acid sequencing of the
protein
 can also be determined by sequencing the gene
and then using the codon information to define the
protein sequence
 amino acid analysis means percentages; (less
Sequence of a.a informative than the sequence)
bonded to form
polypeptide
*occurs at the
ribosome

Primary structure
 A slight change in primary structure can affect a protein’s
conformation and ability to function.

Primary structure of bovine insulin

  regular recurring arrangement of the amino acid
chain;
 local spatial arrangement of a polypeptide’s
backbone atoms (without regard to side chain
conformation);
α-helix and β-sheet, have regular hydrogen-bonding patterns  main-chain H-bonds that define short-range
Secondary
Structure order in structure

Forms:
 α, 310, ϖ helices
Folding/coiling of  β pleated sheets and the strands that comprise
polypeptide due to them
attractions and
repulsions
 Beta turns
between like parts  More specialized structures like collagen helices
of the a.a
*occurs in the cytosol

α-helix β-sheet Secondary structures

 Amino acids form a coil or spiral
 The coils consist of loops of amino acids held
together by hydrogen bonds (between the –H of
the –NH2 of one amino acid and the O of the
C=O of the acid part of another amino acid
 Each turn of the helix contains an average of 3.6
amino acids
 Flexible and elastic
 Amino acid side chains face outward
 ~ 10 residues long in globular proteins

Examples:
 Alpha-keratin (hair, wool, nails, …)

Charateristics of α-helices Alpha helix

 310 helix is NH to C=O  Consists of parallel strands of
three residues earlier polypeptides held together by H-bonds
 More kinked; 3 residues  Flexible but not elastic
per turn  No defined interval in sequence number
 Often one H-bond of this between amino acids involved in H-bond
kind at N-terminal end of
an otherwise α-helix Example: Silk (strong but resistant to
 ϖ-helix: even rarer: NH to stretching)
C=O five residues earlier

Other helices Beta strands

 Folds straighten H-bonds
 Side-chains roughly
perpendicular from sheet
plane
 Consecutive side chains up,
then down
 Minimizes intra-chain
collisions between bulky
side chains
Sheets: roughly planar
 N-to-C directions are the same for both
strands
 You need to get from the C-end of one strand
to the N-end of the other strand somehow
 H-bonds at more of an angle relative to the
approximate strand directions
 Therefore, more pleated than anti-parallel
sheet
Parallel Beta sheet
 Neighboring strands extend in opposite  Antiparallel
directions beta sheets
 Complementary C=O…N bonds from top to
running parallel
bottom and bottom to top strand
 Slightly pleated for optimal H-bond strength
to the silk fiber
Example: Silk fibrion axis
 Multiple
repeats of (Gly-
Ser-Gly-Ala-
Gly-Ala)n

Anti-parallel beta sheet Silk fibroin

Beta turns Collagen Triple Helix
  determined by a variety of interactions of the R groups and
between R groups
 The overall 3-D arrangement of atoms in a single
polypeptide chain
 Described in terms of sequence, topology, overall fold,
domains
 Gives proteins their specific biologic activity
 interactions include
 hydrogen
bonds ( polar
and/or charged
areas)
 ionic bonds
between charged
R groups, and
 hydrophobic
interactions
 van der Waals
interactions among
hydrophobic R
groups.

Tertiary Structures Tertiary Structures

 Alternating α, β create parallel β-pleated Stabilized by
 Salt bridges: formed between positively and
sheet negatively charged groups within the protein
structure (example: carboxyl and amino side chains
 Bends around as it goes to create barrel found in glu, lys, arg, asp
 van der Waals interactions,
 Hydrogen bonds (can form between different
segments of the coil)
 Disulfide bonds (can form between cysteine groups in
the different parts of the coil)
 Hydrophobic bonds (can be formed in nonpolar amino
acids folded on the “inside” of the protein)
 Polar group interactions (formed between polar amino
acids on the “outside” of the protein molecule and
water molecules)

Example of tertiary structure:

TIM Barrel Tertiary Structures
• Occurs when two or more protein
units (each with its own primary,
secondary, and tertiary structure)
combine to form a complex unit
• Spatial arrangement of subunits of
proteins composed of multiple
polypeptides (protein complexes)
• Individual chains can be identical
or different
• If they’re the same, they can
be coded for by the same gene
• If they’re different, you need
more than one gene

Quatenary Structures Levels of protein structure

Not all proteins have all four levels of structure
◦ Monomeric proteins don’t have quaternary
structure
◦ Tertiary structure: subsumed into
secondary structure for many structural
proteins (keratin, silk fibroin, …)
◦ Some proteins (usually small ones) have no
definite secondary or tertiary structure;
they flop around!
 The amount of protein present in food is
determined by determining the amount of N
present
 The average %N in a protein is 16% or 1/6 of
the amount of protein.
Example:
A 100g sample of food yields 4 g of N on
chemical analysis. What is the amount of
protein?
Answer: ?

Percent Composition
 Is based on solubility, composition, (2) Classification According to Composition
function or shape
Conjugated proteins are classified based on the nature of
(1) Classification According to Solubility
non-protein portion of the molecule

Classification of Proteins Classification of Proteins

 Cont’n . . (2) Classification According to Composition Cont’n . . (2) Classification According to Composition

Glycoproteins Structural glycoproteins: collagen

• (carbohydrate: hexoses, mannose, galactose, pentoses • Lubricants: mucin and mucous secretions
arabinose and xylose, and sialic acids)
• Glucose is not found in glycoproteins except for collagen
• Transportation molecules:
• Human cell membranes are 5% carbohydrate present in • Immunoglobulins: interferon
glycoproteins and glycolipids • Hormones: thyrotropin (TSH)
• Enzymes: hydrolases and nucleases
Examples: • Hormone receptor sites
glycophorin – found in membranes of human erythrocytes
Heparin – inhibits blood clotting
• Specification of human blood types

Classification of Proteins Classification of Proteins

 Cont’n . . (2) Classification According to Composition
Lipoproteins (proteins containing lipids;
part of cell membranes)
• Plasma lipoproteins (consist of a neutral lipid
core of TAG and cholesterol ester that is
surrounded and stabilized by free cholesterol,
protein, and phospholipid.
-The relative proportions of nonpolar lipid, protein, and
polar lipid determine the density, size, and charge f the
resulting lipoproteins
Classification of Proteins
Cont’n . . (2) Classification According to Composition
• Chylomicrons
• Produced in the intestinal mucosa used to
transport dietary lipids into the blood plasma
via the thoracic lymph duct
• Removed from the plasma with a half life of
5-15 min
• Responsible for the creamed-tomato-soup
appearance of the blood following a meal
containing fats
Classification of Proteins
 Cont’n . . (2) Classification According to Composition
• VLD lipoproteins
• Transport TAG synthesized by the liver to
other parts of the body
Note: the breakdown of VLDL produce intermediate
density lipoproteins (IDL) and low density lipoprotein
(LDL)
• LDL provides cholesterol for cellular needs;
in excess, thought to promote coronary
heart disease by clogging coronary artery
walls and eventually develop into
atherosclerotic plaque
Classification of Proteins
Cont’n . . (2) Classification According to Composition
• HD lipoproteins (HDL)
- Involve in the catabolism of other lipoproteins
• Lipoprotein (a)
-Recently detected lipoprotein with similar structure as that
of human plasminogen
-Links atherosclerosis and thrombosis but found to be an
independent risk factor for coronary heart disease
↑ LDL: increases risk of coronary artery disease ↑ HDL: reduces
the risk of coronary artery disease in women
Women HDL: 55 mg/100 mL Men HDL: 45 mg/100 mL
- HDL is increased by aerobic exercise and running
- Marathon runner average HDL: 65 mg/100 mL
Classification of Proteins
 (3) Classification According to Shape (4) Classification According to Function
 Globular proteins – consists of polypeptides
folded into shape of a “ball”; soluble in water or
form colloidal dispersions
◦ Length to width ration: <10
◦ Examples: hemoglobin, albumins, globulins

 Fibrous proteins – consists of parallel polypeptide

chains that are coiled and stretch out; insoluble
in water
◦ Length to width ration: >10
◦ Examples: collagen, fibrin, myosin

Classification of Proteins Classification of Proteins

 Protein structure
determines protein
function.

Protein structure and function

1.Involved in structure: tendons ligaments blood clots
(e.g. collagen and keratin)
2.Contractile proteins in movement: muscle, microtubules
(cytoskelton, mitotic spindle, cilia, flagella)
1. Most proteins which move around (e.g.
albumen, casein in milk)
2. Proteins with binding sites:
enzymes, haemoglobin, immunoglobulins,
membrane receptor sites

Fibrous proteins Globular Proteins

 CATALYTIC: enzymes  Colloidal Nature (forms colloidal dispersion with
STORAGE: ovalbumen (in eggs), casein (in milk), water)
zein (in maize) ◦ Can pass through a filter paper but not a membrane
TRANSPORT: haemoglobin -Proteins present in the blood stream cannot pass
through capillaries and should remain in the blood
COMMUNICATION: hormones (eg insulin) and stream otherwise there is damage with the membranes
neurotransmitters of the kidneys - nephritis
CONTRACTILE: actin, myosin, dynein (in  Denaturation (unfolding and rearrangement of
microtubules) the secondary and tertiary structures of a
PROTECTIVE: Immunoglobulin, fibrinogen, blood protein without breaking the peptide bonds
clotting factors ◦ Protein loses its biological activity
TOXINS: snake venom ◦ Reversible denaturation – the protein can be restored
STRUCTURAL: cell membrane proteins, keratin to its original conformation by reversing the conditions
(hair), collagen that caused denaturation else its irreversible
◦ Primary structure is unchanged by denaturing

Protein Classification by function Properties

 Alteration of the protein’s
shape and
 Primary structure is
unchanged by denaturing
Properties: Denaturation
 Alcohol can coagulate all proteins except
prolamines
◦ Forms hydrogen bonds that compete with naturally
occurring H-bonds in the polypeptide; irreversible
 Salts of Heavy Metals
◦ very poisonous when ingested
◦ disrupt the salt bridges and disulfide bonds in the
protein
◦ irreversible
 Bichloride of mercury: HgCl2 (Antidote: egg white and
must be removed from the body through emetic)
 Lunar caustic: AgNO3 (mild sol’n: disinfectant in the
eyes of neonates; strong solutions: cauterize fissures
and destroy excessive granulation tissues
Denaturizing Agent
 Heat  pH
◦ Disrupts intermolecular interactions ◦ Change in pH can disrupt H-bonds and salt
 Mild: reversible
 Intense: irreversible
bridges
Testing urine for presence of protein is done by  Acids
heating  Bases
 Alkaloidal Reagents ◦ Casein in milk is coagulated in the stomach to
◦ Irreversible; disrupts H-bonds and salt bridges form curd when comes in contact with HCl.
 Tannic acid (used for treatment of burns) ◦ Heller’s Ring test: Testing urine for presence of
 Picric acid
albumin with HNO3 (white ring)
 Radiation can coagulate proteins
◦ Long period of exposure to acid or base,
◦ Can be irreversible if H-bonds and hydrophobic
bonds are disrupted peptide bonds are broken
 UV, X-ray

Denaturizing Agent Denaturizing Agent

 Oxidizing and reducing agents  When the amino acid pool reaches
◦ Irreversible; disrupts disulfide bonds capacity the amino acids are broken
 Oxidizing agent: HNO3 down to their component parts for other
 Reducing agents: sulfides and oxalates uses
 First deamination must occur (primarily
 Salting Out
in the liver and may also occur in the
◦ Proteins are insoluble in saturated salt
kidneys) to produce ammonia
solutions and precipitate out unchanged.
 Carbon-containing remnants are
 Proteins can be separated from a mixture by
saturated solution of salt where they coagulate
converted to:
◦ glucose, if they are glucogenic amino acids,
and removed through filtration and purified via
through gluconeogenesis
dialysis
◦ fatty acids and stored as triglycerides in
 Mechanical agitation adipose tissue

Denaturizing Agent Properties: Deamination

 Healthy, nonpregnant adults should
consume enough to replace what is used
every day
◦ The goal is to achieve the equilibrium.
 A pregnant woman, people recovering
from surgery or injury, and growing
children should consume enough to build
new tissue

How much protein do you need? Nitrogen Balance and Imbalance

 High quality protein
 •_______________
 •_____________________________
 •_____________________________
 It helps to be aware of:
 •Amino acid score
 •Limiting protein
 •Protein digestibility corrected amino acid
score (PDCAAS)
 •Biological value of protein rates absorption
and retention of protein for use
Not all protein is created equal
 Complete proteins
 •Contain all ________ essential amino acids
 •Usually __________ source are complete
proteins
 •Are considered higher quality
 Incomplete proteins
 •Low in one or more essential amino acid
 •Usually ____________ sources are
incomplete
Protein Quality
 Protein intake recommendations Too much protein Too little protein
•
 •_______% of total daily kilocalories Protein-energy malnutrition
 •Adults over 18
poses risks of (PEM)
• Protein is used for energy rather
 -______ g/kg daily ◦ heart disease than its other functions in the body
• Other important nutrients are in
 American College of Sports Medicine, the ◦ kidney stones short supply
• More prevalent in infants and
American Dietetic Association, and other ◦ calcium loss from children
•17,000 children die each day as a
experts advocate bones result
• Without adequate protein
 •________% more protein for competitive ◦ colon cancer • Cells lining the GI tract are not
athletes participating in endurance exercise sufficiently replaced as they
or resistance exercise ◦ Displacement of slough off
• Digestive function is inhibited
 •Typically this population eats more and other nutrient-rich, • Absorption of food is reduced
disease preventing • Intestinal bacteria gets into the
therefore gets additional protein blood and causes septicemia
foods • Immune system is
compromised due to
malnutrition and cannot fight
infection
Protein Needs Eating too much or too little protein
Kwashiorkor Marasmus
 Results from a severe
 Severe protein deficiency deficiency in kilocalories
◦ Generally result of a diet high in ◦ Frail, emaciated
grains and deficient in protein appearance
◦ Weakened and appear
 Symptoms range from apathetic
◦ Edema in legs, feet, and stomach ◦ Many cannot stand without
support
◦ Muscle tone and strength diminish
◦ Looks old
◦ Hair is brittle and easy to pull out ◦ Hair is thin, dry, and lacks
◦ Appear pale, sad, and apathetic sheen
◦ Prone to infection, rapid heart ◦ Body temperature and
blood pressure are low
rate, excess fluid in lungs, ◦ Prone to dehydration,
pneumonia, septicemia, and water infections, and
and electrolyte imbalances (Image from unnecessary blood clotting
http://www.thachers.org/pediat
rics.htm

Types of PEM Types of PEM

Marasmic Kwashiorkor  Medical and nutritional treatment can
 Chronic deficiency in dramatically reduce mortality rate
kilocalories and protein  Should be carefully and slowly implemented
◦ Have edema in legs and Step 1 – Address life-threatening factors
arms  Severe dehydration
◦ Have a “skin and bones”  Fluid and nutrient imbalances
appearance Step 2 – Restore depleted tissue
◦ With treatment the  Gradually provide nutritionally dense kilocalories and
edema subsides and high-quality protein
appearance becomes Step 3 – Transition to foods and introduce physical
more like someone with activity
marasmus

Types of PEM Treatment for PEM

End