Announcement …

Extra Class: 27th Jan 19 (Sunday)

10AM-10:55 AM: PSàL2(III), SNàL3(IV)

11:30AM-12:25PM : PSàL2(I), SNàL3(II)

NO CLASS : 7th Feb 2019, Thursday

L4: Proteins, Fats…

Dr. P. Satpati,
BSBE, IIT Guwahati
 Polypeptide (or Protein) Folds in 3D

Linear poly-Peptide Folded Poly-peptide

(Native structure of protein)

In water, hydrophobic residues (shown as black circles) tend to hide from

water, there by spontaneously folding protein to its native structure.
A protein is functional
only in its native structure

Chemicals like, urea,

GdnHCl, and Heat, unfold
protein.
Urea Guanidine
These are called
denaturing agents. hydrochloride

Extent of unfolding can be

measured by determining
residual function of the
protein

Tm = Melting point. At this

point the protein is 50%
unfolded
 Anfinsen’s Experiment

• Sequence determines structures

• Proof : renaturation of ribonuclease by
Anfinsen after denaturation
– Correct disulfide bonds

Transition state

Unfolded ∆G = 5-15 kcal/mol

state
Folded state

Reaction process
 How proteins fold ?
Lets take a small protein = say 101 aa

Number of peptide bonds = 100

Assumption : Each aa can have 3 main chain rotation angle (Φ ,Ψ)

[I mean three possible minima in the (Φ ,Ψ) space ].

Total number of minima/structure = 3100 =5x1047

Typical rotations take ~ 10-13 Sec

So a search of all conformation will take

=(5x1047)x10-13 = 5x1034 sec = (5x1034)/(365x24x3600) = 1.6x1027 Years

Age of the universe from big bang ~ 14×109 years

small proteins fold spontaneously on a millisecond or even microsecond time scale.

Levinthal's paradox 6
 Sickle-cell Disease
A single Base Mutation:

Hydrophilic Hydrophobic
 Sickle-cell Disease

•Glu " Val mutation generates a

hydrophobic patch in each β subunit.
•In deoxygenated state such
hydrophobic patches get exposed.
•Two hemoglobin interacts through
those hydrophobic patch and stick.

•Forms elongated strands of sticking

hemoglobins
•Crystallize and precipitates

•RBC changes shape

•Oxygen carrying capacity decrease
•Sickle shaped RBC blocks blood vessels
•Increased lysis of RBC

Sickle cell Normal

 Molecular Representation

ATP

Space filling
Ball-and-stick
Two ball can fuse if they are bonded
Ball for atom and stick for bond
Size and color of a ball depend upon atom
 Molecular Representation
A protein usually have thousands of atoms.
Ball-and-stick or Space-filling representation are not suitable to show a protein

Space-filling model
 Molecular Representation

Molecular Representation
Ribbon Diagram
Helix
Ribbon (Cartoon)

Ribbon Diagram is
better for
representation of a
protein

β strand
N terminal
C terminal

$Very good to understand the fold architecture of a protein.

$Note the type of ribbon for different secondary structure and
meaning of arrow head.
Molecular Representation

Molecular Surface

Suitable to:
Understand charges on
surface;
Detect active
site/pockets
 Protein Chemistry of Human Hair
•Main constituent of hair : α keratin
•It’s a helical protein.
•Two copies coil over each other. Forms intermolecular disulphide bonds
•Further coiling leads to thick fibrous structure.
 Protein Chemistry of Human Hair
Curling of Hair:
 Human Hemoglobin

Heme Gr.

Adult Hemoglobin

•Made up of two identical subunit α and β, each present in two copies

•Heme Gr. binds oxygen
Sources of Protein from diet

Total daily requirement for protein

for males is ~ 56g/day,
for females it is ~ 46 g/day
9 Essential amino acids
(Lecture 1, Essential nutrients )
Fats/Lipids
Fats with Structural or Biological Importance

Fatty Acids
•SFA
•MUFA
•PUFA
•Essential fatty acids
Ø N-3 fatty acids (w-3 FA)
Ø N-6 fatty acids (w-6 FA)
 SATURATED
(SFA)

MONOUNSATURATED
(MUFA)

CIS VS. TRANS

POLYUNSATURATED
(PUFA)
 Lipids
q Lipids are non-polar (hydrophobic) compounds, soluble in organic solvents.
q Most membrane lipids are amphipathic, having a non-polar end and a polar end.
q Fatty acids consist of a hydrocarbon chain with a carboxylic acid at one end.
q A 16-C fatty acid:
O
CH3(CH2)14-COO- C
non-polar polar 4
3 1 O
2

qDouble bonds in fatty acids usually have the

cis configuration. fatty acid with a cis- 9

double bond
qMost naturally occurring fatty acids have an
even number of carbon atoms.
v There is free rotation about C-C bonds in the fatty acid hydrocarbon, except about double bond.
v Each cis double bond causes a kink in the chain.
v Rotation about other C-C bonds would permit a more linear structure than shown, but there would
be a kink.
 Partially hydrogenated

Deep fat frying

Trans fatty acids behave like saturated fat in the body.

 Nomenclature of fatty acids

A 16-C fatty acid with one cis double bond between C atoms 9-10 may be represented as
16:1 cis D9.

O
Some fatty acids and their common names: C
14:0 myristic acid; 4
3 1 O
2
16:0 palmitic acid;
18:0 stearic acid; 9
18:1 cisD9 oleic acid fatty acid with a cis-
18:2 cisD9,12 linoleic acid double bond
18:3 cisD9,12,15 a-linonenic acid
20:4 cisD5,8,11,14 arachidonic acid
20:5 cisD5,8,11,14,17 eicosapentaenoic acid (an omega-3)
Two Essential fatty acids (Lecture 1, Essential nutrients )
 Properties of fatty acids

• Saturated fatty acids are solid at room temperature.

• Melting point depends on chain length and degree of unsaturation.

1. Unsaturated fatty acids have lower melting point
2. Shorter fatty acids have lower melting point

• Cis double bonds disrupts intermolecular packing and therefore lower melting temperature.
Three major kind of membrane lipids

Ø Phospholipids

Ø Glycolipids

Ø Cholesterol
 Phospholipids
Ø Phospholipids are abundant in all biological membrane
Ø A phospholipid is constructed from four components: One or more
fatty acids, a platform where fatty acids are attached, a phosphate ,
and an alcohol attached to phosphate
Ø Fatty acid component gives hydrophobic barrier , rest of the molecule
has hydrophilic properties and interacts with aqueous membrane

• 2 classes of phospholipids
-Glycerophospholipids/Phosphoglycerides -glycerol backbone
-Sphingomyelin-sphingosine backbone
• Glycerophospholipids
-essential for membrane structure
-Most abundant membrane lipids
-No genetic defect in humans
• Sphingolipids
-occur chiefly in the cell membranes of the brain and nervous tissue
 Glycerophospholipids/Phosphoglycerides
O
o Glycerophospholipids (phosphoglycerides), are common
constituents of cellular membranes. O H2C O C R2
o They have a glycerol backbone. R1 C O CH O
o Hydroxyls at C1 & C2 are esterified to fatty acids.
H2C O P O
o In phosphatidate, the simplest phosphoglyceride, the C3
is esterified with a phosphate group(Pi) O
phosphatidate

o In most glycerophospholipids (phosphoglycerides), O

Pi is in turn esterified to OH of a polar head group (X): e.g.,
O H2C O C R2
serine, choline, ethanolamine, glycerol, or inositol.
o The 2 fatty acids tend to be non-identical. They may differ in R1 C O CH O
length and/or the presence/absence of double bonds.
H2C O P O X

O
glycerophospholipid
Common Phosphoglycerides found in membrane
 Sphingolipids OH OH
H
H2C C CH
Ø Sphingolipids are derivatives of the lipid sphingosine, which has a
H3N+ CH
long hydrocarbon tail, and a polar domain that includes an amino
group. HC

(CH 2 )12

sphingosine CH 3

Ø Sphingosine may be reversibly phosphorylated to produce the signal O P O

molecule sphingosine-1-phosphate.
O OH
Ø Other derivatives of sphingosine are commonly found as constituents H
of biological membranes. H2 C C CH

H3N+ CH

HC

(CH2 )12
sphingosine-1-P
CH3
 Sphingolipids
OH OH
H
The amino group of sphingosine can form an amide bond with a fatty acid H2C C CH
carboxyl, to yield a ceramide.
In the more complex sphingolipids, a polar “head group" is esterified to NH CH
the terminal hydroxyl of the sphingosine moiety of the ceramide.
O C HC

CH3 O R (CH 2 )12

H2 H2
+
H3C N C C O P O ceramide CH 3
CH3 O OH
phosphocholine H
H2C C CH Sphingomyelin has a phosphocholine or
sphingosine phosphethanolamine head group.
NH CH
Sphingomyelins are common constituent of plasma
O C HC membranes
fatty acid Sphingomyelin, with a phosphocholine head group, is
R (CH2 )12
similar in size and shape to the glycerophospholipid
Sphingomyelin CH3 phosphatidyl choline.
 Glycolipids

§ Sugar containing lipids

§ Glycolipids in animal cells are derived from
Sphingosine
CH2OH
§ A cerebroside is a sphingolipid (ceramide) or simplest
glycoside with a monosaccharide such as glucose or OH O
galactose as polar head group. H OH
OH H O
H
H H H2C C CH
§ A ganglioside is a ceramide with a polar head group
that is a complex oligosaccharide, including the acidic H OH NH CH
sugar derivative sialic acid.
O C HC
§ Cerebrosides and gangliosides, collectively called
glycosphingolipids, are commonly found in the outer R (CH2 )12
leaflet of the plasma membrane bilayer, with their
cerebroside with
sugar chains extending out from the cell surface.
-galactose head group CH3
Triglycerides
medium chain triglycerides
- weight gain

Fig. 6-3, p. 132

 Cholesterol

Ø Cholesterol is a Lipid based on steroid nucleus

Ø Cholesterol, an important constituent of cell membranes, has a rigid ring system and a short
branched hydrocarbon tail.
Ø Cholesterol is largely hydrophobic.
Ø Cholesterol has one polar group, a hydroxyl, making it amphipathic.
 Cholesterol
1. Almost all cholesterol in our body is made by
our body. NOT from out Diet.

2. Body makes 3000 mg/day

Why?
1. Cell membranes (Brain: lots and lots of cholesterol)
2. BILE production
3. Vitamin D, A, K2, E
4. Adrenal hormone (Stress hormone)
5. Sex hormones
6. Myelin synthesis (lipid layer around nervous system)
7. Helps immune system (control WBC)
8. Bind and neutralize toxin from bacteria
Based on the density, there are five classes of lipoproteins (from high to low)

1. High-density lipoprotein (HDL),

2. Low-density lipoprotein (LDL),
3. Intermediate density lipoprotein (IDL),
4. Very-low-density lipoprotein (VLDL),
5. Chylomicron (CM).