Lecture 3

Molecules of Life II:

Lipids and Proteins

LIF101
 Lipids Fatty, oily, or waxy organic compounds

Mostly made up of hydrocarbons hence they show very little

tendency to dissolve in water and are “hydrophobic”.
http://www.biochem.arizona.edu/classes/bioc462/462 http://www.familyhealthavenue.com/2009/

Functions of lipids :
a/NOTES/LIPIDS/Lipids.html 04/know-something-about-triglycerides/

1) Main energy reservoirs.

Fat : Triglyceride
2) Structural materials e.g. in Fatty acids
the cell membrane and
surface coatings.

3) Signaling molecules:
communication between cells http://wellbeinganddiseases.com/?p=220
http://alevelnotes.com/Biological-Membranes/128
Sterols
Phospholipids
Waxes
 Fatty acids
Organic compound that consists of a chain of
carbon atoms with an acidic carboxyl group Stearic acid : Saturated fatty acid
at one end and hydrogen atoms occupying
most of all the remaining bonding sites.

Carbon chain of saturated types has single

bonds only; that of unsaturated types has
one or more double bonds

Oleic acid : Monounsaturated fatty acid

Linoleic acid : Polyunsaturated fatty acid

 Fats: Lipids that have one, two or three fatty acids
attached to glycerol
Animal fats : butter, lard etc.
Plant fats : groundnut oil, sunflower oil, coconut oil etc.

Triglycerides
Most natural fats from animal and plant sources are made up of triglycerides: fats having
three fatty acid tails attached to glycerol.

http://www.familyhealthavenue.com/2009/
04/know-something-about-triglycerides/
Triglycerides are the body’s most abundant lipids and the richest
source of energy.

The energy yield per gram is twice that of starch.

Triglycerides are stored

as droplets in cells of
body fat.

A thick layer of
http://medicineworld.org/stories/lead/12-2010/fat-cells-become-
useful-stem-cells.html

triglycerides under the

skin of some animals such
as penguins help insulate
their body against near
freezing temperatures of
their habitat. http://www.bbc.co.uk/southyorksh
ire/content/image_galleries/kev_o
_donnell_antarctic_gallery.shtml
Most animal fats have many saturated
fatty acids hence they pack together by
weak interactions. Thus they are solid at
temperatures where most plant fats
remain liquid.

Plant fats have many monounsaturated

and polyunsaturated fatty acids which
have “kinks” in their structure and hence
cannot have strong packing interactions
and thus remain liquid. http://healthfuleatingtips.wordpress.com/2011/03/14/saturated-and-trans-fats/

In unsaturated fatty acids there are

two possible arrangements around
the C=C double bond:
One produces a bend or kink and is
the “cis” conformation and the other
is almost straight and is the “trans”
conformation.

http://biology.clc.uc.edu/courses/bio104/lipids.htm
Trans fats
Fast foods like french fries have a high
proportion of trans fats as the oil is
reused many times to fry the food and
this converts many of the cis
conformations to trans. Processed
foods like margarine also undergo a
process called partial hydrogenation
which increases their shelf-life but also http://thevitaminm.com/2011/01/07/study-trans-fat-labeling/
http://thevitaminm.com/2011/01/07/study-trans-fat-
labeling/

produces more trans fats.

Trans fats in hydrogenated vegetable oils raise blood cholesterol more than any other fat, and
directly alter the function of arteries and veins

Eating as little as 2 grams a day of hydrogenated vegetable oils increases risk of atherosclerosis
(hardening of the arteries), heart attack, and diabetes.

Trans fat consumption has also been linked to cancer of the large intestine (colon).
Phospholipids
Lipid with a highly
polar phosphate group
in its hydrophilic
head, and two
nonpolar, hydrophobic
fatty-acid tails.

http://alevelnotes.com/Biological-Membranes/128
It is the main constituent of eukaryotic cell membranes which is made up of a bilayer
of phospholipids. The heads of one layer are in the interior of the cell which is a
watery environment and the heads of the other layer are dissolved in the fluid
exterior of the cells.

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/phosphb.htm

https://www.ck12.org/biology/phospholipid-bilayer/lesson/Phospholipid-Bilayers-BIO/
 Sterols and their derivatives
Sterols are the lipids that do not have a fatty acid component. All sterols have a rigid backbone of
four fused carbon-rings and differ with respect to the number position and type of functional groups .

https://courses.lumenlearning.com/wm-
biology1/chapter/reading-signaling-molecules/

Sterol backbone
http://www.anabolic-
bible.org/ShowPage.aspx?callpage=Synthetic_De
velopment
http://wellbeinganddiseases.com/?p=220
https://in.pinterest.com/pin/424464333608451003/

Sterols are present in cell membranes. Cholesterol

is the most common type in animal tissues.
Cholesterol can be used to produce Vitamin D,
steroids and bile salts. Steroids include hormones
such as testosterone and estrogen, bile salts help
in digestion of fats in the small intestine.

http://xbodyconcepts.com/can-vitamin-d-boost-
https://en.wikipedia.org/wiki/Bile_acid testosterone-levels/
 Excess fat in the
coronary artery
diet may result in
atherosclerotic high blood
plaque
cholesterol leading
to the formation of
atherosclerotic
plaques which block
the blood vessels of
cardiac muscle
the heart causing a
(heart muscle)
http://www.utsouthwestern.edu/utsw/cda/dept14857/files/1145
heart attack.
32.html
 Waxes
The lipids called waxes have long chain fatty acids tightly packed and linked to long-chain
alcohols or to carbon rings.

They have a firm consistency and are water repellent. Many above ground parts of plants including
leaves, stems and fruits are covered by a cuticle that has waxes in it. This coating helps the plants
conserve water and keep off insects.

http://www.flickr.com/photos/atomicshark/2523
524390/

Waxy coating on cherries

https://www.quora.com/What-would-happen-if-a-leaf-did-not-have-a-cuticle

Waxy cuticle on leaf

 http://shootingforasmile.blogspot.com/2011/02/du http://www.gpscellphonetrackingtips.com/what-is-gps-cell-phone-tracking/
ck-close-up.html

Water repellent feathers Honeycomb made of beeswax

In many animals waxy Wax is the material of choice for

secretions are part of the honeycombs as it is waterproof and
coatings that lubricate, can maintain the temperature in the
protect and impart pliability beehive. Bees use it to make
to skin or hair and in water hexagonal chambers for storage of
birds it keeps feathers dry. honey.
 Important points

What are the different types of lipids ?

What are the main functions of lipids in

living systems?

What is the difference between cis and trans

fatty acids?

What is the biological implication of this?

Molecules of Life III
Proteins
Proteins Of all the biological molecules proteins are the most diverse.
Proteins are the workhorses in a cell.
http://www.richard-

Some examples of what proteins can do:

http://lorenkarney- http://photographysammy. seaman.com/Arthropods/
biologyblog.blogspot.com/ blogspot.com/2010/06/spid Usa/Butterflies/Illinois/ind
2010/11/enzymes.html er-web-i-hate-spiders-but-i- ex.html
love.html

1) Protein enzymes drive the rates of

metabolic reactions and make them
faster.
2) Structural proteins perform diverse
roles as constituents of spider webs,
feathers, butterfly wings, cartilage and
bone.
3) Transport proteins move ions across
the cell membrane and carry molecules
http://kids.mongabay.co
http://www.orthoandsportspt m/elementary/animals/s
carlet_macaw.html
from one part of the body to another
.com/article.php?aid=250

through body fluids like blood.

http://www.mc.vanderbilt.edu/lens/article/?id=177&pg=2

4) Protein hormones and other signaling

molecules change cellular activities.
5) Proteins defend our bodies against
disease causing bacteria.

https://www.pharmatching.com/blog/categ
http://happyhealthybalance.blogspot.com/2010/05/ins ory/monoclonals/
ulin-sugar-fat.html
 Amino acids the building blocks of proteins
Generalized structural
Cells build an enormous diversity of proteins from formula for amino acids
their pools of only twenty types of amino acids

An amino acid comprises of a central

carbon atom bonded to an amino group, a
carboxyl group, a hydrogen atom and one
or more atoms known as the “R” group.
Polar amino acids
http://macrotomicro.blogspot.com/2011/04/amino-
acids.html

Nonpolar amino acids

Valine Phenylalanine
Tyrosine: Lysine: Glutamate:
uncharged positively negatively charged
charged Proline
 Primary structure of proteins
Amino acids are linked one after the other through peptide bonds to form proteins

http://en.wikipedia.org/wiki/Amino_acid http://www.physchem.co.za/OB12-mat/organic5.htm

When a peptide bond joins two amino acids we have a dipeptide. When there are three
or more it is a polypeptide. The carbon backbone has a -N-C-C-N-C-C- structure. For
each protein different amino acids are selected one at a time from the twenty available.
This sequence of amino acids is unique for every protein and it is called the primary
structure of the protein. The primary structure is prescribed by DNA.
YGGFL is a different polypeptide than LFGGY
 Primary structure of proteins
Proteins can be broadly classified into two structural classes

Fibrous proteins Globular proteins

Polypeptide chains are organized as strands or In the case of globular proteins one or more
sheets. Collectively many such molecules contribute polypeptide chains are folded in compact rounded
towards the shape and internal organization of the shapes. Most enzymes are globular proteins.
cell.

Collagen

http://www.fei.com/resources/image http://www.physorg.com/news167
-gallery/knee-joint-capsule-7329.aspx 574452.html
http://www.tumblr.com/tagged/t
https://chempolymerproject.wikispaces. ertiary+structure
com/Collagen+-+B-+rgam
 How does a protein’s three-dimensional
structure emerge?
The primary structure of the protein gives rise to the protein’s shape
in the following ways:

1) It allows hydrogen bonds to form between the C=O and N-H groups
of different amino acids along the length of the polypeptide chain.

2) It puts “R” groups into positions that allow them to interact.

Through their interactions the chain is forced to bend and twist.
 Second level of protein structure
Hydrogen bonds form at short intervals along the new polypeptide chain and they give
rise to a coiled or extended pattern known as the secondary structure of the protein.

Think of the polypeptide chain as a set of rigid playing cards

joined by links that can swivel a bit. Each card is a peptide group.
Atoms on either side of it can rotate slightly around their covalent
bonds and form bonds with neighboring atoms.
Alpha helix (α helix)
Features:
1. It is a rod like structure.

2. Backbone is inside while side chains

are on the outside.

3. Hydrogen bonding between CO and

NH groups of the main chain
stabilizes the structure.

4. CO group of residue R hydrogen

bonds with the NH group of residue
R+4.

5. Rise per residue is 1.5Å and

rotation per residue is 100 degrees,
therefore, residues per turn is 3.6.

6. Most α-helices observed naturally

are right-handed helices.
The helical content of a protein may vary anywhere between 0% to 100%.

75% of AAs in Ferritin, an iron storage protein is in alpha-helices.

α-helices are usually less than 45Å long. However, two or more α-helices can entwine to form a very stable
structure, which can have a length of 1000Å or more. Such α-helical coiled coils are found in many structural
proteins e.g. myosin, tropomyosin in muscle, Fibrin in blood, Keratin in hair etc.

α-helical
coiled coil
 Beta sheet (β sheet)
Where residues per turn is 2 (n=2) it is a β-pleated sheet structure. There are two kinds of β-pleated sheet
structures either the chains (strands) are such that in two successive chains they have same directionality
for N > C or they are parallel chains (parallel β-sheet) or they are in opposite/anti-parallel orientation (anti-
parallel β-sheet). Features:
1. Distance between two successive amino acids is
3.5Å.

Anti-parallel 2. The side chains are at 180° to each other.

β sheet
3. Adjacent β-strands are linked by hydrogen
bonds.

4. In antiparallel β-sheets the hydrogen bonds

between the CO and NH of adjacent strands
form between groups that are diametrically
opposite to each other.
Parallel β
sheet 5. In parallel β-sheets hydrogen bonds between
CO group of one amino acids forms with the
NH group of two amino acids downstream in
the other strand.

6. β-strands are depicted by arrows

schematically.
β-sheet is an important structural element in many proteins e.g. fatty-acid binding proteins, important for
lipid metabolism, are almost exclusively built of β-sheets.

Many β-strands (4-10 or more) may come together in a protein. These β-strands may be all parallel to each
other or anti-parallel or mixed.

A and B are ball and stick and ribbon model of the same polypeptide, respectively. β-
strands may have twists. Side view of the schematic in B demonstrates the twists.

A protein rich in β-sheets, a fatty acid binding protein.

 Important points
What are the different functions of proteins?

In the structure of an amino acid, what are the various

classes of “R” groups that are present in amino acids?

What is the primary structure of a protein

and what is it determined by?

What are the secondary structure of a proteins?

What are  helices and β sheets?

What are the features of these structures in a protein?

Resource:
Chapter 3: Molecules of life

Biology Concepts and Applications

8th edition

By

Cecie Starr
Christine A. Evers
Lisa Starr