Chemistry in our life

CCC 407, 1.5 Credits, 3L/week

Dr. Nidhi Malhotra

nidhi.malhotra@snu.edu.in
Research Block, First floor, R-112
 Course

COURSE CONTENT:

• Chemistry in humans: Eye, Brain, Cholesterol, Cell membranes, vitamins, enzymes, fatty acids, acidity etc.
• Chemistry in daily life: Role of colourants, adulterants (FDA), carcinogens, toiletries, hair styling, recycling codes etc.
• Chemistry in special fields: Electrolysis, cement, Cathode ray tube to LCDs, implants, specialty plastics, self-cleaning glasses,
diapers, sutures, eye-lens, solar cells, OLEDs etc.

RECOMMENDED BOOK(S):

• No specific books, learning will be based on class notes, e-literature, internet

• Chemistry in your life, Sec Ed, Colin Baird
• Lecture slides will have reference separately mentioned for each topic
• Watch HowStuffWorks

ASSESSMENT SCHEME:

• Quiz (1, 60%), Assignment/Game (1, 40%)

• Passing scheme: 40% and above- to pass the exam; A-grade ≥ 90%
• Attendance ≥75%
 About my academic Journey

Accomplishments

• Academic Topper
• Science Meritorious Award
• Excellence in doctoral research award
M.Sc. Biophysical Chemistry B.Sc. Chemistry (H) • Excellence in HPC based research award
(IIT Delhi) (St. Stephens College, DU) • Impactful research record published in reputed
PhD journals like “Nature Communications”,
(IIT Delhi)
“Autophagy” etc.

“Everything that living things do can be understood in

Teaching Experience PostDocs
(St. Stephens College, SRCASW) (University of Delaware, USA terms of jigglings and wigglings of atoms” – Feynman
IGIB, ICGEB, Delhi)
 Chemistry

Why are we studying this course?

 Our Eyes: A Magical Tool

Eyes, the windows to the soul, are more than just a pair of organs that allow us to see the world

Smile of a child on seeing his parents Desire to watch TV Appreciating the beauty of nature by gazing it
 Is there any chemistry behind vision??

Let’s break into different scenarios and understand how it happens

Let’s start with two daily life examples…

 Chemistry of Vision

Bright Light Dark Room

Why can’t we see an object for a moment in a dark Why do we see different colors?
room after exposing ourselves from bright sunlight?
 Why do we see?

Of Course: How does eyes work??

Because of the eyes and the light!!

 How does eye work?

Iris

Cornea

Retina

Lens
 How does eye work?

• First, light passes through the cornea (the clear front layer of the eye). The cornea is shaped like a
dome and bends light to help the eye focus.

• Some of this light enters the eye through an opening called the pupil. The iris (the colored part of the
eye) controls how much light the pupil lets in.

• Next, light passes through the lens (a clear inner part of the eye). The lens works together with the
cornea to focus light correctly on the retina.

• When light hits the retina (a light-sensitive layer of tissue at the back of the eye), special cells called
photoreceptors turn the light into electrical signals.

• These electrical signals travel from the retina through the optic nerve to the brain. Then the brain turns
the signals into the images you see.

• The image on the retina of the eye is upside down, but the brain processes this information and
interprets it as up.

https://www.nei.nih.gov/learn-about-eye-health/healthy-vision/how-eyes-work#:~:text=When%20light%20hits%20the%20retina,into%20the%20images%20you%20see.
How does eye work: Rods and Cones

• Two types of nerve cells are placed around retina: the rods and
the cones. These are photoreceptors found at the outermost
layer of the retina.

• The cone cells work to detect colour, while the rod cells detect
low-light contrasts.

• Rods work at very low levels of light (scotopic vision). We use

this for night vision since only a few bits of light (photons) can
activate a rod.

• Cones provide vision in good light conditions (photopic vision)

and they are used to see color.

• These two come together to convert the light into signals, which
are then sent to the brain.

https://www.wikilectures.eu/w/Biochemistry_of_the_vision_process
 Before we proceed further, let’s understand isomerism!

• In order to understand the chemical basis of rod vision, we need to understand the ‘isomerism’

• Isomers are different molecules even though they have same

molecular formula
• They have different properties [melting point (mp) and boiling point
(bp)]
 Cis-Trans Isomerism

• Geometrical isomers

• Isomers that have the same connectivity of their atoms but a different
arrangement of their atoms in space due to the presence of either a ring or a
carbon–carbon double bond
 Chemical basis of Rod Vision

• 130 million rods

• Rods contain chromophore RHODOPSIN which is covalently

bound complex of protein OPSIN and 11-cis-RETINAL (derivative
of vitamin A). Rhodopsin is the photosensitive pigment in the rod
photoreceptor cell.

• When light hits the retina, it is absorbed. Absorption leads

to excitation of the membrane, which results in isomerization of
11-cis-retinal to ALL-TRANS-RETINAL.

• The consequence of the photon impact is uncoupling of the

dye from the protein. Rhodopsin thus breaks down into opsin
and all-trans-retinal. Also, the conformational changes in the
protein molecule occur that trigger a cascade of reactions that
Cis ultimately leads to a nerve signal being sent to the brain.
RETINAL
Trans RETINAL
• In the dark', the trans isomer is converted back to 11-cis-retinal
(retinal isomerase), the opsin+11-cis-retinal complex is formed
OPSIN OPSIN
again, and the process is repeated after further irradiation
= Wald cycle.
Active form
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561911/#:~:text=Upon%20absorption%20of%20a%20photon,reduced%20to%20all%2Dtrans%20retinol
Cis-Trans isomerism in vision
Why can’t we see an object for a moment in a dark room after exposing
ourselves from bright sunlight?
Bright Light Dark Room

https://www.scientificamerican.com/article/experts-eyes-adjust-to-darkness/
Expansion and contraction of pupil

• Your eyes adapt to various light conditions by increasing

or restricting the size of the pupil (the black hole in the
middle of your eye). When you've been out in the sun the
pupil is tiny and only allowing a little light to enter. Then
when you go into the dark room there isn't enough light left
that gets through the narrow pupil to give a clear image.

• Spend a little time in the dark and the eye will quickly adapt
to the new light level and objects will begin to appear
again.

• One of the most amazing things about human vision is the

incredible range it has. We can see in very bright sunlight,
and we can also see in nearly total darkness. If you spend
much time working with a camera, you know how amazing
this range is. Film that works well outdoors is nearly
useless indoors, and vice versa.
 • The range that our eyes have comes from three different parts of the eye:
• Pupil contracts and expands depending on the amount of light, and can physically
block the amount of light entering the eye in bright situations.
• Rod and cone cells in the retina - Our eyes sense light with two different types of
cells: rods and cones. Cone cells can perceive color in bright light. Rod cells
perceive black and white images and work best in low light.
• Rhodopsin - Rhodopsin is a chemical found in the rods.
• Rhodopsin is the key to night vision -- it is the chemical that the rods use to absorb
photons and perceive light. When a molecule of rhodopsin absorbs a photon, it splits
into a retinal and an opsin molecule. These molecules later recombine naturally back
into rhodopsin at a fixed rate, and recombination is fairly slow.
• So, when you expose your eyes to bright light, all of the rhodopsin breaks down
into retinal and opsin. If you then turn out the lights and try to see in the dark,
you can't. The cones need a lot of light, so they are useless, and there is no
rhodopsin now so the rods are useless, too. Over the course of several minutes,
however, the retinal and opsin recombine back into rhodopsin, and you can see
again.

https://health.howstuffworks.com/human-body/systems/eye/eyes-adjust-darkness.htm#:~:text=So%2C%20when%20you%20expose%20your,the%20rods%20are%20useless%2C%20too.
A fun fact !!
• The retinal found in the eye is derived from vitamin A. If a person's
diet is low in vitamin A, there is not enough retinal in the rods and
therefore not enough rhodopsin. People who lack vitamin A often
suffer from night blindness -- they cannot see in the dark
Why do we see different colors?

Chemistry colors our world!!

Let’s revise again!!

We see because of the light and our eyes

Rods Cones
 Light as a wave

Water Waves Light Waves

https://kids.frontiersin.org/articles/10.3389/frym.2013.00010
 Light is part of Electromagnetic Spectrum

• The light you can see is just a small part of

something bigger called the electromagnetic
(EM) spectrum.
Wavelength
• All parts of the electromagnetic spectrum can be
thought of as sets of waves moving through
space. The distance between two waves that
follow each other is called a wavelength.

• Only certain wavelengths of light can be

detected by human eye.
 Color is reflected light

• White light contains all colors.

• When an object is illuminated, some of the light source’s wavelengths are absorbed and some are reflected.
• The reflected wavelength create what we perceive as color.

• If no light is reflected (or if there is no illumination), the object appears black.

https://www.lifepixel.com/infrared-photography-primer/ch2-basic-theory-color-is-reflected-light
 Color Perception
•Adding red, green, and blue light in different amounts
leads to all possible colors of light.
•Red, green, and blue are the primary additive colors of light
 Why is a black car hotter than a white car in the summer?

• Remember light is energy. Heat is another form

of energy.

• A white car reflects all wavelengths of light.

• A black car absorbs all wavelengths of light,

absorbing the energy and turning it to heat
What happens at atomic level?
 Color Perception

• A molecule with an energy-level gap that corresponds to visible light

appears colored (pigment).
• Remember: The cone cells work to detect colour!
• Pigments absorb certain colors of light, reflecting other colors, which hit
the cone cells. There are three types of cone cells corresponding to
the primary colors: Red-sensing cones, Green-sensing cones, and
Blue-sensing cones.
• A colored object will excite all three types of cones, but at varying
degrees. For example, a green ball will stimulate the green cones to a
large extent, but also the red cones to a lesser extent and blue cones to
an even lesser extent. We perceive color based on the superposition of Color Blindness
different spectra conveyed to the brain.
•Color blindness is an inheritable disorder in which a person cannot
distinguish between colors. Color blindness happens when one or more
types of cone cells are absent or not functioning properly.
 Human vs dog
•Dogs lack a green receptor and can’t distinguish red from
green.
 Colors in art

•Paints are a homogeneous mixture of a pigment, which

provides color, and a binder, which cements the pigment
to the solid support after drying.
Why do plants show different color leaves in different season?
 Why do plants show different color leaves in different season?

Sunlight Other pigments in plants:

Pigment Class Compound Type Colours

Porphyrin Chlorophyll Green
Carotenoid Carotene and Yellow, Orange, Red
Lycopene

Xanthophyll Yellow

• Chlorophyll is produced in response to sunlight. It is chief Flavonoid Flavone Yellow

pigment involved in photosynthesis

• Plants contain other pigments that reflect different colors, but Flavonol Yellow
these are often masked by Chlorophyll.

• Light is not needed in order for a plant to produce

Anthocyanin Red, Blue, Purple,
Carotenoids, therefore these pigments are always present in Magenta
a living plant even in autumn season when there is less
sunlight unlike chlorophyll.
Why do plants show different color leaves in different season?

• Chlorophyll is a green pigment that gives most plants their color.

• Look green because it absorbs other colors of light such as
red and blue, so in a way the green light is reflected out since
the pigment does not absorb it.
• Plants contain other pigments that reflect different colors, but
these are often masked by Chlorophyll.
• For example: Carotenoids. As the seasons change - During
autumn, when the days begin to shorten, and the amount of
sunlight decreases result in the less amount of chlorophyll
produced hence chlorophyll in the leaves of trees is dramatically
reduced. Hence the leaves appear less green.
• This is when the colors of the carotenoids become more
prevalent and is what you see when the leaves appear to change
color.
• When green leaves "turn colors" in the fall, or turn yellow due to
nutrient limitation or disease, the chlorophylls are breaking down
and being re-absorbed, allowing the other pigments to show through.
chlorophyll a (which is teal-green), chlorophyll
b (which is yellow-green)
 Soil Acidity affects leaf color

• Flavonoid includes Flavone and

Flavol, which are yellow, and the
Anthocyanins, which may be red,
blue, or purple, depending on the
pH.
• Production of this class of
pigments is dependent on the
availability of carbohydrates within
a plant.
• Anthocyanin colour changes with
pH, so soil acidity affects leaf
colour.
Different structure so different colour
 Summary

• When leaves appear green, it is because they contain an abundance

of chlorophyll.

• Chlorophyll masks other pigment colours.

• Anthocyanins masks Carotenoids.

• Before the leaves fall, plants recover the nutrients stored in the
leaves with the help of Anthocyanins. Due to which the production of
it increases giving a brighter reddish colour to the leaves.
• Leaves with good amounts of both anthocyanins and Carotenoids
will appear orange.

• Leaves with Carotenoids but little or no anthocyanins will appear

yellow.

• In the absence of these pigments, other plant chemicals also can

affect leaf colour. An example includes tannins, which are
responsible for the brownish colour of some oak leaves.
Common Sources of Pigments

Marigolds Grape
Lutein pigment Juice
Anthocyanins pigment

Beets Cochineal
Betalains pigment Beetles
Carminic acid pigment

Walnut hulls
Pyrogallol and hydro juglone pigment
 Other Examples: Photosynthetic organisms

Different photosynthetic organisms use different combinations

of pigments, which have different colors because they absorb
and reflect different frequencies of light.
• Plants and green algae (plants are really advanced green
algae) contain chlorophyll a (which is teal-green),
chlorophyll b (which is yellow-green), and beta-carotene
(which is yellow), thus giving them a green color.
• Brown algae and their unicellular relatives have chlorophyll a,
chlorophyll c, and lipid pigments called fucoxanthins, which
together give them a golden-brown color.
• Red algae possess chlorophyll a and lipid-based pigments
called phycobilins, which give them the brilliant red (or deep
blue) color.
• These different combinations of pigments are more or less
efficient at collecting light at certain frequencies and at certain
levels of light intensity (too much will damage the pigment).
Thus, they parcel out the Sun's energy to make the most use
of it and to not compete with other photosynthetic organisms.