Chemistry of Life

Chemistry of Life

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Chemistry of Life

• Flowers emit a chemical perfume that attracts butterflies, but the plant also makes a noxious chemical in its leaves which discourages the butterfly from laying her eggs there.

• Insects interact via chemical messages that range from “stay away” to “come mate with me”.

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Rattlebox Moth

• Secrete a noxious chemical for defense, particularly against spiders.

• This moth is a native of Central Florida. • Its name comes from the rattlebox plant, the

source of the moth’s defensive chemical. • This chemical also has an important role in its

mating strategy. • While the moth was a caterpillar, it ate the

leaves from the rattlebox plant and stored this chemical in its body.

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Rattlebox Moth

• While both male and female caterpillars contain this chemical, the female moth receives an extra dose at mating.

• During the eight hour copulation, the male passes a large mass of sperm, nutrients, and this chemical to the female, supplying additional protection for her and for their offspring.

• Only a human bridegroom would buy life insurance for his bride.

• This classy moth gives a gift she can really use-- a life insurance policy that pays off every time her life is in danger.

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•Nature’s Chemical Language– The rattlebox moth

• Produces chemicals important for mating and defense

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Rattlebox Moth

• During the courtship dance, the male moth release is into the air puffs of this chemical; the female, sensing it, can assess how much of this chemical he has.

• There are some kinds of chemical signaling in humans as well. For instance, chemicals in the armpit of a male can apparently regularize a female companion’s ovulatory cycle.

• Chemicals play many more roles in life than signaling. Chemicals make up our bodies as well as the bodies of other organisms, and they also make up the physical environment. To understand biology, we should first look at where it all begins: chemistry.

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Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

An element is an atom with a certain number of protons (electrical charges) circling around it in an orbit.

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ELEMENTS

• 96% of the human body is composed of just four elements. – Carbon (C)– Hydrogen (H)– Oxygen (O)– Nitrogen (N)

• The other 4% of elements in our body– Calcium, phosphorus, potassium, sulfur, sodium,

chlorine, and magnesium. – These elements are involved in important functions

such as bone formation, nerve signaling, and DNA synthesis.

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Trace Elements• Iron

– Needed by all forms of life for transporting the oxygen in the blood.

• Iodine– only required by certain species; it is an

ingredient of a hormone produced by the thyroid gland. Iodine is commonly added to table salt to prevent the formation of goiters.

• Fluorine– added to water in some communities to reduce

tooth decay• Zinc• Manganese

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Goiter

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Vitamin-Fortified Foods

• Chemicals are added to food to help preserve it, make it more nutritious, or simply to make it look better.

• Iron, for example, is a trace element that is commonly added to foods.

• You can actually see the iron that has been added to a fortified cereal by crushing the cereal and then stirring a magnet through it.

• Vitamins are also frequently added to cereal. • A vitamin consists of more than one element and is an

example of a compound, which we will consider next: Elements combine to larger units called compounds.

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Trace elementsare essential tohuman health andmay be added to food or water

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Compounds• Two or more elements• Compounds are much more common than pure

elements. • In fact, few elements exist in a pure state in nature.

Many compounds consist of only two elements; for instance table salt (sodium chloride) has equal parts of the elements sodium and chlorine.

• Pure sodium is a metal and pure chlorine is a poisonous gas. Chemically combined, however, they form a common seasoning.

• This example shows the emergence of novel properties with a higher level of structural organization. We will see this in biology to, as we study the adaptations of organisms as they evolved.

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Elements can combine to form compounds

Sodium Chlorine Sodium Chloride

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Compounds

• Hydrogen (H) and Oxygen (O) = H2O

• Sodium (Na) and Chlorine (Cl) = NaCl

• Demonstrates new properties with a higher level of structural organization

• Carbon, hydrogen, oxygen, and nitrogen form most of the compounds in living organisms

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– Sodium and chloride ions • Bond to form sodium chloride, common table salt

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Compounds

• Most of the compounds in living organisms contain at least three or four different elements, mainly carbon, hydrogen, oxygen, and nitrogen.

• Vitamin K, for example, is formed of just carbon, hydrogen, and oxygen.

• Proteins are compounds containing carbon, hydrogen, oxygen, nitrogen, and a small amount of sulfur.

• Different arrangements of the elements determine unique properties for each compound.

• There are two groups of compounds in our bodies; organic and inorganic.

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INORGANIC COMPOUNDS

• Contain NO carbon atoms

• SALTS– Found in body fluids and is needed for

muscle contraction and nerve conduction.

• WATER– The body is 70% water.– It keeps the body from overheating– It also prevents drastic changes in

temperature.18

Water

• If you have ever burned your finger on a metal pot while waiting for the water in it to boil, you know that water heats up much more slowly than metal.

• Water has a better ability to resist temperature change than most other substances.

• Earth's giant water supply moderates temperatures, keeping them within limits that permit life.

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Water

• A large body of water can store a huge amount of heat from the sun during warm periods.

• At cooler times, heat given off from the gradually cooling water can warm the air.

• That's why coastal areas generally have milder climates than inland regions.

• Water's resistance to temperature change also stabilizes ocean temperatures, creating a favorable environment for marine life.

• And at 70% of your body weight, water helps moderate your internal temperature.

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Water

• Liquids vaporize into a gas when some of their molecules move fast enough.

• When heat is applied to a liquid, it makes the molecules move faster and bump into each other, causing the hydrogen bonds break, allowing vaporization to occur.

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Water Molecule

(–) (–)

(+) (+)

O

HH

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Water molecules form weak bonds between each other called hydrogen bonds

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)

(–)

O

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Ice is less dense than liquid water– Hydrogen bonds hold molecules in ice farther

apart than in liquid water

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogen bond

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– Insects can walk on water due to surface tension

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Water

• Another way water moderates temperatures is by evaporative cooling.

• When a substance evaporates, the surface of the liquid remaining behind cools down as the hottest molecules leave.

• Evaporative cooling helps prevent land-dwelling organisms from overheating.

• Evaporation from a plant’s leaves keeps them from becoming too warm in the sun, just as sweating helps to dissipate our excess body heat.

• On a much larger scale, the evaporation of surface waters cools tropical seas.

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How do land organisms keep from overheating?

• Evaporative cooling – Plant’s leaves – Human sweating– Evaporation of surface

waters cools tropical seas.

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Water is the solvent of life

• Solution: a liquid consisting of a uniform mixture of two or more substances.

• Solvent: the dissolving agent• Solute: the substance that is dissolved

• Water is the solvent inside all cells, in blood, and in plants, and it dissolves an enormous variety of solutes necessary for life.

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The chemistry of life • The chemistry of life is sensitive to acidic

and basic conditions• In water solutions, a very small percentage of

the water molecules actually break apart into ions.

• The ions formed are called hydrogen ions (H+) and hydroxide ions (OH-).

• The proper balance of these ions is very critical for the proper functioning of an organism.

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Acids and Bases

• Some water molecules break apart into ions. – Hydrogen ions (H+)– Hydroxide ions (OH-)

• Acid: excess hydrogen ions (H+)– hydrochloric acid in your stomach

• Base: excess hydroxide ions (OH-)– Ammonia is a base

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Acids and Bases

• We use the pH scale to describe how acidic or basic a solution is.

• The scale ranges from 0 (most acidic) to 14 (most basic).

• Pure water and other solutions that are neither acidic nor basic are said to be neutral; they have a pH of 7.

• The pH of the solution inside most living cells is close to 7.

• Even a slight change in pH can be harmful.31

pH scale

• Neutral: pH = 7

• Acid: pH < 7

• Base: pH > 7

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale0

1

2

3

4

5

6

7

8

9

10

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Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleachIn

crea

sing

ly A

CID

IC(H

ighe

r co

ncen

trat

ion

of H

+)

NEUTRAL[H+]=[OH–]

H+ H+

H+ OH– H+

H+ H+

OH– H+ H+

OH–

OH–

H+ H+OH–

OH– OH–

H+ H+H+

OH–

OH–

OH– OH–

OH–OH– H+ Incr

easi

ngly

BA

SIC

(Low

er c

once

ntra

tion

of H

+)

OH–

H+

14

13

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Acid Rain

• Imagine arriving for a long awaited vacation at a mountain lake only to discover that since your last visit a few years ago, all fish and other forms of life in the lake have perished because of increased acidity of the water.

• Over the past quarter-century, thousands of lakes in North America, Europe, and Asia have suffered that fate. This problem is due to acid rain.

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Acid Rain

• Acid rain = pH well below 7• Results from sulfur and nitrogen in the

air. • These elements react with water vapor in

the air to form sulfuric acid and nitric acid, which fall to the earth in rain or snow.

• Acid rain with a pH of 1.7 (almost as acetic as the digestive juices in the human stomach) has been recorded in Los Angeles.

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Acid Rain

• Sulfur and nitrogen in the air comes from the burning of fossil fuels such as coal, oil, and gas.

• Electrical power plants that burn coal produce more of these pollutants than any other single source.

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Sulfur and nitrogen in the air comes from the burning of fossil fuels

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The Effect of Acid Rain

• Lakes: – most pronounced in the spring– Kills eggs and young fish

• Forests:– Ions bind with essential minerals needed

for plant growth– Leaves behind toxic levels of aluminum

• Cities: – corrosion of buildings and statues

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Acid Rain in Lakes

• The surface snow melts first, drains down, and sends much of the acid that has accumulated over the winter into lakes and streams all at once.

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Lakes

Most pronounced in the spring

Kills eggs and young fish

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Acid Rain in Forests

• Acid rain has also taken a toll on forests. When acid precipitation falls on land, it washes away mineral ions, such as calcium and magnesium, which are essential nutrients for plant growth.

• At the same time, minerals such as aluminum reach toxic concentrations.

• In cities, acid precipitation causes a great deal of corrosion of buildings and statues.

• That is why laws were enacted that require reductions in emissions to help alleviate the problem.

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Forests

Ions bind with essential minerals needed for plant growth

Leaves behind toxic levels of aluminum

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CitiesCorrosion of buildings and statues

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Chemistry of Life

• Every organism has a delicate biochemistry that needs to be maintained.

• One spring, a baby finch collapsed with exhaustion on my patio.

• Since it was exhausted, it probably wasn’t good at finding food and water yet.

• That means it was dehydrated and hungry. • I knew to get an eyedropper and give it water with sugar

in it because those are the two main things it needs right away.

• We discussed water, now let’s get to sugars.

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ORGANIC COMPOUNDS

• Always contain carbon– Carbohydrates– Lipids– Proteins

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CARBOHYDRATES

• Store energy for a short time – Simple (sugars) – Complex (starches)

• Cellulose (fiber) is in plants only

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SIMPLE CARBOHYDRATES

• Known as sugars• Quick source of

energy• Burned off fast

– Glucose– Sucrose– Fructose– Lactose (some people

are lactose intolerant)

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Lactose Intolerance

• Got milk? Most of the world's people cannot easily digest milk-based foods.

• Milk and other dairy products have long been recognized as highly nutritious foods, rich and proteins and minerals necessary for good teeth and strong bones.

• But for millions of people, those health benefits come with digestive discomfort.

• Such people suffer from lactose intolerance, or the inability to properly break down lactose, the main sugar found in milk.

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Lactose intolerance is common world-wide

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Lactose Intolerance• For those with lactose intolerance, the problem starts once

lactose passes through the stomach and enters the small intestine.

• To absorb this sugar, digestive cells need to secrete an enzyme called lactase, which is necessary to break down lactose.

• An enzyme is a protein that breaks down larger molecules into smaller ones.

• Those with lactose intolerance produce insufficient amounts of the enzyme and the lactose cannot be properly digested.

• This leads to symptoms of nausea, cramps, diarrhea, and gas. • .

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Lactose Intolerance

• At birth, nearly everyone produces enough lactase• Therefore, milk provides excellent nourishment for

infants. • But after the age of two, lactase levels start to decline in

most of the world’s populations. In the United States, 75% of African Americans and Native Americans and 90% of Asian-Americans are lactase deficient once they reach their teenage years.

• People of European descent are the only group that does not suffer much from lactose intolerance.

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Lactose

• Present in bottled salad dressings, lunchmeat, prescription drugs.

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Lactose

• Currently, lactose intolerance cannot be corrected by gene therapy to treat the underlying cause

• The symptoms of lactose intolerance can be controlled through diet. – In many Asian cultures, beverages are made

from soy or rice instead of milk.– Milk-based foods pre-treated with lactase. – Lactase in pill form can be taken with food

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Lactose

• Lactose intolerance, with its interplay between genes and milk sugar, illustrates the importance of biological molecules to the functioning of living cells and to human health.

• In people who easily digest milk, lactose (a sugar), is broken down by lactase (a protein), which is produced by a gene made of DNA (a nucleic acid).

• If the gene for lactase production is not active, lactase is not present.

• And the presence of lactase can mean the difference between delight and discomfort when someone contemplates an ice cream sundae.

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“Sweet” Taste Receptors

• The taste we describe as sweet has been a beloved sensation throughout human history.

• However, sugars are not the only substances perceived as sweet; there are other chemicals that can trigger the same sensation.

• We perceive sweetness when molecules of a substance attach to the “sweet” taste receptors on our tongue, triggering a message to the brain.

• Many different kinds of molecules can bind to our “sweet” taste receptors, each causing a similar message to be sent.

• The glucose and fructose in honey taste sweet but so does the laboratory-produced compound called aspartamine (Equal and NutraSweet).

• Compared to table sugar (sucrose), fruit sugar (fructose) is four times sweeter.

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• We perceive sweetness when molecules of a substance attach to the “sweet” taste receptors on our tongue.

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• Aspartamine (Equal and NutraSweet)

• Compounds that bind more tightly to “sweet” taste receptors send stronger “sweet” messages to the brain.

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• The chemical shape of a compound determines how well it fits into a taste receptor.

• Compounds that bind more tightly to “sweet” taste receptors send stronger “sweet” messages to the brain.

• Some artificial sweeteners are much sweeter than sucrose because their molecules fit more snugly into our sweet taste receptors than natural sugars.

• Neotame, a new artificial sweetener that received FDA approval in 2002, has been rated 8000 times sweeter than sucrose. Therefore, smaller quantities are needed.

• However, some sugar substitutes also bind to other kinds of taste receptors on the tongue. For example, a sweetener may have a bitter aftertaste because it also binds to “bitter” receptors.

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STARCH• The storage form of

glucose in plants • When we eat breads, corn,

rice, potatoes, and cakes, we convert it to glucose.

• These don’t break down to glucose as easily, so they tend to get stored and are only broken down when there is not enough glucose available.

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CELLULOSE

• Only found in plant cell walls

• Our body is unable to break it down, so it passes through our digestive tract.

• That is what is referred to as eating fiber.

• The fiber portion of is the wall of each plant cell.

Eating fiber helps a person who has constipation. Foods that are high in fiber are most likely derived from plants.

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Fiber

• Fresh fruits, vegetables, and grains are rich in fiber. • The fiber portion of each of these foods is the wall of each cell. • The contents of each cell contain the carbohydrates which can be

digested. • This is one reason you should chew your food well; crushing up the

cell walls will release the nutrients. • If you swallow a whole kernel of corn, it will pass right through your

digestive tract without being digested.

• You may have heard the term cellulite referring to fat. However, there is no such thing; it is just regular fat, which we’ll talk about now. Some companies made up the term and said their cream can dissolve it: Wrong!

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LIPIDS• Lipids don’t

dissolve in water.– FATS AND OILS

• Fats are animal lipids• Oils are plant lipids

– STEROIDS

When we ingest (eat) oils, we convert them to fats. One gram of fat stores more than twice as much energy as one gram of starch.

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FATS

• Long-term energy storage • Insulate against heat loss• Forms protective cushions around organs

1) SATURATED FATTY ACIDS are solid at room temperature, like butter and lard

(animal fats).

2) UNSATURATED FATTY ACIDS are liquid at room temperature, such as vegetable oils (plant fats)

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Fats

• Most plant fats are unsaturated oils, whereas most animal fats are saturated solids.

• Diets rich in saturated fats contribute to cardiovascular disease by promoting a condition called atherosclerosis.

• In this condition, the lipids deposits called plaques build up within the walls of blood vessels, reducing blood flow.

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Atherosclerosis

• Caused by diets rich in saturated fats

• The lipids deposits (plaques) build up within the walls of blood vessels, reducing blood flow.

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STEROIDS

• Formed from cholesterol

• Cholesterol is found in the cell membranes of our body.

• Examples of steroids that our body makes are estrogen and testosterone.

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Anabolic Steroids

• Synthetic form of the male hormone testosterone

• Testosterone causes a buildup (anabolism) in muscle and bone mass in males during puberty and maintains masculine traits throughout life.

• Because anabolic steroids structurally resemble testosterone, they also mimic some of its effects.

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Anabolic Steroids

• As a prescription, steroids are used to treat anemia and diseases that destroy body muscle.

• Overdosing may cause violent moods swings (“steroid rage”) and deep depression.

• The liver may be damaged, leading to cancer. • High blood pressure• The body reduces its output of natural male sex

hormones– Men: shrunken testicles, reduced sex drive, infertility, and breast

enlargement.– Women: menstrual cycle disruption and development of

masculine characteristics, including facial hair. – Teenagers: bones may stop growing, stunting growth.

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Steroid Abuse

• Despite risks associated with steroid use, some athletes use steroids to gain a competitive edge.

• Sports organizations banned their use, implement drug testing, and penalize violators.

• In 2003, the discovery of a new designer steroid rocked the sports world.

• THG is a drug modified to avoid detection in ordinary drug testing.

• The drug was discovered when a track coach mailed a syringe containing a sample of it to the US Anti-Doping Agency.

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Steroid Abuse

• With that sample, the agency was able to develop a test that revealed the substance’s use among track and field athletes and professional football players, so the International Olympic Committee has begun retesting frozen and urine samples from the 2002 Winter Games.

• The US FDA declared THG an illegal steroid. • In 2004, a British sprinter became the first athlete to be

penalized for its use, with a permanent exclusion from the Olympics following his positive test for THG.

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Olympic Drug Testing

• THG was a new steroid that was not detectable in ordinary drug testing before 2003.

• Performance-enhancing drugs bar an athlete from getting a medal.

• Blood doping: blood is removed from an athlete's body several weeks before a competition and then re-injected into the body right before the event.

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Performance-Enhancing Drugs

• Discussion

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PROTEINS • PROTEINS are compounds that make up most of our

body. • Our hair, nails, tissues, ligaments, cartilage,

bone, tendons, muscles, and organs are made of proteins.

• Other proteins we have are enzymes, which function to speed up metabolic reactions and break down larger compounds into smaller ones.

• A protein is made from a string of amino acids. Each of our many thousands of different kinds of proteins has a unique shape that corresponds to a specific function.

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PROTEINS

• Other types of proteins include the anti-bodies of our immune system, hormones that coordinate bodily activities, hemoglobin in red blood cells which deliver oxygen to working muscles, transport proteins that move sugar molecules into cells for energy, storage proteins, the protein of egg white, and milk proteins which provide amino acids for baby mammals.

• Plants also have storage proteins for the developing embryos in their seeds.

• Since proteins are made of amino acids, in order to understand what a protein is, we have to talk about amino acids (AA’s).

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AMINO ACIDS• The building blocks of protein

• They are tiny compounds, made of just a carbon atom and a few other atoms.

• Although there are many thousands of different types of proteins, they are all made up of a various combination of only 20 amino acids.

• They are like beads on a necklace. How they are arranged on the string determines the type of necklace. Each bead is an amino acid, and the whole necklace is the protein.

• A protein’s specific shape determines its function. A bunch of the same types of necklaces (proteins) woven together makes up our tissues.

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PROTEINS

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Denatured Proteins

• If a protein becomes denatured, the amino acid chain unravels, causing a loss in shape and, as a result, function.

• Things that can denature a protein include salt concentration, pH, and excessive heat.

• You can see an example of protein becoming denatured by frying an egg. Heat quickly denatures the clear protein surrounding the yoke, making them solid, white, and opaque.

• One of the reasons why extremely high fevers are so dangerous is that some proteins in the body become denatured and cannot function.

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Denatured Proteins

• Denatured proteins are those whose amino acid chains becomes unraveled, and results in loss of function.

• Proteins are denatured by– salt concentration– pH– excessive heat

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NUCLEIC ACIDS

• Special type of amino acids that make up DNA and RNA

• DNA makes up our genes

• Genes – store information about how to replicate,

including how to arrange the amino acids in the new cell to form the proper proteins for the body.

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TYPES OF NUCLEIC ACIDS

• DNA– The genetic material that organisms inherit

from their parents consists of DNA. – Genes are the specific stretch of a DNA

molecule that programs the amino acid sequences.

• RNA– Messenger molecules that take a copy of the

DNA blueprint out of the nucleus and into the cell where it is used to make proteins

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NUCLEOTIDES

Nucleic acids are made of nucleotides

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DNA and RNA

• An architect who spends a lot of time designing an original blueprint for a building does not take this precious document down to the dusty construction site.

• Instead, he makes a copy and leaves the original at home in a safe place.

• Likewise, DNA in the nucleus does not put its genetic information to work directly by leaving the nucleus.

• It works through an intermediary called RNA, which can enter the nucleus from the cytoplasm, make a copy of the gene and take it outside of the nucleus into the cytoplasm, were the protein is actually built.

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DNA and RNA

• To do this, the information in DNA is first copied onto a strand of messenger RNA (mRNA), which is like stamping an impression in clay.

• Since the clay impression is not an exact copy of the original, but is instead a reverse copy, the DNA then needs to be translated before the protein is built.

• This is done by transcription RNA (tRNA). • After the protein is built in the cytoplasm, it is either used

by that cell or transported outside of the cell so it can be taken wherever else in the organism it is needed.

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NUCLEOTIDES

• Nucleic acids are made out of a string of nucleotides

• There are only four types:– adenine (A)– thymine (T)– cytosine (C)– guanine (G)

A sample protein sequence: AATCAGCT

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NUCLEOTIDES

• A sample protein sequence: AATCAGC• If you were to remove the last letter in that sequence, a

completely different protein would form. (Click) • Likewise, if you were to substitute the last letter in that

sequence for a different letter, you would also get a completely different protein. (Click)

• And of course, if you insert additional letters, you would have a new protein.

TA

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NUCLEOTIDES

• Actually, a DNA “string of beads” is actually double-stranded.

• Each of the nucleotides (A,T,C,G) on one strand fits like a puzzle piece into the nucleotides on the other strand.

• The nucleotide adenine (A) always pairs up with thymine (T), and cytosine (C) always pairs up with guanine (G)…these are called base pairs.

• Therefore the two strands of DNA lock together like a jigsaw puzzle.

• The two strands of this DNA “string of beads” are also twisted like a coiled telephone cord. This structure is called a double helix.

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NUCLEOTIDES

• Each of the nucleotides (A,T,C,G) on one strand fits like a puzzle piece into the nucleotides on the other strand.

• adenine (A) pairs up with thymine (T)

• cytosine (C) pairs up with guanine (G)

• These are called base pairs.

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DNA

• The two strands of this DNA are also twisted into a double helix

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DNA

• Most DNA molecules are very long, with thousands or even millions of base pairs.

• One long DNA molecule may contain many genes, each one being a specific series of hundreds or thousands of nucleotides.

• The specific sequence of nucleotides in a gene is the information that programs the primary structure of a protein.

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ATP

• The type of protein that provides all the energy to cells.

• When food is broken down to glucose for energy, ATP is what is released, which is the actual energy molecule.

• The more ATP that is produced, the more energy we have.

• When we inhale oxygen, it is used in a process called respiration, which produces ATP for energy. That is why we breathe.

• Just remember that ATP is an energy molecule.89

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Chemistry of Life