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The Chemistry of Life

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Allen Weltig

on 15 September 2015

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Transcript of The Chemistry of Life

The Chemistry of Life
1. Explain the importance of water to living things.

Unit 2-Biochemistry and Digestion
Part 1. Chemistry of Life- Chapter 2
Composition of Matter, Water, Acids and Bases

Part 2. Biochemistry- Chapter 3
Carbon Compounds, Macromolecules, Enzymes

Part 3. Digestive System- Chapter 48
Nutrients, Anatomy and function of Digestion
Use your STAR Sheet!!!!
The ATOM is the basic unit of matter

The subatomic particles of a Helium atom—

Positively charged protons
Uncharged neutrons

Bound together in the nucleus

Negatively charged electrons move in the space around the nucleus.
The electrons are found in energy fields that orbit the nucleus.


Let's Look at Carbon



The number of PROTONS AND NEUTRONS is the
So for Carbon (C), the Atomic Mass is 12.
ELEMENT: Pure substance that consists entirely of one type of atom

Radiation from certain isotopes can be used to treat cancer and to kill bacteria that cause food to spoil.
Figure 2-2: Isotopes of Carbon
6 electrons
6 protons
7 neutrons

6 electrons
6 protons
8 neutrons

6 electrons
6 protons
6 neutrons

Radioactive carbon-14

Nonradioactive carbon-13

Nonradioactive carbon-12

Ex: Hydrogen (H) and Oxygen (O) are gases at room temperature, but can combine to form Water (H20)

Most matter in the world are compounds

Chemical compounds are represented by a symbol




Important things to note about enzymes:

Enzymes give reactants a place to meet
Enzymes will usually end in “-ase”
Chemical reactions can be expressed using a chemical equation:

How does the body use carbohydrates?
What are the three monosaccharides?
What are the three disaccharides?
How does the body use lipids?
What are the two parts of a lipid?
What is a hormone?
How does the body use amino acids?
How does the body use nucleic acids?

Carbon Dioxide is an exception– it is inorganic
Nucleotide’s Job- cellular energy
Ex: ATP is a nucleotide

Nucleic Acid Polymer is many nucleotides linked together
There are two types of Nucleic Acids

DNA has Deoxyribose as its 5-Carbon Sugar
RNA has Ribose

CARRIERS-- lots of things have to travel through our blood-many of those things are hydrophobic, like steroids and oxygen gas. 

Some control the rate of reactions and regulate cell processes. Others transport substances into or out of cells or help fight disease. Some are used to form bones and muscles.

Proteins: Macromolecules that contain NITROGEN as well as Carbon, Hydrogen and Oxygen

Lipid used by the endocrine system to send messages

Common Types of Lipids
Also known as fats, waxes, oils
EX: glucose, fructose, cellulose
Why is water important?
Ex: Sodium Hydroxide
NaOH -> Na+ + OH-

The pH scale ranges from 0 to 14.
Pure water has a pH of 7

SUSPENSION: mixtures of water and nondissolved material
Adhesion between water and a glass causes water to rise in a narrow tube against the force of gravity (Capillary Action).  

Capillary action is a force that draws water out of the roots of a plant up to the stems and leaves
Water is the GREATEST SOLVENT on Earth!

The combination of atoms in a covalent bond form a MOLECULE.

A molecule is the smallest particle of a covalently bonded compound.

Ex: Hydrogen and Oxygen bond covalently to form a molecule of H20

Most covalent bonds can be either single, double, or triple depending on the amount of electrons shared in the bond.

Single Bond: Atoms share two electrons
Double Bond: Atoms share four electrons
Triple Bond: Atoms share six electrons

In this type of bond an atom will lose or gain an electron and the resulting compound will have an electric charge.

In ionic bonds the outer energy levels will be filled. 
Ex: Ionic bonds form between Sodium and Chlorine in table salt

Animated enzyme-link broken

Enzymes lower the amount of energy needed for reactions to occur by binding to the compounds individually


Some reactions vital to living are too slow or have activation energies that are too high to occur. These reactions are made possible because cells produce CATALYSTS.

Chemical reactions that release energy often occur SPONTANEOUSLY. Chemical reactions that absorb energy will not occur without a source of energy.


Carbon dioxide is not soluble in water, and so your blood could not carry very much of it to the lungs without a chemical reaction to make it more soluble.

 Chemical reactions always involve the BREAKING of bonds in reactants and the FORMATION of new bonds in products.
Ex: Polymerization


Answer: Amino Acid

Does the molecule have C, H, O?
No? It's NOT an Organic Compound!
Proteins are made of long chains of amino acids folded into complex structures

Type of protein used to assist chemical reactions

They are not reactants

Enable cells to notice chemical signals from the blood and from other cells.
PIGMENTATION-- like the melanin in your skin or the pigment in your iris
Peptide Bond is a covalent bond between an amino group and a carboxyl group.
Water is lost

Lipids that make up cell membranes
It's fashionable to avoid fats but we need them to survive and they make food palatable.
Lipids can be classified as:
Hydrolysis means adding an H2O to break apart polymers
Results in the loss of an H2O molecule

Controlling the pH is important for homeostasis

Ex: NH3 + H2O -> NH4+ + OH-

Ex: Hydrochloric acid in your stomach to digest food
In a salt-water solution, table salt is the SOLUTE— the substance that is dissolved.

All components are evenly distributed

A simple solution mixture has two parts: solute, solvent

Therefore, water normally tends to have the smallest surface possible, i.e. it has a high SURFACE TENSION

Water is very cohesive because of hydrogen bonding

Drops of water form beads on smooth surfaces because of cohesion

The attraction between the hydrogen atom on one water molecule and the oxygen atom on another water molecule is an example of a HYDROGEN BOND.

Let’s Review what we just talked about…

This intermolecular force of attraction is called…
Van der Waals Forces!!
Because of their structures, atoms of different elements do not all have the same ability to attract electrons.

In this type of bond, an atom will share its electrons with another atom and the charge will be neutral.
In covalent bonding the outer energy levels will NOT be filled. 
Chemical compounds are formed by the interaction of atoms in a process known as
LOCK and KEY: Each enzyme is specific for one and ONLY one substrate (one lock - one key)
To stay alive, organisms need to carry out reactions that require energy.
Every organism MUST have a source of energy to carry out chemical reactions
Plants from sunlight
Animals from plants/ animals

Answer: Carbohydrate- Monosaccharide

Section 2-3

Nucleotide Parts:
Nitrogenous Base
Phosphate Group
5-Carbon Sugar
Contain –NH2 and –COOH
R Group is how each amino acid differs

When fatty acids and glycerol combine, it is an example of DEHYRDATION SYNTHESIS
When they break apart, it releases energy and is called HYDROLYSIS
Fatty acids are chains of Carbon and Hydrogen

Water molecules can dissociate into ions of its own in the following reaction:
Surface tension is what permits water striders and other insects to walk across the surface of water and what enables a paper clip to float

Because of its make up, a water molecule is slightly polar (has a positive and negative end).

If you have ever seen a photograph of Earth from space, you know that much of the planet is covered by water. Water makes life on Earth possible. If life as we know it exists on some other planet, water must be present to support that life.

The elements or compounds that ENTER into a chemical reaction are known as REACTANTS.



Answer: Lipid

What type of molecule is this?

Atoms or Molecules + Water

Larger Molecule

Each line = a pair of electrons

Triple Covalent Bond



Each line = a pair of electrons

Double Covalent Bond



When placed in water, the ions break away from the salt crystal and are surrounded by water molecules. The ions gradually become dispersed in the water and form a SOLUTION.

Figure 2-9: NaCI Solution

Section 2-2







Energy-Releasing Reaction

Energy-Absorbing Reaction





Activation Energy


Chemists call the energy that is needed to get a reaction started the ACTIVATION ENERGY.


Reaction pathway
with enzyme

with enzyme

Activation energy
without enzyme

Reaction pathway
without enzyme

ENZYMES are molecules that serve as biological catalysts and speed up chemical reactions in cells.

Go to Section:

Figure 2-3: Ionic Bonding

Section 2-1

Protons +17
Electrons -18
Charge -1

Protons +11
Electrons -10
Charge +1

Protons +17
Electrons -17
Charge 0

Protons +11
Electrons -11
Charge 0

of electron

Chloride ion (Cl-)

Sodium ion (Na+)

Chlorine atom (Cl)

Sodium atom (Na)


Each line = a pair of electrons

Amino Acids


Fats and oils

Sugars and


Nucleic acids



Carbon, hydrogen, oxygen, nitrogen,
oxygen, nitrogen,

Carbon, hydrogen,

Carbon, hydrogen,
which contain

which contain

which contain

that consist of

that consist of

that consist of

which contain

that consist of


Carbon Compounds

When two or more elements combine in definite proportions to form substances CHEMICAL COMPOUNDS are produced
Lady-Seraphim- deviantart.com
Ex: Blood- it is mostly water (which contains many dissolved compounds) but also contains cells and other undissolved particles that remain in suspension as it moves


Water is neutral because the number of positive hydrogen ions produced is equal to the number of negative hydroxide ions.
3. Identify acidic and basic solutions and be able to construct a pH scale.
4. Describe key properties of water (cohesion, adhesion, surface tension) and give examples.
2. Differentiate between solutions and suspensions.
Atomic Structure Consists of:
Nucleus- at the center of atom
Subatomic Particles:
Neutron- neutral
Proton-positively charged
Electron-negatively charged

The nucleus makes up 99.9% of the mass of the atom
The electrons make up the rest of the atomic mass
The number of PROTONS in an atom of an element is the
ATOMIC NUMBER of the atom.
So, for Carbon (C), the Atomic Number is 6.
Because they have the same number of electrons, all isotopes of an element have the same chemical properties.
ISOTOPES: Atoms of the same element that differ in the number of neutrons they contain



Some isotopes are radioactive, meaning that their nuclei are unstable and break down at a constant rate over time.
Radioactive Carbon Dating

The physical and chemical properties of a compound are usually very different from those of the elements from which it is formed.
The amount of electrons an atom gains, loses or shares will determine the TYPE of bonds it will form and the atoms it will combine with.
What determines whether or not two atoms will combine?
The ability to bond is determined by the amount of electrons in the outer energy level.

This produces a strong bond and is characteristic of most chemicals found in living organisms.
A slight attraction can develop between the oppositely charged regions of nearby molecules.
Even when the sharing is equal, the rapid movement of electrons can create regions on a molecule that have a tiny positive or negative charge.
They are not as strong as covalent or ionic bonds, but can still hold molecules together (especially large ones)
What kind of bonds join the atoms in a water molecule?
Covalent Bonds
How many electrons are shared between hydrogen and oxygen in a water molecule?
Two (Single Covalent)
Water is the single most abundant compound in most living things
Covers 75% of Earth; makes up 45-95% of living things
Naturally found as a liquid

Water expands as it freezes unlike most substances
Thus, ice is less dense than liquid and FLOATS
 Because of their partial positive and negative charges, polar molecules such as water can attract each other
COHESION: An attraction between molecules of the SAME substance
Water molecules at the surface of water are surrounded partially by air and partially by water. Each molecule will form as many hydrogen bonds with it water neighbors as possible.
But hydrogen bonds within the liquid are all filled, and more stable- Cohesion.
ADHESION: An attraction between molecules of
DIFFERENT substances.
Cohesion holds the column of water together as it rises
When one substance dissolves into another, a SOLUTION is formed.
Because of the polarity of water, it can dissolve substances that are polar or ionic.
Water is the SOLVENT— the substance in which the solute dissolves
Some materials do not dissolve when placed in water but separate into pieces so small that they do not settle out.
Some of the most important biological fluids are both suspensions and solutions
H+ and OH- ions are the most reactive ions in nature.
The pH Scale is a measurement system to indicate the concentration of H+ ions in a solution.
Indicates the strength of an acid or a base
At NEUTRAL, the concentration of H+ ions and OH- ions are equal.
Pure water has a pH of 7
ACID -- A compound that produces H+ ions in solution
Solutions with a pH below 7 are called ACIDIC because they have more H+ ions than OH- ions
The Lower the pH, the greater the acidity
Strong Acids: pH between 1 and 3
HCl -> H+ + Cl-
BASE – A compound that produces hydroxide ions (OH-) in solution
Solutions with a pH above 7 are called BASIC, or ALAKLINE,
because they have more OH- ions than H+ ions
Strong Bases: pH between 11 and 14
Many bases don’t contain OH- ions but they produce them by accepting an H+ from water. 
BUFFERS: Weak acids or bases that can react with strong acids or bases to prevent sharp, sudden fluctuations in pH.
What is the pH scale and what does it tell us?
What is a buffer?
What is a base?
What is an acid?
What is surface tension?
youtube.com: Buffers and Exercise
If pH of fluids in cells of the body is too high or low, it will affect the chemical reactions that take place in that cell
One way the body controls pH is through BUFFERS
Macromolecules are formed by polymerization
Smaller units(MONOMERS) join to form larger POLYMERS
Four main types of Organic Molecules:
Nucleic Acids
“giant molecules”
Compounds made of
Carbon, Hydrogen, Oxygen in 1:2:1 (CHO)
Used as a main source of energy for living things
Sugars and starches
Monosaccharides (“single sugar”)
Ex: Glucose, Galactose, Fructose
Ex: Sucrose, Maltose, Lactose
Polysaccharides (“many sugars”)
Ex: Storage Polymers: Glycogen-animals, Starch-plants
Structural Polymers: Cellulose- plants, Chitin- insects, fungi
(“2 sugars”- 2 monosaccharides)
Ex: Putting monomers together to form polymers
Ex: glucose + glucose = maltose
The monomers of organic compounds join together by a chemical reaction know as DEHYDRATION SYNTHESIS to make polymers.
Dehydration is an ANABOLIC (energy consuming) reaction
Two monosaccharides can join by dehydration synthesis to form a disaccharide
Turn Turn Turn it around
The reverse reaction of breaking up polymers is accomplished by
Hydrolysis is a CATABOLIC (energy releasing) reaction
Energy is released when bonds are broken
Ex: Splitting apart polymers to form monomers
SUBUNITS of Lipids-
NOTE: Lipids do NOT have true Monomers!
Fatty Acid Chains (Chains of Carbon and Hydrogen)
NOT Water Soluble - Hydrophobic
6 12 6
Use your STAR Sheet!!!!
4. Explain the role of enzymes in living things and their importance.
3. Demonstrate how enzymes can affect the rate of chemical reactions.
2. Explain how chemical reactions affect chemical bonds in compounds.
1. Describe the functions, monomers, and examples of each of the 4 macromolecules
Hydrolysis occurs when we eat carbs and break them down for energy (E is released when bonds are broken).

Overall Jobs: store energy, form membranes, act as waterproof coverings
Waxes- plant rigidity (cuticle), ear wax
Steroids- cholesterol, steroid hormones
Phospholipids- part of biological membranes
Triglycerides- "fats" and "oils" - used for long-term sugar storage or for insulation of a multicellular organism.
Polyunsaturated- Fatty acid contains MORE THAN ONE double bond
Unsaturated- fatty acid contains at least one carbon-carbon DOUBLE bond
Saturated- Each carbon atom in a lipid’s fatty acid chain is joined to another atom by a SINGLE bond
Fats are the highest energy food.
Fats, in the form of blubber, keep large animals insulated from the cold.

You find fats in both plants and animals.
Plant oils are used in a diverse range of products, such as cosmetics, margarine, soaps, candles, and printing inks.
Polar/Hydrophilic Head
Nonpolar/Hydrophobic Tail
Amino group
Fatty Acid chain
96.3% of human body made up of:
Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N), Phosphorous (P) and Sulfur (S)

CHEMICAL REACTION: Any process in which a chemical change takes place (changes one set of chemicals into another set of chemicals).
Remember: What is Hydrolysis? What is Dehydration Synthesis?

The elements or compounds PRODUCED by a chemical reaction are known as PRODUCTS.
2H2 + O2 -> 2H2O
2H2O -> 2H2 + O2
Your body is constantly converting chemicals from one substance to another.
In the lungs, the reaction is reversed—producing carbon dioxide gas, which you exhale
H2CO3 -> CO2 + H2O

CO2 + H2O -> H2CO3
 As it enters the blood, carbon dioxide reacts with water to produce carbonic acid (highly soluble)
 The chemical reaction for this is
Energy is released or absorbed when chemical bonds form or are broken.
Some chemical reactions release energy, and other reactions absorb energy.
Those are called...?
Catalysts are substances that speed up the RATE of a chemical reaction.
They do so by LOWERING the rxn’s Activation Energy

See -ase? Think...
Speeds up the reaction between carbon dioxide and water by 10 million times.
CO2 + H2O -> H2CO3

Ex: Carbonic Anhydrase (enzyme)
Enzymes catalyze almost every important chemical reaction in living things.
Without Enzymes, the chemical reactions in the body would occur to slowly to support life.
A single organism may contain 1000s of different enzymes, each specific to a different chemical reaction.
Enzymes are specific—each enzyme only catalyzes (speeds up) one type of chemical reaction
There are tons of enzymes!!
This process is similar to a LOCK AND KEY in which the SUBSTRATE fits into the ACTIVE SITE of the enzyme
Active site: part of the enzyme that fits with the substrate

Note that the active site has a specific fit for this particular substrate and no other.

Enzymes are destroyed by excessive heat (denatured).
Enzymes are sensitive to pH.
Enzymes are generally specific to only one reaction or type of reaction.
There are 20 different amino acids
Amino Acids: contain amino group on one end (-NH2) and a carboxyl group on the other (-COOH), and R group
A covalent bond called Peptide Bonds link them together to form a protein
Monomer: Amino Acids;
Polymer: Protein
Amino group
Amino group
This is an example of dehydration synthesis.
Proteins are involved in practically every function performed by a cell, including regulation of cellular functions.
STRUCTURE-- proteins have many roles in structure
Cellular structure:  proteins make up our cytoskeleton-- our cell skeleton-- that gives our cells shape and enables movement
Other structure:  the protein called keratin is the one that makes up the bulk of your hair and nails, gives structure
ENZYMES-- these are proteins that help to promote a chemical reaction; enzymes help us to only carry out appropriate reactions
CHANNELS-- protein pores that run like tunnels across the lipid bilayer will allow specific materials that we need, like glucose, to slip through the membrane.
We have to wrap those hydrophobic things up in something that can interact with water (like a little hydrophilic coat), and that something is a carrier protein.  Ex: hemoglobin.
MOVEMENT-- it is only because our cells have protein cytoskeletons that our cells can move.  As long as our cells can move, we can move, too.
CELL ATTACHMENT-- these face the outside of the cell membrane and allow the cell to stick to other cells or to non-cellular material in the outside world.
RECEPTORS-- these face the outside of the cell and recognize chemicals like hormones that pass by
Made of C, H, O, N, P
MONOMER: Nucleotides
DNA’s Job- holds the genetic code
It contains the information so that our cells know how to make all the proteins they need
RNA’s Job- reading our genetic code—
RNA is used to read the DNA and provide the instructions contained within the DNA to the rest of the cell so that the cell can make the appropriate proteins.

1a. If a carboxyl group present.... Go to 2?
1b If carboxyl group absent.... Carbohydrate
Remember: Nucleic Acids will have the three parts of a nucleotide to look for: 5-carbon sugar, phosphate and nitrogenous base
2a. If nitrogen present............ amino acid
2b. If nitrogen absent............. fat
Organic Compounds contain Carbon– inorganic compounds DO NOT
In Carbohydrate molecules, the ratio of hydrogen to oxygen is 2:1
In fats and oils the ratio of hydrogen to oxygen is MUCH greater than 2:1
Amino acids contain an amino group (NH2) AND acid group (COOH)
must collide with enough energy to break existing bonds and form new ones.
The enzyme releases the products, and then can be re-used.
Substrates remain attached to the enzyme until the reaction is complete.
Each active site is specific for certain reactants—like a lock and key.
Substrates (reactants) bind to a specific place on the enzyme called the
Reactants are called
have the purpose
have the purpose of
have the purpose of
have the purpose of
have the purpose of
energy source
long term storage,
store and read genetic code
structure, transport, ENZYME
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