Unit 3 Lesson 2Elements, Atoms, Molecules,

Carbon Atoms and Organic Molecules

John LevasseurSpringfield Central high School

Questions to Ponder From Lesson 1 What is chemistry?What are atoms, elements and molecules?What are the key six elements found in living things?

What is the periodic table?

What are chloroplasts and mitochondria?

What are entities and processes and properties. What is respiration?

What is ATP? What is the relationship between chloroplasts and mitochondria? 

What is photosynthesis? 

What are the similarities between carbon and silicon? Why do the similarities between carbon and silicon exist?

What are organic molecules?

What are the four key organic molecules that make living things?

Why is carbon the element of life?

Use the carbon atom to explain concept that form determines function; explain why the carbon atom’s shape determines the properties of the element carbon that allow carbon to be the element of life.

Explain how the form of H2O determines that water is a polar molecule. Be sure to discuss the properties that water has because the H2O molecule is polar.

Explain how ions are formed; then explain the ionic bonding

process that makes table salt.

Describe how amino acids join together to form peptide bonds.

Questions to AnswerDaily Problem Set Unit 3- #1

Draw and describe the structure of a carbon atom; be sure to label subatomic particles, the particles’ charges and energy levels.

Matter is composed of elements.◦ Matter is anything that has mass and volume

Elements are substances that consist of only one kind of atom and cannot be decomposed into simpler substances.

There are over 90 elements occurring in nature.◦ There are 6 elements that makes up most of, (98%) the mass of

living things. Carbon Hydrogen Oxygen Nitrogen Phosphorus Sulfur

Smallest piece of matter that still retains properties of an element is an atom.

lement

• What is matter? • What are elements?• What are atoms?

• What are the 6 key elements for life?

Atoms change form when they become ions.A change in form will mean a change in function

Atoms and Ions Atoms - the smallest particle of an element that has the

physical and chemical properties of that element. Atoms are made from three types of subatomic particles.

◦ Proton positively charged and found in the nucleus◦ Neutron no charge and found in the nucleus◦ Electron negatively charged and found outside the nucleus in the energy

levels Atoms must contain equal numbers of electrons and protons.

◦ If an atom gains or loses electrons it becomes an Ion. Positively charged ions are made when an atom loses an electron

Positive ions an called Cations. Negatively charged ions are made when an atom gains an electron

Negative ions are called Anions.

How are ions made from atoms?

What are anions and cations?

The number of protons in an atom will determine what type of element.◦ The atomic number of an

element is the number of protons in that element’s atoms’ nuclei

The Atom’s Nucleus

Electrons are a subatomic particle Electrons have negative charges. Electrons are found in the outer

regions surrounding the nucleus called energy levels also known as energy shells.

The outermost energy level is called the valence level. ◦ The electrons found in the valence level

is called the valence electron.◦ The number of valence electrons

determine the chemical reactions of the element.

◦ How an atom behaves when it encounters other atoms is determined by valence electrons.

The Atom’s Electrons(e-)

• What are electrons?• What is the valence level

in an atom?

 Isotopes of Atoms ◦ Isotopes are atoms of the same element that

have different masses due to different number of neutrons. 

Examples of Isotopes:  • Hydrogen has 3 isotopes 

1. Usually Hydrogen has only a proton in its nucleus 2. Hydrogen has an isotope known as Deuterium.

Deuterium has one proton and one neutron. 3. Hydrogen has another isotope known as Tritium. Tritium

has one proton and two neutrons.

Isotopes

• What are isotopes?

• What happens to an atom if the

proton numbers changes?

• What happens to an atom if the

neutron number changes?

What do the numbers on the periodic table tells us?

• What are elemental symbols?

• What is the atomic number?

• What is the mass number?

• Name the six elements above.• State the number of protons,

neutrons and electrons in an atom of each.

A little game called: Name that Element!What does the element do for living things?

Can you determine how many protons there are?

Can you determine how many valence electrons

there are?

Chemical Reactions◦ A chemical reaction is a process where one or

more substances are transformed into one or more different substance. Chemical reactions do not destroy or create

matter Chemicals reactions rearrange atoms from one

compound into another.

◦ 2H2 + O2 2H2O Covalent Bonds

◦ When atoms are bonded together by sharing electrons in the atoms’ valence energy level a covalent bond is formed; Covalent bonds are made between elements that

are nonmetals Ionic Bonds

◦ When ions are attracted toward each other due to opposite charges, electrostatic attraction, a bond is formed called an ionic bond’ Ionic bonds are formed between ions of metal

elements, (+ charged) and ions of non-metal elements (- charged)

Chemical Reactions and Ionic & Covalent Bonds

• What is a chemical reaction?• What are covalent and ionic

bonds?• What is the law in science that

matter is not created nor destroyed?

Watch this Animation

Water (H2O) has a Polar Covalent BondThe form of water molecules determines the function and properties of water. 

Water is a polar molecule; which means that one side of the molecule attracts more electrons, (or negative charges).

Attracting more electrons to the oxygen side of the molecule means that water has a slight negative charge on the oxygen side and a slight positive charge on the hydrogen side.

Water is a polar molecule because of its shape. 

Water has a slightly positive charge on the H2 side.  H2O has a slightly negative charge on the O side. 

Different shape Different properties

Why is water a polar molecule?

Water’s two key properties: ◦ Adhesion and Cohesion

Adhesion: water sticks to charged entities◦ Water has adhesion because H2O is a

polar molecule Cohesion: water molecules stick to

other water molecules◦ Water has cohesion because H2O is a

polar molecule 

Water Molecules’ Emergent Properties

Cohesion

• Explain why water is a polar molecule.

• What is adhesion?

• Why will water adhere to charged

surfaces?

• What is cohesion?

Watch this animation

Different Representation of Molecules

We often see molecules modeled in different ways so that we can better understand the form of molecules, which in turn allows us to understand the properties of molecules.

Some of the common modeling types of molecules.

•Molecular Formula

•Skeletal

•Ball and Stick

• Lewis Dot Structures

• Structural Formula

The Element Carbon

• Organic Molecules are Molecules Made with the Element Carbon.

• Carbon is a Very Special Element for Life; Carbon Atoms Hold Together the Organic Molecules That Living Things Are Made From.

• There Are Four key Organic Molecules to Know: • Carbohydrates, • Proteins, • Lipids • Nucleic Acids.

Carbon is the element of life; what is the role of carbon in organisms?• Carbon is element

number 6 on the Periodic Table.

• Carbon has 6 protons and 6 electrons

• Carbon has 4 electrons in its valence (outermost) energy level.

Why is carbon so special?

Carbon Bonds

• A carbon atom becomes stable when it forms four covalent bonds and fills the valence level.

• Carbon atoms can form covalent bonds with other atoms.• Carbon bonds with other elements’ atom.• Carbon bonds with other carbon atom

Carbon atoms can form multiple bonds (that are very strong) with other carbon atoms.

•   Single carbon-carbon bond

• Double carbon-carbon bonds

• Triple carbon-carbon bonds

The Reasons why carbon is the Element of Life.

Carbon has a special ability to form covalent bonds because of the form of the carbon atom

What types of bonds can a carbon atom form with other

carbon atoms?Why are these bonds

important?

Basic Structures of Carbon Molecules Carbon atoms can form multiple bonds (that are very strong) with other carbon atoms

Carbon atoms bonded together can make different shapes (forms). 

Here  are examples of the different forms: • Straight Chains

• Branched Chain 

• Rings

Since carbon based organic molecules can be arranged into seemingly

endless numbers of forms, organic molecules can perform seemingly

endless numbers of functions.

We now know that form determines function. ◦ This concept holds true a all the levels of scale

We also know that organic molecules are those molecules that have a carbon backbone and are found in living things. ◦ These organic molecules make the structures and perform the chemical

reactions of organisms Each organic molecule group has small molecules (monomers) that

are linked to form a larger organic molecule (macromolecule). ◦ Monomers can be joined together to form polymers that are the large

macromolecules made of three to millions of monomer subunits. ◦ Sections of these monomers have distinct forms that give the molecule certain

functions These sections of molecules are called functional groups .

Functional groups are clusters of atoms with characteristic structure and functions.

The specific molecular structures of many organic molecules are due to specific arrangements of atoms into functional groups. These functional groups give molecules their distinctive chemical properties.

Functional Groups in Organic Molecules

What 6 elements do you expect to see in the common functional groups?

Concept of Scale and The Key Organic Molecules of Life

We need to remember to consider the levels of scale when we're  discussing life's chemistry: • Subatomic particles- Protons, neutrons and electrons• Atoms- the smallest particle of defined elemental matter.• Functional groups- groups of atoms bonded together within a molecule that allow the molecule to perform some particular function.• Molecule- Atoms joined together by covalent bonds.•Subunit, (monomer)- molecules that can be joined together to form large polymers.•Macromolecule, (polymer)- Large molecules made by joining smaller molecules

Macromolecules

Subunits

Molecules

Functional Group

Atoms

Subatomic Particles

Life substances:The Four Key Organic Molecules 

Monomer PolymerMonosaccharide

s Carbohydrate

Glycerol and Fatty Acid Chains Lipids

Amino Acids Proteins

Nucleotides Nucleic Acids

• As you know there are four key Organic Molecules to Know: • Carbohydrates, • Proteins, • Lipids • Nucleic Acids.• These four organic molecules are large molecules,

(polymers) made by joining smaller molecules, (monomers). • These four large molecules are known as macromolecules or polymers; the smaller molecules that make them up are known as subunits or monomers.

Watch this Animation

Carbohydrates• Carbohydrates are used by cells to store and release energy. Energy is stored in the carbon bonds.• Carbohydrates are also used as structural components of plants and insects. • Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen, in a ration of 1 carbon : 2 hydrogen : 1 oxygen.

• The basic formula for carbohydrates is : (CH2O)n.• Carbohydrates are broken into 3 groups:

• monosaccharides,• disaccharides,• polysaccharides• Carbohydrates are macromolecules made

by joining simple sugars, (momosaccharides) together.

• Monosacharides are simple single sugars.

• Key monosaccharides include:• glucose (C6H12O6), • fructose (same formula but

different structure than glucose). • ribose (C5H10O5), (an important part

of nucleic acids)

Advanced Animation

Disaccharides: Two Monosaccharides joined by a condensation

reaction, (AKA. Dehydration Synthesis)◦ Example of a disaccharide: sucrose◦ Sucrose is table sugar (C12H22O11)◦ Sucrose’s chemical formula once again shows how

glucose (C6H12O6) and fructose (C6H12O6) are joined by the condensation of a water (H2O) molecule. . C6H12O6 + C6H12O6 -->C12H22O11 + H2O

Carbohydrates (cont.)• Explain a condensation reaction,

aka dehydration synthesis.• What is a Disaccharid

e?

An Animation on Condensation and Hydrolysis

•What form of carbohydrate is energy storage for plants?

•What form of carbohydrate is energy storage for fungi and

animals?

Polysaccharides:◦Polysaccharides are polymers of many

monosaccharide monomers joined by condensation reactions. Examples of polysaccharides: starch, glycogen, and

cellulose. Starch is a polymer of many glucose molecules used as energy

storage in plants. Glycogen is a polysaccharide of glucose monomers that stores

energy for bacteria, fungus, and animals. Humans and other vertebrates store glycogen in their liver.

Cellulose is a polysaccharide of glucose monomers that plants use for structure.

Carbohydrates (cont.)

Lipids•Lipids: are organic macromolecules that have a large proportion of carbon to hydrogen bonds with less oxygen.• Example: lipid in beef C57H110O6.

• Lipids are more commonly known as fats, waxes, and oils.• Lipids are insoluble in water. Lipids do not form solutions in water.• Lipids are non-polar molecules. This means there is no side of the molecule with a positive or negative charge. The molecule is perfectly balanced.• Remember water (H2O) is a polar molecule and water will

attach to any charged particle.• It is this capability of water that allows solutions to form.

• Since lipids are non-polar (have no charge) H2O molecules cannot adhere to lipids.

Why are lipids insoluble in water?What is the ration

relationship between C, H, and O in lipids?

Lipids (cont.)•). Lipids are used in cells for energy storage, insulation, and protective coating (to reduce H2O loss• We will learn how lipids make up the cell membrane.Phosphlipid bilayer• Lipids are macromolecules made of two simpler molecules: glycerol and fatty acids.• Steroids have glycerol with one fatty acid chain.• Phospolipids have a phosphate group attached to a glycerol with two fatty acid chains.• Triglycerides have a glycerol with three fatty acid chains.Molecular structure of triglycerol.• Steroids (and other hormones) are lipids.

Proteins: are large complex polymers composed of smaller monomers, (simpler molecules) known as amino acids. ◦ Amino acids are composed of the elements: carbon, hydrogen, oxygen,

nitrogen, and sulfur. ◦ There are 20 amino acids.

In humans there are 9 essential amino acids that the body cannot make and must take in with diet.

In humans, there are 11 non-essential amino acids that a healthy body makes, Conditionally essential amino acids are the 6 nonessential amino acids that the

body may not be able to make due to illness or poor nutrition and then must be obtained through diet.  

The 20 amino acids can form millions of different combinations to form millions of different proteins.

Amino acids have two distinctive functional groups: ◦ amino group (NH2) ◦ carboxyl group (COOH).

The structure of a generalized amino acid:

Proteins

• What are amino acids?•What are the functional groups of

amino acids?• How many amino acids make up

all the proteins?

The covalent bonds that join amino acids are called peptide bonds◦ Proteins are also known as polypeptides.

Proteins (cont.)

Amino Acid Condensation Reaction

Where are the amino groups?

Where are the carboxyl groups?

How is the peptide bond formed?

Proteins (cont.)• Proteins play many roles and perform many functions in living organisms.• Proteins are often used as structural components of organisms.• The coats of viruses are bacteria are made of protein.• Muscle tissue is protein and lipids.

• Other uses of proteins:• Transporting oxygen in the blood• Providing immunity• Regulating other proteins• Regulating chemical reactions (this is the job of enzymes).

•Enzymes• Enzymes are proteins that change the rate of chemical reactions• Enzymes are involved in nearly all metabolic processes.• Enzymes are like a lock and key to regulate chemical reactions.

No surprise, the shape of enzymes allow them to be catalysts for chemical reactions in living things.

Enzymes are chemical catalysts.Catalysts are substances usually used in small amounts relative to the reactants, that modifies and increases the rate of a reaction without being consumed in the process.

Watch this Animation

Proteins (cont.)• Protein Structure:

• There are four levels to the structure of proteins:

• Proteins are the “work horses” of organic molecules. Proteins perform countless functions in living things. • Think of the innumerable chemical

reactions that enzymes catalyze. • Proteins must have the ability to organize the 20 amino acids into countless shapes.

• Primary•Secondary•Tertiary•Quaternary

Watch this Animation

Watch this Animation

MA Framework Question: Explain the role of enzymes as catalysts that lower the activation energy of biochemical reactions. Identify factors, such as pH and temperature, that have an effect on enzymes.

Proteins (cont.)• Remember: enzymes are chemical catalysts that make chemical reactions happen faster or slower.

• Enzyme activity is influenced by several factors.  Environmental conditions, such as pH, temperature, or salt concentration may change the three dimensional shape of an enzyme, altering its rate of activity and/or its ability to bind the substrate.

• Note how an enzyme’s shape allows it to perform this function

• Chemical reactions often require an input of energy to get the reaction started. • Many enzymes function by lowering the activation energy of reactions. By bringing the reactants closer together, chemical bonds may be weakened and reactions will proceed faster than without the catalyst.

Enzyme Specificity Animation

Nucleic Acids

Nucleotides are important for several reasons. First the genetic material (DNA) is a polymer of four different nucleotides. The genetic information is coded in the sequence of nucleotides in a DNA molecule. Polymers of nucleotides such as DNA and the several types of RNA in the body are called nucleic acids.  Nucleotides and related compounds are also important energy carrying compounds. Among the ones commonly encountered are ATP, and NADH.

Nucleic acids are polymers of nucleotides joined together to make large macromolecules. The important nucleic acids are deoxyribonucleic acid(DNA) and various types of ribonucleic acids(RNA).

Nucleotides are monomers consisting of a phosphate group, a five carbon sugar(either ribose or deoxyribose) and a one or two ring nitrogen containing base. 

The four nucleotides that make the DNA molecule

Watch This Animation

Nucleic Acids (cont.)The Functions of Nucleic Acids• The primary function of nucleic acids is to store and transmit genetic information. • Other functions of Nucleic Acids include:• Transport of amino acids• Energy storage and release

The Central Dogma of Biology• DNA is Replicated into more DNA• DNA is Transcribed into RNA• RNA is Translated into Proteins

•ATP is the chemical energy that cells actually use. •ATP is produced when organisms release the energy in carbohydrates and lipids. •ATP release energy and breaks down into ADP as cells require energy.

Nucleic Acids (cont.)Deoxyribonucleic Acid (DNA) & Ribonucleic Acid

• DNA, (Deoxyribonucleic acid), is the molecule of heredity.  • Genes are sections of a long

DNA molecule that encode the directions for one protein.• Genes are coded messages

of how, when and where to make proteins.

• The information stored in DNA's chemical code is transcribed into RNA.• RNA  delivers the DNA's

information to the site of protein synthesis

See this animation

Nucleic Acids (cont.)Adenosine Triphosphate (ATP) - Nature's Energy Store

•All living things require a continual supply of energy in order to function. •Cells require energy for all the processes which keep the organism alive. •Examples of cell processes that require energy:• Synthesis of organic molecules• Active transport of molecules and other cell nutrients

•The molecule adenosine triphosphate, (ATP) is the nucleic acid that is the currency of energy in cells .•ATP works by releasing the endmost phosphate group when catalyzed by an enzyme. This reaction releases energy. •The reaction’s product is adenosine diphosphate (ADP), and the extra phosphate functional group as well as the energy.

http://student.ccbcmd.edu/courses/bio141/lecguide/unit6/metabolism/energy/adpan.html

Questions to Ponder From Lesson 3What are atoms, ions, elements and molecules?What makes carbon the element of life?What are the key six elements found in living things?

What are the four basic organic molecules for lifeWhat is a macromolecule or a polymer?What is a subunit or monomer?

What are the three types of carbohydrates? What are the four key organic molecules’ subunits?What is a functional group?

Where can you find carbon on the periodic table? How many  electrons  can carbon share?

What are the basic shapes that carbon molecules can make?What are single, double and triple bonds?

What type of reaction joins monomers into polymers?What functions can lipids perform?What key functional groups are found in amino acids?What is the function of enzymes?What is the central dogma of biology?What are the functions of nucleic acids?

Choose and

answer 7

questions