Chemistry of Life

Chapter 2

1

Section 2.1 – Atoms, Ions and Molecules

Section 2.2 – Properties of water

Section 2.3 – Carbon-based Molecules

Section 2.4 – Chemical Reactions

Section 2.5 - Enzymes

Atoms, Ions and Molecules Living things and non-living things are

made of matter

- Matter – anything that occupies

space and has mass

- Mass – the amount of matter in an

object

2

Matter is made up of atoms.

- Atom – smallest particle of matter that

can exist and still have the properties

of that particular kind of matter.

- 3 Parts make up an atom

1. proton – positive charged particle

Affects the IDENTITY of element

2. electron – negative charged particle

affects reactivity

3. neutron – neutral/ no charge

affects mass

- Atoms make up elements3

Atoms make up elements- Element – substance consisting entirely of one type

of atom.

- Cannot be broken down into simpler

substances.

- Just 4 elements make up 96% of the human

body’s mass

- Carbon (C) Nitrogen (N)

- Oxygen (O) Hydrogen (H)

- Elements are found on the periodic table.

4

Sodium, reacts violently with water

http://ruminatingdude.blogspot.com/2005/08/justifying-what-we-teach-in-hs.html

Video

Chlorine gas used in chemical warfare is

Deadly stuff!5

Pacific Steel

Chlorine Gas

Leak

Aug 2015

Chlorine is very soluble in water

and forms a strong acid when

dissolved. The chemical symbol for

chlorine is Cl. The formula for

chlorine gas is Cl2

But chemically combined…

NaCl = Table salt!

Compound – two or more elements that are chemically combined - Can be broken down into smaller substances

Ex: water – made up of hydrogen and oxygen = H2O

NaCl - table salt (sodium and chlorine)

6

Contrast:

How are elements different from compounds?

Ex. Li+

Ex. F-

Ex. Ca+

Ex. O-

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Ion - Is an atom that has gained or lost an

electron,

- Anion – The atom gains an electron

- Cation – the atom loses an electron

Apply:

What determines whether an atom becomes a positive ion or a negative

ion?

Ionic bond: Metal + Non metal

(transferred electrons)

Strongest bond

Covalent bond: Nonmetal + nonmetal

(shared electrons)

Second strongest bond

Molecule - The smallest part of a covalent

compound that still has all the properties of

the compound

Example: the smallest unit possible of water10

Compounds

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Summarize:

What happens to electrons in outer energy levels when two atoms form

a covalent bond?

Checkpoint

What distinguished one element from another?

Describe how an ionic compound is formed and

how a covalent compound is formed.

What is the difference between and ionic bond

and a covalent bond?

13

Chemistry of Life

Chapter 2

14

Section 2.1 – Atoms, Ions and Molecules

Section 2.2 – Properties of water

Section 2.3 – Carbon-based Molecules

Section 2.4 – Chemical Reactions

Section 2.5 - Enzymes

2.2 Properties of Water KEY CONCEPT

Water’s unique properties allow life to exist on Earth.

15

Life depends on hydrogen bonds in water.

OHH

_

++

• Water is a polar molecule.

– Polar molecules have slightly charged regions.

– Nonpolar molecules do

not have charged regions.

- Hydrogen bonds form between slightly

positive hydrogen atoms and slightly

negative atoms.

OHH

_

++

Properties of water1. High Specific Heat- water resists changes

in temperature.

Example: Ocean Temp

2. Cohesion – Attraction of molecules of the

same substance.

1 molecule of water sticking to another molecule

of water (droplets)

3. Adhesion – Attraction of molecules of

different substances.

Water molecules sticking to other things.

Water sticking to glass.

Water sticking to the inside stem of a plant.16

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• Hydrogen bonds are responsible for four

important properties of water.

1. Polarity

2. High specific heat

3. Cohesion

4. Adhesion

Two additional properties of water:

5. Capillary Action - the ability to move upward against

gravity. Due to the combined properties of adhesion and

cohesion.

6. Surface Tension - because water is polar and bonds with

other water molecules it creates hydrogen bonds that create

a small amount of tension on the surface.

Properties of water video (3:52 min)

Compare:

How are hydrogen bonds similar to ionic bonds?

19

Many compounds dissolve in water.

solution

• A solution - when one

substance dissolves in

another.

• “Like dissolves like.”

– Polar solvents dissolve polar solutes.

– Nonpolar solvents dissolve nonpolar solutes.

– Polar substances and nonpolar substances

generally remain separate.

– homogeneous mixture.

– Solvents dissolve other

substances.

– Solutes dissolve in a

solvent.

Connect:

What are the solvent and solutes in a beverage you drink?

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Some compounds form acids or bases.

• An acid releases a

hydrogen ion when it

dissolves in water.

– high H+ concentration

– pH less than 7

more acidic

stomach acid pH between 1 and 3

• A base removes

hydrogen ions from a

solution.

– low H+ concentration

– pH greater than 7

bile pH between 8 and 9

more basic

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• A neutral solution has a pH of 7.

pure water pH 7

Apply:

Cells have higher H+ concentrations than blood. Which has a higher

pH ? WHY?

Check Point How do polar molecules form hydrogen bonds?

What determines whether or not a compound

will dissolve in water?

Compare acids and bases

Name one example, from everyday life, of

adhesion and cohesion.

Hank water video (11:17 min)24

Chemistry of Life

Chapter 2

25

Section 2.1 – Atoms, Ions and Molecules

Section 2.2 – Properties of water

Section 2.3 – Carbon-based Molecules

Section 2.4 – Chemical Reactions

Section 2.5 - Enzymes

The Necessities/ Chemistry of Life: CARBON

All organisms must breakdown their food to use

the nutrients found in it.

Nutrients are made of molecules

C, H, O, P, Ca, N, S

– the 7 main elements that make up living things.

Carbon Hydrogen Oxygen Phosphorus

Calcium Nitrogen Sulfur

2-3 Carbon Based Molecules- Organic

Carbon atoms have unique bonding properties.

Carbon forms covalent bonds with up to four other

atoms, including other carbon atoms.

Carbon-based molecules have three general types

of structures.

– Straight chain, branched or rings

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The Chemistry Of Life…. CARBON Carbon Based Molecules

Most molecules that make up living

things are based on carbon atoms

Carbon can form up to 4 covalent

bonds (shared)

There are 3 basic structures,

because of Carbon’s unique ability to

form 4 covalent bonds.

Straight chains

and rings

Branched chain

Ring

Benzene is a component of products

derived from coal and petroleum and

is found in gasoline and other fuels.

Benzene is used in the manufacture of

plastics

It is the simplest

alkane and the

main component

of natural gas.

The relative

abundance of

methane on Earth

makes it an

attractive fuel,

a liquid

hydrocarbon

present in

petroleum. It

serves as a

standard in

the system

of octane

numbers.

It is an important

industrial chemical used

as a monomer in the

production of synthetic

rubber

a colorless pungent-smelling

hydrocarbon gas, which burns

with a bright flame, used in

welding and formerly in

lighting

Carbon-Based Molecules

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• Most Living things are made up of Carbon.

(Organic)

• Many carbon-based molecules are made of

many small subunits bonded together.

• Monomer = 1 molecule.

• Polymer = many monomers bonded together.

Chains can bond with rings forming very large,

very complex molecules.

CONNECTING LOOPS and making …CHAINS

MONOMER – the subunit in the

completed molecule.

POLYMER – the large, or macromolecule made of

many monomers bonded together.

The Chemistry Of Life…. CARBON

MONOMER that makes up a polymer, can

be made of the same or different monomers.

POLYMER – can be called a

“MACROMOLECULE”.

(made from the same or different monomers).

The Chemistry Of Life…. CARBON

Synthesize:

Write your own analogy for the formation of a polymer from monomer.

The Necessities/ Chemistry of Life: CARBON

Four Main Types of Carbon-based molecules

Carbohydrates

Lipids

Proteins

Nucleic acids

All different structures

All different functions

All formed from carbon chains and rings

Four Main types of carbon

based molecules

1. Carbohydrates Sugars and starches

2. Lipids Fats and oils

3. Nucleic Acids DNA and RNA

4. Proteins Amino acids

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1. Carbohydrates

Molecules made of C, H, O (1:2:1)

Broken down into usable chemical

energy that the body can use.

Include sugars and starches

Monosaccharides include simple

sugars (C6H12O6) – glucose, fructose

Polysaccaharides

Glycogen, starches, and cellulose

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Carbohydrates - Function Carbohydrates can be broken down to

provide energy for cells.

Some carbohydrates are part of cell

structure.

36

Polymer (starch)

Starch is a polymer of

glucose monomers that

often has a branched

structure.

Polymer (cellulose)

Cellulose is a polymer

of glucose monomers

that has a straight, rigid

structure

monomer

Carbohydrates

Polysaccharides:

Glycogen – storage in animals

(glucose/sugar)

Starches – made and stored by plants.

Cellulose – makes up the cell wall of a plant

- structure

37

Carbohydrates – molecules made of sugars.

simple sugars can bond together to make larger

sugar molecules.

polysaccharides are polymers of monosaccharides.

The Necessities/ Chemistry of Life - FOOD

MONOMER POLYMER EXAMPLE

Glucose Carbohydrate

Cellulose

Makes up cell walls in

plant cells

Contain Carbon,

Hydrogen, Oxygen

in a 1:2:1 ratio

Biochemical Reactions -

• Dehydration Synthesis –anabolic reaction -

polymers are formed

monomer + monomer polymer + water

• Example: monosaccharide + monosaccharide disaccharide + water

• Hydrolysis –large molecules ( polymers)

broken into simpler ones (monomers)

polymer + water monomer + monomer• Example

disaccharide + water monosaccharide +monosaccharide

•

2. Lipids Molecules made of C, H, O no fixed ratio

Store large amounts of chemical energy in

organisms.

Include fats, oils, waxes and cholesterol

Fats – found in foods such as meat and butter.

Oil – olive oil, peanut oil

Cholesterol – your body needs a certain

amount to function but

too much can cause

problems.40

Lipids

Lipids are nonpolar molecules

-fats, oils, and cholesterol.

– contain carbon chains called fatty acids.

– fatty acids bonded to glycerol.

41

Triglyceride

Lipids: structure

42

• Fats and oils have different types of fatty

acids.

– saturated fatty acids (single bonds)

– unsaturated fatty acids (at least one double bond

Lipids: Functions– broken down as a source of energy

– make up cell membranes

– used to make hormones

43

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• Phospholipids make up all cell

membranes.

– Polar phosphate “head”

– Nonpolar fatty acid “tails”

Phospholipid

3. Protein Molecules made of C, H, O and N

A protein is a polymer made of monomers called

amino acids.

Organisms use 20 different amino acids to

build proteins.

Your body makes 12 of the 20 amino acids.

The rest come from foods you eat such as

meat, beans and nuts.

Proteins differ in the number and order of amino

acids.

45

Proteins – made from amino acids

Our bodies make 12 of the 20 needed.

The food we eat gives us the other 8 that are

necessary

Different number and/or order of amino acids

produce different proteins.

Hemoglobin (574 amino acids)…

helps blood transport oxygen.

If one amino acid changes,

the structure changes

IT doesn’t work properly !

Red Blood cells (round vs sickled)

The Necessities/ Chemistry of Life - FOOD

Proteins

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– linked by peptide bonds.

– differ in side groups, or R groups.

– 20 different amino acids are used to

build proteins in organisms.

Protein is required by the body for the growth,

maintenance and repair of all cells.

Protein is a major component of all muscles,

tissues and organs.

Needed for metabolism, digestion and the

transportation of nutrients and oxygen in the

blood.

The main nutrient that keeps our hair shiny

and healthy, our nails strong, our skin fresh and

glowing and our bones strong and healthy.48

Protein

The Necessities/ Chemistry of Life - FOOD Proteins – made from amino acids

MONOMER POLYMER EXAMPLE

Amino acids Protein

Hemoglobin

Muscle

Contain carbon, hydrogen,

oxygen, nitrogen and

sometimes sulfur

Hemoglobin is used to

transport oxygen

in the blood

4. Nucleic Acids Molecules made of C, H, O, N and P

Nucleic acids are polymers, made from

monomers called nucleotides.

50

– Nucleotides are made of a sugar,

phosphate group, and a nitrogen

base.A phosphate group nitrogen-containing molecule,

called a base

deoxyribose (sugar)

Nucleic Acids There are 2 types of Nucleic

Acids

DNA and RNA

DNA - stores the information

for putting amino acids

together to make proteins.

DeoxyriboNucleic Acid

RNA – helps to build

proteins.

RiboNucleic Acid51

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Each Nucleotide has

a specific matched partner

A – T

(Adenine) – (Thymine)

G – C

(Guanine) – (Cytosine)

In RNA

A – U

(Adenine) – (Uracil)

Nucleic Acids

53

– DNA stores genetic information.

DNA

RNA

– RNA builds proteins.

The Necessities/ Chemistry of Life - ATP

Nucleic Acid

MONOMER POLYMER EXAMPLE

Nucleotide Nucleic AcidsDNA

RNA

DNA is the blueprint/

code for the genetic

information

Apply:

What is the relationship between proteins and nucleic acids?

Check Point What is the relationship between a monomer

and a polymer?

How are nucleic acids and proteins polymers?

How are carbohydrates and lipids similar?

Different?

How does the property of carbon account for

the variety of organic compounds?56

Chemistry of Life

Chapter 2

57

Section 2.1 – Atoms, Ions and Molecules

Section 2.2 – Properties of water

Section 2.3 – Carbon-based Molecules

Section 2.4 – Chemical Reactions

Section 2.5 - Enzymes

2.4 Chemical Reactions

58

Bonds break and form during chemical reactions.

• Chemical reactions change substances into different ones by

breaking and forming chemical bonds.

– Reactants: changed during a chemical reaction.

– Products: made by a chemical reaction.

CO2 + H2O H2CO3

CO2 + H2O H2CO3

2.4 Chemical Reactions

59

• A reaction is at equilibrium when reactants and products form

at the same rate.

• Bond energy - the amount of energy that it takes to break a

bond.

– Energy is added to break bonds.

– Energy is released when bonds form.

CO2 + H2O H2CO3

H2CO3 CO2 + H2O

60

Carbonic acid is a weak acid that is created

when carbon dioxide (CO2) is dissolved in

water (H2O),

resulting in the chemical formula H2CO3

It gives carbonated beverages their sharp taste.

Apply:

Explain why concentration is important in a chemical reaction.

62

Chemical reactions release or absorb energy.

• Activation energy - amount of energy needed to

start a chemical reaction.

63

• Exothermic reactions release more energy than

they absorb.

– Reactants have higher bond energies than products.

– Excess energy is released by the reaction.

– Endothermic reactions cause the surroundings to feel

warmer

64

• Endothermic reactions absorb more energy than

they release.

– Reactants have lower bond energies than products.

– Energy is absorbed by the reaction to make up the

difference.

– Endothermic reactions cause the surroundings to feel

cooler

Analyze:

How is activation energy related to bond energy?

Check point Hydrogen peroxide breaks down into water and

hydrogen gas. Explain why this is a chemical

reaction. What are the reactants? What are the

products?

How do endothermic and exothermic reactions

differ?

66

Chemistry of Life

Chapter 2

67

Section 2.1 – Atoms, Ions and Molecules

Section 2.2 – Properties of water

Section 2.3 – Carbon-based Molecules

Section 2.4 – Chemical Reactions

Section 2.5 - Enzymes

2.5 Enzymes A catalyst lowers activation energy.

Catalysts are substances that speed up chemical

reactions.

decrease activation energy

increase reaction rate

68

Summarize:

Describe two functions of catalysts in chemical reactions.

70

Enzymes allow chemical reactions to occur under

tightly controlled conditions.

• Enzymes are catalysts in living things.

– Enzymes are needed for almost all processes.

– Most enzymes are proteins.

Enzymes

Enzymes

71

• An enzyme’s structure allows only certain reactants

to bind to the enzyme.

– Substrates - reactant

– active site

substrates

(reactants)

enzyme

Substrates bind to an

enzyme at certain places

called active sites.

Enzymes

72

• The lock-and-key model helps show how

enzymes work.

– substrates brought together

– bonds in substrates weakened

Substrates bind to an

enzyme at certain

places called active

sites.

The enzyme brings

substrates together

and weakens their

bonds.

The catalyzed reaction forms

a product that is released

from the enzyme.

Apply:

How does the structure of an enzyme affect its function?

Check Point How does a catalyst affect the activation energy

of a chemical reaction?

Describe how the interaction between an

enzyme and a substrate changes a chemical

reaction

Some organisms live in very hot or acidic

environments. Would their enzymes work in a

person’s cells?74