Chemistry of Life

Chapter Two

1

Biology and Chemistry

Biology = study of life

Chemistry = study of matter

and the changes it undergoes

Matter – anything that takes up

space and has mass

Life is made up of atoms

2

2.1 Atoms, Ions, and Molecules

Atoms

Building blocks of

matter

Tiny

Models

Help explain structure

and properties

3

Atomic Structure

Three subatomic particles:

Protons (p+)

Neutrons (no)

Electrons (e-)

4

Subatomic Particles

Protons

Same size as no

Inside nucleus

Positive charge

Same number as e-

Identifies element

5

Subatomic Particles

Neutrons

Same size as p+

Inside nucleus

No charge

Helps hold nucleus

together

6

Subatomic Particles

Electrons

Smallest

Outside nucleus

Negative charge

Same number as p+

Involved in chemical reactions

7

Atomic Review

Nucleus

Core of atom

Dense

p+ and no

e- are outside the

nucleus

Atoms are neutral

Same # of p+ as e-

8

Elements

Pure; made of just one

kind of atom

>100 different kinds

91 natural

~25 found in organisms

Represented by chemical

symbols

9

10

Elements Differ in # of p+ in atoms

Atomic number = # of p+ in atom

Ex:

Carbon = 6

Oxygen = 8

Hydrogen = 1

What element is shown?

11

Elements

Atomic Mass – sum

of p+ and no in an

atom

“atomic weight”

12

Isotope

Atoms of the same element that differ in

the # no

Same element

Same # p+

Same # e-

Different # no

Ex: Hydrogen

13

Mystery Atom

How many protons?

How many electrons?

What is the atomic number?

What is the name?

What is its chemical symbol?

14

In Your Own Words: Differentiate between an

atom and an element:

What is an atom?

What is an element?

How are they related?

15

Compounds Made up of two or more different

kinds of atoms joined together represented by chemical formulas

Formulas tell type of elements and proportion (# of atoms of each element)

Ex: Water = H2O

Sodium chloride = NaCl

Carbon dioxide = CO2

16

Chemical Bonding Atoms join with other atoms to form compounds

Force that holds the atoms together = chemical bond

17

Chemical Bonds

Atomic “Glue”

Three basic types:

Ionic bonds

Covalent bonds

Hydrogen bonds

18

Ion An atom that has gained or

lost one or more electron

Now different # of p+ and e-

Not neutral

Has a charge!

19

Ions

Cation – an atom that

has lost one or more

electrons

positive charge

Anion – an atom that

has gained one or

more electrons

negative charge

20

Atoms Want Stability

21

Ionic Bonding

Ex: NaCl = Table Salt

Na gives up an e-

Becomes cation

Cl takes in an e-

Becomes anion

Opposites attract and

BOND

22

Ionic Bonding

23

Covalent Bonding

Atoms share e- to gain

stability

Fill outer shell with e-

24

Covalent Bonds

Molecule – two or more

atoms held together by

a covalent bond

25

Covalent Molecules

Ex:

Water

Carbon dioxide

Oxygen

26

2.2 Properties of Water

~70% of your body is water

~2/3 of molecules in your body

Hydrogen Bonding

Weak bond between

polar molecules

Holds molecules

together

Water = good example

Often between slightly

positive H atom and

slightly negative N or O

atom

Opposite charges attract

28

Polar Molecules

Overall molecule is

neutral

e- shared unequally

One end positive

One end negative

Ex: Water

29

Hydrogen Bonding in Water

30

Water in Living Things Your cells: filled AND surrounded by water

All living things need water

Properties of water 7 min British

31

Properties Related to H bonding

1) Specific heat

2) Cohesion

3) Adhesion

32

1)High Specific Heat

Water:

Heats up slowly

Cools down slowly

Helps regulate body

temperature

Evaporation

33

2) Cohesion

Force of attraction between similar substances

Ex: Hydrogen bonding in water

Creates surface tension

surface doesn’t break easily

34

35

3) Adhesion

Attraction between different substances

Ex: Water is attracted to other polar substances

Adhesion is stronger than cohesion in water molecules

Explains water meniscus

Adhesion

Powers capillary action

Water moves upward

through tiny tubes against

gravity

Ex: water moving up a

plant

37

Aqueous Solutions Solution of a substance dissolved in water

Solution - mixture of evenly distributed

substances (homogeneous)

38

Solution Parts

Solvent – does the dissolving

Solute- gets dissolved

Concentration – the amount of solute

dissolved in solvent

Polarity of Water

Review:

Overall molecule = neutral

One end = positive

One end = negative

Opposites attract

40

“Like Dissolves Like”

Water dissolves ionic

compounds and polar

molecules best

Ionic compounds

break apart into ions

in water

Ions have charges

41

Sodium Chloride in Water

42

Sodium chloride is an example of :

43

Oil and Water do NOT mix!

Nonpolar and polar do

NOT mix

Nonpolar substances

do not dissolve well in

water

Important to organisms

Nonpolar membranes

44

Acid

Compound that releases a hydrogen

ion (H+) - when dissolved in water

H+ is a proton

45

Bases Compounds that form hydroxide ions

(OH-) when dissolved in water

Reduces concentration of H+

OH- react with H+ to form H2O

46

Acids and Bases

47

pH Scale Measures concentration

of H+ in a solution

pH scale runs from 0-14

below 7 = acidic

above 7 = basic

pH equal to 7 is neutral

48

pH Scale Each step is a ten fold change in H+ concentration!

Ex: pH 4 is ________x more acidic than pH of 6?

49

pH of Common Household Items

50

pH Range in organisms

Very narrow

Ex:

human blood pH 7.35-7.45

Azalea plant pH 4.5

Buffers – help regulate pH

binds to H+ when too many, and releases H+

when not enough

Thinker. . .

Cells have a higher concentration of

Hydrogen ions than blood.

Which has a higher pH – blood or a cell?

Why?

2.3 Carbon Compounds

= Organic compound

Contain C

“building block

of life”

Usually forms:

4 covalent

bonds

Long chains or

rings 53

Carbon Molecules

Monomer – subunit of the molecule

Polymer – Many monomers bonded

together

large molecule (macromolecule)

Classes of Organic Compounds

1) Carbohydrates

2) Lipids

3) Proteins

4) Nucleic Acids

55

1) Carbohydrates

Made of C, H, and O

Often 1:2:1 ratio

Most have 5 or 6 C

atoms

Key energy source

Monomer (building

block) =

monosaccharides

56

A) Monosaccharides

Simple sugars

Mono = “one”

Saccharide =“sugar”

Examples:

Glucose

Fructose

Galactose

57

B) Disaccharides

Double sugars

Di = “two”

Two

monosaccharides

joined

Ex: Sucrose =

table sugar

glucose + Fructose

58

C) Polysaccharides Poly = “many”

Polymers of monosaccharides

Macromolecules

Macro = “big”

59

Polysaccharides

Some store energy

Plants = starch

Animals = glycogen

In plants, they also

provide support

Ex: Cellulose in cell

walls

60

61

2) Lipids

Not soluble in water

Nonpolar

Examples:

Fats

Oils

Waxes

Steroids

Cholesterol

Phospholipids

Cell membranes

62

Lipids include Fats Store lots of energy

Building blocks:

1) Fatty acids – chain of C bonded to H

2) Glycerol

Triglyceride = 3 fatty acids + glycerol

Many lipids

63

Saturated Fatty Acids

Lots of C – H single

bonds

Generally solids at room

temp

Ex: Animal fats

Butter

Lard

Grease

64

Unsaturated Fatty Acids

Some double bonds

Bends molecule

Can’t pack tightly together to become solid

Generally liquids at room temp

Most plant oils

Some fish oils

65

Hydrogenated fats

“Trans Fats”

Made when unsaturated fat has H added Becomes more solid

More “saturated” with H

Tastes better. Lasts longer. Not good for you!

Not natural!

66

Phospholipids

Make up cell

membranes

Contain

Glycerol

2 fatty acids

Nonpolar “tails”

Phosphate group

(PO4-)

Polar “head”

67

Cholesterol

Ring structure

Too much = not good

Necessary for:

Cell membrane structure

Steroid hormone production

Ex: testosterone, estrogen

68

3) Proteins

Important to life

Ex: enzymes

Promote chemical

reactions

Ex: structural proteins

Collagen

Keratin

Fibrin

Hemoglobin 69

Proteins Large molecules = macromolecules

Building blocks = Amino acids (aa)

70

Amino Acids

Twenty different aa

Some polar

Some nonpolar

Fold into shapes

Our body makes 12

Get other 8 from food

71

Amino Acids

Contain C,H,O,N and sometimes S

Most varied organic compound

All have:

C bonded to H

Amino group (NH2)

Carboxyl group (COOH)

Only differ in R-group (side chain)

Examples of aa

AA Bonding

Form Peptide bonds

covalent bonds

Linked chains =

polypeptides

Protein = 1 or more

polypeptides

Proteins

AA sequence

determines structure

and function

Ex: hemoglobin

In RBCs

One incorrect aa = sickle

cell anemia

4) Nucleic Acids

long chain-like

molecule

Nucleotides =

building blocks

(monomer)

Store protein making

info

76

Nucleotides

3 parts

Phosphate

group

Sugar

Nitrogen

base

77

Two kinds

1) DNA

Two strands

Spiral shape

Stores hereditary info

makes up chromosomes

78

Two kinds of nucleic acids

2) RNA

One strand

3 different types

Key role in making proteins

Can act as enzyme

79

ATP

Adenosine triphosphate

Single nucleotide with 2

extra phosphate groups

Energy “currency”

Fuels cell activities

80

ATP

81

2.4 Chemical Reactions

Change substances into different

substances by making and breaking bonds

Reactants – substances changed

Products – substances made

Bond Energy – amount of energy needed to

break a bond between 2 atoms

Energy

Ability to move or

change matter

Many forms:

Light

Heat

Chemical

Electrical

Mechanical (motion)

83

Energy Conversions

can change from one

form to another

Ex:

Kicking a ball

Frying an egg

84

Chemical Reactions Energy stored or

released

Atoms rearranged

1000s of reactions

per cell per second!

85

Chemical Reactions

Reactants

Starting materials

Before reaction

Products

Ending materials

After reaction

Arrow = “yields”

86

Energy in Chemical Reactions

Involve energy changes

Bonds are broken and formed

Energy is either absorbed or released

87

Energy-Releasing Reaction

Exothermic

Gives off energy

Ex:

Squid and firefly

light

Water freezing

Cellular respiration

88

Energy-Absorbing Reaction

Endothermic

Takes in energy

Ex:

Melting of ice

Photosynthesis

89

Metabolism

Sum of all chemical

reactions in

organism

Energy comes from

food

90

Activation Energy Energy needed to

start a chemical

reaction

Energy absorbed

“chemical push”

Amount needed varies

Analogy: To get a

boulder to roll

downhill, First you

must push it up

91

2.5 Enzymes Act as catalysts

Speed up chemical

reactions (rxs) in cells

Lower activation

energy

92

Cells and Energy

Cells must have “fuel”

Chemical rxs in cells occur:

Quickly

Low temperatures

93

Enzymes Required for Life

Help maintain

homeostasis

w/o enzymes rxs

would be too slow

Life could not exist

94

Carbonic Anhydrase

Enzyme in blood

Helps convert CO2

and H2O into carbonic

acid

Carried to lungs

Converted back into

carbon dioxide and

water

95

Do not write; just an example Without Carbonic

anhydrase

Slow rx

2000 molecules per hour

converted

Not fast enough

Millions of cells release

CO2

96

Do not write; just an example

With enzyme

600,000 molecules

per second

Increases rate a

million times!

97

Do not write; just an example

Catalase

enzyme

Helps breakdown

hydrogen peroxide

(toxic to cells)

Reduce activation

energy

quicker

98

Enzyme Specificity Each enzyme acts only on a specific substrate

(reactant)

Substrate

Substance on which an enzyme acts

“Lock and key” model

99

Active Sites

Shape is everything!

Enzymes bend

slightly around

substrate

Active site - site on

enzyme where

substrate temporarily

binds

100

Enzymes

101

Factors That Affect Enzymes

1)Temperature

Operate best within

certain range

102

Factors That Affect Enzymes

2) pH

Operate best within

certain range

Thinker: If the HCl in

the stomach has a pH

of ~2, which enzyme

on the chart would

function best here?

103

Enzyme Activity

Many different ones

Each for different rx

Not used up

Used over

104