chapter 2 the chemistry of biology copyright © the mcgraw-hill companies, inc. permission required...

Chapter 2

The Chemistry of Biology

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.1

Shells

Hydrogen

Carbon6 protons

6 neutrons6 electrons

Nucleus

(b)

proton

neutron

electron

Nucleus

Nucleus

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

1 proton1 electron

2

Atoms, Bonds, and Molecules• Matter - all materials that

occupy space and have mass. Matter is composed of atoms

• Atom - simplest form of matter not divisible into simpler substances

– Protons: (+) subatomic particles

– Neutrons: neutral subatomic particles

– Electrons: (-) subatomic particles

3

Different Types of Atoms

• All atoms share the same fundamental structure

• Element - pure substances with a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors

Shells

Hydrogen

Carbon6 protons


Nucleus

(b)

proton

neutron

electron

Nucleus

Nucleus


1 proton1 electron

The Major Elements of Life

4

5

Characteristics of ElementsAtomic number – number of protons

Mass number – number of protons and neutrons

Isotopes – variant forms of the same element that differ in the number of neutrons

Atomic weight – average mass numbers of all isotopic forms

Electron orbitals – volumes of space surrounding the atomic nucleus where electrons are likely to be found

(a) Orbitals

Shell 1

Shell 2

ShellHydrogen

Carbon

ShellsHydrogen

Carbon6 protons


Nucleus

(b)

proton

neutron

electron

Nucleus

Nucleus

1 proton1 electron

Biologically Important Atoms

6

Mg

S 16

SULFUR

AT. MASS 32.06

Cl 17

CHLORINE

AT. MASS 35.45

P 15

PHOSPHORUS

AT. MASS 30.97

Ca 20

CALCIUM

AT. MASS 40.08

K 19

POTASSIUM

AT. MASS 39.10

Na 11

SODIUM

AT. MASS 22.99

O 8

OXYGEN

2 • 6

AT. MASS 16.00

N 7

NITROGEN

2 • 5

AT. MASS 14.00

C 6

CARBON

2 • 4

AT. MASS 12.01

Mg 12

MAGNESIUM

2 • 8 • 2

AT. MASS 24.30

Chemical symbol

Atomic number

Chemical name

NumberOf e– inEachEnergylevel PQS N


AT. MASS 1.00

1

H

HYDROGEN

1p

12p

H

c

6p

7p

N 8p

O

2 • 8 • 1

11p

Na

2 • 8 • 8 • 1

2 • 8 • 8 • 219p

20p

K

Ca

2 • 8 • 5 2 • 8 • 6

P S

2 • 8 • 7

Cl

15p 16p

17p

H

Li Be

Na Mg

K Ca

Rb Sr

Cs Ba

Fr Ra

Mn

Tc

Re

Fe

Ru

Os

Co

Rh

Ir

Ni

Pd

Pt

Sc Ti V Cr Cu Zn Ga Gs As Se Br Kr

Al Si P S Cl Ar

B C N O F Ne

He

1

Concept Check:

If two atoms have the same number of protons and electrons but different numbers of neutrons, they would be

A. Different elements

B. Isotopes of the same element

C. Ions of the same element

D. Orbitals of the same element

7

8

Bonds and Molecules

• Molecule - a chemical substance that results from the combination of two or more atoms

• Compounds - molecules that are combinations of two or more different elements

• Formula/Mass weight - sum of all of the atomic masses of the atoms a molecule contains

• Chemical bonds - when 2 or more atoms share, donate, or accept electrons to form molecules and compounds– 3 types: covalent, ionic, and hydrogen

8

3 Types of Chemical Bonds1. Covalent bonds –

electrons are shared among atoms

– Polar covalent bonds – unequal sharing

– Nonpolar covalent bonds – equal sharing

Covalent Bonds

Single

Double


Covalent Bonds

10

Hydrogen molecule

Single bond

H2

e–

e–

e–e–H +

+ Hydrogen atom

H

Hydrogen atom

1p+ 1p+ 1p+1pH H


8n 8n8p+ 8p+

Molecular oxygen (O2)

Double bond

O O

6p+

6n 1p+

1p+

1p+

1p+

Methane (CH4)

H

H

H

H

C

H H

H

H

C

Polarity

11

(–)

H H

H H

(+) (+)

(a) (b)

8p+

1p+ 1p+

O

(+) (+)

O


(–)

12

3 Types of Chemical Bonds

2. Ionic bonds – electrons are transferred to one atom forming positively charged cations and negatively charged anions


Ionic Bond

(+) (–)

Ionic Bonding

13

11p+

12n

Na

[Na]+ [Cl]–

Cl

Sodium Chloride

(c)

17p+

18n

Chlorine atom (Cl)

12


(a) Sodium atom (Na)

(b) Na Cl

(d)© Kathy Park Talaro

Cl2 Cl2

Na1

Cl2 Cl

2

Cl2

Cl2

Cl2

Na1

Na1

Na1Na

1

Na1

NaCl crystals

Cl2

Cl2

Na1

1

2

2

1

HH

O

11

1 2

2


11p1

17p2

Sodium ion (Na1)

(cation)

Chlorine atom (Cl2)

(anion)

Na1

14

3 Types of Chemical Bonds

3. Hydrogen bonds – weak bonds between hydrogen and other atoms

Hydrogen Bond

H

O

or

N

Molecule B

Molecule A


(+)

(–)

1

Hydrogen bonds

Water moleculeH

O

H

O

H

H

H

OH

H

O

H

O

H

H

1

2

1

2

2

2

1

1 1

1

11


14

Concept Check:

Molecules where atoms share electrons contain

A. Covalent Bonds

B. Ionic Bonds

C. Hydrogen Bonds

15

16

Oxidation-Reduction Reactions

Energy exchange in cells is a result of the movement of electrons from one molecule to another.

Oxidation – the loss of electrons

Reduction – the gaining of electrons

Redox reactions

Na

Reducing agent gives up electrons.

Oxidizing agent accepts electrons.

Oxidized cation Reduced anion

2 8 1 Na 2 8Cl 2 8 7 Cl 2 8 8

1 2


Chemical Shorthand

• Reactants - molecules starting a reaction• Products - substances left by a reaction• Synthesis reaction - the reactants bond together in a

manner that produces an entirely new molecule

• Decomposition reaction - the bonds on a single reactant molecule are broken to release two or more products

• Exchange reaction - the reactants trade portions between each other and release products that are combinations of the two

17

S O2 SO2+

2H2O O22H2O2 +

NaCl H2OHCl ++ NaOH

18

Solutions

Solutes – Na+ & Cl-

Solvent – H2O

Solution – a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent

Cl2 Cl2

Na1

Cl2 Cl

2

Cl2

Cl2

Cl2

Na1

Na1

Na1Na

1

Na1

NaCl crystals

Cl2

Cl2

Na1

1

2

2

1

HH

O

11

1 2

2


11p1

17p2

Sodium ion (Na1)(cation)

Chlorine atom (Cl2)(anion)

Na1

Aqueous Solutions

19

• Hydrophilic molecules - dissolve in water• Hydrophobic molecules - repel water• Amphipathic molecules - have both hydrophilic

and hydrophobic properties

Cl

Hydrogen

Oxygen Water molecules

Na


20

Acidity, Alkalinity, and the pH Scale

• Ionization of H2O releases hydrogen ions [H+] and hydroxyl ions [OH-]• pH scale – ranges from 0 to 14, expresses the concentration of H+ ions

• pH is the negative logarithm of the concentration of H+ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

[H+]

1 2 3 4

Increasing acidity

Increasing basicity

2.0

acid

sprin

g wat

er

2.3

lemon

juice

2.4

vineg

ar

3.0

red

wine

3.5

saue

rkra

ut

4.2

beer

4.6

acid

rain

5.0

chee

se

5 6 7 8 9 10 11 12 13 14

6.0

yogu

rt

6.6

cow's

milk

7.0

distill

ed w

ater

7.4

hum

an b

lood

8.0

seaw

ater

8.4

sodiu

m b

icarb

onat

e

9.2

bora

x, alk

aline

soils

10.5

milk

of m

agne

sia

11.5

hou

seho

ld am

mon

ia

12.4

limew

ater

0pH

13.2

ove

n cle

aner

1 M

pot

assiu

m h

ydro

xide

0.1

M h

ydro

chlor

ic ac

id

Acidic Neutral Basic (alkaline)

[OH–]

pH and Ion Concentration

21

Concept Check:

If solution A has a pH of 2 and solution B has a pH of 4, which of the following is true?

A. Solution A has 2 times more H+ ions than solution B

B. Solution B has 2 times more H+ ions than solution A

C.Solution A has 10 times more H+ ions than solution B

D.Solution B has 10 times more H+ ions than solution A

E. Solution A has 100 times more H+ ions than solution B22

23

The Chemistry of Carbon and Organic Compounds

• Organic chemicals – compounds containing carbon bonded to hydrogens

• Carbon is the fundamental element of life– Contains 4 atoms in its outer orbital– Can form single, double, or triple covalent bonds– Can form linear, branched, or ringed molecules

The Versatility of Bonding in Carbon

24(a)

C O

C N

C C

C C

C N

C H

(b)

Branched

C C C C C

C C

C

C

Ringed

C

CC

C

C

C

C

C

C

C

C OC O

CC N N

CC

C C

C

CC

C

C H C H

Linear

C C C C C C

C

C C

1

1

CN N1

1

1

1


C C C C

C C C

C

C

NH2

TABLE 2.3Representative Functional Groups and Organic Compounds That Contain Them

Formula of Functional Group Name Can Be Found in

Hydroxyl Alcohols, carbohydrates

Carboxyl Fatty acids, proteins, organic acids

Amino Proteins, nucleic acids

Ester Lipids

Sulfhydryl Cysteine (amino acid), proteins

Carbonyl, terminal end

Aldehydes, polysaccharides

Carbonyl, internal

Ketones, polysaccharides

Phosphate DNA, RNA, ATP

R*

R

O H

C

O

OH

R C

H

H

R C

O

O R

R C

H

H

SH

R C

O

H

R C

O

CC

R O

O

P

OH

OH


Functional Groups of Organic Compounds

• Accessory molecules that bind to organic compounds

• Confer unique reactive properties on the whole molecule

25

26

Macromolecules• Biochemicals are organic compounds produced

by living things

• Macromolecules: large compounds assembled from smaller subunits– Monomer: a repeating subunit– Polymer: a chain of monomers

• 4 Biological Macromolecules: Carbohydrates, Lipids, Proteins, Nucleic Acids

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.Biological Macromolecules

27

28

Carbohydrates

• Sugars and polysaccharides• General formula (CH2O)n

• Aldehydes and ketones

C1

HOCH2

CH2OH

Fructose

O

HO H

H OH

H OH

H OH

H

Ketone group

H

OH

HOH

1

2

3

6

Galactose

H O

H OH

HO H

H OH

H OH

H

OCH2OH

HO

H

H

OHH

OH

OH

H

H

1

23

4

5

6

HO H

O

H

H

O

HOH

4

5

Glucose

H O

H OH

HO H

H OH

H OH

H OH

H

Aldehyde group

O

CH2OH

H

HO

H

OHH

OH

OH

H

H

1

23

4

5

6

H

C2

C3

C4

C5

C6

C1

C2

C3

C4

C5

C6

C1

C2

C3

C4

C5

C6


29

Carbohydrates

• Saccharide: simple carbohydrate– Monosaccharide: 3-7 carbons– Disaccharide: two monosaccharides– Polysaccharide: five or more monosaccharides

29

Polysaccharide

O

O

O

O

O

O

O

O O

O

O

O

O

O

CH2

O

DisaccharideMonosaccharide


O O O

CH2

(c)

(d)

(b)

(a)

H2OC

O

H

COH

C C1

CO H

CC

COH

CO

CC

OH

H

C C C

1H

HH

OH

H

O

OH

H

HO

C

CC

C

C

OH H

OH

O

HH

C

CC

C

O

CH2OHCH2OHCH2OHCH2OH

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH

H

HH

OH

H

O

OH

H

C

CC

C

C

OH

H

HH

OH

H

O

OH

H

HO

C

CC

C

C

Maltose

H

HH

OH

H

O

OH

HC

CC

C

OH

Glucose1

1

H

HH

OH

H

O

O

H

HOC

CC

C

C

OH HO

Glucose

1

OH H

OH

O

H

OH

HC

CC

C

1

1

CC

C C

CC

C

H

H H

OH

H

O

OH

H

HOC

CC

C

C

OH

Glucose

H2O

1 H2O

H2O

6 6

CH2OH

H

HH

OH

H

O

OH

H

HO

C

CC

C

OH

GlucoseGalactose 1

1 C

6CH2OH

H

H

OH

H

O

OHC

CC

C

CH

6

6 6

6

1

6

6

1

6

O

O

Sucrose

Lactose

Fructose

HO

H

CH

CH2OH

H

HH

OH

H

O

OH

OHC

CC

C

H

O C

6CH2OH

H

H

OH

H

O

OHC

CC

C

H

6

HO

H

C

3

1

23

5

1

23

44

5

1

23

4

5

1

23

4

5

1

23

4

5

1

23

4

5

1

2

4

5

2

4

5

3

1

23

4

5

2

4

5

3

1(b)

23

4

5

1(b)

23

4

5

1(b) 1(b)


30

Carbohydrates• Subunits linked by

glycosidic bonds

• Dehydration synthesis: loss of water in a polymerization reaction

31

Carbohydrates

• Functions – cell structure, adhesion, and metabolism

CH2OH

H

H

OH

H

O

OH

H

O

CH2OH

H

H H

OH

H

O

OH

H

O

H

O

CH2OH

H

H H

OH

H

O

OH

H O

Branch O

CH2OH

H

H H

O

H

O

OH

H

O

C

H

H H

OH

H

O

OH

H

Branchpoint

OH OH

CH2OH

O

CH2OH

HOH

OH

H

H

H H

OH

H

O

OH H

O

H

H

OH

CH2OHH

OH

OH

HH

H

OH

OO

CH2OH

H

H H

OH

H

O

OH H

O

Hbonds

(a) Cellulose (b) Starch

14 1414

5

6

14

14

6

5

3 2

3 2

5

6

3 2

5

6

3 2

5

6

3 2

14 141414


32

Lipids

• Long or complex, hydrophobic, C - H chains• Triglycerides, phospholipids in membranes,

steroids like cholesterol• Functions

– Triglycerides – energy storage– Phospholipid – major cell membrane component– Steroids – cell membrane component

Triglycerides: 3 fatty acids bound to glycerol

33

• Triglycerides are used for energy storage

• Could be saturated or unsaturated

C C C C C C C C C C C C C C C

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

HC

H

H

O

HO

Linolenic acid, an unsaturated fatty acid

Palmitic acid, a saturated fatty acid

HC C C C C C C C C C CC C C C

H

H

H

H

H H H

H

H H H H H H

H

H H

H

H H

HO

C

H

H

O

C

H

H

C

H H H H

1

Fatty acids Triglycerides

2


Phospholipids: glycerol with 2 fatty acids and a phosphate group

34

• Bilayers of phospholipids form membranes

Glycerol

Charged headPhosphate

Tail

Doublebond Creates a kink.

Fatty acids

(a) (b)

Variable alcohol group

Water

Polar lipid molecule

Polar head

Nonpolartails

1 Phospholipids in single layer

2 Phospholipid bilayer

Water Water

O OC C

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HC

HCH

HCH

HCH

O

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

HCH

O

CHHC

HHCHOP O2O

H

HCHHCH

HCHHCH

HCH

HCHHCH

HCH

H

O

HC

HCH

R


Membrane Lipids

35

• Cholesterol is inserted into the phospholipid bilayer

CH2–C


Glycolipid

Globular protein

Protein

Cholesterol

Phospholipids

Cellmembrane

Site forester bondwith a fattyacid

Cholesterol

H2

HCH2C

CH C

C

C CH2

H2C

H2C

HO

C

CH2

CH2

CH3

CH3

CH3CH3

CH2

CH2

H

CH

HC

CH–CH3

CH

CH2–CH

Concept Check:

Triglycerides that have double bonds in their fatty acids are best described as

A. Saturated

B. Unsaturated

C. Phospholipids

D. Cholesterol

36

37

Proteins

• Predominant molecules in cells• Monomer – amino acids – 20 essential AA’s• Polymer – peptide, polypeptide, protein• Subunits linked by peptide bonds• Fold into very specific 3-D shapes• Functions – support, enzymes, transport,

defense, movement

38

Amino Acids

• Amino acids are the monomers that make up a protein polymer

Formation of a Peptide Bond

39

• Amino acids are attached through peptide bonds to form proteins

N C

R1

H

C

O

N

H

C C

R3

H

C

O

N

H

C C

H

R2

C

O

N

H

C C

H

R4

C

H

+ 3H2O

N C

R1H

H

C

O

OH

N

H

H

C C

R3

H

C OH

O

N

H

H

C C

H

R2

C

OH

O

N

H

H

C C

H

R4

C

O

OH

Bond forming

H

H

H

O


40

Protein Structure

• Primary Structure

• Secondary Structure

• Tertiary Structure

• Quaternary Structure

The primary structure is a series of amino acids bound in a chain. Amino acids display small charged functional groups (red symbols).

The tertiary structure forms when portions of the secondary structure further interact by forming covalent disulfide bonds and additional interactions. From this emerges a stable three-dimensional molecule. Depending on the protein, this may be the final functional state.

The quaternary structure exists only inproteins that consist of more than onepolypeptide chain. Shown here is amodel of the cholera toxin, composedof five separate polypeptides, eachone shown in a different color.

The secondary structure develops when CO – and NH –groups on adjacent amino acids form hydrogen bonds. This action folds the chain into local configurations called the helix and -pleated sheet. Most proteins have both types of secondary structures.

Secondary structure

Projected 3-dimensional shape (note grooves and projections)

Quaternary structure

Disulfide bond

S

Tertiary structure

helix-pleated sheet

1

2

3

4

Detail of hydrogen bond

NC

CN

N

ON

CC

C O

H O

O H

C

Amino acids

Primary structure


Image courtesy RCSB Protein Data Bank, www.pdp.org

S

41

Nucleic Acids• DNA and RNA• Nucleotide monomer• DNA – deoxyribonucleic

acid– A,T,C,G – nitrogen bases– Double helix – Function – hereditary

material

• RNA – ribonucleic acid– A,U,C,G – nitrogen bases– Function – organize protein

synthesis H bonds

Backbone

Backbone

DNA

(b) In DNA, the polymer is composed of alternating deoxyribose (D) and phosphate (P) with nitrogen bases (A,T,C,G) attached to the deoxyribose. DNA almost always exists in pairs of strands, oriented so that the bases are paired across the central axis of the molecule.

(a) A nucleotide, composed of a phosphate, a pentose sugar, and a nitrogen base (either A,T,C,G, or U) is the monomer of both DNA and RNA.

Phosphate

N base

Pentose sugar

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

P

(c) In RNA, the polymer is composed of alternating ribose (R) and phosphate (P) attached to nitrogen bases (A,U,C,G), but it is usually a single strand.

RNA

A T

C G

G C

T A

A T

C G

U

A

C

G

C

A

D

D

D

D

D

D

D

D

D

D

D

D

R

R

R

R

R

R


Nucleotide Components

42

• DNA Nucleotides:– Deoxyribose– C, G, A or T

• RNA Nucleotides:– Ribose– C, G, A or U

OHOCH2OH

HHH

OH

H

OH

Ribose

(a) Pentose sugars

(c) Pyrimidine bases

Uracil (U)

HOCH2OH

HHH

OH

H

H

Deoxyribose

Thymine (T) Cytosine (C)

OHH

H O

H

O

N

N

HH3C

H O

H

N

HH

H

H O

H

N

N

N

N

(b) Purine bases

Adenine (A) Guanine (G)

O

H

H

N

H

H

H

N

H

HH

H

H

N

NN

NNN

NN

O


Double Helix of DNA• DNA is formed by

two very long polynucleotide strands linked along their length by hydrogen bonds

43O

OO

OPP

Hydrogen bonds

Base pairs

Backbonestrands

DT A D

PP

DC

G D

D DA T

P

O

O OO

OO

OO


DNA Passing on the Genetic Message

• Each strand is copied• Replication is guided

by base pairing• End result is two

separate double strands

44G C

T

G

TA

C

A

A

C

A

G C

T

G

T

G

C

A

C

T

G

T

Cells

Two double strands

Two single strandsNew bases

H-bonding severed

Events in Cell Division Events in DNA Replication

A T

C G

A T

G C

G

A T

G C


45

ATP: The Energy Molecule of Cells

• Adenosine triphosphate– Nucleotide - adenine, ribose, three phosphates

• Function - transfer and storage of energy

N

2

N4

56

3

OH OH

OCH2–O P O P O P O

O O O

O– O– O–


Adenosine diphosphate (ADP)

Adenosine triphosphate (ATP)

Adenosine

87

N9

N

NH2

1

Concept Check:

Which of the following is TRUE about RNA?

A. It is a double stranded molecule

B. It contains the sugar deoxyribose

C. It contains the nitrogenous base Uracil

D. It holds the genetic information

E. All of the above are true

46

chapter 2 the chemistry of biology copyright © the mcgraw-hill companies, inc. permission required...

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element orbitals

different numbers of

chemical substance

element ions

different elements isotopes

subatomic particlesneutrons

compounds3 types