Chapter 2 - Professor Welday's Weebly...

Copyright © 2013 Pearson Education, Inc.Lectures prepared by Christine L. Case

© 2013 Pearson Education, Inc. Lectures prepared by Christine L. Case

Chemical Principles

Chapter 2

1

© 2013 Pearson Education, Inc.

The Structure of Atoms

� Chemistry is the study of interactions between atoms and molecules

� The atom is the smallest unit of matter that enters into chemical reactions

� Atoms interact to form molecules

2



� Atoms are composed of� Electrons : negatively charged particles� Protons : positively charged particles� Neutrons : uncharged particles

3



� Protons and neutrons are in the nucleus� Electrons move around the nucleus

4


Figure 2.1 The structure of an atom.

.

Electron shells

Nucleus

Electron (e −)

Neutron (n 0)

Proton (p +)

5


� Each chemical element has a different number of protons

� Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen:

816O 8

17O 818O

Chemical Elements 6


Electronic Configurations

� Electrons are arranged in electron shells corresponding to different energy levels

7


Insert Table 2.1

Table 2.1 The Elements of Life 8


How Atoms Form Molecules

� Atoms combine to complete the outermost shell� The number of missing or extra electrons in this shell

is known as the valence� Molecules hold together because the valence

electrons of the combining atoms form attractive forces, called chemical bonds , between the atomic nuclei

9


Chemical Bonds

� A compound contains different kinds of atoms

H2O

10


Ionic Bonds

� The number of protons and electrons is equal in an atom

� Ions are charged atoms that have gained or lost electrons

11


Figure 2.2a Ionic bond formation.

A sodium atom (Na) loses one electron to an electro n acceptor and forms a sodium ion (Na +). A chlorine atom (Cl) accepts one electron from an ele ctron donor to become a chloride ion (Cl –).

Sodium ion(Na+)

Sodium atom(electron donor)

Chlorine atom(electron acceptor)

Chloride ion(Cl–)

Loss ofelectron

Gain ofelectron

12


Ionic Bonds

� Ionic bonds are attractions between ions of opposite charge� One atom loses electrons, and another gains electrons

13


Figure 2.2b Ionic bond formation.

The sodium and chloride ions are attracted because of their opposite charges and are held together by an ionic bond to form a molecule of sod ium chloride.

Chloride ion(Cl–)

Sodium ion(Na+)

Sodium chloride moleculeNa+ Cl–

NaCl

14


Covalent Bonds

� Covalent bonds form when two atoms share one or more pairs of electrons

15


Figure 2.3 Covalent bond formation.

Atomic Diagram

Structural Formula

Molecular Formula A single covalent bond

forms between two hydrogen atoms to form a hydrogen molecule.

Hydrogen atoms

Hydrogen

Hydrogen molecule Carbon

atom

Hydrogen atoms Methane

molecule

Single covalent bonds between four hydrogen atoms and a carbon atom, forming a methane molecule.

Methane

16


Hydrogen Bonds

� Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

17


Insert Fig 2.4b

Figure 2.4b Hydrogen bond formation in water.

Hydrogenbond

18


H2O

2H = 2 ×××× 1 = 2

O = 16

MW = 18

1 mole weighs 18 g

Molecular Weight and Moles

� The sum of the atomic weights in a molecule is the molecular weight

� One mole of a substance is its molecular weight in grams

19


Check Your Understanding

� Differentiate an ionic bond from a covalent bond. 2-2

20


Learning Objective

Chemical Reactions

2-3 Diagram three basic types of chemical reactions.

21


Chemical Reactions

� Chemical reactions involve the making or breaking of bonds between atoms

� A change in chemical energy occurs during a chemical reaction

� Endergonic reactions absorb energy� Exergonic reactions release energy

22


� Occur when atoms, ions, or molecules combine to form new, larger molecules

� Anabolism is the synthesis of molecules in a cell

Synthesis Reactions

A + B ABAtom, ion,

or molecule AAtom, ion,

or molecule BNew molecule

AB

Combinesto form

23


� Occur when a molecule is split into smaller molecules, ions, or atoms

� Catabolism is the decomposition reactions in a cell

Decomposition Reactions

A + BABAtom, ion,

or molecule AAtom, ion,

or molecule BNew molecule

AB

Breaksdown into

24


Exchange Reactions

� Are part synthesis and part decomposition

NaCl + H2ONaOH + HCl

25


Reversible Reactions

� Can readily go in either direction� Each direction may need special conditions

A + BWater

ABHeat

26


Check Your Understanding� This chemical reaction below is used to remove

chlorine from water. What type of reaction is it? 2-3

HClO + Na2SO3 Na2SO4 + HCl

27


Important Biological Molecules

� Organic compounds always contain carbon and hydrogen

� Inorganic compounds typically lack carbon

28


Learning Objectives

Inorganic Compounds

2-4 List several properties of water that are important to living systems.

2-5 Define acid, base, salt, and pH.

29


Water

� Inorganic� Polar molecule� Solvent

� Polar substances dissociate, forming solutes

30


Insert Fig 2.4a

Figure 2.4a Hydrogen bond formation in water. 31


Insert Fig 2.5

Figure 2.5 How water acts as a solvent for sodium c hloride (NaCl).

Sodium chloride crystal

Sodium iondissolved in water

Chloride iondissolved in water

32


� H+ and OH− participate in chemical reactions

R—R′ + H2O → R—OH + H—R′

Maltose + H2O → Glucose + Glucose

Water 33


Maltose + H2O → Glucose + Glucose

Glucose C6H12O6

Glucose +C6H12O6

Total C12H24O12

Maltose C12H22O11

The difference is:

Water 34


Water

� H bonds absorb heat� Makes water a temperature buffer

35


Insert Fig 2.4b

Figure 2.4b Hydrogen bond formation in water.

Hydrogenbond

36


Insert Fig 2.6

Figure 2.6 Acids, bases, and salts.

Acid Base Salt

HCl NaClNaOH

37


Acids

� Substances that dissociate into one or more H+

HCl → H+ + Cl−

38


Insert Fig 2.6a

Figure 2.6a Acids, bases, and salts.

Acid

HCl

39


Bases

� Substances that dissociate into one or more OH−

NaOH → Na+ + OH−

40


Insert Fig 2.6b

Figure 2.6b Acids, bases, and salts.

Base

NaOH

41


Salts

� Substances that dissociate into cations and anions, neither of which is H+ or OH−

NaCl → Na+ + Cl−

42


Insert Fig 2.6c

Figure 2.6c Acids, bases, and salts.

Salt

NaCl

43


Acid-Base Balance

� The amount of H+ in a solution is expressed as pH� pH = −log[H+]� Increasing [H+] increases acidity� Increasing [OH−] increases alkalinity� Most organisms grow best between pH 6.5 and 8.5

44


Insert Fig 2.7

Figure 2.7 The pH scale.

pH scale

Stomach acid

Lemon juice

Grapefruit juice

WineTomato juice

UrineMilkPure water

Seawater

Milk of magnesia

Household ammonia

Household bleach

Oven cleanerLimewaterBasic solution

Neutral solution

Acidic solution

Human blood

45



� Why is the polarity of a water molecule important? 2-4

� Antacids neutralize acid by the following reaction.

Identify the acid, base, and salt. 2-5

Mg(OH)2 + 2HCl → MgCl2 + H2O

46


Learning Objectives

Organic Compounds

2-6 Distinguish organic and inorganic compounds.2-7 Define functional group.

47


� The chain of carbon atoms in an organic molecule is the carbon skeleton

Structure and Chemistry 48


� Functional groups are responsible for most of the chemical properties of a particular organic compound

Structure and Chemistry 49


50


Insert Table 2.4(two slides if possible)

Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (Part 1 of 2) 51


Insert Table 2.4(two slides if possible)

Table 2.4 Representative Functional Groups and the Compounds in Which They Are Found (Part 2 of 2) 52


� Identify the functional groups in an amino acid

Functional Groups 53


54



� Define organic. 2-6� Add the appropriate functional group(s) to the ethyl

group below to produce each of the following compounds: ethanol, acetic acid, acetaldehyde, ethanolamine, diethyl ether. 2-7

55


Learning Objectives

Organic Compounds

2-8 Identify the building blocks of carbohydrates.2-9 Differentiate simple lipids, complex lipids, and

steroids.2-10 Identify the building blocks and structure of

proteins.2-11 Identify the building blocks of nucleic acids.2-12 Describe the role of ATP in cellular activities.

56


Organic Compounds

� Small organic molecules can combine into large macromolecules

� Macromolecules are polymers consisting of many small repeating molecules

� The smaller molecules are called monomers

57


� Monomers join by dehydration synthesis or condensation reactions

Polymers 58


59


Carbohydrates

� Cell structures and energy sources� Consist of C, H, and O with the formula (CH2O)n

� Monosaccharides are simple sugars with three to seven carbon atoms

60


Carbohydrates

� Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis

� Disaccharides can be broken down by hydrolysis

61


Insert Fig 2.8

Figure 2.8 Dehydration synthesis and hydrolysis.

GlucoseC6H12O6

FructoseC6H12O6

Dehydrationsynthesis

HydrolysisSucroseC12H22O11

Water

62


Carbohydrates

� Oligosaccharides consist of 2 to 20 monosaccharides

� Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis� Starch, glycogen, dextran, and cellulose are polymers of

glucose that are covalently bonded differently� Chitin is a polymer of two sugars repeating many times

63



� Give an example of a monosaccharide, a disaccharide, and a polysaccharide. 2-8

64


Lipids

� Primary components of cell membranes� Consist of C, H, and O� Are nonpolar and insoluble in water

65


Simple Lipids

� Fats or triglycerides� Contain glycerol and fatty acids; formed by

dehydration synthesis

66


Figure 2.9c Structural formulas of simple lipids.

Palmitic acid (saturated)(C15H31COOH)

+

Ester linkage

Molecule of fat (triglyceride)

H2O

H2O

Stearic acid (saturated)(C17H35COOH)

+

cisconfiguration

Oleic acid (unsaturated)(C17H33COOH)

+ H2O

Glycerol

67


Simple Lipids

� Saturated fat : no double bonds� Unsaturated fat : one or more double bonds in the

fatty acids� Cis: H atoms on the same side of the double bond� Trans: H atoms on opposite sides of the double bond

68


Figure 2.9c Structural formulas of simple lipids.

Palmitic acid (saturated)(C15H31COOH)

+

Ester linkage

Molecule of fat (triglyceride)

H2O

H2O

Stearic acid (saturated)(C17H35COOH)

+

cisconfiguration

Oleic acid (unsaturated)(C17H33COOH)

+ H2O

Glycerol

69


Complex Lipids

� Contain C, H, and O + P, N, or S� Membranes are made of phospholipids

70


Figure 2.9ab Structural formulas of simple lipids.

Carboxyl group

Hydrocarbon chain

Glycerol

Fatty acid (palmitic acid, Saturated)C15H31COOH

71


Steroids

� Four carbon rings with an –OH group attached to one ring

� Part of membranes

72


Insert Fig 2.11

Figure 2.11 Cholesterol, a steroid. 73


Proteins

� Are essential in cell structure and function� Enzymes are proteins that speed chemical reactions� Transporter proteins move chemicals across

membranes� Flagella are made of proteins� Some bacterial toxins are proteins

74


Amino Acids

� Proteins consist of subunits called amino acids

75


Figure 2.12 Amino acid structure.

Sidegroup

Aminogroup

Carboxylgroup

Generalized amino acid

Cyclicsidegroup

Tyrosine

76


Amino Acids

� Exist in either of two stereoisomers : D or L� L-forms are most often found in nature

77


Insert Fig 2.13

Figure 2.13 The L- and D-isomers of an amino acid, s hown with ball-and-stick models.

L-amino acid D-amino acid

Left hand Right hand

Mirror78


Peptide Bonds

� Peptide bonds between amino acids are formed by dehydration synthesis

79


Figure 2.14 Peptide bond formation by dehydration s ynthesis.

Glycine Alanine

Dehydrationsynthesis

Peptide bond

Glycylalanine(a dipeptide)

Water

80


Levels of Protein Structure

� The primary structure is a polypeptide chain

81


Figure 2.15a Protein structure.

Peptide bonds

Primary structure: polypeptide strand (amino acid sequence)

82



� The secondary structure occurs when the amino acid chain folds and coils in a regular helix or pleats

83


Figure 2.15b Protein structure.

Hydrogen bond

Secondary structure:helix and pleated sheet (with three polypeptide strands) Helix

Pleated sheet

84



� The tertiary structure occurs when the helix folds irregularly, forming disulfide bridges, hydrogen bonds, and ionic bonds between amino acids in the chain

85


Figure 2.15c Protein structure.

Disulfidebridge

Tertiary structure: helix and pleated sheets fold into a 3D shape

Hydrogenbond

Disulfide bridge(between cysteine

molecules)

Ionic bond

Details of tertiary structure bonds

Hydrophobic interaction

Polypeptidestrand

86



� The quaternary structure consists of two or more polypeptides

87


Figure 2.15d Protein structure.

Quaternary structure: the relationship of several folded polypeptide chains, forming a protein

88


Figure 2.15 Protein structure.

Peptide bonds

Primary structure: polypeptide strand (amino acid sequence)

Hydrogen bond

Secondary structure:helix and pleated sheet (with three polypeptide strands)

Helix

Pleated sheet

Disulfidebridge

Tertiary structure: helix and pleated sheets fold into a 3D shape

Quaternary structure: the relationship of several folded polypeptide chains, forming a protein

Hydrogenbond

Disulfide bridge(between cysteine

molecules)

Ionic bond

Details of tertiary structure bonds

Hydrophobic interaction

Polypeptidestrand

89



� Conjugated proteins consist of amino acids and other organic molecules� Glycoproteins� Nucleoproteins� Lipoproteins

90


Nucleic Acids

� Consist of nucleotides� Nucleotides consist of

� Pentose� Phosphate group� Nitrogen-containing (purine or pyrimidine ) base

� Nucleosides consist of � Pentose� Nitrogen-containing base

91


DNA

� Deoxyribonucleic acid� Has deoxyribose� Exists as a double helix� A hydrogen bonds with T� C hydrogen bonds with G

92


Insert Fig 2.16

Figure 2.16 The Structure of DNA.

Phosphate Sugar Adenine (A) Thymine (T) Sugar Phosphate

Adenine nucleotide

The carbon atoms in thesugars are identified by adding a marker, ’ (for example, 5’, pronounced “5-prime”). This differentiates them from the carbon atoms in the nucleo-bases, such as Thymine.

Adenine and Thymine (as well as Cytosine and Guanin e, not shown here) are nitrogenous bases or nucleobases.

Hydrogen bonds

Individual DNA nucleotides are composed of a deoxyribose sugar molecule covalently bonded to a phosphate group at the 5’ carbon, and to a nitrogen-containing base at the 3’ carbon. The two nucleotides shown here are held together by hydrogen bonds.

Sugars

PhosphatesSugar-phosphate backbone

The sugar-phosphate backbone of one strand is upside down, or antiparallel, relative to the backbone of the other strand.

DNA double helix

DNA’s double-helical, ladder-like form is made up of many nucleotides base pairs forming the rungs, and the repeating sugar-phosphate combination,forming the backbone.

Thymine nucleotide

93


RNA

� Ribonucleic acid� Has ribose� Is single-stranded� A hydrogen bonds with U� C hydrogen bonds with G

94


Insert Fig 2.17

Figure 2.17 A uracil nucleotide of RNA.

Phosphate

Uracil (U)

Ribose

95


� Adenosine triphosphate� Has ribose, adenine, and three phosphate groups

ATP 96


Insert Fig 2.18

Figure 2.18 The structure of ATP.

Phosphates

Adenosine

Ribose

Adenine

97


� Is made by dehydration synthesis� Is broken by hydrolysis to liberate useful energy

for the cell

ATP 98


99

Chapter 2 - Professor Welday's Weebly...

Documents

Transcript of Chapter 2 - Professor Welday's Weebly...