Chemistry - Spring 2013 (Student Copy)

Chapter 2
Chemistry
Copyright 2010 Pearson Education, Inc.
Q&A
A Salmonella bacterium releases a regulatory molecule containing amino acids and phosphate that causes a human cells cytoskeleton to change shape, thereby allowing the bacterium to enter the cell. What type of chemical is this regulatory molecule?
The Structure of Atoms

Learning Objectives 2-1 Describe the structure of an atom and its relation to the physical properties of elements.

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

Atoms are composed of
Protons Positive charge Located in nucleus 1 atomic unit Neutrons No charge Located in nucleus 1 atomic unit Electrons Negative charge Orbit nucleus No significant weight

Protons and neutrons are in the nucleus Electrons move around the nucleus
Electron shell
Figure 2.1
Chemical Elements
Atomic number: # Protons in Atom Atomic weight: Sum of Protons and Neutrons in Atom Atomic symbol: Letter(s) representing each element Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen:
8 16
8 17
8 18
Chemical Elements
Atom can: Gain/Lose Electrons Lose Excess Neutrons Never Gain/Lose Protons
The Elements of Life
Table 2.1
Electronic Configurations
Electrons are arranged in electron shells corresponding to different energy levels
Table 2.2
Table 2.2
Check Your Understanding

12 How does 14 C differ from 6 6 C? What is the atomic number of each carbon atom? The atomic weight? 2-1
How Atoms Form Molecules

Learning Objectives 2-2 Define ionic bond, covalent bond, hydrogen bond, molecular weight, and mole.
How Atoms Form Molecules

Atoms combine to complete the outermost shell Valence: Number of missing or extra electrons in the outermost shell The # electrons in the valence affects the behavior of the atom The atom is stable when the valence is full The atom is unstable/reactive when the valence is incomplete
Chemical Bonds
Join atoms by valence electrons Atoms tend to Gain, Lose, or Share electrons to fill their valence Types of chemical bonds:
Ionic Covalent Hydrogen
Ionic Bonds
Transfer of electrons from one atom to another Atoms that gain electrons have net negative charge Atoms that lose electrons have net positive charge Ion: Atom with a net charge Ionic Bond: Attraction between oppositely charged ions.
Ionic Bonds
Figure 2.2a
Ionic Bonds
Atoms with 1-3 valence electrons tend to lose them Atoms with 5-7 valence electrons tend to gain additional electrons Ionic bonds common in inorganic molecules Ionically formed compounds dissolve easily in water electrolytes
Ionic Bonds
Figure 2.2b
Covalent Bonds
Covalent bonds form when two atoms share one or more pairs of electrons
Figure 2.3a
Covalent Bonds
Carbon may form up to 4 covalent bonds
Figure 2.3b
Covalent Bonds
Carbon may share up to 3 pairs of electrons with another atom
Hydrogen Bonds
Weak attraction between slightly positive hydrogen atom and slightly negative atom (O, N)
Figure 2.4
Hydrogen Bonds
May form within same molecule or between molecules Easily broken by temperature or pH Common between H2O molecules, amino acids, nucleic acids Results in 3-D shape of proteins
Hydrogen Bonds
Why is ice less dense than liquid water?
Hydrogen Bonds
What causes capillary action to occur in these tubes?
Why does the water travel higher in the thinner tube?
Chemical Bonds Review
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
H2O 2H O MW 1 mole weighs =21 = 2 = 16 = 18 18g
Check Your Understanding Differentiate an ionic bond from a covalent bond. 22
Chemical Reactions
Learning Objectives 2-3 Diagram three basic types of chemical reactions.
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
Synthesis Reactions
A
Atom, ion, or molecule A
B
Atom, ion, or molecule B
Combines to form
AB
New molecule AB
Anabolism is the synthesis of molecules in a cell
Decomposition Reactions
AB
New molecule AB
Breaks down into
A
Atom, ion, or molecule A
B
Atom, ion, or molecule B
Catabolism is the decomposition reactions in a cell
Exchange Reactions
NaOH +
HCl
NaCl
+ H2O
Reversible Reactions
Can readily go in either direction Each direction may need special conditions
Heat
+ B
AB
Water
Redox Reactions
Coupled Oxidation/Reduction Reactions Oxidation releases electrons Reduction causes atom to receive electrons Essential to biochemical processes
Check Your Understanding This chemical reaction below is used to remove chlorine from water. HClO + Na2SO3 Na2SO4 + HCl
What type of reaction is it? 2-3
Important Biological Molecules

Organic compounds always contain carbon and hydrogen Inorganic compounds typically lack carbon
Inorganic Compounds
Learning Objectives 2-4 List several properties of water that are important to living systems. 2-5 Define acid, base, salt, and pH.
Water
Inorganic Polar, Solvent Temperature buffer 2/3 by weight (human)
Figure 2.4a
Water
Figure 2.5
Water
H+ and OH participate in chemical reactions RR + H2O ROH + HR
Maltose + H2O Glucose + Glucose
Water
Maltose + H2O Glucose + Glucose Glucose C6H12O6
Glucose
Total Maltose
+C6H12O6
C12H24O12 C12H22O11
The difference is:

Water
H bonds absorb heat
Figure 2.4b
Acids, Bases, and Salts
Figure 2.6
Acids
Substances that release H+ in solution pH < 7
HCl H+ + Cl
Figure 2.6a
Bases
Substances that release OH in solution pH > 7
NaOH Na+ + OH
Figure 2.6b
Salts
Ionic compounds Dissociate in H2O Dont release H+ or OH Act as electrolytes NaCl Na+ + Cl
Figure 2.6c
pH
Power of hydrogen Scale to indicate relative [H+] and [OH] pH = log[H+] 0 14 7 is neutral (water) Most organisms grow best between pH 6.5 and 8.5
The pH Scale
Figure 2.7
Check Your Understanding Why is the polarity of a water molecule important? 2-4 Antacids neutralize acid by the following reaction.
Mg(OH)2 + 2HCl MgCl2 + H2O

Identify the acid, base, and salt. 2-5
Organic Compounds
Learning Objectives 2-6 Distinguish organic and inorganic compounds. 2-7 Define functional group.
Structure and Chemistry

The chain of carbon atoms in an organic molecule is the carbon skeleton
Structure and Chemistry

Functional groups are responsible for most of the chemical properties of a particular organic compound.
Functional Groups
Table 2.3
Functional Groups
Table 2.3
Functional Groups
Identify the functional groups in an amino acid:
Check Your Understanding 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
Organic Compounds
Learning Objectives 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.
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
Polymers
Monomers join by dehydration synthesis or condensation reactions
Chemical Reaction Terminology Review

Match the following terms under Synthesis or Decomposition. - Endergonic - Catabolism - Hydrolysis - Anabolism - Exergonic - Dehydration (Condensation) Synthesis Decomposition
Carbohydrates
Cell structures and primary energy source Consist of C, H, and O with the formula (CH2O)n Monosaccharides are simple sugars with 3 to 7 carbon atoms
Carbohydrates
Disaccharides are formed when 2 monosaccharides are joined in a dehydration synthesis Disaccharides can be broken down by hydrolysis
Dehydration Synthesis and Hydrololysis
Figure 2.8
Carbohydrates
Oligosaccharides consist of 2 to 20 monosaccharides Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis
Check Your Understanding Give an example of a monosaccharide, a disaccharide, and a polysaccharide. 2-8
Lipids
Essential components of cell membranes Consist of C, H, and O Are nonpolar and insoluble in water
Simple Lipids
Fats or triglycerides Contain glycerol and 3 fatty acids; formed by dehydration synthesis
Structural Formulas of Simple Lipids
Figure 2.9c
Simple Lipids
Saturated (with hydrogen) - No double bonds Unsaturated fat: One or more double bonds in the fatty acids
Cis vs. Trans Fatty Acids

cis: H atoms on the same side of the double bond
trans: H atoms on opposite sides of the double bond
Complex Lipids
Contain C, H, and O + P, N, or S Membranes are made of phospholipids
Figure 2.10a
Complex Lipids
Figure 2.10
Steroids
4 carbon rings with an OH group attached to one ring
Figure 2.11
Check Your Understanding How do simple lipids differ from complex lipids? 2-9
Proteins
Consist of C, H, O, and N Amino Acids (AAs) Joined by peptide bond into chain = polypeptide Structural (peptidoglycan) or regulatory (enzyme) Complex, 3-D shape
Amino Acids
Proteins consist of subunits called amino acids
Figure 2.12
Amino Acids
Exist in either of two stereoisomers: D or L. L-forms are most often found in nature.
Amino Acids
When growing in an animal, Bacillus anthracis produces a capsule that is resistant to phagocytosis. The capsule is composed of D-glutamic acid. Why is this capsule resistant to digestion by the host's phagocytes?
Figure 2.13
Peptide Bonds
Peptide bonds between amino acids are formed by dehydration synthesis
Figure 2.14
Levels of Protein Structure

Primary structure:
Figure 2.15a

Secondary structure:
Figure 2.15b

Tertiary structure: irregular folding due to bonding between AAs in the polypeptide chain
disulfide bonds hydrogen bonds ionic bonds
Figure 2.15c

Quaternary structure:
Figure 2.15d
Protein Structure - Review
Figure 2.15

Conjugated proteins consist of amino acids and other organic molecules
Glycoproteins Nucleoproteins Lipoproteins
Q&A
A Salmonella bacterium releases a regulatory molecule containing amino acids and phosphate that causes a human cells cytoskeleton to change shape, thereby allowing the bacterium to enter the cell. What type of chemical is this regulatory molecule?
Check Your Understanding What two functional groups are in all amino acids? 2-10
Nucleic Acids
Consist of nucleotides
1) Pentose (5-C sugar: deoxyribose or ribose) 2) Phosphate group 3) Nitrogenous base (purine or pyrimidine)
DNA, RNA, ATP Acidic, found in nucleus Sugar-phosphate backbone + bases as rungs of ladder
Nucleic Acids
Nitrogenous Bases:
Figure 2.16
DNA
Deoxyribonucleic acid Has deoxyribose Exists as a double helix A hydrogen bonds with T G hydrogen bonds with C
DNA
Figure 2.16
RNA
Ribonucleic acid Has ribose Is single-stranded A hydrogen bonds with U C hydrogen bonds with G
DNA vs. RNA

DNA Deoxyribose A-T, C-G Double stranded Codes for proteins Nucleus
RNA
ATP
Adenosine triphosphate
Ribose Adenine 3 phosphate groups
The Structure of ATP
ATP
Is made by dehydration synthesis Is broken by hydrolysis to liberate useful energy for the cell
Check Your Understanding Which can provide more energy for a cell and why: ATP or ADP? 2-12

Chemistry - Spring 2013 (Student Copy)

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Chapter 2

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

The Structure of Atoms

Copyright 2010 Pearson Education, Inc.

The Structure of Atoms

Copyright 2010 Pearson Education, Inc.

The Structure of Atoms

The Structure of Atoms

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

The Elements of Life

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Check Your Understanding

Copyright 2010 Pearson Education, Inc.

How Atoms Form Molecules

Copyright 2010 Pearson Education, Inc.

How Atoms Form Molecules

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Why does the water travel higher in the thinner tube?

Copyright 2010 Pearson Education, Inc.

Chemical Bonds Review

Copyright 2010 Pearson Education, Inc.

Molecular Weight and Moles

H2O 2H O MW 1 mole weighs =21 = 2 = 16 = 18 18g

Copyright 2010 Pearson Education, Inc.

Check Your Understanding Differentiate an ionic bond from a covalent bond. 22

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Anabolism is the synthesis of molecules in a cell

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Breaks down into

Catabolism is the decomposition reactions in a cell

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Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

What type of reaction is it? 2-3

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Important Biological Molecules

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Copyright 2010 Pearson Education, Inc.

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Copyright 2010 Pearson Education, Inc.

Maltose + H2O Glucose + Glucose

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The difference is:

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