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Chemistry
Chapter 2
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Q&A
A Salmonella bacteriumreleases a regulatory
molecule containing amino
acids and phosphate that
causes a human cellscytoskeleton to change
shape, thereby allowing
the bacterium to enter the
cell. What type of chemical
is this regulatory molecule?
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Learning Objectives
The Structure of Atoms
2-1 Describe the structure of an atom and its relation
to the physical properties of elements.
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The Structure of Atoms
Chemistry is the study of interactions betweenatoms and molecules
The atom is the smallest unit of matter that enters
into chemical reactions
Atoms interact to form molecules
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The Structure of Atoms
Atoms are composed of
ProtonsPositive charge
Located in nucleus
1 atomic unit
Neutrons
No charge
Located in nucleus
1 atomic unit Electrons
Negative charge
Orbit nucleus
No significant weight
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The Structure of Atoms
Protons and neutrons are in the nucleus
Electrons move around the nucleusElectron shell
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O
8
16 O
8
17 O
8
18
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:
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Chemical Elements
Atom can:
Gain/Lose Electrons
Lose Excess Neutrons
Never Gain/Lose Protons
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The Elements of Life
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Electronic Configurations
Electrons are arranged in electron shellscorresponding to different energy levels
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Electronic Configurations
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Electronic Configurations
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Check Your Understanding How does C differ from C? What is the atomic
number of each carbon atom?
The atomic weight? 2-1
14
6
12
6
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Learning Objectives2-2 Define ionic bond, covalent bond, hydrogen bond,
molecular weight, and mole.
How Atoms Form Molecules
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How Atoms Form Molecules
Atoms combine to complete the outermost shell
Valence: Number of missing or extra electrons inthe 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
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Chemical Bonds
Join atoms by valence electrons
Atoms tend to Gain, Lose, orShare electrons to fill
their valence
Types of chemical bonds:
Ionic
Covalent
Hydrogen
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Ionic Bonds
Transferof 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.
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Ionic Bonds
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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
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Ionic Bonds
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Covalent Bonds
Covalent bonds form when two atoms share one ormore pairs of electrons
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Covalent Bonds
Carbon may form up to 4 covalent bonds
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Covalent Bonds
Carbon may share up to 3 pairs of electrons withanother atom
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Hydrogen Bonds
Weak attraction between slightlypositive hydrogen atom and
slightly negative atom (O, N)
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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
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Hydrogen Bonds
Why is ice less dense
than liquid water?
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Hydrogen Bonds
What causes capillary
action to occur in thesetubes?
Why does the water
travel higher in the
thinner tube?
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Chemical Bonds Review
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H2O
2H = 2 1 = 2
O = 16
MW = 18
1 mole weighs 18g
Molecular Weight and Moles
The sum of the atomicweights in a molecule is
the molecular weight
One mole of a substance
is its molecular weight ingrams
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Check Your Understanding Differentiate an ionic bond from a covalent bond. 2-
2
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Learning Objectives
Chemical Reactions
2-3 Diagram three basic types of chemical reactions.
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Chemical Reactions
Chemical reactions involve the making or breakingof bonds between atoms
A change in chemical energy occurs during a
chemical reaction
Endergonic reactions absorb energy
Exergonic reactions release energy
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Anabolism is the synthesis of molecules in a cell
A + B ABAtom, ion,or molecule A
Atom, ion,or molecule B
New molecule
AB
Combines
to form
Synthesis Reactions
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Catabolism is the decomposition reactions in a cell
A + BABAtom, ion,
or molecule A
Atom, ion,
or molecule B
New molecule
AB
Breaks
down into
Decomposition Reactions
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NaCl + H2ONaOH + HCl
Exchange Reactions
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A + BWater
AB
Heat
Reversible Reactions
Can readily go in either direction
Each direction may need special conditions
R d R ti
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Redox Reactions
Coupled Oxidation/Reduction Reactions
Oxidation releases electrons
Reduction causes atom to receive electrons
Essential to biochemical processes
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Check Your Understanding
HClO + Na2SO3Na2SO4 + HCl
This chemical reaction below is used to removechlorine from water.
What type of reaction is it? 2-3
I t t Bi l i l M l l
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Important Biological Molecules
Organic compounds always contain carbon andhydrogen
Inorganic compounds typically lack carbon
I i C d
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Learning Objectives
Inorganic Compounds
2-4 List several properties of water that are important
to living systems.
2-5 Define acid, base, salt, andpH.
W t
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Water
Inorganic
Polar, Solvent
Temperature buffer
2/3 by weight (human)
W t
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Water
W t
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RR + H2O ROH + HR
Maltose + H2O Glucose + Glucose
Water
H+ and OH
participate in chemical reactions
W t
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Maltose + H2O Glucose + Glucose
Glucose C6H12O6
Glucose +C6H12O6
Total C12H24O12
Maltose C12H22O11
The difference is:
Water
W t
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Water
H bonds absorb heat
A id B d S lt
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Acids, Bases, and Salts
Acids
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Acids
Substances that releaseH+ in solution
pH < 7
HCl H+ + Cl
Bases
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Bases
Substances that releaseOH in solution
pH > 7
NaOH Na+ + OH
Salts
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Salts
Ionic compounds
Dissociate in H2O
Dont release H+ or OH
Act as electrolytes
NaCl Na+ + Cl
pH
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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
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The pH Scale
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Check Your Understanding
Mg(OH)2 + 2HCl MgCl2 +H2O
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
Organic Compounds
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Learning Objectives
Organic Compounds
2-6 Distinguish organic and inorganic compounds.
2-7 Define functional group.
Structure and Chemistry
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Structure and Chemistry
The chain of carbon atoms in an organic molecule is
the carbon skeleton
Structure and Chemistry
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Structure and Chemistry
Functional groups are responsible for most of the
chemical properties of a particular organic
compound.
Functional Groups
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Functional Groups
Functional Groups
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Functional Groups
Functional Groups
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Functional Groups
Identify the functional groups in an amino acid:
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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
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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.
Organic Compounds
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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
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Monomers join by dehydration synthesis or
condensation reactions
Polymers
O
Chemical Reaction Terminology Review
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Chemical Reaction Terminology Review
DecompositionSynthesis
Match the following terms under Synthesis or
Decomposition.- Endergonic - Catabolism
- Hydrolysis - Anabolism
- Exergonic - Dehydration (Condensation)
Carbohydrates
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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
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Carbohydrates
Disaccharides are formed when 2
monosaccharides are joined in a dehydration
synthesis
Disaccharides can be broken down by hydrolysis
Dehydration Synthesis and Hydrololysis
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Dehydration Synthesis and Hydrololysis
Carbohydrates
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Carbohydrates
Oligosaccharides consist of 2 to 20
monosaccharides
Polysaccharides consist of tens or hundreds of
monosaccharides joined through dehydration
synthesis
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Check Your Understanding
Give an example of a monosaccharide, a
disaccharide, and a polysaccharide. 2-8
Lipids
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Lipids
Essential components of cell membranes
Consist of C, H, and O
Are nonpolar and insoluble in water
Simple Lipids
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Simple Lipids
Fats ortriglycerides
Contain glycerol and 3 fatty acids; formed by
dehydration synthesis
Structural Formulas of Simple Lipids
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Structural Formulas of Simple Lipids
Simple Lipids
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Simple Lipids
Saturated (with hydrogen) - No double bonds
Unsaturated fat: One or more double bonds in thefatty acids
Cis vs. Trans Fatty Acids
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Cis vs. Trans Fatty Acids
c is: H atomson the same
side of the
double bond
t rans : H atoms
on opposite
sides of the
double bond
Complex Lipids
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Co p e p ds
Contain C, H, and O + P,
N, or S
Membranes are made of
phospholipids
Complex Lipids
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p p
Steroids
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Copyright 2010 Pearson Education, Inc.Figure 2.11
4 carbon rings with anOH group attached to one
ring
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Check Your Understanding
How do simple lipids differ from complex lipids? 2-9
Proteins
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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
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Proteins consist of subunits called amino acids
Amino Acids
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Exist in either of two stereoisomers:
D orL.
L-forms are most often found in nature.
Amino Acids
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Copyright 2010 Pearson Education, Inc. Figure 2.13
When growing in an
animal, Bacillusanthracis 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?
Peptide Bonds
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p
Peptide bonds between amino acids are formed by
dehydration synthesis
Levels of Protein Structure
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Primary structure:
Levels of Protein Structure
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Secondary structure:
Levels of Protein Structure
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Tertiary structure: irregular folding due to bonding
between AAs in the polypeptide chain
disulfide bonds
hydrogen bonds
ionic bonds
Levels of Protein Structure
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Levels of Protein Structure
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Quaternary structure:
Protein Structure - Review
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Levels of Protein Structure
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Conjugated proteins consist of amino acids and
other organic molecules
Glycoproteins
Nucleoproteins
Lipoproteins
Q&A
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A Salmonella bacterium
releases a regulatory
molecule containing
amino acids and
phosphate that causesa human cells
cytoskeleton to change
shape, thereby allowing
the bacterium to enterthe cell. What type of
chemical is this
regulatory molecule?
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Check Your Understanding
What two functional groups are in all amino acids?
2-10
Nucleic Acids
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Consist ofnucleotides
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
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Nitrogenous Bases:
DNA
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Deoxyribonucleic acid
Has deoxyribose
Exists as a double helix
A hydrogen bonds with T
G hydrogen bonds with C
DNA
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RNA
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Ribonucleic acid
Has ribose
Is single-stranded
A hydrogen bonds with U
C hydrogen bonds with G
DNA vs. RNA
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RNA DNA
Deoxyribose
A-T, C-G
Double stranded
Codes for proteins
Nucleus
ATP
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Adenosine triphosphate
Ribose Adenine
3 phosphate groups
The Structure of ATP
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ATP
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Is made by dehydration synthesis
Is broken by hydrolysis to liberate useful energy
for the cell
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Check Your Understanding
Which can provide more energy for a cell and why:
ATP or ADP? 2-12
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