1. Marieb Chapter 2 Part B: Chemistry Comes Alive
12/10/11
Student version

2. Study of chemical composition and reactions of living matter
Biochemistry
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Study of chemical composition and reactions of living matter
All chemicals are either organic or inorganic
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3. Both equally essential for life
Classes of Compounds
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Inorganic compounds
Do not contain carbon (exception is CO2)
Organic compounds
Contain carbon, are usually large, and atoms are covalently bonded
Both equally essential for life
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4. Water in Living Organisms
12/10/11
Most abundant inorganic compound
60%–80% volume of living cells
Most important inorganic compound
Due to water’s properties
Let’s discuss this!
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5. High heat of vaporization
Properties of Water
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High heat capacity
Absorbs and releases heat with little temperature change
Prevents sudden changes in temperature
High heat of vaporization
Evaporation requires large amounts of heat
Useful cooling mechanism
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6. Properties of Water Acts as a polar solvent
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Acts as a polar solvent
Dissolves and dissociates ionic substances
Forms layers around large charged molecules, e.g., proteins (colloid formation)
Body’s major transport medium
Most biological molecules are happy in it (uhm, dissolve!)
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7. Figure 2.12 Dissociation of salt in water.
12/10/11 δ+
δ– δ+
Water molecule
Salt
crystal
Ions in
solution
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8. Formed or used in some chemical reactions
Properties of Water
12/10/11
Formed or used in some chemical reactions
Necessary part of hydrolysis and dehydration synthesis reactions
Used as cushioning
Protects certain organs from physical trauma, e.g., cerebrospinal fluid
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9. What Are Salts?
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Ions ( ) conduct electrical currents in solution
Ions play specialized roles in body functions
Ionic balance vital for homeostasis
Contain cations other than H+ and anions other than OH–
Common electrolytes found in the body
sodium, chloride, carbonate, potassium, calcium, phosphates
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10. Acids and Bases Both form electrolytes Acids are Bases are
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Both form electrolytes
Acids are
Release H+ (a bare proton) in solution
HCl  H+ + Cl–
Bases are
Take up H+ from solution or release OH- into solution
NaOH  Na+ + OH–
OH– accepts an available proton (H+) to form water
OH– + H+  H2O
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11. Some Important Acids and Bases in Body
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Important acids
HCl, HC2H3O2 (acetic acid), and H2CO3
Important bases
Bicarbonate ion (HCO3–) and ammonia (NH3)
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12. pH: Acid-base Concentration
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• Relative free [H+] of a solution measured in a special way
• As free [H+] increases, acidity increases
[OH–] decreases as [H+] increases
pH decreases
• As free [H+] decreases, alkalinity increases
[OH–] increases as [H+] decreases
pH increases
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13. pH: Acid-base Concentration
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pH = negative logarithm of [H+] in moles per liter
pH scale ranges from 0–14
Because pH scale is logarithmic (like the Richter Scale)
A pH 5 solution is 10 times more acidic than a pH 6 solution
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14. pH: Expression Of Acid-base Concentration
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Acidic solutions
 [H+],  pH
Acidic pH:
Neutral solutions
Equal numbers of H+ and OH–
All neutral solutions are pH
Pure water is pH neutral
pH of pure water = pH 7: [H+] = 10–7 m
Alkaline (basic) solutions
 [H+],  pH
Alkaline pH:
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15. Figure 2.13 The pH scale and pH values of representative substances.
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Concentration
(moles/liter)
[OH−]
[H+] pH
Examples
100
10−14 14
1M Sodium
hydroxide (pH=14)
10−1
10−13 13
Oven cleaner, lye
(pH=13.5)
10−2
10−12 12
Household ammonia
(pH=10.5–11.5)
10−3
10−11 11
Increasingly basic
10−4
10−10 10
Household bleach
(pH=9.5)
10−5
10−9 9
Egg white (pH=8)
10−6
10−8 8
Blood (pH=7.4)
10−7
10−7 7
Neutral
Milk (pH=6.3–6.6)
10−8
10−6 6
10−9
10−5 5
Black coffee (pH=5)
10−10
10−4 4
Wine (pH=2.5–3.5)
Increasingly acidic
10−11
10−3 3
10−12
10−2 2
Lemon juice; gastric
juice (pH=2)
10−13
10−1 1
1M Hydrochloric
acid (pH=0)
10−14
100
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16. 12/10/11
pH Paper

17. Strong and Weak Acids and Bases
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Strong and Weak Acids and Bases
strong
weak

18. Acid-base Homeostasis
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A pH change interferes with cell function and may damage living tissue
Even a slight change in pH can be fatal
What are the extremes of pH of the blood?
Lowest = Highest =
pH is regulated by kidneys, lungs, and chemical buffers (observe in Lab Expt. 2)
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19. Buffers Acidity reflects only free H+ in solution
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Acidity reflects only free H+ in solution
Buffers resist abrupt and large swings in pH
Release hydrogen ions if pH rises
Bind hydrogen ions if pH falls
Carbonic acid-bicarbonate system (important buffer system of blood):
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20. • All three present in solution. • What happens if we add H+? -
Buffers
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• H2CO3 H+ + HCO3-
• All three present in solution.
• What happens if we add H+? -
• What happens if we add OH-?

21. Where Do We Find Buffers?
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22. Molecules that contain
Organic Compounds
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Molecules that contain
Except CO2 and CO, which are considered inorganic
Carbon always shares electrons; never gains or loses them
Carbon forms four covalent bonds with other elements
Unique to living systems
Carbohydrates, lipids, proteins, and nucleic acids
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23. (ex.= glycogen, DNA, proteins)
Organic Compounds
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Many are
(ex.= glycogen, DNA, proteins)
Chains of similar units called
(I call them the “building blocks”)
Polymers are synthesized by dehydration synthesis ( )
Polymers are broken down by hydrolysis reactions ( )
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24. Figure 2.14 Dehydration Synthesis and Hydrolysis.
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Dehydration synthesis
Monomers are joined by removal of OH from one monomer
and removal of H from the other at the site of bond formation. +
Monomer 1
Monomer 2
Monomers linked by covalent bond
Hydrolysis
Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other.
Monomer 1 +
Monomer 2
Monomers linked by covalent bond
Example reactions
Dehydration synthesis of sucrose and its breakdown by hydrolysis
Water is
released +
Water is
consumed
Glucose
Fructose
Sucrose
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25. Come in monomers and polymers Contain C, H, and O [formula =(CH20)n]
Carbohydrates
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Sugars and starches
Come in monomers and polymers
Contain C, H, and O [formula =(CH20)n]
Three classes
Monosaccharides – one sugar
Disaccharides – two sugars covalently bonded
Polysaccharides – many sugars covalently bonded
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26. Functions of carbohydrates
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Functions of carbohydrates
Major source of cellular fuel (e.g., glucose)
Structural molecules
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27. These are the monomers of carbohydrates Important monosaccharides
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Simple sugars
These are the monomers of carbohydrates
Important monosaccharides
Pentose sugars
Ribose and deoxyribose (in DNA and RNA)
Hexose sugars
Glucose (blood sugar)
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28. Simple carbohydrate molecules important to the body.
Figure 2.15a
Simple carbohydrate molecules important to the body.
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Monosaccharides
Monomers of carbohydrates
Example
Hexose sugars (the hexoses shown here are isomers)
Example
Pentose sugars
Glucose
Fructose
Galactose
Deoxyribose
Ribose
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29. Double sugars (two covalently linked monomers)
Disaccharides
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Double sugars (two covalently linked monomers)
Also called simple carbohydrates
Too large to pass through cell membranes
Important disaccharides
Sucrose, maltose, lactose
We have enzymes to break these down
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30. Simple carbohydrate molecules important to the body.
Figure 2.15b
Simple carbohydrate molecules important to the body.
12/10/11
Disaccharides
Consist of two linked monosaccharides
Example
Sucrose, maltose, and lactose
(these disaccharides are isomers)
Glucose
Fructose
Glucose
Glucose
Galactose
Glucose
Sucrose
Maltose
Lactose
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31. Polymers of monosaccharides Complex sugars Important polysaccharides
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Polymers of monosaccharides
Complex sugars
Important polysaccharides
Plant starch
Animal starch (glycogen)
Cellulose (woody plants)
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32. Figure 2.15c Carbohydrate molecules important to the body.
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Polysaccharides
Long chains (polymers) of linked monosaccharides
Example
This polysaccharide is a simplified representation of
glycogen, a polysaccharide formed from glucose units.
Glycogen
PLAY
Animation: Polysaccharides
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33. Contain C, H, O (less than in carbohydrates), and sometimes P
Lipids
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Contain C, H, O (less than in carbohydrates), and sometimes P
Insoluble in water
Main types:
PLAY
Animation: Fats
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34. Neutral Fats or Triglycerides
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Called fats when solid (lard, butter)
Oils when liquid (canola oil)
Composed of three fatty acids covalently bonded to a glycerol molecule
Main functions
Energy storage
Insulation
Protection
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35. Dehydration Synthesis
Figure 2.16a Lipids.
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Dehydration Synthesis
Triglyceride formation
Three fatty acid chains are bound to glycerol by dehydration synthesis. + +
Glycerol
3 fatty acid chains
3 water
molecules
Triglyceride, or neutral fat
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36. Saturation of Fatty Acids
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Saturated fatty acids
Single covalent bonds between C atoms
Maximum number of H atoms
Solid animal fats, e.g., butter
and lard
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37. Saturation of Fatty Acids
Unsaturated fatty acids
One or more double bonds between C atoms
Reduced number of H atoms
Plant oils, e.g., olive oil

38. Saturation of Fatty Acids

39. Saturation of Fatty Acids
Trans fats – modified oils –
Omega-3 fatty acids –

40. Saturation of Fatty Acids

41. Types Of Fat

42. Modified triglycerides:
Phospholipids
12/10/11
Modified triglycerides:
Glycerol + two fatty acids and a phosphorus (P) - containing group
“Head” and “tail” regions have different properties
Important in cell membrane structure
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43. Phosphorus-containing
Figure 2.16b Lipids.
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“Typical” structure of a phospholipid molecule
Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.
Example
Phosphatidylcholine
Polar “head”
Nonpolar “tails”
(schematic
phospholipid)
Glycerol
backbone
Phosphorus-containing
group
(polar “head”)
2 fatty acid chains
(nonpolar “tails”)
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44. Steroids—interlocking four-ring structure
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Steroids—interlocking four-ring structure
Cholesterol, vitamin D, steroid hormones, and bile salts
Most important steroid
Important in cell membranes, vitamin D synthesis, steroid hormones, and bile salts
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45. Four interlocking hydrocarbon rings
Figure 2.16c Lipids.
12/10/11
Simplified structure of a steroid
Four interlocking hydrocarbon rings
form a steroid.
Example
Cholesterol (cholesterol is the
basis for all steroids formed in the body)
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46. 12/10/11
Anabolic Steroids

47. Derived from a fatty acid (arachidonic acid) in cell membranes
Eicosanoids
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Many different ones
Derived from a fatty acid (arachidonic acid) in cell membranes
Most important eicosanoid
Prostaglandins
Role in blood clotting, control of blood pressure, inflammation, and labor contractions
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48. Other Lipids in the Body
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Fat-soluble vitamins
Vitamins A, D, E, and K
Lipoproteins
Transport fats in the blood (LDL, HDL)
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49. Proteins Contain C, H, O, N, and sometimes S and P
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Contain C, H, O, N, and sometimes S and P
Proteins are polymers
Amino acids (20 types) are the monomers in proteins
Joined by covalent bonds called peptide bonds
Contain amine group and acid group
Can act as either acid or base
All identical except for “R group” (in green on figure)
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50. Figure 2.17 Amino acid structures.
12/10/11
Amine
group
Acid
group
Generalized
structure of all
amino acids.
Glycine
is the simplest
amino acid.
Aspartic acid
(an acidic amino
acid) has an acid
group (—COOH)
in the R group.
Lysine
(a basic amino
acid) has an amine
group (—NH2) in
the R group.
Cysteine
(a basic amino acid)
has a sulfhydryl (—SH)
group in the R group,
which suggests that
this amino acid is likely
to participate in
intramolecular bonding.
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51. Figure 2.18 Amino acids are linked together by peptide bonds.
12/10/11
Dehydration synthesis:
The acid group of one amino
acid is bonded to the amine
group of the next, with loss
of a water molecule.
Peptide
bond +
Amino acid
Amino acid
Dipeptide
Hydrolysis: Peptide bonds
linking amino acids together
are broken when water is
added to the bond.
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52. Figure 2.19a Levels of protein structure.
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Amino acid
Amino acid
Amino acid
Amino acid
Amino acid
Primary structure:
The sequence of
amino acids forms
the polypeptide chain.
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53. Figure 2.19b Levels of protein structure.
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Secondary
structure:
The primary chain
forms spirals
(α-helices) and
sheets (β-sheets).
α-Helix: The primary chain is coiled
to form a spiral structure, which is
stabilized by hydrogen bonds.
β-Sheet: The primary chain “zig-zags”
back and forth forming a “pleated”
sheet. Adjacent strands are held
together by hydrogen bonds.
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54. Figure 2.19c Levels of protein structure.
12/10/11
Tertiary structure:
Superimposed on secondary structure.
α-Helices and/or β-sheets are folded up
to form a compact globular molecule
held together by intramolecular bonds.
Tertiary structure of
prealbumin (transthyretin),
a protein that transports
the thyroid hormone
thyroxine in blood and
cerebrospinal fluid.
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55. Figure 2.19d Levels of protein structure.
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Quaternary structure:
Two or more polypeptide chains,
each with its own tertiary structure,
combine to form a functional
protein.
Quaternary structure of a
functional prealbumin
molecule. Two identical
prealbumin subunits join
head to tail to form the
dimer.
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56. Fibrous and Globular Proteins
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(structural) proteins
Most have tertiary or quaternary structure (3-D)
Provide mechanical support and strength
Examples:
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57. Fibrous and Globular Proteins
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(functional) proteins
Compact, spherical, water-soluble and sensitive to environmental changes
Tertiary or quaternary structure (3-D)
Specific functional regions (active sites)
Examples:
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58. Fibrous and Globular Proteins

59. Usually reversible if normal conditions restored
Protein Denaturation
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Denaturation
Globular proteins unfold and lose functional, 3-D shape
activity destroyed
Can be cause by decreased pH, increased ions, or increased temperature
Usually reversible if normal conditions restored
Irreversible if changes are extreme
e.g., cooking meat
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60. Protein Denaturation

61. Globular proteins that act as biological catalysts
Enzymes
12/10/11
Globular proteins that act as biological catalysts
Regulate and increase speed of chemical reactions
Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!)
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62. Figure 2.20 Enzymes lower the activation energy
required for a reaction.
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WITHOUT ENZYME
WITH ENZYME
Activation
energy
required
Less activation
energy required
Energy
Reactants
Energy
Reactants
Product
Product
Progress of reaction
Progress of reaction
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63. Characteristics of Enzymes
12/10/11
Some functional enzymes consist of two parts
Protein portion
Cofactor (metal ion) or coenzyme (organic molecule often a vitamin)
Enzymes are specific
Act on specific substrate
Usually end in the suffix “ ”
Often named for the reaction they catalyze
Hydrolases, oxidases
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64. Enzyme Action

65. Figure 2.21 Mechanism of enzyme action.
12/10/11
Slide 1
Product (P)
e.g., dipeptide
Substrates (S)
e.g., amino acids
Energy is
absorbed;
bond is
formed.
Water is
released.
Peptide
bond +
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
Substrates bind at active
site, temporarily forming an
enzyme-substrate complex. 1
The E-S complex
undergoes internal
rearrangements that
form the product. 2
Enzyme (E)
The enzyme releases
the product of the
reaction. 3
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66. Enzyme Action

67. Enzyme Action

68. Enzyme Action Enzyme Reactants Product Reactants approach enzyme
bind to enzyme
Enzyme
changes shape
Products
are released

69. Deoxyribonucleic acid ( ) and ribonucleic acid ( )
Nucleic Acids
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Deoxyribonucleic acid ( ) and ribonucleic acid ( )
Largest molecules in the body
Contain C, O, H, N, and P
Polymers
Monomer = nucleotide a
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70. Nucleotides - The Building Blocks of DNA and RNA
Adenine (A)
Cytosine (C)
Thymine (T)
Guanine (G)
Phosphate
Deoxyribose
Figure 2.23

71. Deoxyribonucleic Acid (DNA)
12/10/11
Utilizes four nitrogen bases:
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), and Thymine (T)
Base-pair rule – each base pairs with its complementary base
A always pairs with T; G always pairs with C
Double-stranded helical molecule (double helix) in the cell nucleus
Pentose sugar is deoxyribose
Provides instructions for protein synthesis
Replicates before cell division ensuring genetic continuity
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72. Figure 2.22 Structure of DNA.
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Sugar:
Deoxyribose
Base:
Adenine (A)
Phosphate
Thymine (T)
Sugar
Phosphate
Adenine nucleotide
Thymine nucleotide
Hydrogen
bond
Deoxyribose
sugar
Sugar-
phosphate
backbone
Phosphate
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
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73. Base pair
Phosphate
Sugar
Nucleotide

74. Ribonucleic Acid (RNA)
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Four bases:
Adenine (A), Guanine (G), Cytosine (C), and Uracil (U)
Pentose sugar is ribose
Single-stranded molecule mostly active outside the nucleus
Three varieties of RNA carry out the DNA orders for protein synthesis
Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
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75. Phosphate
Ribose
Uracil

76. Structure and function of adenosine triphosphate (ATP)
ATP Carries Energy
12/10/11
Structure and function of adenosine triphosphate (ATP)
Nucleotide – adenosine triphosphate
Universal energy source
Bonds between phosphate groups contain potential energy
Breaking the bonds releases energy
ATP → ADP + P + energy
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77. Figure 2.23 Structure of ATP (adenosine triphosphate).
12/10/11
High-energy phosphate
bonds can be hydrolyzed
to release energy.
Adenine
Phosphate groups
Ribose
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
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78. Function of ATP Phosphorylation
12/10/11
Phosphorylation
Phosphates are enzymatically transferred to and energize other molecules
Such “primed” molecules perform cellular work (life processes) using the phosphate bond energy
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79. Figure 2.24 Three examples of cellular work driven by energy from ATP.
12/10/11
Solute +
Membrane
protein
Transport work: ATP phosphorylates transport proteins,
activating them to transport solutes (ions, for example)
across cell membranes. +
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
Mechanical work: ATP phosphorylates contractile pro-
teins in muscle cells so the cells can shorten. +
Chemical work: ATP phosphorylates key reactants, providing
energy to drive energy-absorbing chemical reactions.
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