Chapter 2: The Chemical Level of Organization

1
Chapter 2 The Chemical Level of Organization
2
Introduction to Chemistry

• Matter is made up of atoms
• Atoms join together to form chemicals with
  different characteristics
• Chemical characteristics determine physiology at
  the molecular and cellular level

3
Atomic Particles

• Proton
• positive, 1 mass unit
• Neutron
• neutral, 1 mass unit
• Electron
• negative, low mass

4
Particles and Mass

• Atomic number
• number of protons
• Mass number
• number of protons plus neutrons
• Atomic weight
• exact mass of all particles (daltons)

5
Isotopes

• 2 or more elements with equal numbers of protons
  but different numbers of neutrons

6
Elements in the Human Body
Table 21
7
How do atoms form molecules and compounds?
8
Molecules and Compounds

• Molecules
• atoms joined by strong bonds
• Compounds
• atoms joined by strong or weak bonds

9
Chemical Bonds

• Ionic bonds
• attraction between cations () and anions (-)
• Covalent bonds
• strong electron bonds
• Non polar covalent bonds equal sharing of
  electrons
• Polar covalent bonds unequal sharing of
  electrons
• Hydrogen bonds
• weak polar bonds

10
Ionic Bonds
Are atoms with positive or negative charge
Figure 23a
11
Covalent Bond

• Formed between atoms that share electrons

Free Radicals Ion or molecule that
contain unpaired electrons in the outermost
shell. - Extremely Reactive -Typically
enter into destructive reactions
-Damage/destroy vital compounds
12
Hydrogen Bonds

• Attractive force between polar covalent molecules
• Weak force that holds molecules together
• Hydrogen bonds between H2O molecules cause
  surface tension

Figure 26
13
How is it possible for two samples of hydrogen to
contain the same number of atoms, yet have
different weights?
A. One sample has more bonds. B. One sample
contains fewer electrons, decreasing weight. C.
One sample contains more of hydrogens heavier
isotope(s). D. One sample includes more protons,
increasing weight.
14
Both oxygen and neon are gases at room
temperature. Oxygen combines readily with other
elements, but neon does not. Why?
A. Neon has 8 electrons in its valence shell,
oxygen has only 6. B. Neon cannot undergo
bonding due to its polarity. C. Neon is
exergonic. D. Neons molecular weight is too low
to allow bonding.
15
Both oxygen and neon are gases at room
temperature. Oxygen combines readily with other
elements, but neon does not. Why?
A. Neon has 8 electrons in its valence shell,
oxygen has only 6. B. Neon cannot undergo
bonding due to its polarity. C. Neon is
exergonic. D. Neons molecular weight is too low
to allow bonding.
16
Which kind of bond holds atoms in a water
molecule together? What attracts water
molecules to one another?
A. polar covalent bonds hydrogen bonds B.
ionic bonds charge interactions C. hydrogen
bonds charge interactions D. covalent bonds
hydrogen bonds
17
Why are chemical reactions important to
physiology?
18
Energy

• Energy
• the capacity to do work
• Work
• a change in mass or distance

19
Forms of Energy

• Kinetic energy
• energy of motion
• Potential energy
• stored energy
• Chemical energy
• potential energy stored in chemical bonds
• When energy is exchanged, heat is produced
• - cells cannot capture it or use it for work

20
Break Down, Build Up

• Decomposition reaction (catabolism)
• AB ??A B
• Synthesis reaction (anabolism)
• A B ??AB
• Exchange reaction (reversible)
• AB CD ??AD CB
• If Water is Involved
• Hydrolysis
• ABCDE H2O ??ABCH HODE
• Dehydration synthesis (condensation)
• ABCH HODE ??ABCDE H2O

21
KEY CONCEPT

• Reversible reactions seek equilibrium, balancing
  opposing reaction rates
• Add or remove reactants
• reaction rates adjust to reach a new equilibrium

22
How do enzymes control metabolism?
23
Activation Energy

• Chemical reactions in cells cannot start without
  help
• Activation energy gets a reaction started

Figure 27
24
Materials in Reactions

• Reactants
• materials going into a reaction
• Products
• materials coming out of a reaction
• Enzymes
• proteins that lower the activation energy of a
  reaction

25
Energy In, Energy Out

• Exergonic reactions
• produce more energy than they use
• Heat will be the by-product
• Endergonic reactions
• use more energy than they produce
• Most chemical reactions that sustain life cannot
  occur unless the right enzymes are present

26
In cells, glucose, a six-carbon molecule, is
converted into two three-carbon molecules by a
reaction that releases energy. How would you
classify this reaction?
A. endergonic B. exergonic C. decomposition D. B
and C
27
In cells, glucose, a six-carbon molecule, is
converted into two three-carbon molecules by a
reaction that releases energy. How would you
classify this reaction?
A. endergonic B. exergonic C. decomposition D. B
and C
28
Why are enzymes needed in our cells?
A. to promote chemical reactions B. for
chemical reactions to proceed under
conditions compatible with life C. to
lower activation energy requirements D.
all of the above
29
What is the difference between organic and
inorganic compounds?
30
Organic and Inorganic Molecules

• Organic
• molecules based on carbon and hydrogen
• Inorganic
• molecules not based on carbon and hydrogen

31
Essential Molecules

• Nutrients
• essential molecules obtained from food
• Metabolites
• molecules made or broken down in the body

32
Why is water so important to life?
33
Properties of Water

• Solubility
• waters ability to dissolve a solute in a solvent
  to make a solution
• Reactivity
• most body chemistry uses or occurs in water
• High heat capacity
• waters ability to absorb and retain heat
• Lubrication
• to moisten and reduce friction
• Water is the key structural and functional
  component of cells and their control mechanisms,
  the nucleic acids

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Aqueous Solutions
Polar water molecules form hydration spheres
around ions and small polar molecules to keep
them in solution
Figure 28
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Electrolytes

• Inorganic ions conduct electricity in solution
• Electrolyte imbalance seriously disturbs vital
  body functions

36
Molecules and Water

• Hydrophilic
• hydro water, philos loving
• reacts with water
• Hydrophobic
• phobos fear
• does not react with water

37
Solutions

• Suspension
• a solution in which particles settle (sediment)
• Concentration
• the amount of solute in a solvent (mol/L, mg/mL)

38
What is pH and why do we need buffers?
39
pH Neutral, Acid, or Base?

• pH
• the concentration of hydrogen ions (H) in a
  solution
• Neutral pH
• a balance of H and OH
• pure water 7.0
• Acid (acidic) pH lower than 7.0
• high H concentration, low OH concentration
• Base (basic) pH higher than 7.0
• low H concentration, high OH concentration

40
pH Scale

• Has an inverse relationship with H
  concentration
• more H ions mean lower pH, less H ions mean
  higher pH

Figure 29
41
KEY CONCEPT

• pH of body fluids measures free H ions in
  solution
• Excess H ions (low pH) Acidosis
• damages cells and tissues
• alters proteins
• interferes with normal physiological functions
• Excess OH ions (high pH) Alkalosis
• Uncontrollable and sustained skeletal muscle
  contractions

42
Controlling pH

• Salts
• positive or negative ions in solution
• contain no H or OH (NaCl)
• Buffers
• weak acid/salt compounds
• neutralizes either strong acid or strong base

43
Why does a solution of table salt conduct
electricity, but a sugar solution does not?
A. Electrical conductivity requires ions. B.
Sugar forms a colloid, salt forms a
suspension. C. Electricity is absorbed by
glucose molecules. D. Table salt is hydrophobic,
sugar is hydrophilic.
44
How does an antacid help decrease stomach
discomfort?
A. by reducing buffering capacity of the
stomach B. by decreasing pH of stomach
contents C. by reacting a weak acid with a
stronger one D. by neutralizing acid using a
weak base
45
What kinds of organic compounds are there, and
how do they work?
Organic Compounds
46
Functional Groups of Organic Compounds

• Molecular groups which allow molecules to
  interact with other molecules

Table 24
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Carbohydrates

• Consist of CHO in 121 ratio
• 1. Monosaccharides
• simple sugars with 3 to 7 carbon atoms (glucose)
• Glucose important metabolic fuel
• 2. Disaccharides
• 2 simple sugars condensed by dehydration
  synthesis (sucrose)

48
Simple Sugars

• Structural Formula
• Straight-chain form
• Ring from
• 3-D
• Isomers Glucose vs. Fructose
• - Same chemical formula
• but different shape

Figure 210
49
Polysaccharides

• Chains of many simple sugars (glycogen)
• Formation
• Dehydration synthesis
• Breakdown
• Hydrolysis synthesis

Glycogen made and stored in muscle cells
Figure 212
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Carbohydrate Functions
Polysaccharides Glycogen made
and stored in muscle cells Cellulose structural
component of plants -Ruminant Animals
Cattle, sheep, and deer
Table 25
51
The Ruminant Stomach
Ruminant stomach is polygastric four
compartments -Rumen
-Reticulum -Abomasum
-Omasum
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Rumen

• Occupies 80 of the stomach
• Muscular Pillar
• Contract to mix feed
• Digest starch and fibers
• Microbes produce VFAs
• Lined with Papillae
• pH of 5.8-7.0
• Provide a suitable environment for bacteria and
  protozoa

53
KEY CONCEPT

• Carbohydrates are quick energy sources and
  components of membranes
• Lipids have many functions, including membrane
  structure and energy storage
• Provides 2x more energy then carbohydrates

54
Lipids

• Mainly hydrophobic molecules such as fats, oils,
  and waxes
• Made mostly of carbon and hydrogen atoms (12),
  and some oxygen
• Less oxygen then carbon

55
Classes of Lipids

• Fatty acids
• Eicosanoids
• Glycerides
• Steroids
• Phospholipids and glycolipids

56
Fatty Acids

• Carboxyl group -COOH
• Hydrophilic
• Hydrocarbon tail
• Hydrophobic
• Longer tail lower solubility
• Saturated vs. Unsaturated
• Saturated solid at room temp.
• Cause solid plaques in arteries
• Unsaturated liquid at room temp.
• Healthier

Figure 213
57
Eicosanoids

• Used for cellular communication
• Never burned for energy
• 1. Leukotrienes
• active in immune system
• Used by cells to signal injury
• 2. Prostaglandins local hormones
• Used for cell-to-cell signaling to coordinate
  events

58
Steroids

• 4 carbon ring with attached carbon chains
• Not burned for energy

Figure 216
59
Types of Steroids

• Cholesterol
• cell membrane formation and maintenance, cell
  division, and osmotic stability
• Estrogens and testosterone
• Regulation of sexual function
• Corticosteroids and calcitrol
• Tissue metabolism and mineral balance
• Bile salts
• Processing of dietary fats

60
Glycerides

• Glycerides are the fatty acids attached to a
  glycerol molecule
• Triglyceride are the 3 fatty-acid tails, fat
  storage molecule

• Fat Deposits are Important
• Energy Storage
• Insulation
• Mechanical Protection
• -Knees and Eye Sockets

Figure 215
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Phospholipids Vs. GlycolipidsCombination Lipids
Cell Membranes are Composed of these lipids
Hydrophilic
Diglyceride
Hydrophobic
Figure 217a, b
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Phospholipids Vs. GlycolipidsCombination Lipids
Spontaneous formation of Micelle
Figure 217c
63
5 Lipid Types
Table 26
64
A food contains organic molecules with the
elements C, H, and O in a ratio of 121. What
class of compounds do these molecules belong to,
and what are their major functions in the body?
A. lipids energy source B. proteins support
and movement C. nucleic acids determining
inherited characteristics D. carbohydrates
energy source
65
When two monosaccharides undergo a dehydration
synthesis reaction, which type of molecule is
formed?
A. polypeptide B. disaccharide C.
eichosanoid D. polysaccharide
66
Which kind of lipid would be found in a sample of
fatty tissue taken from beneath the skin?
A. eichosanoid B. steroid C. triglyceride D.
phospholipid
67
Which lipids would you find in human cell
membranes?
A. cholesterol B. glycolipids C.
phospholipids D. all of the above
68
Protein Structure

• Proteins are the most abundant and important
  organic molecules
• Basic elements
• carbon (C), hydrogen (H), oxygen (O), and
  nitrogen (N)
• Basic building blocks
• 20 amino acids

69
Protein Functions

• 7 major protein functions
• support structural proteins
• movement contractile proteins
• transport transport proteins
• buffering regulation of pH
• metabolic regulation enzymes
• coordination and control hormones
• defense antibodies

70
Proteins

• Proteins
• control anatomical structure and physiological
  function
• determine cell shape and tissue properties
• perform almost all cell functions

71
Amino Acid Structure

• central carbon
• hydrogen
• amino group (NH2)
• carboxylic acid group (COOH)
• variable side chain or R group

Figure 2-18
72
Peptide Bond

• A dehydration synthesis between
• amino group of 1
• amino acid
• and the carboxylic acid group of another amino
  acid
• producing a peptide

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Primary Structure

• Polypeptide
• Linear sequence of amino acids
• How many amino acids were bound together
• What order they are bound

Figure 220a
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Secondary Structure

• Hydrogen bonds form spirals or pleats

Figure 220b
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Tertiary Structure

• Secondary structure folds into a unique shape
• Global coiling or folding due to R group
  interaction

Figure 220c
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Quaternary Structure

• Final protein shape
• several tertiary structures together

Fibrous proteins - structural sheets
Globular proteins - soluble spheres
with active functions
Figure 220d
77
Shape and Function

• Protein function is based on shape
• Shape is based on sequence of amino acids
• Denaturation
• loss of shape and function due to heat or pH

78
Enzymes

• Enzymes are catalysts
• proteins that lower the activation energy of a
  chemical reaction
• are not changed or used up in the reaction

79
How Enzymes Work
Substrates reactants in enzymatic
reactions Active site location on an enzyme that
fits a particular substrate
Figure 221
80
Enzyme Helpers

• Cofactor
• an ion or molecule that binds to an enzyme before
  substrates can bind
• Coenzyme
• nonprotein organic cofactors (vitamins)
• Isozymes
• 2 enzymes that can catalyze the same reaction

81
Enzyme Characteristics

• Specificity
• one enzyme catalyzes one reaction
• Saturation limits
• an enzymes maximum work rate
• Regulation
• the ability to turn off and on

82
Conjugated Protein

• Glycoproteins
• large protein small carbohydrate
• includes enzymes, antibodies, hormones, and mucus
  production
• Proteoglycans
• large polysaccharides polypeptides
• promote viscosity

83
Proteins are chains of which small organic
molecules?
A. saccharides B. fatty acids C. amino acids D.
nucleic acids
84
Which level of protein structure would be
affected by an agent that breaks hydrogen bonds?
A. the primary level of protein structure B. the
secondary level of protein structure C. the
tertiary level of protein structure D. the
protein structure would NOT be affected by this
agent
85
Why does boiling a protein affect its structural
and functional properties?
A. Heat denatures the protein, causing
unfolding. B. Heat causes the formation of
additional quaternary structure. C. Heating
rearranges the primary structure of the
protein. D. Heat alters the radical groups on
the amino acids.
86
Why does boiling a protein affect its structural
and functional properties?
A. Heat denatures the protein, causing
unfolding. B. Heat causes the formation of
additional quaternary structure. C. Heating
rearranges the primary structure of the
protein. D. Heat alters the radical groups on
the amino acids.
87
How might a change in an enzymes active site
affect its functions?
A. increased activity due to a better fit with
the substrate B. decreased activity due to a
poor substrate fit C. inhibited activity due to
no substrate fit D. all of the above
88
Nucleic Acids

• C, H, O, N, and P
• Large organic molecules, found in the nucleus,
  which store and process information at the
  molecular level
• DNA deoxyribonucleic acid
• RNA ribonucleic acid

89
DNA and RNA

• DNA
• Determines inherited characteristics
• Directs protein synthesis
• Controls enzyme production
• Controls metabolism
• RNA
• Codes intermediate steps in protein synthesis

90
KEY CONCEPT

• DNA in the cell nucleus contains the information
  needed to construct all of the proteins in the
  body

91
Nucleotides

• Are the building blocks of DNA
• Have 3 molecular parts
• sugar (deoxyribose)
• phosphate group
• nitrogenous base (A, G, T, C)

92
The Bases
Figure 222b, c
93
Complementary Bases

• Purines pair with pyrimidines
• DNA
• adenine (A) and thymine (T)
• cytosine (C) and guanine (G)
• RNA
• uracil (U) replaces thymine (T)

94
RNA and DNA

• RNA
• a single strand
• DNA
• a double helix joined at bases by hydrogen bonds

95
Protein SynthesisThree forms of RNA

• messenger RNA (mRNA)
• Protein blueprint or instructions
• transfer RNA (tRNA)
• Carry amino acids to the place where proteins are
  being synthesized
• ribosomal RNA (rRNA)
• Forms the site of protein synthesis in the cell
• Factory ribosomes

96
High-Energy CompoundsADP and ATP

• - Assembled using RNA Nucleotides
• - Bonds are broken easily by cells to release
  energy as needed
• During digestion and cellular respiration
• energy from food is transferred to high energy
  compounds for quick and easy access.

97
ADP to ATPPhosphorylation

• ADP vs. ATP
• adenosine diphosphate (ADP)
• 2 phosphate groups (di 2)
• adenosine triphosphate (ATP)
• 3 phosphate groups (tri 3)
• Adding a phosphate group to ADP with a
  high-energy bound to form the high-energy
  compound ATP
• ATPase
• the enzyme that catalyzes phophorylation

98
The Energy Molecule

• Chemical energy stored in phosphate bonds

Figure 224
99
A large organic molecule composed of the sugar
ribose, nitrogenous bases, and phosphate groups
is which kind of nucleic acid?
A. DNA B. ATP C. tRNA D. RNA
100
What molecule is produced by the phosphorylation
of ADP?
A. ATPase B. ATP C. Adenosine Diphosphate D.
Uridine Triphosphate
101
Compounds Important to Physiology
Table 28
102
SUMMARY

• Atoms, molecules, and chemical bonds control
  cellular physiology
• Metabolism and energy work within the cell
• Importance of organic and inorganic nutrients and
  metabolites

103
SUMMARY

• Role of water and solubility in metabolism and
  cell structure
• Chemistry of acids and bases, pH and buffers
• Structure and function of carbohydrates, lipids,
  proteins, and nucleic acids