Transcript Chapter 2: The Chemical Level of Organization

Chapter 2:
The Chemical
Level of Organization
1
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
2
Atomic Particles
• Proton:
– positive, 1 mass unit
• Neutron:
– neutral, 1 mass unit
• Electron:
– negative, low mass
3
Particles and Mass
• Atomic number:
– number of protons
• Mass number:
– number of protons plus neutrons
• Atomic weight:
– exact mass of all particles (daltons)
4
Isotopes
• 2 or more elements with equal
numbers of protons but different
numbers of neutrons
Electron
shell
n
e
p+
(a) Hydrogen-1
(electron-shell model)
p+
e
(b)
n
Hydrogen-2
deuterium
e
p+
(c)
n
Hydrogen-3,
tritium
5
Elements in the Human Body
6
Table 2–1
How do atoms form
molecules and compounds?
7
Molecules and Compounds
• Molecules:
– atoms joined by strong bonds
• Compounds:
– atoms joined by strong or weak bonds
8
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
9
Ionic Bonds
Are atoms with positive or negative charge
10
Figure 2–3a
Covalent Bond
• Formed between atoms that share electrons
Molecule
Electron-Shell Model and
Structural Formula
Hydrogen
(H2)
H–H
Oxygen
(O2)
O=O
Carbon
Dioxide
(CO2)
O=C=O
Nitric
Oxide
(NO)
N=O
Free Radicals:
Ion or molecule that
contain unpaired
electrons in the outermost
shell.
- Extremely Reactive
-Typically enter into
destructive reactions
-Damage/destroy vital
compounds
11
Hydrogen Bonds
• Attractive force
between polar
covalent molecules
• Weak force that
holds molecules
together
• Hydrogen bonds
between H2O
molecules cause
surface tension
12
Figure 2–6
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
hydrogen’s heavier isotope(s).
D. One sample includes more
protons, increasing weight.
13
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. Neon’s molecular weight is too
low to allow bonding.
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. Neon’s molecular weight is too
low to allow bonding.
15
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
16
Why are chemical reactions
important to physiology?
17
Energy
• Energy:
– the capacity to do work
• Work:
– a change in mass or distance
18
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
19
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:
A—B—C—D—E + H2O A—B—C—H + HO—D—E
• Dehydration synthesis (condensation):
A—B—C—H + HO—D—E A—B—C—D—E + H2O
20
KEY CONCEPT
• Reversible reactions seek equilibrium,
balancing opposing reaction rates
• Add or remove reactants:
– reaction rates adjust to reach a new
equilibrium
21
How do enzymes
control metabolism?
22
Activation Energy
• Chemical reactions in cells cannot start
without help
• Activation energy gets a reaction
started
23
Figure 2–7
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
24
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
25
In cells, glucose, a six-carbon
molecule, is converted into two threecarbon molecules by a reaction that
releases energy.
How would you classify this reaction?
A. endergonic
B. exergonic
C. decomposition
D. B and C
26
In cells, glucose, a six-carbon
molecule, is converted into two threecarbon molecules by a reaction that
releases energy.
How would you classify this reaction?
A. endergonic
B. exergonic
C. decomposition
D. B and C
27
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
28
What is the difference
between organic and
inorganic compounds?
29
Organic and Inorganic Molecules
• Organic:
– molecules based on carbon and hydrogen
• Inorganic:
– molecules not based on carbon and
hydrogen
30
Essential Molecules
• Nutrients:
– essential molecules obtained from food
• Metabolites:
– molecules made or broken down in the
body
31
Why is water so
important to life?
32
Properties of Water
• Solubility:
– water’s ability to dissolve a solute in a solvent to
make a solution
• Reactivity:
– most body chemistry uses or occurs in water
• High heat capacity:
– water’s 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
33
Aqueous Solutions
Polar water molecules form hydration
spheres around ions and small polar molecules
to keep them in solution
34
Figure 2–8
Electrolytes
• Inorganic ions: conduct electricity in
solution
• Electrolyte imbalance seriously disturbs
vital body functions
35
Molecules and Water
• Hydrophilic:
– hydro = water, philos = loving
– reacts with water
• Hydrophobic:
– phobos = fear
– does not react with water
36
Solutions
• Suspension:
– a solution in which particles settle
(sediment)
• Concentration:
– the amount of solute in a solvent (mol/L,
mg/mL)
37
What is pH and why
do we need buffers?
38
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
39
pH Scale
• Has an inverse relationship with H
concentration:
+
– more H+ ions mean lower pH, less H+ ions
mean higher pH
40
Figure 2–9
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
41
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
42
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.
43
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
44
Organic Compounds
What kinds of organic
compounds are there,
and how do they work?
45
Functional Groups of Organic Compounds
• Molecular groups which allow
molecules to interact with other
molecules
46
Table 2–4
Carbohydrates
• Consist of C:H:O in 1:2:1 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)
47
Simple Sugars
Structural Formula:
• Straight-chain form
• Ring from
• 3-D
Isomers: Glucose vs. Fructose:
- Same chemical formula
but different shape
48
Figure 2–10
Polysaccharides
• Chains of many simple
sugars (glycogen)
• Formation:
– Dehydration synthesis
• Breakdown:
– Hydrolysis synthesis
Glycogen: made and stored in muscle cells
49
Figure 2–12
Carbohydrate Functions
Polysaccharides
Glycogen: made and stored in muscle cells
Cellulose: structural component of plants
-Ruminant Animals: Cattle, sheep, and deer
50
Table 2–5
The Ruminant Stomach
Ruminant stomach is polygastric: four compartments
-Rumen
-Reticulum
-Abomasum
-Omasum
51
Rumen
Occupies 80% of the stomach
Muscular Pillar
Contract to mix feed
Digest starch and fibers
Microbes produce VFA’s
Lined with Papillae
pH of 5.8-7.0
Provide a suitable environment for bacteria and protozoa
52
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
53
Lipids
• Mainly hydrophobic molecules such as
fats, oils, and waxes
• Made mostly of carbon and hydrogen
atoms (1:2), and some oxygen
– Less oxygen then carbon
54
Classes of Lipids
•
•
•
•
•
Fatty acids
Eicosanoids
Glycerides
Steroids
Phospholipids and glycolipids
55
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
56
Figure 2–13
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
57
Steroids
• 4 carbon ring with attached carbon chains
• Not burned for energy
58
Figure 2–16
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
59
Glycerides
• Glycerides: are
the fatty acids
attached to a
glycerol molecule
• Triglyceride: are
Fat Deposits are Important
the 3 fatty-acid
1. Energy Storage
tails, fat storage
2. Insulation
molecule
3. Mechanical Protection
-Knees and Eye Sockets
60
Figure 2–15
Phospholipids Vs. Glycolipids
Combination Lipids
Cell Membranes are Composed of these lipids
Hydrophilic
Diglyceride
Hydrophobic
61
Figure 2–17a, b
Phospholipids Vs. Glycolipids
Combination Lipids
Spontaneous formation of Micelle
62
Figure 2–17c
5 Lipid Types
63
Table 2–6
A food contains organic molecules with the
elements C, H, and O in a ratio of 1:2:1.
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
64
When two monosaccharides undergo a
dehydration synthesis reaction, which
type of molecule is formed?
A.
B.
C.
D.
polypeptide
disaccharide
eichosanoid
polysaccharide
65
Which kind of lipid would be found in
a sample of fatty tissue taken from
beneath the skin?
A.
B.
C.
D.
eichosanoid
steroid
triglyceride
phospholipid
66
Which lipids would you find in human
cell membranes?
A.
B.
C.
D.
cholesterol
glycolipids
phospholipids
all of the above
67
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
68
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
69
Proteins
• Proteins:
– control anatomical structure and
physiological function
– determine cell shape and tissue properties
– perform almost all cell functions
70
Amino Acid Structure
1.
2.
3.
4.
central carbon
hydrogen
amino group (—NH2)
carboxylic acid
group (—COOH)
5. variable side chain
or R group
71
Figure 2-18
Peptide Bond
• A dehydration
synthesis between:
– amino group of 1
amino acid
– and the carboxylic
acid group of another
amino acid
– producing a peptide
72
Primary Structure
• Polypeptide:
– Linear sequence of amino acids
• How many amino acids were bound together
• What order they are bound
73
Figure 2–20a
Secondary Structure
• Hydrogen bonds form spirals or pleats
74
Figure 2–20b
Tertiary Structure
• Secondary structure folds into a unique shape
• Global coiling or folding due to R group
interaction
75
Figure 2–20c
Quaternary Structure
• Final protein shape:
– several tertiary structures together
Fibrous proteins:
- structural sheets
Globular proteins:
- soluble spheres
with active functions
76
Figure 2–20d
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
77
Enzymes
• Enzymes are catalysts:
– proteins that lower the activation energy
of a chemical reaction
– are not changed or used up in the reaction
78
How Enzymes Work
Substrates: reactants in enzymatic reactions
Active site: location on an enzyme that fits a
particular substrate
79
Figure 2–21
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
80
Enzyme Characteristics
• Specificity:
– one enzyme catalyzes one reaction
• Saturation limits:
– an enzyme’s maximum work rate
• Regulation:
– the ability to turn off and on
81
Conjugated Protein
• Glycoproteins:
– large protein + small carbohydrate
• includes enzymes, antibodies, hormones, and
mucus production
• Proteoglycans:
– large polysaccharides + polypeptides
• promote viscosity
82
Proteins are chains of which small
organic molecules?
A.
B.
C.
D.
saccharides
fatty acids
amino acids
nucleic acids
83
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
84
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.
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
How might a change in an enzyme’s
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
87
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
88
DNA and RNA
DNA
• Determines inherited characteristics
• Directs protein synthesis
• Controls enzyme production
• Controls metabolism
RNA
• Codes intermediate steps in protein
synthesis
89
KEY CONCEPT
• DNA in the cell nucleus contains the
information needed to construct all of
the proteins in the body
90
Nucleotides
• Are the building blocks of DNA
• Have 3 molecular parts:
– sugar (deoxyribose)
– phosphate group
– nitrogenous base (A, G, T, C)
91
The Bases
92
Figure 2–22b, c
Complementary Bases
• Purines pair with pyrimidines:
• DNA:
– adenine (A) and thymine (T)
– cytosine (C) and guanine (G)
• RNA:
– uracil (U) replaces thymine (T)
93
RNA and DNA
• RNA:
– a single strand
• DNA:
– a double helix joined at bases by hydrogen
bonds
94
Protein Synthesis:
Three 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
95
High-Energy Compounds:
ADP 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.
96
ADP to ATP:
Phosphorylation
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 highenergy bound to form the high-energy
compound ATP
• ATPase:
– the enzyme that catalyzes phophorylation
97
The Energy Molecule
• Chemical energy stored in phosphate
bonds
98
Figure 2–24
A large organic molecule composed of
the sugar ribose, nitrogenous bases, and
phosphate groups is which kind of
nucleic acid?
A.
B.
C.
D.
DNA
ATP
tRNA
RNA
99
What molecule is produced by the
phosphorylation of ADP?
A.
B.
C.
D.
ATPase
ATP
Adenosine Diphosphate
Uridine Triphosphate
100
Compounds Important
to Physiology
101
Table 2–8
SUMMARY
• Atoms, molecules, and chemical bonds
control cellular physiology
• Metabolism and energy work within the
cell
• Importance of organic and inorganic
nutrients and metabolites
102
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
103