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IV. Stages of a Scientific Investigation
Steps in the scientific method:
(1) Observation
Francesco Redi in 1600’s!
!Maggots appear on fresh meat left uncovered.
!Flies swarm over raw meat
(2) Hypothesis
A tentative testable explanation of an observed event.
!
Maggots appear on fresh meat left uncovered because flies
land on the meat and lay eggs.
IV. Stages of a Scientific Investigation
Steps in the scientific method ...
(3) Experiment
a study to test a hypothesis
Simple experiments
Test single variable AT A TIME
– Experimental Variable
– AKA the “Treatment”
Control all other variables
– Hold them constant in “controls”
Maggots
No maggots
What were his results?
1
IV. Stages of a Scientific Investigation
Steps in the scientific method ...
(4) Conclusion
In this case, the hypothesis is
supported by the results of the
experiment
Maggots
No maggots
IV. Stages of a Scientific Investigation
O!Q ! H ! P ! Controlled Experiments ! Conclusions
"
Manuscript preparation for publication
"
Peer Review
"
Publication
"
Replication by other scientists
"
Acceptance by the scientific community
2
IV. Stages of a Scientific Investigation
Science is a human endeavor.
Real scientific advances often involve:
–
–
accidents and insight
lucky guesses
–
controversies between scientists
i.e. Discovery of penicillin by Alexander
Fleming, 1928
Penicillin prevents the growth of staphylococci bacteria,
an organism causing serious infection at that time
Theory: Scientific versus general
3
Theory: Scientific versus general
In one episode of 'Cheers', Cliff is seated at the bar describing the Buffalo Theory to
Norm. "Well you see, Norm, it's like this... A herd of buffalo can only move as
fast as the slowest buffalo. And when the herd is hunted, it's the slowest and
weakest ones at the back that are killed first. This natural selection is good for
the herd as a whole, because the general speed and health of the whole group
keeps improving by the regular killing of the weakest members.”
1.
A set of statements or principles devised to explain a
group of facts or phenomena, especially one that has been
repeatedly tested or is widely accepted and can be used to
make predictions about natural phenomena.
Theory: Scientific versus general
In one episode of 'Cheers', Cliff is seated at the bar describing the Buffalo Theory to
Norm. "Well you see, Norm, it's like this... A herd of buffalo can only move as
fast as the slowest buffalo. And when the herd is hunted, it's the slowest and
weakest ones at the back that are killed first. This natural selection is good for
the herd as a whole, because the general speed and health of the whole group
keeps improving by the regular killing of the weakest members.”
“In much the same way, the human brain can only operate as fast as the
slowest brain cells. Now, as we know, excessive intake of alcohol kills brain cells.
But naturally, it attacks the slowest and weakest brain cells first. In this way,
regular consumption of beer eliminates the weaker brain cells, making the brain a
faster and more efficient machine. And that, Norm, is why you always feel
smarter after a few beers...."
1.
A set of statements or principles devised to explain a
group of facts or phenomena, especially one that has been
repeatedly tested or is widely accepted and can be used to
make predictions about natural phenomena.
2.
An assumption based on limited information or knowledge;
a conjecture.e; a conjecture.
4
V. What is a Scientific Theory?
Examples of Theories in Science:
1. Cell Theory
2. Theory of Relativity
3. Theory of Evolution
Theory: Scientific versus general
Cell theory
5
Theory: Scientific versus general
Stem Cell theory
Theory: Scientific versus general
Stem Cell use in wound repair
6
Theory: Scientific versus general
Stem Cell use in wound repair
Theory: Scientific versus general
Stem Cell use in wound repair
7
Debate is an important part of science
Not a current scientific debate
• Natural selection and evolution versus Creative Design
8
Not a current scientific debate
• Natural selection and evolution versus Creative Design
V. What is a Scientific Theory?
Example of the Development of a Theory: Evolution
Accepted “Belief” in 1831: Species have been specifically
created and are unchangeable over time.
Darwin’s Evidence to the Contrary:
Fossil record
Geographical Variability
Island Modifications
9
V. What is a Scientific Theory?
The Basics of the Theory of Evolution
Darwin & Wallace 1800’s
(1) Genetic variation: exists among members of a
population
(2) Inheritance of variations: parents to offspring
(3) Natural selection: Enhanced survival/reproduction
of organisms with adaptations to survive
!Present-day organisms descended, with
modification, from pre-existing forms
…or…‘Change over time’
V. What is a Scientific Theory?
Further Evidence Supporting the Theory of Evolution:
1. The Fossil Record
2. The Age of the Earth
3. The Mechanisms of Heredity
4. Comparative Anatomy
5. Molecular and Phylogenetic Evidence (DNA)
Figure 1.13
10
V. What is a Scientific Theory?
What is Biology?
Unifying Themes of Biology
1. Cell theory
2. Molecular basis of inheritance
3. Evolution
VI. Unifying Themes in Biology
What is Biology?
1. Cell Theory
Robert Hooke (1665): Discovered cells
Schleiden and Schwann (1839): “All living things are
composed of cells”
Modern Cell Theory: All living organisms are made of cells,
and all living cells come from other living cells.
2. Molecular basis of inheritance
DNA encodes genes which make-up and control living organisms.
Heredity is dependent on the faithful copying of the cell’s DNA into
daughter cells.
11
3. Evolution
! conservation
Some fundamentally important characteristics of earlier
organisms are preserved and passed on to future generations.
e.g. Histones (chief proteins of chromatin)
! adaptation
Life-forms have evolved varying characteristics to adapt to varied environments.
This has resulted in incredible diversity.
Chapter 2: Nature of Molecules
I. Atoms
II. Chemical Bonds
III. Importance of water
12
Chapter 2: Nature of Molecules
I. What are atoms?
Units of Matter (=has mass and occupies space)
• Composed of even smaller particles:
Atomic Nucleus:
Protons (+)
Neutrons (#)
Electrons:
(-) charge
orbit nucleus
lighter mass
Neutral Atoms have # Protons = # Electrons
Chapter 2: Nature of Molecules
Atoms make up structure of elements
Elements:
• can’t be broken down or
converted to another
substance
• Atomic number =
# protons
• Atomic mass =
# protons + # neutrons
(each weighs ~1 dalton)
• Each element has
unique chemical
properties!
7
14.01
13
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Frequency of Elements in the Earth’s Crust
8
1
3
4
5
Li Be
11
12
Na Mg
19
2
O
H
20
K Ca Sc Ti
21
22
23
24
25
37
38
39
40
41
42
43
55
56
57
72
73
74
87
88
89
104
105
26
Fe
6
B 14
13 Si
Al
C
9
7
10
F Ne
N
15
P
16
17
18
36
S Cl Ar
27
28
29
30
31
32
33
34
35
44
45
46
47
48
49
50
51
52
53
I
Xe
75
76
77
78
79
80
81
82
83
84
85
86
106
107
108
109
110
58
59
60
61
62
63
64
65
66
67
68
69
70
71
90
91
92
93
94
95
96
97
98
99
100
101
102
103
V Cr Mn
Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te
Cs Ba La Hf Ta W Re Os Ir
Fr Ra Ac
He
54
Pt Au Hg Tl Pb Bi Po At Rn
(Lanthanide Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
series)
(Actinide series) Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
Chemical Composition of the Human Body
14
Chapter 2: Nature of Molecules
Helium Atom Structure
–
Electron
cloud
2e–
–
+
+
+
+
Nucleus
Atomic number?
Atomic mass?
2 +
Protons
2
Neutrons
2 –
Electrons
Chapter 2: Nature of Molecules
Carbon Atom Structure
Electron
cloud
6e–
+
+
Atomic number?
Atomic mass?
Nucleus
6
+
Protons
6
Neutrons
6
– Electrons
15
Chapter 2: Nature of Molecules
Isotopes: Versions of an element with different # neutrons
• Both naturally and artificially occurring
Isotopes of Carbon
Chapter 2: Nature of Molecules
Summary of Isotopes
•
•
•
•
•
92 naturally occurring elements
270 stable isotopes
50 natural radioisotopes
1000’s artificial isotopes
Radioactivity is released by unstable isotopes
Radioactive isotopes: an isotope in which the nucleus
decays spontaneously, giving off particles and/or
energy (radiation). The decay occurs to increase
stability.
There are different types of radioactivity: Beta, Alpha, and Gamma
16
Electrons:
Chapter 2: Nature of Molecules
A) Repel each other (- charge)
B) Are attracted to the nucleus (+ charge)
Electrons orbit nucleus in 3-D space
$ electron shells (energy levels)
• First shell (2 e-)
• Second shell (8 e-)
• Etc..
Closest shell to nucleus fills first
Chapter 2: Nature of Molecules
Inert atoms: Outer shell either completely full, or completely
empty
Reactive atoms: Partially filled outermost shell
Which of these is
more reactive?
17
Chapter 2: Nature of Molecules
Patterns of the Periodic Table
Take Home: Reactivity can be predicted by position!
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Energy Levels or Electron Shells
ed
as
ele
yr
erg
En
–
M
Energy
level
3
L
Energy
level
2
K
Energy
level
1
+
++
+ +
+
+
En
erg
ya
bs
or
be
d
–
K
L
Energy
level
1
Energy
level
2
M
Energy
level
3
18
Chapter 2: Nature of Molecules
II. Chemical bonds
• Interaction of atoms to stabilize outermost e- shells
• Result from gaining, losing, or sharing electrons
Molecule:
2 or more atoms (same or different) held
together by interactions of outer e- shells
H2
H2O
Compound: 2 or more different atoms held together by
interactive forces
Chemical Reaction: Making or breaking of chemical bonds
Chapter 2: Nature of Molecules
Molecules Have Emergent Properties
Sodium
Chlorine
Sodium Chloride
19
Chapter 2: Nature of Molecules
Chemical Bond Types
1. Covalent bond
Attractive force between atoms that are sharing
electrons
H2
• Common in biological
molecules
! Proteins, Lipids,
Sharing of
electrons
Carbohydrates
• Crucial for life
Covalent bonds = Strong bonds
Chapter 2: Nature of Molecules
Covalent bond Types
Single covalent bonds:
H-H
Share 1 pair electrons
Double covalent bonds:
O=O
Share 2 pairs of electrons
Triple covalent bonds:
N=N
Share 3 pairs of electrons
20
Chapter 2: Nature of Molecules
Patterns of covalent bonds
Chapter 2: Nature of Molecules
Types of covalent bonds
a. non-polar covalent bonds
• Equal sharing of e-
Oxygen Molecule
21
Chapter 2: Nature of Molecules
Types of covalent bonds
b. polar covalent bonds
• unequal sharing of e• due to unequal nuclear attraction for e-; Oxygen is more
electronegative than Hydrogen
• poles have partial charges (although the molecule is electrically
neutral)
=POLAR MOLECULE
Water Molecule
Chapter 2: Nature of Molecules
Chemical Bond Types
2. Ionic bonds
Atoms are
electrically
charged
22
Chapter 2: Nature of Molecules
Chemical Bond Types
2. Ionic Bond:
Attractive force between atoms that have lost or
gained e- (ions: charged atoms)
Transfer of
electrons
Chapter 2: Nature of Molecules
Ionic bonds are weaker than Covalent Bonds
23
Chapter 2: Nature of Molecules
Chemical Bond Types
3. Hydrogen Bonds:
EX: Attraction between
water molecules
In each water molecule:
O = partial (-) charge
H = partial (+) charge
(Due to polar covalent bonds)
•
•
Partial charges attract
molecules together
Weakest of 3 bond types,
“transient” bonds
Water Molecule*
Chapter 2: Nature of Molecules
III. Why is Water So Important? READ pgs 28-32
1. Water is an extremely good solvent
(UNIVERSAL SOLVENT)
Can dissolve solutes into solutions
EX: Water dissolves NaCl (salt)
WHY?
• Polar nature of water,
partial charges
•
What type of substances
will water dissolve?
24
Chapter 2: Nature of Molecules
Hydrophilic molecules
• Have electrical attraction
for water molecules
• Ions, polar molecules
• Sugars, amino acids
• Dissolve in H20
Hydrophobic molecules
• Uncharged, non-polar
• Fats, oils
• Clump together in H2O
Chapter 2: Nature of Molecules
Why is Water So Important?
2. Water molecules stick together (Cohesion)
• Polar nature of water ! H-bonds
Creates surface tension
Water molecules also Adhere to other molecules
25
Chapter 2: Nature of Molecules
Why is Water So Important?
3. Water-based solutions can be acidic, basic or neutral
When H+ >> OH- = Acidic Solution
.........Think H+Cl- + H2O.........
When H+ << OH- = Basic solution
.........Think Na+OH- + H2O.........
Chapter 2: Nature of Molecules
• The pH of a solution
explains how
acidic/basic it is
• Negative log scale
of the [H+]
26
Chapter 2: Nature of Molecules
Buffers maintain a solution at a relatively constant pH
– pH stability essential for living cells to function
– Takes up or donates H+ in response to changes in pH
Example buffer: Bicarbonate and Carbonic Acid
Blood getting acidic? (“too much” H+)
HCO3+
H+
$ H2CO3
(Bicarbonate ion)
(Carbonic acid)
Bicarbonate takes up H+
Blood getting basic? (“too little” H+)
H2CO3
+
OH$ HCO3(Carbonic acid)
(Bicarbonate ion)
+
H 2O
(water)
Carbonic acid donates H+ to combine with [OH-]
Chapter 2: Nature of Molecules
Why is Water So Important?
4. It moderates the effects of temperature changes.
Background: Temperature relates to speed of molecules
low temps
slow speeds
high temps
fast speeds
A) Water heats slowly
• Energy must first break H-bonds...
Water has a high specific heat: E to heat 1g substance 1oC
Water :
1 calorie
Alcohol :
0.6 cal
Granite:
0.02 cal
Water has a high heat of vaporization
• (E to convert liquid to gas)
27
Chapter 2: Nature of Molecules
Why is Water So Important?
4. It moderates the effects of temperature changes.
Background: Temperature relates to speed of molecules
low temps
slow speeds
high temps
fast speeds
A) Water heats slowly
B) Water cools and freezes slowly
• Ice has a very organized structure
• Large amount of E must be removed to form ice crystals
Chapter 2: Nature of Molecules
5. Water forms Ice:
Ice is less dense than water:
B/C hydrogen bonds in ice space the
water molecules relatively far apart
Critical for
winter insulation
in lakes and
ponds
28
Chapter 3: Biological Molecules
I. Carbon and Organic Molecules
II. Synthesis of Organic Molecules
III. Biological Macromolecules
A.
B.
C.
D.
Carbohydrates
Lipids
Proteins
Nucleic Acids
Chapter 3: Biological Molecules
I. Carbon and Organic Molecules:
A. What does Organic really mean?
Organic: carbon-based
compounds that include
hydrogen
Organisms can synthesize
and use Organic
molecules
Inorganic: everything else…
29
Chapter 3: Biological Molecules
I. Carbon and Organic Molecules:
B. Carbon Chemistry
Why is carbon so important?
1) Forms basis of organic molecules :
– carbon skeleton
2) Wide diversity of C-based molecules
a. variety of carbon bonding
b. diverse Functional Groups
Chapter 3: Biological Molecules
B. Carbon Chemistry
1) Forms basis of organic molecules :
! carbon skeleton of varying lengths
Ethane and Propane are examples of Hydrocarbons: molecules
consisting of only carbon and hydrogen
! Covalent bonds between carbon and hydrogen are energyrich
30
Chapter 3: Biological Molecules
B. Carbon Chemistry
1) Forms basis of organic molecules:
How can it do this?
Protons
Neutrons
Electrons
a. Carbon has 4 valence electrons
b. A carbon atom can form four covalent bonds allowing
it to build large and diverse organic compounds
Chapter 3: Biological Molecules
B. Carbon Chemistry
2) Wide diversity of C-based molecules
a. variety of carbon bonding schemes
31
Chapter 3: Biological Molecules
2) Wide diversity of C-based molecules
a. variety of carbon bonding schemes
b. diverse functional groups
! groups of atoms attached to carbon
! groups confer specific chemical properties onto the
molecules
Chapter 3: Biological Molecules
See Figure 3.2
b. diverse functional groups
•
Hydrogen
•
Hydroxyl
•
Carboxyl
(Carboxylic acid)
Amine
or Amino
Polar / Nonpolar
Ex: Almost all
biochemical molecules
•
Polar
Ex: Sugars
•
Polar & acidic
•
Ex: Amino acids
•
Polar & basic
•
Ex: Amino acids,
proteins
32
Chapter 3: Biological Molecules
b. diverse functional groups
Sex Hormones: A Small Difference Makes a Huge Difference!
OH
Estradiol
HO
Female lion
Testosterone
OH
O
Male lion
Chapter 3: Biological Molecules
II. How are large organic molecules synthesized?
• Assembling smaller subunits: modular approach
monomer + monomer ... = polymer
• Generally joined or split by adding or removing H2O
Dehydration
synthesis =
polymer
building
Hydrolysis =
polymer
breaking
33
Chapter 3: Biological Molecules
III. Biological Macromolecules
Four major classes of Biological Macromolecules:
A. Carbohydrates
B. Lipids
C. Proteins
D. Nucleic Acids
! All macromolecules that are polymers are
constructed using DEHYDRATION SYNTHESIS
and broken down by HYDROLYSIS!
Chapter 3: Biological Molecules
III. Biological Molecules :
A. Carbohydrates
• molecules composed of Carbon, Hydrogen & Oxygen
• 1:2:1 ratio
(CH O)
2
x
C3H603
C6H1206
Composed of water-soluble sugar molecules:
– Monosaccharides: single sugar
– Disaccharides: two sugars
– Polysaccharides: many sugars (long chains)
34
Biological Molecules: Carbohydrates
1. Monosaccharides
O
H
C6H12O6
C
H
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
Glucose
H
C
OH
C
O
HO
C
H
H
C
OH
H
C
OH
H
C
OH
Carbonyl
Group
Hydroxyl
Groups
H
H
Fructose
Biological Molecules: Carbohydrates
Fig. 3.26
1. Monosaccharides
Fructose
Glucose
Galactose
H
H
H
H C OH
C O
HO C H
H C OH
H C
OH
H C OH
H
Structural
isomer
C O
H C OH
HO C H
H C OH
H C OH
H C OH
H
C O
Stereoisomer
H C
OH
HO C H
HO C H
H C OH
H C OH
H
Structural isomer: identical chemical groups bonded to different
carbon atoms
Stereoisomer: identical chemical groups bonded to the same
carbon atoms but in different orientations
35
Biological Molecules: Carbohydrates
1. Monosaccharides
Chain form
Ring form
Some important sugars:
6-carbon: hexoses
5-carbon: pentoses
glucose: most common
ribose - RNA
fructose: fruit sugar
deoxyribose- DNA
galactose: part of milk sugar
Biological Molecules: Carbohydrates
1. Monosaccharides
Three representations of the ring form of glucose
6 CH2OH
5C
H
CH2OH
O
H
H
4C
OH
OH
3C
H
H
C 1
H
C2
OH
HO
O
H
OH
H
H
OH
H
O
OH
OH
Structural
formula
Abbreviated
structure
Simplified
structure
36
Biological Molecules: Carbohydrates
1.
Monosaccharides
Fig.
3.23(TE Art)
H
3-carbon C
1
sugar
5-carbon sugars
O
5 CH2OH
H C OH
2
H C OH
3
H
Glyceraldehyde
6-carbon sugars
6 CH2OH
O H
H5 H
4 OH H 1
OH
HO3
2
H
OH
Glucose
5 CH2OH
O
OH
1
4 H
H H
H
3
2
OH OH
Ribose
O
OH
1
H
H
2
OH H
Deoxyribose
4
H
H3
6 CH2OH
5
OH
OH
1
4 H
OH H
H
H
2
3
H OH
Galactose
6 CH2OH
O
H
5
H HO 2
CH2OH
HO
3 1
4
OH H
Fructose
Biological Molecules: Carbohydrates
2. Disaccharides
• transport of sugars and short-term energy storage
• two monosaccharides joined together
Fig. 3.27
CH2OH
O
H H
H
OH H
HO
OH
H
OH
Glucose
CH2OH
O
HO
H
H
HO
CH2OH
OH H
Fructose
CH2OH
O
H
H
H
OH H
HO
OH
CH2OH
O
H H
H
H
OH
OH
HO
H
OH
Glucose
H
OH
Glucose
H2O
H2O
CH2OH
CH2OH
O
O
H H
H
H
OH H
H
HO
O
HO
CH2OH
H
OH
OH
Sucrose
H
CH2OH
CH2OH
O
O
H H H
H H
H
H
OH
H
OH
O
HO
OH
H
OH
H
OH
Maltose
Dehydration Synthesis
37
Biological Molecules: Carbohydrates
3. Polysaccharides
OH
CH 2O
O
OH
CH2OH
O
O
OH
OH O
CH
2O
O H
a) Longer term energy storage:
OH
2
CH O O
OH
CH
2 OH
O
CH
2O
O H
OH O
i) Plant Starch (Amylose):
• in seeds and roots
• Forms spiral of 1,000’s of glucose molecules
ii) Glycogen
• energy storage in animals
• stored in liver and muscles
• branched amylose chains
OH O
b) Structural polysaccharides:
i) Cellulose: Plant cell walls
ii) Chitin: Fungal cell walls, insect exoskeletons
Biological Molecules: Carbohydrates
Fig. 3.28
3. Polysaccharides
CH2OH
O H
H
1
4
OH H
OH
HO
H
OH
H
CH2OH
CH2OH
CH2OH
CH2OH
O H H
O H H
O H H
O H
H H
H
H
14 H
OH H O OH H O OH H O OH H
% form of glucose
H
OH
H
OH
H
H
OH
Starch
OH
Starch: chain of %-glucose subunits
Cellulose
O
Plant
cell wall
CH2OH
O OH
H
H
4 OH H 1
HO
H
H OH
& form of glucose
OH H O
H
OH O
CH2OH
H
O
OH
H
O
CH2OH
HH H
H H H CH2OH
O
H
OH H O
H
O
OH
O
OH H 14
H
H
CH
OH
2
H OH
H
Cellulose: chain of &- glucose subunits
38
Biological Molecules: Carbohydrates
3. Polysaccharides
Chitin:
Like cellulose, but with nitrogen
group
! Structural building material of
arthropods and fungi
O
O
N H
O C
CH3
CH2OH
CH3
O C
N H
CH2OH
O O
N H
O C
CH3
O O
CH2OH
O O
CH3
O C
N H
CH2OH
CH2OH
O O
N H
O C
CH3
Biological Molecules: Lipids
B. Lipids
•
Large non-polar regions: mostly C & H
•
insoluble in water: hydrophobic
Functions:
1) Oils, fats: Energy storage
2) Phospholipids: membranes
3) Waxes: waterproofing
4) Steroids: membranes & hormones
39
Biological Molecules: Lipids
1) Oils & Fats
• Contain:
only C, H, O
• function:
energy storage (stored chemical bonds)
• formed via dehydration synthesis
glycerol + 3 fatty acids
H2 O
=
triglycerol
triglycerol
+
water
Biological Molecules: Lipids
1) Oils & Fats
Fatty Acid !
Hydrocarbon chain
Carboxyl
Group
40
Biological Molecules: Lipids
1) Oils & Fats
Components: Fatty Acids
a) Saturated: No C=C double bonds (solid at RT)
Fig. 3.22
Biological Molecules: Lipids
1) Oils & Fats
Components: Fatty Acids
b) Unsaturated: One or more C=C double bonds (liquid at RT)
Fig. 3.22
41
Biological Molecules: Lipids
1) Oils & Fats
Beef Fat
Linseed oil
Olive Oil
Butter: Saturated or Unsaturated?
2) Phospholipids
Biological Molecules: Lipids
• Forms core of cell membranes
• 1 glycerol, 2 Fatty acids, & 1 polar group (Phosphate)
Hydrophilic
Polar Head
Hydrophobic
Nonpolar Tails
42
Hydrophillic and Hydrophobic nature of cell membranes
Watery environment: Polar
Hydrophilic heads
(polar)
Hydrophobic tails
(non-polar)
Hydrophilic heads
(polar)
Watery environment: Polar
Biological Molecules: Lipids
3) Waxes
•
Similar to fats: highly saturated
•
solid at room temperature
•
waterproof coatings
on plants
on fur and exoskeletons
beehives
43
Biological Molecules: Lipids
4) Steroids: ring structures
Estradiol
a) Steroid
Hormones
b) Steroid
Cholesterol
Testosterone
– Essential
substance in
membranes
Cholesterol
Chapter 3: Biological Molecules
I. Carbon and Organic Molecules
II. Synthesis of Organic Molecules
III. Biological Macromolecules
A.
B.
C.
D.
Carbohydrates
Lipids
Proteins
Nucleic Acids
44
Biological Molecules: Proteins
C. Proteins
•
•
Polymers of amino
acids
Roles in cell
1. Support
EX:
– Hair, nails
– Muscles
2. Motion
– Antibodies
3. Defense
– Egg white
4. Storage
5. Regulation
6. Enzyme catalysis
7. Transport
– Hormones
– Enzymes
– Hemoglobin
Biological Molecules: Proteins
Amino Acids: 20 kinds
Carboxylic Acid
Amino
Group
R
• Different sequence of amino
acids makes different proteins
“R” Group
• R- groups influence “behavior”
45
Biological Molecules: Proteins
Amino Acid Structure
Nonpolar
Fig. 3.6
Biological Molecules: Proteins
Amino Acid Structure
Polar Uncharged
Fig. 3.6
46
Biological Molecules: Proteins
Amino Acid Structure
Charged
Fig. 3.6
Biological Molecules: Proteins
Amino Acid Structure
Aromatic
Fig. 3.6
47
Biological Molecules: Proteins
Special Function Amino Acids
CH3
S
CH2 CH
NH+2
Proline
(Pro)
SH
CH2
CH2 CH2
C O
O
CH2
CH2
–
H3 N +
C C O– H3N
+
C C O–
H O
H O
Methionine
(Met)
Cysteine
(Cys)
Fig. 3.6
Biological Molecules: Proteins
Amino Acids: 20 kinds
• Joined by dehydration synthesis ! Proteins
• Proteins have peptide bonds between Amino Acids
• Polar bonds!
Fig. 3.5
48
Biological Molecules: Proteins
Protein Structure: Shape dictates function
Primary Protein Structure
1
R
H H O
R
R
H H O
H H
C C N C C N C C N C C N C C N C
H O
H H O
H H O
R
R
R
• Polypeptide bonds (Covalent Bonds!) between amino acids
• Primary Protein Structure dictates all subsequent Structure!
Fig. 3.8
Biological Molecules: Proteins
Protein Structure
Fig. 3.8
Secondary Protein Structure
Tensile strength e.g. silk
Flexible e.g. wool
• Hydrogen Bonding!
49
Biological Molecules: Proteins
Protein Structure
Tertiary Structure
All proteins show
at least this much
structure!
Fig. 3.8
• Positioning of the various motifs
• Nonpolar side groups are folded into the interior
(hydrophobic exclusion)
• Further locked in place by both Ionic bonds and
Dissulfide bonds (covalent bonds)
Biological Molecules: Proteins
Protein Structure
Bonds Stabilize Protein Structure
Cysteine
1. Hydrogen Bond
2. Disulfide bridge
3. Ionic bond
4. Van der Waals attraction
5. Hydrophobic Exclusion
Fig. 3.7
50
Biological Molecules: Proteins
Protein Structure
Tertiary Structure: Domains
Fig. 3.8
• Structural regions (exons) within a larger protein
• Each domain folds into a structurally independent
functional unit
• Modular units of 100 to 250+ amino acids
Biological Molecules: Proteins
Protein Structure
Quaternary Protein Structure
Fig. 3.8
51
Biological Molecules: Proteins
Denaturation is a Change in Protein Structure
Folded
protein
Denaturation does not
impact primary
structure, but can
disrupt all subsequent
levels of structure
Denaturation
Denatured
protein
Fig. 3.10
Biological Molecules: Proteins
Protein folding is critical to protein function
• Proteins can be denatured when the pH, temperature,
or ionic concentration of the surrounding solution is
changed
52
Biological Molecules: Proteins
Protein Folding
! Directed by chaperone proteins?
Read pg. 46
Biological Molecules: Proteins
Defective protein folding is an important mechanism
underlying the pathogenesis of many diseases.
53
Biological Molecules: Proteins
Normal Protein Folding is Critical to Function
Prion (Bad) PrPSc
30% %-helix
43% &-sheet
Normal (Good) PrPC
43% %-helix
Biological Molecules: Nucleic Acids
D. Nucleic Acids
1) Polymers of nucleotide subunits (EX: DNA & RNA)
3-part
nucleotide
structure
NH2
OH
HO
P
O
2. Phosphate Group
O
N C C N
CH2
O
HC
Deoxyribose
N C N CH
H
H
or
H
H
3. Nitrogenous
Ribose
Base (varies)
OH
H
1. Pentose Sugar
Deoxyribose nucleotides !
DNA: molecule of heredity
Ribose nucleotides
RNA: carries code—directs
protein synthesis
!
54
Biological Molecules: Nucleic Acids
A Nucleotide is a
monomer of a nucleic
acid
Nitrogenous base
NH2
N
N
Phosphate group
N
O
O
–
N
P O CH2
O–
O
OH in RNA
OH
R
Sugar
H in DNA
Biological Molecules: Nucleic Acids
Nitrogen Bases of Nucleic Acids
55
Biological Molecules: Nucleic Acids
Nucleic Acid Structure
Nucleotides are
linked through
dehydration
synthesis
reactions and the
formation of
Phosphodiester
Bonds
Biological Molecules: Nucleic Acids
Fig. 3.16(TE
Art)
DNA
Structure
Double Helix
Sugar-phosphate
"backbone"
P
C
P
G
P
P
A
T
C
P
Hydrogen bonds
P
C
G
Paired Nitrogen
P
Bases
O
P
G
T
A
P
P
Nucleotide
OH
3’ end
5’ end
56
Biological Molecules: Nucleic Acids
Fig.
3.17b(TE
Art)
RNA
Structure
P
P
P
P
C
A
Ribose (sugar)
G
Phosphate
P
U
A
Nitrogenous
Bases
U
P
RNA vs. DNA
P
1. Ribose versus Deoxyribose
Sugar
2. Uracil instead of Thymine
G
3. Mostly single stranded
Biological Molecules: Nucleic Acids
D. Nucleic Acids
2) Single nucleotide subunits
Cyclic AMP:
(Cyclic Adenosine Monophosphate)
Intracellular communication
“Messenger”
ATP:
(Adenosine Triphosphate)
Energy transfer
57