Download The Chemical Context of Life

LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 2
The Chemical Context of Life
Lectures by
Erin Barley
Kathleen Fitzpatrick
1
© 2011 Pearson Education, Inc.
Overview: A Chemical Connection to Biology
• Biology is a multidisciplinary science
• Living organisms are subject to basic laws of
physics and chemistry
• One example is the use of formic acid by ants to
maintain “devil’s gardens,” stands of Duroia trees
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 2.1
EXPERIMENT
Cedrela
sapling
Insect
barrier
Duroia
tree
Inside,
unprotected
Devil’s
garden
Outside,
protected
Inside,
protected
Outside,
unprotected
RESULTS
Dead leaf tissue (cm2)
after one day
Figure 2.2
16
12
8
4
0
Outside,
Inside,
Inside,
Outside,
unprotected protected unprotected protected
Cedrela saplings, inside and outside devil’s gardens
Concept 2.1: Matter consists of chemical elements in
pure form and in combinations called compounds
• Organisms are composed of matter 物質
• Matter is anything that takes up space and
has mass*
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Elements and Compounds
• Matter is made up of elements
• An element 元素 is a substance that
cannot be broken down to other
substances by chemical reactions
• A compound 化合物 is a substance
consisting of two or more elements in a
fixed ratio
• A compound has characteristics different
from those of its elements
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-3 The emergent properties of a compound.
Sodium
Chlorine
Sodium
chloride
The Elements of Life
• About 25 of the 92 elements are essential to life
• Carbon, hydrogen, oxygen, and nitrogen make up
96% of living matter
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
• Trace elements are those required by an organism in
minute quantities ex. Fe, I ect.
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Table 2.1
Fig. 2-4
(a) Nitrogen deficiency
The effect of nitrogen deficiency in
corn. In the controlled experiment,
the taller plants on the left are
growing in nitrogen-rich soil, and
the shorter plants on the right in
nitrogen-poor soil.
(b) Iodine deficiency
Goiter is an enlargement of the
thyroid gland, resulting from a
deficiency of the trace element
iodine. It can probably be
reversed by iodine supplements.
Case Study: Evolution of Tolerance to Toxic
Elements
• Some elements can be toxic, for example,
arsenic (As 砷)
• Some species can become adapted to
environments containing toxic elements
– For example, some plant communities are
adapted to serpentine , which contains
chromium (Cr), nickel (Ni), and cobalt (Co)
© 2011 Pearson Education, Inc.
Figure 2.4
Concept 2.2: An element’s properties
depend on the structure of its atoms
• Each element consists of unique atoms 原子
• An atom is the smallest unit of matter that still
retains the properties of an element
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Subatomic Particles
• Atoms are composed of subatomic particles
• Relevant subatomic particles include:
– Neutrons 中子 (no electrical charge)
– Protons 質子 (positive charge)
– Electrons 電子 (negative charge)
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• Neutrons and protons form the atomic
nucleus 原子核
• Electrons form a cloud around the nucleus
• Neutron mass and proton mass are almost
identical and are measured in daltons
(1.7 X 10-24 gram)
© 2011 Pearson Education, Inc.
Fig. 2-5
Cloud of negative
charge (2 electrons)
(a)
Nucleus
Electrons
(b)
Simplified models of a helium (He) atom.
The helium nucleus consists of 2 neutrons (brown) and 2
protons (pink). Two electrons (yellow) exist outside the nucleus.
Atomic Number and Atomic Mass
• Atoms of the various elements differ in number
of subatomic particles
• An element’s atomic number 原子序 is the
number of protons in its nucleus (ex. 2He)
• An element’s mass number 質量數 is the sum
of protons + neutrons in the nucleus
(ex. 24He or 1123Na)
• Atomic mass 原子量, the atom’s total mass,
can be approximated by the mass number
(ex. Na is 23 daltons (22.9898 daltons precisely))
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Isotopes
• All atoms of an element have the same number
of protons but may differ in number of neutrons
• Isotopes are two atoms of an element that
differ in number of neutrons
C isotopes
All 3 have 6 protons
- 612C, 98.93%
Stable isotopes
- 613C, 1.07%
- 614C, even rare
Radioactive isotopes
(unstable isotopes)
Atomic mass of C is 12.0107
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Two isotopes of sodium.
• Radioactive isotopes decay spontaneously,
giving off particles and energy.
– Number of protons changes, and transforms to a
different element. Ex. Radioactive carbon →
nitrogen.
• Some applications of radioactive isotopes in
biological research are:
– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Figure 2.6a
10°C 15°C 20°C
TECHNIQUE
Compounds including 35°C Incubators
radioactive tracer 45°C
(bright blue)
20°C
10°C
15°C
50°C
Human cells
1 Human cells
are incubated
with compounds used to make
DNA. One compound is labeled
with 3H.
2 Cells from each
incubator are
placed in tubes;
their DNA is
isolated; and
unused labeled
compounds are
removed.
25°C
30°C
35°C
40°C
45°C
50°C
10° 15° 20° 25° 30° 35° 40° 45° 50°
DNA (old and new)
Figure 2.6b
TECHNIQUE
3 The test tubes are placed in a scintillation counter.
Figure 2.6c
Counts per minute
( 1,000)
RESULTS
30
20
Optimum
temperature
for DNA
synthesis
10
0
10
20 30 40 50
Temperature (°C)
Figure 2.7
A PET scan, a medical use for radioactive
isotopes.
PET, an acronym for positron-emission tomography, detects
locations of intense chemical activity in the body. The bright
yellow spot marks an elevated level of radioactively labelled
glucose, which in turn indicated high metabolic activity, a
hallmark of cancerous tissue.
Cancerous
throat
tissue
核子試爆給的
生物線索
對瑞典斯德哥爾摩諾貝爾醫學研究所的弗瑞森（Jonas Frisen）來說，挫折是發明之母
。弗瑞森是一名神經科學家，專門研究腦組織的再生，他想知道人體各器官組織的年
齡，卻苦無方法。如果能為人體組織定年的話，他就能夠確定人類腦組織是否會部份
、或甚至完全再生，以及會多常再生。他說：「這個問題困擾著我。」一般用來標記
細胞然後觀察它們在動物體內生命週期的技術，由於使用到有毒化學藥劑，因此不適
用於人類，使得人類組織再生的問題，一直懸而未解。
然後弗瑞森得知1955年後出生的人，體內都帶有天然標記。自1955年到1963年制訂「
核子武器部份限定條約」為止，許多在地面上進行的核子武器試爆，釋放出大量的碳
14（14C）同位素到大氣中，這些14C很快飄浮擴散到全球，然後植物細胞攝取了14C
，動物吃植物，而以動、植物為食的人類，細胞也吸收了同位素，弗瑞森現在可以追
查這些14C的蹤跡。
透過測量DNA分子的14C含量，然後比對大氣層中14C含量，弗瑞森終於建立了一套能
夠回答細胞年齡疑問的試驗，2004年他將結果發表在《細胞》上，他發現人體中許多
部位都比整個身體年輕許多：30多歲的受試者，消化道組織的空腸細胞還不到16歲；
快40歲的受試者，其骨骼肌只有15歲。
地表上的核彈試爆導致大氣層
中14C激增900％，在人類組織
內留下了可以用來定年的微量
標記。
然而最讓科學家驚訝的是腦組織。弗瑞森檢查了小腦和大腦枕葉皮質的細胞，這兩個
組織的神經元，年紀都吻合或接近受試者的實際年齡，顯示這些部位在受試者出生時
就形成了，而通常不會進行更替。
這項發現是不是表示腦組織再生療法沒有希望，弗瑞森認為現在還言之過早。他承認
：「我不會這麼說，只是機會比有旺盛的再生現象小一點。」他迫不及待想繼續這項
研究，舉例來說，看看中風患者腦組織的神經元受損後能否再生，他也計畫研究心肌
和胰臟內製造胰島素的β細胞，這兩種組織的再生能力，一直引發激烈的爭議，也是
再生療法最感興趣的部位。弗瑞森希望其他研究人員也能利用這種技術，來研究他們
最感興趣的器官。
原子彈試爆時代殘留的14C在1965年後就快速減少，每11年減少一半，根據布赫茲的說
法，1990年後人類細胞殘留的同位素信號就很微弱。弗瑞森說，科學家可以為那段時
期儲存的組織樣本約略定年。現在布赫茲也將這種方法應用在法醫研究上。自己也出
生在該時期的布赫茲說：「嬰兒潮世代是個相當龐大的族群，這個技術肯定對我後半
期研究事業助益匪淺。」
【本文轉載自科學人2006年1月號】
The Energy Levels of Electrons
• During a chemical reaction, their nuclei do no
interact, but only electron involved.
• Energy 能量 is the capacity to cause change
• Potential energy 位能 is the energy that
matter has because of its location or structure
• The electrons of an atom differ in their amounts
of potential energy
• An electron’s state of potential energy is called
its energy level, or electron shell 電子層
Fig. 2-8
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons
Third shell (highest energy
level)
Second shell (higher
energy level)
First shell (lowest energy
level)
(b)
Atomic
nucleus
Energy
absorbed
Energy
lost
Electron Distribution and Chemical Properties
• The chemical behavior of an atom is
determined by the distribution of electrons in
electron shells
• The periodic table of the elements shows the
electron distribution for each element
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Fig. 2-9 Electron-distribution diagrams for the first 18 elements
in the periodic table.
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electrondistribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium Magnesium Aluminum
12Mg
11Na
13Al
Third
shell
• Valence electrons 價電子 are those in the
outermost shell, or valence shell 價層
• The chemical behavior of an atom is mostly
determined by the valence electrons
• Elements with a full valence shell are
chemically inert (chemical unreactive); ex. He,
Ne, Ar, etc.
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Electron Orbitals
• An orbital 軌域 is the three-dimensional space
where an electron is found 90% of the time
• Each electron shell consists of a specific number
of orbitals
© 2011 Pearson Education, Inc.
Figure 2.10
First shell
Neon, with two filled
Shells (10 electrons)
Second shell
(a) Electron distribution diagram
First shell
Second shell
y
x
1s orbital
2s orbital
z
Three 2p orbitals
(b) Separate electron orbitals
1s, 2s, and
2p orbitals
(c) Superimposed electron orbitals
Concept 2.3: The formation and function of
molecules depend on chemical bonding between
atoms
• Atoms with incomplete valence shells can
share or transfer valence electrons with
certain other atoms
• These interactions usually result in atoms
staying close together, held by attractions
called chemical bonds 化學鍵
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Covalent Bonds
• A covalent bond 共價鍵 is the sharing of a
pair of valence electrons by two atoms
• In a covalent bond, the shared electrons count
as part of each atom’s valence shell
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Fig. 2-11
Hydrogen
atoms (2 H)
Hydrogen
molecule (H2)
• A molecule consists of two or more atoms held
together by covalent bonds
• A single covalent bond, or single bond, is the
sharing of one pair of valence electrons
For example H:H (H–H)
• A double covalent bond, or double bond, is
the sharing of two pairs of valence electrons
For example O::O (O=O)
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• The notation used to represent atoms and
bonding is called a structural formula 結
構式
– For example, H–H
• This can be abbreviated further with a
molecular formula 分子式
– For example, H2
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Fig. 2-12
Name and
Molecular
Formula
Two hydrogen atoms
can form a single
bone.
Two oxygen atoms
share two pairs of
electrons to form a
double bond.
Two hydrogen atoms
and one oxygen atom
are joined by covalent
bonds to produce a
molecule of water.
Four hydrogen atoms
can satisfy the
valence of one
carbon atom, forming
methane.
ElectronLewis Dot
Spacedistribution Structure and filling
Model
Diagram
Structural
Formula
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
(d) Methane (CH4)
Animation: Covalent Bonds
• Covalent bonds can form between atoms of the
same element or atoms of different elements
• A compound is a combination of two or more
different elements
• Bonding capacity is called the atom’s valence
價數
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• Electronegativity 陰電性 is an atom’s
attraction for the electrons in a covalent bond
• The more electronegative an atom, the more
strongly it pulls shared electrons toward itself
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• In a nonpolar covalent bond 非極性共價
鍵, the atoms share the electron equally,
ex. H2, O2, CH4.
• In a polar covalent bond 極性共價鍵, one
atom is more electronegative, and the
atoms do not share the electron equally,
ex. H2O
• Unequal sharing of electrons causes a
partial positive or negative charge for each
atom or molecule
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Fig. 2-13
Because O is more electronegative than
H, shared electrons are pulled more
toward O.
–
This results in a partial
negative charge on the
oxygen and a partial
positive charge on the
hydrogen.
O
+
H
H
H2O
+
Ionic Bonds
• Atoms sometimes strip electrons from their
bonding partners
• An example is the transfer of an electron
from sodium to chlorine
• After the transfer of an electron, both
atoms have charges
• A charged atom (or molecule) is called an
ion離子
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Fig. 2-14 Electron transfer and ionic bonding
The lone valence electron
of a sodium atom is
transferred to join the 7
valence electrons of a
chlorine atom.
Each resulting ion has a
completed valence shell.
An ionic bond can form
between the oppositely
charged ions.
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
• A cation 陽離子 is a positively charged ion
• An anion 陰離子 is a negatively charged ion
• An ionic bond 離子鍵 is an attraction between
an anion and a cation
Animation: Ionic Bonds
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• Compounds formed by ionic bonds are called
ionic compounds, or salts
• Salts, such as sodium chloride (table salt), are
often found in nature as crystals
Na+
Cl–
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Weak Chemical Bonds
• Most of the strongest bonds in organisms
are covalent bonds that form a cell’s
molecules
• Weak chemical bonds, such as ionic
bonds and hydrogen bonds, are also
important
• Weak chemical bonds reinforce shapes of
large molecules and help molecules
adhere to each other
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Hydrogen Bonds
• A hydrogen bond forms when a
hydrogen atom covalently bonded to
one electronegative atom is also
attracted to another electronegative
atom
• In living cells, the electronegative
partners are usually oxygen or nitrogen
atoms
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Fig. 2-16

+
Water (H2O)
+
Hydrogen bond

Ammonia (NH3)
+
+
+
Van der Waals Interactions
• If electrons are distributed asymmetrically in
molecules or atoms, they can result in “hot
spots” of positive or negative charge
• Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges
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Figure 2.UN01
• Collectively, such interactions
can be strong, as between
molecules of a gecko’s toe
hairs and a wall surface
Molecular Shape and Function
• A molecule’s shape is usually very important to
its function
• A molecule’s shape is determined by the
positions of its atoms’ valence orbitals
• In a covalent bond, the s and p orbitals may
hybridize, creating specific molecular shapes
© 2011 Pearson Education, Inc.
Figure 2.17
s orbital
Four hybrid orbitals
z
Three p orbitals
x
y
Tetrahedron
(a) Hybridization of orbitals
Space-Filling
Model
Ball-and-Stick
Model
Hybrid-Orbital Model
(with ball-and-stick
model superimposed)
Unbonded
Electron
pair
104.5o
Water (H2O)
Methane (CH4)
(b) Molecular-shape models
• Biological molecules recognize and interact with
each other with a specificity based on molecular
shape
• Molecules with similar shapes can have similar
biological effects
© 2011 Pearson Education, Inc.
Figure 2.18
A molecular mimic
Carbon
Hydrogen
Natural endorphin
Nitrogen
Sulfur
Oxygen
Morphine
Morphine affects pain perception
and emotional state by mimicking
the brain’s natural endorphins 腦內啡
(a) Structures of endorphin and morphine
Natural
endorphin
Brain cell
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors
Concept 2.4: Chemical reactions make and break
chemical bonds
• Chemical reactions are the making and
breaking of chemical bonds
• The starting molecules of a chemical
reaction are called reactants
• The final molecules of a chemical reaction
are called products
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Fig. 2-UN2
2 H2
O2
Reactants
2 H2 O
Reaction
Products
• Photosynthesis is an important chemical
reaction
• Sunlight powers the conversion of carbon
dioxide and water to glucose and oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2
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Fig. 2-19
• Some chemical reactions go to completion:
all reactants are converted to products
• All chemical reactions are reversible:
products of the forward reaction become
reactants for the reverse reaction
• Chemical equilibrium is reached when the
forward and reverse reaction rates are equal
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
You should now be able to:
1. Identify the four major elements
2. Distinguish between the following pairs of
terms: neutron and proton, atomic number
and mass number, atomic weight and
mass number
3. Distinguish between and discuss the
biological importance of the following:
nonpolar covalent bonds, polar covalent
bonds, ionic bonds, hydrogen bonds, and
van der Waals interactions
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings