Cơ sở hóa học

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CƠ SỞ HÓA HỌC CỦA SỰ SỐNG
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NỘI DUNG BÀI GIẢNG
Vật chất, nguyên tố và nguyên tử
Cấu trúc nguyên tử
Liên kết hóa học
Tính chất hóa học của nước
Axít, Bazơ và pH
Cấu trúc và chức năng phân tử lớn
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VẬT CHẤT
Vật chất là bất cứ vật gì có khối lượng và thể tích
Hữu hình (Tangible)
Có thể tồn tại dưới nhiều dạng
Rắn (Solid)
Lỏng (Liquid)
Khí (Gas)
Plasma
Bao gồm nhiều
nguyên tố
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NGUYÊN TỐ
Một nguyên tố không thể phân chia thành các chất đơn giản bằng các phản ứng hóa học bình thường
Có khoảng 100 nguyên tố khác nhau
Mỗi nguyên tố có một ký hiệu nhất định
Ví dụ: Carbon (C), hydrogen (H), v.v.
Nước (H2O), glucose, v.v không phải là nguyên tố.
Chlorine (Cl)
Sodium Chloride (NaCl)
Sodium (Na)
X
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ELEMENTS
Có khoảng 25 nguyên tố cần thiết cho sự sống
Gần 96% khối lượng vật chất sống là từ 4 nguyên tố cơ bản
Carbon (C)
Hydrogen (H)
Nitrogen (N)
Oxygen (O)
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nguyên tử
An atom is the smallest unit into which an element can be subdivided while retaining its properties
Comprised of smaller “subatomic” particles
Protons + charge mass ≈ 1 amu
Neutrons no charge mass ≈ 1 amu
Electrons - charge mass <<< 1 amu


(1 atomic mass unit (amu) ≈ 1 Dalton ≈ 1.7 * 10-24 g)
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ATOMIC STRUCTURE
Protons and neutrons form an atom’s nucleus
Electrons are present outside of the nucleus
Helium (He) atom
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ATOMIC NUMBER
Atoms of different elements possess different numbers of protons
The number of protons in an atom is termed its atomic number
This number defines the element
1
2
3
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ATOMIC MASS
Protons and neutrons have significant mass
The number of protons plus neutrons in an atom is termed its atomic mass
Electrons have negligible mass
This number is slightly variable for many elements
H
He
Li
1
1
2
4
7
3
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ISOTOPES
Isotopes are atoms of the same element possessing different atomic masses
Due to different numbers of neutrons
Identical chemical behavior
H
1
1
1
2
3
1
H
H
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ISOTOPES
Some isotopes are stable
e.g., 1H, 2H, 12C, 13C, etc.
Some isotopes are unstable
e.g., 3H, 14C, 32P, 35S, etc.
“Radioactive”
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ISOTOPES
Radioactive isotopes
Decay at a constant rate into
more stable forms
May decay into another element
e.g., 14C  N
Various uses
Important research tools
Monitor biological processes
Diagnostic tools in medicine
Determine age of fossils
Sometimes produce superheroes
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ISOTOPES
Each radioactive isotope has a fixed rate of decay
Unaffected by temperature, pressure etc.
The time required for half of a sample to decay is termed the radioisotope’s half-life
e.g., Half-life of 14C is ~5,730 years
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ISOTOPES
Fossils contain isotopes of elements that accumulated while they were alive
Accumulation stops upon
death
Death tends to reduce
one’s appetite
Accumulated isotopes
slowly decay into more
stable isotopes
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ISOTOPES
Ages of fossils can be determined using radiometric dating
Compares accumulating “daughter” isotope to remaining “parent” isotope
e.g., Carbon dating is useful for dating fossils up to 75,000 years old
13 half-lives
Radioisotopes with
longer half-lives can
be used to date older
fossils
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ELECTRON SHELLS
Electrons vary in the amount of energy they possess
Each electron exists within a discrete energy level
These energy levels are
represented by electron
shells
Most atoms possess
multiple electron shells
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ELECTRON SHELLS
Electrons exist within electron shells
The first shell must be completely filled before electrons are placed in the second shell, etc.
The first shell can hold 2 electrons
The next few electrons can each hold 8 electrons
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CHEMICAL BONDS
Atoms are most stable when their outermost electron shell is completely full
Making and breaking chemical bonds involves the exchange or rearrangement of electrons
Atoms will tend to react such that their outermost electron shell becomes completely full
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CHEMICAL BONDS
How would you expect F and Cl to react?
Li and Na?
He, Ne, and Ar?
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IONS
A sodium atom possesses a single electron in its outermost electron shell
Tends to lose this electron
Loss of the electron
produces a sodium ion
A charged form of a
sodium atom
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IONS
A chlorine atom possesses seven electrons in its outermost electron shell
Tends to gain a single electron
Gain of this electron produces a chloride ion
A charged form of
a chlorine atom
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IONIC BONDS
The attraction between oppositely charged ions is termed an ionic bond
Compounds formed by ionic bonds are called “ionic compounds” or “salts”
Indefinite size and number of ions
Ions present in a fixed ratio
e.g., 1:1 ratio in NaCl
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COVALENT BONDS
Electrons are not always gained or lost
Molecules can be formed when electrons are shared
Sharing is always in pair(s) of electrons
Shared electrons contribute to electron shells of both atoms
This sharing of electrons is termed a covalent bond
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COVALENT BONDS
The sharing of a pair of electrons forms a covalent bond
A double covalent bond involves the sharing of two pairs of electrons
A triple covalent bond
involves the sharing of
three pairs of electrons
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COVALENT BONDS
Electron sharing can be equal or unequal
Equal sharing results in no separation of charges
Nonpolar covalent bonds
Methane
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COVALENT BONDS
Electron sharing can be equal or unequal
Unequal sharing results in a separation of charges
Polar covalent bonds
Electronegative atoms such as oxygen and nitrogen tend to attract electrons
more strongly than
carbon or hydrogen
They thereby possess
partial negative charges
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COVALENT BONDS
Water is a polar molecule
The hydrogen atoms possess partial positive charges
The oxygen atom possesses a partial negative charge
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HYDROGEN BONDS
Attraction between a hydrogen atom bearing a partial positive charge and another atom bearing a partial negative charge
Much weaker than covalent or ionic bonds
~1/20 as strong
Many weak bonds can add
up to a significant force
Transient
Constantly breaking and
reforming
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CHEMISTRY OF WATER
Water is a critically important molecule
Most of the Earth’s surface is submerged in water
Life on Earth began
in water
Life evolved in water
for 3 billion years
before spreading onto
land
The abundance of
water is a major
reason why the Earth
is habitable
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CHEMISTRY OF WATER
Water is the most prevalent molecule within living organisms
Cells are about 70 – 95% water
Most cells are themselves surrounded by water
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CHEMISTRY OF WATER
Water molecules possess polar covalent bonds
Able to participate in H-bonds
Water molecules
interact with each other
Water is held together
by these H-bonds
Cohesion
Water attaches to other
ions and molecules
Adhesion
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CHEMISTRY OF WATER
Cohesion and adhesion allow transport of water against gravity
Fluid movement into capillary tubes or xylem vessels
“Capillary action”
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CHEMISTRY OF WATER
Surface tension results from cohesion
Difficult to break the surface of water
e.g., Water strider, skipping rocks, etc.
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WATER AS A SOLVENT
Water is a powerful and versatile solvent
A wide variety of molecules and ions dissolve in water
e.g., Sugars, salts, some proteins, etc.
Interacts well with polar or charged molecules and ions
Most chemical reactions within organisms occur in a water medium
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WATER AS A SOLVENT
Polar or charged molecules and ions are hydrophilic
Interact favorably with water
Hydration shells surround ions from salts
Similar structures surround polar molecules
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WATER AS A SOLVENT
Many molecules and ions dissolve in water
A solution is formed
Water is the solvent
The salt, sugar, dye, etc. is the solute
A solution in which water is the
solvent is termed an aqueous solution
Chicago River before St. Patrick`s Day
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WATER AS A SOLVENT
Not all hydrophilic molecules dissolve in water
Typical of very large hydrophilic molecules
e.g., Cotton consists of very large molecules of cellulose
A towel dries your body, but does not dissolve in the water
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DISSOCIATION OF WATER
Most water molecules exist as H2O (H-O-H)
A small fraction of water molecules exist in a dissociated state
~1 in 554 million molecules in pure water
A hydrogen atom shifts from one water molecule to another
H-O-H  H+ & OH- (hydrogen ion & hydroxide ion)
2H2O  H3O+ & OH- (hydronium ion & hydroxide ion)
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DISSOCIATION OF WATER
H+ and OH- are formed when H2O dissociates
Very reactive
Equal concentrations in pure water
10-7 mol/L
Concentrations are not always equal
Can be altered by the addition of acids or bases
As [H+] ↑, [OH-] ↓, and vice versa
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ACIDS, BASES, AND pH
An acid is a substance that increases the H+ concentration of a solution
Generally donates additional H+
e.g., HCl  H+ & Cl-
A base is a substance that decreases the H+ concentration of a solution
Either absorbs H+ or donates OH-
e.g., NH3+ & H+  NH4
e.g., NaOH  Na+ & OH-
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ACIDS, BASES, AND pH
pH is a quantitative measure of [H+]
Pure water is pH 7
(neutral)
Equal concentrations of
H+ and OH-
Acidic solution contain
more H+ than OH-
pH < 7
Basic solutions contain
more OH- than H+
pH > 7
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ACIDS, BASES, AND pH
pH is a quantitative measure of [H+]
Ranges from 0 (most
acidic) to 14 (most basic)
Each pH unit represents
a tenfold change in the
concentration of H+
e.g., pH 4 has 100 times
more H+ than pH 6
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ACIDS, BASES, AND pH
The interior pH of most cells is close to 7
Even slight changes in pH can be harmful to cells and organisms
Chemical processes of the cell are very sensitive to concentrations of H+ and OH-
The shapes of biological molecules can be altered by changes in H+ and OH- concentrations
e.g., Enzymes, etc.
Altered shape can reduce function
Biological fluids contain buffers
Substances or systems that minimize changes in pH by accepting or donating H+
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ACID PRECIPITATION
Acid precipitation represents a serious assault on water quality
Uncontaminated rain has a pH of about 5.6
Slightly acidic due to carbonic acid formed from dissolved CO2
CO2 & H2O  H2CO3  H+ & HCO3-
Acid precipitation is more acidic than this
pH 4.3 rain has been measured in the U.S.
20 times more acidic than normal rain
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ACID PRECIPITATION
Acid precipitation
Caused primarily by the presence in the atmosphere of sulfur oxides and nitrogen oxides
React with water to form strong acids
Fall to earth with rain or snow
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ACID PRECIPITATION
Acid precipitation
The burning of fossil fuels in factories and automobiles is a major source of acid precipitation
Electrical power plants burning coal produce more of these pollutants than any other source
Winds carry these pollutants away
Acid rain may fall far from industrial
centers
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ACID PRECIPITATION
Acid precipitation
Can damage life in lakes and streams
Can remove mineral ions from soil
e.g., Calcium and magnesium ions
Essential nutrients
Ordinarily help to buffer soil
Can increase the
solubility of certain ions
e.g., Aluminum can
reach toxic concentrations
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REFERENCES
Campbell, Neil A. and Reese, Jane B. Biology, 7th edition. Pearson Education, Inc. 2005.
Campbell, Neil A., Reese, Jane B., Taylor, Martha R., and Simon, Eric J. Biology, Concepts and Connections, 5th edition. Pearson Education, Inc. 2006.
Nester, Eugene W., Anderson, Denise G., Roberts, C. Evans Jr., and Nester, Martha T. Microbiology, A Human Perspective, 5th edition. McGraw-Hill Companies, Inc. 2007.
Limson, Janice. 2002. http://www.scienceinafrica.co.za/2002/june/lactose.htm