Transcript Basic_Chemistry___Biochemistry__Ch_2__S2

Basic Chemistry & Biochemistry
Chapter 2
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Outline
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Basic Chemistry
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Chemical Bonds
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Elements
Atoms
Ions, Molecules & Compounds
Ionic, Covalent, & Hydrogen Bonding
Properties of Water
Acids, Bases & Buffers
Molecules of Life
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Carbohydrates, Lipids, Proteins, Nucleic acids,
ATP
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Basic Chemistry
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There are 92 naturally-occurring elements.
– About 96% of human body is composed
of just four elements.
 Oxygen
 Carbon
 Hydrogen
 Nitrogen
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Atoms
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An atom is the smallest unit of matter that
retains an element’s physical and chemical
properties.
– Positively-charged protons and neutral
neutrons are located in the nucleus.
– Negatively-charged electrons orbit the
nucleus in shells.
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Figure 2.1 The structure of an atom.
Nucleus
Nucleus
Helium atom
Helium atom
2 protons (p+)
2 neutrons (n0)
2 electrons (e–)
2 protons (p+)
2 neutrons (n0)
2 electrons (e–)
(a) Planetary model
(b) Orbital model
KEY:
Proton
Neutron
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Electron
Electron cloud
Second
electron
shell
First
electron
shell
1p+
6p+
6n0
7p+
7n0
Hydrogen (H)
Atomic number = 1
Mass number = 1 or 2
Atomic mass = 1.01
Carbon (C)
Atomic number = 6
Mass number = 12 or 13
Atomic mass = 12.01
Nitrogen (N)
Atomic number = 7
Mass number = 14 or 15
Atomic mass = 14.01
Fourth
electron
shell
Third
electron
shell
8p+
8n0
Oxygen (O)
Atomic number = 8
Mass number = 16, 17, or 18
Atomic mass = 16.00
Fifth
electron
shell
11p+
12n0
17p+
18n0
19p+
20n0
Sodium (Na)
Atomic number = 11
Mass number = 23
Atomic mass = 22.99
Chlorine (Cl)
Atomic number = 17
Mass number = 35 or 37
Atomic mass = 35.45
Potassium (K)
Atomic number = 19
Mass number = 39, 40, or 41
Atomic mass = 39.10
Atomic number = number of protons in an atom
Mass number = number of protons and neutrons in an atom (boldface indicates most common isotope)
Atomic mass = average mass of all stable atoms of a given element in daltons
53p+
74n0
Iodine (I)
Atomic number = 53
Mass number = 127
Atomic mass = 126.90
Ions, Molecules & Compounds
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During ionization, atoms give up or take on
an electron to stabilize their outer shells
An ion is an atom that has a positive or
negative charge; has gained or lost an
electron
A molecule consists of two or more atoms
bonded together, sharing electrons
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Ionic Bonds
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Ions are particles that carry a positive (+) or
negative (-) charge
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The attraction between oppositely charged ions forms
an ionic bond
 Example: bones & teeth; ions deposited into a matrix
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Elemental Sodium:
11protons, 11electrons
Na
Na
Atom
Electron
donated
(a) Sodium: 1 valence electron
Ion
Elemental Chlorine:
17protons, 17electrons
Electron
accepted
Cl
Cl
Atom
Ion
(b) Chlorine: 7 valence electrons
Na
Cl
(c) Ionic bond in sodium chloride (NaCl)
Covalent Bonds
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In covalent bonds, atoms share electrons
instead of losing or gaining them; strongest
bonds
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A single bond is formed when atoms share a
single pair of electrons
A double bond is formed when atoms share
two pairs of electrons
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Figure 2.7 Formation of covalent bonds.
Reacting atoms
H
Resulting molecules
H
H
Hydrogen
Hydrogen
atom
atom
(a) Formation of a single covalent bond
O
O
Oxygen atom
Oxygen atom
H
or
Molecule of
hydrogen gas (H2)
O
O
or
Key to why we are
carbon-based life
forms: Carbon can
make four bonds
with other atoms
Molecule of oxygen gas (O2)
(b) Formation of a double covalent bond
H
H
H
C
H
C
H
H
H
H
Hydrogen atoms
Carbon atom
Molecule of methane gas (CH4)
(c) Formation of four single covalent bonds
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Hydrogen Bonding
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Nonpolar & Polar Covalent Bonds
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Nonpolar covalent bond: both atoms share electrons
equally
Polar covalent bond: unequal sharing of electrons
Polar covalent bonds lead to hydrogen bonding
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Example: H2O, water.
Electrons in water molecule – spend more time circling
larger oxygen atom than smaller hydrogen atom; leads
to charge distribution across the whole molecule
Hydrogen bonding in water imparts very special
characteristics to water that are extremely important for
life; water is the most important molecule for life
Hydrogen bonding in other biological molecules will be
extremely important for structure/function relationships
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Figure 2.8 Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules.
Non-polar
covalent bond
(a) Carbon dioxide (CO2)
δ–
Polar
covalent bond
δ+
δ+
(b) Water (H2O)
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Hydrogen Bonding between Water Molecules
Water is a polar molecule with the oxygen
end being slightly negative and the
hydrogen end being slightly positive.
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H
H
O
d– d–
Water
molecule
d–
d–
H
H
O
d– Na+ –
d
d–
d–
d–
Hydrated sodium ion
Na+
H O
Cl–
H
d+
Crystal of NaCl
d+
d+
Cl–
d+
d+
d+
Hydrated chloride ion
Properties of Water Critical for Life
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Water is liquid at room temperature.
Water is a solvent for polar molecules.
Water molecules are cohesive.
Water temperature rises and falls slowly.
Water has a high heat of vaporization.
Frozen water is less dense than liquid water.
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Density of Ice vs. Liquid Water
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Acids and Bases
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Acids dissociate in water and release
hydrogen ions (H+).
Bases take up hydrogen ions (H+) or release
hydroxide ions (OH-).
– Buffers prevent large changes in amounts
of acids and bases in body by taking up
excess hydrogen ions or hydroxide ions.
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HCl
H+
KOH
Cl–
(a) Acid
K+
OH–
(b) Base
KCl
K+
Cl–
(c) Salt
The pH Scale
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Molecules of Life
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Organic Compounds
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Molecules containing carbon
Carbon can make four bonds with many types of atoms
including itself; can form large molecules
Result: many different types of organic molecules each
with a unique structure and therefore function
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Molecules of Life
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Four categories of molecules are unique to
cells.
– Carbohydrates.
– Lipids.
– Proteins.
– Nucleic Acids.
 ATP
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Carbohydrates
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Carbohydrates function for quick and shortterm energy storage
– Monosaccharide (simple sugar).
 Glucose.
– Disaccharide.
 Sucrose: Glucose + Fructose
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Glucose
All atoms written out
Standard shorthand
Figure 2.14 Carbohydrates.
(a) Simple sugar (monosaccharide)
(b) Double sugar (disaccharide)
(c) Starch (polysaccharide)
Dehydration
synthesis
H2O
Hydrolysis
Glucose
Fructose
Sucrose
(d) Dehydration synthesis and hydrolysis of a molecule of sucrose
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Water
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Complex Carbohydrates
Polysaccharides.
– Glycogen – storage form of carbohydrates
in animals
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Lipids (Fats)
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Lipids contain more energy per gram than any other
biological molecule; long-term energy storage
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Do not dissolve in water
 Absence of polar groups
Types of Lipids
 Fatty acids
 Triglycerides
 Phospholipids
 Steroids
 Animal origin, solid at room temperature
 Plant origin, liquid at room temperature
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Saturated and Unsaturated Fatty Acids
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A fatty acid is a carbon-hydrogen chain ending
with -COOH
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Saturated fatty acids: contain only single bonds
between the carbon atoms; saturated with hydrogen
Unsaturated fatty acids: contain one or more double
bonds in the carbon chain; not saturated with hydrogen
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Ester linkage
Palmitic acid (C15H31COOH) +
(Saturated)
Stearic acid (C17H35COOH) +
(Saturated)
Oleic acid (C17H33COOH) +
(Monounsaturated)
(c) Triglyceride (fat) molecule
Fatty Acid Stacking
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Figure 2.16 Examples of saturated and unsaturated fats and fatty acids.
Structural formula of a
saturated fat molecule.
(a) Saturated fat. At room temperature, the
molecules of a saturated fat such as this
butter are packed closely together, forming
a solid.
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Structural formula of an
unsaturated fat molecule.
(b) Unsaturated fat. At room temperature,
the molecules of an unsaturated fat such as
this olive oil cannot pack together closely
enough to solidify because of the kinks in
some of their fatty acid chains.
Phospholipids
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Phospholipids contain a phosphate head
and fatty acid tails.
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Polar head and non-polar tails
 Soluble in water
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Polar head
Phosphate
group
Polar
head
Polar
heads
Nonpolar
tails
Cell
membrane
Polar
heads
Nonpolar tails
Nonpolar tails
(b) Simplified way to
draw a phospholipid
(a) Chemical structure of a phospholipid
(c) Arrangement of phospholipids in
a portion of a cell membrane
How Detergents Work
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Steroids
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Steroids are lipids with a backbone of four
fused carbon rings
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Examples: cholesterol, estradiol, testosterone,
cortisol
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Hydrocarbon tail
4 rings
Hydroxyl group
Cholesterol
Estradiol (an estrogen or female
sex hormone)
Testosterone (a male
sex hormone)
Cortisol
Proteins
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Proteins are macromolecules with amino acid
subunits
– An amino acid has a central carbon atom bonded
to a hydrogen and three groups.
 Polypeptide – Single chain of amino acids
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Figure 2.17 Amino acid structures.
Amine
group
Acid
group
(a) Generalized
structure of
all amino
acids.
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(b) Glycine is
the simplest
amino acid.
(c) Aspartic acid (d)
(an acidic
amino acid)
has an acid
group (—COOH)
in the R group.
Lysine (a
(e) Cysteine (a
basic amino
basic amino
acid) has an
acid) has a
amine group
sulfhydryl
(—NH2) in the
(—SH) group in
R group.
the R group,
which suggests
that this amino
acid is likely to
participate in
intramolecular
bonding.
Proteins
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Essential Amino Acids
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Levels of Protein Organization
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Primary Structure
– Linear sequence of amino acids
Secondary Structure
– Polypeptide takes on orientation in space
Tertiary Structure
– Final three-dimensional shape
Quaternary Structure
– Proteins with more than one polypeptide
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Proteins (Cont.)
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Enzymes: proteins that catalyze chemical
reactions; most names end in the suffix -ase
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Are catalysts- help reactions to occur but are not part of
the product or changed by the reaction
Master molecules of metabolism
Highly specific
Very efficient
Subject to a variety of cellular controls
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Figure 2.20 A simplified view of enzyme action.
Energy is
absorbed;
bond is
formed.
Substrates (S)
e.g., amino acids
Water is
released.
H2O
Product (P)
e.g., dipeptide
Peptide
bond
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
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1 Substrates bind at active
site, temporarily forming an
enzyme-substrate complex.
2 The E-S complex
undergoes internal
rearrangements that
form the product.
Enzyme (E)
3 The enzyme
releases the product
of the reaction.
Nucleic Acids
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Nucleic acids are huge macromolecules
composed of nucleotides.
– A nucleotide is constructed of a phosphate, a
pentose sugar, and a nitrogenous base.
– Deoxyribonucleic acid (DNA)
 Information storage on how to make proteins
– Ribonucleic acid (RNA)
 Helper molecule for DNA related to protein
synthesis
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Figure 2.21a Structure of DNA.
Deoxyribose
Phosphate sugar Adenine (A)
(a) Adenine nucleotide
(Chemical structure)
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Figure 2.21 Structure of DNA.
Deoxyribose
Phosphate sugar Adenine (A)
KEY:
Thymine (T)
Adenine (A)
(a) Adenine nucleotide
(Chemical structure)
(b) Adenine nucleotide
(Diagrammatic
representation)
Cytosine (C)
Guanine (G)
Hydrogen
bond
Deoxyribose
sugar
Phosphate
(c) Computer-generated image of
a DNA molecule
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(d) Diagram of a DNA molecule
(ATP) Adenosine Triphosphate
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ATP is the primary cellular energy carrier
– Energy currency of cells
– Breaks down to adenosine diphosphate
(ADP) and a molecule of inorganic
phosphate, releasing energy to drive
cellular metabolism
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Figure 2.22a ATP—structure and hydrolysis.
Adenine
High
energy
bonds
P
P
P
Ribose
Phosphates
(a) Adenosine triphosphate (ATP)
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Figure 2.26
Release of Energy for Cell to Do Work
Adenosine
H2O
Hydrolysis of ATP
produces useful energy
for the cell
Adenine (A)
Adenosine
P P P
(ATP)
Triphosphate
H2O
Adenosine
P P
(ADP)
Energy for ATP synthesis
comes from food or body
stores of glycogen or fat
Ribose
The structure of ATP.
The breakdown and synthesis of ATP.
The breakdown (hydrolysis) of ATP yields
energy for the cell. The reaction is reversible,
meaning that ATP may be resynthesized
using energy from other sources.
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Need to Know
Main chemical elements in the body
1.
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Life is based on the chemistry of carbon, hydrogen,
nitrogen, and oxygen
Know difference between ions and molecules
Chemical bonds
2.
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Know difference between ionic, covalent, and
hydrogen bonding
Know the reason why life is based on carbon
Properties of water
3.
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Understand how hydrogen bonding contributes to the
unique properties of water
Understand how the unique properties of water allow
for life
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Need to Know (Cont.)
Acid-Base balance and buffers
4.
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Understand importance of acid-base balance and how
buffers work
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5.
Need to Know (Cont.)
Molecules of life- built by putting subunits
together
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Carbohydrates
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Carbon-oxygen ring structures
Know the most important subunit is glucose
Types: mono, di, polysaccharides
Quick energy, short-term storage of energy
Lipids




Know the subunits- three fatty acid chains bond to
one glycerol molecule to make triglyceride
Long carbon-hydrogen chains
Long-term energy storage
Types: fatty acids, triglycerides, phospholipids,
steroids, other
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Need to Know (Cont.)
6.
Molecules of life (Cont.)
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Proteins:





Carbon-nitrogen chains (amino acids) with side
groups
Know the subunits are amino acids- 20 different
kinds- 10 essential, 10 non-essential
Functions of proteins
Level of structural organization; interaction of
structure with function
Enzymes for biochemical regulation
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Need to Know (Cont.)
7.
Molecules of life (Cont.)
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Nucleic Acids- ex. DNA- subunits are
nucleotides




Nucleotide are make of nitrogenous base +
pentose sugar + phosphate group
Storage of how to make every protein- also called
genetic material (DNA)- subunits of DNA are
nucleotides- adenine, thymine, cytosine, guanine
Protein making blueprint is RNA (to be discussed
in a later chapter)
Energy currency of the cell is ATP; proteins can
get energy from it to do work
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