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Chapter 2
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Why study chemistry?
A clear understanding of chemistry is
essential for the study of physiology.
This is because organ functions
depends on cellular functions, which
occur as a result of chemical reactions.
Definitions
Chemistry = Science that exams the composition and interactions of matter
Biochemistry = Chemistry of living things
Matter = Anything that has mass and takes up space
(Solids, liquids, gasses)
Elements are listed
on a Periodic Table
Element = Fundamental substance of matter
(e.g. Carbon, Nitrogen, Oxygen)
C
6
12.01
N
7
14.01
O
8
15.99
Definitions
Atom = Smallest functional particle of an element
Molecule = two or more atoms chemically joined together.
Compound = Two or more different elements chemically bonded
together (e.g. H2O = water, C6H12O6 = glucose)
Molecule of an element = two or more identical atoms chemically
bonded together. (e.g. H2 = hydrogen molecule, O2 = oxygen molecule)
Elements of the Body
Bulk elements make up 99.9% of our body:
Hydrogen (H)
Oxygen (O)
Carbon (C)
Nitrogen (N)
Sulfur (S)
Magnesium (Mg)
Sodium (Na)
Potassium (K)
Calcium (Ca)
Chlorine (Cl)
Phosphorus (P)
Trace elements make up less than 0.1% of our body:
Cobalt (Co)
Zinc (Zn)
Manganese (Mn)
Iron (Fe)
Iodine (I)
Copper (Cu)
Fluorine (F)
Atomic Structure
•
electron
atom - the smallest particles of an element
that still have the properties of that element.
• subatomic particles:
Proton – single positive charge
Neutron – carries no electrical charge
Electron – single negative charge
An atom contains a central nucleus
composed of protons and neutrons.
Electrons orbit the nucleus.
neutron
proton
-
-
+
+
+
-
+
nucleus
-
Subatomic Particles
Electrical Charge:
Proton: +1
Electron: -1
Neutron: No charge
Atomic Mass:
Proton: 1 (atomic mass unit)
Neutron: 1 (atomic mass unit)
Electron: 0
Most atoms contain equal number of protons
and electrons, so an atom contains no overall
net charge and is neutral.
Atomic Number and Atomic Weight
Atomic Number:
• The number of protons in one atom.
• Atomic number identifies an element.
O
8
15.99
Example. The atomic number
of oxygen is 8. Oxygen, and
only oxygen has 8 protons.
Atomic Weight (mass):
• The sum of protons and neutrons in one atom.
• Remember, the weight of electrons is negligible.
atomic number and atomic weight
+
-
-
+
-
-
+
+
+
-
+
+
-
-
Isotopes - atoms of an element with the same atomic
number, but different atomic weights.
• number of neutrons of an element varies between atoms.
Isotopes of carbon
C
12
6
C
13
6
C
14
6
C
6
12.01
Atomic weight
(mass) of carbon
*The atomic weight of an element is an average of the isotopes present.
Electron Shells: Electrons encircle the nucleus in discrete orbits,
called electron shells. Each shell can contain only a fixed number
of electrons.
1st shell holds 2 electrons
2nd shell holds 8 electrons
3rd shell holds 8 electrons
-
-
-
-
-
-
-
-
-
-
nucleus
Octet rule: rule of thumb that except for
the 1st shell, each atom reacts to have 8
electrons in its outer (valence) shell.
* Lower shells are filled first.
-
-
-
-
-
-
-
Examples of filling electron shells
Helium
Atomic number = 2
Atomic weight = 4
(2 electrons fill the 1st electron shell)
Carbon
Atomic number = 6
Atomic weight = 12
(The first 2 electrons fill the inner shell, and
the remaining 4 electrons are placed the 2nd
electron shell).
Ions
Ion - atom that readily gain or loose electrons
Cation: an ion that is deficient in electrons
• positively charged ions
Anion: an ion that has additional electrons
• negatively charged ions
+
-
Example of a cation
11
Na
23
-
Sodium readily loses an electron.
+
Na
Sodium cation
Example of an anion
Chlorine readily accepts an
additional electron
Cl
17
35
Cl
Chloride anion
Chemical Bonds
11
Na
Ionic bond
23
Cl
17
35
Complete exchange of electrons
+
+
Na
Sodium cation
_
Opposite charges attract
Cl
Chloride anion
Ionic bonds do not form molecules
+
-
+
+
-
+
+
-
+
-
+
+
Chemical Bonds
non-polar covalent bonds
Nonpolar covalent bonds occur when the atoms share the
electrons equally, so the molecule has no overall charge.
Two hydrogen atoms share
their electrons equally. Thus,
the hydrogen molecule has no
overall charge and is nonpolar.
+
H
H
H-H
Structural formula of
the hydrogen molecule
CH4
Structural
formula
molecular
formula
polar covalent bonds
• Water is a polar molecule because the oxygen atom tends to pull
the electrons away from hydrogen.
• The oxygen end has a slight negative charge, while the hydrogen
end has a slight positive charge.
partial negative charge
δ-
O
H
H
Structural
formula
δ+
partial positive charge
δ+
H2O
molecular
formula
Types of covalent bonds
O
H
H
(H2O)
O O
(O2)
N N
(N2)
Chemical Bonds
δ-
• slightly positive (hydrogen) end of a polar
molecule weakly attracts to the slightly
negative end of another molecule
Hydrogen bonds
O
H
δ+
H
δ+
Chemical Bonds
• weak bonds at room temperature, but
are strong enough to form ice
• Stabilize large proteins, DNA, and RNA
End of Section 2, Chapter 2
Types of chemical bonds
Chemical Reactions
Synthesis
joins molecules together
A + B
A
Products
Reactants
Decomposition
breaks chemical bonds
A
B
A + B
B
Exchange (replacement)
breaks bonds and makes new bonds
A
B
Reversible
products can also yield the reactants
+ C
D
A + B
A
C + B
A
B
D


Activation Energy – Energy required to initiate a reaction
A Catalyst increases the rate of the reaction without being
consumed by the reaction
Activation energy
without catalyst
Activation energy
with a catalyst
Catalysts lower the activation
energy required to initiate a reaction
Acids, Bases, and Salts
Electrolytes – dissociate in water to release ions.
Hydration shell
NaCl
Na+
+
Cl-
Acids, Bases, and Salts
Acid - electrolyte that releases H+ (hydrogen ions /protons) in solution
• Example: HCl
H+ +
Cl
Hydrochloric
acid
Base (alkaline) - electrolyte that removes H+ from solution
• Many bases release hydroxide ions (OH-)
• Example:
NaOH
Sodium
Hydroxide
Na+ + OHOH- + H+
The hydroxide further reacts
with H+ to form water
H2O
Acids, Bases, and Salts
Salt – electrolyte formed by the reaction between
an acid and a base (alkaline)
Acid + Base → Salt + water
HCl + NaOH → NaCl + H2O
Acid and Base Concentrations
pH
• pH measures the concentration of hydrogen ions [H+] in a solution
• As pH decreases, [H+] increases = solution is more acidic
acidic property
increasing
pH
0
alkaline property increasing
7
neutral
14
Hydrogen ion concentration vs. pH
[H+] grams/Liter
1.0
Small changes in pH reflect large changes in [H+]0.1
0.01
1 pH = 10 fold change in [H+]
0.001
2 pH = 100 fold change in [H+]
0.0001
3 pH = 1000 fold change in [H+]
0.00001
pH
0
1
2
3
4
Increasingly acidic
5
0.000001
6
0.0000001
7
0.00000001
8
0.000000001
9
0.0000000001
10
0.00000000001
11
0.000000000001
12
0.0000000000001
13
0.00000000000001
14
neutral
Increasingly
alkaline
pH of Blood
Average pH of blood = 7.35 - 7.45
Acidosis = blood pH less than 7.3
Symptoms include fatigue, disorientation, and difficulty breathing.
Alkalosis = blood pH greater than 7.5
Symptoms include agitation and dizziness
Blood contains several buffers
Buffer = resists changes to pH
Chemicals of the Cell
Organic Vs. Inorganic Molecules
Organic molecules
Compounds with carbon
May form macromolecules
Includes proteins, carbohydrates, lipids, nucleic acids
Inorganic molecules
Compounds that lack Carbon (exception is CO2)
Usually dissociate in water
Inorganic Chemicals
Water (H2O) - 2/3 of weight in a person
Transports gasses, nutrients, wastes, hormones, ect.
Oxygen (O2) - Used in cellular respiration
Carbon Dioxide (CO2) - Waste of metabolic reactions
Inorganic Salts
Na+, Cl-, K+, Ca2+, Mg2+, HCO3-, PO42-
Organic Molecules
C
12
6
-
Carbon
• Organic molecules contain carbon
• Carbon forms 4 covalent bonds
-
C
-
-
• Carbon-to-Carbon bonds can form long
hydrocarbon chains and hydrocarbon rings
H H H H H H H H H H
HO C C C C C C C C C C H
H H H H H H H H H
Fatty acid – example of an organic molecule
++
+
+ +
+
Glucose (C6H12O6)
-
Organic Synthesis
Organic Synthesis
Small molecules (monomers) join together to form
larger molecules (polymers)
Several Monomers
Polymer
Organic molecules
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates
Monosaccharides (simple sugars)
•
2:1 ratio of Hydrogen to Oxygen (eg. C6H12O6)
•
Polar molecules – water soluble
Glucose
Fructose
Disaccharides (double sugars)
Maltose
Lactose
Sucrose
Carbohydrates
Polysaccharides (complex carbohydrates)
Large molecules composed of several monosaccharides and
disaccharides joined together
•
Starch – easily digested
•
Cellulose- Plant polysaccharide, indigestible by humans
Dietary Fiber
•
Glycogen – storage form of energy, synthesized by liver
Each ring represents a
monosaccharide
Lipids
Lipids
Fat (triglyceride)
Lipids
Fat (triglyceride)
Saturated fatty acid
• All carbon-to-carbon single bonds
Unsaturated fatty acid
• Contains one or more carbon-to-carbon double bonds
Lipids
Fat (triglyceride)
Unsaturated Fat
Saturated Fat
Lipids
Phospholipids
Non-polar region is
water insoluble
Polar region is
water soluble
Hydrophilic
head
Hydrophobic
tails
Lipids
Steroids
• Small hydrocarbon rings
• Includes
Proteins
Proteins have many functions:
• Proteins provide structural material.
• Some act as chemical messengers (hormones, neurotransmitters).
• Many proteins are receptors.
• Most enzymes are proteins.
• They are a source of energy.
Proteins
Enzymes catalyze reactions (increases rate), but
are not consumed by the reaction (reusable).
Substrates
Product
A
A
Active Site
B
A
B
Active Site
Enzyme
Active Site
Enzyme-Substrate Complex
Synthesis reaction involving an enzyme
B
Active Site
Enzyme is unchanged
Proteins
Amino Acids
• Amino Acids are the monomers of proteins
1. Central carbon
2. Amine group
4. Hydrogen
3. Carboxyl group
5. R group (R – rest of molecule)
• Each amino acid is determined by
1 of 20 different R groups.
Proteins
Amino Acids
• The 20 amino acids are determined by 20 different R groups
Glutamine
Aspartic Acid
glycine
Proteins
Amino Acids
• Amino Acids are linked together by peptide bonds
• Dipeptide – two amino acids bonded together
• Polypeptide – several amino acids linked together
Amino acid
A dipeptide formed from two
amino acids. Peptide bond
in red .
Portion of a polypeptide chain.
Peptide bonds are in red.
Proteins
Protein Structure
Proteins
Protein Structure
Proteins
Protein Structure
Proteins
Protein Structure
a) The primary structure is the sequence of amino
acids that make up the polypeptide chain.
b) The secondary structure, which can take the
form of an alpha-helix or a beta-pleated sheet, is
maintained by hydrogen bonds between amino
acids in different regions of the original polypeptide
strand.
c) The tertiary structure occurs as a result of further
folding and bonding of the secondary structure.
d) The quaternary structure occurs as a result of
interactions between two or more tertiary subunits.
The example shown here is hemoglobin, a protein in
red blood cells which transports oxygen to body
tissues.
Proteins
Conformation - shape of a protein.
• The shape of a protein determines its function.
Denature - Treatment that alters the shape of a protein to make it
nonfunctional
• Heat, pH changes, radiation, certain chemicals may
denature proteins
Nucleic Acids
Overview
Includes DNA and RNA
Genetic information
Consists of monomers, called nucleotides
Nucleic Acids
Nucleotide
• Nucleotides are the monomers of Nucleic Acids
• 3 Components of a Nucleotide
o 5 Carbon Sugar (S)
o Nitrogenous Base (B)
o Phosphate Group (P)
• Dinucleotide – two nucleotides bonded together
Nucleic Acids
Ribonucleic Acid (RNA)
• The sugar in RNA is ribose
• RNA is a single-stranded nucleic acid
Nucleic Acids
Deoxyribonucleic Acid (RNA)
• The sugar in DNA is deoxyribose
• DNA is a double-stranded helix
• Encodes genetic information for protein
synthesis.
Hydrogen bonds
Compound
Building Blocks
Examples
Carbohydrates
Monosaccharides
Glucose, starch, glycogen
Lipids
Glycerol, fatty acids,
phosphate group
Triglycerides, phospholipids,
steroids
Proteins
Amino Acids
Hemoglobin, Albumin
Nucleic Acids
Nucleotides
RNA, DNA
Attribution
•
•
•
•
•
•
•
•
•
•
•
Rock salt crystals: CC BY-SA 2.0 (http://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/d/d0/Rock_salt_crystal.jpg
Icicle: CCO public domain, via pixabay. http://pixabay.com/en/icicle-ice-cold-frost-frosty-93727/
Protein: CC BY-SA 3.0 http://upload.wikimedia.org/wikipedia/commons/1/10/Protein_NP_PDB_1m73.png
Chemist: CCO http://pixabay.com/en/experiment-chemistry-liquid-220023/
Periodic Table: CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/6/61/Periodic-table.jpg
DNA molecule: CCO public domain, by Yikrazuul, via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/c/c3/DNA_Furchen.png
Glucose: By NEUROtiker (Own work) [Public domain], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/c/c6/Alpha-D-Glucopyranose.svg
Fructose: By NEUROtiker (讨论 · 贡献) (自己的作品) [Public domain], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/6/67/Beta-D-Fructofuranose.svg
Lactose: By NEUROtiker (Own work) [Public domain], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/3/36/Lactose_Haworth.svg
Maltose: By NEUROtiker (Travail personnel) [Public domain], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/9/93/Maltose_Haworth.svg
Sucrose: By Don A. Carlson [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 3.0
(http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/b/b3/Sucrose-inkscape.svg
Attribution
•
•
•
•
DNA molecule: By Yikrazuul [Public domain], via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/c/c3/DNA_Furchen.png
3-helix bundle: CC BY-SA 3.0, via Wikimedia Commons
http://upload.wikimedia.org/wikipedia/commons/b/b7/Vti1a_Nterm_3helix_bundle_1vcs_model2.png
Alpha-helix and beta-sheet: By Holger87 (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/bysa/3.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/0/05/Protein_structure.png
Peptide Bonds: By OpenStax College [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia
Commons http://upload.wikimedia.org/wikipedia/commons/2/26/225_Peptide_Bond-01.jpg