Bio 11 Lecture- Chemistry II

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Bio 11 Lecture- Chemistry II

• Chemical reactions, Ions, pH, functional groups,
  organic molecules

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Lecture outline

• Chemical Bonds review
• 5. Ions
• 6. pH
• 7. Functional groups
• 8. Organic molecules
• 4. Chemical Reactions
• 9. Carbohydrates

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What part(s) of an elements atoms determines
its mass?

• A. Protons
• B. Neutrons
• C. Electrons
• D. Protons Neutrons
• E. Electrons/Protons

4
What part(s) of an elements atoms define the
element?

• A. Protons
• B. Neutrons
• C. Electrons
• D. Protons Neutrons
• E. Electrons/Protons

5
What part(s) of an elements atoms differentiate
its isotopes?

• A. Protons
• B. Neutrons
• C. Electrons
• D. Protons Neutrons
• E. Electrons/Protons

6
What part of atoms determine how they bond with
other atoms?

• A. Protons
• B. Neutrons
• C. Electrons
• D. Protons Neutrons
• E. Electrons/Protons

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Basic atomic structure- protons, neutrons, and
electrons
8
The periodic table logically arranges and
describes all matter
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Molecules, compounds, chemical reactions, and
bonding
10
Elements combine in chemical reactions to form
compounds

• Molecules- 2 or more atoms combined in a specific
  way
• Compounds- different elements in a molecule, in
  exact, whole-number ratios, joined by a chemical
  bond
• 2 major means of intramolecular chemical bonding
  Covalent (incl. polar and nonpolar) and Ionic

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Valence electrons determine bonding
12
Atoms seek complete valence electron shells (the
octet rule)
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In Ionic bonding, atoms strip valence electrons
from partners, forming ions
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Atoms are stable when their outer shells are
filled with electrons

• Shell 1 Holds 2 electrons
• Shell 2 Holds 8
• Shell 3 Holds 8
• Hydrogen- 1p, 1e, seeks a second electron in its
  outermost shell
• Carbon seeks 4
• The electrons in the outermost shell are called
  valence electrons

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Noble gases have a stable electron structure

• Their outer orbitals have a full complement of
  electrons
• Noble gases are very unreactive

16
In ionic bonding, an atom takes an electron from
another atom, forming 2 ions
LE 2-7
Transfer of electron
Na Sodium ion
Cl- Chloride ion
Sodium chloride (NaCl)
Na Sodium atom
Cl Chlorine atom
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5. Ions

• Ions- Charged atoms or molecules
• Anion- negative ion
• Cation- positive ion
• Ionization- reaction producing ions
• Salt- a neutral compound comprised of ions

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LE 2-7a-2
Na Sodium ion
Cl- Chloride ion
Sodium chloride (NaCl)
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LE 2-7b
Na
Cl-
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Water dissolves many ionic compounds (like
dissolves like)
Individual soluble ions are not physically bound
to each other
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In covalent bonding, pairs of valence electrons
are shared, and molecules are formed
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LE 2-17a

2 H2
O2
2 H2O

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LE 2-6b
Nitrogen (N) Atomic number 7
Oxygen (O) Atomic number 8
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In neutral molecules, carbon always forms 4 bonds
Structural formula
Ball-and-stick model
Space-filling model
Methane
The 4 single bonds of carbon point to the corners
of a tetrahedron.
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LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.
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LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
Butane and Isobutane are _______________of each
other.
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LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary
in location.
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LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.
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Organic Chemistry

• The chemistry of carbon
• Hydrocarbons are the most basic example
• Combustible
• Can form rings

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The variety of carbon compounds is limitless
inorganic - lack carbon atoms organic - with
carbon (plus hydrogen) biochemical - organic
molecule in life carbohydrates proteins
lipids nucleic acids
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Covalent bonds hold together the macromolecules
of life

• Living things create macromolecular products for
  structure
• 6CO2(g) 6H2O(l) h? ? C6H12O6(s) 6O2(g)
• Macromolecules as reactants are broken down for
  energy
• C6H12O6(s) 6O2(g) ? 6CO2(g) 6H2O(l)
• All the reactions of a living thing are called
  its metabolism

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Electronegativity determines properties of
covalently bonded molecules
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Electronegativity electron greediness

• Atoms in covalently bonded molecules do not
  always share electrons equally
• This creates polar molecules
• Polar regions of water molecules interact to form
  hydrogen bonds
• Hydrogen bonds weak/temporary intermolecular
  forces

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Some electronegativity values

• Hydrogen 2.20
• Oxygen 3.44
• Carbon 2.55
• Chlorine 3.16
• Sodium 0.93

• Difference between
• H and O 1.22
• H and C 0.35

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Hydrogen bonding in water determine many of
waters unique properties

• H-bonds can form a lattice (ice)
• H-bonds require much energy to break
• H-bonds give water surface tension

Hydrogen bond
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Water dissolves many ionic compounds (like
dissolves like)
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Intermolecular Hydrogen bonds give water its
surface tension
0
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Intermolecular Hydrogen bonds require much heat
in order to be broken
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Water also forms ions sometimes

• H2O ? H OH-

• Spontaneously happens to water molecules
• 1/ 107 water molecules are ionized in distilled
  water
• In dH2O, H OH-
• salt - neutral molecule releases ions
• acid releases hydrogen H, burns
• base releases hydroxide OH, slimy

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pH is a measure of acidity/basicity

• pH -log H (logarithmic scale)
• pH 1? 6.9 acid
• pH 7.1?14 base
• pH 7? neutral
• buffers - absorb excess H or OH
• - stomach 2, urine 5-7.8, blood 7.4
• Acids donate H to water
• Bases remove H from water (or donate OH- to
  water)
• Proteins are very sensitive to small changes in pH

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LE 2-15
pH scale
H
H
H
OH?
H
Lemon juice, gastric juice
H
OH?
H
H
H
Grapefruit juice, soft drink
Increasingly ACIDIC (Higher concentration of H)
Acidic solution
Tomato juice
Human urine
OH?
OH?
NEUTRAL H??????-
Pure water
OH?
H
H
Human blood
OH?
OH?
H
H
H
Seawater
Neutral solution
Increasingly BASIC (Lower concentration of H)
Milk of magnesia
Household ammonia
OH?
OH?
OH?
OH?
H
Household bleach
OH?
OH?
H
Oven cleaner
Basic solution
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7. FUNCTIONAL GROUPS

• hydroxide group OH amino group
  NH2 carboxyl group COOH phosphate group
  PO4 methyl group CH3

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The physical/ chemical properties of carbon
skeletons can be modified by functional groups
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2.20 Part 2
figure 02-20b.jpg

• Figure 2.20 Part 2

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Functional groups can radically change the
function of a molecule
Estradiol
Female lion
Testosterone
Male lion
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• The six functional groups that are most important
  in the chemistry of life
• Hydroxyl group (alcohols)
• Carbonyl group
• Carboxyl group (carboxylic acids)
• Amino group
• Sulfhydryl group
• Phosphate group
• Methyl group

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LE 4-10aa
STRUCTURE
(may be written HO)
Ethanol, the alcohol present in alcoholic
beverages
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Is polar as a result of the electronegative
oxygen atom drawing electrons toward itself.
Alcohols (their specific names usually end in -ol)
Attracts water molecules, helping dissolve
organic compounds such as sugars (see Figure 5.3).
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LE 4-10ab
Acetone, the simplest ketone
EXAMPLE
STRUCTURE
Acetone, the simplest ketone
Propanal, an aldehyde
NAME OF COMPOUNDS
Ketones if the carbonyl group is within a carbon
skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is at the end of
the carbon skeleton
A ketone and an aldehyde may be structural
isomers with different properties, as is the
case for acetone and propanal.
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LE 4-10ac
EXAMPLE
STRUCTURE
Acetic acid, which gives vinegar its sour taste
FUNCTIONAL PROPERTIES
NAME OF COMPOUNDS
Has acidic properties because it is a source of
hydrogen ions.
Carboxylic acids, or organic acids
The covalent bond between oxygen and hydrogen is
so polar that hydrogen ions (H) tend
to dissociate reversibly for example,
Acetic acid
Acetate ion
In cells, found in the ionic form, which is
called a carboxylate group.
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LE 4-10ba
EXAMPLE
STRUCTURE
Glycine
Because it also has a carboxyl group, glycine is
both an amine and a carboxylic acid compounds
with both groups are called amino acids.
FUNCTIONAL PROPERTIES
NAME OF COMPOUNDS
Acts as a base can pick up a proton from the
surrounding solution
Amine
(nonionized)
(ionized)
Ionized, with a charge of 1, under cellular
conditions
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LE 4-10bb
EXAMPLE
STRUCTURE
(may be written HS)
Ethanethiol
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can interact to help
stabilize protein structure (see Figure 5.20).
Thiols
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LE 4-10bc
EXAMPLE
STRUCTURE
Glycerol phosphate
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Makes the molecule of which it is a part an anion
(negatively charged ion).
Organic phosphates
Can transfer energy between organic
molecules.





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Organic molecules are good energy sources
Energy is required to form covalent bonds energy
is released when bonds are broken
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Most molecules in living things fall into four
categories

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

These all exhibit modular construction
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Modular housing
Made of interchangeable parts
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Freight trains have modular assembly
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Modular assembly allows a wide variety of
products from a few pieces
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Most biopolymers of life are formed by
dehydration synthesis
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Hydrolysis is the reverse reaction (Catabolic)
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4. CHEMICAL REACTIONS 

• metabolism - all chemical reactions in body -
  reactants products  synthesis - build larger
  molecule CH3-OH H-CH3 CH3-CH3
  H2O  hydrolysis - break down molecule  CH3-CH3
  H2O CH3-OH H-CH3 exchange reaction -
  example AB CD AD CB

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Carbohydrates

• Carbon Hydro
• Formula (CH2O)n
• Different from hydrocarbons
• Soluble in water
• Includes table sugar, honey, starch, glycogen,
  cellulose, high fructose corn syrup
• Glucose is the monomer

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Glucose can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds
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Glucose Glucose Maltose (A Sugar
dimer)
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Chain can be extended to thousands
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9. Carbohydrates

• functions
• - principle source of energy (4 kcal/g)
• - structure energy storage in plants
•  atoms - C H O
• structure - ring or chain of 5-6 Cs
•  monosaccharide

• - single sugars (example glucose)
•  disaccharide
• - double sugars (example sucrose)
•  polysaccharide
• - polymer or chain of 100s sugars
• - starch cellulose (mostly plants)
• - glycogen (animals, esp. liver)

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Proteins are polymers made of 20 different kinds
of amino acid monomers
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Table 3.2 Part 2
table 03-02bc.jpg

• Table 3.2 Part 2

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Table 3.2 Part 3
table 03-02d.jpg

• Table 3.2 Part 3

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Proteins Polymers of Amino Acids

• Amino acids are covalently bonded together by
  peptide linkages. Review Figure 3.4

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3.4
figure 03-04.jpg

• Modular assembly of amino acids through
  dehydration synthesis

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Proteins have an incredible variety of structures
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Proteins have an incredible variety of functions
Hair, skin, fingernails, muscles, eye pigments,
are all made of protein
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11. Proteins

• functions - energy (4 kcal/g)
• - structure in animals (meat)
• - enzymes (speed up reg chem rxs) 
• atoms - C H O N
• amino acid
• - central C, hydrogen H
• - amino group NH2
• - carboxyl group COOH
• - R-group (20 different)
• polypeptide - polymer of amino acids
•  protein - 1 or more polypeptides

• 4 levels of structure - necessary
• for protein function, esp. enzymes
• I primary structure - sequence of
• amino acids in polypeptide chain
• II secondary structure
• - coiling or folding of chain
• - hydrogen bonds between regions
• III tertiary structure
• - folding of coiled-folded chain
• IV quaternary structure
• - linkage to other polypeptides

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Lipids

• Non-polar
• High-energy molecules
• For energy storage
• Forms cell membranes
• Hormones
• Members of family include oils, fats, waxes, and
  cholesterol (steroids)

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Lipids are non-polar

• Therefore, they are hydrophobic

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Triglycerides are a primary lipid structure
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Dehydration synthesis links fatty acids to
glycerol
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Fatty acids can be saturated and unsaturated (cis
and trans)
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10. Lipids

• functions
• - energy storage (9 kcal/g)
• - also animal structure (blubber)
•  
• atoms - C H O
•  
• structure - glycerol 3 fatty acids
•  
• oil - liquid, unsaturated (missing Hs)
•  
• fat - solid, saturated (maximum Hs)
• - promotes heart disease
•  
• others
• - steroids, phospholipids, waxes

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Nucleic acids

• Informational molecules in cells
• Include DNA, RNA, and ATP/ADP
• Have other functions

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Nulceotides are the subunits of nucleic acids

• Consist of a sugar, a phosphate, and a
  nitrogen-containing base
• Sugar can be deoxygenated

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12. Nucleic Acids

• function - not energy
• - genetics (genes chromosomes)
•  
• atoms - C H O N P S
•  
• structure - chain of 100s nucleotides
•  
• examples - DNA, RNA, ATP
•  
•  

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Review

• Atomic structure- protons, neutrons electrons
• Valence electrons
• Carbon
• Functional groups
• Carbohydrate structure
• Protein structure
• Lipid structure

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Things left unsaid

• Isotopes of all elements exist (some of these are
  radioactive)
• Electronegativity determines polarity of covalent
  bonds, and thus solubility
• Water has important physical properties essential
  to life on earth
• Isomers have the same molecular formula but not
  the same shape in space
• Nucleic acids are comprised of nucleotide
  monomers