Transcript Chem for Bio11

Chemistry for Bio 11
Chemistry is relevant to Biological
Concepts
• All Living things are made of matter
• The interactions of matter are described by
chemical principles
• Biolgists are interested in:
– Biochemical reactions
– Complex biological molecules
– Chemical energy
– The chemical environment
Biochemical reactions
• All living things are
collections of a vast
number of chemical
reactions
• Even the simplest living
things contain
impossibly complex
pathways
Complex biological molecules
• All living things are
made of complex
macromolecules
• Chemical principles
rule their assembly
Chemical energy
Photosynthesis creates molecules rich in energy:
• 6CO2(g)+ 6H2O(l) + hν  C6H12O6(s) + 6O2(g)
The Chemical Environment
• The physical properties
of water determine the
fate of life on earth
• pH, salinity and other
chemical factors
influence
Basic principles of chemistry
Atoms
Atoms are the smallest individual unit
of matter
• Atoms are comprised of
protons, neutrons and
electrons
Proton: Charge= +1,
Mass= 1
Neutron: Chg= 0, mass= 1
Electron: Chg = -1, mass=
~0
Mass= p + n
Charge = p - e
LE 2-4a
Electron
cloud
6e–
2e–
Nucleus
2
Protons
2
Neutrons
2
Electrons
Helium atom
Mass
number = 4
6
Protons
6
Neutrons
6
Electrons
Carbon atom
Mass
number = 12
Elements are defined by the number
of their protons
• There are 92 naturally
occurring elements
• Many others have been
synthesized
Atomic number: # protons
Atomic mass: protons
Isotopes- different atoms of
same element, with
different # neutrons
Atomic weight: Naturally
occurring average of
isotopes of a substance
96% of human tissue is comprised of 6
elements
• Carbon, Hydrogen,
Nitrogen, Oxygen,
Phosphorous, Sulfur
(CHNOPS)
• 25 elements serve
known functions in the
body, incl. Ca, K, Na, Cl,
Mg, Fe
Atomic structure
• Protons and electrons in
the nucleus
• Electrons orbit around
• Bohr atom- classic
model featuring
electrons in “planetary”
orbitals
• Each orbit holds a
determined number of
electrons (first holds
two, 2nd and 3rd hold
eight
The number of neutrons in atoms
is variable
• Isotopes
• Some isotopes are
stable, others are
radioactive
Isotopes of carbon have important
applications in biology and archaeology
Other radioactive isotopes are also
important
Electron cloud model
• Currently accepted
model of atomic
structure
• 90% probability cloud
• Mostly empty space
• Unfilled orbitals found
in unstable, reactive
elements
• Therefore, orbitals
influence bonding
Molecules, compounds, chemical
reactions, and bonding
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
Atoms are stable when their outer
shells are filled with electrons
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•
•
•
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
Noble gases have a stable electron
structure
• Their outer orbitals
have a full complement
of electrons
• Noble gases are very
unreactive
LE 2-7
In ionic bonding, an atom takes an
electron from another atom, forming 2
ions
Transfer of
electron
Na+
Sodium ion
Na
Sodium atom
Cl
Chlorine atom
ClChloride ion
Sodium chloride (NaCl)
5. Ions
• Ions- Charged atoms or
molecules
• Anion- negative ion
• Cation- positive ion
• Ionization- reaction
producing ions
• Salt- a neutral
compound comprised
of ions
LE 2-7a-2
Na+
Sodium ion
ClChloride ion
Sodium chloride (NaCl)
LE 2-7b
Na+
Cl-
Water dissolves many ionic
compounds (“like dissolves like”)
Individual soluble ions are not physically bound to
each other
In covalent bonding, pairs of valence electrons
are shared, and molecules are formed
LE 2-17a
+
2 H2
+
O2
2 H2O
LE 2-6b
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
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.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Organic Chemistry
• The chemistry of carbon
• Hydrocarbons are the
most basic example
– Combustible
– Can form rings
The variety of carbon compounds is
limitless
All terrestrial life is based on carbon
Biological Chemistry II: pH,
Intermolecular forces and
biomolecules
Bio 11
Covalent bonds hold together the
macromolecules of life
• Living things create
macromolecular products for
structure:
• 6CO2(g)+ 6H2O(l) + hν  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
Electronegativity determines properties
of covalently bonded molecules
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
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
Hydrogen bonding in water determine
many of water’s unique properties
• H-bonds can form a
lattice (ice)
• H-bonds require much
energy to break
• H-bonds give water
surface tension
Hydrogen bond
Water dissolves many ionic
compounds (“like dissolves like”)
Intermolecular Hydrogen bonds give water its
surface tension
Intermolecular Hydrogen bonds require
much heat in order to be broken
Hydrogen bonds don’t only happen
between water molecules
• Ethanol contains –OH
group and can form Hbonds
• H-bonds can form
between nitrogen and
hydrogen
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
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
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
Acids donate [H+] to water
Bases remove [H+] from water (or donate [OH-]
to water)
• Proteins are very sensitive to small changes in
pH
Ionization reactions can increase or
decrease pH
• NaCl  Na+ + Cl• HCl  H+ + Cl• NaOH  Na+ + OHH+ + OH-  H2O
LE 2-15
pH scale
H+
H+
H+
H+ OH
+
OH- H
H+
H+
Lemon juice, gastric juice
H+
Grapefruit juice, soft drink
Acidic solution
Tomato juice
Human urine
OH-
OH-
-
H+
H+ OH
OH OHH+
H+
H+
Neutral solution
NEUTRAL
[H+[
-
Pure water
Human blood
Seawater
Milk of magnesia
Household ammonia
OHOHOH-
OHH+
H+
OH-
Household bleach
OH-
Basic solution
Oven cleaner
Figure 2.16b
Figure 2.16a
7. FUNCTIONAL GROUPS
hydroxide group
– OH
amino group – NH2
carboxyl group
– COOH
phosphate group – PO4
methyl group – CH3
The physical/
chemical
properties of
carbon skeletons
can be modified
by functional
groups
figure 02-20b.jpg
2.20 –
Part 2
Figure 2.20 – Part 2
Functional groups can radically change the
function of a molecule
Estradiol
Female lion
Testosterone
Male lion
• 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*
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
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.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
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.
LE 4-10ba
STRUCTURE
EXAMPLE
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.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
Thiols
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
Organic molecules are good energy sources
Energy is required to form covalent bonds;
energy is released when bonds are broken
Most molecules in living things fall into
four categories
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•
•
•
Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction
Modular housing
Made of interchangeable parts
Freight trains have modular assembly
Modular assembly allows a wide
variety of products from a few pieces
Most biopolymers of life are formed by
dehydration synthesis
Hydrolysis is
the reverse
reaction
(Catabolic)
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
Glucose can cyclize to form a ring
structure
Atoms in bonds are free to rotate around the bonds
Glucose + Glucose = Maltose
Sugar dimer)
(A
Sugars are not limited to 6 carbons
• Sugars can be from 3
to 8 sugars
• 6 and 5-carbon
varieties are the
most common
(pentoses and
hexoses)
Two common sugar dimers
Raffinose, a sugar trimer, can be
found in legumes
Chain can be extended to thousands
9. Carbohydrates
• functions
- principle source of energy
(4 kcal/g)
- structure & energy storage
in plants
atoms - C H O
structure - ring or chain of 56 C’s
monosaccharide
- single sugars (example:
glucose)
disaccharide
- double sugars (example:
sucrose)
polysaccharide
- polymer or chain of 100’s
sugars
- starch & cellulose (mostly
plants)
- glycogen (animals, esp.
liver)
Proteins are made of amino acids
Proteins are polymers made of 20
different kinds of amino acid monomers
table 03-02bc.jpg
Table 3.2 – Part 2
Table 3.2 – Part 2
table 03-02d.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3
figure 03-04.jpg
Modular assembly
of amino acids
through
dehydration
synthesis
Formation of a
peptide bond
3.4
Proteins have an incredible variety of
structures
Proteins have an incredible variety of
functions
Hair, skin, fingernails, muscles, eye pigments, are all
made of protein
Enzymes are critical protein
machines
• Enzymes speed up
chemical reactions in
the body
• Their shape is necessary
to their function
• Shape is dependent on
protein structure
Proteins have four levels of
structure
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•
•
•
•
Primary
Secondary
Tertiary
Quaternary
Protein structure
depends on all these
levels of interaction
Primary structure
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•
•
•
•
Determined by the sequence of amino acids
Amino acids linked by peptide bonds
Chain is called polypeptide
Sequence proceeds from “N-terminus” to “C-terminus”
Amino acid sequence determined by DNA code
Secondary structure
• Hydrogen bonding between amino acid side chains
• Amino group hydrogens bind with Oxygens from carboxyl
end
Alpha-helix and Beta-sheet are two
important 2o structural motifs
Tertiary structure
• The folding interactions from
amino acid side chains of a
polypeptide
• The folding of 2o domains
upon each other
• Interactions can be ionic, Hbonds, hydrophobic, or
covalent
• Proper 3o structure depends
on pH, temperature
A lightbulb filament has multiple
levels of structure
Quaternary structure
• The interactions of
multiple polypeptides
to form a functional
protein
London dispersion/induced dipole
intermolecular interactions occur
between hydrophobic molecules
• Between hydrophobic/ non-polar/ lipophilic molecules
• Effects are cumulative over large hydrocarbon chains
Lipids
•
•
•
•
•
•
Non-polar
High-energy molecules
For energy storage
Forms cell membranes
Hormones
Members of family
include oils, fats, waxes,
and cholesterol
(steroids)
Hydrocarbons are nonpolar
• So are lipids
• Nonpolar substances
are usually insoluble in
water
• Interact through
London dispersion/
induced dipole
interactions
Lipids are non-polar
• Therefore, they are
hydrophobic
• C and H are similarly
electronegative
• Do not mix easily with
water
• C-H bond is high in
energy
• Lipids make good energy
storage molecules
Triglycerides are a primary lipid structure
Dehydration synthesis links fatty acids to
glycerol
Fatty acids can be saturated and
unsaturated (“cis” and “trans”)
Cis- and Trans- fatty acids are
isomers
• Melting point is very
different because of
shape
• Health effects are very
different
Triglycerides can be modified to
form phospholipids
• Phospholipids are
amphipathic- having a
polar and nonpolar
region
• Hyrophilic head,
hydrophobic tails
• Primary constituent of
cell membranes
Steroids and cholesterol are also lipids
Estradiol
Female lion
Cholesterol
Testosterone
Male lion
Isoprenoids constitute another
important subcategory of lipids
• The 5-carbon isoprene
subunit can be used to form
many important compounds
• Artemisinin is an important
antimalarial isoprenoid
Nucleic acids
• Informational molecules
in cells
• Include DNA, RNA, and
ATP/ADP
• DNA is the code to
make a protein
• Living things are made
up of protein
• Have other functions
Nulceotides are the subunits of nucleic
acids
• Consist of a sugar, a
phosphate, and a
nitrogen-containing
base
• Sugar can be
deoxygenated
• Bases contain the
genetic information
Hydrogen bonds hold the two sides
of the DNA ladder together
• DNA bases have –OH
and –NH2 groups
• Sides of ladder are
covalently bonded
• Rungs held together
with H-bonds
Review
•
•
•
•
•
•
•
•
•
Atomic structure- protons, neutrons electrons
Valence electrons
Carbon
pH
Functional groups
Carbohydrate structure
Protein structure
Lipid structure
Nucleic acid structure