Transcript Chemistry for Bio 11

Chemistry for Bio 9
Which of the following is/are
properties of life?
1. Cellular structure
2. the ability to take in energy and use it
3. the ability to respond to stimuli from the
environment
4. the ability to reproduce
5. All of the choices are correct.
Lecture outline
• Chemistry- definition, scope, and relevance to
biology
• Classification of matter
• The atom and subatomic particles
• Chemical bonding & reactions
• Chemistry of water
• Acids, Bases, and the pH scale
Chemistry is relevant to Biological
Concepts
• Chemistry is the study of matter and its
interactions
• All Living things are made of matter
• Biolgists are interested in:
– Complex biological molecules
– Chemical energy
– Biochemical reactions
– The chemical environment
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)
• Earth has been transformed by chemical
reactions peformed by living things
Biochemical reactions
• All living things are
collections of a vast
number of chemical
reactions
• Even the simplest living
things contain
impossibly complex
pathways
The Chemical Environment
• The physical properties
of water determine the
fate of life on earth
• pH, salinity and other
chemical factors
influence
• Living things are
profoundly influenced
by their chemical
environment
Chemical reactions performed by living
things have transformed earth over billions
of years of its history
Classification of matter
Classification of matter
Mixtures can be homogeneous or heterogeneous
Mixtures can vary in composition of their ingredients
Compounds are defined substances with proportional
amounts of ingredients: water, carbon dioxide, etc.
Elements cannot be broken down into ingredients by
chemical processes
Basic principles of chemistry
The periodic table is an organized display
of all the elements in the universe
The Structure of the Atom
Subatomic particles- protons,
neutrons electrons
Orbitals and the nucleus
All matter is ultimately comprised of
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
Reading the Periodic Table
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 (mass number) =
protons + neutrons of an
individual atom
Atomic weight= Naturally
occurring average of isotopes
of a substance
The number of neutrons in atoms
of a single element is variable
• Isotopes are variants of
an element,
differentiated by
numbers of neutrons
• Some isotopes are
stable, others are
radioactive
Some isotopes are common, others
rare
Many Isotopes for an element can exist;
radioisotopes are radioactive
Radioisotopes can be used in medical
diagnosis- Radioisotopes of iodine target
the thyroid gland
How is atomic weight different
from atomic mass?
The sodium atom contains 11 electrons, 11
protons, and 12 neutrons. What is the
mass number (atomic mass) of sodium?
1.
2.
3.
4.
5.
0
11
22
23
34
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
• Trace elements are
essential, but in small
quantities
A compound
1. A) is a pure element.
2. B) is less common than a pure element.
3. C) contains two or more elements in a fixed
ratio.
4. D) is exemplified by sodium.
5. E) is a solution.
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
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
Electrons in the outermost shell of an
atom are called valence electrons
Intramolecular Chemical Bonds:
Ionic, Covalent, and the
formation of molecules
Atoms are stable when their valence
shells are filled with electrons
• What atoms are
these?
• How could they
satisfy their
valence shells?
Noble gases have a stable electron
structure
• Their outer orbitals
have a full complement
of electrons
• Noble gases are very
unreactive
Elements combine in chemical
reactions to form compounds
• Molecules- 2 or more atoms combined in specific ways
• Compounds- different elements in a molecule, in exact,
whole-number ratios, joined by a chemical bond
• 2 major kinds of intramolecular chemical bonds:
Covalent (incl. polar and nonpolar) and Ionic
LE 2-7
In ionic bonding, an atom takes an
electron from another atom, forming
ions
Transfer of
electron
Na+
Sodium ion
Na
Sodium atom
Cl
Chlorine atom
ClChloride ion
Sodium chloride (NaCl)
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-
The nucleus of an atom contains
1.
2.
3.
4.
5.
protons and neutrons.
protons and electrons.
only neutrons.
only protons.
only electrons.
In covalent bonding, electrons are
shared
• Atoms form as many
bonds as they have
vacancies in their
outermost electron
orbitals
• Atoms are bound
together by the sharing of
electrons
• Chemical reactions often
involve the exchange of
covalent bonds
LE 2-6b
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
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
Many chemical reactions solely involve
exchange of covalent bonding partners
+
Chemical reactions performed by your body
create essential molecules your body needs
Beta-carotene
Vitamin A
(2 molecules)
Electronegativity and its effect
on chemical bonds
Ionic bonds, covalent bonds, and
intermolecular forces
Electronegativity values can predict
how atoms will bond
In covalent bonds, electrons do not always
share time between bond partners equally
•
•
•
•
•
•
Comparisions of electronegativity
Na: 0.9
H: 2.1
C: 2.5
N: 3.0
Cl: 3.0
O: 3.5
Electronegativity = “electron
greediness”
• Large differences in polarity of
atoms in a bond creates polar
molecules
• Relative electronegativity of
Hydrogen and oxygen makes
water a very polar molecule
• Polar- regions of positivity and
negativity
• By Oxygen, water is (slightly)
negative
• By Hydrogens, water is (slightly)
positive
Intermolecular forces and the
chemistry of water
Polarity and hydrophilicity,
Nonpolarity and hydrophobicity,
hydrogen bonding, and the chemistry
of water
Water is a “universal solvent” and dissolves
many polar and ionic compounds (“like
dissolves like”)
The polarity of water allows
hydrogen bonding
• Polar regions of water
molecules interact to
form hydrogen bonds
• Hydrogen bonds:
weak/temporary
intermolecular forces
between positive and
negative regions
Other molecules can engage in Hbonding, w/ water or other substances
Hydrogen bonds hold together the
two strands of a DNA double helix
Hydrogen bonding in water determine
many of water’s unique properties
• H-bonds can form a
lattice (ice)
• H-bonds require much
energy (usually heat) to
break
• H-bonds give water
surface tension
Hydrogen bond
Hydrogen Bonds help to make water cohesive,
allowing water surface tension and capillary
action
Capillary action allows redwoods
to grow to heights over 300 feet
Just as heat breaks H-bonds, as water
cools, more H-bonds form
Hydrogen bond
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
Because H-bonds have a fixed distance, the
crystal lattice of water makes ice less dense
Hydrogen bonds require energy to
break- water has a high specific heat
Water’s high
specific heat
allows
evaporative
cooling
-and makes
sweating an
effective cooling
mechanism
Due to water’s high specific
heat, proximity to water has
a stabilizing effect on
regional temperature
Nonpolar molecules are mostly
neutral
• C: 2.5, H: 2.1
• Very few positive or negative
regions, if any
• Hydrocarbons- compounds
solely made of hydrogen and
carbon, e.g. fats, oils, & gas
• Nonpolar substances are
hydrophobic and do not mix
well with water
Acids, bases, and the pH scale
Since ions do not share electrons,
they may separate in solution
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-]
Because Oxygen is much more
electronegative than Hydrogen,
water can occasionally Ionize
• H2O  H+ + OH• Also called dissociation
• Ions quickly reform into water:
–
H+ + OH-  H2O
• Approx 1 in 10,000,000 water molecules is
dissociated at any given time (that is, 10-7)
Other substances ionize
•
•
•
•
•
•
Usually ionic compounds
Many ionize completely
Salt: NaCl  Na+ + ClHydrochloric acid: HCl  H+ + ClSodium Hydroxide: NaOH Na+ + OHSubstances which ionize can affect the pH of a
water solution
pH is a measure of acidity/basicity
•
•
•
•
•
pH = -log [H+] (logarithmic scale)
pH 1 6.9: acid
pH 7.114: base
Acids donate [H+] to water- cause burns
Bases remove [H+] from water (or donate [OH-]
to water) – often have a slimy feel
• Strong acids & bases are ~equally nasty
• Proteins are sensitive to small changes in pH
LE 2-15
pH scale
H+
H+
H+
-
H+ OH
+
OH- H
H+
Lemon juice, gastric juice
H+
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
OHOHOH-
Household ammonia
OH-
H+
H+
OH-
Household bleach
OHOven cleaner
Basic solution
Acid rain pollution can cause tremendous
ecological damage
SO2 (g)+ H2O SO2·H2O
SO2·H2O H++HSO3HSO3- H++SO32-
Mechanism of acid rain
More effects of acid rain
Buffers can help control changes in
pH
The Relationships between Two Different Drinking
Water Fluoride Levels, Dental Fluorosis and Bone
Mineral Density of Children
•
S.R. Grobler*, A.J. Louw, U.M.E. Chikte, R.J. Rossouw and T.J. van W. Kotze Oral and Dental Research Institute, Faculty of
Dentistry, University of the Western Cape, Republic of South Africa
Abstract: This field study included the whole population of children aged 10–15 years (77
from a 0.19 mg/L F area; 89 from a 3.00 mg/L F area), with similar nutritional, dietary
habits and similar ethnic and socioeconomic status. The fluoride concentration in the
drinking water, the bone mineral content, the bone density and the degree of dental
fluorosis were determined. The left radius was measured for bone width, bone
mineral content, and bone mineral density. The mean fluorosis score was 1.3 in the
low fluoride area and 3.6 in high fluoride area. More than half the children in the low
fluoride area had no fluorosis (scores 0 and 1) while only 5% in the high fluoride area
had none. Severe fluorosis (30%) was only observed in the high fluoride area. The
Wilcoxon Rank Sum Test indicated that fluorosis levels differed significantly (p < 0.05)
between the two areas. No relationships were found between dental fluorosis and
bone width or between fluorosis and bone mineral density in the two areas
(Spearment Rank correlations). A significant positive correlation was found in the
high fluoride area between bone mineral density over age. In the 12-13 and 13-14
year age groups in the high fluoride area, girls had higher bone mineral densities.
However, a significant negative correlation (p<0.02) was found in low fluoride area
(0.19 mg/L F) over age.
Water's surface tension and heat storage
capacity is accounted for by its
1.
2.
3.
4.
5.
orbitals.
weight.
hydrogen bonds.
mass.
size.