Lecture 2 - Chemistry - Bio 105 - Napa Valley College 2...8/27/2013 10 Atomic Atomic WWeight eight =...
Transcript of Lecture 2 - Chemistry - Bio 105 - Napa Valley College 2...8/27/2013 10 Atomic Atomic WWeight eight =...
8/27/2013
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Chemistry
Biology 105
Lecture 2
Reading: Chapter 2 (pages 20-29)
Outline
Why study chemistry???
Elements Atoms Isotopes Periodic Table Electrons
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Bonding Bonds Covalent bonds Polarity
Ionic bonds Hydrogen bonding
Water Acids and Bases
Why study chemistry?
Chemistry is the basis for studying much of biology.
The biology of the human body follows the rules of physics and chemistry.
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You need to understand enough about chemistry to know what kinds of things will cross a membrane, and what the biological compounds are that make-up cells. What is a protein?
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Definitions and the Basics
Matter is anything that takes up space and has mass.
Atoms are units of matter that cannot be
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broken down into simpler substances.
An element is a “pure” form of matter containing only one kind of atom.
Elements in nature
Text page 22
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The Atom
We used to think that an atom could not be divided, but now we know atoms are composed of parts (particles):
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Protons – carry a positive charge
Neutrons – have no charge (neutral)
Electrons – carry a negative charge
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Table 2.1 Review of Subatomic Particles
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The Atom
Protons and neutrons are in the center of the atom.
Electrons orbit around the outer edge in orbitals.
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In each atom the # electrons = # protons.
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Chemistry and Biology
Copyright © 2009 Pearson Education, Inc. Figure 2.1c
Shell Model of Electrons
Electrons can be visualized as residing in shells around the nucleus.
The first shell can have up to two electrons.
The second shell can have up to eight electrons.
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The second shell can have up to eight electrons.
The third, fourth … shells can have up to eight electrons.
Protons are found in the …
50%50%1. Nucleus
2. Orbital shells
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Nucl
eus
Orb
ital s
hells
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How many electrons can be in the 1st shell?
25% 25%25%25%1. One
2. Two
3. Four
4 Ei ht
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One
Tw
o F
our
Eig
ht
4. Eight
How many electrons can be in the 2nd shell?
25% 25%25%25%1. One
2. Two
3. Four
4 Ei ht
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One
Tw
o F
our
Eig
ht
4. Eight
Periodic Table of Elements
Copyright © 2009 Pearson Education, Inc. Figure 2.2
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The atomic number = the # of protons in an atomThe atomic number = the # of protons in an atom
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The atomic number the # of protons in an atomThe atomic number the # of protons in an atom
Atoms have equal numbers of protons and Atoms have equal numbers of protons and electrons.electrons.
Particle Mass
Proton = 1 amu
Neutron = 1 amu
Electron = negligible
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How many electrons does Be have?
25% 25%25%25%
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4 5 9 13
1. 4
2. 5
3. 9
4. 13
Isotopes
Atoms with the same number of protons but different numbers of neutrons are called isotopes.
Isotopes of Hydrogen:
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Radioactive Isotopes
In 1896, Henri Becquerel placed a rock on unexposed photographic plates inside a drawer. The rock contained uranium.
The isotopes of uranium emit energy.
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After a few days the plate had an image of the rock.
A co-worker, Marie Curie, named this radioactivity. This is known as a radioisotope.
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Radioactive Isotopes
Radioisotopes are isotopes that are unstable, and become more stable by emitting energy and particles.
In contrast, most isotopes are stable.
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Radioisotopes in Medicine
PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled
with an unstable isotope
Cancer cells are growing faster and take up more of the compound than normal cells
Ab l ti t k l f th d
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Abnormal tissue takes up less of the compounds
Isotopes in Medicine
Copyright © 2009 Pearson Education, Inc. Figure 2.4
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Isotopes are atoms of the same element that differ in their number of …
25% 25%25%25%1. Protons
2. Electrons
3. Neutrons
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Pro
tons
Ele
ctro
ns
Neu
trons
None
of the
abo
ve
4. None of the above
Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic number is ___.
25% 25%25%25%1. Six
2. Eight
3. Twelve
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Six
Eig
ht
Tw
elve
Tw
enty
-four
4. Twenty-four
Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic weight is ___.
25% 25%25%25%1. Six
2. Eight
3. Twelve
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Six
Eig
ht
Tw
elve
Tw
enty
-four
4. Twenty-four
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Atomic Atomic WWeight eight = an average of the isotopes= an average of the isotopes
MassMass NumberNumber = round the atomic weight= round the atomic weight
Atomic number
Atomic weight
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Mass Mass Number Number round the atomic weight round the atomic weight
Mass Number = (Number of Protons) + (Number Mass Number = (Number of Protons) + (Number of Neutrons)of Neutrons)
Number of Neutrons = Number of Neutrons = (Mass Number) (Mass Number) –– (Number (Number of of Protons)Protons)
For any element:For any element:
Number of Protons = Atomic Number of Protons = Atomic NumberNumber
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Number of Electrons = Number of Electrons = Number of Number of Protons = Protons = Atomic Atomic NumberNumber
Number of Neutrons = Mass Number Number of Neutrons = Mass Number -- Atomic Atomic NumberNumber
For Be:For Be:
Number of ProtonsNumber of Protons= Atomic Number = = Atomic Number = 44
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Number of ElectronsNumber of Electrons= = Number Number of Protons = of Protons = 44
Number of NeutronsNumber of Neutrons= Mass Number = Mass Number -- Atomic Number Atomic Number
= 9 = 9 -- 4 = 54 = 5
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Chemical Bonds
Chemical bonds are unions between electron structures from different atoms.
Molecules are when two or more atoms join together. The atoms can be the same element (H ) diff t l t (H O)
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(H2) or different elements (H2O).
When different elements join, the molecule is referred to as a compound molecule.
Electrons and Bonding
If the outer shell is full, then it is non-reactive and stable = does not form chemical bonds.
Incompletely filled outer orbital, then atom is reactive and will form chemical bonds.
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How many bonds it can form depends on how many empty spots in outer shell.
How many neutrons does Li have?
25% 25%25%25%
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3 4 7 10
1. 3
2. 4
3. 7
4. 10
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Chemistry and Biology
Copyright © 2009 Pearson Education, Inc. Figure 2.8
Chemical Bonds
Covalent bonds
Ionic bonds
Hydrogen bonds
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Covalent Bonds
Covalent bonds: The strongest bonds
They form when two or more atoms share the electrons in their outer shells.
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How many bonds can form?
Each atom wants their outer shell filled.
Hydrogen only has one electron in its shell – it wants two, so it can form one bond.
Carbon has four electrons in its outer shell – it wants eight, so it can form four bonds.
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Double Bond
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How many bonds can carbon form?
25% 25%25%25%
1. One
2. Two
3. Three
4. Four
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One
Tw
o
Thre
e F
our
How many bonds can hydrogen form?
25% 25%25%25%
1. One
2. Two
3. Three
4. Four
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One
Tw
o
Thre
e F
our
How many bonds can helium form?
25% 25%25%25%
1. None
2. One
3. Two
4. Three
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None
One
Tw
o
Thre
e
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How many bonds can nitrogen form?
25% 25%25%25%
1. One
2. Two
3. Three
4. Four
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One
Tw
o
Thre
e F
our
How many bonds can oxygen form?
25% 25%25%25%
1. One
2. Two
3. Three
4. Four
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One
Tw
o
Thre
e F
our
Covalent Bonding
When two atoms with unpaired electrons in the outermost shell come together and share electrons.
Each atom has an attractive force for the other
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atom’s unshared electrons, but not enough to take them completely away.
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Covalent Bonding
Covalent bonds can be polar or nonpolar.
Nonpolar bonds: the atoms have the same pull on the shared electrons (H2).
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Polar bonds: the atoms don’t equally share the electrons (H2O).
Polar Covalent Bond
Copyright © 2009 Pearson Education, Inc. Figure 2.11a
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Polarity
Some atoms have a greater pull on shared electrons than other atoms.
The measure of this pull is electronegativity.
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When a bond is made between atoms with different electronegativities, it is a polar bond.
The greater the pull, the more electronegative (remember that electrons are negative).
Polarity
Polar covalent bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons.
Common examples in biological molecules
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include: Oxygen
Nitrogen
Sulfur
Polarity
The oxygen side of water is slightly negative and the hydrogen sides are slightly positive.
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C
H
H O
H
HO
H
H
H2
OH2C C
O
Water Alcohol
Ketone Aldehyde
C
H
H H
H
H3C
H2C
CH2
CH
H3C
C
CH2
C
CH3
H3C
H2C
CH2
H2C
CH2
H2C
CH2
CH3
Hydrocarbons
NHH
CH3
SH
CH3
HC
HC
CH
CH
CH
HC
Oxygen containing: Carboxyl = -COOH
Hydroxyl (alcohol) = -OH Phosphate = -PO4
Carbonyl:K t CO
Polar Groups
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Ketone = -CO Aldehyde = -CHO
Nitrogen containing = amino (-NH2) Sulfur containing = -SH
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CH3CH2CH2OH
CarboxylCarboxyl
AlcoholAlcohol
KetoneKetone
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CH3-O-CH2CH3
CH3CH2CH3
AldehydeAldehyde
EtherEther
HydrocarbonsHydrocarbons
Nonpolar Compounds
Hydrocarbons – lots of carbons and hydrogensbonded together.
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Terminology
Hydrophilic (water-loving) – polar molecules that are attracted to water.
Hydrophobic (water-fearing) – nonpolarmolecules that are pushed aside by water.
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p y
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Chemical Formulas
When we write compounds, we often write them as a formula that tells how many atoms of each element are present, but not the way the molecule is put together.
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You often can determine the way the molecule is put together by knowing how many bonds each element can form.
Examples
How would you draw this compound? H2O
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O H
H
Examples
How would you draw this compound? C4H10
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C C C C
H
H
H H H
H
H
H
H
H
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Examples
How would you draw this compound? C4H8
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C C C C
H
H
H H
H
H
H
H
Examples
How would you draw this compound? CO2
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C OO
Examples
How would you draw this compound? C2H4O
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C C H
H
H
H O
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Hydrogen Bonding
Weak attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge (an electronegative atom such as oxygen, nitrogen, or sulfur).
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Hydrogen Bonding
Individually weak, but many together can be strong.
Determines shape of many biological molecules, including proteins and DNA.
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, g p
Hydrogen Bonds
Copyright © 2009 Pearson Education, Inc. Figure 2.11b
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Ionic Bonds
Ion = atom that has gained or lost electrons It no longer has a balance between protons and
electrons.
It has a positive or negative charge.
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Ionic bond is an association between ions of opposite charge.
Ionic Bond
Copyright © 2009 Pearson Education, Inc. Figure 2.10
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Chemical Bonds
Copyright © 2009 Pearson Education, Inc. Table 2.2
Water – The Life Giving Molecule
Why are we so interested in finding evidence of water on Mars?
What would it mean if we did not find evidence of water? Or if we find evidence? Does it matter what form the water is?
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matter what form the water is?
Life exists here because water is abundant!
Water’s Abundance
71% of the Earth’s surface is water 97.5% of the water is salt water Freshwater only accounts for 2.5% of water Only 0.53% is available to us to drink (rivers,
lakes, ground water)
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66% of the human body is water by weight 75-85% of a cell’s weight is water
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Water
Water is polar and forms hydrogen bonds.
Water is a great example of hydrogen bonding – the hydrogen bonds give water many of its unique characteristics.
H
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O
H
OH
H
Exists in Three Forms
Water exists in three forms Solid - Ice
Liquid
Vapor
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Water Exists in Three Forms – (1) Ice (Solid)
As water approaches 0˚C, its freezing temperature, the molecules slow down.
Water forms more hydrogen bonds at lower temperature and forms a lattice structure.
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p
The ice is less dense due to the lattice structure and to the fact that there are less molecules present than in the same volume of liquid.
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Ice Caps
The floating property of ice allows the ArticOcean’s ice cap to exist.
This is the habitat for polar bears and young seals, as well as many other species.
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These ice caps are melting, and as they melt the habitat for these species shrinks.
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So what does all this mean?
The polarity and ability to form hydrogen bonds give water its properties.
Properties of Water
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There are four properties of water…
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1. Water is an excellent polar solvent
Because water is polar and forms hydrogen bonds, it acts as a solvent for polar molecules.
Like dissolves in like, so polar molecules dissolve in water.
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Water is considered the best polar solvent –due in great part to its ability to form hydrogen bonds with other molecules.
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Why is this property important?
Blood is approx 55% water, so the fact that water is a good solvent makes blood a good way to transport things around.
Cells are made up of mainly water: the water
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keeps salts in your cells, blood, and tissues in solution.
2. Water has cohesion
Due to the hydrogen bonding, water has cohesion (the water molecules cling together).
Cohesion is the capacity to resist breaking under tension.
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2. Water has cohesion
What allows bugs to walk on water?
Hydrogen-bonds create surface tension
At the surface of water, where water meets air, the water molecules are being pulled down with a much greater force than they are being pulled
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up towards the air.
The cohesion of water allows blood to move more easily through the blood vessels.
Also is responsible for moving water in plants
Why is this property important?
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3. Water has high heat capacity
It takes a great deal of energy to raise the temperature of water.
When you increase the temperature of something, the molecules in it move faster.
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Hydrogen bonds keep the water molecules in place, so it takes lots of energy to break the bonds and heat the water.
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Water in our bodies keeps us at a constant temperature.
Why is this property important?
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4. Water has high heat of vaporization
It takes a great deal of energy to make water evaporate (change water from a liquid to a gas).
Hydrogen bonds must be broken in order to
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change water from liquid to vapor.
Sweat is mainly water, so when we sweat the body uses its heat to vaporize the water –cooling us off.
Why is this property important?
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H2 is a(n)
33% 33%33%1. Atom
2. Molecule
3. Compound molecule
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Ato
m
Mole
cule
Com
pound m
olecu
le
molecule
Hydrophobic molecules are __________ by water.
50%50%1. Attracted
2. Repelled
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Attr
acte
d
Rep
elle
d
What type of bond between water molecules creates surface tension that gives water cohesion?
33% 33%33%1. Ionic
2. Covalent
3 Hydrogen
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Ioni
c
Cova
lent
Hyd
roge
n
3. Hydrogen
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Water…
33% 33%33%1. Makes ionic bonds
2. Is nonpolar
3. Is polar
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Mak
es io
nic b
onds
Is n
onpola
r
Is p
olar
Which property of water provides the cooling effect of sweating?
25% 25%25%25%1. Cohesiveness
2. High heat capacity
3. High heat of vaporization
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Cohes
iven
ess
Hig
h hea
t cap
acity
Hig
h hea
t of v
apor
iz...
Exc
elle
nt s
olven
t
vaporization
4. Excellent solvent
Acids and Bases
We are already familiar with acids and bases.
Common acids: Lemon juice
Sodas
Vinegar
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Common bases: Ammonia
Many household cleaners
Bleach
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Acids and Bases
Acids – substances that donates hydrogen ions when in solution:
HCl H+ + Cl-
Bases – substances that accept hydrogen ions when in solution:
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NaOH Na+ + OH-
In solution:
H+ + Cl- + Na+ + OH- H2O + NaCl
pH Scale
The strength of acids and bases is measured using the pH scale.
pH = -log10[H+]
[H+] = concentration in moles per liter
It is an inverse relationship:
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p Higher pH = lower concentration of H+
Logarithmic: Each point increase in pH represents a ten-fold
decrease in H+ concentration.
pH Scale
Scale from 0 – 14 0 is the most acidic
14 is the most basic
7 is neutral (pure water)
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Acids and Bases
Copyright © 2009 Pearson Education, Inc. Table 2.3
The higher the pH a solution has, the higher the H+ concentration.
50%50%1. True
2. False
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Tru
e
Fal
se
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Is a pH of 8 acidic or basic?
50%50%1. Acidic
2. Basic
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Aci
dic
Bas
ic
Biological Fluids
Blood – pH 7.35 Changes in pH of ± 0.1 can damage cells. pH of 7.8 can be lethal!
Biological fluids have buffers to keep the pH stable
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stable.
Most biological fluids are between 6 – 8.
Stomach fluid – pH of under 2
Buffers
Buffers resist pH changes because they are chemicals that can take up excess H+ or OH-.
Our body wants to keep its fluids at an even pH.
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Blood contains buffers that are weak acids that can dissociate into ions.
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Buffers
For example, when CO2 enters the blood it combines with H2O to form carbonic acid (H2CO3).
This weak acid dissociates to form H+ and
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bicarbonate ion (HCO3-).
Acids in the Environment
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Acid Rain
The two main sources of acid rain are H2SO4
and HNO3.
Most of H2SO4 pollution comes from electric power plants.
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Most of HNO3 pollution comes from cars, buses, etc.
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Effects of Acid Rain
Acid rain acidifies lakes and streams.
More acidic water leaches more heavy metalsfrom the soil than normal water.
Declining frog and fish populations may be due
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more to increased metal concentrations in the water than due to the acidic water itself.
Important Concepts
Reading for next lecture: Chapter 2 (pages 29 –39)
What are the three particles of an atom, where are they located, what are their charges, and masses?
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Be able to determine how many bonds each element can form.
Be able to recognize if a molecule is drawn correctly.
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Important Concepts
Be able to read the periodic table to determine the number of protons, neutrons, and electrons in the atoms of all the biologically important elements.
What are the three most common elements in
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the human body?
Be able to draw the atom of any biologically important element, with the correct number of protons, neutrons, and electrons. Be able to draw the electrons in their correct shell(s).
Important Concepts
Be able to identify polar and nonpolar molecules.
Be able to describe the types of chemical bonds.
Be able to draw a water molecule and hydrogen b di b l l
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bonding between water molecules.
Be able to describe the four properties of water and their importance in living organisms.
Understand the pH scale.
Important Concepts
What are three electronegative elements found in biological molecules?
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Definitions
Matter, atom, element, isotope, radioisotope, chemical bond, single bond, double bond, molecule, compound molecule, ion, ionic bond, covalent bond, nonpolar bond, polar bond, electronegativity, hydrogen bond, hydrophilic, h d h bi h i id b b ff
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hydrophobic, cohesion, acid, base, buffer, logarithmic, inverse, pH, solvent, solute, solution