Lec 1.1 & 1.2 - org of life, subatomic particles

LCC Biol 121, Kitty O'Neil, Instructor 1/8/2010

Course details
• Office Hours – Tu 2:30 – 3:00, Tu & Th 6:00 – 6:40PM
– in the LSARC (AS455)
Biology 121 – Biological – Plus additional time as needed, before & after class
• 2 Textbooks –
Foundations for Physiology – Essentials of Biology, 2nd ed., Sylvia Mader
Instructor: – Lab manual, Wagner
• LCC Angel website - http://angel.lcc.edu
Kitty O’Neil
• Attendance – doesn’t count for anything, or does it?
oneil17@lcc.edu • Grades, exams, quizzes, homeworks
• Additional learning resources

Date Part Lecture Title
1/14/2010 1 Basic chemistry 1.1 Organization of Life / Atoms

Course details 1/14/2010
1/21/2010
1/21/2010
1
1
1
1.2
1.3
1.4
Subatomic Particles / Ionic bonds
Covalent Bonds and Polarity
Water and pH
1/28/2010 1 1.5 pH and Buffers
1/28/2010 2 Basic organic chemistry 2.1 Organic Compounds
2/4/2010 Exam 1
• Office Hours – Tu 2:30 – 3:00, Tu & Th 6:00 – 6:40PM 2/4/2010 2 2.2 Functional Groups and Reactions
2/11/2010 2 2.3 Carbohydrates
– in the LSARC (AS455) 2/11/2010
2/18/2010
2
2
2.4
2.5
Lipids
Proteins and Nucleic Acids
– Plus additional time as needed, before & after class 2/18/2010
2/25/2010
3 Cells and organelles 3.1 Cells and Organelles
Exam 2

• 2 Textbooks – 2/25/2010
3/4/2010
3
3
3.2
3.3
Cytoskeleton
Membranes and Transport

– Essentials of Biology, 2nd ed., Sylvia Mader 3/4/2010
3/18/2010
3 3.4 Osmosis and Capillary Dynamics
Exam 3
3/18/2010 4 Cellular energy metabolism 4.1 Reduction and Oxidation
– Lab manual, Wagner 3/25/2010 4 4.2 Glycolysis and the Kreb’s Cycle
3/25/2010 4 4.3 Electron Transport Chain
• LCC Angel website - http://angel.lcc.edu 4/1/2010
4/1/2010
4
5 Genetic Information
4.4
5.1
Other Energy Sources, Energy Wrap Up
DNA & Replication
• Attendance – doesn’t count for anything, or does it? 4/8/2010
4/8/2010 5 5.2
Exam 4
RNA, Transcription

• Grades, exams, quizzes, homeworks 4/15/2010
4/15/2010
5
5
5.3
5.4
Proteins, Translation
Regulation of Gene Expression
4/22/2010 5 5.5 Mendelian Genetics
• Additional learning resources 4/22/2010
4/29/2010
5
5
5.6
5.7
Beyond Mendel Part I
Beyond Mendel Part II
Cell Division · Meiosis in Humans · Chromosomal
4/29/2010 5 5.8 Abnormalities
Exam 5

1


Course details LCC Withdrawal Policy
• In-class participation is encouraged
• Schedule – approximate

• Periodic Table –
– KEEP THIS IN YOUR NOTEBOOK! We’ll need to
refer to it in class during Part 1 of the course.

Biology 121

? Lecture 1.1
Biology Defined
Organization of Life

Q of the Day :: Define “Life” -- what
characteristics typify a living creature??
 Defining Life is a question
you might address in a
philosophy class
 In biology, we can satisfy
ourselves by describing
common characteristics of
life.
 What those important
characteristics are depends
on………who you ask.

2


Life is cellular Life uses energy
• Life is not defined by its • How do living things survive?
size • All living things process
• From a unicellular amoeba energy –
to a brontosaurus… – Eat, or ingest nutrients
• All life is composed of – Excrete waste
individual units called cells – Harvest energy in a useable
form
• The cell is the smallest
unit of a living organism • Collectively, these processes
are called “metabolism”

Life can sense its environment, respond
Life reproduces itself
Life can maintain homeostasis
• All life forms can sense and • How does life continue?
respond to stimuli in their
environments • All life forms duplicate
– See plants respond to themselves, through
light sexual or asexual
http://www.ncsu.edu/project/agron
auts/mission4_6.htm means, by duplicating
• Living organisms can their genetic material
maintain homeostasis – (DNA)
internal conditions
different from
surrounding environment

Life is highly complex, but highly
organized Summing it all Up…
• There is a large array and variety 1. life is cellular (the cell is the
of living organisms…. smallest unit considered
“alive” )
– Single cell organisms
– Multicellular organisms 2. life takes in and uses
energy
– Microorganisms
3. life responds to the
– Plants and animals environment
• ….but all are composed of the 4. life maintains homeostasis
same essential elements 5. life reproduces itself
• organization is hierarchal 6. life is highly complex and
organized

3


More about the Hierarchal Can you organize these units, from
Organization of Life smallest to largest?

Here are the answers. Let’s go
through each level individually. “Cell and tissue, shell and bone, leaf
and flower, are so many portions of
matter, and it is in obedience to the
laws of physics that their particles
have been moved, moulded, and
conformed.”
7: organism 1: atom 4: cell 5: organ

-D’Arcy Thompson, 1917
from On Growth and Form

3: organelle 2: molecules and compounds 6: organ system

Molecule -- when two or more atoms
Atom – the smallest unit of matter
interact, they form a molecule
• Although this is the
smallest in the series you • Molecules are formed
had to choose from, we’ll when individual atoms
see later that each atom or bond together. This
“element” is actually molecule is called ATP
composed of smaller (adenosine
subunits, called subatomic triphosphate), and is
particles, named protons, the energy currency for
neutrons and electrons. most cells.
• The atom is the smallest • A compound
unit of an element

4


Organelle -- many molecules working
together to perform a single function
Cell – the smallest unit of life
for the cell • Organelles work
• This is a photograph of
a mitochondria, one of
together within a
the organelles present living cell
in eukaryotic organisms.
• Cells parcel out their
workload to various
organelles, or “little
organs”.
• Mitochondria are the
organelles responsible
for making ATP.

Tissue -- two or more cells working Organ -- two or more tissues performing
together to perform a function a function
• Not a choice in your
series! But you will
learn a great deal • This picture of the
about tissues in lungs also has other
Biology 201, Human organs included --
Anatomy. This Areolar connective you can see the
hierarchal level and tissue
trachea and the
the remaining levels
bronchi.
are specific to Bone -- the
multicellular strongest
connective tissue
organisms.

Adipose – storing fat

Organ System -- two or more organs Organism -- All 11 organ systems working
performing a function for the organism cooperatively to form one individual
• This is an example of
• There are 11 organ a multicellular
systems in the organism
human body. You’ll
• Plants, animals, fungi
cover them
progressively in Biol …
201 and 202

5


Population - Community
• A group of the same • All populations in
type of organism one particular
located together in location
one area • Plant community in a
prairie
• Microorganism
community in our GI
tract

Ecosystem Biosphere
• A community + the physical • All the ecosystems
environment in which it exists making up the earth
and interacts • Earth, water,
atmosphere and
organisms

Learning Goal: Be able to rank order
Biol 121 is concerned with Levels 1-5
levels of organization
1. Subatomic particles 1. Subatomic particles
2. Atoms 2. Atoms
3. Molecules
4. Organelles 3. Molecules
5. Cells 4. Organelles
6. Tissues 5. Cells
7. Organs 6. Tissues
8. Organ systems 7. Organs
9. Multicellular Organism 8. Organ systems
10.Population -- a group of the same kind of organisms occupying the 9. Organism
same area 10.Population -- a group of the same kind of organisms occupying the
11.Community -- Populations of different species occupying the same area same area
11.Community -- Populations of different species occupying the same
12.Ecosystem -- The community AND the physical environment area
13.Biosphere -- all regions sustaining life 12.Ecosystem -- The community AND the physical environment
13.Biosphere -- all regions sustaining life

6


Biol 201 and 202 are concerned with You would learn about Levels 9-13 in an
organismal/environmental biology course like
Levels 5-9 128 or 120
1. Subatomic particles 1. Subatomic particles
2. Atoms 2. Atoms
3. Molecules 3. Molecules
4. Organelles 4. Organelles
5. Cells 5. Cells
6. Tissues
6. Tissues 7. Organs
7. Organs 8. Organ systems
8. Organ systems 9. Organism
9. Organism 10. Population -- a group of the same kind of organisms
10.Population -- a group of the same kind of organisms occupying the
occupying the same area
same area 11. Community -- Populations of different species
11.Community -- Populations of different species occupying the same area occupying the same area
12.Ecosystem -- The community AND the physical environment 12. Ecosystem -- The community AND the physical
13.Biosphere -- all regions sustaining life environment
13. Biosphere -- all regions sustaining life

Biology 121
Lecture 1.2
Basic Chemistry
Electron Shells

Elements Atom
• Fundamental forms of matter • Smallest particles that retain properties of an element
• Can’t be broken apart by normal means is an ATOM
• 92 occur naturally on Earth • Positively charged nucleus surrounded by cloud of
negatively charged electrons
• Most common elements in living organisms:
• Made up of subatomic particles:
– Oxygen (O) – Protons (+)
– Hydrogen (H) – Electrons (-)
– Carbon (C) – Neutrons (no charge)
– Nitrogen (N) • Has mass (we can think of mass as weight)
• Occupies space

7


Representing the Hydrogen Atom How Much Do You Know About Atoms?

• Atoms are composed of 3 subatomic
particles, called protons, neutrons and
electrons.
• Each has a characteristics charge and mass
associated with it:
Particle Charge Mass Location
Proton + 1 amu* nucleus
Neutron 0 1 amu nucleus
Electron - 0 amu shells
Fig. 2-2, p.20
* 1 Amu is a unit of mass (atomic mass unit), like a pound or gram, but much, much, smaller.

Atomic particles arranged in pattern Atomic Mass
• The MASS of the atom is concentrated in its • It’s time to mention another important concept
nucleus. regarding atomic weights……..
– Determined by numbers of protons and neutrons
– Positively charged protons and uncharged
neutrons are tightly packed in the nucleus

• The VOLUME of the atom is determined by the
negatively charged electrons
– Electrons orbit the nucleus in a series of concentric
6.02 x 10 23
‘shells’

What Does It Mean?? Why is it handy?
• A dozen is………..12 • Avogadro’s Number is a convenient amount of very
small things to count out, like 6.02 X 1023 protons
• A gross is…………..144 • 6.02 X 1023 protons weigh exactly 1.00 grams.
• A triple is……………..3 • 6.02 X 1023 H atoms weigh exactly 1.00 grams.
• A century is…………….100 • 6.02 X 1023 amu weigh exactly 1.00 grams.
• And Avogadro’s Number is…….6.02 X 1023 • Avogadro’s number relates the mass of a proton,
which is unimaginably and immeasurably small, to
something more tangible-- the gram
• In other words……it’s a predetermined, • 6.02 X 1023 molecules = 1 mole.
arbitrary number chosen for matters of • More information about Avogadro and his number
‘handiness.’ later

8


Compare 1 atom to 1 mole Protons -- the identity of the element

• Protons are positively charged
subatomic particles that have
a mass of 1 amu
1 egg 1 dozen eggs • They are located in the
(0.14 lbs) (12 eggs, 1.5 lbs) nucleus. See the green “dot”
at the right? It’s a proton.
• This particular atom contains
1 proton and 1 electron.
1 atom of C 1 mole of C
(12 amu) (6.02 · 1023 atoms , 7.22 · 1024 amu, 12 g)

Hydrogen Elements have abbreviations
 Hydrogen is the simplest atom. H
contains one proton • Each atom has a one or two letter short hand
abbreviation. The first letter is capitalized, the
• If a second proton were added to the nucleus, it
wouldn’t be H any longer. It’d be Helium. In fact, second is small case. They are derived from
every atom has its own characteristic number of the name of the atom:
protons. Each atom has an atomic number,
which reflects its proton total. H Hydrogen
He Helium
• For each proton in the nucleus, there must be a
C Carbon
corresponding electron in the shell to balance the
charges. The atomic number also reflects the Co Cobalt
number of electrons in a particular atom.

• The Periodic Chart of the elements contains all of Name that element! Don’t use your
the atoms, listed in atomic number order, reading in
rows from left to right. In most periodic charts, the
periodic chart
atomic number is on the top.
• H = Hydrogen
• He = ???
• Ne = ???
• C = ???
• Si = ??
• P = ??
• Na = ???

• Know the symbols for elements 1 through 20

9


Name that element! Name that Atom!
• Based on the number of protons (dark blue circles), which
• H = hydrogen atom is represented by each picture? For this, you DO
• He = Helium need to use your periodic chart.

• Ne = Neon
• C = Carbon proton

• Si = Silicon neutron

• P = Phosphorus
• Na = Sodium (from the Latin, Natrium)

Name that Atom! Neutrons -- add mass but no charge
Here are the answers!

• Neutrons are subatomic
particles that weigh 1
amu (same as a proton),
1 proton = Hydrogen (H) • but they are neutral,
6 protons = Carbon (C)
which means they have
no associated charge
(unlike a proton).

2 protons = Helium (He)
12 protons = Magnesium (Mg)

Atomic Mass (Weight) Calculate the atomic mass for these atoms
• Since both protons and neutrons (but not electrons…) contribute
mass (weight) to an atom, each atom has a characteristic atomic
weight, the total of all its protons and neutrons
• On most periodic charts, that number is written beneath the atom’s
symbol
Hydrogen (H)
Carbon (C)

Helium (He)
Magnesium (Mg)

10


Atomic Mass In Summary…
• The atomic number is a whole number, and is equal
to the number of protons in the nucleus of that atom.
Since protons and electrons are equal to neutralize
charges, it also tells you how many electrons are in
Hydrogen (H) has 0 neutrons Carbon (C) has 6 neutrons the shells.
and 1 proton and 6 protons – Atomic number = number of protons or electrons
Atomic Weight = 1 amu Atomic weight = 12 amu
• The atomic weight is a decimal number, and is the
sum of the protons and the neutrons. You know the
number of protons from the atomic number, the
number of neutrons is the difference between atomic
number and atomic weight.
Helium (He) has 2 neutrons
Magnesium (Mg) has 12 neutrons – Atomic wt – atomic number = number of neutrons
and 2 protons
Atomic weight = 4 amu
and 12 protons – Atomic wt = no. of protons + no. of neutrons
Atomic weight = 24 amu

Problems Problems
• How many neutrons are in one atom of the • How many neutrons are in one atom of the
following elements? following elements?
• Need to know 3 things… • Need to know 3 things…

Element N Li B F Element N Li B F
Atomic Wt Atomic Wt 14 7 11 19
No. Protons No. Protons 7 3 5 9
No. Neutrons No. Neutrons 14-7 = 7 7-3 = 4 11–5 = 6 19-9 = 10

Practice Problems Practice Problems - Answers

Atom: C Be Atom: C Be Si Na O He
Atomic number: 6 14 Atomic number: 6 4 14 11 8 2
Atomic weight: 12 22.99 Atomic weight: 12 9.012 28.09 22.99 16.00 4.003
No. Protons 6 8 No. Protons 6 4 14 11 8 2
No. Neutrons 6 2 No. Neutrons 6 5 14 12 8 2
No. Electrons 6 No. Electrons 6 4 14 11 8 2

Know how to calculate these parameters for elements 1
through 20.

11


Atomic Mass Atomic Mass
• Although atomic numbers are reported as whole • Atoms can exist in multiple forms in nature, with
digits, atomic weights are generally reported as differing numbers of neutrons. These forms are
decimals called isotopes (same atom, different form)
• C weighs 12.01 amu • Isotopes vary in number of neutrons; protons and
• Al weights 26.98 amu electrons remain the same.
• H weighs 1.008 amu
• If protons and neutrons each weigh 1.00 amu, where
does the extra “weight” of the atom come from?

Atomic Mass -- Part II Atomic Mass -- Part II
• Hydrogen typically has 1 proton and 0 neutrons, • Isotopes are indicated by writing the atomic symbol, with the
weighing a total of 1 amu.
specific weight of that isotope in the upper left hand corner
• But alternate, isotopic forms of H exist;
– Deuterim, 1 proton and 1 neutron, 2 amu, stable – 1H is hydrogen
– Tritium, 1 proton and 2 neutrons, 3 amu, unstable or – 2H is deuterium
radioactive – 3H is tritium

Hydrogen = 1H Deuterium = 2H Tritium = 3H
Stable Stable Radioactive

Atomic Mass Radioisotopes
• Have an unstable nucleus that emits
• The atomic mass indicated on
energy and particles as it ‘decays’
the periodic chart represents
our knowledge about the • Radioactive decay transforms
average mass, distributed radioisotope into a different element
among all the known isotopes • Decay occurs at a fixed, predictable
of each atom, that exist in the rate
universe. • Emissions from the radioactive
isotope can be detected with special
instruments
Isotope Rel. Abund. Half-life
12C 98.9% C is stable with 6 neutrons • Following movement of radioactivity
13C 1.1% C is stable with 7 neutrons
is useful in many areas of biology
14C
and health care
trace 5730 y

12


Radioactive Isotopes and Health Care Isotopes
• Radioactive isotopes have
two very special places in
the health care industry
– Diagnostics
– Therapeutics How many protons?
• Nuclear Energy Institute’s What element is it?
Informational Website to How many neutrons?
learn more about Nuclear What’s the atomic mass?
Medicine What is the isotope?
– http://www.nei.org/

Isotopes

Biology 121
Lecture 1.2
How many protons? 1 1 1 6 6
What element is it? H H H C C Basic Chemistry
How many neutrons? 0 1 2 6 8
What’s the atomic mass? 1 2 3 12 14
Electron Shells
What is the isotope? 1H 2H 3H 12C 14C

hydrogen deuterium tritium

Electrons -- the Bonding Story Electron Shells
• Electrons are the negatively charged subatomic • Electrons spin and rotate
particles without mass that make up the volume around the nucleus of an
of the atom
atom, but are constrained
• Electrons are SOCIAL -- they prefer:
to particular paths. They
– Being paired
live in shells
– Living in full shells
• Electrons repel each other • Similar to layers of an onion,
or floors of a hotel.
• Electrons are attracted to protons in the nucleus
• Electrons determine how atoms interact with or
bond with each other.

13


What keeps electrons constrained to What keeps electrons constrained to
their shells? their shells?
• Answer, part 1 • Answer, part 2

 But, they don’t fly off into space…  Opposite charges attract

Negatively charged electrons are attracted to
the positive charges on the protons
Electron shells
• There are specific places
(distances) around the
nucleus where the
opposing centrifugal forces
(away) and charge forces
(toward) exactly balance
one another.
• These are the “shells”
where electrons reside
• Shells closest to nucleus are
lower energy and are filled
first.

Electron shells Electron shells
• The first shell, • The second shell, a
closest to the bit farther from the
nucleus, is quite ► nucleus, is a bit
small, only large larger, and can
►
enough for 2 accommodate 8
electrons electrons

14


Electron shells Electron shells
• The third shell, a bit • As we are only
farther from the dealing with elements
nucleus, is also a bit 1-20, and we can
larger, but still only account for 18
accommodates 8 electrons with three
electrons shells (2 + 8 + 8), only
►
the last two elements
(K and Ca) need to
use the 4th shell. ►

Electron shells Filling electron shells
• Helium example:
• As you might imagine, – Helium has atomic number 2, indicating it has 2
this ‘shell’ description protons and 2 electrons.
is a slight – The two electrons will both fit in the first shell.
oversimplification.
• But that’s all we need
for now. We won’t
worry about how
complicated shells can
really be in Biol 121. – The last, outermost shell with an electron in it is
the atom’s “valence” or outer shell. The first shell
is the valence shell for He.

Filling electron shells Filling electron shells
• Lithium example:
– Lithium has atomic number 3, indicating it has 3 • Draw the electron shells for the following atoms --
protons and 3 electrons. using your periodic chart.
– The first two electrons will both fit in the first shell.
The third electron goes into the second shell.

H C O

– The second shell is the valence shell for Li.
Na Cl

15


Electron Shells - Answers Noble Gases
• Argon, like Helium, has a full
valence shell
• Some atoms have full valence
shells. They’re called the Noble
Hydrogen 1 e- Carbon 2 + 4 = 6 e- Oxygen 2 + 6 = 8 e-
Gases -- they do not react or
bond with other elements. You
can find them in a nice neat
column on the periodic chart,
on the farthest to the right.

Sodium 2 + 8 + 1 = 11 e- Chlorine 2 + 8 + 7 = 17 e-

Let’s look at another column in the Oxygen and Sulfur are also in the same
periodic chart…. column (16) of the periodic chart

 Oxygen  Sulfur
 8 e- = 2 in the first and  16e- = 2 in the first, 8
6 in the second in the second and 6 in
(valence) shell the third (valence)
shell

And O and S have the same number of Periodic Table is organized
electrons (6) in their valence shells • The periodic chart is not a random
arrangement of atoms, they are all
conveniently arranged for your viewing
pleasure,
• Elements in column (we call them groups or
families of elements) having the same number
 Oxygen  Sulfur of valence electrons.
 8 e- = 2 in the first and  16e- = 2 in the first, 8 • Families of elements have similar bonding
6 in the second in the second and 6 in capabilities
shell

16


Is there a similar significance to the rows on the Noble Gases
periodic chart?
• Remember Helium and
Argon, who both had full
valence shells? They are
the noble gases.
• Noble gases end each row.
The next atom is written in
the next row (period) of
the chart.
• What is the significance of
that?

Oxygen and Sulfur have the same number of
Oxygen is found in the second period (row), its
electrons (6) in their valence shells, but they are
second shell is occupied
in different shells

 Oxygen  Sulfur  Oxygen  Sulfur
 8 e- = 2 in the first and  16e- = 2 in the first, 8  8 e- = 2 in the first and  16e- = 2 in the first, 8
6 in the second in the second and 6 in 6 in the second in the second and 6 in
(valence) shell the third (valence) (valence) shell the third (valence)
shell shell

Sulfur is found in the third period (row), its third In Summary….Location, location,
shell is occupied location

 Oxygen  Sulfur
 8 e- = 2 in the first and  16e- = 2 in the first, 8
6 in the second in the second and 6 in
shell

17


The period (row) represents which shell is the valence Lecture 1.1 and 1.2 Study Guide
shell
The group (column) represents how many electrons • Biology overview and Subatomic particles
are in that valence shell – Name and describe the characteristics of life
– Know the levels of organization of life from least
to most complex
– Know the name, charge, location, and mass of the
subatomic particles
– Know the names (spelled correctly!) and symbols
for elements 1-20
– Know what a mole is, what Avogadro’s number is
and how they are both used

18

Lec 1.1 & 1.2 - org of life, subatomic particles

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Lec 1.1 & 1.2 - org of life, subatomic particles