lec 1.1 & 1.2 - org of life, subatomic particles

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

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Biology 121 – Biological Foundations for Physiology

Instructor:

Kitty O’Neil

[email protected]

Course details

• Office Hours – Tu 2:30 – 3:00, Tu & Th 6:00 – 6:40PM – in the LSARC (AS455)

– Plus additional time as needed, before & after class

• 2 Textbooks –– Essentials of Biology, 2nd ed., Sylvia Mader

– Lab manual, Wagner

• LCC Angel website - http://angel. lcc.edu

• Attendance – doesn’t count for anything, or does it?

• Grades, exams, quizzes, homeworks

• Additional learning resources

Course details

• Office Hours – Tu 2:30 – 3:00, Tu & Th 6:00 – 6:40PM – in the LSARC (AS455)

– Plus additional time as needed, before & after class

• 2 Textbooks –– Essentials of Biology, 2nd ed., Sylvia Mader

– Lab manual, Wagner

• LCC Angel website - http://angel. lcc.edu

• Attendance – doesn’t count for anything, or does it?

• Grades, exams, quizzes, homeworks

• Additional learning resources

Date Part Lecture Title

1/14/2010 1 Basic chemistry 1.1 Organization of Life / Atoms

1/14/2010 1 1.2 Subatomic Particles / Ionic bonds

1/21/2010 1 1.3 Covalent Bonds and Polarity

1/21/2010 1 1.4 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

2/4/2010 2 2.2 Functional Groups and Reactions

2/11/2010 2 2.3 Carbohydrates

2/11/2010 2 2.4 Lipids

2/18/2010 2 2.5 Proteins and Nucleic Acids

2/18/2010 3 Cells and organelles 3.1 Cells and Organelles

2/25/2010 Exam 2

2/25/2010 3 3.2 Cytoskeleton

3/4/2010 3 3.3 Membranes and Transport

3/4/2010 3 3.4 Osmosis and Capillary Dynamics

3/18/2010 Exam 3

3/18/2010 4 Cellular energy metabolism 4.1 Reduction and Oxidation

3/25/2010 4 4.2 Glycolysis and the Kreb’s Cycle

3/25/2010 4 4.3 Electron Transport Chain

4/1/2010 4 4.4 Other Energy Sources, Energy Wrap Up

4/1/2010 5 Genetic Information 5.1 DNA & Replication

4/8/2010 Exam 4

4/8/2010 5 5.2 RNA, Transcription

4/15/2010 5 5.3 Proteins, Translation

4/15/2010 5 5.4 Regulation of Gene Expression

4/22/2010 5 5.5 Mendelian Genetics

4/22/2010 5 5.6 Beyond Mendel Part I

4/29/2010 5 5.7 Beyond Mendel Part II

4/29/2010 5 5.8Cell Division · Meiosis in Humans · Chromosomal AbnormalitiesExam 5

http://angel.lcc.edu/

http://angel.lcc.edu/


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Course details

• 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.

LCC Withdrawal Policy

?Biology 121Lecture 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.


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Life is cellular

• Life is not defined by its size

• From a unicellular amoeba to a brontosaurus…

• All life is composed of individual units called cells

• The cell is the smallest unit of a living organism

Life uses energy

• How do living things survive?

• All living things process energy –

– Eat, or ingest nutrients

– Excrete waste

– Harvest energy in a useable form

• Collectively, these processes are called “metabolism”

Life can sense its environment, respondLife can maintain homeostasis

• All life forms can sense and respond to stimuli in their environments– See plants respond to

light http://www.ncsu.edu/project/agronauts/mission4_6.htm

• Living organisms can maintain homeostasis –internal conditions different from surrounding environment

Life reproduces itself

• How does life continue?

• All life forms duplicate themselves, through sexual or asexual means, by duplicating their genetic material (DNA)

Life is highly complex, but highly organized

• There is a large array and variety of living organisms….

– Single cell organisms

– Multicellular organisms

– Microorganisms

– Plants and animals

• ….but all are composed of the same essential elements

• organization is hierarchal

Summing it all Up…

1. life is cellular (the cell is the smallest unit considered “alive” )

2. life takes in and uses energy

3. life responds to the environment

4. life maintains homeostasis

5. life reproduces itself

6. life is highly complex andorganized

http://www.ncsu.edu/project/agronauts/mission4_6.htm

http://www.ncsu.edu/project/agronauts/mission4_6.htm


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More about the Hierarchal Organization of Life

Can you organize these units, from smallest to largest?

Here are the answers. Let’s go through each level individually.

7: organism 1: atom 4: cell 5: organ

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

“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.”

-D’Arcy Thompson, 1917

from On Growth and Form

Atom – the smallest unit of matter

• Although this is the smallest in the series you had to choose from, we’ll see later that each atom or “element” is actually composed of smaller subunits, called subatomic particles, named protons, neutrons and electrons.

• The atom is the smallest unit of an element

Molecule -- when two or more atoms interact, they form a molecule

• Molecules are formed when individual atoms bond together. This molecule is called ATP (adenosine triphosphate), and is the energy currency for most cells.

• A compound


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Organelle -- many molecules working together to perform a single function

for the cell• This is a photograph of

a mitochondria, one of the organelles present in eukaryotic organisms.

• Cells parcel out their workload to various organelles, or “little organs”.

• Mitochondria are the organelles responsible for making ATP.

Cell – the smallest unit of life

• Organelles work together within a living cell

Tissue -- two or more cells working together to perform a function

• Not a choice in your series! But you will learn a great deal about tissues in Biology 201, Human Anatomy. This hierarchal level and the remaining levels are specific to multicellularorganisms.

Areolar connective tissue

Bone -- the strongest connective tissue

Adipose – storing fat

Organ -- two or more tissues performing a function

• This picture of the lungs also has other organs included --you can see the trachea and the bronchi.

Organ System -- two or more organs performing a function for the organism

• There are 11 organ systems in the human body. You’ll cover them progressively in Biol201 and 202

Organism -- All 11 organ systems working cooperatively to form one individual

• This is an example of a multicellularorganism

• Plants, animals, fungi …


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Population -

• A group of the same type of organism located together in one area

Community

• All populations in one particular location

• Plant community in a prairie

• Microorganism community in our GI tract

Ecosystem

• A community + the physical environment in which it exists and interacts

Biosphere

• All the ecosystems making up the earth

• Earth, water, atmosphere and organisms

Learning Goal: Be able to rank order levels of organization

1. Subatomic particles2. Atoms3. Molecules 4. Organelles5. Cells6. Tissues7. Organs8. Organ systems9. Multicellular Organism10.Population -- a group of the same kind of organisms occupying the

same area11.Community -- Populations of different species occupying the same area12.Ecosystem -- The community AND the physical environment13.Biosphere -- all regions sustaining life

Biol 121 is concerned with Levels 1-5

1. Subatomic particles2. Atoms3. Molecules 4. Organelles5. Cells6. Tissues7. Organs8. Organ systems9. Organism10.Population -- a group of the same kind of organisms occupying the

same area11.Community -- Populations of different species occupying the same

area12.Ecosystem -- The community AND the physical environment13.Biosphere -- all regions sustaining life


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Biol 201 and 202 are concerned with Levels 5-9

1. Subatomic particles2. Atoms3. Molecules 4. Organelles

5. Cells6. Tissues7. Organs8. Organ systems9. Organism10.Population -- a group of the same kind of organisms occupying the

same area11.Community -- Populations of different species occupying the same area12.Ecosystem -- The community AND the physical environment13.Biosphere -- all regions sustaining life

You would learn about Levels 9-13 in an organismal/environmental biology course like

128 or 1201. Subatomic particles2. Atoms3. Molecules 4. Organelles5. Cells6. Tissues7. Organs8. Organ systems

9. Organism10. Population -- a group of the same kind of organisms

occupying the same area11. Community -- Populations of different species

occupying the same area12. Ecosystem -- The community AND the physical

environment13. Biosphere -- all regions sustaining life

Biology 121Lecture 1.2

Basic ChemistryElectron Shells

Elements

• Fundamental forms of matter

• Can’t be broken apart by normal means

• 92 occur naturally on Earth

• Most common elements in living organisms:

– Oxygen (O)

– Hydrogen (H)

– Carbon (C)

– Nitrogen (N)

Atom

• Smallest particles that retain properties of an element is an ATOM

• Positively charged nucleus surrounded by cloud of negatively charged electrons

• Made up of subatomic particles:

– Protons (+)

– Electrons (-)

– Neutrons (no charge)

• Has mass (we can think of mass as weight)• Occupies space


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Fig. 2-2, p.20

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

* 1 Amu is a unit of mass (atomic mass unit), like a pound or gram, but much, much, smaller.

Atomic particles arranged in pattern

• The MASS of the atom is concentrated in its nucleus.– 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

‘shells’

Atomic Mass

• It’s time to mention another important concept regarding atomic weights……..

6.02 x 1023

What Does It Mean??

• A dozen is………..12

• A gross is…………..144

• A triple is……………..3

• A century is…………….100

• And Avogadro’s Number is…….6.02 X 1023

• In other words……it’s a predetermined, arbitrary number chosen for matters of ‘handiness.’

Why is it handy?

• Avogadro’s Number is a convenient amount of very small things to count out, like 6.02 X 1023 protons

• 6.02 X 1023 protons weigh exactly 1.00 grams.• 6.02 X 1023 H atoms weigh exactly 1.00 grams.• 6.02 X 1023 amu weigh exactly 1.00 grams.• Avogadro’s number relates the mass of a proton,

which is unimaginably and immeasurably small, to something more tangible-- the gram

• 6.02 X 1023 molecules = 1 mole.• More information about Avogadro and his number

later


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Compare 1 atom to 1 mole

1 egg(0.14 lbs)

1 dozen eggs(12 eggs, 1.5 lbs)

1 atom of C(12 amu)

1 mole of C(6.02 · 1023 atoms , 7.22 · 1024 amu, 12 g)

Protons -- the identity of the element

• Protons are positively charged subatomic particles that have a mass of 1 amu

• They are located in the nucleus. See the green “dot” at the right? It’s a proton.

• This particular atom contains 1 proton and 1 electron.

Hydrogen

• If a second proton were added to the nucleus, it wouldn’t be H any longer. It’d be Helium. In fact, every atom has its own characteristic number of protons. Each atom has an atomic number, which reflects its proton total.

• For each proton in the nucleus, there must be a corresponding electron in the shell to balance the charges. The atomic number also reflects the number of electrons in a particular atom.

Hydrogen is the simplest atom. H contains one proton

Elements have abbreviations

• Each atom has a one or two letter short hand abbreviation. The first letter is capitalized, the second is small case. They are derived from the name of the atom:

H Hydrogen

He Helium

C Carbon

Co Cobalt

• The Periodic Chart of the elements contains all of the atoms, listed in atomic number order, reading in rows from left to right. In most periodic charts, the atomic number is on the top.

Name that element! Don’t use your periodic chart

• H = Hydrogen• He = ???• Ne = ???• C = ???• Si = ??• P = ??• Na = ???

• Know the symbols for elements 1 through 20


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Name that element!

• H = hydrogen

• He = Helium

• Ne = Neon

• C = Carbon

• Si = Silicon

• P = Phosphorus

• Na = Sodium (from the Latin, Natrium)

Name that Atom!

• Based on the number of protons (dark blue circles), which atom is represented by each picture? For this, you DO need to use your periodic chart.

proton

neutron

Name that Atom!Here are the answers!

1 proton = Hydrogen (H)6 protons = Carbon (C)

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

Neutrons -- add mass but no charge

• Neutrons are subatomic particles that weigh 1 amu (same as a proton),

• but they are neutral,which means they have no associated charge (unlike a proton).

Atomic Mass (Weight)• 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

Calculate the atomic mass for these atoms

Hydrogen (H)Carbon (C)

Helium (He)Magnesium (Mg)


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Atomic Mass

Hydrogen (H) has 0 neutrons

and 1 proton

Atomic Weight = 1 amu

Carbon (C) has 6 neutrons

and 6 protons

Atomic weight = 12 amu

Helium (He) has 2 neutrons

and 2 protons


Magnesium (Mg) has 12 neutrons

and 12 protons


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 the shells.

– Atomic number = number of protons or electrons

• 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.

– Atomic wt – atomic number = number of neutrons

– Atomic wt = no. of protons + no. of neutrons

Problems

• How many neutrons are in one atom of the following elements?

• Need to know 3 things…

Element N Li B F

Atomic Wt

No. Protons

No. Neutrons

Problems

• How many neutrons are in one atom of the following elements?

• Need to know 3 things…

Element N Li B F

Atomic Wt 14 7 11 19

No. Protons 7 3 5 9

No. Neutrons 14-7 = 7 7-3 = 4 11–5 = 6 19-9 = 10

Practice Problems

Atom: C Be

Atomic number: 6 14

Atomic weight: 12 22.99

No. Protons 6 8

No. Neutrons 6 2

No. Electrons 6

Practice Problems - Answers

Atom: C Be Si Na O He

Atomic number: 6 4 14 11 8 2

Atomic weight: 12 9.012 28.09 22.99 16.00 4.003

No. Protons 6 4 14 11 8 2

No. Neutrons 6 5 14 12 8 2

No. Electrons 6 4 14 11 8 2

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


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Atomic Mass

• Although atomic numbers are reported as whole digits, atomic weights are generally reported as decimals

• C weighs 12.01 amu

• Al weights 26.98 amu

• 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

• Atoms can exist in multiple forms in nature, with differing numbers of neutrons. These forms are called isotopes (same atom, different form)

• Isotopes vary in number of neutrons; protons and electrons remain the same.

Atomic Mass -- Part II• Hydrogen typically has 1 proton and 0 neutrons,

weighing a total of 1 amu. • But alternate, isotopic forms of H exist;

– Deuterim, 1 proton and 1 neutron, 2 amu, stable– Tritium, 1 proton and 2 neutrons, 3 amu, unstable or

radioactive

Atomic Mass -- Part II

• Isotopes are indicated by writing the atomic symbol, with the specific weight of that isotope in the upper left hand corner

– 1H is hydrogen

– 2H is deuterium

– 3H is tritium

Deuterium = 2H

Stable

Hydrogen = 1H

Stable

Tritium = 3H

Radioactive

Atomic Mass

• The atomic mass indicated on the periodic chart represents our knowledge about the average mass, distributed among all the known isotopes of each atom, that exist in the universe.

Isotope Rel. Abund. Half-life

12C 98.9% C is stable with 6 neutrons13C 1.1% C is stable with 7 neutrons

14C trace 5730 y

Radioisotopes

• Have an unstable nucleus that emits energy and particles as it ‘decays’

• Radioactive decay transforms radioisotope into a different element

• Decay occurs at a fixed, predictable rate

• Emissions from the radioactive isotope can be detected with special instruments

• Following movement of radioactivity is useful in many areas of biology and health care


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Radioactive Isotopes and Health Care

• Radioactive isotopes have two very special places in the health care industry– Diagnostics

– Therapeutics

• Nuclear Energy Institute’s Informational Website to learn more about Nuclear Medicine– http://www.nei.org/

Isotopes

How many protons?

What element is it?

How many neutrons?

What’s the atomic mass?

What is the isotope?

Isotopes

How many protons? 1 1 1 6 6

What element is it? H H H C C

How many neutrons? 0 1 2 6 8

What’s the atomic mass? 1 2 3 12 14

What is the isotope? 1H 2H 3H 12C 14C

hydrogen deuterium tritium

Biology 121Lecture 1.2

Basic Chemistry

Electron Shells

Electrons -- the Bonding Story

• Electrons are the negatively charged subatomic particles without mass that make up the volume of the atom

• Electrons are SOCIAL -- they prefer:– Being paired– Living in full shells

• Electrons repel each other

• Electrons are attracted to protons in the nucleus• Electrons determine how atoms interact with or

bond with each other.

Electron Shells

• Electrons spin and rotate around the nucleus of an atom, but are constrained to particular paths. They live in shells

• Similar to layers of an onion, or floors of a hotel.

http://www.nei.org/


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What keeps electrons constrained to their shells?

• Answer, part 1

But, they don’t fly off into space…

What keeps electrons constrained to their shells?

• Answer, part 2

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

• The first shell, closest to the nucleus, is quite small, only large enough for 2 electrons

►

Electron shells

• The second shell, a bit farther from the nucleus, is a bit larger, and can accommodate 8 electrons

►


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Electron shells

• The third shell, a bit farther from the nucleus, is also a bit larger, but still only accommodates 8 electrons

►

Electron shells

• As we are only dealing with elements 1-20, and we can account for 18 electrons with three shells (2 + 8 + 8), only the last two elements (K and Ca) need to use the 4th shell. ►

Electron shells

• As you might imagine, this ‘shell’ description is a slight oversimplification.

• But that’s all we need for now. We won’t worry about how complicated shells can really be in Biol 121.

Filling electron shells• Helium example:

– Helium has atomic number 2, indicating it has 2 protons and 2 electrons.

– The two electrons will both fit in the first shell.

– 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• Lithium example:

– Lithium has atomic number 3, indicating it has 3 protons and 3 electrons.

– The first two electrons will both fit in the first shell. The third electron goes into the second shell.

– The second shell is the valence shell for Li.

Filling electron shells

• Draw the electron shells for the following atoms --using your periodic chart.

H C O

Na Cl


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Electron Shells - Answers

Oxygen 2 + 6 = 8 e-Hydrogen 1 e-

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

Carbon 2 + 4 = 6 e-

Noble Gases

• Argon, like Helium, has a full valence shell

• Some atoms have full valence shells. They’re called the Noble 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.

Let’s look at another column in the periodic chart….

Sulfur

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

Oxygen

8 e- = 2 in the first and 6 in the second (valence) shell

Oxygen and Sulfur are also in the same column (16) of the periodic chart

And O and S have the same number of electrons (6) in their valence shells

Oxygen


Sulfur


Periodic Table is organized

• 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 of valence electrons.

• Families of elements have similar bonding capabilities


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Is there a similar significance to the rows on the periodic chart?

Noble Gases

• 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 electrons (6) in their valence shells, but they are

in different shells

Oxygen


Sulfur


Oxygen is found in the second period (row), its second shell is occupied

Oxygen


Sulfur


Sulfur is found in the third period (row), its thirdshell is occupied

Oxygen


Sulfur


In Summary….Location, location, location


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The period (row) represents which shell is the valence shell

The group (column) represents how many electrons are in that valence shell

Lecture 1.1 and 1.2 Study Guide

• Biology overview and Subatomic particles– 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

lec 1.1 & 1.2 - org of life, subatomic particles

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