Download Atom Molecule

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The first part of this slide show is chemistry review! We
are not recovering this section in class. Therefore IF
YOU NEED HELP with this material, come see me
ASAP!
Thank you!
CHEMISTRY
The study of matter.
(Anything that has mass
and takes up space)
•Why chemistry in biology class?
When we spent all that time studying diffusion, solutes, semipermeable membranes and water, we were really looking at
the way that matter behaves and how the cell is affected by
that matter (chemicals).
When we studied the organelles, they are all composed of
chemicals, work with chemicals, produce chemicals.
Soon you’ll see that chemistry (bio-chem) is really studying how
life uses chemicals to live…..but before we can talk about what
the cells do with the chemicals, you need to understand a bit
more about chemistry!
But, before we move on, if you aren’t convinced that you are a
series of chemicals and their actions:
The U.S. Bureau of Chemistry and Soils invested
many a hard-earned tax dollars in calculating
the chemical and mineral composition of the
human body, which breaks down as follows:
65% Oxygen
• 18% Carbon
• 10% Hydrogen
• 3% Nitrogen
• 1.5% Calcium
• 1% Phosphorous
•
•0.35% Potassium
•0.25% Sulfur
•0.15% Sodium
•0.15% Chlorine
•0.05% Magnesium
•0.0004% Iron
•0.00004% Iodine
•What you need to know:
• Basic
components of an atom. (With
charges)
• How electrons fill orbits. (Valence)
• Basics about periodic table, how to
determine; # of neutrons, electrons, protons
and mass
• When atoms will react
• Turn
to a partner and
tell them all the things
you already know
about these topics.
•Elements
•A
substance that
contains all the
same type of
atom.
• Fundamental
forms of matter
• 92
occur naturally
on Earth
Most Common Elements in Living
Organisms (the ones you need to
know)
Oxygen
Hydrogen
Carbon
Nitrogen
Phosphorus
•What Are Atoms?
•
•
•
Smallest particles that retain properties of an
element
Atoms can’t be broken apart by normal
means
Made up of subatomic particles:
•
•
•
Protons (+) Found in the nucleus/add to mass
Neutrons (no charge) Found inside the nucleus/add
to mass
Electrons (-) Located outside the nucleus
• Draw
a picture of an
atom and label the 3
subatomic particles.
• Check
your drawing
with your neighbor to
see if they match.
•Atomic Number
• Number
of protons and electrons (in
neutral atom)
• All atoms of an element have the same
atomic number
• Atomic number of hydrogen
• Atomic number of carbon
**Look on your practice sheet**
Mass Number
Number of protons
+
Number of neutrons
Mass number (rounded) – atomic
number = neutrons
On your practice sheet…
Fill in the protons, neutrons and electrons
for each of the elements on the sheet.
•Counting Atoms!
• CH4 Carbon=_______ Hydrogen=_____________
• COH4(CH2)4 Carbon=___ Oxygen=_____Hydrogen=_____
•
Multiply all the atoms in the parenthesis with the co-efficient and then
add like atoms together!
• C2(COH)5CH3 Carbon=___Oxygen=___Hydrogen=___
What Determines If Atoms Will
Interact?
The number and arrangement
of their electrons
•Electrons
Carry a negative charge
• Repel one another (like magnets)
• Are attracted to protons in the nucleus(- to +)
• Move in orbitals = volumes of space that
surround the nucleus
•
Electron Orbitals
• Orbitals,
based on their size can hold
different amounts of electrons.
• Atoms differ in the number of
occupied orbitals
• Orbitals closest to nucleus are smaller
in size and have lower energy and are
filled first
• Filling pattern is 2,8,8
•Shell Model
SODIUM
11p+ , 11e-
•
First shell
•
•
CHLORINE
17p+ , 17e-
2 electrons
Second shell
•
holds up to 8
electrons
CARBON
6p+ , 6e-
OXYGEN
8p+ , 8e-
HYDROGEN
1p+ , 1e-
HELIUM
2p+ , 2e-
On your practice sheet…
Draw the shell models for Hydrogen,
Carbon and Oxygen
Electron Vacancies
Unfilled shells make atoms likely
to react
• Hydrogen, carbon, oxygen, and nitrogen all
have vacancies in their outer shells
• This means these atoms like to bond with other
atoms to fill their shells. (Orbitals)
• The outer most shell is called the valence
•
Filled Valence = Happy atom
Electrons will move, or be
shared between atoms to
try and fill the outer shell.
• If the outer shell is already
full (noble gas) it is very
unlikely to react.
• If there is only 1 space to fill
or only 1 in the valence level
they are volatile.
• Determine what charge the
atom would have with a full
valence shell.
•
On your practice sheet…
Determine the number of valence
electrons for each of the atoms.
And the typical charge for that element
based on the valence number.
•Here is where we will pick it up in
class…
Chemical Bonds, Molecules,
& Compounds
• Bond
is union between electron
structures of atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only
one element - O2
• Molecules of compounds contain more
than one element - H2O
2 Important types of Bonds found in
Biological Molecules
• Ionic
Bonds
• Covalent Bonds
Ionic Bonding
This bond is the
transfer of
electrons from one
atom to another
• One atom loses
electrons,
becomes
positively charged
ion
• Another atom gains these electrons, becomes
negatively charged ion
• Charge difference attracts the two ions to each
other
•
Formation of NaCl
electron transfer
sodium
atom
11 p +
sodium
ion
11 p +
10 e-
chlorine
atom
17 p +
17 e-
chlorine
ion
17 p +
18 e-
Ionic bonds will create ions.
Ions are charged atoms.
This charge is the result of an atom gaining
or losing electrons in the bond.
A + ion (ion with a positive charge) is called a cation.
A – ion (ion with a negative charge)is called an anion.
Think about electrons and explain how the above occurs.
Covalent Bonding
Atoms share a pair or pairs of
electrons to fill outermost shell
(valence)no giving or taking of
electrons
Covalent Bonding
Two oxygen
atoms,
each with six
electrons, would
like to fill their
valence (need 2
more electrons
each). So the 2
atoms share four
electrons in a
covalent bond.
molecular oxygen (O2)
O=O
Fig. 2-8b(2), p.25
Covalent Bonding
Oxygen has
vacancies for two
electrons in its
outer orbital. Two
hydrogen atoms
can each share an
electron with an
oxygen. The result
is a covalent bond
forming a water
molecule.
water (H2O)
H—O—H
Bonding Video
Fig. 2-8b(3), p.25
How to tell Ionic or Covalent??
Typically covalent bonds are formed
between atoms of the same element
and when more than 2 atoms are
involved in the bond.
• Tell
your neighbor how you can tell if a
compound has ionic or covalent bonds
just by looking at the formula.
N2
CH3
KF
Hydrogen Bonding
• Hydrogen's
bonding to
carbon, nitrogen,
other hydrogen's
• These
are special
bonds important
to bio.
• Where have we
seen hydrogen
bonds before?
Video reminder
So now that you have the basics of chem,
what’s your body doing with all these
chemicals and bonded atoms?
Before we can answer that, you need to
know that all living creatures MUST
follow the Physical Laws of our planet.
• 1st Law of Thermodynamics:
energy/mass can not be created or
destroyed, only converted.
• 2nd Law of Thermodynamics:
energy/matter can not be converted
at 100% efficiency.
Think – Pair - Share
• How
do you think the Laws of
Thermodynamics will impact life?
So to get enough energy for the cells to
work, we need atoms reacting
together…
•
•
•
•
Chemical reactions are the conversion (change)
of substances from one form into another. (1st
Law of Thermodynamics)
Follows the Law of Conservation of Matter
This is the basic formula: Substrate  Product
2 things are necessary for a chemical reaction to
occur
1) Substrates (Reactants) - what is being
converted
2) Activation Energy – Energy for reaction to take
place
•
•
•
If there are substrates and activation energy,
then a chemical reaction can take place
and produce products. Depending on the
type of reaction, energy can be produced!
Catalyst – something that speeds up a
reaction but does not undergo any changes
In cells, almost every
reaction has a catalyst
called an enzyme!
Example:
Substrate + Enzyme 
• The
products of a chemical reaction
can either be larger (putting things
together) or they can be smaller
(breaking things down) than what we
started with.
Metabolism
• If
we break down the original
substance it is called a catabolic
pathway.
EX: H2O  H + H + O
• If
we build up the original substances it
is called anabolic pathway.
EX: H + H + O  H2O
Mnemonic device
• Think
of a way to remember the
cataboic and anabolic pathways
Ion Formation
• Sometimes
molecules that are
catabolized create ions.
• Atom
loses electron(s), becomes
positively charged ion (Cation)
• Atom gains electron(s), becomes
negatively charged ion (Anion)
• Ions
can be very reactive
• Especially
OH- and H+
Mnemonic device
• Think
of a way to remember the type of
ions that are cations and anions.
•The pH Scale
• Measures
H+ concentration of fluid
• Change of 1 on scale means 10X
change in H+ concentration
Highest H+
Lowest H+
0---------------------7-------------------14
Acidic
Neutral
Basic
•Examples of pH
•
Pure water is neutral with pH of 7.0
•
Acidic (Below 7.0) High % H+
•
•
Stomach acid: pH 1.0 - 3.0
•
Lemon juice: pH 2.3
Basic/alkaline (Above 7.0) High % OH•
Seawater: pH 7.8 - 8.3
•
Baking soda: pH 9.0
•
(buffers)
The pH Scale
Fig. 2-12, p.28
What about Water??!
• Polar
molecule
o High
specific heat
o Cohesion
o Adhesion
o Less dense as a solid
o Universal solvent
•Water Is a Polar Molecule
• Oxygen
end has a
slight negative charge
O
• Hydrogen
end has a
slight positive charge
• So
let’s look at water’s
additional traits that
occur because it is
polar…..
H
+
H
+
High Specific Heat
• This
means it takes a
lot of energy for
water to change
phases. (From solid
to liquid to gas).
• This is also sometimes
called temperature
insulating.
Cohesion and Adhesion
• Cohesion:
water loves water
• Adhesion:
water loves other surfaces
Low Density Solid
Ice less dense as a
solid than a liquid!
Universal solvent
Because water carries a slight negative
and positive charge on it, it readily and
easily dissolves most solutes!
MOST important trait???
Check your understanding:
In terms of the math, what is the actual
difference between a pH of 8 and 13?
• In terms of the chemistry, what is the
difference between a pH of 8 and 13?
• What does the term “polar” mean?
• Where in an atom are each sub-atomic
particle located?
• What things are needed for a chemical
reaction to run?
• What is the name of all biological catalysts?
•
SUPER CARBON
* Abundant!
* Able to share 4 outer
valence electrons!
* Versatile!
* Stable!
O-Chem (organic chemisty)
Organic compounds are critical to the
structure and function of all living things.
• There are 4 main categories (classes/groups)
of organic compounds they are all polymers
(very large structures);
1) Carbohydrates
2) Proteins
3) Nucleic Acids
4) Lipids
• All of these (1-4) will be made out of different
monomers (single, smaller structures that
bond together)
•
How can we get 4 different functioning
groups (classes) of organic compounds
from the same basic component?
(Carbon)
• By
using things called functional groups!
• Functional groups are lone atoms or
clusters of atoms, bonded to a carbon
chain (backbone)* the bonding of
those functional groups alters the
properties of the carbon skeleton.
* C-C-C-C-C-C-C-C
•Carbohydrates
Large compounds
(polymer)
• Used in the body
for energy and
structure
• Made up of
monomers called
saccharides
(simple sugars, like
glucose)
•
glucose
fructose
• Monosaccharides
(like
glucose) bond together
to form disaccharides
(like sucrose) bond
together to form
polysaccharides or
complex carbohydrates
(like starch) (Prefixes are
a hint; mono, di, poly)
• Examples: Pasta,
potatoes
Carbohydrates- 3 main levels of
carb structure
Monosaccharides
•
Example: C6H12O6
•
Glucose
Disaccharides
Sucrose
• 2 mono bonded
Polysaccharides
• Complex
carbohydrates
• 2 di bonded
•
• Large
Proteins
compounds (polymer)
• Used in the body to form tissues, cell
membrane gates
• Made up of monomers called amino acids
• Single amino acids are bonded together
using peptide bonds.
• EX: Meat, eggs, fish
Think – Pair - Share
• What’s
another name for a
biological catalyst?
• What
do they do?
• Where
are they in a chemical
equation?
Make a Prediction
• Would
your body like to use a single
enzyme for more than one reaction?
Why or why not?
• Will
your body want to regulate (start
and stop) chemical reactions at
different times throughout your life?
• Enzymes
are efficient as ONE enzyme can
run many different reactions! (Convert
multiple substrates)
Lock and Key!
If I block the lock (enzyme) the key
(substrate) won’t fit and won’t be converted
to product! (regulation!)
2 Ways to block the active site
Denaturation
• Disruption
of three-dimensional shape
of the protein
• Breakage
of bonds (hydrogen bonds
that form the shape of the protein)
• Causes
of denaturation:
pH
Temperature
• Destroying
function
protein shape disrupts
Tell a partner the last time
you denatured a protein.
Why is this important to cells?
Nucleic Acids
• Large
compounds
(polymer)
• DNA and RNA
• Made of monomers
called nucleotides
which are a
phosphate, sugar
and a nitrogenous
base. (A,T,G,C or U)
LIPIDS
• Large
compounds (polymer)
• Used in the body for insulation, cell
membrane structure and energy
• Made up of the monomers; 3 fatty
acids and 1 glycerol
• All are hydrophobic
• EX: Butter, oil
Special,
modified lipids
• If
the fatty acids are in a ring
format, they are called sterols. Ex:
cholesterol and steroids
• If
we remove one fatty acid and
add a
phosphate we get phospholipids.