Biochemistry Notes

2010-2011
 Chemical Symbols
*Capitals matter!
*Element symbols contain ONE capital
letter followed by lowercase letter(s) if
necessary.

Metal that forms

bright blue solid
compounds.
Co vs CO Poison gas
 How many elements and
compounds do you know??

• See the provided sheet and let’s fill it in

together- write down any you do not
already know!
Parts of the atom
Nucleus has:
Protons=positive charge
Neutrons=no charge

Shells have:
Electrons=negative
charge
 Electron Orbitals
• Region where there is 90%
probability of finding an electron.
• Can’t pinpoint
the location of
an electron.
• Density of dots
represents
degree of
probability.
 Atomic number

Equals the # of protons in an atom-

all protons are located in the atom nucleus

Proton # is also the # of electrons-

As long as they remain equal, the atom is
neutral in charge
 ATOMIC MASS
• Sum of the protons and neutrons in the
nucleus of an atom.

To find neutrons:
• Mass # - proton # =
# of neutrons
• Let’s see how this works…..
 Element properties
determined by proton #
 Making Bohr Model
• Each shell has a maximum # of e- it can hold:
• 1st = 2
• 2nd = 8
• 3rd = 18
• BUT when filling the 3rd, goes to 8 and then the next
e- is in the 4th shell!
• SO for Bio- we will memorize:
2-8-8-extra
 Let’s Practice!
• Use the periodic table in your text or
planner. Make Bohr models of the
following:
N O Mg Ca
K Na Cl H F
 Isotopes
• Isotopes are elements that have the
same Proton # but different # of
neutrons-are radioactive
 Radioactive isotopes
• When a nucleus breaks apart, it
gives off radiation that can be
detected and used for many
C 12: C 14 ratio

Radioactivity and rate of

decay of C 14 to C 12 used to
determine age of “young”
fossils

P
 Ionic Bonding
• Ionic Bonds: One atom gives up electrons and
another takes it. This make them become ions.

• Ions:
o Charged atoms
• Give up e- ---> become positive (+)
• Take e- ---> become negative ( - )

AFTER they become charged, then they BOND

called IONIC bonding because
o Attraction between + and - ions
o Ex: Li f or HCl or NaCl
How ionic bond made: LiF
 Did you hear about…..?
• Two atoms are walking down the street.

• One says,” Wait, I think I lost an electron.”

• The other says,” Are you sure?”

• The first one says, “Yeah, I’m positive.”

 Covalent Bonding
Compound in which the atoms are
held
•Atoms
together by covalent bonds. share e-
•Ex: CO2, H2O

Methane (CH4)
Comparing Covalent and Ionic
Bonding
 Let’s Practice!
• Get into groups of 2
• Using the package of supplies provided and
the paper template, follow directions to make
bonds between the given molecules. When
you believe you have it right, call me over!
• BE PREPARED to explain what and why you
set it up the way you did.
 Inorganic Molecules
• Contain C or H, usually not both
QuickTime™
needed to seeand
decompressor thisa
1. Acids - have H in solution
+ are

HCl H+ and Cl-

QuickTime™
decompressor and a
are needed to see this picture.
2 Bases - have OH- in solution
NaOH Na+ and OH-
 Acids/Bases
3. Acid + base ---> salt + H2O
(neutralizes)
Ex: HCl + NaOH ---> NaCl + H2O

HCl + KOH ----> KCl + H2O

 pH = parts Hydrogen
pH scale Normal Baking
rain Blood soda Ammonia Strong
base
Strong
acid
0 QuickTime™ and a
bleach
decompressor
Battery are needed to see this picture.
acid
or basic
Stomach Acid Distilled
Acid rain Water
Lemon
juice
Vinegar
 pH effects Ecosystems
• Availability of nutrients to plants effected by pH
• Soil pH can effect flower and fruit production
• Acid rain- disrupt ecological processes/nutrient cycles
• Plants can change pH by decomposition or uptake of
nutrients/water and animal waste can change soil
ex: pine needles are very acidic
• APPLICATION: gardeners apply lime to buffer acidic
soil
 6. pH Buffers in organisms
• Acid pH can effect shapes of molecules and how they
work in your body
• Maintain normal pH conditions like in the bloodstream
-blood should be 7.4
• one of the homeostatic mechanisms of the body.
• Most of the human body is pH around 7. Stomach pH ~2
• Ex: alkaseltzer for acid indigestion
– Buffers in bloodstream: balance pH
• Bufferin - in aspirin, which is salycilic acid - helps
neutralize & doesn’t add more acid to stomach
 7. Ulcers & heartburn
a. ulcers: blisters on stomach lining
* Most not caused by stress
* Most common cause: bacteria in stomach
lining, producing acid.
 Ulcers con’t
1. Normally lining replaced as acids eat it
away.
2. Lining eaten away if bacteria there - can’t
keep up replacement
Blister from burn: ulcer
3. If perforated: acidic contents dumped on
body organs - not protected from burning
- life threatening
4. Crackers/bread help with acid indigestion
and acid reflux because they are basic -
help buffer pH
 Heartburn con’t
b. Has nothing to do with
the heart
Cause: stomach contents
go back through cardiac
sphincter
- esophagus burn is more
accurate term
- Pregnant women:
stomach squished: more
reflux
The Structure of Water
Two hydrogen atoms are each joined to an oxygen
atom by a single covalent bond van der Waals

 
forces:
The weak
attraction between
                                                                                       the hydrogen atom
                     
of one molecule
and a slightly
negative atom
within another
molecule
 Properties of Water
- A. Stable: covalent bonds btw O and H
not easily broken

Why is that important to life?

 Answer:
- Our bodies are mostly H2O
- We remain stable
 B. Good medium
- Can’t compress it, flows easily,
dissolves a lot of substances

What is that important to life?

 Answer
- Allows dissolving across membranes,
blood flows, etc.
- Diffusion depends on it
 c. High specific heat
- Absorbs/loses a lot of heat before changing
temperature
- 1. H2O temperature stable - like in ponds as well as
bodies
- Warmer in ocean in Aug than June--took all winter to cool
- 2. Evaporative coolant - can dump heat from body
reactions into H2O of bloodstream to radiate as
sweat.

What is that important to life?

 Answer
- Maintains body temp:
- Homeostasis
 D. Density v Temp
1. Densest at 4ºC
Lightest at 0ºC

What is that
important to life?
 Answer:
Ice floats, liquid cold
H2O sinks =
organisms can live
through winter under
ice/ whole pond
doesn’t freeze
H2O continues to flow
in rivers
 E. Solubility of O2vs. T
1. Cold H2O holds more O2than warm

Why is that important to life?

 Answer
1.Fish die if H2O warm
1.Not because of temp. but because of
loss of O2
1.Best fishing is in cold H2O not in warm
tropics - water clear because of few
microorganisms - base of food chain
The tendency of
molecules of the
same kind to stick to
one another is called
cohesion.

The type of attraction

that occurs between
unlike molecules is
called adhesion.

(van der Waals forces)

 Hydrogen Bonding
1.Adhesion = H2O sticks to things
2.Cohesion = H2O sticks to itself
3.Q: Why important to life?

QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
 Answer:
1. Stable liquid
2. Climbs up xylem in plants against
gravity
3. H bond - easily broken - changes
state easily
4. Drops of water Applied: Insects/geckos “stick” to
things

Ex. Why ice expands

Summary of water prop
erties