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Basic Biochemistry 2010,Part 1

Basic Biochemistry 2010,Part 1

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Published by: julie raines on Nov 30, 2010
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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.




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 atomall protons are located in the atom nucleus Proton # is also the # of electronsAs long as they remain equal, the atom is neutral in charge

‡ 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 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 ³young´ fossils


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

Charged atoms

‡ Give up e- ---> become positive (+) ‡ Take e- ---> become negative ( - ) AFTER they become charged, then they BOND called IONIC bonding because
o o

Attraction between + and - ions 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, ³Yeah, I¶m positive.´

Covalent Bonding
Compound in which the atoms are held ‡Atoms share etogether by covalent bonds.
‡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
QuickTi eΠand a deco ressor are needed to see this icture.


2 Bases - have OH- in solution NaOH Na+ and OH-

QuickTi eΠand a deco ressor are needed to see this icture.



‡ Contain C or H, usually not both 1. Acids - have H+ in solution HCl H+ and Cl-

£¢ ¢

3. Acid + base ---> salt + H2O (neutralizes) Ex: HCl + NaOH ---> NaCl + H2O HCl + KOH ----> KCl + H2O

pH = parts Hydrogen
pH scale
Strong acid Normal rain


Baking soda Ammonia

Strong base


Battery acid

uickTime and a decompressor are needed to see this picture.


or basic
Stomach Acid Acid rain Distilled Water
Lemon juice


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. 2. Normally lining replaced as acids eat it away. Lining eaten away if bacteria there - can¶t keep up replacement
Blister from burn: ulcer



If perforated: acidic contents dumped on body organs - not protected from burning - life threatening 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?

- 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?

- 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?

- Maintains body temp: - Homeostasis

D. Density v Temp
1. Densest at 4ºC Lightest at 0ºC What is that important to life?

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?

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. : Why important to life?

ickTime and a T FF ncompressed decompressor are needed to see this pict re.

1. Stable liquid 2. Climbs up xylem in plants against gravity 3. H bond - easily broken - changes state easily Applied: Insects/geckos ³stick´ to things

4. Drops of water

Ex. Why ice expands

Summary of water properties

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