Biochemistry!

Biochemistry is one of the crossover fields of chemistry. Biochemists have to understand both the living world and the chemical world. Even if you don't want to become a biochemist, you'll still have to understand atoms and molecules as a biologist.

Ch 2, 3, 6

2.1  Chemical Elements

Chemistry as it related to biology

QOD: (after quiz) Read the article, or as much as you can, and try to answer the questions: 1. Why does the doctor not recommend the

use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever.

2. Are there any exceptions?3. What is recommended to treat fever?

Why? Your should have thorough answers, including evidence you find in the article.

A. MatterWhat is matter?

Biochemistry Ch 2.1Write a vocabulary list for yourself: try to define the ones you remember:

• Element• Compound• Protons• Neutrons• Electrons• Atomic number• Atomics Mass• Isotope• Orbital

Matter: “stuff” has mass, takes up space

Made up of elements: substance that cannot be broken down into other substances by a chem rxn

Compound: consist of 2 or more elements in a fixed ratio

• Six elements:

C, H, N, O, P, S: make up 98% of living things.

• C, H, O and N make up about 96%

“SHNOPS”

B. Atomic Structure

a. Protons (p+): positively charged particles; neutrons have no charge; both have about 1 atomic mass unit of weight. Both are found in the nucleusb. Electrons (e-) are negatively charged particles that orbit the nucleus

Atomic number= number of protons- can’t change or it changes the atom

Atomic mass: about equal to the sum of its protons and neutrons

All atoms of an element have the same number of protons, the atom's atomic number

Periodic Table

(mass)

Interactive Periodic Table  |  Cartoon Periodic Table

Isotopes

Isotopes are atoms with the same number of protons but differ in number of neutrons; e.g., a carbon atom has six protons but may have more or less than usual six neutrons.

Carbon 14  - Break it Down!

Carbon- 12 is the most common form of carbon, it has 6 protons, 6 electrons, and 6 neutrons It is called Carbon 12 because that is its weight  (6 + 6 )

Carbon 14 has 2 extra neutrons, its weight is 14  (6 + 8 ); it is an isotope of carbon

A carbon with eight rather than six neutrons is unstable; it releases rays and subatomic particles and is a radioactive isotope.

Sample Question: A 200 g sample of muskopfonian is left in a container , the half life of muskopfonian is 1 hour. How much of the sample will be left after 4 hours?

Answer:

200 x .5 =  100 (hour 1)100 x .5  =  50  (hour 2)50 x .5 = 25 (hour 3)25 x .5 = 12.5 (hour 4)

or 200 x .54 = 12.5

Low levels of radiation such as radioactive iodine or glucose allow researchers to trace the location and activity of  the atom in living tissues; therefore these isotopes are called tracers                                 which are used in CAT scans

 High levels of radiation can cause cancerous tissues and destroy cells; careful use of radiation in turn can sterilize products and kill cancer cells.

Pick your favorite element from the table.  Turn and tell your lab partner how many protons, electrons and neutrons it has, and what it's atomic weight is (if you can see it). Have your table partner then name the element.

E. Electrons and Energy

1. Electrons occupy an orbital at some level near or distant from the nucleus of the atom.

S orbital: innermost, hold 2 elections

P orbital: after s, holds 8 elections

Outer elections have more energy and are less stable. So?

2. Electrons can be used to store and release energy!3. When atoms absorb energy during photosynthesis, electrons are boosted to higher energy levels.4. The innermost shell of an atom is complete with two electrons; all other shells are complete with eight electrons.5. The outermost shell is the valance shell, and the number of valance e- in the outermost shell determine many of the atoms properties

DRAW IT!     QUICK!!1. Draw six protons in the nucleus of the atom. 2. Draw six neutrons in the nucleus of the atom.3. Draw two electrons in the first energy level and label them with their charge.4. Draw four electrons in the second energy level and label them with their charge.5. What element is it!? __________                           (the future of the human race depends on it!)

What can easily be added to carbon to complete it’s valence shell?

2.2 Elements and Compounds

A. Compounds: When two or more different elements react or bond together, they form a compound (e.g., H2O).

 Electrons possess energy and bonds that exist between atoms in molecules contain energy.

Glycine

B. Ionic Bonding

Ionic bonds: when electrons are transferred from one atom to another.

- Attraction of oppositely charged ions holds the two atoms together in an ionic bond.

- Losing or gaining elections gives ions a filled outer shell, so they are more stable

Ex: sodium (Na+) and Chlorine (Cl- ) make NaCl

Why and how do ionic bonds form?

Cation: positively charged ion anion:

negatively charged ion

Attraction of oppositely charged ions holds the two atoms together in an ionic bond.

C. Covalent Bonding

• Hydrogen can give up an electron to become a hydrogen ion (H+) or share an electron with another atom to complete its outer shell of two electrons.

Covalent bonds: when two atoms share electrons so each atom has octet of electrons in the outer shell.

• Strongest type of bond

Carbon has amazing bonding properties, as we will learn in the next chapter

Structural formulas represent shared atom as a line between two atoms; a line represent the sharing of 2 electionse.g., single covalent bond (H-H), double covalent bond (O=O)

Three dimensional shape of molecules is not represented by structural formulas but shape is critical in understanding the biological action of molecules: action of insulin, HIV receptors, etc.

D. Nonpolar and Polar Covalent Bonds1. In nonpolar covalent bonds, sharing of electrons is equal = no

charge2. With polar covalent bonds, the sharing of electrons is unequal. =

chargeEx: water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; the oxygen atom with more protons dominates the H2O association.

              *The oxygen then assumes a small negative charge *

Oxygen is more electronegative than hydrogen

Hydrogen Bond: weak attractive force between slightly positive hydrogen atom of one molecule and slightly negative atom in another or the same molecule.• Weakest bond• mainly between O, N, F and an atom of hydrogen• Many hydrogen bonds taken together are relatively strong.• Hydrogen bonds between complex molecules of cells help maintain structure and

function.

Hydrogen bonds create surface tension.

Notice the e- spend more time around the oxygen molecule: it’s has more protons to attract the elections

*the shape allows for one side to be more + and the other more -

Van der Waals Interactions

When you have a molecule which is electrically dipolar (equal but opposite in charge) you have attraction between the negative pole of one molecule and positive pole of the other molecule. They are usually weaker than hydrogen bounds but exist in all matter

Biological molecules recognize and interact with each other with specificity based on their shape

List the 4 main types of bonds from weakest to strongest:

van der waalhydrogenioniccovalent

Draw these example and Name the type of bond.What elements are in each bond?

1 2

Name the type of bond.What elements are in each bond?

3

4

QOD: Properties of water, acids and bases

A. In your notebook, create a chart listing the properties of water, and why each property is important. Include example whenever possible

use pages 29-31

http://vimeo.com/37064053

Property Explanation Importance Example

1. High Specific Heat

2. High heat of vaporization

3. Universal solvent

4. Cohesive and Adhesive

5. Less Dense as solid

Examples of charts

water

Property 1 Property 2 Property 3 Property 4 Property 5

Explanation

example

Pg 29-31https://www.youtube.com/watch?v=0eNSnj4ZfZ8

https://www.youtube.com/watch?v=aVmU3CLxvgU

2.3. Chemistry of Water

A. Facts

1. All living things are 70.90% water.2. Because water is a polar molecule, water molecules are hydrogen bonded to each other.3. With hydrogen bonding, water is liquid between 0 C and 100 C which is critical for life.

http://www.johnkyrk.com/H2O.html

B. Properties of Water

1. High Specific Heat: The temperature of liquid water rises and falls more slowly than that of most other liquids.

- Most water stays a liquid Because water holds more heat, its temperature falls more slowly than other liquids; this protects organisms from rapid temperature changes, living things don't freeze or boil easily

Calorie is amount of heat energy required to raise temperature of one gram of water 1o C.

http://science.howstuffworks.com/environmental/458-how-water-works-video.htm

2. Water has a high heat of vaporization.

a. Hydrogen bonds between water molecules require a large amount of heat to break.b. This property moderates earth's surface temperature; permits living systems to exist here.c. When animals sweat, evaporation of the sweat takes away body heat, thus cooling the animal.

Heat of vaporizationEvaporative cooling

Organisms rely on heat of vaporization to remove body heat

3. Water is universal solvent, and facilitates chemical reactions both outside of and within living systems..

a. Water is a universal solvent because it dissolves a great number of solutes.b. Ionized or polar molecules attracted to water are hydrophilic.c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic.

Solvents dissolve other substances (solutes) and do not lose their own properties.

If we use a simple and easy example, we can get a handle on the idea. Take a glass of warm water, put a teaspoon of table salt in it, and stir it. The salt will dissolve in the water and "disappear" from view. The water is the solvent here, the salt is the solute in this example, and the resulting salt water is a solution that we created. It's that simple.

Hydrophobic vs Hydrophilic

4. Liquid water is cohesive & adhesiveCohesion = H bonds between water molecules; H2O molecules tend to stick together.Adhesive= ability of water to cling to other polar molecules

importance= Higher surface tensionTransport H2O against gravity in plants = capillary action

And this hasmade all the difference!

Ice! I could use more ice!

5. Ice floats

Most (all?) substances are more dense when they are solid, but

not water… Ice floats! H bonds form a crystal allowing life to survive the winter

B. Create a Venn Diagram Comparing Acids and Bases Substances with hydrogen

ions (H+) Substances with hydroxide

ions (OH–) Taste sour Taste bitter Feel slippery pH greater that 7 pH lower that 7

• Stomach acid• Citrus fruit: orange• Soap• Cleaning products• Baking soda• vinegar

Neutral = pH of 7

QOD: Properties of water, acids and bases

Acids and Bases

Covalently bonded water molecules ionize; the atoms dissociate into ions.• When water ionizes or dissociates, it releases a small

(107 moles/liter) but equal number of H+ and OH ions; thus, its pH is neutral.

• Water dissociates into hydrogen and hydroxide ions: 

Acid molecules dissociate in water, releasing hydrogen ions (H+) ions: HCl ¨ H+ + Cl-.

Bases are molecules that take up hydrogen ions or release hydroxide ions. NaOH ¨ Na+ + OH-.

See also:  Acid & Base Coloring

-One mole of water has 107 moles/liter of hydrogen ions; therefore, has neutral pH of 7. -Acid is a substance with pH less than 7; base is a substance with pH greater than 7.-As logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher pH unit;

* Buffers keep pH steady and within normal limits in living organisms.. http://www.johnkyrk.com/pH.html

The pH scale indicates acidity and basicity (alkalinity) of a solution.

Chemistry in Biology

Substances that dissociates into hydrogen ions (H+)

Taste sour pH lower than 7

Acids

Examples• Stomach acid• Citrus fruit: orange• vinegar

Substances that dissociated into hydroxide ions (OH–)

Taste bitter Feel slippery pH greater than 7

Base

Examples• Soap• Baking soda• Cleaning

products

pH Scale

10–1

H+ IonConcentration

Examples of Solutions

Stomach acid, Lemon juice

1

pH100 Hydrochloric acid0

10–2 2

10–3 Vinegar, cola, beer3

10–4 Tomatoes4

10–5 Black coffee, Rainwater5

10–6 Urine, Saliva6

10–7 Pure water, Blood7

10–8 Seawater8

10–9 Baking soda9

10–10 Great Salt Lake10

10–11 Household ammonia11

10–12 Household bleach12

10–13 Oven cleaner13

10–14 Sodium hydroxide14

tenfold changein H+ ions

pH1 pH210-1 10-2

10 times less H+

pH8 pH710-8 10-7

10 times more H+

pH10 pH810-10 10-8

100 times more H+

AP Biology

pH of cells must be kept ~7 to maintain homeostasis!

Buffers: solutions used to stabilize the pH of a solution

Control pH by using buffers reservoir of H+

donate H+ when [H+] falls absorb H+ when [H+] rises

100

1

2

3

4

5

6

7

8

9

3Amount of base added

Bufferingrange

4 52

pH

Buffers & cellular regulation

AP Biology

BICARBONATE BUFFER SYSTEM:

H2O + CO2 H2CO3 HCO3 -+ H+

HCO3- = Bicarbonate (weak base)H2CO3 = Carbonic acid (weak acid)

Major buffer system in bloodMaintains blood pH between 7.38 and 7.42

2009-2010

He’s gonnaearn a Darwin Award!

AnyQuestions?

http://www.darwinawards.com/

http://youtube.com/v/d0zION8xjbM

1. The only atom that has a nucleus with no neutrons is _________.

A) argonB) carbonC) oxygenD) hydrogen

2. Which of the following elements is NOT one of the six that make up 98% of most organisms' body weight?

A) hydrogenB) nitrogenC) carbonD) iron

Which of the following statements is true?A) All isotopes give off subatomic

particles.B) All isotopes are radioactive.C) All isotopes have the same number of

protons.D) All isotopes have the same number of

neutrons.What type of bond is formed when atoms share electrons?

A) ionicB) covalentC) hydrogen

If an atom has an atomic number of 17 and an atomic mass of 35, the number of neutrons in its nucleus equals _____.

A) 17B) 18C) 52

Which bond is most easily broken?A) a hydrogen bondB) a triple covalent bondC) a single covalent bond

Hydrophobic molecules tend to be _________.

A) nonpolarB) inorganic mineralsC) ionicD) water soluble

The calcium ion (Ca2+) _____.A) has accepted two protonsB) has given away two electronsC) will form a covalent bond with the chlorine ion (Cl-)D) All of these

The three isotopes of carbon 12C, 13C and 14C have different numbers of _______?

A) electronsB) protonsC) neutrons

The combined number of ___________ will determine the number of electrons in orbital(s) around a neutral atom.

A) orbitalsB) neutronsC) bondsD) protons

Which of the following statements is true?A) There are two polar covalent bonds in

water.B) There are two ionic bonds in water.C) There is one ionic and one covalent

bond in water.D) Electrons are less attracted to oxygen

than hydrogen.

The two parallel strands of DNA are held together by _______ bonds.

A) nonpolarB) hydrogenC) ionicD) covalent

The calcium ion (Ca2+) _____.A) has accepted two protonsB) has given away two electronsC) will form a covalent bond with the

chlorine ion (Cl-)D) All of these

Hydrogen bonds form when ___________.A) atoms share electronsB) a slightly negative atom is attracted to a slightly positive atomC) atoms gain electronsD) atoms lose protons

Which of the following has a basic pH?A) lemon juiceB) milk of magnesiaC) tomatoesD) hydrochloric acid

Aquatic living things are able to survive the winter thanks to which property of water?

A) It is less dense as a solid than as a liquid.

B) It is cohesive and adhesive.C) It is the universal solvent.D) It resists changes of state (from liquid

to ice or liquid to steam).

QOD:In a group of 4, each pick one paragraph of the article to read. (note: paragraph 2 is the hardest one, the back page will be more helpful) When you are done reading, discuss as a group and try to answer the question: 1. Why does the doctor not recommend

the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever.

2. Why do movie theaters put so much salt on popcorn?