Talk:Biology, Answering the Big Questions of Life/Atoms and Molecules

This is my draft, I need to edit it.

The ancient Greek Philosophers looked at the world and tried to describe it.

(Democritus and Leucippus, Greek philosophers in the 5th century BC, presented the first theory of atoms )

They wanted to know what things were made of. They new that the things in the world had substance. They take up space. You can touch them and push against them. They called this substance that all things are made of ...

Matter

Matter is defined as any substance in the universe that has mass and occupies space.

Mass is a measure of how much substance is in an object. On earth we measure mass by weighing an object. Weight, however can change. An person who weighs 180 pounds on the Earth would only weigh about 30 pounds on the moon.

Anyway, These same Greek philosophers wanted to find out what the universe is built of, so they wondered ...

What if we cut this piece of chalk in half, and then cut that piece of chalk in half, and so on and so on.

Wouldn't there eventually be some place where we couldn't cut any more? Some fundamental unit that the universe was made of?

They called this object an Atom.

Atom - a(not) tom (to cut) - The smallest unit of matter. also -The smallest component of an element that still has the properties of that element. (The atomic theory is one of the most basic theories of science. It says that all matter is made up of atoms.) What is an element? To understand element we need to go further ahead in time to the middle ages when Alchemy was king.

The ancient alchemists began to study matter in their search for the philosopher's stone that could turn lead into gold.

Well to do that, you need to understand what gold is, and what lead is.

Ancient alchemists found that atoms can be combined to make all the things found on Earth, but that some things are in a pure state, that is that all of the atoms in them are the same type of atom.

Element - matter composed only of one type of atom -matter composed of atoms that have all the same atomic number.

There are 92 naturally occuring (technidium may be an exception though) elements found on Earth. Elements such as Iron, silver, oxygen, hydrogen, Nitrogen, Sulfur, Calcium, and Gold

We list these elements on a chart called the periodic table of elements. Which gives data about them and is organized to show trends in how the elements interact with each other.

The study of matter and it's transformations is called Chemistry.

Now back to the atom. We could name elements and what properties they had, but we did not understand why they acted as they did until we were able to understand the structure of an atom. This was discovered in the late 19th and 20th centuries by many different scientists.

(For more on this, see physics - The study of the fundamental laws of nature) Atomic structure - DRAW

proton - Particle in nucleus. positive charge +1. Weight = 1 Dalton (unit named after scientist who proposed the modern atomic theory)

neutron - Particle in nucleus. no charge. Weight = 1 Dalton electron - negatively charged particle -1, circles nucleus. Weight 1/1836 Daltons (about 9.11 × 10−31 kg)

Atomic number - number of protons in an atom. Atomic mass - number of protons and neutrons in an atom.

Return to definition: Element - -matter composed of atoms that have all the same atomic number.

He (Helium) atomic number 2 - 2 protons 2 electrons ( no charge) atomic mass 4 - 2 protons 2 neutrons (ignore mass of electrons)

isotope - atoms of the same element that have different # of neutrons He 3 - isotope of helium

Atomic weight - Average atomic mass of atoms in an element. Includes differences due to different percentages of isotopes. measured in grams.

On earth Atomic mass is about the same as atomic weight. Assume the same.

THE DISCOVERY of the structure of the atom changed how we looked at the world. For one, it explained chemistry and the rules of the periodic table. The ways that atoms combine are determined by protons and electrons.

electrons don't simply float everywhere. They are found at descrete distances from the nucleus in an area called an orbital. These orbitals form layers of electrons around the nucleus called shells.

As atoms get bigger, they have more electrons, and they have more shells.

.He. . .Li. An orbital can only hold a fixed number of electrons. When the shell is filled, electrons must begin to fill a new orbital.

Atoms prefer to have their outer shell completely filled.

1s2 2s2 2p6 3s2 3p6 4s2 3d10

Atoms can lose or gain electrons. This changes the charge.

A charged atom is called an Ion. Na outer shell has one e-  often loses it to make Na+ ion.

molecule - Two or more atoms linked by a chemical bond

Ionic bond - a bond formed when two or more atoms lose or gain electrons to form an ion.

Na + Cl - They stick to each other to form a neutral molecule NaCl (table salt).

(loss of electrons - oxidation gain of electrons - reduction Redox reactions important to biology )

Sometimes atoms share an electron Covalent bond - when two or more atoms share electrons

Water H2O DRAW with partial charges

Periodic table - (except noble gasses) ones on outside tend to ionize and form ionic bonds. Ones in middle tend to form covalent bonds.

Different atoms have different numbers of electrons in their outer shell. Determines electrons they have to form covalent bonds

H 1 O 2 N 3 C 4 S 5

molecules DRAW H2O, NH3, CH4

H2O atomic mass/weight oxygen 16, hydrogen 1 2H@1=2 2O@16=16 H2O=18 AMU ( Atomic mass units)

You can convert molecules to grams using a unit called a mole. defined such that One MOLE of something equals the weight in grams equal to the number of AMUs. Mole - That amount of the substance containing exactly the same number of grams as the number of the atomic weight of the substance. equal to a particular number of atoms or molecules called Avogadro's number 6.022x10 23

Use - One mole oxygen (16 grams) plus 2 moles hydrogen (2 grams) can be used to make one mole water molecules (18 grams)

Next: Properties of water pH Other types of bonds electrostatic (ionic) hydrogen ( a type of covalent) Van Der Waals Hydrophobic interactions

Structure of water polar partial + and - charges mickey mouse ears shape

Properties of water inportant for living organisms 1. Universal Solvent Water Ionizes, polar, surrounds molecules, dissolves many substances especially dissolves charged and polar substances.

This means that the cytoplasm in your cells, which are made of water, can contain many many different kinds of molecules.

Hydrophilic - water loving hydrophobic - water hating

Hydrophobic molecules are repelled by water. "Squeezed out" of it called the "hydrophobic effect"

Remember plasma membrane. - water squeezes non-polar molecules together. Inside and outide stay separate.

2. high heat of vaporization

Water requres lots of heat to change from water into steam. 2,452J/g. This means that evaporating water (sweat) can cool your body in high temperatures.

3. High specific heat Specific heat is the amount of energy required to raise the temperature of one kilogram of the substance by one kelvin. Liquid water heats up very slowly.

This means that it water helps organisms maintain a constant body temperature. It also keeps lake and ocean temperatures constant.

4.Strong surface tension

The surface of the water makes a film that resists breaking. This is why certain insects can skate on the surface of the water.

5. High cohesive strength Water molecules stick to each other very strongly. Therefore it will cling to charged substances and form a coat on them. The cohesive force also pulls water up small spaces like straws called "capillary action". Capillary action is why water can be pulled from the ground to the tops of trees.

6. Ice floats Water is most dense at 4C therefore ice is less dense and will float. This fact means that in the winter, ice insulates lakes and makes it possible for aquatic animals to survive the winter.

Lecture 11 - macromolecules

1. Take roll 2. Return tests / take late labs 3. Remind them this is chapter 3 4. lecture

Macromolecules I. Intro On Wednesday we talked about chemistry. All things are made of Atoms. That atoms have different numbers of protons neutrons and electrons. The number of protons decides the element. Atomic number. That the number of electrons decides the bonding.

We also talked about Moles, the periodic table of elements, and the properties of water.

We will continue talking about chemical bonds, discuss pH and end with a discussion of the macromolecules that make up living organisms.

CHON TRANSPARENCY - COMMON LIVING ELEMENTS

II. weak bonds

As well as the strong ionic and covalent bonds(50-110kC/mole), there are many weaker bonds that help keep molecules together.

A. electrostatic / aqueous ionic bonds (5kC/mole) result from the attraction between two ionized atoms or functional groups. Ionic bonds become very weak in water.

-COO - and NH3 +

B. hydrogen bonds (4-5kC/mole) result from electrostatic attraction between a covalently bonded hydrogen atom which has a partial positive charge, and electronegative atoms such as oxygen and nitrogen.

N-H --- O=C-

C. Van der Waals interactions (1-2 kC/mol) A weak attraction between the protons of one atom and the electron cloud of the neighboring atoms even in uncharged (neutral) atoms.

D. hydrophobic attractions (1-3kC/mole) Uncharged hydrophobic molecules will group together in water. Mostly due to molecules avoiding water, not so much them being attracted to each other. "water and oil don't mix"

In large molecules, these weaker forces play important roles in helping them molecules function and keep their shape.

III. Properties of water - Ionization A. Water Ionizes One property of water that we did not mention last time is that water can ionize. That is to say that water can break down from the neutral molecule H2O to two charged molecules H+ and OH-.

Any body of water will normally have a small number of ionized water molecules in it at any time.

B. Acids and bases Sometimes a molecule dissolved in water will release H+ ions into the water. This makes the H+ concentration increase so that there are more H+ ions than OH ions.

A molecule that can donate a hydrogen atom is called an acid.

Some molecules can attract and bind a hydrogen atom taking it out of solution. Such a chemical is called a base.

When water contains an acid it is said to be acidic. When water contains a base it is said to be alkaline or basic.

C. pH 1. We can measure how acidic or basic water is using a scale called pH.

2. pH is the log base 10 of the [H+] conc.

pH=log10[H+]

1 liter of pure water has a H+ conc. of 1x10 -7 We call this pH 7 neutral ( pH=log10[H+] pH=-log10[10-7] pH=-(-7) pH=7 )

3. Notice the exponent is a negative one, this means that a smaller exponent means a larger number of H+ ions.

Numbers below 7 are acidic Numbers above 7 are basic

The scale goes from 1 - 14 TRANSPARENCY e.g. pH 1 = 10-1 H+ One tenth of a mole of H+/liter pH 14 = 10-14 H+ one hundred trillionth of a mole of H+ per liter

TRANSPARENCY

4. Remember the scale is logarithmic Each number means 10 times more than the previous

D. Buffers So every time you add a substance you have the possibility of changing the pH by a large amount. We can moderate the affect of pH change by adding a Buffer. TRANSPARENCY A buffer is a substance that stabilizes the pH by absorbing and releasing H+ ions. It is usually a combination of a weak acid and it's conjugate base.

TRANSPARENCY

The cytoplasm and many other parts of living organism are buffered to prevent large changes in the pH.

IV. Functional groups we defined Molecules as two or more molecules bonded together. Some parts of a molecule have recognizable structures. These are some important groups of atoms that are found on larger molecules.

TRANSPARENCY

-OH hydroxyl group a chemical with such a group is called an alcohol. C=O Carbonyl group

-COOH Carboxyl group a molecule with this group is called a carboxylic acid.

-NH2 amino group a molecule with this group is called an amine.

-PO4 phosphate group

V. classes of macromolecules

A. Intro In living systems, we deal with very large molecules. We call these molecules MACROMOLECULES. Macromolecules are made of subunits called monomers. These monomers are combined to make complex polymers.

Often polymers formed by hydrolysis, a reaction where water is removed to form a bond between monomers. TRANSPARENCY There are four classes of macromolecules in living systems: Carbohydrates, Lipids, Nucleic Acids, and Proteins TRANSPARENCY polymer			monomer Carbohydrates		sugars Lipids			fatty acids Nucleic acids		nucleotides proteins			amino acids

B. Carbohydrates - Sugars and starches {Carbon chain hydrated (water)} Note the water molecules across almost every carbon node. Often form rings of 4,5 or 6 carbons. Formula {C(H2O)}n

most abundant source of carbon in living organisms.

monosaccharides: fructose, glucose, ribose TRANSPARENCY disaccharides: lactose, sucrose (table sugar) TRANSPARENCY polysaccharides: starch, cellulose, glycogen TRANSPARENCY chitin - polymers of glucosamine found in insect skeleton, shellfish, and fungi.

Sugar groups found on proteins in the cell membrane. Glycoproteins.

C. Lipids - Fats and oils Lipids are insoluble in water. Create compartments in cells. Stores the most energy of biological macromolecules.

Triglycerides have a glycerol molecule bound to three fatty acids. TRANSPARENCY Show fatty acid, glycerol

Saturated - straight Unsaturated - bent or kinked - contains double bonds. Unsaturated lipids stay liquid at higher temperatures.

Substitute one fatty acid in a triglyceride with a phosphate group and you make, a phospholipid! TRANSPARENCY Phospholipids 1. form micelles and bilayers in water. TRANSPARENCY 2. are amphipathic - having one side charged and one side hydrophobic. 3. Often have nitrogen groups on the phosphate.

Other lipids cholesterol - important in membrane fluidity vitamins such as vitamin A Steroids such as estrogen and testosterone TRANSPARENCY (Notice the difference in appearance. Lipids also form chains and rings, but they don't have internal oxygens, and the rings tend to be 6 carbon saturated or unsaturated. Notice the large lengths of (CH)n.

D. Nucleic acids - DNA and RNA

Nucleic acids are giant linear polymers that are used in the cell to store information. They are made of three parts. a sugar a phosphate group and a nitrogen containing base TRANSPARENCY There are two major nucleic acids used in the cell. Ribonucleic Acid RNA Deoxyribonucleic Acid DNA TRANSPARENCY Sugar (ribose or deoxyribose) Phosphate Base - a single or double ring of carbon and nitrogen attached to the sugar. DNA has 4 Adenine, cytosine, Guanine, and Thiamine ACGT RNA has 4 Adenine, cytosine, guanine, and Uracil ACGU TRANSPARENCY The bases can hydrogen bond to each other. C=G, A=T, A=U DNA is usually double stranded RNA is usually single stranded

5' and 3' ends

Knowing the sequence of one strand tells you the sequence of the other "complementary" strand.

ATP is a nucleic acid

E. proteins monomers amino acids small proteins are called peptides Carbon atoms with - one carboxyl group - one amino group - a hydrogen - and a variable group called R

Amino acids polymerize by hydrolysis this reaction forms a peptide bond. TRANSPARENCY The R groups determine the properties of the protien. They hang off of a linear chain formed by the series of peptide bonds. TRANSPARENCY

Proteins will fold in specific ways. They call this it's primary secondary tertiary and Quaternary structure TRANSPARENCY

primary - chain secondary - Alpha helix and beta pleated sheet tertiary - folding due to all of the weak forces we talked about before. S groups can covalently bond sulfur bond.

Proteins will spontaneously fold into specific shapes. The sequence of the protein determines it's shape and function.

The field of study dealing with protein structure and function is proteomics.

Most of the functions of a cell are catalyzed by proteins. Proteins act as enzymes - molecules that make chemical reactions happen easier with lower energy cost. TRANSPARENCY Enzymes also have structural functions in the cell.

Show examples of macromolecules. explain how to identify them. Show locations in a cell/organism TRANSPARENCY peptidoglycan - protein sugar