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AP Biology Unit 1: The Chemistry of Life

Chapters: 2, 3, 4, & 5

Cris Robson

on 30 July 2013

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Transcript of AP Biology Unit 1: The Chemistry of Life

Chapters: 2, 3, 4, & 5
Unit 1: The Chemistry of Life
Chapter 2 should be REVIEW from Chemistry - we will not be spending much time on this chapter - I expect that you learned this information in Chemistry!
Chapter 2: The Chemical Context of Life
Focus Question:
Why is water essential to living things?

Chapter 3: Water and the Fitness of the Environment
Why is Carbon essential?
Chapter 4: Carbon and the Molecular Diversity of Life
Chapter 5: The Structure and Function of Macromolecules
Atomic Number
Mass Number
Basic Vocabulary you should know:
The types of chemical bonds you need to know for AP Bio:
1. Covalent Bonding - nonpolar & polar
2. Ionic Bonding
3. Hydrogen Bonding
Chemical Bonding
If you don't know this vocabulary, I suggest you look up the definitions in your textbook and make notecards.

They will not be on a vocab quiz, but you need to know these terms to understand basic Biological concepts!
Review Questions
What are those properties?
Water has special properties that make it the ideal molecule for living organisms
Cohesion is the attraction between like substances.
This occurs in water between each molecule because of Hydrogen bonds.
Cohesion makes it possible for some insects to 'walk on water' and for water to be drawn up plants.
A covalent bond is the sharing of a pair of valence electrons by two atoms.
Covalent Bonding
Hydrogen Bonding
Ionic Bonding
Nonpolar Covalent Bond:
Polar Covalent Bond:
Electronegativity: an atom’s ability to attract electrons.
Therefore - the more electronegative an atom, the more strongly it attracts shared electrons
A nonpolar covalent bond is formed by an equal attraction/pull of electrons between atoms. This means that the atoms have same electronegativities.
A polar covalent bond is formed by an unequal attraction/pull of electrons between atoms. Therefore, atoms have different electronegativities.
Water is an example of a polar covalent bond.
The Oxygen is more electronegative, therefore it pulls the electrons with more force than the Hydrogen atoms do. This gives the oxygen a more negative charge and the Hydrogens a more positive charge.
Two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely away from another atom.

This produces an anion and a cation.
An anion is a negatively charged atom (more electrons than protons = a net negative charge)

Example: Chlorine
Because of the opposite charges of the cation and the anion, they attract one another in an ionic bond.
Example: Sodium Chloride
A cation is a positively charged atom (fewer electrons than protons = a net positive charge)
Chlorine will accept an electron to complete the octet rule (full outer shells) Once this occurs, Chlorine now has 18 electrons and only 17 protons.

Recall that protons are positively charged and electrons are negatively charged.

Once the electron transfers to the Chlorine atom, the atom becomes more electronegative. (It was previously neutral with an equal amount of protons and electrons)
Sodium will give away an electron to satisfy the octet rule (full outer shells) Once this occurs, Sodium now has 10 electrons and 11 protons.

Recall that protons are positively charged and electrons are negatively charged.

Once the electron transfers away from the Sodium atom, the atom becomes less electronegative. (It was previously neutral with an equal amount of protons and electrons)
1. Sodium gave an electron to the Chlorine
2. Chlorine becomes more electronegative;
Sodium becomes less electronegative
3. Sodium and Chlorine are attracted to create an ionic bond because of their opposite charges.
Weak chemical bonds play important roles in the chemistry of life.

Weak bonds make properties of life possible, they form brief associations between molecules.
A Hydrogen bond is formed by the charge attraction when a Hydrogen atom covalently bonded to one electronegative atom is attracted to (the negative end of) another electronegative atom.
How do they form brief associations?
Hydrogen bonding!
Recall that Hydrogen atoms have a very low electronegativity...they only have one electron and one proton.

When Hydrogen atoms are covalently bonded to other atoms (like oxygen) they become more positively charged because of the polarity that is formed in that molecule. (Remember - the oxygen atom has a stronger pull on the electrons making it more negative and the hydrogen more positive)
Why are Hydrogen bonds important?
The advantage of weak bonding is that the contact between the molecules can be brief; the molecules come together, respond to one another in some way, and then separate.

An example of why this is important:
Chemical signaling in the brain - one brain cell signals another by releasing molecules that use weak bonds to dock onto receptor molecules on the nearby surface of a receiving cell. The bonds last just long enough to trigger a momentary response by the receiving cell. If the signal molecules attached by stronger bonds, the receiving cell would continue to respond long after the transmitting cell ceased dispatching the message, with perhaps disastrous consequences.
Imagine what it would be like, for instance, if your brain continued to perceive the ringing sound of a bell for hours after nerve cells transmitted the information from the ears to the brain...
2. Why is hydrogen bonding so important to life processes?
1. What are the four main types of bonds that are essential to life processes? - briefly describe each and give an example.
Chemical Reactions Make and Break Chemical Bonds:

Chemical reactions are the process of making and breaking chemical bonds leading to changes in the composition of matter.

Reactants undergo changes into products

Matter is conserved (rearranged) and reactions are reversible
Hydrogen gas
Oxygen gas
Notice that matter is conserved - there is an equal number of Hydrogen atoms on the reactant side as on the product side. There is an equal number of oxygen atoms on the reactant side and the product side.
3. Describe what a chemical reaction is.
Answer the following questions (these are graded)
Because water has the capability to hydrogen bond it has:
A High Specific Heat: the amount of energy needed to increase the temperature of 1 gram of a substance 1 degree Celsius (changes temp slowly) – ex. Pan is hot before water boils

A High Heat of Vaporization: the amount of heat energy needed to change a liquid to a gas (or evaporate)

A High Heat of Fusion: the energy needed to convert a substance from a liquid to a solid (freezing, in the case of water)
What is so special about water??
4. Think about it - (answer this question)
why are these three traits of water important for living organisms? (p 43-44 may help you)
Adhesion is the clinging of one substance to another
Adhesion of water to the walls of the vessels helps counter the downward pull of gravity.
Adhesion and cohesion work together in plants:
Cohesion due to hydrogen bonding contributes to the transport of water against gravity in plants.
Water reaches the leaves through microscopic vessels that extend up ward from the roots.
Water that evaporates from a leaf is replaced by water from the vessels in the veins of the leaf. Hydrogen bonds cause water molecules leaving the veins to tug on molecules farther down in the vessel, and the upward pull is transmitted along the vessel all the way down to the roots.

It's kind of like an assembly line! a new water molecule replaces one that has left the leaf...
Water makes a versatile solvent, because of it's polarity.
Water is the solvent of LIFE:
Water adheres to other unlike molecules.

When water adheres to the walls of narrow tubing or to absorbent solids like paper, it demonstrates capillary action.
when paper towels absorb water, you can watch the water travel up the paper towel - try it at home!
an aqueous solution is one where water is the solvent.
If you don't know the terminology for solvent, solute and solution - LOOK THEM UP!!!
When you add salt (sodium chloride) to water, the salt dissolves...but think for a moment...what is really happening at the molecular level?
5. Explain what is happening in this diagram
What determines and acid vs. a base?
pH - What does it MEAN??
8. Describe adhesion vs. cohesion
An acid is a substance that increases the hydrogen ion (H+) concentration of a solution.
A substance that reduces the Hydrogen ion (H+) concentration in a solution is a base.

Essentially this means there are more Hydroxide Ions (OH-)
The pH Scale
Reactions of living organisms are very sensitive to levels of pH
It is critical to maintain proper pH in an environment where cells and tissues are present.
6. Why do you think this is the case? In your learning about water, how do you think pH plays a role?

An optimum pH is essential for cellular metabolism (10 x -7)
At any given time, a fixed proportion of a volume of water will be:
H+ (hydrogen ions) Acids
OH- (hydroxide ions) Bases
And the rest will be H2O
Instructions for using the prezi:
as you read through the prezi, take notes on concepts you don't quite understand.
You can follow along in the book with each chapter to read more if you have questions.
You need to answer the questions (highlighted in red text and they are numbered) with complete detailed answers - this will be turned in.
Also, if you have further questions as you move through the prezi, write them down so you can ask them during class.
9. what are properties of water that make it so important to living things?
10. Explain the difference between an acid and a base?
11. what happens (at the molecular level) when you add salt to water?
12. In your own words, describe the properties of water that make it possible to defy gravity so that it can travel up a tree.
7. Draw a water molecule and show the polar ends.
Organic molecules are those that have carbon.
In living systems, large organic molecules, called macromolecules, may consist of hundreds or thousands of atoms.
Most macromolecules are polymers.
Remember a polymer is a larger molecule that consists of a single unit (monomer) repeated many times.
Many organic molecules share similar properties because they have similar clusters of atoms: functional groups.
13. Define "Organic Chemistry"
Organic Chemistry: The study of carbon containing compounds.
Four of carbon’s six electrons are available to form bonds with other atoms

You will always see four lines connecting a carbon atom to other atoms.

Complex molecules can be formed by stringing carbon atoms together in a straight line.
Because Carbon can make so many bonds, it can bond in different shapes - including ring structures OR chains.
CHAIN structure
RING structure
Carbon molecules are grey - hydrogen is red
14. Why does carbon make a good 'backbone' element?
Hydrocarbons are carbon compounds with carbon and hydrogen only.
There is variation within hydrocarbon structures
15. What is a hydrocarbon?
16. What are the 4 variations of hydrocarbon structures? Draw each one.
Functional groups are added to a hydrocarbon chain
Functional groups give the molecule a particular property, such as acidity or polarity.
17. Describe what a functional group is, and why are they important?
Isomers are molecules with identical molecular formulas but different structural formulas

Different types of Isomers exist:
18. Describe the three types of isomers and give examples.
Different Isomers:
The variation in carbon skeletons contributes to the diversity of organic molecules.
Polymer: most macromolecules are polymers…a single unit repeated many times, hence “poly”mer
Monomer: a single unit (“mono”mer) that makes up a polymer
Macromolecule: a large organic molecule, made of multiple polymers
Lipids are a class of substances that are insoluble in water, but are soluble in non-polar substances (ether, chloroform)

Fats are energy storage molecules, they store more energy per gram than carbohydrates!
Nucleic Acids
How are monomers attached or detached?

Dehydration Synthesis: polymerization reactions during which monomers are covalently linked, producing net removal of a water molecule for each covalent linkage (De-hydrate = remove water)

Hydrolysis is a reaction process that breaks covalent bonds between monomers by the addition of water molecules. (Hydro = water; lysis = to break; Hydrolysis = to break using water)
Start to break down words and learn their roots! - the vocabulary will make WAY more sense!
Dehydration synthesis - note where the waters are coming from.
A monosaccharide (sugar) is the simplest kind of carbohydrate. It consists of a single (mono) molecule like fructose or glucose.

All sugar molecules have the formula (CH2 O) n, where n is any number from 3 to 8.

For glucose, n is 6, and its formula is C6H12O6

The formula for fructose is also C6H12O6
Two forms of glucose, seen below, differ only in a reversal of the H and OH on the first carbon.

Even very small changes in the position of certain atoms may dramatically change the molecule
Common Disaccharides:
Maltose= Glucose+Glucose (beer)
Lactose= Glucose+Galactose (milk)
Sucrose= Glucose+Fructose (table sugar/fruit sugar)
All saccharides are storage molecules, they store energy to be used by living system
19. What is the difference between starch (above) and cellulose (below)?
Di (two) sacchar (sugar): a double sugar that consists of two monosaccharides joined by a glycosidic linkage.

Glycosidic linkage: a covalent bond formed by a condensation/dehydration (water is removed) reaction between two sugar monomers, for example maltose:
20. Describe a dehydration reaction.
21. Describe hydrolysis.
22. What are the four classes of biomolecules?
23. What is a monosaccharide? A disaccharide?
24. What is the main purpose of carbohydrates for living organisms?
A polysaccharide consists of a series of connected monosaccharides. A polysaccharide is a polymer. (poly = many; mono = one)

Cells hydrolyze (add water to break apart) storage polysaccharides into sugars as needed.

Common storage polysaccharides are STARCH, GLYCOGEN, CELLULOSE, and CHITIN.
Starch is an alpha-glucose polymer that is an energy storage molecule in plants

Starch has two forms:
Amylose and Amylopectin
25. Describe the four types of storage carbohydrate biomolecules.
Glycogen: an άalpha-glucose polymer that is a storage polysaccharide in animal cells.
Glycogen polymers are more tightly branched than starch
Glycogen is stored in the muscle and liver of humans and other vertebrates
Cellulose is a polymer of beta-glucose molecules.
It serves as a structural molecule in the walls of plant cells.
Cellulose is the major component in wood.
Chitin is a polymer similar to cellulose, but each beta-glucose molecule has a nitrogen containing group attached.
Chitin serves as a structural molecule in the walls of fungus cells, exoskeletons of insects, and mollusks
There are three major groups of lipids:
Triglycerides, phospholipids, and steroids
What's the difference between Saturated and Unsaturated fatty acids??
A saturated fatty acid has a single covalent bond between each pair of carbon atoms, and each carbon has 2 hydrogen bonded to it. The carbon is “saturated” with hydrogen

Unsaturated fatty acids have a double covalent bond and each of the two carbons in this bond have only one hydrogen atom bonded to it.
solid at room temp
more processed &
less healthy fats
liquid at room temp
healthier fats
Phospholipids: look just like a lipid except that one of the fatty acid chains is replaced by a phosphate group (hence, “phospho” lipid)
A phospholipid is amphipathic (a molecule which is polar in a region and nonpolar in another), meaning it has a hydrophilic “head” and hydophobic “tail”
Phospholipids are oriented in a sandwich-like fashion formation with the tails grouped together on the inside (away from water)
All cell membranes are made from phospholipids!
Steroids are characterized by a backbone of four linked carbon rings.
Examples include cholesterol (a component of cell membranes), hormones, testosterone and estrogen.
Triglycerides (fats, oils, waxes)
They consist of 3 fatty-acids attached to a glycerol molecule.
(Fatty acids are hydrocarbon chains with a carboxyl group at one end of the chain)
Proteins can be grouped according to their functions:
Structural proteins: keratin, hair, horns, collagen, connective tissue, spider silk
Storage proteins: casein in milk & ovalbumin in egg whites
Transport proteins: found on cell membranes that transport materials into and out of cell, hemoglobin
Defensive proteins: antibodies to fight infection
Enzymes: regulate the rate of chemical reactions
For a protein to function properly, it has to be folded into a specific structure. Protein folding has four levels of “folding”
The primary structure of a protein describes the order of amino acids. Using 3 letters to represent each amino acid.
Secondary structure of a protein is a 3D shape that results from hydrogen bonding between the amino and carboxyl groups of adjacent amino acids.

The bonding produces a spiral (alpha helix)
The bonding produces a folded (pleated sheet)

Proteins whose shape is dominated by these 2 patterns, form fibrous proteins
Tertiary structure of a protein includes additional 3D shaping. The following factor contribute to tertiary “folding”
Hydrogen bonding between R groups of amino acids
Ionic bonding between R groups of amino acids
Hydrophobic effect
Disulfide Bonds, when the sulfur atoms in two cysteine amino acids bond….”Disulfide Bridge”
Quaternary structure describes a protein that is assembled from two or more separate peptide chain.
Ex. Hemoglobin consists of 4 peptide chains held together by hydrogen bonding, R-groups interactions, and disulfide bonds
26. Three types of lipids: describe their shapes and function.
27. Explain how proteins are folded
The genetic information of a cell is stored in molecules of DNA.

The DNA, in turn, passes its genetic instructions to RNA for directing various metabolic activities of the cell

DNA is a polymer of nucleotides. A nucleotide includes:
Nitrogen Base (A,T,C,G)
5-carbon sugar (deoxyribose)
Phosphate group
The nitrogen bases are A, T, C, G
A and G are “Purines” double-ring bases
T and C are “Pyrimidines” single-ring bases

You can remember which bases are purine because only the two purines end with “nine”: adenine and guanine

Remember base pairing rules A-T and C-G
The two strands of DNA are antiparallel, that is, they run in opposite directions.

One is arranged in the 5’3’ direction the other in the 3’5’ direction
RNA differs from DNA in the following ways:
The sugar in RNA is ribose, not deoxyribose
The thymine does not occur in RNA, it is replaced with uracil

RNA is a single-stranded molecule and does not form a double helix as DNA does.
Primary Structure:
Quaternary Structure:
Secondary Structure:
Tertiary Structure:
28. What is a nucleotide composed of?
29. What is the difference between the purines and pyrimidines?
30. Describe the differences between DNA and RNA
Full transcript