Quiz 2 Study Guide CHAPTER 2

Extra Notes on Water:

1. Many molecules of water connect with hydrogen bonds and this gives liquid water
structure, and this is cohesion.
 Cohesion, along with adhesion, is responsible for the transport of water
molecules against gravity from the roots of trees up to the leaves.
• Adhesion is the connection made between water and other substances – when
water molecules from hydrogen bonds with cellulose in plant cell walls.

2. Water is a very good solvent – because of its polarity. Water can dissolve ionic
substances and/or polar substances. Each water molecule has polar bonds with slight
negative charge at the oxygen atom and slight positive charge at each of the hydrogen
atoms which attract opposite ion charges (like NaCl or and acid like HCl or base like
NaOH or other polar molecules).
 An “aqueous” solution is one where water is the solvent

3. Water has a high specific heat and has the ability to moderate temperature.

Carbon:
Know the 4 elements most common in organic molecules

– Carbon, Hydrogen, Oxygen and Nitrogen

Know carbon shares four (4) electrons with another atom (or atoms) to form
covalent bonds to complete its valence shell. – This is why carbon can bond to form
macromolecules

Organic molecules contain carbon.

Know carbon makes up the backbone of organic molecules.
The hydrocarbon chain is a common backbone of organic molecules.
Recall: Carbon has 4 valence electrons and when it bonds with other substances, like
Hydrogen, it forms a tetrahedral shape due to the orbitals of the shared valence
electrons. The shape is symmetrical and nonpolar.
Know CO2 is not organic, but inorganic, because carbon is sharing electrons with
oxygen. In order for a molecule to be organic, carbon shares electrons with hydrogen.

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Double Bonds between carbon atoms = Adjacent carbon atoms can share two pairs of
electrons, forming a double bond between them. Double bonds between two carbon
atoms require more energy to break than single bonds between two carbon atoms.
The double bond is shorter than a single bond and is not free to rotate.
Double bonds between two carbon atoms are found in hydrocarbon chains and in
rings.

Isomers:
Two molecules with the same chemical formula may be arranged differently to
produce different structures. = Isomers
Structure dictates function, so these molecules with the same molecular formula but
different structures will have different functions.

Isoleucine will have a different function than leucine because they have different
molecular structures, even though they have the same molecular formula.

- Structural isomers have different covalent arrangements of their atoms.

- Cis-trans isomers have the same covalent bonds but differ in their spatial
arrangements.
In cis-trans isomers, two carbon atoms have a double bond between. Please Note:

- Enantiomers are isomers that are mirror images of each other

Enantiomers are important in the pharmaceutical industry.
One isomer will be biologically active in a person and the other isomer will be
biologically inactive.

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L-Dopa is active
D- Dopa is inactive,
and can interfere with
L-Dopa

Be able to identify and distinguish:

Organic Molecules
What are the 4 types of organic molecules?
Proteins
Nucleic acids
Carbohydrates
Lipids

Know the basic functions of each type of organic molecule:

1. Proteins provide structural support and act as catalysts to facilitate chemical
reactions.
2. Nucleic acids encode and transmit genetic information.
3. Carbohydrates provide structural support for many organisms and a source of
energy.
4. Lipids make up cell membranes, store energy, and are important in cell
communication.

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Know the 2 biochemical reactions that occur to assemble and disassemble
macromolecules:
Be able to identify if a reaction is dehydration synthesis or hydrolysis.

Assembling Macromolecules:
Dehydration Synthesis (or AKA – Condensation)
Water is removed
H2O will be in the product!
Two smaller molecules are combined to produce
a larger molecule plus water.

Disassembling Macromolecules:
Hydrolysis
A water molecule is added, breaking a bond for
hydrolysis to occur.
H2O is in the reactants!
One larger molecule is broken down into two
smaller molecules.
Examples of Dehydration Synthesis and Hydrolysis:

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Example of dehydration synthesis to produce a peptide bond and polypeptide:

A dehydration synthesis reaction joins a

dipeptide with an amino acid to form a
peptide bond and polypeptide. During
the reaction water is removed and the
products are the polypeptide and
water.

Proteins:
What is the monomer of proteins? Amino acid
What is the basic structure of amino acids?

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How do amino acids form a peptide bond?

through dehydration synthesis

Peptide Formation: 2 examples below

What is a polypeptide?

3 or more amino acids bonded together by peptide bonds

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Be able to recognize an amino acid R group as to being hydrophilic or hydrophobic.
Review the Chart in the text and PowerPoint Slides – Figure 5.2

Know that if the R group has hydrocarbons (-CH3) or hydrocarbon chains or carbon
rings, then the amino acid will be nonpolar and hydrophobic.

Know that if the R group has a hydroxyl group (-OH), carbonyl group ( =O or CHO),
carboxylic group (-COOH), amine group (-NH2), amide group (O=C-NH2), then the group
will be polar or charged and hydrophilic and reactive.

Nucleic Acids and Nucleotides

What is the monomer of nucleic acids? (monomer = subunit)

Nucleotide

What is the structure of a nucleotide?

5 Carbon sugar (Ribose – RNA or Deoxyribose – DNA)

Nitrogen Base
Phosphate Group

Nitrogen Base

Phosphate Groups 5 Carbon Sugar

Nitrogen Base

Notice that the 5 carbon sugars differ at Carbon

#2
– Ribose has a hydroxyl group (-OH) and
Deoxyribose only has a hydrogen (H & no “O”)
Know each nucleotide contains either a purine or pyrimidine nitrogen base.
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 This base found only in DNA

This base found only in RNA

The bases in nucleic acids are single-ring pyrimidines (T, C, U)

or double-ring purines (A, G).

DNA complementary base pairs: Adenine bonds to Thymine (A – T)

Guanine bonds to Cytosine (G – C)

RNA – When RNA is copying DNA: Uracil (U) replaces Thymine

1. Adjacent pairs of nucleotides are joined together by phosphodiester bonds.

2. The phosphate group of one nucleotide is joined to the sugar unit in another
nucleotide.
3. The formation of this bond results in the loss of a water molecule.

The formation of the phosphodiester bond establishes the 5’ to 3’ direction in which

DNA will replicate itself in later chapters.

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 NOTE: The bond forms between the
phosphate group and the 3’ Carbon of the last
nucleotide.

1. DNA consists of two strands of nucleotides twisted around each other in the
form of a double helix.
2. The sugar–phosphate backbones wrap around the outside, and the bases form
complementary base-pairing A-T, G-C.
3. The base pairing in the middle results from hydrogen bonding between the
bases.

Why is it beneficial for hydrogen bonds

to form between nucleotide bases?

- Because DNA “unzips” down the middle.

Hydrogen bonds are weak bonds, which
makes it easier for the DNA molecule to
unwind.

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Carbohydrates:
1. Carbohydrates, or sugars, are composed of C, H, and O.
2. The simplest carbohydrates are saccharides, which contain five or six carbons.
They can be linear but are more commonly cyclic.
3. Sugars containing an aldehyde group are aldose sugars, and those containing a
ketone group are called ketose sugars.
Glucose, Galactose and Fructose each have 6 carbons, 12 hydrogens, and 6 oxygens but
differ in their arrangements of the atoms. They are isomers – same molecular formula,
but different structural arrangement.

Types of Sugar Molecules = monosaccharide, disaccharide or polysaccharide

1. A monosaccharide contains one sugar molecule. It is often a subunit, or monomer,

of more complex sugars. Virtually all monosaccharides in a cell are in cyclic form.

2. Disaccharides contain two bonded monosaccharides.

3. Polysaccharides contain more than two monosaccharide monomers and are formed
through dehydration reactions. Some, but not all, sugars have glycosidic linkages.

4. Complex carbohydrates are long, braided chains of monosaccharide monomers.

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Monosaccharide: a single ring / monomer of polysaccharides

Polysaccharide: Two monomers are joined by a glycosidic linkage**

**Glycosidic linkage is circled in red**

Carbon #1 of first glucose subunit is bonded to Carbon #4 of following glucose subunit.
1,4 – glycosidic linkage

How are two glucose subunits joined together in starch?

By a glycosidic linkage

Straight chain Polysaccharide? = starch

Polysaccharide chain with branches in structure and only found in animals?
Glycogen
Polysaccharide made up of parallel chains of glucose subunits joined by hydrogen
bonds between the two chains and only found in plants?
Cellulose
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Lipids:

All lipids are hydrophobic

Different types of lipids have different structures, but they are all hydorphobic

Fatty acids are long chains of carbons attached to a carboxyl group at one end.

Recall: Fatty acid chains can be short or long

Which fatty acid chains would be more stabilized by van der Waals interactions –
short or long?
WHY? Because the long fatty acid chains can form more Van der Waals interactions
between the hydrophobic groups

Saturated versus unsaturated fatty acids have different structure based on the
presence of C-C double bonds.

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Animal fats are saturated with hydrogens. (like butter) The molecules can pack together
more tightly. This explains why animal fats are solids at room temperatures

Note how the Saturated Fatty Acid Chains lie straight and flat and the
Unsaturated Fatty Acid Chain in the diagram to the right has a kink in the chain where
the carbon-carbon double bond is located.

What will prevent the fatty acid chains from packing to tightly in warm weather?
The kinks in the C-C double bonds
Saturated fats will remain packed together because the chains are saturated with
hydrogens.
That is why butter is a solid at room temperature and oil is a liquid at room
temperature.

Van der Waals Interactions

Hydrocarbon chains of fatty acids contain no polar

covalent bonds and are uncharged.

In van der Waals forces, the constant motion of electrons

leads to regions of slight charges, and these charges are
attracted to or repelled by neighboring molecules.

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Van der Waals forces are weaker than hydrogen bonds, but many act together to
stabilize molecules.

The length of the hydrocarbon chains increases these forces.

Longer fatty acid chain = more Van der Waals Interactions

Lipids: Steroids

Cholesterol is a steroid.
Cholesterol is found in the lipid bilayer of animal cell membranes.
Cholesterol is a precursor to steroid hormones – estrogen, progesterone and
testosterone.

Lipids: Phospholipids
Phospholipids =
major component of cell membrane
Have both hydrophilic and hydrophobic properties
Phosphate head = hydrophilic
Fatty acid tails = hydrophobic

What is the term describing both hydrophilic and

hydrophobic properties?

Amphipathic
Phospholipids are amphipathic

Phospholipids spontaneously form membranes.

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