Chemical Structures and Properties of Biologically Important Molecules

Question 1

What are key characteristics of organic molecules?

Answer 1

• have C-H bonds
• generally have covalent bonds

Question 2

What are key characteristics of inorganic molecules?

Answer 2

• may contain C, but lack H
• usually contain metals
• generally have ionic bonds

Question 3

When do covalent bonds form?

Answer 3

• covalent bonds form when electrons are shared

Question 4

What are the two types of covalent bonds?

Answer 4

1. Nonpolar (pure) covalent bonds: electrons are shared equally
2. Polar covalent bonds: electrons are shared unequally

Question 5

When do ionic bonds form?

Answer 5

• form when electrons are transferred

Question 6

What is the distinction between a cation and an anion?

Answer 6

• cations lose electrons and are positively-charged
• anions gain electrons and are negatively-charged

Question 7

What elements can participate in hydrogen bonding?

Answer 7

• Occurs only between polar molecules with hydrogen atoms bonded directly to F, O, or N

Question 8

Why is carbon such an important element for biological molecules? Why are carbon-containing compounds so diverse and stable?

Answer 8

• valence of four - carbon forms four covalent bonds w/other atoms, which gives it diversity in structure and function
• covalent bonds - carbon covalent bonds have high bond energies, which makes them stable
• diverse - carbon-containing compounds are extremely diverse (ie many functional groups)
• tetrahedral - b/c carbon has a tetrahedral geometry, it can form stereoisomers

Question 9

What are key characteristics of water?

Answer 9

• polar
• excellent solvent
• high specific heat
• high heat of evaporation
• strong cohesive/adhesive forces
• less dense as solid than liquid

Question 10

What is the most important characteristic of water?

Answer 10

• its polarity, b/c this accounts for all of its other characteristics

Question 11

How is water polar?

Answer 11

• water has a bent geometry (104.5⁰)
• oxygen = highly electronegative = draws electrons towards it = partial negative charge
• hydrogen = electropositive = electrons are drawn from it = partial positive charge

Question 12

Why is water considered an excellent solvent?

Answer 12

• b/c it is polar, it can dissolve many polar/ionic solutes

Question 13

Why is the high specific heat of water important?

Answer 13

• it takes a lot of energy to raise the temperature of water by a degree
• this helps keep the surrounding environment temperature regulated/consistent

Question 14

Why is the high heat of vaporization of water important?

Answer 14

• it takes a lot of energy to change water from liquid to a gas
• this helps cool down organisms via evaporative cooling

Question 15

Why are the strong cohesive forces of water important?

Answer 15

• water molecules have a strong attraction to other water molecules b/c H-bonds
• this creates surface tension and enables fluid transport of substances

Question 16

Why are the strong adhesive forces of water important?

Answer 16

• water molecules have a strong attraction to other non-water molecules because of partial charges
• this allows it to stick to other substances besides itself and enables fluid transport of substances

Question 17

Why is it important that water is less dense as a solid than as a liquid?

Answer 17

• this causes ice to float and keeps ponds/lakes/oceans from freezing solid during the winter, which allows life to continue below the surface

Question 18

What are the 4 macromolecules?

Answer 18

1. proteins
2. carbohydrates
3. nucleic acids
4. lipids

Question 19

What is the basic structure of an amino acid?

Answer 19

• an alpha carbon surrounded by:
  
  • carboxyl group (-COOH)
  • amino group (-NH2)
  • hydrogen atom
  • side-chain (r-group)

Question 20

What determines the chemical characteristics of a specific AA?

Answer 20

• the side-chain chemistry

Question 21

How do peptide bonds form?

Answer 21

• peptide bonds form between adjacent AA in a chain via a dehydration synthesis reaction between the carboxyl group of one AA and the amino group of the second AA, releasing water
• this reaction is not easily reversible b/c it is catalyzed by enzymes and the peptide bond is extremely stable

Question 22

What determines the primary structure of a protein?

Answer 22

• the linear sequence of the AA in a polypeptide chain

Question 23

What determines the secondary structure of a protein?

Answer 23

• local interactions between AAs via hydrogen bonds between the carbonyl oxygen and the amino nitrogen

Question 24

When do alpha helices form?

Answer 24

• secondary structures that form via hydrogen bond interactions between AAs four residues apart on the same chain

Question 25

When do beta-sheets form?

Answer 25

* form via hydrogen bond interactions between AAs on separate chains

Question 26

What determines the tertiary structure of proteins?

Answer 26

* determined by long-range hydrophobic/hydrophilic interactions between the R-groups of AAs on separate

Question 27

When do proteins have quaternary structure?

Answer 27

* only when the protein contains more than one subunit

Question 28

What is the general structure of a monosaccharide?

Answer 28

* general formula = (CH₂O)_n [n determines the specific type] * ~3-7 carbons * carbonyl group * hydroxyl group

Question 29

How are glycosidic bonds formed?

Answer 29

* glycosidic bonds are formed between two monosaccharides via an oxygen atom after a dehydration reaction that releases water

Question 30

What are the two most abundant storage polysaccharides?

Answer 30

* starch (plant cells) * glycogen (animal cells)

Question 31

What are the two types of starch?

Answer 31

1. amylose: straight-chain polymer of glucose, ~20% of starch content 2. amylopectin: branched-chain polymer of glucose, ~80% of starch content

Question 32

What are the two most abundant structural polysaccharides? What are the differences between the two?

Answer 32

1. Cellulose: * Polymer of glucose * Plant/algae cell walls 2. Chitin: * Polymer of glucosamine (contains N) * Arthropod exoskeletons and fungi cell walls

Question 33

What is the basic structure of a fatty acid? What is the most key characteristic of fatty acids?

Answer 33

* long hydrocarbon chain (non-polar) * carboxyl group at one end (polar) Amphipathic: both polar and nonpolar

Question 34

What is the distinction between saturated fatty acids and unsaturated fatty acids?

Answer 34

* Saturated fatty acids: no double-bonds in tails; long, straight chains that pack together well * Unsaturated fatty acids: one or more double-bonds; result in a kink in a chain that prevents tight packing

Question 35

What is a triacylglycerol?

Answer 35

* Composed of a glycerol molecule with 3 fatty acids linked to it * Ester bonds link fatty acids to glycerol * Main function = store energy

Question 36

What is a phospholipid?

Answer 36

* Composed of one glycerol, two fatty acids, and phosphorus * Main function = bilayer of membrane

Question 37

What is the basic structure of nucleotides?

Answer 37

* Nitrogen-containing base * Pentose * One or more phosphate groups

Question 38

What are the two types of nucleotide bases?

Answer 38

* pyrimidine: one-carbon/nitrogen ring: uracil, cytosine, thymine * purine: two-carbon/nitrogen rings: guanine, adenine

Question 39

What are the two types of pentose sugars?

Answer 39

* ribose: has a hydroxyl group on 2'C * deoxyribose: lacks a hydroxyl group on 2'C

Question 40

How are nucleotides linked to one another?

Answer 40

* phosphodiester (covalent) bonds between the phosphate group of one nucleotide and the C'3 of the pentose sugar * creates an alternating backbone of sugar-phosphate-sugar

Question 41

How do bases pair?

Answer 41

* purines and pyrimidines pair up * A forms two H-bonds w/T (or U) * G forms three H-bonds with C