College Biology Test #2

III. Amino Acids

A. Building blocks of proteins

B. Basic formula

R-CH₂NH₂-COOH

where the R group can be literally any organic molecule

C. Though there are literally an infinite number of possible amino acids, only 20 are 

used by living things

D. The 20 amino acids are lumped into 3 basic categories, based on the broad chemical properties of their R groups

a. polar, uncharged R groups

b. electrically charged R groups

1. negatively charged

2. positively charged

c. apolar

V. Proteins

A. Amino acid polymer

B. Levels of protein structure

a. primary-order in which amino acids are joined together (note 

that any amino acid can be joined to any other)

b. secondary-regular coils and folds formed by hydrogen bonding between amino acids within the strand, forming a 2 

dimensional structure

c. tertiary-3 dimensional structure in the strand, resulting from 

interactions between R-groups (e.g., apolar sections will be attracted to other apolar sections in the strand, charged sections will be attracted to other charged sections, etc.)

d. conformation: the 3 dimensional shape for any given protein 

that allows it to function most effectively/efficiently (note that proteins can have multiple 3 dimensional shapes)

c. denaturation

1. process whereby a protein's preferred conformation is changed, functionally inhibiting or more commonly inactivating that protein

2. processes that can denature proteins

i. high temperatures

ii. changes in pH

3. protein denaturation can be temporary or permanent, depending upon the severity of the denaturing conditions (cooking is irreversible denaturation of 

protein with the purpose of making some item more palatable and/or more digestible)

VI. Enzymes

A. protein catalysts that make a huge range of biological processes possible

B. Properties of catalysts

a. alter the rate of a chemical reaction (usually speed it up) 

without being used up in the process

b. selectively act on molecules but not others

C. Function depends critically upon an exact conformation

D. Roughly consist of 2 regions

a. the structural region (determines overall enzyme shape)

b. the binding region: 

E. Enzyme function-lock and key model

VII. Nucleotides, RNA, and DNA

A. Nucleotides

a. composition

1. a nitrogenous base

2. a pentose, either ribose or deoxyribose (deoxyribose differs from ribose in having one less -OH attached)

3. one or more phosphate groups (abbreviated P)

b. 5 types of nucleotides are used in living things 

1. adenine (A) (both ribose and deoxyribose versions)

2. thymine (T) (deoxyribose version only)

3. uracil (U) (ribose version only, equivalent to thymine)

4. guanine (both ribose and deoxyribose forms)

5. cytosine (both ribose and deoxyribose forms)

c. special property of nucleotides-nucleotides can selectively 

hydrogen bond to each other through their bases (nucleotides that can stick in this fashion are called complements)

• A binds to T and U

• C binds to G

B. Nucleotide polymers-DNA and RNA

VIII. Adenosine Triphosphate (ATP) and Adenosine Diphosphate (ADP)

A. ATP is the ultimate energy source for all cell activities

B. Structures

A-P-P-P = ATP A-P-P = ADP

(A= adenosine, P= phosphate)

C. A-P-P-P gives rise to A-P-P + P + energy (the second P-P bond 

is unstable, and can decay to release energy)

D. The energy released by the decay of the third phosphate powers 

almost every single important process in a cell