Topic 1, Lecture 1

Question 1

What are the four categories of organic molecules?

Answer 1

Carbohydrates, Lipids, Proteins, and Nucleic Acids

Question 2

What are the small organic building blocks of the cell?

Answer 2

Sugars, Fatty Acids. Amino Acids, Nucleotides

Question 3

What are the larger organic molecules of the cell?

Answer 3

Polysaccharides, glycogen, and starch (in plants)
Fats and Membrane Lipids
Proteins
Nucleic Acids

Question 4

Describe the abundance of macromolecules in cells.

Answer 4

70% Water
30% Chemicals

Question 5

What is the chemistry definition of acid vs base?

Answer 5

Acid- Proton Donor
Base- Proton Acceptor

Question 6

Define condensation reaction.

Answer 6

Two molecules are joined together by a covalent bond and loses a small molecule

Question 7

What is the primary structure of a protein?

Answer 7

Sequence of amino acids

Question 8

What is the most basic definition of secondary protein structure?

Answer 8

Protein Folds: alpha helices and beta sheets

Question 9

What percent of protein structure can be accounted for by alpha helices and beta sheets?

Answer 9

60%

Question 10

What is the most important aspect of hydrogen bonding in secondary protein structure?

Answer 10

Hydrogen bonds between hydrogens connecting to oxygens on the opposite side of a different amino acid.

Question 11

How often will there be hydrogen bonds between amino acids?

Answer 11

About every four amino acids, specifically 3.6

Question 12

Are the hydrogen bonds between alpha helices hydrophilic or hydrophobic?

Answer 12

Hydrophilic

Question 13

How does secondary structure protect the hydrogen bonding from its aqueous environment?

Answer 13

By putting the side chains on the outside

Question 14

Why is secondary structure so common?

Answer 14

It is an easy way to take a polymer and make it a more defined structure

Question 15

Why does some secondary structure turn out to be helices and the others sheets?

Answer 15

The side chains allow for differences between alpha helix and beta sheets because one is more energetically favorable than the other.

Question 16

Describe beta pleated sheets.

Answer 16

three strands that use hydrogen bonding to lay next to each other. The formation depends on side chains, just like alpha helices.

Question 17

What is a motif? Give an example.

Answer 17

a combination of secondary structure (a subcategory). For example, if two alpha helices twisted around each other.

Question 18

What is the basic description of tertiary protein structure?

Answer 18

Final protein folding event

Question 19

Describe domains.

Answer 19

distinct regions of tertiary structure that are an independently folded region of a protein.
They can also be referred to as a modular unit. They probably perform a very specific function.

Question 20

Why are understanding domains important?

Answer 20

Knowing what specific domains do can allow for an insight into the function of the protein even if the other portions of the protein are unknown. not always obvious that two different domains are distinct.

Question 21

What is a random coil?

Answer 21

Portions of proteins that do not fold

Question 22

Describe quaternary structure of amino acids.

Answer 22

a complex of more than one polypeptide chain. These function as an n-mer.

Question 23

What are macromolecular machines?

Answer 23

a combination of proteins that perform a specific function. These are sometimes made up of other molecules besides proteins, i.e. RNA. They perform highly specialized functions.

Question 24

what are the alpha helix breakers?

Answer 24

glycine and proline

Question 25

what is affinity?

Answer 25

on and off rate of two things that come together