Topic 1, Lecture 1 Flashcards
What are the four categories of organic molecules?
Carbohydrates, Lipids, Proteins, and Nucleic Acids
What are the small organic building blocks of the cell?
Sugars, Fatty Acids. Amino Acids, Nucleotides
What are the larger organic molecules of the cell?
Polysaccharides, glycogen, and starch (in plants)
Fats and Membrane Lipids
Proteins
Nucleic Acids
Describe the abundance of macromolecules in cells.
70% Water
30% Chemicals
What is the chemistry definition of acid vs base?
Acid- Proton Donor
Base- Proton Acceptor
Define condensation reaction.
Two molecules are joined together by a covalent bond and loses a small molecule
What is the primary structure of a protein?
Sequence of amino acids
What is the most basic definition of secondary protein structure?
Protein Folds: alpha helices and beta sheets
What percent of protein structure can be accounted for by alpha helices and beta sheets?
60%
What is the most important aspect of hydrogen bonding in secondary protein structure?
Hydrogen bonds between hydrogens connecting to oxygens on the opposite side of a different amino acid.
How often will there be hydrogen bonds between amino acids?
About every four amino acids, specifically 3.6
Are the hydrogen bonds between alpha helices hydrophilic or hydrophobic?
Hydrophilic
How does secondary structure protect the hydrogen bonding from its aqueous environment?
By putting the side chains on the outside
Why is secondary structure so common?
It is an easy way to take a polymer and make it a more defined structure
Why does some secondary structure turn out to be helices and the others sheets?
The side chains allow for differences between alpha helix and beta sheets because one is more energetically favorable than the other.
Describe beta pleated sheets.
three strands that use hydrogen bonding to lay next to each other. The formation depends on side chains, just like alpha helices.
What is a motif? Give an example.
a combination of secondary structure (a subcategory). For example, if two alpha helices twisted around each other.
What is the basic description of tertiary protein structure?
Final protein folding event
Describe domains.
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.
Why are understanding domains important?
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.
What is a random coil?
Portions of proteins that do not fold
Describe quaternary structure of amino acids.
a complex of more than one polypeptide chain. These function as an n-mer.
What are macromolecular machines?
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.
what are the alpha helix breakers?
glycine and proline
what is affinity?
on and off rate of two things that come together
