Lecture 1: Biochemistry and Protein Structure Review Flashcards
Kilocalorie
the amount of energy need to raise the temperature of one liter of water one ˚C
Relative strength of bond types
Covalent > Ionic (electrostatic interactions) > Hydrogen > Van der Waals
Electrostatic attractions are ____ in aqueous solutions
weakened
Hydrogen Bonds
Highly directional, unlike a typical electrostatic interaction, and is strongest when a straight line can be drawn between all three atoms involved
Amino acids that form a protein are often ___ bonded together
Hydrogen
___ bonds exist between the G and C bases in a DNA double helix
Hydrogen
Hydrophilic molecules
composed of ions or polar molecules that attract water molecules through electrical charge effects
Hydrophobic Molecules
Molecules that contain a preponderance of nonpolar bonds. Insoluble in water. Most hydrocarbons are hydrophobic molecules.
Van der Waals Interactions
weak attractive force generated by induced flickering dipoles in neighboring atoms
Hydrophobic Forces
Non really a “bond”, but interactions that push nonpolar surfaces out of hydrogen bonding water networks where they would otherwise physically interfere with the highly favorable interactions between water molecules
Which of the following represent covalent interactions?
a) peptide bond formation during the translation of epidermal growth factor (EGF)
b) hydrogen bond formation during folding of the newly translated EGF
c) ionic bond formation during folding of the newly translated EGF
d) disulfide formation during folding of the newly translated EGF
e) binding of EGF to the EGF receptor
a) peptide bond formation during the translation of epidermal growth factor (EGF)
d) disulfide formation during folding of the newly translated EGF
What are the four basic building blocks of the cells? And what larger units do they make up?
Phospholipid structure
Polar head group (choline is common), phosphoric acid, glycerol backbone, fatty acid tails
Amino acid structure
Nucleotide structure
Difference between a nucleotide and a nucleoside
nucleotides are the constituents of DNA and RNA not nucleosides
Most macromolecules fold into ___ stable shape or conformation
One
_____ bonds specify shape and interaction properties of macromolecules
Non covalent
The shape and properties of a protein is determined by its _____
amino acid sequence
Environmental pH determines the charged state of some amino acid side chains
• Five amino acids side chains can carry a charge
– D, E, H, K, R
Proteins are structurally polar
• Polypeptide sequences are always written in an Amino terminal (N, NH2) to Carboxyl terminal (C, COOH) direction
Protein conformations are restricted by __ interactions
steric
What three noncovalent interactions help shape protein conformations?
Electrostatic interactions, Hydrogen bonds, Van der Waals attractions
___ interactions also regulate protein conformation
Hydrophobic
The 3D shape of a protein is determined by its amino acid sequence. What proves this?
What secondary structure is this and how is it formed?
- Alpha Helix
- Particular sets of phi/psi angles and main chain hydrogen bonds between peptide bond can result in the common fold.
What secondary structure is this?
Beta sheet
Which beta sheet is parallel and which is antiparallel?
A) antiparallel
B) parallel
What secondary structure is this and how is it formed?
Coiled coil- alpha helices wrap around eachother to minimize exposure of hydrophobic amino acid side chains to the aqueous environment.
What is this an example of?
Secondary structure elements combining to form tertiary structure
Src family kinases are an example of?
The fact that many large proteins are composed of several to many smaller independent modules
