Chem and Bio Review Flashcards
Angstrom
10 Å = 1 nm
Distance between atoms
Nanometer
1 nm = 10^-9 m
Dimensions in macromolecules
Micron/micrometer
1 μm = 10^-6 m
Dimensions of cells and cellular structures (organelles and bacteria)
Biochemicals are primarily composed of which atoms?
Hydrogen, Carbon, Oxygen, Phosphorus, Nitrogen, and Sulfur
Amine
Structure RNH2 or RN+H3 R2NH or R2N+H2 R3N or R3N+H Functional group: amino group
Alcohol
Structure: ROH
Functional group: hydroxyl group
Thiol
Structure: RSH
Functional group: sulfhydryl group
Ether
Structure: ROR
Linkage: ether linkage —O—
Aldehyde
Structure: RCHO
Functional group: carbonyl group
Ketone
Structure: R2C=O
Functional group: carbonyl group
Carboxylic acid
Structure: RC=OOH or RC=OO-
Functional group: carboxyl group (neutral) or carboxylate group (negative charge)
Ester
Structure: RC=OOR
Functional group: acyl group RC=O
Linkage: ester linkage -C=OO-
Thioester
Structure: RC=OSR
Functional group: acyl group
Linkage: thioester linkage
Amide
Structure:
RC=O-NH2
RC=O-NHR
RC=O-NHR2
Functional group: amido group (O=C—N—) or acyl group
Imine
Structure:
R=NH or R=N+H2
R=NR or R=NHR
Functional group: imino group (C=N)
Phosphate ester
R-phosphate group
Functional group: phosphoryl group
Diphosphate ester
Structure:
R-phosphate group 1-phosphate group 2
Functional group: phosphoanhydride group
Phosphate diester
Structure:
R-phosphate group-r
Linkage: phosphodiester linkage
What are covalent forces?
Shared electrons between atoms
Determine how monomers link together to form biological polymers
1-2 Å
What are the non-covalent forces?
- Electrostatic
- Hydrogen bonds
- van der Waals interactions
- Hydrophobic interactions
What are the properties of electrostatic interactions?
- Ion pairs (full positive with full negative)
a. 86 kJ/mol
b. up to 10 Å
c. Strength falls off with 1/d^2 (falls off slowly over distance)
d. depends on pH - Dipole-dipole (neutral molecules)
a. due to uneven distribution of charge in a molecule
b. 9 kJ/mol (weaker electrostatic interaction)
c. 3-10 Å
d. Causes charge separation
What are the properties of hydrogen bonds?
A. Need an electron pair donor and acceptor
B. Happens between H and O or N
C. Linear (makes this interaction stronger than dipole-dipole)
D. 1.5-2 Å (short interaction due to linearity)
What are the properties of van der Waals interactions?
A. Weak attractive forces found in all atoms due to attractive and repulsive components (nuclei and electron clouds)
B. Electron cloud overlap = strong repulsion
C. Attraction proportion to 1/r^6 (Falls off rapidly with distance) but increases over distance
D. Repulsion proportional to 1/r^12 (stronger over longer distances than attraction)
E. 3.5-4 Å
F. Weak individually but sum of many is significant
What are the properties of hydrophobic interactions?
A. Hydrophobic molecules do not interact with water
B. Disrupt the water network maintained by hydrogen bonds (energetically unfavorable)
C. Wants to minimize this disruption through the hydrophobic effect (clustering of hydrophobic molecules to allow water molecules to be close to each other)
D. Exclusion effect
E. important for membranes and amphipathic molecules
F. Increases entropy of water molecules