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
Why is water important in biochemistry?
Water is always around in cells and acts as the solution that reactions happen in
What are the chemical properties of water?
a. polar
b. non-linear/bent (104.5 degrees)
c. hydrogen bond donor and acceptor
d. van der Waals radius of H= 1.2 Å
e. van der Waals radius of O= 1.4 Å
f. O—H covalent bond distance= 0.958 Å
Water as solvent
A. irregular network of hydrogen bonded molecules
b. rapidly fluctuating (H bonds are constantly breaking and forming)
c. polar and ionic molecules are able to dissolve in water
Autoioniziation of water and equilibrium of water
H2O ⇌ H+ and OH-
Keq= [H+] [OH-]/ [H2O]= (10^-7)^2/55.5
Kw=10^-14 M^2=[H+] [OH-]
Kw=Keq (55.5)
pH
pH= -log [H+] pkw= pH + pOH=14
What is pH determined by?
The concentrations of acid and bases in solution (water)
What is acid strength determined by?
Ka (association constant)
HA + H2O ⇌ H+ + A- (conjugate acid and conjugate base)
K= [H+] [A-]/ [HA] [H2O]
Ka=K [H20]= [H+] [A-]/[HA]
What are properties of buffers?
a. Resist pH changes
b. Often weak acids with conjugate bases (create strong conjugate bases)
c. Critical for biological organisms
What are the classes of biological polymers?
- Proteins (largest and most diverse class, do most of the work in cells)
- Nucleic acids (DNA-genome storage/organization and RNA-diverse jobs)
- Polysaccharides (linear and branched)
- Lipids (chemically diverse)
What are the features of biological polymers?
- Directional (DNA is read 5’ to 3’)
- Informational
- Structures in three dimensions
- Held together by many weak molecular forces
How are macromolecules built and deconstructured?
- Condensation reactions form macromolecules
2. Molecules are hydrolyzed to break them apart
What are properties of proteins?
- Polymers of amino acids
- Formed by amide linkages
- Backbone/ main chain is hydrophillic
- Backbone is the same between different proteins
- Side chains determine folds and different chemical properties
- Directionality= amino (N) to carboxy (C) termini
What are the properties of peptide bonds?
- Rigid and planar
- Has resonance (some double bond character)
- No rotation around C—N bond due to resonance
What are the components of amino acids monomers?
- Alpha carbon
- Amine group
- Carboxyl group
- R group/side chain
