Lecture 1 -3 Flashcards
3 important noncovalent bonds
(all about charges) Electrostatic interactions, Hydrogen bonds, Van der waals interactions.
Bond length increases or decrease with its strength
inverse, as bond is stronger, length decreases. and vice versa
avg length and E of C-C bond, and compared to those of the 3 important non covalent bonds
C-C 1.5A 85 kcal/mol,
Electrostatic ranges, 3A 1.4-55 kcal/mol (range depends on D,
Hydrogen bonding 2.6-3.5A 1-5kcal/mol
Van der Waals 3.6A 0.5-1 kcal/mol
Coulombs law
E = kqq/Dr
D in coulombs law stands for and is defined as?
Dielectric constant, Basically think of it as the ENVIRONMENT, and like r, the higher the D the less energy required to hold together or break apart a bond.
what are the first two laws of Thermo and describe
- Energy is neither created nor destroyed
2. Entropy, tendancy toward disorder
Understand the concept of free E , what is shows and what it means
Gibbs eqn, shows difference in E of pdts and reactants. Spontaneity, If positive, then non spontaneous
What is responsible for driving chemical reactions
Concentrations, know le chatleirs
What’s hydrophobic effect
the Energy released when 2 separate hydrophobic entities come together. Due to H bonds of water surround the matter needing to be broken.
Know the difference b/c Thermo and rxn velocity (kinetics)
thermo is spontaneity (but could happen in years), Kinetics is velocity and deals with (enzymes, rxn rates, activation energy)
non spontaneous and spontaneous rxns are called ?
Endergonic and exergonic
Delta G is DE or INDE pendant on the path?
Independant
is delta G ‘ (naut/std.) a usable value
no, lab value only, never determins spontaneity
Delta G equations (2)
G = G’ +RT ln([B]/[A]) and G’= - RT ln Keq
Biological pH range where proteins are biologically stable
pH 7.37- 7.43
Describe the 4 levels of Protein structure
Primary: sequence of linked A.A’s
2 - Non-covalent interactions, mostly Hydrogen bonding forming 3D structure: A coils and B sheets
3. the secondary structure, folding on eachother from distant AA chain interactions
4. different proteins subunits from distinct polypeptide chains coming together
are all A.A. Chiral?
No 1 is not , which is glycine
Are all A.A. the same Chirality? Which D or L?
other than Glycine, Yes, they are L.
Which is not a true/standard A.A. of those you know and why?
Proline does not have a NH3 on backbone. but an NH2
How can you tell the general Pka/Ph of A.A.’s?
Acidic AA - have low pH and want to donate H, and will do so at Physio. pH, therefore becoming (-) negatively charged. opposite for Basic AA’s which are postively charged from accepting a H.
Which are the essential A.A.
PVT TIM HALL
Which A.A. is found in collagen/cartilage? and why
Glycine is rigid and great for structure, it makes up 30% of the A.A.’s in these tissues.
Which A.A. creates the kinks in tertiary structure
Proline b/c its ring structure makes it more conformationally restricted.
Two A.A.s have 2 Chiral Centers, which ones?
I and T
Which A.A. is most important precursor for happy feelings and why?
W b/c it is the precursor for seritonin. also melatonin (sleepiness)
Which A.A.’s are the BCAA? and whats that stand for?
Branched Chain AA’s, L I V
What are BCAA’s known for?
They burn efficiently as fuel and are good for the TCA cycle.
remember that Nonpolar/hydrophobic AA’s hate what?
Hate charges and any polarity.
near physiological Ph, what is an AA called b/c of charge?
Zwitterion, has a positive and negative charge on different atoms in the same compound. NOT amphoteric which means It can act as an acid or a base.
approx pka of the COOH and NH3 end of an AA?
pka = 3 and 8
with few exceptions, which of the 20 AA in humans are also are the AA building blocks of Prokaryotes (bacteria) and archaea?
The same 20 AA construct Eurkaryotes, prokaryotes and Archaea with few exceptions.
Hydrophobicity in AA allow for their structure to?
pack tightly and there be little space, since they push water away and cause a hydrophobic effect.
the 20 AA rotate plane polarized light which way?
counterclockwise or “S”
Which three AA have OH groups
S T Y and are therefore polar
name of the bond between amino and carboxyl of adjacent AA’s is called?
Peptide or amide bond
is forming peptide/amide bonds, favorable?
nope, endothermic and required energy.
Which end is said to be the beginning and how are AA added
N is beginning…. N adds to C
pKa’s for 3 Basic Amino acids?
H - 6
K - 10.8
R - 12.5
pKa’s for Acidic AA R groups
both are 4.1
pKa for N and C terminus of AA?
N = 8 C = 3
pKa for Cysteine?
8.3
physiological Bases and their dissociation constants
generally know
HCO3- + H - > H2CO3
Bicarbonate Carbonic acid
(base) (conjugate acid)
NH3 + H –>. NH4+
Ammonia Ammonium ion
(base) (conjugate acid)
physiological acids and their dissociation constants
generally know
CH3COCH2COOH –> H+ + CH3COCH2COO -
Acetoacetic acid Acetoacetate
(acid) (conjugate base)
CH3CH(OH)CH2COOH –>. H+ + CH3CH(OH)CH2COO
beta-Hydroxybutyric acid beta-Hydroxybutyrate
(acid) (conjugate base)
