Lecture 1 -3

Question 1

3 important noncovalent bonds

Answer 1

(all about charges) Electrostatic interactions, Hydrogen bonds, Van der waals interactions.

Question 2

Bond length increases or decrease with its strength

Answer 2

inverse, as bond is stronger, length decreases. and vice versa

Question 3

avg length and E of C-C bond, and compared to those of the 3 important non covalent bonds

Answer 3

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

Question 4

Coulombs law

Answer 4

E = kqq/Dr

Question 5

D in coulombs law stands for and is defined as?

Answer 5

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.

Question 6

what are the first two laws of Thermo and describe

Answer 6

1. Energy is neither created nor destroyed

2. Entropy, tendancy toward disorder

Question 7

Understand the concept of free E , what is shows and what it means

Answer 7

Gibbs eqn, shows difference in E of pdts and reactants. Spontaneity, If positive, then non spontaneous

Question 8

What is responsible for driving chemical reactions

Answer 8

Concentrations, know le chatleirs

Question 9

What’s hydrophobic effect

Answer 9

the Energy released when 2 separate hydrophobic entities come together. Due to H bonds of water surround the matter needing to be broken.

Question 10

Know the difference b/c Thermo and rxn velocity (kinetics)

Answer 10

thermo is spontaneity (but could happen in years), Kinetics is velocity and deals with (enzymes, rxn rates, activation energy)

Question 11

non spontaneous and spontaneous rxns are called ?

Answer 11

Endergonic and exergonic

Question 12

Delta G is DE or INDE pendant on the path?

Answer 12

Independant

Question 13

is delta G ‘ (naut/std.) a usable value

Answer 13

no, lab value only, never determins spontaneity

Question 14

Delta G equations (2)

Answer 14

G = G’ +RT ln([B]/[A]) and G’= - RT ln Keq

Question 15

Biological pH range where proteins are biologically stable

Answer 15

pH 7.37- 7.43

Question 16

Describe the 4 levels of Protein structure

Answer 16

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

Question 17

are all A.A. Chiral?

Answer 17

No 1 is not , which is glycine

Question 18

Are all A.A. the same Chirality? Which D or L?

Answer 18

other than Glycine, Yes, they are L.

Question 19

Which is not a true/standard A.A. of those you know and why?

Answer 19

Proline does not have a NH3 on backbone. but an NH2

Question 20

How can you tell the general Pka/Ph of A.A.’s?

Answer 20

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.

Question 21

Which are the essential A.A.

Answer 21

PVT TIM HALL

Question 22

Which A.A. is found in collagen/cartilage? and why

Answer 22

Glycine is rigid and great for structure, it makes up 30% of the A.A.’s in these tissues.

Question 23

Which A.A. creates the kinks in tertiary structure

Answer 23

Proline b/c its ring structure makes it more conformationally restricted.

Question 24

Two A.A.s have 2 Chiral Centers, which ones?

Answer 24

I and T

Question 25

Which A.A. is most important precursor for happy feelings and why?

Answer 25

W b/c it is the precursor for seritonin. also melatonin (sleepiness)

Question 26

Which A.A.'s are the BCAA? and whats that stand for?

Answer 26

Branched Chain AA's, L I V

Question 27

What are BCAA's known for?

Answer 27

They burn efficiently as fuel and are good for the TCA cycle.

Question 28

remember that Nonpolar/hydrophobic AA's hate what?

Answer 28

Hate charges and any polarity.

Question 29

near physiological Ph, what is an AA called b/c of charge?

Answer 29

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.

Question 30

approx pka of the COOH and NH3 end of an AA?

Answer 30

pka = 3 and 8

Question 31

with few exceptions, which of the 20 AA in humans are also are the AA building blocks of Prokaryotes (bacteria) and archaea?

Answer 31

The same 20 AA construct Eurkaryotes, prokaryotes and Archaea with few exceptions.

Question 32

Hydrophobicity in AA allow for their structure to?

Answer 32

pack tightly and there be little space, since they push water away and cause a hydrophobic effect.

Question 33

the 20 AA rotate plane polarized light which way?

Answer 33

counterclockwise or "S"

Question 34

Which three AA have OH groups

Answer 34

S T Y and are therefore polar

Question 35

name of the bond between amino and carboxyl of adjacent AA's is called?

Answer 35

Peptide or amide bond

Question 36

is forming peptide/amide bonds, favorable?

Answer 36

nope, endothermic and required energy.

Question 37

Which end is said to be the beginning and how are AA added

Answer 37

N is beginning.... N adds to C

Question 38

pKa's for 3 Basic Amino acids?

Answer 38

H - 6 K - 10.8 R - 12.5

Question 39

pKa's for Acidic AA R groups

Answer 39

both are 4.1

Question 40

pKa for N and C terminus of AA?

Answer 40

``` N = 8 C = 3 ```

Question 41

pKa for Cysteine?

Answer 41

8.3

Question 42

physiological Bases and their dissociation constants | generally know

Answer 42

HCO3- + H - > H2CO3 Bicarbonate Carbonic acid (base) (conjugate acid) NH3 + H -->. NH4+ Ammonia Ammonium ion (base) (conjugate acid)

Question 42

physiological acids and their dissociation constants | generally know

Answer 42

CH3COCH2COOH --> H+ + CH3COCH2COO - Acetoacetic acid Acetoacetate (acid) (conjugate base) CH3CH(OH)CH2COOH -->. H+ + CH3CH(OH)CH2COO beta-Hydroxybutyric acid beta-Hydroxybutyrate (acid) (conjugate base)