Midterm 1 Learning Objectives

Question 1

The Hydrophobic Effect

Answer 1

• non local interactions compared to other weak interactions
• Driven by 2nd law of Thermodynamics
• total entropy of system increases for a spontaneous process

Question 2

Protein Folding Paradox

Answer 2

• increase in entropy of water more than compensates for reduced conformational entropy
• hydrophobic effect drives collapse & folding of globular proteins

Question 3

Folding of peptide ____(increases or decreases) entropy of chain

Answer 3

decreases

Question 4

Stabilization energy

Answer 4

much greater for ionic vs. vdw

Question 5

The tendency of an acid to ionize

Answer 5

pKa

Question 6

Difference between Aldose and Ketose structure

Answer 6

carbonyl at C1 for aldehyde and carbonyl at C2 for ketone

Question 7

How to find out if a sugar a reducing sugar?

Answer 7

If the anomeric carbon contains a hydroxyl, then it is reducing!!

Question 8

How to find out if a sugar is a non-reducing sugar?

Answer 8

If the anomeric carbon does not contain a hydroxyl group, then it is NON-REDUCING!!

Question 9

What can a reducing sugar access?

Answer 9

A reducing sugar can access the open/linear confromation

ex. Beta glucose

Question 10

Sugars in sucrose:

Answer 10

glucose and fructose

Question 11

Sugars in Lactose

Answer 11

galactose and glucose

Question 12

Sugars in Maltose

Answer 12

Glucose and glucose

Question 13

Define the chemical reaction of monosaccharide cyclization

Answer 13

When an OH does a nucleophilic attack to an aldeyhyde or ketone and adds an OH group. The outcome becomes a hemiacetyl, or hemiketal

Question 14

Define glycosidic bond.

Answer 14

Glycosidic bond is a covalent bond that joins two monosaccharides between the anomeric carbon and either an O or an N.

Question 15

_______ (condensation/hydrolysis) of monosaccharides form disaccharides

Answer 15

Condensation of monosaccharides for disaccharides

Question 16

Glycogen

Answer 16

• how glucose is stored in animal cells (liver and muscle)

- highly branched glucose homopolymers

Question 17

Two types of glucose storage in plants (starch)

Answer 17

Amylose and Amylopectin

Question 18

Amylose

Answer 18

unbranched homopolymer

Question 19

Amyloopectin

Answer 19

branched but frequency is less than glycogen

Question 20

Type of linkage in glycogen

Answer 20

Alpha 1,4 glycosidic bonds and/or alpha 1,6 glycosidic bonds

Question 21

Types of linkage in cellulose

Answer 21

Beta 1,4 linkages; strands are held together via H-bonding network

Question 22

Micelle formation is driven by what force?

Answer 22

Hydrophobic effect

Question 23

Micelles vs. Liposomes

Answer 23

Micelles is a non-covalent structure and is not a bilayer.Lipoomes are 3D spherical balls with an aqueous interior, with a spontaneous self assembly that is driven by the hydrophobic effect and it’s structure stabilized by vdw forces between alkyl chains.

Question 24

Function of Integral Membrane Proteins

Answer 24

Disrupt membrane in order to purify protein

Question 25

Function of Peripheral Protein

Answer 25

maintain membrane integrity; increase salt concentration, and change the pH. It is polar/charged.

Question 26

Building blocks for DNA polymer

Answer 26

nucleotides

Question 27

Building blocks of nucleotides

Answer 27

sugar, base, and phosphate

Question 28

Glycosylation vs Glycation

Answer 28

Glycosylation is the enzymatic addition of sugars to protein, while glycation also is NON-enzymatic addition of sugars to protein

Question 29

Forces that stabilize the double helix structure:

Answer 29

Electrostatic Interactions and VDW

Question 30

Architectural elements of the double helix

Answer 30

1. ) 2 chains are antiparallel 2. ) phosphate groups on the outside 3. ) Bases are nearly perpendicular to sugar

Question 31

Sugar Pucker of B-form DNA

Answer 31

C2' endo: the H group on C2' is on the SAME SIDE of C5'

Question 32

Sugar Pucker of A-form DNA

Answer 32

C3' endo

Question 33

Which structure (1,2,3,4) of protein are in intramolecular interactions?

Answer 33

2 and 3

Question 34

Which protein structure is in intermolecular forces?

Answer 34

4th

Question 35

Anfinsen's Dogma when product is 100% active:

Answer 35

1. ) Remove urea | 2. ) then Betamercapoethanol

Question 36

Anfinsen's Dogma when product is 1% active:

Answer 36

1. ) remove BME | 2. ) Then remove urea

Question 37

What is an assay?

Answer 37

Measure of enzyme activity, purity, quantity

Question 38

Affinity

Answer 38

measure of the strength of the interaction

Question 39

Define F as fractional occupancy

Answer 39

F=[L] / kd+[L]

Question 40

Affinity Chromatography Purification

Answer 40

ligand binds to specific protein | ex. Glucose binding protein

Question 41

Ion Exchange Chromatography

Answer 41

separate protein based on charge

Question 42

Size Exclusion/Gel Filtration Chromatography

Answer 42

based on size

Question 43

Protein turnover

Answer 43

Balance between protein synthesis and protein degration

Question 44

Serine 195

Answer 44

modified to act as the nucleophile via DIPF

Question 45

Oxyanion Hole

Answer 45

stabilizes the tetrahedral intermediate of the chymotrypsin reaction since the oxygen would have a negative charge. The charge is stabilized by interactions with NH groups from the protein in the hole

Question 46

Histidine 57

Answer 46

active site and it is reactive. Acts as the Base

Question 47

Aspartate 102

Answer 47

positions the His57 to make it a stronger base

Question 48

Catalytic Strategies

Answer 48

1. ) covalent catalysis 2. ) acid-base catalysis 3. ) Metal Catalysis 4. ) Catalysis by Approximation

Question 49

How does 2,3 Bispohosphoglycerate affect hemoglobin's affinity for oxygen?

Answer 49

the negative charged polyanions molecule binds in the (+) charged pocket and negatively regulates affinity of hemoglobin

Question 50

Role of 2,3 BPG in regulating the affinity of fetal hemoglobin for oxygen

Answer 50

reduce affinity for hemoglobin, resulting in a higher affinity overall for oxygen

Question 51

Bohr Effect

Answer 51

pH influences O2 binding - as CO2 accumulates in the tissues, it diffuses into the blood, reacting with water. - This reaction then forms carbonic acid (H2CO3) - then it disassociates, forming hydrogen ions - more H+ decreases the pH - decreased pH forms salt bridge - T state stabilized