Test 1: Ch. 1 Pka's/acidity + Ch. 2

Front 1

How long are typical single covalent bonds?

Back 1

1.54 Angstrom

Front 2

What is the typical bond length of hydrogen bonds?

Back 2

2.9 Angstrom

Salt bridges can be both hydrogen bonding and non-hydrogen bonding, thus length ranges from 2.6-3.5

But we'll just say hydrogen bonds are shorter, so 2.9

Front 3

What formula capitulates the 2nd law of thermodynamics?

Back 3

Front 4

What is the henderson Hasselbalch equation?

Back 4

pH = pKa + log([A-]/[HA])

Front 5

What is the ratio of acceptor/donor when pH = 4 and pKa = 5?

Back 5

1:10

Front 6

What is the ratio of acceptor/donor when pH = 7 and pKa = 5?

Back 6

100:1

Front 7

When pKa - pH > 0, is there more acid or base?

Aka, when pKa > pH, is there more acid or base?

Back 7

Base!

Protonated Form

Front 8

When pKa - pH < 0, is there more acid or base?

Aka, when pKa < pH, is there more acid or base?

Back 8

Acid!

Deprotonated Form

Front 9

What amino acids are negatively charged at physiological pH?

Back 9

Glutamate (E) and Aspartate (D)

Front 10

What amino acids are positively charged at physiological pH?

Back 10

Arginine (R) and Lysine (K) and SOMETIMES Histidine (H)

Front 11

Are most amino acids L or R stereochemically?

Back 11

Only L amino acids constitute proteins

Front 12

What does E6V mean? And in what disease is this substitution found?

Back 12

The 6th glutamate is replaced with a valine. This is sickle cell anemia

Front 13

Why does bringing a positive charge into proximity or ionizable groups decrease pKa while a negative charge increases it?

Back 13

A positive charge would increase the likelihood of donating a H+ ion because it would stabilize the resulting negative charge, thus lower pKa

Front 14

Why does burying a positively charged ionizable group in a hydrophobic environment decrease pKa while pKa increases for negatively charged ionizable groups?

Back 14

Postively charged groups will do their best to act nonpolar (Chargeless) because like dissolves like, so that means that rather than more like a base and less like an acid so that the -OH can remain neutral

Front 15

Phi is the rotation about the ___ bond

Back 15

N-C Bond

Front 16

Psi is the rotation about the ___ bond

Back 16

C - C=O bond

Front 17

Where is the disfavored region of a ramachandram plot?

Back 17

Quadrant 4 near {90, -90}

Front 18

Where are beta sheets found in a ramachadran plot?

Back 18

Quadrant 2 between -180 to -60 phi and ~0 to 180 psi

Front 19

Where are right handed alpha helices found in a ramachadran plot?

Back 19

Horizontal sliver in quadrant 3

From -180 to -60 phi and -70 to -50 psi

Front 20

Where are left handed alpha helices found in a ramachadran plot?

Back 20

Vertical sliver in quadrant 1

From 55 to 65 phi and ~0 to 80 psi

Front 21

What is the x-axis of a ramachadran plot?

Back 21

Rotation about the N-C bond, phi values

Front 22

What is the y-axis of a ramachadran plot?

Back 22

Rotation about the C - C=O, psi values

Front 23

What is the major stabalizing form of secondary structure?

Back 23

Hydrogen bonding between -C=O and H-N- in the backbone

Front 24

Are alpha helices mostly right or left handed?

Back 24

Almost exclusively right handed

Front 25

How many residues are there per turn in an alpha helix?

Back 25

3.6 residues

Front 26

How large is the rise per turn in an alpha helix?

Back 26

5.4 angstrom

Front 27

CO and NH form hydrogen bonds with amino acids ___ residues ahead in sequence

Back 27

4

Front 28

Why is it unfavorable to have Serine, Aspartate, or Asparagine residues in alpha helices?

Back 28

S, D, and N disrupt alpha helices because their side chains compete for hydrogen bonds with the backbone atoms

Front 29

How does Threonine, Valine, and Isoleucine disrupt an alpha helix?

Back 29

Steric clashes

Front 30

How does the hydrogen bonding scheme of parallel and antiparallel bonding differ in beta sheets?

Back 30

Antiparallel sheets hydrogen bond 1 amino acid on strand A to 1 amino acids on strand B

Parallel sheets hydrogen bond 1 amino acid on strand A to 2 different amino acids on strand B

Front 31

What type of bonding stabilizes the 3* structure of proteins?

Back 31

Hydrophobic and van der waals interactions

Front 32

Where would you expect to find sulfur bridges in cells?

Back 32

Extracellular proteins, bacterial periplasms, ER, and Golgi because they are all oxidative envrionment which is needed for bond formation

Front 33

What about the cytosol makes it an unfit environment for sulfur bridges to form?

Back 33

Cytosol is a reductive environment which would convert a cystine bridge to 2 cysteine residues

Front 34

What are common hydrogen bond donors found in proteins? What makes it a donor rather than an acceptor?

Back 34

-OH, -NH3+, and -NH-

Donors have the H and are usually more electron deficient

Front 35

What are hydrogen bond acceptors found in proteins?

Back 35

Lone electrons such as C=O and NH2 electrons

Front 36

What is the typical length of a salt bridge aka electrostatic interaction?

Back 36

3 angstoms

Front 37

What is the typical bond length of a van der waals interaction?

Back 37

3.6 angstom

ranges from 2.5-4.6

Front 38

Sort bonds from Strongest to weakest

(Covalent, van der waals, hydrogen, and electrostatic)

Back 38

Covalent > Electrostatic > Hydrogen > Van der waals

Front 39

What does levinthal's paradox teach us about protein folding?

Back 39

There's an enormous difference between predicted and actual folding time which tells us that protein folding is not random guess and check ---> Cumulative selection

Front 40

What are the 4 ways to denature a protein?

Back 40

1) Acid/Base treatment

2) Heat

3) Detergents

4) Reducing agents

Front 41

What 2 hydrogen-bond disrupting compounds do we commonly use to denature a protein?

Back 41

Urea and Guanidinium Chloride

Front 42

How do organic solvents denature proteins?

Back 42

Lower dielectric constant, increase electrostatic interactions, and weakens hydrophobic effect within the protein

Front 43

What detergent do we commonly use to denature proteins and how does it do it?

Back 43

SDS works by binding to nonpolar core of protein and destabilizing native structure

Front 44

What structural level is most effected by heating a protein and why?

Back 44

Tertiary structure because heat effects long range interaction first

Front 45

How does Rosetta software predict protein structure?

Back 45

Rosetta simulates protein folding process to predict structure

Front 46

Does 1 peptide sequence always equal 1 structural paradigm? If so, how?

Back 46

No, there needs to be states with diminished stability, flexible regions, and a new binding surface that is revealed upon alternate folding thus expanding biological function

Front 47

How do we prevent pathogenic misfolding of proteins?

Back 47

Molecular chaperones, UPR, and quality control processes

Front 48

Is the proteome of nucleosome larger?

Back 48

Proteome due to the post-translational modification possible and the existence of quarternary structures

Front 49

What is the formula for a change in entropy of the surroundings?

Back 49

Front 50

Derive the Henderson-Hasslebach from Equilibrium constant for the deprotonation of an acid

Back 50

Ka = [H+][A-]/[HA] --> log(Ka) = log [H+] + log([A-]/[HA]) --> -pKa = -pH + log([A-]/[HA]) --> pH = pKa + log([A-]/[HA])

Front 51

What compound do we commonly use to reduce disulfide bridges?

Back 51

Beta-mercaptoethanol

Front 52

What are the standard state conditions of a delta G naught

Back 52

pH=7 and 25*C

Front 53

What is the formula for free energy and equilibriums?

Back 53

delta G naught = -RT ln(k)

Front 54

Order bonds from shortest to longest

{covalent, hydrogen, van der waals, electrostatic aka salt bridge}

Back 54

Covalent < Electrostatic < Hydrogen < Van der Waals