Protein Structure and Function Lecture 5

Question 0

How can you distinguish between the L form and D form enantiomer?

Answer 0

The CORN rule; the amino acid reads CORN from left to right when the hydrogen is in the back

Question 1

amino acids are asymmetric and have a chiral center (except ___), so they can exist as ____

Answer 1

glycine; enantiomers

Question 2

If the pH is below the acid’s pKa, is the acid likely to be charged?

Answer 2

no it will be neutral; acids will either be neutral or have a -1 charge

Question 3

what is the central dogma for protein sequencing from a DNA sequence?

Answer 3

DNA makes RNA makes protein

Question 4

Interactions between side chains of aspartate and arginine at neutral pH would be ____.

Answer 4

ionic

Question 5

most polypeptides contain between ___ and ___ amino acids

Answer 5

50; 2000

Question 6

What is the average molecular weight for an amino acid?

Answer 6

110 daltons

Question 7

the molecular weight of most proteins is between ____ and ____ daltons or ___ and ___ kD.

Answer 7

5500, 220,000; 5.5, 220

Question 8

some proteins contain _____ bonds that cross link between the cysteine residues by the oxidation of cysteine.

Answer 8

disulfide

Question 9

intracellular proteins often ___ disulfides while extracellular proteins often ____ them.

Answer 9

lack; have

Question 10

____ proteins have a common ancestral protein.

Answer 10

homologous

Question 11

phylogenetic trees based on ___ ____ are consistent with trees based on ribosomal ___ ____ or morphology.

Answer 11

protein homology; RNA sequences

Question 12

cytochrome c is a very important protein in every cell; between many species, there are ___ conserved amino acids; eight are ____ and three are ___

Answer 12

22; glycine; proline

Question 13

proteins with similar ____ normally have similar ____

Answer 13

function; structure

Question 14

___ is more conserved than sequence.

Answer 14

structure

Question 15

What is Levinthal’s paradox?

Answer 15

folding for most small proteins is extremely fast; the enormous difference between calculated and actual folding time

Question 16

What protein did Christian Anfinsen work on to create Anfinsen’s dogma?

Answer 16

ribonuclease A

Question 17

What is Anfinsen’s dogma?

Answer 17

For small, globular proteins, the native structure is determined only by the protein’s sequence. The native structure is a unique, stable, and kinetically accessible minimum of the free energy for a given environment.
Simplified: Primary structure determines tertiary structure.

Question 18

Disulfide bonds form ___ the protein folds.

Answer 18

after

Question 19

define denaturation

Answer 19

disruption of native conformation of a protein, with loss of biological activity (use heat or chemicals)

Question 20

proteins fold ____ by ____ bonds and ____ interactions.

Answer 20

cooperatively; hydrogen; hydrophobic

Question 21

what are the 4 principles of the protein folding problem?

Answer 21

1. bury hydrophobic groups
2. expose charged groups or neutralize with salt bridges
3. expose polar groups or satisfy hydrogen bonding
4. obey stereochemical restraints

Question 22

___ ___ results in the disordered peptide condensing around a weakly ordered ___ ___, which is either a small turn or a short stretch of local secondary structure.

Answer 22

hydrophobic collapse; folding nucleus

Question 23

hydrophobic amino acids are typically buried in the ___

Answer 23

core

Question 24

The structures of ___ and ___ ___ are due to the hydrophobic effect.

Answer 24

micelles; soluble proteins

Question 25

amino acids pack together like ___ ___ to fill the interior (or core) of a protein

Answer 25

puzzle pieces

Question 26

___ represent the free energy potential of folding proteins

Answer 26

funnels

Question 27

In protein folding, the __ ___ ___ assist subsequent ___ and ____.

Answer 27

first few interactions; alignment; folding

Question 28

what is the driving force of protein folding? there is a large increase in ___ as ___ is released to bulk solvent

Answer 28

hydrophobic interactions (hydrophobic effect); entropy; water

Question 29

Protein folding occurs by ___ ___. Partly correct folding ___ are retained because they are slightly more ___ than unfolded regions. Thus, proteins don’t fold ___ ___.

Answer 29

cumulative selection; intermediates; stable; completely randomly

Question 30

what are the stages of protein folding?

Answer 30

1. hydrophobic collapse
2. nucleation-condensation
3. partially structured intermediate
4. native conformation

Question 31

during the folding process, the polypeptide collapses into an intermediate ___ ___ due to the ___ effect. The backbone is then rearranged to achieve a stable ____ conformation.

Answer 31

molten globule; hydrophobic; native

Question 32

____ collapse and ____ structure form at the same time

Answer 32

hydrophobic; secondary

Question 33

What happens if the protein gets stuck while folding?

Answer 33

It’s either directed to a chaperonin to be fixed or protease to be degraded.

Question 34

chaperonin assisted protein folding requires ___ through the ___ of several ___ molecules.

Answer 34

energy; hydrolysis; ATP

Question 35

what do chaperonins do?

Answer 35

-prevent incorrect protein aggregation

Question 36

for chaperonins, protein folding takes place inside the ___ ___

Answer 36

central cavity

Question 37

two examples of chaperonin

Answer 37

HSP60; GroE

Question 38

Who won the nobel prize in 1962 for “hemoglobin the 1st protein structure”?

Answer 38

max f. perutz

Question 39

how do you bury the the hydrophobic side-chains in the core of a protein and still satisfy the strong dipole and hydrogen bonding needs of the peptide backbone?

Answer 39

the alpha helix (2ndary structure)

Question 40

who discovered the alpha helix in 1951?

Answer 40

linus pauling

Question 41

in an alpha helix, the ___ of residue 1 accepts a proton from the ___ or residue n+__.

Answer 41

carbonyl; amide; 4

Question 42

in an alpha helix, how many residues are there per turn?

Answer 42

3.6

Question 43

in an alpha helix, the H-bond is between atoms _ and __.

Answer 43

1; 13

Question 44

for every turn of the alpha helix, there are between _ and _ H-bonds.

Answer 44

3;4

Question 45

what is the pitch and rise of an alpha helix?

Answer 45

pitch: advance per helix turn; 0.54 nm
rise: advance per amino acid residue; 0.15 nm

Question 46

___ ___ are often found on the surface of proteins.

Answer 46

amphipathic helices

Question 47

what does amphipathic mean for an alpha helix?

Answer 47

one side of the surface of the alpha helix has hydrophilic AA’s and the opposite side has hydrophobic AA’s

Question 48

residues are spaced ___ degrees apart in the helical wheel

Answer 48

100

Question 49

with beta sheets, there’s no such thing as a ___ ___.

Answer 49

lone strand

Question 50

____ beta sheets are more stable and stronger than ____ beta sheets due to the more ____ hydrogen bonds.

Answer 50

anti-parallel; parallel; linear

Question 51

native conformation is achieved by rotating the main and side chain ___ ___.

Answer 51

torsion angles

Question 52

what are the three torsion angles in the main chain?

Answer 52

omega; phi; psi

Question 53

Between trans and cis isomers, there is a strong preference for ___ due to steric clash. ____ is a special case though. It permits both trans and cis conformers.

Answer 53

trans ; proline