Medical Biochemistry Lecture 4

Question 1

Primary Structure

Answer 1

protein adopt specific three-dimensional conformations

Question 2

Native fold

Answer 2

has a large number of favorable interactions within the protein

Question 3

What does protein. structure have?

Answer 3

the lowest Gibbs free energy

Question 4

True or False: This structure can fulfill a specific biological function

Answer 4

True

Question 5

Hydrophobic effect

Answer 5

water makes the best hydrogen bonds with itself and is disrupted by other molecules
-Hydrophobic groups aggregate, hiding their entire surface from water, which creates a structured salvation layer around the molecule

Question 6

Van der Waals (London dispersion)

Answer 6

-attractive force due to induced dipoles in all atoms
-important to the stability in the interior of the protein

Question 7

hydrogen bonds

Answer 7

-Interaction of N-H and C=O if the peptide bond leads to local regular structure such as alpha helices and Beta sheets
-Maximized in protein structure, allow polar molecules to traverse interior protein

Question 8

Ionic interactions

Answer 8

-long range strong interactions between permanently charged groups
-salt-bridges, especially buried in the hydrophobic environment strongly stabilize proteins

Question 9

Disulfide Bridge

Answer 9

-mostly in secreted proteins
-generally not found in reducing environment of cell

Question 10

What are the four levels of protein structure?

Answer 10

Primary, Secondary, Tertiary, Quaternary

Question 11

Peptide bond

Answer 11

partial double bond

Question 12

Resonansance in peptide bonds allows a what configuration because of steric hindrance

Answer 12

trans

Question 13

Is rotation around the peptide bond permitted?

Answer 13

no

Question 14

Is rotation around connected on the alpha carbon permitted

Answer 14

yes

Question 15

bulky R groups generally are on what sides?

Answer 15

opposite

Question 16

phi

Answer 16

angle around alpha carbine: amide nitrogen bond

Question 17

psi

Answer 17

angle around the alpha carbon-carbonyl carbon bond

Question 18

In a fully exited polypeptide, both phi and psi are what degrees

Answer 18

180

Question 19

The peptide are _____
but bulk-R groups on adjacent alpha carbons can interfere

Answer 19

planar

Question 20

What two possible conformations can peptide bonds exist?

Answer 20

trans highly favorable except for proline( which can be found 6 percent in cis conformation in beta turns)

Question 21

Secondary structures

Answer 21

local spatial arrangement of the polypeptide backbone

Question 22

Secondary structure of alpha helix

Answer 22

-stabilized by H-bond between new\arby residues
-25% of amino acids in this conformation(highly variable between proteins)

Question 23

Secondary structure of beta sheets

Answer 23

stabilized by H-bond between adjacent segments that may be far away

Question 24

Random coli

Answer 24

irregular arrangement of the polypeptide chain

Question 25

alpha helix

Answer 25

the helical backbone is held together by hydrogen bonds between an amide hydrogen of one amino acid and a carbonyl oxygen four amino acids away, maximizing bonds

Question 26

What hand helix is 3.6 residues (5.4) per turn giving a twist?

Answer 26

right

Question 27

Peptide bond are aligned roughly parallel with

Answer 27

helical axis

Question 28

another characteristics of the alpha helix

Answer 28

sides pot out and roughly perpendicular with the helical axis

Question 29

What is the inner diameter

Answer 29

4-5 A

Question 30

What residues align nicely on top of each other

Answer 30

1 and 8

Question 31

Peptide bond has a strong dipole movement with

Answer 31

- carbonyl, + amide

Question 32

where does negatively charge residues occurs

Answer 32

near the positive end of the helix dipole

Question 33

All polypeptides sequences adopt an alpha helical structures

Answer 33

False: Not all polypeptide sequences adopt an alpha helical structures

Question 34

Small hydrophobic residues such as what are strong helix formers

Answer 34

Ala and Leu

Question 35

What amino acid serves as a helix breaker and why?

Answer 35

Pro because the rotation around the N-C alpha bond is impossible

Question 36

What other amino acids serves as a helix breaker and why?

Answer 36

Gly because the tiny R group supports other conformations

Question 37

Attraction or repulsive interactions between side chains 3-4 amino acids apart will affect

Answer 37

formation

Question 38

Why is non polar side chains along each alpha helix can be arranged?

Answer 38

their side chain groups contact another helix

Question 39

coiled coil

Answer 39

this allows side groups to pack neatly only when the alpa helices interact at 18 degrees from parallel. If alpha helices remained parallel, could stain contact for only few residues

Question 40

Multiple coils

Answer 40

helical bundle

Question 41

What can an alpha helix supercoiling be

Answer 41

tertiary or quaternary

Question 42

Beta sheets

Answer 42

the planarity of the peptide bond ad tetrahedral geometry of the alpha carbon create a pleated sheet-like structure

Question 43

How are the side chains in beta sheets?

Answer 43

alternating in up and down direction

Question 44

How are beta sheets in proteins?

Answer 44

twist in a right-handed manner

Question 45

Whare the two orientation of beta sheets?

Answer 45

parallel and antiparallel

Question 46

Parallel Beta sheets

Answer 46

the H-bonds strands run in the same direction; bent H-bonds(weaker)

Question 47

Antiparallel B-sheets

Answer 47

the H-bonds stands run in opposite direction, linear H-bonds (stronger)

Question 48

When does beta turns occurs?

Answer 48

frequently when the strands of the B sheet changes direction

Question 49

How is 180 degree accomplished in a B turn?

Answer 49

over 4 amino acids

Question 50

How is the turn stabilized?

Answer 50

H-bond from carbonyl oxygen to amide proton three residues down the sequence

Question 51

What are common in B turns?

Answer 51

Proline(cis) in position 2 or a flexible glycine in position 3

Question 52

Tertiary structure

Answer 52

overall spatial arrangement of atoms in a protein

Question 53

How is tertiary structure stabilized?

Answer 53

numerous weak and strong interactions between amino acids side chain, often far apart in the primary sequence

Question 54

What are the two major class of tertiary structure?

Answer 54

fibrous and globular(water or lipid soluble)

Question 55

what do proteins have?

Answer 55

motifs(folds)

Question 56

What is the strongest influence on protein folding?

Answer 56

Burial of hydrophobic(non polar) side chains into the core of the polypeptide's structure

Question 57

What happens in aqueous solution regarding the hydrophobic core?

Answer 57

proteins with a large number of non polar side groups will tend to internalize the non polar residues and be more stable than proteins containing mostly polar groups

Question 58

True or False: Polar bonds can H-bond with water, and thus a smaller free energy would be gained from packing polar groups vs non polar groups

Answer 58

True

Question 59

Change is G is more positive than non polar packing

Answer 59

False

Question 60

Why do some alpha helices have alternating polar and non polar amino acids

Answer 60

to improve packing of helical bundles

Question 61

Transmembrane proteins have a long stretches of how many non polar amino acids to cross the membrane?

Answer 61

20