Biochemistry Of Macromolecules - Exam 1

Front 1

protein conformation

Back 1

the spatial arrangements of atoms

Front 2

native protein

Back 2

protein in any of its functional, folded conformations

Front 3

stability (of a protein)

Back 3

tendency to maintain a native conformation

Front 4

Why does the environment within cells usually preclude the formation of --S--S-- bonds?

Back 4

the environment is highly reducing

Front 5

In eukaryotes, disulfide bonds are usually found in what types of proteins?

Back 5

secreted, extracelluar proteins (i.e. the hormone insulin)

Front 6

Give an example of an organism that would have many different types of proteins containing disulfide bonds.

Back 6

thermophilic bacteria, because disulfide bonds help to stabilize their proteins

Front 7

Describe the solvation layer of a protein and state what causes it.

Back 7

a highly structured shell of water molecules around the molecule that results from the optimal arrangements of hydrogen bonds

Front 8

What effect does an increase in hydrophobic interactions within the protein have on the solvation layer?

Back 8

the extent of the solvation layer decreases because each hydrophobic group no longer presents its entire surface to the solution

Front 9

salt bridge

Back 9

interaction of oppositely charged groups that form an ion pair

Front 10

equation for the force (F), meaning strength, of ionic interactions

Back 10

F = (Q1Q2) / (E * r^2)

Front 11

Salt bridges are typically stabilizing for a protein when they are located in what spatial region? Why?

Back 11

Toward the interior of the protein (buried from the water outside) because the dielectric constant (E) is lower in the nonpolar protein interior than near the polar aqueous solvent

Front 12

Why does the alpha-helix protein conformation form more readily than many others?

Back 12

stabilized by H bonds between the H attached to the electronegative N of a peptide linkage and the electronegative carbonyl O of of the 4th amino acid further down the chain
(starting w amino terminus side)

Front 13

How many H bonds stabilize one turn of an alpha-helix?

Back 13

3-4

Front 14

What amino acid shows the greatest tendency to form alpha-helices?

Back 14

alanine (Ala)

Front 15

How will a long block of glutamate (Glu, E) residues affect an alpha-helix at pH=7.0? Why?

Back 15

disrupt the helix because the negitively charged carbonyl groups of adjacent Glu residues repel each other

Front 16

How will a close rogether group of Asn, Ser, Thr, and Cys residues affect an alpha-helix? Why?

Back 16

stabilize because of their bulk and shape

Front 17

How will a group of close together Lys and/or Arg affect an alpha-helix? Why?

Back 17

destabilize b/c + charged R groups will repel each other

Front 18

Why structure do Gly residues like to form and why?

Back 18

coiled structures because Gly has the most conformational flexibility of the amino acids

Front 19

Which 2 amino acids have the least tendency to form alpha-helices and why?

Back 19

Pro, b/c (1) the N atom is part of a rigid ring so rotation about the N--Calpha bond is not possibile, (2) the N of the peptide bond has no H for H bonding, and
Gly, b/c of its conformational flexibility

Front 20

Compare the repeat period of amino acids in a parallel B sheet and antiparallel B sheet.

Back 20

repeat period is shorter for parallel conformation (6.5A vs. 7A)

Front 21

Describe the R groups prevalent when 2 beta sheets are close together in protein.

Back 21

R groups are small, like in Gly and Ala residues

Front 22

Why do Gly and Pro often occur in B turns?

Back 22

Gly b/c its small and flexible
Pro b/c peptide bonds involving the imino N of Pro usually form cis conformation, which helps tight turns

Front 23

Where are B turns found spatially in a protein? Why?

Back 23

near the surface, b/c the peptide groups of the central 2 amino acids can H bond w/ water

Front 24

Glycine

Back 24

Gly, G

Front 25

Alanine

Back 25

Ala, A

Front 26

Proline

Back 26

Pro, P

Front 27

Valine

Back 27

Val, V

Front 28

Isoleucine

Back 28

Ile, I

Front 29

Methionine

Back 29

Met, M

Front 30

Phenylalanine

Back 30

Phe, F

Front 31

Tyrosine

Back 31

Tyr, Y

Front 32

Tryptophan

Back 32

Trp, W

Front 33

Serine

Back 33

Ser, S

Front 34

Threonine

Back 34

Thr, T

Front 35

Cysteine

Back 35

Cys, C

Front 36

Asparagine

Back 36

Asn, N

Front 37

Glutamine

Back 37

Gln, Q

Front 38

Lysine

Back 38

Lys, K

Front 39

Histidine

Back 39

His, H

Front 40

Arginine

Back 40

Arg, R

Front 41

Aspartate

Back 41

Asp, D

Front 42

Glutamate

Back 42

Glu, E

Front 43

Leucine

Back 43

Leu, L

Front 44

Describe the structure and properties of a fibrous protein.

Back 44

protein w/ polypeptide chains arranged in long strands or sheets;
usually consist largely of a single type of secondary structure and have a simple tertiary structure;
insoluble in water b/c of many hydrophobic residues in center and on surface

Front 45

Describe the sturcutre of a globular protein.

Back 45

protein w/ polypeptide chains folded into spherical or globular shapes;
usually have several types of secondary structure

Front 46

domain

Back 46

part of a polypeptide chain that is independently stable or could undergo movements as a single entity w/ respect to the entire protein

Front 47

Rules of protein folding

Back 47

1. hydrophobic interactions contribute largely to stability, and burial of R groups to exclude water requires at least 2 layers of secondary structure
2. if in the same protein, alpha helices and beta sheets are usually found in different structural layers, b/c beta sheet backbone can't H bond to alpha helix
3. amino acids adjacent in protein chain are usually stacked next to each other in folding
4. connections between common elements of secondary structure cannot cross or form knots
5. beta conformation is most stable when individual segments are twisted slightly in a right-handed sense

Front 48

alpha/beta barrel

Back 48

a series of beta-alpha-beta loops arranged so that the beta strands form a barrel;
often found w/ binding site of enzymes

Front 49

protein family

Back 49

proteins with significant similarity in primary structure and/or similar tertiary structure and function

Front 50

protein superfamilies

Back 50

two or more protein families that make use of the same structural motif and have functional similarities
(may have little similarity in amino acid sequence)

Front 51

multimer

Back 51

multisubunit protein

Front 52

oligomer

Back 52

multimer w/ just a few subunits

Front 53

protomer

Back 53

a repeating structural unit in a multimer (can be a single subunit or a group of subunits)

Front 54

rotational symmetry (of an oligomer)

Back 54

individual subunits are superimposed on others (correspond spatially) by rotation about one or more rotational axes;
these proteins form CLOSED structures

Front 55

helical symmetry (of an oligomer)

Back 55

individual subunits are superimposed on others (correspond spatially) by a helical rotation;
these proteins form OPEN-ENDED structures, with subunits added in a spiral
i.e. can be found in virus capsids; also encloses viral RNA; can help form actin filaments of muscle

Front 56

cyclic symmetry

Back 56

type of rotational symmetry involving rotation about a single axis
(denoted Cn, w/ n as # subunits related by the axis)

Front 57

dihedral symmetry

Back 57

type of rotational symmetry in which a twofold rotational axis intersects an n-fold axis at right angles
(denoted Dn, w/ n as # subunits related)

Front 58

icosahedral symmetry

Back 58

when symmetry occurs in shape of icosahedron (regular 12-cornered polyhedron w/ 20 equilateral triangular faces);
each face can be brought to coincidence w/ another face by rotation about one or more of 3 axes;
i.e. common structure of capsids (virus coats); poliovirus

Front 59

denaturation

Back 59

loss of 3-dimensional structure sufficient to cause loss of function

Front 60

What can cause proteins to become denatured?

Back 60

1) heat, b/c it affects weak interactions like H bonds
2) extremes of pH
3) miscible organic solvents, like alcohol or acetone
4) certain solutes, like urea and guanidine hydrochloride
5) detergents

Front 61

molecular chaperones

Back 61

proteins that interact w/ partially folded or improperly folded polypeptides by (a) facilitating correct folding pathways or (b) providing microenvironments in which folding can occur

Front 62

Hsp70

Back 62

class of molecular chaperones abundant in cells stressed by high temperatures;
bind to regions of unfolded polypeptides that are rich in hydrophobic residues, preventing inappropriate aggregation;
also block the folding of proteins that must remain unfolded

Front 63

chaperonins

Back 63

class of molecular chaperones required for the folding of some cellular proteins that do not fold spontaneously;
use a system called GroEL/GroES

Front 64

GroEL/GroES

Back 64

system in chaperonins that assists folding:
unfolded proteins are bound w/in pockets of the GroEL complex, and pockets are capped transiently by the GroES "lid". GroEL undergoes conformational changes, coupled w/ ATP hydrolysis and the binding/release of GroES, which promote folding of the bound protein

Front 65

protein disulfide isomerase (PDI)

Back 65

enzyme that helps protein folding by catalyzing the interchange, or shuffling, of disulfide bonds until the bonds of the native conformation are formed

Front 66

peptide prolyl cis-trans isomerase (PPI)

Back 66

enzyme that helps protein folding by catalyzeing the interconversion of the cis and trans isomers of Pro residue peptide bonds, which can be a slow step in folding if Pro peptide bonds are in cis formation

Front 67

amyloidoses

Back 67

any of a group of diseases where a soluble protein that is normally secreted from the cell is secreted in a misfolded state and converted into an insoluble extracellular amyloid
i.e. type 2 diabetes, Alzheimer's disease

Front 68

amyloid

Back 68

insoluble extracellular protein that is highly ordered and unbranched, w/ many beta sheet structures (oriented perpendicular to the axis of the fiber)