Biochemistry Chapter 2 Mams

Front 1

What isomer form do amino acids in living organisms take?

Back 1

The L isomer

Front 2

zwitterion

Back 2

having both + and - functional groups.

Front 3

what is the pKa at which the COOH deprotonates?


The amino group?

Back 3

2 and 9 respectively

Front 4

Which amino acid contains an additional chiral center.

Back 4

isoleucine

Front 5

which 2 amino acids are common in bends and turns? why?

Back 5

proline (it is a fused ring)

Glycine ( no R group = flexible)

Front 6

the ring structure in tryptophan is called a _______ group

Back 6

indole

Front 7

Which two amino acids have a terminal carboxamide in their side chains?

Back 7

glutamine (Q) and Asparagine (N)

Front 8

name the positively charged amino acids.

Back 8

Lysine Arginine Histidine

Front 9

Which amino acids are negatively charged?

Back 9

Aspartate (D) and Glutamate (E)

Front 10

what end of a peptide is taken to be the beginning of a polypeptide?

Back 10

the amino (N) terminus

Front 11

oligopeptide

Back 11

a peptide composed of a small number of amino acids.

Front 12

1 dalton = ___ amu

Back 12

1 amu = 1 dalton

Front 13

which amino acids can form disulfide bonds?

are these covalent forces?

Back 13

cysteine and yes these are covalent.

Front 14

What is unique about the peptide bond geometry?

Back 14

it is planar due to the partial double bond character of the carbonyl and peptide linkage. (OCN)

Front 15

how many atoms lie in the plane of a peptide bond?

Back 15

6

Front 16

Almost all amino acids are linked by _________ (cis or trans) peptide bonds.

Back 16

Trans

Front 17

what prevents cis peptide bonds?

Back 17

steric clash.

Front 18

what amino acid is most ocmmonly included in rare cis peptide bonds?

Back 18

proline

Front 19

What is the psi angle?

Back 19

bond between the alpha carbon and carbonyl

Front 20

What is the phi angle?

Back 20

bond between the nitrogen and the alpha carbon

Front 21

what does a ramachandran plot tell you?

Back 21

the allowed values of phi and psi and their relative frequencies. (can be used to predict structural variants.

Front 22

What is the distance between strands in the beta sheet and strands in an alpha helix.

Back 22

3.5A and 1.5A respectively.

Front 23

a common reverse turn is linked by what hydrogen bond.

Back 23

the carbony of i with the nitrogen of i+3

Front 24

what protein is the main component of hair and wool?

Back 24

alpha Keratin. a coiled coil. (two right handed alpha helices arranged in a left handed superhelix.

Front 25

what weak interactions link the superhelix of alpha keratin?

Back 25

vanderwalls and ionic interaction.

Front 26

what protein is the main component of skin, bone, tendon, cartilage, and teeth? what is its structural formation?

Back 26

Collagen. a triple helix. Glycine appears at every third residue in the sequence.

Front 27

what two residues play a major role in myoglobin oxygen and iron binding?

Back 27

two histidine residues (the only polar residues inside the myoglobin tertiary structure.)

Front 28

amphipathic

Back 28

having both a hydrophilic and hydrophobic region

Front 29

what agent reversibly removed disulfide linkages?

Back 29

beta-mercaptoethanol

Front 30

name two agents which disrupt noncovelent interactions in a protein

Back 30

urea and guanidinium chloride

Front 31

what proteins inside cells prevent interactions of misfolded proteins?

Back 31

chaparones.

Front 32

Name 3 amino acids common in alpha helices

Back 32

alanine glutamate leucine

Front 33

name 2 amino acids common in beta sheets

Back 33

valine and isoleucine

Front 34

name 3 amino acids common in turns

Back 34

glycine, asparagine, proline

Front 35

Why does proline disrupt alpha helices and beta sheets.

Back 35

It lacks a NH group and also is restricted to a phi angle of about 60degrees.

Front 36

prion

Back 36

an agent similar in size to a virus, but only made of protein.

Front 37

Name the three characteristics of prions.

Back 37

1.) aggregates of a specific protein
2.) resistant to most protein degradation treatments.
3.) largely or completely derived from PrP which is found in the brain.

Front 38

do half folded proteins exist for lengths of time?

Back 38

no. they follow an all or none pathway of cooperative binding.

Front 39

Why can proteins not fold randomly?

Back 39

because it would take universes to try out the google of possible states.

Front 40

how do hormones like epinephrine alter the activity of enzymes?

Back 40

they stimulate phosphorylation of amino acids like serine and threonine

Front 41

what amino acid does insulin trigger the phosphorylation of?

Back 41

tyrosine

Front 42

what three amino acid repeat is responsible for the glowing action of GFP?

Back 42

Ser - Tyr - Gly

Front 43

What is the mass in kilodaltons of the average amino acid?

Back 43

110d

Front 44

what is the average distance per residue in an supercoiled alpha helix?

Back 44

1.5 A

Front 45

what is the average distance per residue in a beta pleated sheet?

Back 45

3.5A

Front 46

is the structure of insulin its most thermodynamically stable form?

Back 46

No, it is a product of adapttions to preproinsulin. A chemical that refreshes disulfide bonds would lead to a new conformation and a loss of function.

Front 47

the free energy release of hydrolysis of a peptide bond is quite large. How can you explain the stability of proteins.

Back 47

there is kinetic restriction due to the large number of h bonds and therefore an enormous activation energy.