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Flashcards in Midterm Deck (212)
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1

name the greek letters in order for the additional carbons in an amino acid

alpha, beta, gamma, delta, epsilon, zeta, eta, theta, phi, chi, psi, omega

2

what is a zwitterionic

charged form ion but charges make atom neutral

3

what determines the charged forms of aa

sidechain properties and pH of medium

4

what is the L form of aa

co, r, n

5

what is the d form of aa

n, r, co

6

what form of aa is almost found exclusively in naturally occurring proteins

L-form

7

is glycine chiral

no due to no side chain

8

what are some functions of proteins

enzymes, motor proteins, structural or cytoskeletal proteins, transport proteins, electron transfer, cell signaling, chaperones, storage proteins

9

proteins are diversified with what type of interactions

covalent and non covalent

10

what is primary structure

the linear amino acid sequence of the polypeptide chain

11

what is the secondary structure

the local structure of linear segments of the polypeptide backbone atoms without regard to conformation of the side chains

12

what is tertiary structure

the overall 3D arrangement of all atoms in a single polypeptide chain

13

what is quaternary structure

the arrangement of separate polypeptide chains (subunits) into the functional protein

14

what creates the peptide bond

condensation of the carboxyl group of aa 1 and amino group aa 2 which form an amide bond

15

what are some factors of the peptide bond

resonance, partial double bond, shorter than single bond but longer than double bond

16

where is the partial dipole in peptide bond

N in amino group and O in carboxyl group

17

polarity is important for the blank of a folded protein

stability

18

the peptide plane is

planar

19

what are the six atoms in the peptide plane

C alpha, carbon, O, N, H and C alpha

20

where is the limited rotation in the primary structure

around the peptide bond, due to resonance

21

what bonds are single and free to rotate

N-Ca and Ca-C

22

what atoms are in the psi angle

Ca-C

23

what atoms are in the phi angle

N-Ca

24

what are dihedral angles

phi and psi

25

omega angle directs what

the orientation of the sidechains between two consecutive aa in a peptide

26

180 degree for omega

trans

27

0 degree for omega

cis

28

which is more energetically favorable, trans or cis

trans due to less steric henderance

29

when do you see cis

when proline involved

30

what is ramachandran plot based on

close contacts between atoms based on their van der waals radii