Protein structure P2

Question 1

what side is the N and C terminus on?

Answer 1

N-terminus on the left side and C-terminus on the right

Question 2

what is a polypeptide?

Answer 2

long chain of AA

Question 3

what is a protein?

Answer 3

large polypeptide with a biological function

Question 4

what is considered a dipeptide?

Answer 4

two AA joined by one peptide form

Question 5

which amino and carboxylate groups retain their charge in a polypeptide?

Answer 5

the terminus groups

Question 6

are peptide bonds covalent or non-covalent?

Answer 6

covalent

Question 7

what is the primary protein structure?

Answer 7

sequence of AA residues

Question 8

what is the secondary protein structure?

Answer 8

local folding of the polypeptide backbone

-alpha helix and B-sheets
-long chain of AA

Question 9

what is protein tertiary structure?

Answer 9

the 3D structure of a long polypeptide including all of its side chains

Question 10

what is quaternary protein structure?

Answer 10

multiple subunits of polypeptide structures

Question 11

what is the characteristic of polypeptide backbone rotation?

Answer 11

rotation of the backbone is limited

Question 12

how many AA are there per turn of an alpha helix?

Answer 12

3.6

Question 13

how many residues per H-bond are there in alpha helices?

Answer 13

the carbonyl O2 of each reisdue forms an H-bond with the backbone -NH grouo FOUR residues downstream

Question 14

which AA in primary structure are close in secondary structure?

Answer 14

amino acids 3-4 residues apart in the primary structure are close in the secondary structure

Question 15

why is proline not common in the middle of an alpha helix?

Answer 15

there is no hydrogen bound to the N
-CH2 is too large to fit and cyclic structure creates kinks in the helix

Question 16

what 2 conformations are seen with B-sheets?

Answer 16

parallel and antiparallel sheets

Question 17

which carbonyl and nitrogens form interactions with each other in B-sheets?

Answer 17

every NH and Carbonyl are forming interactions with each other

Question 18

what types of structures are available to connect B-sheets?

Answer 18

irregular structures
-classified as secondary structures

Question 19

what is the difference in H-bond stabilization between alpha helices and B-sheets?

Answer 19

in alpha-helices H-bonds are between the backbone CO and NH groups in the SAME helices

B-sheet H-bonds are between the backbone CO and NH groups of neighboring strands

Question 20

what makes irregular secondary structures irregular?

Answer 20

they dont have repeating geometry

-alpha helices and B-sheets are regular due to each AA having the same conformation in the backbone

Question 21

what groups can tertiary structures be classified into?

Answer 21

fibrous (elongated)
- insoluble in (aq), long protein filaments
-structural or connective proteins (collagen)

globular (compact)
-soluble in (aq)
-fold on themselves into compact structures with non-polar core and polar surfaces

Question 22

what structures are expected to be seen on the exterior of the tertiary structure as compared to the core?

Answer 22

polar exterior: polar AA, irregular structures (interact with H2O to satisfy H-bond potential)

hydrophobic core: hydrophobic AA, regular structures

*AA 1-2 polar, AA 3-4 hydrophobic

Question 23

what is the driving force that soluble globular proteins adapt their tertiary structure?

Answer 23

hydrophobic effect

Question 24

what force is repsonsible for “fine tuning” and stabilizing secondary and tertiary structures?

Answer 24

weaker forces–> H-bonds and salt bridges

Question 25

True or False: AA residues are capable of forming H-bonds with residues located in the same alpha helix AND neighboring helices

Answer 25

TRUE if they are polar
-serine

Question 26

what are salt bridges?

Answer 26

electrostatic intersactions between closely positioned formal charged groups
form between (-) and (+) charges

Question 27

what are disulfide bonds?

Answer 27

covalent bonds between closely positioned cysteine groups

• these are not formed with methionine because a thiol group (SH) is needed to be oxidized

-helps maintain structure; not a determinant

Question 28

what is a domain in regards to protein structure?

Answer 28

a polypeptide segment that has folded into a single structural unit with a hydrophobic core

-proteins may contain multiple domains

Question 29

what is a motif in regards to protein structure?

Answer 29

a short region of polypeptide with a recognizable 3D shape
- ex. zinc fingers

Question 30

what are prosthetic groups?

Answer 30

non-peptide components that are permanently incorporated into a protein

-provide structure and functional chemical groups

Question 31

what are 2 examples of prosthetic groups?

Answer 31

Zn 2+ in zinc fingers and Heme in hemoglobin

Question 32

what is an apoprotein?

Answer 32

a polypeptide without its prosthetic group

Question 33

what is a holoprotein?

Answer 33

a polypeptide with its prosthetic group

Question 34

why are globular proteins easily denatured?

Answer 34

they are stabilized by weak non-covalent forces

-H-bonds/hydrophobic
-salt bridges

Question 35

what factors have an effect on denaturation?

Answer 35

heat, pH, salt and detergents

Question 36

what can break disulphide bonds?

Answer 36

reducing agents

Question 37

how are quaternary structures named?

Answer 37

by number and type of subunits
-dimer, trimer, tetramer, pentamer

Question 38

what are 2 identical quaternary subunits called?

Answer 38

homodimer

Question 39

what are 2 non-identical quaternary subunits called?

Answer 39

heterodimer

Question 40

what forces stabilize quaternary structures?

Answer 40

the same as tertiary

-hydrophobic interactions
-H-bonds, ion pairs (fine tuning)

Question 41

true or false: polar amino acids in the hydrophobic core of a globular protein are involved in either H-bonding or ion pairs (salt bridges)

Answer 41

TRUE
-depending on protonation state