Lecture 8 - Protein Structure from primary to quaternary

Question 1

what is the primary structure of a protein?

Answer 1

-amino acid sequence in a polypeptide chain

Question 2

what is the secondary structure of a protein?

Answer 2

-helix

Question 3

what is the tertiary structure of a protein?

Answer 3

• one complete protein chain

- beta chain of hemoglobin

Question 4

what is the quaternary structure of a protein?

Answer 4

-the four separate chains of hemoglobin assembled into a oligomeric protein

Question 5

what is the second level of protein structure dictated by?

Answer 5

hydrogen bonds between nearby residues

Question 6

what are protein folds made up of?

Answer 6

secondary structural motifs interrupted by loops

Question 7

how can secondary motifs be identified?

Answer 7

from backbone torsion angle distributions

Question 8

What do backbone torsion angles describe?

Answer 8

-the twisting of the protein peptide backbone

Question 9

Why is the — angle almost always 180?

Answer 9

peptide bond has special resonance structure

Question 10

What does a Ramachandran plot show?

Answer 10

(..,..) angle distribution in a protein

Question 11

what are alpha helices?

Answer 11

right-handed coils

Question 12

how many residues per turn in an alpha helix?

Answer 12

average 3.6 residues per turn

Question 13

What is the average alpha helix lenght?

Answer 13

12 residues, ~3 turns

Question 14

are beta sheets parallel or antiparallel?

Answer 14

• can be both

- anti parallel sheets occur more frequently

Question 15

What is a quality of an antiparallel sheet?

Answer 15

-pleated with repeated distance averaging 7.0

Question 16

What do helices and sheets form?

Answer 16

-a continuum

Question 17

which amino acids favor alpha helices?

Answer 17

ala
cys
leu
met
glu
gln
his
lys

Question 18

which amino acids favor beta sheets?

Answer 18

val
ile
phe
tyr
trp
thr

Question 19

which amino acids favor turns?

Answer 19

gly
ser
asp
asn
pro

Question 20

What is the difference between fibrous and globular proteins?

Answer 20

globular proteins: compact + tightly folded

fibrous proteins: elongated, dominated by helices

Question 21

what do fibrous proteins serve mostly as?

Answer 21

structural elements

Question 22

what is alpha keratin?

Answer 22

coiled coil

Question 23

what is keratin?

Answer 23

-principal component of hair, horn, nail + feathers in birds/animals

Question 24

what is keratincomposed of?

Answer 24

-long alpha helix

Question 25

what do two keratins form?

Answer 25

- hydrophobic interactions to form a coiled coil | - keratin dimer coiled coil

Question 26

what is collagen?

Answer 26

triple helix

Question 27

collagen is the most _______ in ____

Answer 27

- abundant protein | - vertebrates

Question 28

What is collagen the main component of?

Answer 28

bone, teeth, cartilage, tendon, skin, blood vessels

Question 29

how is hydroxyproline made?

Answer 29

- by modifying prolines after the collagen fiber is assembled - requires vitamin C

Question 30

what are 2 methods used to determine tertiary structures?

Answer 30

1. X-ray | 2. NMR

Question 31

what is X-ray?

Answer 31

-differaction method

Question 32

What does X-ray require?

Answer 32

crystal of the protein

Question 33

what does X-ray reveal?

Answer 33

-electron density contours of the molecule

Question 34

what is the structure of a protein in solution identical to?

Answer 34

-largely identical to its crystal structure

Question 35

what is NMR?

Answer 35

- nuclear magnetic resonance | - solution-based method

Question 36

What does NMR measure?

Answer 36

distances between H atoms on the protein

Question 37

what does NMR usually contain?

Answer 37

-ensemble of structures

Question 38

what is the key determinant of side chain locations?

Answer 38

-hydrophobicity

Question 39

AA with nonpolar side chains

Answer 39

``` val ile leu met phe (occur mostly on inside) ```

Question 40

AA with charged side chains

Answer 40

``` arg lys his asp glu (mostly occur on outside) ```

Question 41

AA with polar side chains

Answer 41

``` ser thr asn gln (usually on surface, can be see on inside) ```

Question 42

what do tertiary structures contain?

Answer 42

-combinations fo secondary motifs

Question 43

larger proteins have ______

Answer 43

multiple domains

Question 44

what is a quality of multiple domains in larger proteins?

Answer 44

-each domain folds like a separate unit and has a distinct function

Question 45

are domains the same as subunits?

Answer 45

NO -domains: on same chain -subunits: on different chains

Question 46

what do quaternary structures describe?

Answer 46

how subunits are packed

Question 47

how are subunits assembled?

Answer 47

by van der Waals interactions

Question 48

for identical or near-identical subunits there is often _____

Answer 48

an overall symmetry

Question 49

what are 4 factors involved in the stability of protein folds?

Answer 49

1. hydrophobicity 2. disulfide bonds 3. metal atoms 4. electrostatic interactions

Question 50

Proteins can undergo ____ and _____

Answer 50

denaturation and renaturation

Question 51

what are 2 common denaturants?

Answer 51

1. Guanidinium ion | 2. urea

Question 52

what are the 5 steps of denuration?

Answer 52

1.

Question 53

what are conformations?

Answer 53

-the different geometries the protein can fold into

Question 54

when does the protein have highest conformational entropy?

Answer 54

in its unfolded state

Question 55

What is the entropy of a protein when it is in its unfolded state?

Answer 55

-the protein has highest conformational entropy

Question 56

what is the folding funnel?

Answer 56

-hierarchical pattern of folding

Question 57

what does the folding funnel say about structure and entropy?

Answer 57

...

Question 58

what happens to proteins as they are being synthesized in the ribosome?

Answer 58

they fold

Question 59

what accelerates S-S interchanges?

Answer 59

disulfilde isomerase

Question 60

what does disulfide isomerase do?

Answer 60

accelerates S-S interchanges

Question 61

what is the GroEL-GroES chaperonin complex?

Answer 61

an ATPase motor protein

Question 62

what do chaperone proteins do?

Answer 62

help correct misfolding

Question 63

what are the 4 steps of a chaperone protein?

Answer 63

1.