Chapter 6: Protein structure pt. 1

Question 1

Primary structure (basic)

Answer 1

-amino acid sequence and location of disulfide bonds
- only covalent bonds

Question 2

Secondary Structures (basic)

Answer 2

-Hydrogen bonds: between backbone amide NH of one AA and backbone carbonyl C=O of another

-3D form of LOCAL SEGMENTS of biopolymers to give regular, recurring local conformations

-forms beta and alpha sheets
(alpha helix, beta strand, beta bend, collagen triple helix, loops and turns)

Question 3

Tertiary Structure (basic)

Answer 3

-3D structure of a polypeptide
-bonds form through the hydrophobic effect
-folds stabilized by hydrogen and disulfide
-amino acids far apart in the primary structure may be brought together

-hydrophobic inside
-hydrophilic outside

Question 4

Quaternary Structure (basic)

Answer 4

-organization of subunits on a protein with multiple subunits (oligomer or multimer)
-bonds form through the hydrophobic effect
-have H bonding, ion pair, and all bond that the tertiary structure has but DO NOT see covalent disulfide bonds

-subunits held together by many weak, noncovalent interactions

Question 5

Characteristics of peptide bonds

Answer 5

• 40% DB character
  -trans is the most stable; almost all are trans
  -NO rotation

Question 6

Resonance structure of peptide bonds (rotation)

Answer 6

-rotation can only occur around the alpha carbon of the peptide bond

-C alpha-N: phi
-C alpha C: psi
*both occur clockwise on each side
*fully extended chain= +180 or -180

Question 7

Ramachandran Plot

Answer 7

-calculated plot of all sterically allowed phi and psi angles for a polypeptide chain
-shows that only a limited amount permissible configurations

Question 8

protein secondary struc

Answer 8

-3D form of LOCAL SEGMENTS of biopolymers to give regular, recurring local conformations
- in protei

Question 9

Alpha Helix was proposed by…

Answer 9

Linus Pauling (Robert Corey)
-found that H bonds form between adjacent AA’s to give curled polypeptide helix

Question 10

In the alpha helix the hydrogen bonds occur between…

Answer 10

n and n+4 residues

Question 11

Alpha Helix facts: structure

Answer 11

• Carbonyls pointing up (-)
  -N-term pointing downwards (+)
  -R group points outward (perpendicular to axis)
  -H bonds are parallel to helix axis
• Pitch=5.4 A
  -Residues/turns=3.6 A
  -rise/AA= 1.5A/AA

-most are right handed alpha-helicies
-has dipole (polarity)

-Stable alpha-helicies end with a + charged AA to neutralize dipole movement

-can be amphipathic

Question 12

alpha helix destabilizer

Answer 12

1. Proline: its cyclic sterically destabilizes an alpha helix
2. Steric/ charge repulsion by adjacent bulky like charged amino acids
3. R-groups are too large (tryptophan, tyrosine)
4. R-groups are too small (glycine)

Question 13

alpha-Keratin: structure

Answer 13

-coiled coil
-motif of two amphipathic alpha helices

Question 14

alpha-Keratin: key structural material in….and can detect….

Answer 14

-hair, nails, and skin
-detects heavy metal poisoning

Question 15

alpha-Keratin: bonds and perms

Answer 15

-has disulfide crosslinks (S-S) w covalent bonds since it is rich in Cys

-Perm: reduce -S-S- bonds, 2RSH, curl, re-oxidize to -S-S-

Question 16

Beta-Strands facts

Answer 16

-almost fully extended polypeptide chains
-can come from same polypeptide, completely different sections of a polypeptide or even different polypeptides

Question 17

Beta-sheets facts

Answer 17

multiple beta strands arranged side by side

-Ramachandran plot: beta sheets are at the top left corner of the plot

Question 18

Beta- strands/Sheets (x,y,z)

Answer 18

-Strands (x plane)
-H bonds occur between adjacent strands perpendicular to strand direction (y-axis)
-side chains (r-groups) alternate in pointing above and below the plane perpendicular to H-bonds and strands

Question 19

antiparallel beta sheets

Answer 19

-strands run in opposite N to C-terminal direction
-stronger H bonds because they can be linear

Question 20

parallel beta sheets

Answer 20

strands run in the same N- to C- direction direction

Question 21

Beta structure facts

Answer 21

-extended zig-zag (ruffled) conformation
-6-12 residues usually involved
-repeating units of 2AA residues with distance of 7A
-may be amphipathic

Question 22

Silk fibroin

Answer 22

-stronger than steel
-extended layers of anti-parallel beta sheets of Gly-Ser-GLy-Ala-Gly-Ala
*Ala alternating with Ser/Ala w/ covalent bonds
- Ala from 1 sheet interdigitates w/ Ala from another sheet

Question 23

Collagen (basic)

Answer 23

-main structural protein in the ECM in connective tissues
-most abundant protein in mammals
-1/3 the total protein mass in large animals

-present in: bone matrix, tendons, cartilage, blood vessels, skin

Question 24

Collagen: what is the general repeating unit?

Answer 24

G-P-P-Hyp
(Gly-Pro-Pro-Hydroxyproline)

-Gly residue is invariant (can’t change) and is located among the central axis
-Need glycine for every third residue

Question 25

Collagen: bonding

Answer 25

-H-bonding is interchain: occurs btwn amide NH of one helix to carbonyl oxygens of another helix
interchain involving HydroxyPro (hyp) stabilizes helix
*lysine can hbond w/ hydroxypro??

-NO INTRAchain H-bonding occurs

Question 26

Osteogenesis Imperfecta

Answer 26

-brittle bone disease
-occurs when a mutation in a gene for collagen leads to the substitution of GLY for another amino acid
-prevents the normal production of mature collagen

Question 27

Scurvy (vitamin C deficiency)

Answer 27

-lack of hydroxypro
-not enough interchain H-bonding
-weak collagen

Question 27

Formation of hydroxypro requires…

Answer 27

O2 and ascorbic acid (vitamin C)

-hyrdroxypro is formed by prolylhydroxylase
-hydroxylys is formed by lyslylhydroxylase

Question 28

Collagen Fibrils are also strengthened by what other than hydroxyproline

Answer 28

-intrachain lysine-lysine
-interchain hydroxypyridinium covalent crosslinks

Question 29

Collagen: cross links

Answer 29

-more cross links=less elastic collagen
=more brittle bones/tendons
*sign of old age

Question 30

Loops and turns: general w example

Answer 30

-in non-regular secondary structure
-turns and loops allow chain reversal
-normally on surface of globular protein (hydrophilic)

ex: the omega loop

Question 31

The beta turn (beta bend, tight turn)

Answer 31

-allows polypeptide in antiparallel beta-sheet to reverse direction

-carbonyl O’s are H-bonded to amide H’s btwn residues 1 and 4

-proline is often the 2nd residue in beta-bends

Question 32

X-ray crystallography

Answer 32

-reveals 3D structure in atomic detail
-need crystals of protein
*put them in a buffer

-difficult to get for many proteins

Question 33

X-ray diffraction

Answer 33

-beam is shone through the crystal
-once it hits the crystal the beams gets diffracted
-diffracted beams gets detected by a detector

Question 34

calculating protein structure (x-ray crys/ diffraction)

Answer 34

1. see diffraction pattern
2. fourier transform
3. computer fit to map protein sequence
4. fixed/frozen picture of protein

*resolution measured in A=10x10^-10 (smaller angstrom the better)

Question 35

2D Nosey NMR Spectroscopy

Answer 35

-also a way to determine the structure of protein
-Limitations: need a high concentrations of protein, time consuming, only for proteins with a low molecular weight

Question 36

NMR structure of proetin

Answer 36

proteins are dynamic - “breathe”
-can be displaced up to 2A

Question 37

Cryo-Electron Microscopy (Cryo-EM)

Answer 37

form of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures

-can see membrane proteins