Chapter 6 - Proteins never end

Question 1

Peptide group

Answer 1

6 atoms from aa_n to aa_n+1

occupy same plane (peptide planar)

C_alpha1-C_{alpha 2}

Part of primary structure

Rotate Relative to each other

Question 2

Peptide bonds

Answer 2

partial double bond character causes restricted conformation -> trapped in either trans or cis conformation (usually trans so that the R groups aren’t sterically hindered) -> no peptide bond rotation

Polar - O, partial negative (H-bond acceptor)

N, partial positive (H is H-bond donor)

Question 3

Alpha Helix

Physical features

Answer 3

repeating phi and psi angles along peptide backbone -> predictable physcial features

• right handed helix
• 3.6 aa per turn
• 0.54 nm pitch (advance per turn) and 0.15 nm rise per residue

N——>C

Question 4

Alpha helix

Stabilization

R-group location

Answer 4

Hydrogen bond stabilization: strenth in numbers; parallel to helix axis

R-group location: outside of helix; about every 4th side-chain on the same side

Possible amphipathic properties of helices

Some amino acids prefer alpha helical structure; others (pro and gly) helix breakers

Helix excludes water; van der Waals packing

Stabilizers: Ala-prefer helical phi and psi angles

disruptors - too flexible or inflexible, highly charged or bulky - gly, pro, tyr, arg, lys

Question 5

Beta Sheets

Answer 5

Repeating phi and psi angles along extended peptide backbone -> more flexible

Interstrand hydrogen bonds and right-hand twist

Anti-Parallel (strands run in opposite direction with straigh H-bonds. 2-22 strands, avg 6 residues per strand but up to 15)

Parallel (strands run in same direction with off-set hydrogen bonds; more than 5 strands per sheet, less stable than antiparallel, can be mixed with anti-parallel sheets)

R-Groups project on alternate sides of sheet every other residue along strand

Question 6

Tertiary or 3D structure

Primary stabilizing force

And other stabilizing forces

Answer 6

the basis of protein stability and function

hydrophobic effect (thermodynamic driving force?); 3D arrangement of secondary structures maximizes the hydrophobic effect

Additional stabilizing effect of other noncovalent forces (ionic, hydrogen bonds, and van der Waals); the sum of individual forces is greater than the parts analogy

Disulfide bond contribution to tertiary structure

Question 7

Tertiary Structure

Protein folding process and the denaturing forces

Answer 7

a) Primary structure directs folding process (ms time frame); hydrophobic collapse; molten globule and folding chaperones (when are they needed)
b) Protein denaturation: cooperative process -> Denaturation curve and Tm

Question 8

Quaternary structure

Answer 8

multiple subunits or polypeptides to form a single functional protein

Question 9

Protein structure determination

Answer 9

X-ray crystallography and NMR spectroscopy (intro to techniques)

Question 10

B-Sheets frequently interact in protein structures

Answer 10

side chains project alternately above and below B-sheet plane

Forms amphipathic sheet: hydrophobic side chains face protein interior

amphipathic alpha helices and B-sheets help form hydrophobic interior and hydrophilic surface of proteins

intermolecular h-bonds

right-handed twist to sheet (due to L-amino acid)

Question 11

Variable B-structure in proteins to match function

Answer 11

Barrel structures or sandwiches form from twisted sheets

Form regions or compartments inside proteins for varying conditions and separate environments (i.e. channels through membrane)

Question 12

Beta sheet topology (connectivity of strands)

Answer 12

strands may not be successsive in amino acid sequence

small loop connections between anti-parallel strands

reverse turn or B-bend to change direction

Cross-over loops occur between parallel strands

Question 13

Reverse Turn Features (Type I and II)

Answer 13

occur at protein surfaces

Usually 4 aa arranged in 2 possible ways

• pro fits in due to rigid side-chain
• gly common due to lack of side-chain

h-bond stabilization

Question 14

Helical Wheel Diagram

Answer 14

shows amino acid sequence influence on helix properties

every 4th amino acid in sequence is found on the same face of the helix

Question 15

Alpha-Keratins

Answer 15

major components of hair and nails

tissue specific gene expression

coiled-coil structure - made from 2 polypeptide strands (310 residue central peptide segment)

individual strands: right-handed - overal: left-handed

7 residue pseudo repeat: abcdefg

a & d positions mostly nonpolar - align on one side of helices (hydrophobic strip)

Question 16

Collagen

Answer 16

major component of tendons, skin, bones, and teeth - at least 19 different types

a fibrous protein

major protein in connective tissue of vertebrates

form mirrors function: include tendons (robelike fibers); skin (loosely woven fibers)

Overall role: strength, support, resilency, resistance

Question 17

Higher-order Keratin Structure

Answer 17

N&C-termini of peptides aid protofilament formation

stepwise assembly to form macrofibrils

parallel macrofibrils form hair&nails

cys-rich cross-links form between fibers

Question 18

Collagen

Basic Structure

Answer 18

3 left-handed helical peptides coiled around each other -> right-handed supercoil (quaternary structure - no tertiary structure)

Type I Macro: 285 kdA (good sized); 14 A wide and 3000A long

3 amino acids per turn (3₁₀) helix

rise 0.31 nm per residue (more extended than an alpha helix)

limited amino acid sequence

Question 19

Collagen Triple Helix

Answer 19

multiple repeats of Gly-X-Y

X often Pro

Y usually 4-hydroxyproline

Gly located along central axis of a triple helix (other residues cannot fit)

Amide H from Gly forms H-bond with Carbony from Pro - interchain H-bonds

Question 20

4-Hydroxyproline and 5-Hydroxylysine: post-translational enzyme

Vitamin C deficiency

Answer 20

hydroxylyation requiring vitamin C

hydroxyproline H-bonds between chains

hydroxylysine site of glycosylation (carbohydrate modification)

Vitamin C deficiency (scurvy) leads to lack of proper hydroxylation and defective triple helix (skin lesions, fragile blood vessels, bleeding gums)

Human and guinea pigs cannot synthesize vitamin C

Question 21

Collagen Fibers

Answer 21

Arrangement: staggered array of tropocllagens –> basic unit in tissues

Question 22

Tropocollagen

Answer 22

Triple helix (3 polypeptides about 800 residues each) MW=285kd

opposite twist to individual helices = greater stability

Question 23

Banding pattern in EMs

Answer 23

stagger and overlap of molecules cause a 67 nm repeat with gap and a “hole” regions

-OH groups are glycosylated (carbohydrate)

evidence for bone nucleation site

cross-links form between fibers for additional strength

Question 24

Lysyl oxidase

Answer 24

Converts lys or hydroxlys sidechain to a reactive aldehyde

Question 25

Allysine group

and Cross-links

Answer 25

forms covalent cross-links between tropocollagen -> fibrils

Schiff base forms between lys NH3+ and the aldehyde group of allysine

Two allysine residues condense to form a corss-link, generally intrahelix

HIs and 5-hydroxylysine also contribute cross-links

more crosslinks accumulate with age