Secondary Structure

Question 1

Catalysis

Answer 1

• enzymes for biosynthesis, degredation, energy relations

Question 2

Structure

Answer 2

• proteins for support and protection (collagen, elastin and extensin)

Question 3

Transport

Answer 3

• carriers & membrane transporters (ATPases, antiporters, hemoglobin, lipoproteins).

Question 4

Regulation

Answer 4

• control of gene expression, growth & development (transcription factors, activators, hormones, receptors).

Question 5

Movement

Answer 5

• amoeboid movement, cytoplasmic streaming, chromosome separation, muscle contraction (e.g. tubulin, actin).

Question 6

Storage

Answer 6

• ovalbumin & casein (animals); zein, gluten, phaseolin (corn, wheat, bean).

Question 7

Defense

Answer 7

• keratin (skin), antibodies, fibrinogen & thrombin (clotting).

Question 8

Stress Response

Answer 8

• cytochrome P450, heat shock proteins, DNA repair enzymes.

Question 9

Fibrous Proteins

Answer 9

• rod-like or sheet-like proteins greatly enriched in a-helices or B-pleated sheets

Question 10

Globular proteins

Answer 10

• spherical, water soluble proteins with hydrophilic residues towards the surface
• most chemical work is done by them
• their polypeptide chains are folded into compact structures

Question 11

Membrane Proteins

Answer 11

• spherical/globular proteins embedded in membranes with hydrophobic residues towards the surface
• often “channel” proteins for conducting materials across membranes

Question 12

Primary Structure of proteins

Answer 12

• a portion of the amino acid sequence

- defined number and order of AAs

Question 13

How is protein sequence analysis complicated by multiple chains?

Answer 13

• it does not identify with post-translational modifications
• biosynthesis of insulin as a covalent interaction to create disulfide bonds to hold the chains together (insulin has two chains linked by disulfide bonds)

Question 14

Post translational modification: Insulin processing

Answer 14

• insulin synthesized as an inactive precursor (preproinsulin)
• undergoes enzymatic cleavage to proinsulin, followed by folding and a dsuisulfide bond
• followed by additional enzymatic proteolysis
• allows insulin to be stored as a inactive precursor ready for mobilization on demand

Question 15

Secondary Protein Structure

Answer 15

• the folding or coiling of polypeptide chains into small localized regions of having non-random organization
• two main types: alpha helix and beta pleated sheets
• both stabilized by H bonds between carbonyl and amino groups and all secondary structures MUST follow Paulings law

Question 16

Paulings rules for secondary structures

Answer 16

1. Bond lengths and bond angles should be distorted as little as possible (from X-ray information)
2. No two atoms should approach each other more closely than is allowed by their vdW radii
3. The six atoms in the amide plane must remain coplanar with the alpha carbon
4. Some kind non covalent bonding is necessary to stabilize protein folding

• preferred conformation of polypeptides must allow for max H bonding but satisfy rules 1-3

Question 17

Tertiary Protein Structure

Answer 17

• multiple beta sheets or alpha helices folded

- binds a heme

Question 18

Quaternary Protein Structure

Answer 18

• when 2 or more proteins folded in tertiary interact to form well defined complexes
• four separate protein subunits, two alpha subunits and two beta subunits

Question 19

Alpha Helix

Answer 19

• clockwise corkscrew (right handed)
• R groups extend outwards
• H bonds form between carbonyl and amino groups of every 4th residue
• plane of peptide bond parallel to axis of helix

Question 20

Polyproline helix (polypeptide helix)

Answer 20

• does not meet criteria of alpha helix

- it is left handed and commonly found in glycine

Question 21

Beta Pleated Sheets

Answer 21

• A multi-folded (pleated) sheet-like arrangement of amino acid that is obtained when segments of peptides line up side-by-side.
• perpendicular to AA chain
• lane of peptide bond is parallel to plane of pleat
• R groups alternate above and below the plane of the sheet
• H bonds between carbonyl and amino groups of adjacent chains

Question 22

Two forms of Beta Pleated Sheets

Answer 22

1. Antiparallel configuration

2. Parallel configuration

Question 23

Antiparallel configuration of Beta Pleated Sheets

Answer 23

• shorter, stronger, more stable H bonds

Question 24

Parallel configuration of Beta Pleated Sheets

Answer 24

• longer, weaker, less stable H bond

Question 25

Beta turns

Answer 25

- facilitate peptide folding - antiparallel b-structures have sharp turns in their peptide chains - allow tight reversals in the direction of the peptide chains - B turns are tighter than turns in alpha helices - H bond between the 1st and 4th amino acid (1st and 3rd peptide bond) stabilizes turn

Question 26

a-keratins

Answer 26

- bundles of multiple, cpiled alpha helixes that form fibers ex: hair, wool, outer skin, claws, scales, horns, hoofs

Question 27

B-keratins

Answer 27

- stacked, anti-parallel B-sheets embedded in a matrix of other protein structure (also known as fibroin). ex: spider web silk, silkworm silk, bird feathers & beaks

Question 28

Collagen

Answer 28

- triple helix of polypeptides each having only “a-helix” coils of secondary structure - most abundant protein in animals - triple helix of tropocollagen - quaternary structure of a cross linked collagen - cross linking is via lysinorleucines derived from 2 lysines in diff polypeptides ex: connective tissue in tendons, blood vessels, skin, bone.

Question 29

Cysteines residues form many _______ between polypeptides

Answer 29

- disulfide bridges

Question 30

What is the affect of disulfides in keratin?

Answer 30

- make keratin very rigid and insoluble (important for hair stry

Question 31

Structure of spider silk

Answer 31

- the beta sheet regions of fibroin have a high number of glycines - beta sheets impart strength and a-helices impart flexibility to the strand - stronger than steel

Question 32

Amino acid composition of collagen

Answer 32

- (Gly-Pro-X)n - 1/3 Gly, 1/3 Pro - X is often 5-hydroxylysine - Pro is often hydroxylated

Question 33

Scurvy

Answer 33

- collagen related disease - vitamin C deficiency - Vit C is a cofactor for prolyl hydroxylase (hydroxylates proline and lysine) - results in weakened collagen & connective tissue. - symptoms include gum disease, poor healing of wounds, joint pain

Question 34

Lathyrism

Answer 34

- collagen related disease - consumption of a common range sweet-pea plant (Lathyrus odoratus). - Plant contains a toxin (B-aminopropionitrile) that inactivates lysyl oxidase. - This enzyme facilitates lysine cross-linking in collagen. - Lathyrism results in bone, joint & blood vessel abnormalities.

Question 35

Marfan’s syndrome

Answer 35

- collagen related disease - a genetic disorder of connective tissue - involves mutations in the fibrillin gene. - Fibrillin helps maintain connective tissue integrity. - Symptoms include excessively long limbs, fingers, toes & joint flexibility.

Question 36

Fibrillin

Answer 36

- one of three main proteins of connective tissue | - along with collagen and elastin