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Biochemistry > Secondary Structure > Flashcards

Secondary Structure Flashcards

1
Q

Catalysis

A
  • enzymes for biosynthesis, degredation, energy relations
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2
Q

Structure

A
  • proteins for support and protection (collagen, elastin and extensin)
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3
Q

Transport

A
  • carriers & membrane transporters (ATPases, antiporters, hemoglobin, lipoproteins).
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4
Q

Regulation

A
  • control of gene expression, growth & development (transcription factors, activators, hormones, receptors).
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5
Q

Movement

A
  • amoeboid movement, cytoplasmic streaming, chromosome separation, muscle contraction (e.g. tubulin, actin).
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6
Q

Storage

A
  • ovalbumin & casein (animals); zein, gluten, phaseolin (corn, wheat, bean).
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7
Q

Defense

A
  • keratin (skin), antibodies, fibrinogen & thrombin (clotting).
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8
Q

Stress Response

A
  • cytochrome P450, heat shock proteins, DNA repair enzymes.
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9
Q

Fibrous Proteins

A
  • rod-like or sheet-like proteins greatly enriched in a-helices or B-pleated sheets
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10
Q

Globular proteins

A
  • 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
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11
Q

Membrane Proteins

A
  • spherical/globular proteins embedded in membranes with hydrophobic residues towards the surface
  • often “channel” proteins for conducting materials across membranes
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12
Q

Primary Structure of proteins

A
  • a portion of the amino acid sequence

- defined number and order of AAs

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13
Q

How is protein sequence analysis complicated by multiple chains?

A
  • 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)
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14
Q

Post translational modification: Insulin processing

A
  • 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
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15
Q

Secondary Protein Structure

A
  • 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
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16
Q

Paulings rules for secondary structures

A
  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
17
Q

Tertiary Protein Structure

A
  • multiple beta sheets or alpha helices folded

- binds a heme

18
Q

Quaternary Protein Structure

A
  • 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
19
Q

Alpha Helix

A
  • 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
20
Q

Polyproline helix (polypeptide helix)

A
  • does not meet criteria of alpha helix

- it is left handed and commonly found in glycine

21
Q

Beta Pleated Sheets

A
  • 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
22
Q

Two forms of Beta Pleated Sheets

A
  1. Antiparallel configuration

2. Parallel configuration

23
Q

Antiparallel configuration of Beta Pleated Sheets

A
  • shorter, stronger, more stable H bonds
24
Q

Parallel configuration of Beta Pleated Sheets

A
  • longer, weaker, less stable H bond
25
Q

Beta turns

A
  • 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
26
Q

a-keratins

A
  • bundles of multiple, cpiled alpha helixes that form fibers
    ex: hair, wool, outer skin, claws, scales, horns, hoofs
27
Q

B-keratins

A
  • 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
28
Q

Collagen

A
  • 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.
29
Q

Cysteines residues form many _______ between polypeptides

A
  • disulfide bridges
30
Q

What is the affect of disulfides in keratin?

A
  • make keratin very rigid and insoluble (important for hair stry
31
Q

Structure of spider silk

A
  • 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
32
Q

Amino acid composition of collagen

A
  • (Gly-Pro-X)n
  • 1/3 Gly, 1/3 Pro
  • X is often 5-hydroxylysine
  • Pro is often hydroxylated
33
Q

Scurvy

A
  • 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
34
Q

Lathyrism

A
  • 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.
35
Q

Marfan’s syndrome

A
  • 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.
36
Q

Fibrillin

A
  • one of three main proteins of connective tissue

- along with collagen and elastin

Biochemistry (15 decks)

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