Protein Structure and Function

Question 0

Aliphatic (alkane) Amino Acids

Answer 0

• Proline (pro)
• Glycine (gly) (only AA not chiral)
• Alanine (ala)
• Valine (val)
• Leucine (leu)
• Isoleucine (ile)

ALL ARE HYDROPHOBIC

Question 1

Amino Acid Classification (Hydrophobic/Hydrophilic)

Answer 1

Hydrophobic: Aliphatic, Aromatic, Sulfur containing (only Methionine)

Hydrophilic: Sulfur containing (only Cysteine), Polar/uncharged, Basic/Acidic

Tyrosine is both. (know it as hydrophilic)

Question 2

Aromatic Amino Acids

Answer 2

ALL VERY HYDROPHOBIC (tyrosine is also hydrophilic)

• Phenylalanine (phe)
• Tyrosine (tyr)
• Tryptophan (trp)

Question 3

Sulfur Containing Amino Acids

Answer 3

• Methionine (met) (Very hydrophobic)

- Cysteine (cys) Hydrophilic!

Question 4

Acidic Amino Acids

Answer 4

• Aspartate (Asp)
• Glutamate (Glu)

Negatively charged AA

Question 5

Basic Amino Acids

Answer 5

Histidine- (His) only AA that functions as a buffer in physiol range
Lysine (Lys)
Arginine (Arg)

Question 6

Polar Uncharged AA

Answer 6

Polar side groups, hyrdrophilic in nature

• Serine (ser)
• Threonine (thr)
• Asparagine (asn)
• Glutamine (gln)

Question 7

Peptide

Answer 7

Condensation product of amino acids

• dipeptide = 2 AA
• oligopeptide = up to 20 AA
• polypeptide = >20 AA

Question 8

Protein

Answer 8

A functional polypeptide with a biological role (Native protein)

• sometimes contain non-polypeptides portions as well
• very small proteins are hormones

Question 9

Residue

Answer 9

an amino acid in a peptide

Question 10

Simple and Conjugated Protein Classification

Answer 10

Simple: composed only of amino acid residues

Conjugated: Contain prosthetic groups (metal ions, co-factors, lipids, carbs)
eg. Hemoglobin- Heme

Question 11

Fibrous Proteins

Answer 11

1. polypeptides arranged in long strands or sheets
2. water insoluble (lots of hydrophobic AA’s)
3. Strong but flexible
4. Structural (keratin, collagen)

Question 12

Globular Proteins

Answer 12

1. Polypeptide chains folded into spherical or globular form
2. Water soluble
3. Contain several types of secondary structures
4. Diverse functions (enzymes, regulatory proteins)

Question 13

Protein Function

Answer 13

• Catalysis-enzymes
• Structural (keratin)
• Transport (hemoglobin)
• Transmembrane transport (Na/K pump, ATPases)
• Toxins (rattlesnake venom, ricin)
• Contractile function (actin, myosin)
• Hormones (insulin)
• Storage proteins (seeds and eggs)
• Defensive proteins (antibodies)

Question 14

4 levels of Protein Structure

Answer 14

Primary - genetically encoded sequence of AA
Secondary- folding of the primary sequence into alpha helix or beta sheet
Tertiary- combination of several secondary levels. Highest order for a single polypeptide chain
Quaternary- combination of 2 or more tertiary structures

Question 15

Major common post-translational modifications

Answer 15

1. hydroxylation –> hydroxypro, hydroxylys
2. addition Pi group onto ser, thr
3. addition of sugars to give glycoproteins
4. Disulfide bond formation

Question 16

Disrupters in Polypeptide Chain

Answer 16

• Proline: NO H on N for H-bonding; because of ring, “natural” rotation of chain is disrupted
• Glycine: too much free rotation (no side chain group)
• ser, asp, asn: interfering H-bonds
• ile, val: steric effect

Question 17

Fibrous proteins

Answer 17

contain polypeptide chains organized parallel along a single axis, producing long fibers or large sheets.

• They are mechanically strong, play structural roles in nature
• Difficult to dissolve in water
• eg. a-Keratins and Collagen

Question 18

5 Classes of Tertiary Interaction Bonds

Answer 18

• Hydrophobic force (attraction)
• Van der Waals interactions
• Side Chain H-bonding
• Salt Linkages
• Disulfide linkages

Question 19

Disulfide Bonds

Answer 19

• Stabilize native structure
• Formed after native conformation achieved
• Abundant in secreted proteins but not in intracellular proteins
• Protein disulfide isomerase catalyzes reduction of incorrect disulfide linkages

Question 20

Disulfide linkages (cystine)

Answer 20

• Strong covalent bond
• Result of the oxidation of two cys that were in close proximity in folded protein
• Cannot be broken by changing temperature or pH
• Can be broken by addition of reducing agent that converts cystine back to two cysteine

Question 21

Quaternary Structure

Answer 21

• Organization of multiple chain associations
• Oligomerization- Homo (self), Hetero (different)
• Used in organizing single proteins and protein machines (enzymes)

Question 22

Prion Diseases

Answer 22

• Mad Cow
• New Variant Creutzfeld-Jacob
• Kuru
• Creutzfeld-Jacob
• Fatal Familial Insomnia
• Gertsmann- Straussler Sheinler
• Scrapie

Question 23

Prion

Answer 23

• Smaller than smallest known virus
• Not yet completely characterized
• Most widely accepted theory: Prion = Proteinaceous infectious particle with no DNA or RNA detected.
• Normal Protein: PrPC (C for cellular) comprised of 254 residues; Glycoprotein normally found at cell surface inserted in plasma membrane with a GPI anchor. Found on most cell types, but most abundant in the CNS

Question 25

Prion: Abnormal Protein

Answer 25

- PrPSc (Sc for Scrapie) - Same amino acid sequence and primary structure as normal protein - Secondary structure dominated by beta conformation - When PrPSc contacts PrPC it converts it to the abnormal form - Insoluble in all but strongest solvents - Highly resistant to digestion by proteases - Survives in tissues post-mortem - Extremely resistant toHeat, normal sterilization processes, sunlight - No detectable immune response

Question 26

Prion: Normal Protein

Answer 26

- Secondary Structure dominated by alpha helices - Easily soluble - Easily digested by proteases - encoded by PRNP gene (in humans)