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Biochem Mini 1 > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

0
Q

Aliphatic (alkane) Amino Acids

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

ALL ARE HYDROPHOBIC

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1
Q

Amino Acid Classification (Hydrophobic/Hydrophilic)

A

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

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

Tyrosine is both. (know it as hydrophilic)

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2
Q

Aromatic Amino Acids

A

ALL VERY HYDROPHOBIC (tyrosine is also hydrophilic)

  • Phenylalanine (phe)
  • Tyrosine (tyr)
  • Tryptophan (trp)
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3
Q

Sulfur Containing Amino Acids

A
  • Methionine (met) (Very hydrophobic)

- Cysteine (cys) Hydrophilic!

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4
Q

Acidic Amino Acids

A
  • Aspartate (Asp)
  • Glutamate (Glu)

Negatively charged AA

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5
Q

Basic Amino Acids

A

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

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6
Q

Polar Uncharged AA

A

Polar side groups, hyrdrophilic in nature

  • Serine (ser)
  • Threonine (thr)
  • Asparagine (asn)
  • Glutamine (gln)
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7
Q

Peptide

A

Condensation product of amino acids

  • dipeptide = 2 AA
  • oligopeptide = up to 20 AA
  • polypeptide = >20 AA
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8
Q

Protein

A

A functional polypeptide with a biological role (Native protein)

  • sometimes contain non-polypeptides portions as well
  • very small proteins are hormones
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9
Q

Residue

A

an amino acid in a peptide

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10
Q

Simple and Conjugated Protein Classification

A

Simple: composed only of amino acid residues

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

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11
Q

Fibrous Proteins

A
  1. polypeptides arranged in long strands or sheets
  2. water insoluble (lots of hydrophobic AA’s)
  3. Strong but flexible
  4. Structural (keratin, collagen)
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12
Q

Globular Proteins

A
  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)
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13
Q

Protein Function

A
  • 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)
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14
Q

4 levels of Protein Structure

A

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

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15
Q

Major common post-translational modifications

A
  1. hydroxylation –> hydroxypro, hydroxylys
  2. addition Pi group onto ser, thr
  3. addition of sugars to give glycoproteins
  4. Disulfide bond formation
16
Q

Disrupters in Polypeptide Chain

A
  • 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
17
Q

Fibrous proteins

A

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
18
Q

5 Classes of Tertiary Interaction Bonds

A
  • Hydrophobic force (attraction)
  • Van der Waals interactions
  • Side Chain H-bonding
  • Salt Linkages
  • Disulfide linkages
19
Q

Disulfide Bonds

A
  • 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
20
Q

Disulfide linkages (cystine)

A
  • 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
21
Q

Quaternary Structure

A
  • Organization of multiple chain associations
  • Oligomerization- Homo (self), Hetero (different)
  • Used in organizing single proteins and protein machines (enzymes)
22
Q

Prion Diseases

A
  • Mad Cow
  • New Variant Creutzfeld-Jacob
  • Kuru
  • Creutzfeld-Jacob
  • Fatal Familial Insomnia
  • Gertsmann- Straussler Sheinler
  • Scrapie
23
Q

Prion

A
  • 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
25
Q

Prion: Abnormal Protein

A
  • 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
26
Q

Prion: Normal Protein

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

Biochem Mini 1 (4 decks)

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