Chemistry 506 - Dr. Allen D. Hunter

Transcrição

Chemistry 506
Dr. Hunter’s Class
Chapter 18. 1
Chemistry 506: Allied Health Chemistry 2
Chapter 18: Proteins
Biochemical Amides
Introduction to General, Organic & Biochemistry, 5th Edition by
Bettelheim and March: Chapter 18, Pages 591-622
Outline Notes by Dr. Allen D. Hunter, YSU Department of
Chemistry, 2000.
Outline
1A SECTION(S) 18.1 PROTEIN ROLES .................................................................................................................................... 2
1B SECTION(S) 18.2/3/4 AMINO ACIDS................................................................................................................................... 4
1C SECTION(S) 18.5/6 PEPTIDES AND PROTEINS............................................................................................................. 14
1D SECTION(S) 18.7 PRIMARY STRUCTURE...................................................................................................................... 19
1E SECTION(S) 18.8 SECONDARY STRUCTURE................................................................................................................ 21
1F SECTION(S) 18.9/10/11 TERTIARY AND QUATERNARY STRUCTURE................................................................... 22
2000, Dr. Allen D. Hunter, Department of Chemistry, Youngstown State University
Chemistry 506
1A Section(s)
18.1
Protein Roles
Ø Structural Proteins
Ø Cellular
Ø Bodies
Ø Tendons
Ø Muscles
Ø Bones
Ø Movement Proteins
Ø Intracellular
Ø Cellular
Ø Bodies
Ø Molecular Transport Proteins
Ø Within Cells
Ø Across Membranes
Chapter 18. 2
Chemistry 506
Ø Catalysis Proteins
Ø Digestion
Ø Biochemical Pathways
Ø Protection Proteins
Ø Antibodies
Ø Hormone Proteins
Ø Regulation of Cellular Activity Proteins
Ø Storage Proteins (e.g., Ca+2)
Chapter 18. 3
Chemistry 506
1B Section(s)
18.2/3/4
Amino Acids
Ø General Structure
H
R
C
CO 2 H
NH 2
Ø 20 Commonly Occurring Amino Acids
Ø α-Amino Acids
Ø 19 are chiral at α carbons
Ø Table 18.1 on page 594
Chapter 18. 4
Chemistry 506
Ø Nonpolar Amino Acids
Ø Size
Ø Total Steric Bulk
Ø Distance of bulk from protein backbone
Ø R = H, Glycine, Gly
Ø R = CH3, Methyl, Alanine, Ala
Ø R = CH(CH3)2 , Iso-Propyl , Valine, Val
Chapter 18. 5
Chemistry 506
Chapter 18. 6
Ø R = CH2CH(CH3)2, Iso-Butyl , Leucine, Leu
Ø R = C*H(CH3)(CH2CH3), Sec-Butyl, Isoleucine, Ile
Ø HN{CH2CH2 CH2-ring}CH-CO2 H, Proline, Pro
Chemistry 506
Ø R = CH2-C6H5 , Aromatic, Phenylalanine, Phe
Ø R = CH2CH2-S-CH3, Thioether, Methionine, Met
Chapter 18. 7
Chemistry 506
Ø Neutral Polar Amino Acids
Ø R = CH2-OH, 1° Alcohol, Serine, Ser
Ø R = CH(CH3)-OH, 2° Alcohol, Threonine, Thr
Ø R = CH2-SH, Thiol / Thioalcohol, Cysteine, Cys
Ø R = CH2-(1,4-C6H4)-OH, Phenol, Tyrosine, Tyr
Chapter 18. 8
Chemistry 506
Chapter 18. 9
Ø R = CH2-C(=O)-NH2, Amide, Asparagine, Asn
Ø R = CH2-CH2-C(=O)-NH2 , Amide, Glutamine, Gln
Ø Tryptophan, Trp, Heterocyclic
Ø Aromaticity effects on Nitrogen basicity
Ø R=
H2
C
N
H
Chemistry 506
Ø Acidic Amino Acids
Ø Variable Chain Lengths
Ø R = CH2-CO2 H, Aspartic Acid, Asp
Ø R = CH2CH2-CO2H, Glutamic Acid, Glu
Chapter 18. 10
Chemistry 506
Ø Basic Amino Acids
Ø Variability
Ø Base Distance
Ø Base Strength, Lone pairs on Nitrogen
Ø R = CH2CH2CH2CH2-NH2 , Lysine, Lys
Ø R = CH2CH2CH2NH-C(=NH)-NH2, Arginine, Arg
Ø Histidine, His
Ø R=
H2
C
N
N
H
Chapter 18. 11
Chemistry 506
Chapter 18. 12
Ø Zwitterions
Ø Molecules that contain both a positive charge and a negative
charge
Ø Intramolecular Acid-Base Chemistry
H
H
O
R
C
O
C
R
O
C
N
H
H
H
C
H
N
O
+
H
H
H+
OH-
H
H
O
R
C
H
-
N
C
O
R
C
C
O H
+
H
H
O
-
N
H
H
Ø Isoelectric Point
Ø pH at which Amino Acids are in Zwitterionic form
Chemistry 506
Chapter 18. 13
Ø Cysteine
Ø Cysteine ⇒ Cystine
Ø Oxidation with loss of H2
Ø Thiols ⇒ Disulfides
Ø Reversible Redox (Reduction reverses the reaction)
H2
C
- H2
S
H
H
H2
C
S
S
S
C
H2
Cysteine
C
H2
Cysteine
Cystine
Cystine
H
H
C
R
N
H
H
N
R
C
C
N
H
H
O
R
R
N
O
C
H
H
O
H
H2
C
C
H
S
H
H
O
- H2
N
H
S
H2
C
C
H
S
N
H2C
H
C
H
N
+ H2
O
N
S
C
H2
H
C
H
O
H
C
H
R
O
N
H
N
R
C
C
H
R
O
N
H
H
R
N
H
C
H
Chemistry 506
1C Section(s)
Chapter 18. 14
18.5/6
Peptides and Proteins
Ø Peptide (Amide) Bonds
Ø 6 atom unit
Ø rigid
Ø trans arrangement about amide linkage
Ø planar
Ø Dipeptide example
H
H2N
C
O
O
C
H
N
R
H
C
R
C
OH
Ø Peptide Sizes
Ø Dipeptide, Tripeptide, Tetrapeptide… Polypeptide….Protein
Chemistry 506
Chapter 18. 15
Ø Structures of peptides and proteins specified with 3 letter
codes
Ø 1st start from NH2 groups on the left
Ø Identify side chains
Ø Join Amino Acids by peptide bonds
Ø Typical Exam Questions
Ø Example Ala-Gly-Lys
H
H2N
C
O
O
C
H
O
N
CH3
H
C
C
H
N
H
C
H
C
CH2
OH
H2C
CH2
H2C
N H2
Chemistry 506
Ø Levels of Structure
Ø 1°, Primary Structure
Ø Sequence of Amino Acids in protein backbone
Ø 2°, Secondary Structure
Ø α-Helix and β-Pleated Sheets
Ø 3°, Tertiary Structure
Ø Overall 3D shape/folding of protein chain
Ø 4°, Quaternary Structure
Ø Multiple separate proteins clustered together
Chapter 18. 16
Chemistry 506
Chapter 18. 17
Ø Typical Positions of Amino Acids in Proteins
Ø Core Amino Acid Residues
Ø Nonpolar Amino Acids
Ø Surface Amino Acid Residues
Ø Depends on protein position
Ø Polar/Hydrogen Bonding/Ionic Residues where touch
water
Ø Nonpolar residues where in membrane
Ø Active Site
Ø Acid/Basic/Etc. residues to Catalyze reactions
Ø Nonpolar and Polar/Hydrogen Bonding/Ionic to hold
substrate in Position
Chemistry 506
Ø How proteins keep their shapes
Ø “Hydrophobic” vs. “Hydrophilic” Interactions
Ø Types of Bonds Holding Proteins in their Shapes
Ø Covalent Bonds, Directional
Ø
Disulfide linkages, Directional
Ø Ionic Bonds, Non-directional
Ø Hydrogen Bonds, Directional
Ø Dipole-Dipole Interactions, Non-directional
Ø Van der Waal’s Interactions, Non-Directional
Ø Individually weak but strong in total
Chapter 18. 18
Chemistry 506
1D Section(s)
18.7
Chapter 18. 19
Primary Structure
Ø Sequence
Ø Number of Possibilities
Ø (number of Amino Acids)n
Ø where n is the chain length
Ø Example: 20 AA in mammals ⇒
Ø dipeptides have (20)2 = 400 1° structures
Ø tripeptides have (20)3 = 8,000 1° structures
Ø 1° Structure Determines 2°, 3°, and 4° Structures
Ø Thermodynamics
Ø Kinetics
Ø Types of Structural Variations Found in “the Same” protein
Ø Between individuals in a species
Ø Between sub-populations in a species
Ø Between species
Chemistry 506
Chapter 18. 20
Ø Effects of Structural Variations
Ø Depend on site and nature of substitutions
Ø Some changes have no observable effects
Ø Some changes have effects
Ø On rates
Ø On control
Ø On specificities
Ø Some changes kill activity
Ø These changes work by changing 2°, 3°, and 4° structures
and hence protein reactivity
Chemistry 506
1E Section(s)
18.8
Secondary Structure
Ø Types of 2° structures
Ø Figure 18.5 on page 607
Ø α-Helix
Ø β-Pleated Sheet
Ø Held together by intra-structural Hydrogen Bonds
Ø between backbone groups
Ø N-H Hydrogen Bonds Donors
Ø C=O Hydrogen Bond Acceptors
Ø Random coils/chains
Chapter 18. 21
Chemistry 506
1F Section(s)
Chapter 18. 22
18.9/10/11 Tertiary And Quaternary Structure
Ø Bond Types same as on list above for other structural features
Ø Collagen
Ø Found in human connective tissue, very strong
Ø Figure 18.8 on page 610
Ø Each Collagen molecule is a triple helix (of 3 chains)
Ø Each chain is an individual molecule made up of an αhelix
Ø Twisted together like braiding
Ø Chaperones
Ø Proteins that assist folding to give thermodynamically
preferred structures
Chemistry 506
Chapter 18. 23
Ø Denaturation and Naturation
Ø Often reversible
Ø Can be artificially induced by heat, solvent, salts, etc.
Ø Denaturation
Ø Loss of native 3D structure
Ø Naturation
Ø Gain of native 3D structure
Ø Glycoproteins
Ø Sugars bonded to protein surfaces
Questions: 18.1 to 18.39
Chemistry 506
Chapter 18. 24
Index of Topics and Vocabulary
1
1° ..................................................................................... 16
1° Alcohol.......................................................................... 8
1° Structure Determines 2°, 3°, and 4° Structures.... 19
2
2° ..................................................................................... 16
2° Alcohol.......................................................................... 8
2° structures..................................................................... 21
3
3 letter codes ................................................................... 15
3D shape.......................................................................... 16
3° ..................................................................................... 16
4
4° ..................................................................................... 16
A
Acidic Amino Acids ...................................................... 10
Active Site....................................................................... 17
Ala....................................................................................... 5
Alanine............................................................................... 5
Amide................................................................................. 9
Amino Acids...............................................................4, 12
Antibodies ......................................................................... 3
Arg.................................................................................... 11
Arginine........................................................................... 11
Aromatic............................................................................ 7
Aromaticity ....................................................................... 9
Asn...................................................................................... 9
Asp.................................................................................... 10
Asparagine......................................................................... 9
Aspartic Acid .................................................................. 10
B
Base Distance.................................................................. 11
Base Strength.................................................................. 11
Basic Amino Acids ........................................................ 11
Biochemical Pathways.................................................... 3
Bodies................................................................................. 2
Bonds Holding Proteins in their Shapes..................... 18
Bones .................................................................................. 2
braiding............................................................................ 22
C
Ca+2 ..................................................................................... 3
Catalysis Proteins............................................................. 3
Catalyze reactions .......................................................... 17
Cells .................................................................................... 2
Cellular............................................................................... 2
Chain Lengths................................................................. 10
Chaperones ...................................................................... 22
chiral at α carbons............................................................ 4
Collagen........................................................................... 22
Commonly Occurring Amino Acids............................. 4
connective tissue............................................................. 22
Core Amino Acid Residues .......................................... 17
Covalent Bonds, Directional ........................................ 18
Cys...................................................................................... 8
Cysteine.......................................................................8, 13
Cystine............................................................................. 13
D
Denaturation.................................................................... 23
Digestion............................................................................ 3
Dipeptide......................................................................... 14
dipeptides......................................................................... 19
Dipole-Dipole Interactions, Non-directional............. 18
Distance of bulk from protein backbone...................... 5
Disulfide linkages, Directional.................................... 18
Disulfides......................................................................... 13
F
folding.............................................................................. 22
folding of protein chain................................................. 16
G
Gln...................................................................................... 9
Glu.................................................................................... 10
Glutamic Acid................................................................. 10
Glutamine.......................................................................... 9
Gly ...................................................................................... 5
Glycine............................................................................... 5
Glycoproteins.................................................................. 23
H
heat ................................................................................... 23
Heterocyclic...................................................................... 9
His..................................................................................... 11
Histidine........................................................................... 11
Hormone Proteins............................................................. 3
Hydrogen Bond Acceptors ........................................... 21
Hydrogen Bonds............................................................. 21
Hydrogen Bonds Donors............................................... 21
Hydrogen Bonds, Directional....................................... 18
Hydrophilic...................................................................... 18
Hydrophobic.................................................................... 18
I
Ile ....................................................................................... 6
individuals ....................................................................... 19
Intracellular ....................................................................... 2
Chemistry 506
Chapter 18. 25
Intramolecular Acid-Base Chemistry ......................... 12
Ionic Bonds, Non-directional....................................... 18
Iso-Butyl............................................................................ 6
Isoelectric Point .............................................................. 12
Isoleucine........................................................................... 6
Iso-Propyl.......................................................................... 5
Protection Proteins........................................................... 3
Protein.............................................................................. 14
Protein Roles ..................................................................... 2
protein surfaces............................................................... 23
K
Quaternary Structure...................................................... 16
Questions ......................................................................... 23
Kinetics ............................................................................ 19
L
Q
R
Leu...................................................................................... 6
Leucine............................................................................... 6
Lone pairs........................................................................ 11
Lys.................................................................................... 11
Lysine............................................................................... 11
Redox................................................................................ 13
Reduction......................................................................... 13
Regulation of Cellular Activity Proteins...................... 3
reversible......................................................................... 23
rigid................................................................................... 14
ring...................................................................................... 6
M
S
Membranes ........................................................................ 2
Met...................................................................................... 7
Methionine........................................................................ 7
Methyl................................................................................ 5
Molecular Transport Proteins......................................... 2
Movement Proteins.......................................................... 2
Muscles .............................................................................. 2
native 3D structure......................................................... 23
Naturation........................................................................ 23
negative charge ............................................................... 12
Neutral Polar Amino Acids ............................................ 8
NH2 groups on the left................................................... 15
Nitrogen basicity.............................................................. 9
Nonpolar Amino Acids .............................................5, 17
Nonpolar residues........................................................... 17
salts................................................................................... 23
Sec-Butyl........................................................................... 6
Secondary Structure.................................................16, 21
Sequence.......................................................................... 19
Sequence of Amino Acids in protein backbone........ 16
Ser....................................................................................... 8
Serine.................................................................................. 8
Size..................................................................................... 5
solvent .............................................................................. 23
species.............................................................................. 19
specificities...................................................................... 20
Steric Bulk......................................................................... 5
Storage Proteins................................................................ 3
Structural Proteins............................................................ 2
sub-populations............................................................... 19
Sugars............................................................................... 23
Surface Amino Acid Residues ..................................... 17
O
T
Oxidation with loss of H2 ............................................. 13
Tendons.............................................................................. 2
Tertiary And Quaternary Structure............................. 22
Tertiary Structure........................................................... 16
Tetrapeptide..................................................................... 14
thermodynamically preferred structures..................... 22
Thermodynamics ............................................................ 19
Thioalcohol........................................................................ 8
Thioether............................................................................ 7
Thiols................................................................................ 13
Thr....................................................................................... 8
Threonine........................................................................... 8
tripeptides ........................................................................ 19
triple helix........................................................................ 22
Trp ...................................................................................... 9
Tryptophan ........................................................................ 9
Tyr ...................................................................................... 8
Tyrosine............................................................................. 8
N
P
Peptide.............................................................................. 14
Peptide (Amide) Bonds................................................. 14
peptide bonds .................................................................. 15
Peptides and Proteins..................................................... 14
pH ..................................................................................... 12
Phe...................................................................................... 7
Phenol................................................................................. 8
Phenylalanine.................................................................... 7
planar................................................................................ 14
Polar/Hydrogen Bonding/Ionic Residues................... 17
Polypeptide...................................................................... 14
Positions of Amino Acids in Proteins......................... 17
positive charge................................................................ 12
Primary Structure.....................................................16, 19
Pro....................................................................................... 6
Proline................................................................................ 6
Chemistry 506
Chapter 18. 26
V
α
Val....................................................................................... 5
Valine................................................................................. 5
Van der Waal’s Interactions, Non-Directional.......... 18
α-Amino Acids................................................................. 4
α-helix.............................................................................. 22
α-Helix.......................................................................16, 21
Z
β
Zwitterionic form........................................................... 12
Zwitterions...................................................................... 12
β-Pleated Sheet ............................................................... 21
β-Pleated Sheets ............................................................. 16

Chemistry 506 - Dr. Allen D. Hunter

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