19-1 principles and applications of inorganic, organic, and biological chemistry denniston, topping,...
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19-1
Principles and Applications ofInorganic, Organic, and
Biological ChemistryDenniston, Topping, and Caret
4th ed
Chapter 19
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Power Point to Accompany
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IntroductionProteins:
Provide nitrogen and sulfur for the diet
Most abundant macromolecules in the cell
Carry out most of the work of the cell
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19.1 Cellular Function of Proteins• Are biological catalysts (enzymes)• Are antibodies that fight antigens
(bacteria and viruses)• Transport molecules and ions• Regulate cell function• Provide structural support and
mechanical strength• Are necessary for all forms of
movement• Are sources of amino acids for growth
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Four Levels of Protein Structure
Primary, 1o
the amino acid sequenceSecondary, 2o
3-D arrangement of backbone atoms in space
Tertiary, 3o
3-D arrangement of all the atoms in space
Quaternary, 4o
3-D arrangement of subunit chains
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19.2 The -Amino AcidsAn alpha amino acid is a carboxylic acid
with an amino group on the carbon alpha to the carboxylic acid .
The alpha carbon also has an R group side chain except for glycine which has two Hs.
C C
R1
H
NH3
+O
OGeneric aminoacid at physiologicalpH. C
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If the R group is not H, the AA can exist in two enantiomeric forms (nonsuperimposable mirror image) forms.)
Mirror plane carbon
C
C
R1
HNH3
+
OO
C
C
R1
H NH3
+
O O
Amino acids incorporated into proteins have the L- configuration.
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AA with nonpolar side chains-1
C COO-
CH3
HNH3
+
alanine, alaCH2
C COO-
HNH3
+
phenylalanine,Phe
C COO-
CH2
HNH3
+
CHCH3
CH3
leucine,leu
C COO-
CH
HNH3
+
CH2CH3
CH3
isoleucine, Ile
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AA with nonpolar side chains-2
C COO-
CH
HNH3
+
CH3 CH3CH2
C COO-
HNH3
+
CH2S CH3
C COO-
CH2
HNH2
+
CH2
CH2
valine, val methionine, Met
proline, Pro
C COO-
CH2
HNH3
+
CCHN
Htryptophan, Trp
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AA with polar side chains-1
C COO-
H
HNH3
+
CH2
C COO-
HNH3
+
OH
C COO-
CH2
HNH3
+
SH
glycine, gly serine, ser
cysteine, cys
C COO-
CH
HNH3
+
CH3
OH
threonine, thr
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AA with polar side chains-2
glutamine, Gln
tyrosine, Tyr
C NH2O
CC
HNH3
+OO
CH2
C NH2O
CH2
CC
HNH3
+OO
CH2
asparagine, Asn
OHCC
CH2
HNH3
+OO
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AA: acidic and basic
glutamic acid, GluC OO
CCOO
-
HNH3
+
CH2
C OO
CH2
CCOO
-
HNH3
+
CH2
aspartic acid, Asp
CH2NH
CH2CH2
CNH2
+NH2
CCOO
-
HNH3
+
CH2CH2
CH2
CCOO
-
HNH3
+
CH2
NH3
+
NHCH
CH2
CCOO
-
HNH3
+
CNH
+CH
histidine, Hislysine, Lysarginine, Arg
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19.3 The Peptide BondA peptide is a polymer of about 2-100 amino acids linked by the peptide(amide) bond. As the amino group and the carboxyl group link, water is lost.
C C
R1
H
NH3
+O
OC C
R1
H
NH3
+O
OC C
R1
H
NH3
+O
O
C C
R1
H
NH3
+O
C C
R1
H
NH
OC C
R1
H
NH
OO
Peptide bonds
-H2O -H2O
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Peptide Bond, Cont.There is restricted rotation about the
peptide bond due to resonance. This restricted rotation has important consequences in terms of protein structures.
R
NH3
+
CHCO
NH
C R
NH3
+
CHCO
NH
C
+
-
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Peptides: Structure and NamesStructure left (N-term) to right (C-term)
Structure is based on the repeating sequence
N-C-C-N-C-C-N-C-C
N is the -amino group; white is the a-carbon; and yellow is the carbonyl carbon.
Name peptides by prefixing (L to R) the amino acid name , the ending –ine changed to –yl, and terminating in the COOH end AA name.
E. g. ala-gly is alanyl-glycine
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Names-cont.
Glutathione: the reduced formReduces oxidizing agents by dimerizing toform the disulfide bond with release of 2 H.
SHCH2
CH CH2CH2C
O
NH CH C
OCOO-
NH3
+NH CH2COO
-
-glutamyl-L-cysteineylglycine
N-terminal C-terminal
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Draw: alanyl-glycyl-valine (ala-gly-val)
CNH3
+C
O
NH C C
O
NH C C
O
O Draw theskeleton chain
CNH3
+C
O
NH C C
O
NH C C
O
O
H H H Add hydrogens
CNH3
+
HC
O
NH C C
O
NH C CCH3 CH
O
O
H H H
CH3 CH3
Add R groups
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19.4 Primary StructureThe primary structure of a protein is the
amino acid sequence of the chain.
Primary structures are translations of information contained in the genes.
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19.5 Secondary StructureThe two very important secondary
structures of proteins are:
-helix
-pleated sheet
Both depend on hydrogen bonding between the amide H and the carbonyl O further down the chain or on a parallel chain.
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Helix
Insert Fig 19.5With caption
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B Sheet: Lewis Structure
CH
C
N
CH
C
N
CH
C
N
O
H
H
O
H
O
N-term
C-term C-term
N-term
CH
C
N
CH
C
N
CH
C
N
O
H
H
O
H
O
Parallel sheet
CH
C
N
CH
C
N
CH
C
N
O
H
H
O
H
O
N-term
C-term
C-term
N-term
CH
C
N
CH
C
N
CH
C
N
O
H
H
O
H
O
Antiparallel sheet
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Types of Protein Structure 1Fibrous proteins exist as long stranded molecules: Eg. Silk, collagen, wool. A colagen segment in space-filling mode illustrates this point.
Red spheres represent oxygen, grey carbon, and blue nitrogen
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Types of Protein Structure 2Globular proteins have somewhat spherical shapes. Most enzymes are globular. Eg. myoglobin, hemoglobin. Myoglobin in space-filling mode is the chosen example.
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19.6 Tertiary StructureThe configuration of all the atoms in the
protein chain:
side chains
prosthetic groups
helical and pleated sheet regions
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Tertiary Structure: 2Protein folding attractions:1. Noncovalent forces
a. Inter and intrachain H bondingb. Hydrophobic interactionsc. Electrostatic attractions
+ to - ionic attractiond. Complexation with metal ionse. Ion-dipole
2. Covalent disulfide bridges
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Tertiary interactions: diag.
NH3
+
Polypeptide Chain
COO CH2 S
CH2S
O HC
O O
CH3CH3
CH2OHCH2 OH
CHCH3 CH3CHCH3 CH3 CO
ONH3
+
Mg2+
ionic
disulfide
hydrophobicH bondsor dipoleIon-dipole
metal coord’n
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19.7 Quaternary StructureQuaternary structure is the result of
noncovalent interactions between two or more protein chains.
In some cases the quaternary structure involves binding to a nonprotein group called a prosthetic group.
Hemoglobin has four protein chains and the heme prosthetic group.
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19.8 Overview of Structure and Function
The combination of 1o, 2o, 3o, and 4o structures lead to function.
Some proteins are fibrous and have great strength. They make up the structural parts of cells.
Some proteins are globular and serve as transport, regulatory and enzyme proteins.
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19.19 Myoglobin and HemoglobinHemoglobin transports oxygen to the cells
while myoglobin stores oxygen in skeletal muscle. Both use the heme group to bind oxygen.
Myoglobin has a single protein chain while hemoglobin has four (2 alpha and 2 beta). Each chain has a heme unit.
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The Heme Group
NN
NN
CH2CH2COO-
CH2CH2-OOC
CH3 CH3
CH
CH2
CH3
CH3 CH CH2
Fe(II)Pyrrole ring
N of HisF8 bindstofifth site onthe iron.
His E7 actsas a ”gate” for oxygen.
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Myoglobin: 2o and 3o aspects
Some helical regions
Heme group with iron (orange)at the center
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Hemoglobin (Hb)Oxygen binds to heme in hemoglobin
cooperatively: as one O2 is bound, it
becomes easier for the next to bind. The first oxygen causes 2,3-bisphospho-glycerate (BPG) to leave deoxyhemoglobin. This causes shape changes which favor more reaction with oxygen.
H+ produced by metabolizing cells (low pH) favors oxygen release from Hb and higher pH in the lungs favors binding of oxygen to Hb.
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Hemoglobin: ribbons + hemesEach chain is in ribbon form and color coded.
The heme groups are in space filling form
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Oxygen Transport: Mother-FetusFetal Hb is different from maternal Hb. It does
not bind BPG and therefore has a higher affinity for oxygen. This makes for more efficient oxygen transfer!
Sickle cell hemoglobin (Hb S) has a valine substituted for a glutamic acid in the beta chain. This results in the deoxy version clumping and forming the characteristic sickle cells. People with the disease usually die young but those with only one copy of the gene (sickle cell trait) tend to resist maleria.
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19.10 Protein DenaturationDenaturing destroys the physiological
function of the protein (remove the 2o-4o interactions)..
Heat (coagulation)
Change in pH leads to coagulation or unfolding to to charge repulsion.
Heavy metals
Detergents
Organic solvents
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19.11 Protein Digestion and DietDigestion:
Stomach: pepsin
S. I.: trypsin, chymotrypsin, elastase, etc.
Essential Amino Acids:
Cannot be synthesized by humans
Include: Ile, Leu, Lys, Met, Phe, Thr, Try, Val
Complete protein from animals provides esential AA in proper proportions.
Incomplete protein from vegetable sources must be balanced. E. g. beans (lys + trp) and corn (met)
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THE END
Protein Structure
And Function