amino acids and proteins muhammad jawad hassan assistant professor biochemistry
TRANSCRIPT
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Amino Acids and Proteins
Muhammad Jawad HassanAssistant Professor
Biochemistry
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Objectives
• Structure and Classification of amino acids• Peptide Bond and Primary structure of protein • Secondary Structure of protein, Helices and
Sheets• Tertiary and Quaternary Structure of protein,
domain and motifs• Structure-function relationship of proteins and
disease
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3
Structure dictates function
Protein structureallows DNAreplication withoutdissociation ofreplicatingmachinery
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Protein subunits: amino acids: L & D isomers
Mirror images of each other
R group = side chains
Aminogroup
Carboxylic acid group
Only L amino acids found in proteins. C chiral, L & D isomers not symmetrical, except glycine
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The 20 Amino Acids
The amino acids each have their own shape and charge due to their specific R group.
View the molecular shape of amino acids by clicking on the URL link below:
http://sosnick.uchicago.edu/amino_acids.html
Would the shape of a protein be affected if the wrong amino acid were added to a growing protein chain?
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Ionization state as a function of pH
Physiological pH (measure of [H+])
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Simplest amino acids
Ball & stick
Stereochemical
Fischer projections
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Aliphatic side chains
M: thioether(-S-)
Ile: 2ndchiral center
Aliphaticside chainshydrophobic
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Proline: cyclic structure
Ring structure: Proline conformationally restricted, marked effecton protein architecture
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Aromatic side chains
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Cysteine
Similar to Serine with sulfhydryl, or thiol (-SH) group replacinghydroxyl (-OH) group
-SH more reactive than -OH. -SH pairs form disulfide bonds(aka bridges), key role stabilizing proteins
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The basic amino acids
Polar side chains
Lys & Arg havepositive chargesat neutral pH
His can bepositivelychargednearphysiologicalpHLys side chain
capped withamino group
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Carboxylate & Carboxamide side chains
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pKa of some amino acids
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Amino acid abbreviations
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16
Essential Amino Acids
• 10 amino acids not synthesized by the body
• arg, his, ile, leu, lys, met, phe, thr, trp, val
• Must obtain from the diet
• All in diary products
• 1 or more missing in grains
and vegetables
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Primary structure: Peptide bond, between AAs
Between -carboxyl group of one AA & -amino group of another
2 amino acidsDipeptide
Loss ofH2O
Equilibrium favors hydrolysis, hence,biosynthesis of peptide bonds require free energy input
Peptide bonds are stable kinetically
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Polypeptide chain has direction
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Main chain or backbone
Constant backbone: regularly repeating part
Distinctive side chains (R-groups): variable part
AA unit in a polypeptide is called a residue, which contains,a carbonyl group; good hydrogen-bond acceptor,an NH group (except Pro); good hydrogen-bond donor
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Cross links (disulfide bridges)Prevalent mainly in extracellular proteins
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Bovine insulin: AA sequence1953, Fred Sanger determined aa sequence of insulin, landmark!
Showed for 1st time, protein has precisely defined aa sequenceAlso showed that only L-amino acids were present, linked by peptide bonds
Now, aa sequence of > 100,000 proteins are known
1950s-1960s studies showed aa sequence genetically determinedEach of 20 aa encoded by one or more specific sequences of3 nucleotides.
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Polypeptide bonds are planar
Six atoms (Ca, C, O, N, H, Ca) lie in a plane, in a pair of aa
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Bond lengths in peptide unit
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Trans & cis peptides
Cis configuration has steric hindrance; trans strongly favored
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Rotation of bonds in a polypeptide
Amino group to C & carbonyl group to C are pure single bonds,allow rotationFreedom of rotation allows proteins to fold in different ways
Dihedral angle: measure of rotation about a bondbetween -180o
& +180o
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Ramachandran diagramMost angle combinations (75%) excluded by steric hindranceDark green most favored
Steric exclusion: powerful organizing principle
Limited conformations favor protein folding, favorable entropy of too many conformations opposes folding
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Secondary structure: (1) alpha helix1951, predicted by Pauling & Corey, 6 years before it was seen!
ribbon
ball & stick, sideend view
space-fillingcore
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alpha helix stabilized by hydrogen bonds
CO group of residue n forms H-bond with NH group of Residue n + 4
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Ball & stick model of alpha helix
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Ribbon and cylindrical depiction
Residues related toeach other bya rise of 1.5 Å and a rotation of 100degrees.
3.6 aa residues / turn
Pitch = 5.4 Å(1.5x3.6)
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Ferritin, an iron storage protein
75% alpha helix
Helical content of proteins ranges widely
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Super helix: alpha helical coiled coil
Can be as long as 1000 Å, very stable
Helical cables in these proteins serve a mechanical role,forming stiff bundles of fibers
Found in: • myosin and tropomyosin in muscle,• fibrin in blood clots,• keratin in hair, quills, claws, hoofs, & horns• intermediate filaments (cytoskeleton or internal scaffolding of cells)
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Structure of a beta strand
Side chains are alternately above and below plane of backbone
Distance between adjacent aa = 3.5 AContrast to 1.5 A for alpha helix
Also predicted by Pauling & Corey
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Antiparallel beta sheet
Strands linked by H-bonding between opposite amino acids
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Parallel beta sheetStrands linked by H-bonding of an aa on one strand to twodifferent aa on the adjacent strand
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Structure of mixed beta sheet
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Fatty acid-binding protein
Rich in beta sheets
Arrow pointingto carboxyl-terminal end
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Tertiary structure, myoglobin
O2 carrier inmuscle,
1st protein inatomic detail,
153 aa,
X-ray crystals
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Tertiary structure, myoglobin, schematic
Mainly alpha helices,total = 8 helices (75% of main chain)
Prosthetic (helper)group to bind O2
Heme group isprotoporphyrin IX,& central iron atom
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Distribution of aa in myoglobin
Yellow: hydrophobic aaBlue: charged aaWhite: other aa
Cross-section
Surface, mainly charged aa. Interior, mainly hydrophobic aa
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Quaternary structure, dimerCro protein of bacteriophage lambda
Dimer of identical subunits
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Quaternary structure, tetramer
Humanhemoglobin,two alpha(red)two beta(yellow)subunits,
4 heme groupsCovalent bond…..NO
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Amino acid sequence determines 3D-structureBovine ribonuclease, 1950, C. Anfinsen work
4 disulfide bonds124 amino acids
Denature &renature
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Primary structure determination
•Acid hydrolysis
•Column chromatography
•Ion exchange chromatography
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Reducing disulfied bonds
beta-mercaptoethanol, reduced
oxidized
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Denaturing agent, urea
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Denaturing agent, guanidinium chloride
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Denaturing agent, beta mercaptoethanol
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Ribonuclease: reduction & denaturation
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Finishing touches: covalent modifications
Proteins covalently modified to augment function
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Research Protein
Discuss what you can learn about its structure, function and the organism it
comes from using the skills you learned today and website resources.
You can explore a number of proteins using Cn3D. Go to the following URL:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure
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Thank
You