amino acids and proteins muhammad jawad hassan assistant professor biochemistry
TRANSCRIPT
Amino Acids and Proteins
Muhammad Jawad HassanAssistant Professor
Biochemistry
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
3
Structure dictates function
Protein structureallows DNAreplication withoutdissociation ofreplicatingmachinery
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
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?
Ionization state as a function of pH
Physiological pH (measure of [H+])
Simplest amino acids
Ball & stick
Stereochemical
Fischer projections
Aliphatic side chains
M: thioether(-S-)
Ile: 2ndchiral center
Aliphaticside chainshydrophobic
Proline: cyclic structure
Ring structure: Proline conformationally restricted, marked effecton protein architecture
Aromatic side chains
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
The basic amino acids
Polar side chains
Lys & Arg havepositive chargesat neutral pH
His can bepositivelychargednearphysiologicalpHLys side chain
capped withamino group
Carboxylate & Carboxamide side chains
pKa of some amino acids
Amino acid abbreviations
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
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
Polypeptide chain has direction
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
Cross links (disulfide bridges)Prevalent mainly in extracellular proteins
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.
Polypeptide bonds are planar
Six atoms (Ca, C, O, N, H, Ca) lie in a plane, in a pair of aa
Bond lengths in peptide unit
Trans & cis peptides
Cis configuration has steric hindrance; trans strongly favored
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
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
Secondary structure: (1) alpha helix1951, predicted by Pauling & Corey, 6 years before it was seen!
ribbon
ball & stick, sideend view
space-fillingcore
alpha helix stabilized by hydrogen bonds
CO group of residue n forms H-bond with NH group of Residue n + 4
Ball & stick model of alpha helix
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)
Ferritin, an iron storage protein
75% alpha helix
Helical content of proteins ranges widely
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)
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
Antiparallel beta sheet
Strands linked by H-bonding between opposite amino acids
Parallel beta sheetStrands linked by H-bonding of an aa on one strand to twodifferent aa on the adjacent strand
Structure of mixed beta sheet
Fatty acid-binding protein
Rich in beta sheets
Arrow pointingto carboxyl-terminal end
Tertiary structure, myoglobin
O2 carrier inmuscle,
1st protein inatomic detail,
153 aa,
X-ray crystals
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
Distribution of aa in myoglobin
Yellow: hydrophobic aaBlue: charged aaWhite: other aa
Cross-section
Surface, mainly charged aa. Interior, mainly hydrophobic aa
Quaternary structure, dimerCro protein of bacteriophage lambda
Dimer of identical subunits
Quaternary structure, tetramer
Humanhemoglobin,two alpha(red)two beta(yellow)subunits,
4 heme groupsCovalent bond…..NO
Amino acid sequence determines 3D-structureBovine ribonuclease, 1950, C. Anfinsen work
4 disulfide bonds124 amino acids
Denature &renature
Primary structure determination
•Acid hydrolysis
•Column chromatography
•Ion exchange chromatography
Reducing disulfied bonds
beta-mercaptoethanol, reduced
oxidized
Denaturing agent, urea
Denaturing agent, guanidinium chloride
Denaturing agent, beta mercaptoethanol
Ribonuclease: reduction & denaturation
Finishing touches: covalent modifications
Proteins covalently modified to augment function
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
Thank
You