Download Secondary Structure of Proteins

Amino Acids, Peptides, Proteins and Enzymes
Peptides and proteins are encoded by DNA and are built from amino acids
Amino Acids, Peptides, Proteins and Enzymes
Amino acids (AA)
zwitterionic at
pH 7.4
20 Proteinogenic amino acids – exist as the L-enantiomers *
Spell “CO-R-N” clockwise with H in front
Which amino acid is achiral?
Which amino acids have two chiral carbons?
* Some bacteria use D-amino acids to evade host defense proteases
Physical Properties of Amino Acids
Water soluble
High melting points
Low solubility in organic solvents (Et2O)
Amino acids are abbreviated with a 3-letter or a 1-letter abbreviation
Amino Acid Side Chains Have Different Properties
Non-polar – examples: phenylalanine (Phe, F), valine (Val, V)
Polar – examples: serine (Ser, S), Asparagine (Asn, N)
Acidic – aspartic acid (Asp, D), Glutamic acid (Glu, E)
Basic – Lysine (Lys, K), Arginine (Arg, R)
Peptides and Proteins Differ in the Number of Amino Acid Residues
Dipeptide: 2 AA
N-terminus
C-terminus
Tripeptide: 3 AA
AA1
AA2
AA3
AA4
Tetrapeptide: 4 AA
Oligopeptide: 2-10 AA
Polypeptide: >10 AA
Protein: >50 AA
Amino acid “residues” in peptides and proteins refer
atoms remaining after loss of water in condensation
reactions to synthesize them.
Peptides and Proteins Differ in the Number of Amino Acid Residues
N-terminus
C-terminus
Tetrapeptide
Val-Ala-Gly-Phe
Val
Ala
Gly
Phe
(VAGP)
Biosynthesis: N-terminus to C-terminus
Nomenclature: N-terminus to C-terminus
Drawn: N-terminus to C-terminus
Chemical synthesis: C-terminus to N-terminus
Peptide Bonds: Strong Pi-Donation From Nitrogen to Carbonyl Carbon
S-trans preferred over S-cis
Peptide bonds do not freely rotate
Peptides drawn in plane of paper with side chains extending forward or backward
Peptides and Proteins Are Synthesized In Vivo by Condensation Reactions
Amino acid “residues” in peptides and proteins refer to the remaining atoms
after the loss of water in the condensation reaction.
Peptides and Proteins Are Degraded In Vivo by Hydrolysis Reactions
Hydrolysis of peptides and proteins is catalyzed by proteases
(sometimes peptidases or proteinases)
Examples of Biologically Active Peptides
Aspartame
Artificial sweetener, dipeptide
Glutathione
Antioxidant present in body – thiol can be oxidized to disulfide
sparing other biomolecules from oxidation
Oxytocin (Petocin = name of drug)
Peptide hormone that stimulates uterine contractions, lactation
Many Hormones Are Peptides or Proteins
Hormones are chemical substances secreted by cells or glands that regulate the
metabolic functions of other cells in the body.
Growth hormone (GH) – Anabolic protein hormone, stimulates bone and muscle growth
Antidiuretic hormone (ADH, vasopressin) – Peptide hormone, inhibits urine formation
Parathyroid hormone (PTH) – Protein hormone, controls Ca2+ balance
Insulin is a Peptide Hormone: Stimulates Anabolic Processes
Insulin stimulates the synthesis of energy storage molecules: glycogen, triglycerides, proteins
High blood glucose stimulates insulin secretion
Type 1 diabetes mellitus: Insulin secretion is reduced or absent.
Type 2 diabetes mellitus: Cells are not responsive to insulin.
Lack of insulin activity leads to hyperglycemia (high blood glucose sugar).
Insulin Peptide Chains Covalently Linked by Disulfide Bridges
Amino acid cysteine contains a thiol side chain.
Two cysteine residues within a peptide or protein can form a covalent bond - disulfide bridge.
Oxidation or reduction of cysteine residues to the disulfide bridge?
Insulin and Other Peptide and Protein Therapeutics Administered via Injection
Peptides and protein therapeutics are not orally bioavailable
Proteases would degrade insulin via hydrolysis reactions to inactive fragments –
smaller peptides and constituent amino acids
Other protein and peptide therapeutics:
Trastuzamab (Herceptin)
Infliximab (Remicade)
Human growth hormone (somatropin)
Oxytocin (Petocin)
Erythropoeitin (EPO)
Protein Structure
1) Primary structure – amide bonds
(covalent)
2) Secondary structure – Hydrogen-bonds
(non-covalent)
3) Tertiary structure – Hydrogen-bonds
Dipole-dipole interactions
Hydrophobic interactions
Salt bridges
Disulfide bridges
(non-covalent except disulfides)
4) Quaternary structure – same forces as tertiary
structure
Primary Structure of Proteins is the Sequence of Amino Acids
Amino acids are covalently linked via amide bonds
Primary Structure of Proteins is the Sequence of Amino Acids
With increasing length of peptide or protein chain, an exponential number of
amino acid sequences possible
Consider tripeptide composed of leucine (L), phenylalanine (F), and alanine (A)
How many possible tripeptides can be formed from these three amino acids?
Primary Structure of Proteins is the Sequence of Amino Acids
With increasing length of peptide or protein chain, an exponential number of
amino acid sequences possible
Consider tripeptide composed of leucine (L), phenylalanine (F), and alanine (A)
Six possible tripeptides:
LFA
LAF
ALF
AFL
FLA
FAL
Secondary Structures of Proteins Based on Highly Regular Local Sub-Structures
Alpha (a)-helices and beta (b)-sheets most common types of secondary structures
Based on hydrogen bonding (non-covalent interactions)
Secondary Structure of Proteins: Alpha Helix
Spring-like structure formed by hydrogen bonds between the backbone NH and C=O
groups approximately 4 amino acids apart
Most common type
of secondary
structure
Secondary Structure of Proteins: Beta Sheet
Accordian-like structure formed by hydrogen bonds between backbone NH and C=O groups
in different parts of the same chain or different polypeptide chains
Antiparallel
strands
Parallel
strands
Tertiary Structure of Proteins – Overall Three Dimensional Shape
Next higher level of complexity - folding of the a-helical and/or b-pleated regions
H-bonding, dipole-dipole interactions, London dispersion forces, disulfide bridges
Connecting
turns/loops
Alpha helices
Heme prosthetic
group (binds O2)
Tertiary structure of myoglobin, an oxygen-binding protein in muscle
Quaternary Structure is Found in Some Proteins:
Aggregation of Two or More Polypeptide Chains to Form a Complex
Hemoglobin is formed from four polypeptide chains associated with each other primarily
through hydrophobic interactions (non-polar residues buried, “escape” water)
2 identical a-chains
2 identical b-chains
4 heme prosthetic
groups
Fibrous and Globular Proteins
Fibrous proteins (structural proteins)
Often only secondary structure
Insoluble in water
Chemically stable
Provide mechanical support and tensile strength to tissues
Globular proteins (functional proteins)
Compact, spherical proteins with tertiary structure (some quaternary)
Water soluble
Chemically active
Fibrous (Structural) Proteins
Collagen
Most abundant protein in the body. Tensile strength of bones, tendons, ligaments.
Keratin
Structural protein of hair and nails
Elastin
Durable and flexible – found in ligaments
collagen
elastin
Globular (Functional) Proteins
Enzymes
Protein catalysts
Transport proteins
Hemoglobin (oxygen), lipoproteins (lipids and cholesterol), protein channels (cell membranes)
Metabolic proteins
Hormones
Defense proteins
Antibodies (immunoglobulins), molecular chaperones (aid in protein folding)
chymotrypsin
ion channel protein
Globular Proteins Sensitive to pH and Temperature Changes
Denaturation – Loss of three-dimensional protein structure and function
Intramolecular hydrogen bonds disrupted at high temperature or pH disturbances
Risk of high fever, acidosis, or alkalosis – loss of protein function
Chemical denaturation
1) Reducing agents – Cys disulfide to Cys thiols
2) Detergents - disrupt hydrophobic interactions
Enzymes Are Biological Catalysts - Accelerate Reaction Rates
Enzymes accelerate reaction rates by bringing substrates into proper orientation
for bond breaking / bond formation
E = enzyme
S = substrate (reactant)
P = product
Enzymes are generally very substrate specific, and can be stereospecific.
Some enzymes are less specific, e.g. alcohol dehydrogenase.
Enzyme Specificity Can Vary
Alcohol dehydrogenase catalyzes oxidation of ethanol, methanol, and ethylene glycol
Methanol is toxic – 10 mL can cause blindness due to its metabolite formic acid.
Treatment may include alcohol dehydrogenase inhibitor (fomepizole, Antizol®) and ethanol
Fomepizole and ethanol both compete with methanol for binding alcohol dehydrogenase.
Fomepizole
(Antizol®)
Enzymes Accelerate Reaction Rates by Lowering Their Activation Energy
Enzymes do not alter the equilibrium concentrations of reactant and product
(affect kinetics, not thermodynamics)
Enzyme Activity
• Enzymes operate under specific conditions – pH optimum, temperature optimum
Most near pH 7.4, 37 °C, though some differ
e.g. pepsin at pH 1.5, found in stomach
• May require cofactors – ions or organic compounds (“prosthetic groups” if tightly bound)
Zn2+ (alcohol dehydrogenase, metalloproteases)
Fe2+ (peroxidases)
NADH, NAD+
NADPH, NADP+
FADH2, FAD
CoA
Many Drugs Are Enzyme Inhibitors
Atorvastatin (Lipitor)
HMG-CoA reductase inhibitor
Lowers LDL cholesterol
Celecoxib (Celebrex)
COX-2 inhibitor
Reduces prostaglandin synthesis (NSAID)
Acetazolamide (Diamox)
Carbonic anhydrase inhibitor
Increases loss of bicarbonate via urine
(treatment for alkalosis)
Competitive Enzyme Inhibitors Bind Enzyme Active Site
Competitive enzyme inhibitors generally have similar chemical structure
as endogenous substrate
Methotrexate is an Example of a Competitive Enzyme Inhibitor
Competitive inhibitor of DHFR
Folic acid (vitamin B9)
Important in pregnancy and infancy
Rapidly dividing cells
Methotrexate (MTX)
Inhibits dihydrofolate reductase
Anticancer agent (leukemia)
Antiinflammatory (rheumatoid arthritis)
Non-Competitive Inhibitors Bind Allosteric Site on Enzyme
Substrate
Inhibitor
Enzyme
Substrate
Enzymeinhibitor
complex
Conformational
change
Non-competitive enzyme inhibitors generally have distinct chemical
structure from endogenous substrate.
Non-Competitive Inhibitors Bind Allosteric Site on Enzyme
Acetylcholine
Neurotransmitter
Substrate for acetylcholinesterase
Tacrine (Cognex)
Alzheimer’s disease
Inhibits acetylcholinesterase
Non-competitive inhibitor
of acetylcholinesterase