Proteins, Enzymes and Nucleic Acids The DNA/RNA non-specific Serratia nuclease prefers double-stranded A-form nucleic acids as substrates Gregor Meiss, et al JMB 288: 377–390

Proteins Multipurpose molecules Schematic representation of secondary structures: Image from National Energy Research Scientific Computing Center

Proteins Most structurally & functionally diverse group Function: involved in almost everything –enzymes (pepsin, DNA polymerase) –structure (keratin, collagen) –carriers & transport (hemoglobin, aquaporin) –cell communication signals (insulin & other protein hormones) receptors –defense (antibodies) –movement (actin & myosin) –storage (bean seed proteins)

Proteins Structure –monomer = amino acids 20 different amino acids –polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex molecules complex 3-D shape hemoglobin H2OH2O

Amino acids Structure –central carbon –amino group –carboxyl group (acid) –R group (side chain) variable group different for each amino acid confers unique chemical properties to each amino acid –like 20 different letters of an alphabet –can make many words (proteins) —N——N— H H C—OH || O R | —C— | H

Effect of different R groups: Nonpolar amino acids Why are these nonpolar & hydrophobic?  nonpolar & hydrophobic

Effect of different R groups: Polar amino acids  polar or charged & hydrophilic Why are these polar & hydrophillic?

Building proteins Peptide bonds –covalent bond between NH 2 (amine) of one amino acid & COOH (carboxyl) of another peptide bond dehydration synthesis H2OH2O

Primary (1°) structure Order of amino acids in chain –amino acid sequence determined by gene (DNA) –slight change in amino acid sequence can affect protein’s structure & its function even just one amino acid change can make all the difference! lysozyme: enzyme in tears & mucus that kills bacteria

Sickle cell anemia I’m hydrophilic! But I’m hydrophobic! Just 1 out of 146 amino acids!

Figure 5.21 Primary Structure Secondary and Tertiary Structures Quaternary Structure Function Red Blood Cell Shape  subunit     Exposed hydrophobic region Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. Sickle-cell hemoglobin Normal hemoglobin 10  m Sickle-cell hemoglobin Normal hemoglobin    

Secondary (2°) structure “Local folding” –folding along short sections of polypeptide –interactions between adjacent amino acids H bonds weak bonds between oxygen and hydrogen atoms within the backbone. –forms sections of 3-D structure  -helix  -pleated sheet

Tertiary (3°) structure “Whole molecule folding” –interactions between distant amino acids hydrophobic interactions –cytoplasm is water-based –nonpolar amino acids cluster away from water H bonds & ionic bonds disulfide bridges –covalent bonds between sulfurs in sulfhydryls (S–H) –anchors 3-D shape

Noncovalent Interactions between Proteins and Other Molecules

Figure 5.19 Antibody protein Protein from flu virus

Quaternary (4°) structure More than one polypeptide chain bonded together –only then does polypeptide become functional protein collagen = skin & tendons hemoglobin

Chaperonin proteins Guide protein folding –provide shelter for folding polypeptides –keep the new protein segregated from cytoplasmic influences

Enzymes Biological catalysts –proteins (& RNA) –facilitate chemical reactions increase rate of reaction without being consumed reduce activation energy don’t change free energy (  G) released or required –required for most biological reactions –highly specific thousands of different enzymes in cells –control reactions of life

Figure 8.13 Course of reaction without enzyme E A without enzyme E A with enzyme is lower Course of reaction with enzyme Reactants Products  G is unaffected by enzyme Progress of the reaction Free energy

Induced fit model –3-D structure of enzyme fits substrate –substrate binding cause enzyme to change shape leading to a tighter fit “conformational change” bring chemical groups in position to catalyze reaction

How does it work? Variety of mechanisms to lower activation energy & speed up reaction –synthesis active site orients substrates in correct position for reaction –enzyme brings substrate closer together –digestion active site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules

Enzymes and temperature Different enzymes function in different organisms in different environments 37°C temperature reaction rate 70°C human enzyme hot spring bacteria enzyme (158°F)

Rate of reaction pH (b) Optimal pH for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Two enzymes function in the same organism, but in different environments

Compounds which regulate enzymes Inhibitors –molecules that reduce enzyme activity –competitive inhibition –noncompetitive inhibition –irreversible inhibition –feedback inhibition

Irreversible Inhibition

Reversible Inhibition

Regulatory site (one of four) (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits Active site (one of four) Active form Activator Stabilized active form Oscillation Nonfunctional active site Inactive form Inhibitor Stabilized inactive form Allosteric Regulation of Enzyme Activity

Active site available Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 is no longer able to catalyze the conversion of threonine to intermediate A; pathway is switched off. Isoleucine binds to allosteric site. Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Intermediate B Intermediate C Intermediate D Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 End product (isoleucine) Feedback Inhibition of Metabolic Pathways

Nucleic Acids Information storage

proteins DNA Nucleic Acids Function: –genetic material stores information –genes –blueprint for building proteins »DNA  RNA  proteins transfers information –blueprint for new cells –blueprint for next generation

Nucleotides 3 parts –nitrogen base (C-N ring) –pentose sugar (5C) ribose in RNA deoxyribose in DNA –phosphate (PO 4 ) group

Types of nucleotides 2 types of nucleotides –different nitrogen bases –purines double ring N base adenine (A) guanine (G) –pyrimidines single ring N base cytosine (C) thymine (T) uracil (U) Purine = AG Pure silver!

Nucleic polymer Backbone –sugar to PO 4 bond –phosphodiester bond new base added to sugar of previous base polymer grows in one direction –N bases hang off the sugar-phosphate backbone Dangling bases? Why is this important?

Pairing of nucleotides Nucleotides bond between DNA strands –H bonds –purine :: pyrimidine –A :: T 2 H bonds –G :: C 3 H bonds

Copying DNA Replication –2 strands of DNA helix are complementary have one, can build other

When does a cell copy DNA? When in the life of a cell does DNA have to be copied? –cell reproduction mitosis –gamete production meiosis

Nucleic Acids Are Informational Macromolecules Genome— complete set of DNA in a living organism

An interesting note… ATP Adenosine triphosphate ++  modified nucleotide  adenine (AMP) + P i + P i

RNA

Ghosts of Lectures Past

Building proteins Polypeptide chains have direction –N-terminus = NH 2 end –C-terminus = COOH end –repeated sequence (N-C-C) is the polypeptide backbone can only grow in one direction