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BIBC 100 Midterm 2 Review Session

BIBC 100 Midterm 2 Review Session. (Midterm Tomorrow In Class). DNA. B-DNA Right handed antiparallel double helix Purines AG, Pyrimidines CT (U in RNA) G = C, A=T hydrogen bonds Negatively charged 2’ deoxyribose backbone A-DNA Dehydrated, compressed

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BIBC 100 Midterm 2 Review Session

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  1. BIBC 100Midterm 2 Review Session (Midterm Tomorrow In Class)

  2. DNA • B-DNA • Right handed antiparallel double helix • Purines AG, Pyrimidines CT (U in RNA) • G=C, A=T hydrogen bonds • Negatively charged 2’ deoxyribose backbone • A-DNA • Dehydrated, compressed • Deep, narrow major groove not easily accessible • Z-DNA • Left-handed • Alternating N/M sequences • Tm • Melting temperature at which 50% are SS and 50% are DS • Higher G=C content leads to higher Tm

  3. RNA • A lot more common than DNA • Used in transcription, translation • mRNA (messenger) • mRNA transcript from DNA template • tRNA (transfer) • Attached to an amino acid at CCA 3’ end by amino acyl synthetase • Elongates protein chain in translation at the ribosomes • rRNA (ribosomal) • Makes up structure of ribosomal subunits

  4. RNA • Can form secondary structures/motifs • Stem-loop • Hairpin • Pseudoknots • DNA/RNA and RNA/RNA double helices have A-DNA conformation • Can carry out enzymatic and regulatory activities • mRNA has 5’ 7-methylguanosine cap, but translation starts at first Met (AUG) codon • tRNA carries an anti-codon that wobble-base-pair with the codon (20 aa, 4^3 possible codons)

  5. DNA-Binding Proteins • Bind to the major and minor grooves of B-DNA • Major groove 12A wide 8A deep, binds alpha helices (specific surface pattern for each AT, TA, GC, and CG base pair) • Minor groove 5A wide 8A deep, binds beta sheets (less specificity due to TA/AT and GC/CG base pairs having same exposed surfaces) • Exposed groups • H-bond donor, H-bond acceptor, Hydrogen (VdW), Methyl (VdW) • Motifs • Helix-turn-helix • Zinc finger (Zinc prosthetic group) • Leucine Zipper (heptad coiled-coil hydrophobic stabilization above DNA-Binding domain)

  6. DNA-Binding Proteins • Examples • EcoR1 restriction enzyme (GAATTC palindromic) • Lac repressor in e.coli (actively binds to DNA to prevent txn of lactose metabolism proteins when no lactose is present) • TATA Box Binding Protein (binds TATA box, unwinds DNA, recruits RNA Polymerase to transcribe mRNA from DNA)

  7. DNA Organization • Interphase Chromatin • Unraveled DNA and associated proteins (histones, scaffolds) • Double stranded, but no duplicates • Two types: euchromatin (uncondensed, actively transcribing) and heterochromatin (condensed, repressed) • Mitotic Chromosomes • Condensed heterochromatin, compact, transportable, four arms • Each chromosome has 2x sister (identical) chromatids attached at centromere • Humans have 22 autosomes and 1 sex chromosome (X or Y). Each has its homologous (related in genes, but not identical in content) chromosome, making for 46 total chromosomes in the human diploid (2n) genome

  8. Histones • Interphase chromosomes are organized as 10nm beads-on-a-string conformation • DNA are spaced out with histones attached at regular intervals • 2 winds of DNA around a histone octamer core, with H1 histone linker on the outside (H1 linking creates solenoid structure) • Structure • Core histones 2x (H2A, H2B, H3, H4) • Alpha helical protein • C-terminal covalent modifications • Phosphorylation, monoubiquitination (signaling) • Acetylation (expression) • Methylation (repression)

  9. Sugars • Monomers • alpha-D-glucose (dextrose) • Aldoses, ketoses • Cyclization into pyranose • Dimers • Sucrose (glucose a(1->2) fructose) • Lactose (galactose b(1->4) glucose) • Maltose (glucose a(1->4) glucose) • Anomeric carbon • Attached to anomeric hydroxyl • Either alpha (down) or beta (up) in Haworth • Alpha is cis to D (4’) hydroxyl (same right side in Fischer) • Beta is trans to D (4’) hydroxyl (opposite sides) • Animals cannot break beta glycosidic bonds (but bacteria can)

  10. Sugars • Polymers • Homo/hetero polysaccharides • Glycosidic bond • Alpha – helical structure, compact, energy storage • Animals, bacteria use glycogen glu (1->4) glu – branched every 8-12 res • Plants use starch glu a(1->4) glu • Amylose – unbranched • Amylopectin – branched every 24-30 res • Beta – straight chain, used for structural components • Animals (insects) use chitin gluNAc b(1->4) gluNAc • Plants use cellulose glu b(1->4) glu • Bacteria use peptidoglycan (heteropolysaccharide b(1->4)) • Saturated hydrogen bond network • OH --- O hydrogen bonds • Weak CH --- O hydrogen bonds between sheets

  11. Glycosylation • Proteoglycan • Heavily glycosylated (mostly sugars, little protein) • Covalently attached glycosaminoglycans (GAG) chains ex. Keratan, chondroitin sulfates O-linked to core protein • Hyaluronic acid (polysaccharide) backbone • Makes up extracellular matrix (ECM) • Together with collagen (triple amino acid helix), makes cartilage • Glycoproteins • Mostly proteins with some glycosylation • N-linked glycosylation on the outer (ECM) surface of membrane/transmembrane proteins • Indicates proper protein folding going through ER and Golgi network, used as antigens or ID markers on free proteins such as antibodies (human IgG) • Peptidoglycan • GlcNAc b(1>4) MurNAc backbone • L-Ala-Isoglu-L-Lys-D-Ala at 3’ carbon of MurNAc • E-Amino link on L-Lys to Pentaglycine bridge to Carboxyl end of D-Ala

  12. Glycosylation • O-Linked • Gal b(1->3) GlcNAc alpha linked to Ser/Thr • N-Linked • Asn-X-Ser/Thr sequence protein side • Asn linked to beta GlcNAc • 2xMan-GlcNAc-GlcNAc-Asn sequence oligosaccharide side

  13. Phospholipids • Glycerol backbone (three carbons each attached to OH) • 2 Nonpolar FA tails • Palmitic acid (16C) saturated • Stearic acid (18C) saturated • Oleic/Linoleic acid (16C:1 or 2 or 3) mono or poly unsaturated) • More unsaturation -> Lower Tm • Polar Head group • Phosphate(-) -> Phosphatidic acid (PA) • Phospho(-)choline(+) -> Phosphatidyl choline (PC) • Phospho(-)ethanolamine(+) -> Phosphatidylethanolamine (PE) • Phospho(-)inositol (ring) -> Phosphatidylinositol (PI) • Phospho(-)serine -> Phosphatidylserine (PS) • Phospho(-)glycerol(-) -> Phosphatidylglycerol (PG)

  14. Membranes • Fluid Mosaic • Fluid – Constant movement • Transverse movement – rapid, often • Inversions – very very slow, rare • Both sides are different • Lipid rafts, crystalline/gel and fluid structures • Membrane proteins • Integral (lipoanchored or transmembrane) • Peripheral • Extramembraneous domains • N-linked glycoysylation on ECM side • Transmembrane proteins must have polar resides near polar head groups and nonpolar residues in hydrophobic FA tails (core

  15. Lipids • Usually amphipathic lipids • 1 FA tail is conic, forms micelles (no aqueous interior) – called “detergents” • 2 FA tails is cylindrical, forms vesicles (bilayer forms aqueous interior) • Can be used to dislodge membrane proteins from membrane • DPPC (dipalmitoyl PC) • POPC (palmitooleyl PC)

  16. Cell-Surface Receptor Systems • Movement of membrane proteins depend on membrane fluidity • Tyrosine autophosphorylation when two membrane proteins dimerize • Ligand binding causes conformational change->protein movement->signaling cascade

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