Phu Review 2

Phu Review 2 - BIBC 100 Midterm 2 Review Session (Midterm...

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Unformatted text preview: BIBC 100 Midterm 2 Review Session (Midterm Tomorrow In Class) DNA DNA ► B­DNA ► A­DNA Z­DNA Tm Right handed antiparallel double helix Purines AG, Pyrimidines CT (U in RNA) G=C, A=T hydrogen bonds Negatively charged 2’ deoxyribose backbone Dehydrated, compressed Deep, narrow major groove not easily accessible Left­handed Alternating N/M sequences Melting temperature at which 50% are SS and 50% are DS Higher G=C content leads to higher Tm ► ► RNA RNA ► A lot more common than DNA ► mRNA (messenger) ► tRNA (transfer) ► Used in transcription, translation mRNA transcript from DNA template Attached to an amino acid at CCA 3’ end by amino acyl synthetase Elongates protein chain in translation at the ribosomes Makes up structure of ribosomal subunits ► rRNA (ribosomal) RNA RNA ► Can form secondary structures/motifs ► DNA/RNA and RNA/RNA double helices have A­ Stem­loop Hairpin Pseudoknots DNA conformation ► Can carry out enzymatic and regulatory activities ► mRNA has 5’ 7­methylguanosine cap, but translation starts at first Met (AUG) codon ► tRNA carries an anti­codon that wobble­base­pair with the codon (20 aa, 4^3 possible codons) DNA­Binding Proteins DNA­Binding Proteins ► Bind to the major and minor grooves of B­DNA ► ► Exposed groups Motifs 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) H­bond donor, H­bond acceptor, Hydrogen (VdW), Methyl (VdW) Helix­turn­helix Zinc finger (Zinc prosthetic group) Leucine Zipper (heptad coiled­coil hydrophobic stabilization above DNA­Binding domain) DNA­Binding Proteins DNA­Binding 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) DNA Organization DNA Organization ► Interphase Chromatin ► Mitotic Chromosomes Unraveled DNA and associated proteins (histones, scaffolds) Double stranded, but no duplicates Two types: euchromatin (uncondensed, actively transcribing) and heterochromatin (condensed, repressed) 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 Histones Histones ► ► ► ► Interphase chromosomes are organized as 10nm beads­ on­a­string 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 C­terminal covalent modifications ► Acetylation (expression) ► Methylation (repression) ► Phosphorylation, monoubiquitination (signaling) Sugars Sugars ► Monomers ► Dimers alpha­D­glucose (dextrose) Aldoses, ketoses Cyclization into pyranose Sucrose (glucose a(1­>2) fructose) Lactose (galactose b(1­>4) glucose) Maltose (glucose a(1­>4) glucose) 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) ► Anomeric carbon Sugars Sugars ► Polymers Homo/hetero polysaccharides Glycosidic bond ► Alpha – helical structure, compact, energy storage ► Beta – straight chain, used for structural components Animals, bacteria use glycogen glu (1­>4) glu – branched every 8­12 res Plants use starch glu a(1­>4) glu ► Amylose – unbranched ► Amylopectin – branched every 24­30 res 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 Glycosylation Glycosylation ► Proteoglycan ► Glycoproteins Heavily glycosylated (mostly sugars, little protein) Covalently attached glycosaminoglycans (GAG) chains ex. Keratan, chondroitin sulfates O­linked to core protein Hyaluronic acid (polysaccharide) backbone Makes up extracellular matrix (ECM) Together with collagen (triple amino acid helix), makes cartilage Mostly proteins with some glycosylation N­linked 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) GlcNAc b(1>4) MurNAc backbone L­Ala­Isoglu­L­Lys­D­Ala at 3’ carbon of MurNAc E­Amino link on L­Lys to Pentaglycine bridge to Carboxyl end of D­Ala ► Peptidoglycan Glycosylation Glycosylation ► O­Linked ► N­Linked Gal b(1­>3) GlcNAc alpha linked to Ser/Thr Asn­X­Ser/Thr sequence protein side Asn linked to beta GlcNAc 2xMan­GlcNAc­GlcNAc­Asn sequence oligosaccharide side Phospholipids 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) Membranes Membranes ► Fluid Mosaic ► Membrane proteins Fluid – Constant movement Transverse movement – rapid, often Inversions – very very slow, rare Both sides are different Lipid rafts, crystalline/gel and fluid structures Integral (lipoanchored or transmembrane) Peripheral Extramembraneous domains N­linked glycoysylation on ECM side Transmembrane proteins must have polar resides near polar head groups and nonpolar residues in hydrophobic FA tails (core Lipids 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) Cell­Surface Receptor Systems Cell­Surface 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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This note was uploaded on 01/23/2010 for the course BIBC 100 taught by Professor Nehring during the Summer '07 term at UCSD.

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